Nature Agriculture

The correct name for the liquid endosperm is “coconut water.” It is also called “coconut milk,” but this name concerns a derived product made from a mixture of grated endosperm and milk. The solid edible layer is often referred to as “meat” or “flesh,” words that wrongly suggest animal origin. The fibrous, buoyant mesocarp takes up the largest part of the coconut fruit and is adapted to dispersal by water. It yields coir, a fiber that is used for making ropes, carpets, and mattresses. Among others, the coir is made into rigging and cordage for ships and it is also used for caulking. Coconut has the advantage of not rotting in saltwater. Coconuts can be harvested either by cutting them from the tree or by collecting fallen fruits. Both methods can be applied for the production of copra, although the former has the advantage of removing dead leaves and detecting damage by pests. Because ripe nuts will hang on the tree for another two or three months before falling, the amount of coconut water will be too low for long-distance trade. Therefore, harvesting the nuts by cutting is necessary if they are meant for export. Mostly, coconuts are husked so that the fibrous mesocarp and exocarp is separated from the inner part of the fruit, consisting of the endocarp and the seed . Further processing concerns the drying of the seed into copra. The hard “shells” are split and the “meat” is dried until the moisture content is reduced to about 6 percent. During this process, the “meat” becomes loose and can be separated from the “shell,” raspberry container size which is more effective for drying. If the copra is properly dried, it can be stored almost indefinitely. Coconut oil can be obtained from the copra. Today, the Ababda nomads occasionally use coconuts as containers .

Such containers are called garras or lozes and are mostly made from gourds . They are used for storing meat, animal fat, milk, and rancid butter used as a kind of hair gel. The rancid butter is mixed with additives that enhance the smell. Such containers may be decorated with leather, textile, basketry shells, and beads. The whole-coconut lozes are obtained by removing the “meat,” when it has rotted, through a hole bored through one of the eyes. The small hole is often closed with a stopper made by rolling up a piece of leather adjusted to the size of the hole.The origin of the coconut is still unknown. The possible area of origin is Southeast Asia and Melanesia, whereas India is considered as a possible secondary center of origin . The present distribution comprises the wet tropical lowlands, and the present-day coconut cultivation lies between lat 20° N and 20° S, although the noncommercial growth may extend as far as 27° N and 27° S . There is still scholarly disagreement concerning the introduction of the coconut to East Africa, both with respect to period and dispersal agent. Its spread from India to East Africa by oceanic currents, preceding the distribution by humans, is only based on assumptions, although crossing the Indian Ocean by floating seems to be possible. An early introduction by humans, on the other hand, is plausible, based on the existence of ancient trade contacts between both continents. A reference made by Schuiling and Harries to the Periplus Maris Erythraei is not tenable because it is based on a mistranslation by Schoff of the Greek word nauplios [ναύπλιος]. Egypt fringes the northern distribution line of the coconut. According to Täckholm and Drar , all attempts of cultivating the coconut in Egypt were futile because of unsuitable climatic conditions. The cultivation of coconut palms with the aid of irrigation on the island of Elephantine, near Aswân, is mentioned by Walter .

A striking record concerns the presence of a coconut palm growing near Berenike published by D’Abaza . An English naval officer, who had spent many years in the tropics and must have known the tree very well, made the observation, according to D’Abaza. The observation was confirmed in 1907 by the captain of one of the Khedivial mail boats. Distinguishing the coconut palm from the date palm is, however, quite difficult if no ripe fruits are present. Both trees have a similar shape with scattered, pinnate leaves. Another problem may be the identification of the location, The archaeobotanical record from the Roman Empire is extremely scanty. Excavations at Arikamedu on the southeast coast of India, which cover the period of about 300 BC–AD 200 and later, have yielded remains of the coconut . The presence of all kinds of Roman period remains that have been unearthed attest contact with the West. According to Casson , it could well be that a colony of Westerners resided here who were chiefly engaged in forwarding goods not all the way to Egypt but only to intermediate stations at Muziris and Nelkynda on the southwestern coast of India. Both these sites have not been excavated yet, so nothing can be said about the possible presence of the coconut palm or other plant species there. Anyway, the record of coconut from Arikamedu makes it very likely that the Westerners, putatively present in Arikamedu from the early years of the first century AD until ca. AD 200, would have known it. Unfortunately, no botanical research was carried out in Arikamedu so that only species are recorded that could not have been overlooked: the coconut palm and the palmyra palm . Further botanical evidence of the connection between Berenike and this site, therefore, remains unknown. With the exception of a few husk segments from trench BE99-33, all fragments of coconut unearthed in Berenike concern endocarp fragments. The unbalanced representation of different kinds of fruit fragments in the sub-fossil record suggests that most coconut fruits were traded as dehusked, whole fruits. It is also possible that part of the coconut had been traded as copra, but the chance of recovering such pieces is small, as no detectable waste is produced and recovery relies on discarded pieces.

Unopened coconuts can be kept for consumption until all the liquid endosperm has disappeared. As soon as the coconut is opened, the production of free fatty acids starts and consumption cannot be delayed too long. To exclude the possibility of contamination, a radiocarbon date has been obtained from one fragment, originating from BE96-13.002 and giving 1935 ± 35 BP . The calibrated date coincides with the first two centuries AD. No attempt has been made to convert coconut fragments to whole specimens. Taking into account the scattered distribution of these fragments in trash deposits and the estimated expected finds in the unexcavated area, we can deduce that the coconut was not a rare commodity in either early or late habitation periods. This interpretation is supported by the fact that most coconut fragments were not worked after consumption of its “meat.” So far, only five worked fragments have been unearthed. Two of them, which have holes measuring 7.5 and 13 mm, were found in the same trench . It is possible that they were used for making beads or buttons. In trench BE99-21, a fragment was found with a carved decoration showing a pattern of lines at a right angle. Trench BE99-33 yielded two worked fragments that looked like cups with a diameter of approximately 6.5 cm. One of these fragments still had some resin present along part of its rim. Actually, this low frequency of worked fragments of such an exotic fruit,raspberry plant container having an attractive size and a hard endocarp, making it suitable for fashioning into all kinds of decorative and useful articles, is striking. Even so, it is to be expected that future excavations at Berenike or any other Roman settlement will unearth worked fragments of this nut. As far as the Indian subcontinent is concerned, it is very likely that the coconuts from Berenike would have been imported from ports along the Malabar coast. The most productive area of coconuts in India is confined to its interior and the present name of this state is Kerala, which literally means “the land of the coconut.” The abundance of coconut palms is, for example, expressed in the description of the landscape of Tyndis in a Tamil poem cited by de Romanis , saying that “In its immense fields grow coconut palms laden with fruit, . . .” Due to the activity of pirates, Tyndis was abandoned, as the people moved to the more southerly Muziris and Nelkynda. The cultivation of the coconut palm at isolated spots along the strait of Bab el-Mandeb and the Gulf of Aden, as recorded from the last centuries, leaves open the possibility of a shorter trade route for the coconut. If so, coconuts might have been obtained from Muza or Kanê. Today, this area falls outside the main coconut producing areas and it is, therefore, merely speculative to assume this was an alternative trade route. Coconut fragments belonging to several specimens were also found in Quseir al-Qadim, though dated to the Mamluk period . The only other reference of coconut concerns an Egyptian specimen of unknown age and origin, kept at the Florence museum.

Initially, E. Bonnet did not preclude the possibility of a Greco-Roman date, suggesting that the coconut was merely a curiosity from India . Later, however, he expresses doubt about its ancient date. The coconut is mentioned for the first time on a list that presents all the objects that were collected by Dr. Alessandro Ricci during his travels in Egypt in 1818 and 1822. This list was compiled by M. Arcangelo Migliarini in 1932 on the occasion of the acquisition of the collection by the archduke of Toscane. The coconut is described in the last part of this catalogue as “Un frutto di Cocco. Una mezza scorza di un piccolo cocco” . Because this last part of the list deals with Ricci’s anthropological collection, it is assumed that it is of recent date, despite the fact that a contemporary is of the opinion that it is an old coconut indeed . The reliability of Italian inventories from the nineteenth century and the fact that Riccipays no special attention to the coconut argues for a recent date. But the curious thing is that an ordinary fragment of a coconut is considered as an anthropological object. A definite answer concerning its age, therefore, can only be obtained by radiocarbon dating. It has frequently been suggested that coconut oil was present in Egyptian graves. According to Lucas and Harris , however, this assumption is wrong, because the strong smell is due to a very small proportion of nonoic acid, which had been formed as a result of decomposition of fatty materials.Among the many beads that were found at Berenike, four specimens could be identified as Job’s tears. This bead is made of the false fruit of Job’s tears, a grass species that is closely related to maize . In maize, male and female flowers are arranged in separate inflorescences, in which each female inflorescence consists of a number of fertile flowers and is enclosed by a series of almost bladeless leaves. In Job’s tears, however, each inflorescence bears both female and male flowers, and only the lower fertile flower of each inflorescence is enclosed by a tough and modified sheathing bract or involucre. The slender axis of the inflorescence that bears the male flowers protrudes through the somewhat oblique opening of the callous bract. Once the fruit is detached from the stem, Job’s tears is already effectively a bead, as the basal area has an opening as well as the top. Moreover, the grain is folded lengthwise around the axis, creating a natural groove that facilitates its piercing. The specimen from Berenike has a hard shell, which is indicative of the wild species that is used for bead making. The decorative fruits are mostly tear-shaped to globular in shape, have a white to brown, shiny coating and are 6 to 12 mm long, making them applicable to all kinds of bead work. Although the glossy surface of the Roman specimen from Berenike had disappeared, the shape, the basal perforation, and the characteristic orifice at the top of the fruit justify the identification.

Even when all the water has been absorbed by the soil, which may take a couple of weeks or even months, depending on the amount of water and the soil structure, such play as are still easily recognized because their surfaces are sealed with silt, which bursts open after drying. When all the water has been absorbed, small holes are made in the soil, which are then filled with water. The next day, several seeds of sorghum are put in each hole. Only during the first week, extra water supply is given if necessary. From then on, the farmer only does the weeding . The plants can be harvested after six months and are used as forage for camels. One would assume that the cultivation of cereals such as sorghum and barley is only meaningful if fair sized fields are sown. Evidently, present cultivation of cereals in the Eastern Desert is mostly practiced on a small scale and has an opportunistic character. Sorghumis a crop domesticated in Africa and has a C4-metabolic pathway making its photosynthesis very efficient in an environment characterized by high temperatures and light intensities. Being C3-crops, barley and wheat lack this photosynthetic adaptation to arid conditions and, as a consequence, irrigation is necessary. Long-term irrigation is a disadvantage as the soil may become salty, a condition to which only barley has a considerable tolerance, as far as cereals are concerned. The reason that barley is the preferred crop in drier environments but still suitable for agriculture is that it has a relatively short life cycle. In this way, it succeeds in avoiding water stress. Additionally,seedling grow rack its roots are well developed in the upper soil layer, enabling the plant to benefit from rain showers and morning dew.

Besides problems dealing with water and thermal stress, cereals also have to survive diseases and predation. Crops may be affected by flying animals and microbial diseases such as smut. The leaves of sorghum plants near Arab Saleh, for example, were partly damaged by caterpillars. A fungal disease that was found on sub-fossil remains of barley will be discussed in Chapter 4. Although the grains of sorghum are mostly used as animal fodder—the absence of gluten making it is unsuitable for bread making—it can only be fed in a fresh condition to animals after seed ripening. The presence of the poisonous dhurrin, a cyanogenic glucoside, in the leaves during the growing season and also after drying , makes it necessary to fence off the fields and excludes the possibility of hay making. The dried culms can be used as fuel or as building material. The competition for water in an arid environment results in relatively large distances between plants, so that the spatial distribution of the roots of each plant ensures the uptake of sufficient amounts of water. The relatively large distance between plants is apparent in sorghum fields and kitchen gardens. To reduce water competition, special attention has to be paid to weed control. Nevertheless, in most kitchen gardens, desert plants with a weedy character, such as Sonchus sp., Zygophyllum simplex, and Caylusea hexagyna, were found. In the sorghum field south of Arab Saleh, the following weed plants were recorded: Forsskålea tanacissima, Farsetia ramosissima, Aristida funiculata, A. adscensionis, Tribulus terrestris, Dichanthium foveolatum, Astragalus eremophilus, A. vogelii, Trichodesma ehrenbergii, Zilla spinosa, Acacia tortilis, and Morettia sp. All these species are desert plants and are also found outside the cultivated areas.With respect to the exploitation of plants by man, two terms need to be addressed: cultivation and domestication.

Cultivation concerns the exploitation of plants in its broadest sense, including the harvest of useful products of wild growing plants. Domestication, on the other hand, is restricted to a human-induced process in which plants become dependent on humans for their reproduction . It follows logically from these definitions that domestication implies cultivation. Domesticated plants are mostly recognizable, as such, in an archaeobotanical context, since generative parts, especially, have undergone morphological changes. It may be difficult however to pronounce upon the cultivated status of wild plant species that are considered to be part of the surrounding vegetation in former times. As far as edible plants are concerned, the presence of leftovers unequivocally indicates a cultivated status. But more often, remains of wild plant species are found that do not show clear evidence of a special use. Sometimes, a specific use is known from present-day dwellers, eventually from a more remote area, but mostly no traces of such a use are detectable. In such cases the plant might have been deliberately collected by man but may also have been transported to the site by natural dispersal agents. In the Eastern Desert, both strong winds and irregular occurring torrents are responsible for the transport of plant remains over long distances. Obstacles such as buildings and depressions are excellent seed traps. This process was continuously evidenced during the excavation seasons, where a trench sweep is a daily procedure, and old trenches are filled with sand intermixed with all kinds of plant remains, including tumbleweeds and plants that germinate in such protected safe sites. It may thus be clear that the status of some wild plant species that have been found at Berenike and Shenshef is still obscure.

Some of them have been categorized as cultivated ones, such as beet and Johnson grass , although conclusive evidence is lacking for such a labeling. On the other hand, the potential use of several wild plant species will be mentioned in the next section to compensate for the assumption that they were dispersed by natural dispersal agents. It is assumed that most desert plants with an economic value will have been exploited without intentional planting in gardens or plantations. For this reason, all cultivated plants that grow wild in the Eastern Desert, the Red Sea coastal area, and/or the Gebel Elba area will also be dealt with in the next section. This section presents all cultivated plants from Berenike and Shenshef that have been evidenced by at least non-woody remains. Plants evidenced by wood identification are described by Vermeeren . Some of them will be discussed briefly in the summarizing section. The cultivated plants are described separately in alphabetical order. Each description starts with the scientific name and, as the occasion arises, relevant synonyms are also mentioned. Synonyms that are linked to wild progenitors, such as Olea oleaster Hoffm. & Link. and Vitis sylvestris C.C. Gmel, have been omitted. Next, English, Arabic, and Indian names are presented alphabetically, followed by a description of the plant parts, the trenches in which the plant has been evidenced, the period, the state of preservation, and a reference to a picture of the plant remain. The scientific plant names are mainly based on Wiersema and León . Tentative identifications on a species level are indicated with “cf.” . For example, Monsonia cf. nivea means that only the identification on the genus level is certain, but that the identification to the level of species is only tentative. The common names were obtained from a variety of sources, in which the preferred common English plant name follows Wiersema and León . The Arabic and Indian names are taken mainly from Bedevian , Kamal , Kay , Mandaville , and Dey . These common names refer to whole plants as well as particular plant parts of economic value. All variant spellings have been listed that were found in literature. Doubtless this compilation is by no means complete. The common names are arranged alphabetically and are also indexed. It should be realized that the same name may be used for several plant species, including non-cultivated ones. For each plant, the official names of the recovered remains are mentioned. Sometimes such labels deviate from the names that are commonly used. Such established names may, however, be incorrect and confusing, which is caused by several factors. The main objective of using the official botanical names is that it facilitates an unequivocal description. This, in turn, enables an interpretation with respect to the processing of the plant remains,greenhouse growing racks including preservation techniques that might have been used and a comparison with present-day samples of these plants. To avoid an unreadable text, the botanical names are explained when necessary and eventually also linked to more-popular terms. For the same reason, specific names of fruit types, such as pods and legumes, have been omitted in the description of the botanical remains. First of all, the labeling of “seed” and “fruit” is not always correct.

Strictly speaking, an ovule develops into a seed and an ovary develops into a fruit. This means that a seed is always enclosed by a fruit. Unfortunately, seeds and fruits are not always clearly separated, as for example, the members of the mustard family and the legume family . If only one seed is produced in a fruit, very often the fruit coat is fused with the seed coat. What appears to be a seed is in fact a fruit. Such fruits are produced, for example, by members of the buttercup family and the daisy family .A second factor that obscures the issue is the great variety of fruit types. Thus, the so-called diaspore may either be a seed, a fruit, or even a false fruit. The fig may serve here as an illustrative example. Very often, sub-fossil records mention that seeds or fruits of the fig have been retrieved, but the official labels should be “fruits” and “accessory fruits,” respectively. If the description is unequivocal, for instance in the case of dried fruits, it is not problematic. Unfortunately, this is mostly not the case, as can be deduced, for example, from the codex of ancient Egyptian plant remains by de Vartavan and Amorós , which lacks a sound botanical standardization. Another complication arises from the taphonomic processes and preservation conditions, both resulting in the fragmentation of botanical remains. A correct identification of such fragments should ideally be based on the anatomy of the diaspore. But again, popular names, partly derived from the description of fruit types, are often used instead. Examples of such names are shell, flesh, meat, pip, and kernel. The word stone is used, for example, both for the seed of a date palm fruit and for the endocarp of fruits, which are classified as “drupes,” such as the discarded inner part of an olive fruit. Standardization of descriptions for the archaeobotanical remains of cereals Triticum and Hordeum, including threshing remains, has recently been recommended . Trench numbers, recorded in a consecutive series throughout the whole excavation period, indicate the origin of the botanical remains from Berenike. In Shenshef, on the other hand, the numbering of trenches starts at one in both seasons. A complicating factor in the numbering is that a particular midden has been excavated in three different trenches . Therefore, the numbers of the middens from Shenshef have been used instead to designate the origin of their botanical remains. Only in particular cases, where a more detailed description is considered as informative, are complete locus identifications given. The locations of the trenches and middens are indicated in Figure 4.3 and Figure 4.4. Plant remains can be preserved in different ways: waterlogging, mineralization, desiccation, and charring. Additionally, imprints in pottery, for example, may indirectly maintain the presence of a species in the course of time. The type of preservation depends on environmental conditions and human activity. The plant remains from Berenike and Shenshef are preserved by desiccation and charring. Owing to the extreme arid conditions, plant remains can be preserved by desiccation without special treatments. Basically, this nondestructive mode of preservation is valid for all kinds of plant remains. Differences in fragility, however, allow for bias in favor of the more-solid remains such as seeds and fruits. Since these generative plant parts are, by nature, adapted to survival in the soil, they offer resistance to both mechanical hazards and decay by microorganisms. This kind of preservation is sometimes erroneously mentioned as “mummification,” a qualification that is, however, only applicable to organic subjects that have been treated in a special way to improve preservation. Even plant remains that have been found in tombs and are stored as offerings for the dead do not deserve this special qualification. Charring, on the other hand, is mostly human induced and destructive in character .

In the Ma’aza territory, north of the road between Quseir and Qift, such wet years are reported, among others, 1928–1932, 1949–1951, 1956–1958, and 1977–1985. Seven cloudbursts are recorded by Springuel over the past 15 years in the southern part of the Eastern Desert. The most recent one was in November 1996 and fell over much of the Western and Eastern deserts. However, winter rains mostly result in limited amounts of rainfall. Because the main rain-producing winds come from a northeasterly direction, rainfall is concentrated on the northeastern sides of the mountains. This orographic influence of the Red Sea coastal mountains results in a comparatively well-developed flora on the slopes. The Elba area in particular, located some 260 km south of Berenike, catches much water in this way, and a unique Sudanese flora characterizes its slopes. Most mountain slopes north of the Gebel Elba are, however, almost barren. Especially during nighttime, the evaporation is minimal, and much water sinks into the coarse wadi sand. Some water is caught in rock depressions and is used by animals and humans as a source of drinking water. Even if such rocky clefts are difficult to inspect by eye, the presence of water can easily be checked by throwing a piece of stone. For the Eastern Desert it should thus be realized that the almost-barren orographic relief affects principally the redistribution of rainfall. As a result, the water supply of wadi branches is actually much more than what is calculated on the basis of the mean annual precipitation. This concentration of water is also supported by the presence of impervious surface crusts,blueberry plant pot which are found in hyperarid regions in particular and are virtually water resistant .

Water that penetrates deep into the wadi escapes evaporation and will be available for plants with deep taproots. The amount of water that can sink into the ground will largely depend on the texture of the soil, in which penetration and the coarseness of the soil texture are positively correlated. For this reason, sandy soils offer better water supplies in dry regions than clay soils . Silty depressions are an exceptional case as the concentration of the water may compensate the high field capacity, which hinders water penetration. Groundwater will be drained by an underflow toward the Red Sea or the Nile. Such an underflow was probably used by the Romans in the watering station Kalalat as a source of water for the inhabitants of Berenike. The persistence of this water fl ow is demonstrated by the permanent presence of slow running water in a narrow gorge of Wadi Shenshef, even when preceding winter rains have not been recorded. From the Greek period onward, the groundwater in Arabia, stretching from Kuwait through eastern Arabia to Bahrain, has been exploited via a network of aquifers, which could be tapped for drinking water and irrigation .Atmospheric humidity is an important source of water for plants growing in the Red Sea coastal zone. Evaporation of seawater during daytime replenishes the water content of the air. This water partly condenses again as the temperature of the air sufficiently drops during winter and early spring. Considering the fact that air temperature is lowest just before sunrise, morning dew may therefore be responsible for damp soils. Unlike precipitation, morning dew is a much more steady water source for plants. Referring to agricultural practices in Bactria, Africa, and Cyrene, Pliny even states that crops depend on the dew fall at night for their nourishment. Also Theophrastus emphasizes the contribution of dew to plant growth in regions with no rainfall, including Egypt.

According to Jabbur , who studied the bedouin life in the Syrian Desert, there is so much dew on plants in spring, that some women collect the water in their water skins. This atmospheric humidity is of value for both the fl at coastal plain adjacent to the Red Sea proper and the mountains, which intercept the clouds blown inland. Especially high mountain massifs may receive considerable amounts of rain in this way. This also explains the presence of several mosses and ferns on the higher levels of the Gebel Elba . Fertilization of these plants is only possibly under moist-to-wet conditions.The adaptation of desert plants to water stress is diverse. Several principles can be distinguished and specific combinations of such principles may find their expression in desert plants. One possible adaptation that has arisen by natural selection is the storage of water in leaves, stems, or roots. Such plants are called succulents and are adapted to arid habitats as well as to saline environments. Succulent plants that grow in the Eastern Desert, including the environment of Berenike, are Suaeda monoica Forssk. ex J. F. Gmel, Halopeplis perfoliata Bunge ex Asch., and Aizoon canariense L. A good example of a halophytic succulent is Zygophyllum coccineum, which has swollen stems and leaves and is able to abort part of its leaves and even young shoots to prevent excessive water loss. Other plants have leaves with xeromorphic features. They are called xerophytes and are, by definition, adapted to arid regions. A common feature is the reduction in size and/or number of the leaves, as can be observed by Crotalaria aegyptiaca Benth. and Moringa peregrina Fiori. An extreme example of leaf reduction is demonstrated by Tamarix aphylla H. Karst, a shrub that has only sheath-like leaves. Another way of drought survival is shortening the life cycle. Annual plants that take advantage of the availability of water independent of the season, being either a rain shower or a damp period caused by dewfall, are called ephemerals. 

They include succulents, such as Zygophyllum simplex L.; nonsucculents, including grasses such as Aristida funiculata Trin. & Rupr.; and nongrasses such as Lotononis platycarpa Pic. Serm. Such plants can survive by a quick absorption of the rainwater and dew. Some of them have reasonably long roots, such as species of Aristida, whereas other plant species have only very small and shallow root systems, such as stunted but flowering specimens of Triraphis pumilio R. Br., Eragrostis ciliaris R. Br., and Coelachyrum brevifolium Hochst. & Nees. These plants were frequently found in the environment of Berenike and Shenshef. Some plants may develop temporarily so-called rain or extension roots, which grow in the upper part of the soil and absorb the water from a rain shower or dew . Perennials may also be have as ephemerals. Conversely, some species, such as Zygophyllum simplex, that normally behave as ephemerals, can prolong their life span under favorable conditions . They are as resistant to drought as a seed. Plants that obtain their water directly or through the capillary fringe from the groundwater are called freatophytes. Because in most cases groundwater is only available at considerable depths, freatophytes are predominantly perennial species that are able to develop deeply penetrating taproots. Regeneration of freatophytes will be especially successful during years with heavy showers, resulting in a moist soil from the surface down to the water table over a considerable time span. During this period, long taproots must grow to the water table. As soon as this is reached, the plants will have become independent of the unpredictable rainfall and can survive in an apparent unfavorable environment. A good example of a desert freatophyte is the twisted acacia , which may have a taproot of more than 40 m. Owing to its deep, penetrating root,plastic gardening pots this tree is capable of growing in the fringe of wadi branches. Their presence is even indicative of the many wadi branches that dissect the fl at coastal plains along the Red Sea. The growth of the root starts soon after germination. A seedling under a full-grown tree in Wadi Shenshef of only 2 cm high could be dug out to a length of 25 cm before its fragile root broke off. Examples of herbaceous species with long roots are Aerva javanica Juss. ex Schult., and Aizoon canariense L. Some plants, such as the Nile tamarisk , are capable of initiating condensation of atmospheric moisture by means of special hygroscopic salt crystals under conditions of high humidity . For this reason, drops of water on the surface of the Nile tamarisk taste rather salty. The water condensation is triggered when the humidityof the air exceeds 76 percent . Like dew deposition on the plant surface, which depends on a lower plant surface temperature in relation to the dew point temperature of the adjacent air, this salty water drips from the plant and can be absorbed by the shallow roots. The effectiveness of this self-induced sprinkling is evidenced by the many imprints of raindrops in the damp soil beneath such excretive plants.

The availability of water is, however, no guarantee for the presence of desert plants. This is especially true of regions that do not profit from the dewfall. Here, the irregularity of rainfall is at odds with the presence and longevity of seeds in the soil. Seed banks in desert soils are characterized by a concentration of seeds in the upper 2 cm of soil, with a high degree of spatial heterogeneity and a great seasonal and annual variability. Seeds tend to be concentrated in depressions where water collects and in wind shadows, such as below established plant species . As dispersal distances are generally short, a specific type of ephemeral vegetation may exist for several years . Isolated spots that are completely dependent on unpredictable showers may lack a viable seed bank, and consequently no vegetation will develop after rainfall .The major phytogeographical districts that are distinguished in Egypt are: the Mediterranean coastal strip, the Nile region, the deserts, the mountainous region of the Sinai proper, the oases, and the Sahelian scrub region in and around Gebel Elba . A further division is possible with respect to the Mediterranean area, the Nile Valley, and the deserts . Because the desert vegetation is of prime interest, only the division of the desert vegetation will be discussed in more detail. The Egyptian desert is divided by the Nile Valley into the Western or Libyan Desert and the Eastern or Arabian Desert. Additionally, the Nubian Desert is distinguished, being present on both sides of the Nile south of Aswan. Both the Libyan and Nubian deserts are flat and have several large depressions . On the eastern side of the Nile, three different deserts are distinguished. The Isthmic Desert is located south of the Mediterranean coastal strip on both sides of the Suez Canal. South of this desert, fringed by the Nile and the Gulf of Suez, lies a small desert area consisting of limestone mountains called the Galaga Desert. The Eastern Desert is the third one in the row and extends southward from about lat 26° N to the Gebel Elba region . This large desert is characterized by rugged, igneous mountains that run parallel to the Red Sea on the east side and a rocky plateau on the west side. The Red Sea mountains are dissected by a web of branched wadis that drain off into either the Nile or the Red Sea. Although a detailed labeling of the distribution of the complete Egyptian flora is presented by Täckholm , including a dichotomy between the northern and southern part of the Eastern Desert, which coincides with the territories of the Ma’aza and Ababda nomads, respectively, it has not been used in this study because it is too out-of-date due to many taxonomical revisions and corrections of geographical distribution records during the last decades. Between the mountains and the Red Sea there is a gently sloping coastal plain. Near Berenike this plain is only 8 km wide, but elsewhere it can extend as far as 35 km. This fl at plain is dissected by many wadis draining off into the Red Sea, and its flora differs so much from the flora of the mountainous areas that it represents a separate phytogeographical district. The Egyptian flora comprises almost 2,100 plant species. The distribution of these species over the major phytogeographical regions is presented in Figure 2.8. The analysis is based on the checklist of the Flora of Egypt , the Flora of Egypt and the Key to the Egyptian Grasses .

The first and second instar larvae were grouped into a single ‘larvae’ observation and recovered males and females were counted separately as well as grouped into an ‘adults’ observation . There were clear differences among the mean number of eggs and larvae found across the different plant types . ANOVA indicated a significant interaction between the plant and the developmental stage present on the respective plant . The interaction indicates there was a differential treatment impact with respect to the number of eggs laid and the number of larvae found. The presence of a significant effect of developmental stage indicates that the number of eggs and larvae in clip cages were not similar, i.e. egg mortality was higher with some plants versus others . A correlation coefficient of 0.75 was calculated between the mean numbers of eggs and hatched larvae. Tukey’s HSD rendered a significant plant effect for the total number of eggs and larvae present in the clip cages . More eggs and larvae were found on four types of plants, i.e. citrus , sumac , Star and Jewel . The blueberry varieties Showchaser and O’Neal had significantly lower total number of eggs and larvae and numbers on Emerald and O’Neal were intermediate . The Jewel variety data were slightly skewed, however,planting blueberries in pots as the mean number of eggs and hatched larvae were negatively correlated . Roughly 25% of males and less than 50% of female citrus thrips were recovered from the plants in the bug dorms 14 days post release. The between replicate bug dorm adult survivorship was relatively low.

Of ca. 60 adults of each sex released, male survivors per bug dorm ranged from 13-21 with a mean of 15.4 ± 3.3 [SE]; female counts ranged from 20-37 with a mean of 28.2 ± 6.4 [SE]. The Star variety had the highest mean numbers of adults collected in comparison with other varieties . Data from the bottom two thirds of the plant were pooled together, as there were few thrips collected and eggs found on the lowest third. There were more eggs located on the top third of the plant than the bottom two thirds of the plant across all plant varieties. There were also more larvae found on the top third of the plant than the bottom two thirds, but no differences in larvae found on the bottom two thirds of the plant than eggs present in those areas, for all plant varieties . The Star variety had the numerically highest numbers of total eggs and larvae per plant compared with any other variety. The likelihood ratio chi-square test indicated a significant effect of egg count on the top third of the plant as well as a significant effect of larval count on the two plant locations, i.e. the top third also having the highest count . More eggs were found on the top third of the blueberry plants and there was a higher percent of larvae present on the top third of the plant , regardless of plant variety. However, in the choise test, the Star variety had the highest percent of eggs found and larvae present. The Snowchaser variety had the lowest numbers of thrips counted overall, with fewer eggs, larvae and adults collected on that variety. The Misty variety had fewer larvae present than eggs laid and the number eggs laid were comparable to levels on Emerald.

Under the conditions of these trials , citrus thrips egg hatch typically would take place within 4-9 days , therefore numbers of motile insects counted in both studies would be larvae from the first generation and surviving adults. The primary focus of this work was to determine if there was a difference in the number of eggs laid on the different types plants and our data clearly show this was the case . The no-choice oviposition test showed that the highest number of eggs and larvae were found on citrus and sumac and the blueberry varieties Star and Jewel. Intermediate levels were found on Emerald and Misty, and the lowest numbers on Snowchaser and O’Neal. The Tukey HSD separation for total counts of eggs and larvae group Jewel with the citrus, sumac, and Star, but these data may be skewed due to the negative correlation between the number of eggs laid on the Jewel variety and the number of larvae present. The choice oviposition test also showed a correlation between the number of eggs located and the number of larvae present on the plant. Evaluation of count means showed a difference in citrus thrips numbers on the Star variety over the other blueberry varieties in the test. When given the choice to move about the plants, the citrus thrips’ activities at the time of isolation and counting appear to be similar for Emerald and O’Neal with a mean of less than 10 adults recovered from those plants. In the choice oviposition tests, the negative correlation between egg and larval counts is also apparent for the Jewel variety. Some explanations for this negative correlation could be: first instars eclosing from the egg suffered high mortality, the larvae did not or cannot feed and/or develop well on this variety, and/or the larvae dispersed away from the plant onto other plants. If the latter were the case, then one would expect to see one or more other blueberry varieties with higher numbers of larvae present, but that was not the case and given the fact the canes did not remain in contact with one another, it is unlikely that high levels of larval dispersion to different pots took place.

There are several possibilities which explain the results: 1) females chose to lay eggs preferentially in some varieties over others, 2) egg survivorship influenced the numbers counted/found, 3) first instar egg eclosion varied across variety, 4) differential larval survivorship and development on the plants, and 5) larval dispersion, possibly to other plants, but possibly off the plants with mortality ensuing in unevaluated portions of the bug dorm. The Chi-square values for plant location were significant indicating that there were disparate numbers of eggs laid and larvae counted between the two locations, with the top third of the plants, regardless of variety, preferentially chosen over the bottom two-thirds. This was likely due to the amount of flush growth present on the top third of the plants. Also, given data in our studies, thrips activities appear higher on the top third of the plant; this is likely a good area to sample when looking for thrips on blueberries. Combining all the data, our studies clearly show that the Star variety had more citrus thrips than the other blueberry varieties, and numbers of oviposited eggs found on Star, Jewel, citrus and sumac were similar. This quite possibly is due to Star’s parentage. The Star variety is a variety that produces flowers the earliest and for the longest period during the season and while yield may not be as high as some of the other varieties, it is planted as a season long fruit bearer. Because the high bush blueberries are hybrids of one another and the nurseries have proprietary rights to the genetics of these varieties, we are therefore unsure how closely related the varieties we tested are. Snowchaser was the variety least preferred by the citrus thrips based on our data, however, to our knowledge it is not a variety currently grown commercially in California. There are countless factors that need to be considered to fully understand insect host choice, including but not limited to, host plant finding, host plant acceptance, host plant relatedness, resource concentration, resource availability and host use . The insect’s ability to locate the host plant, settle, feed, reproduce and successfully produce the next generation that achieves reproductive maturity involves countless steps and subtle interactions that are beyond the scope of the work presented here. We provide a platform for further work on the distribution, abundance and avenues for research related to citrus thrips as a pest of blueberries in California. We anticipate citrus thrips will remain a pest of concern to the blueberry industry of California as the industry continues to expand. Citrus thrips, Scirtothrips citri , is a significant insect pest of citrus and mango fruits and has been recognized as a major pest of California citrus since the 1890s . In the USA,blackberries in containers citrus thrips are known from Arizona, California, Texas and somewhat recently, possibly Florida , whereas in Mexico they are reported only from northern Mexico . Based on its past distribution, several authors have reported that citrus thrips is native to southwestern North America and northwestern Mexico . Citrus thrips is primarily a pest of citrus in California, particularly in the San Joaquin and Coachella valleys. They can have a broad host range, including, but not limited to, alfalfa, rose, grape, laurel, cotton, date, fir, lucerne and various grasses, pecans, and other ornamentals. Citrus thrips have been collected from over 55 different plant species .

Their native host plant is hypothesized to be Quercus or more likely Malosma laurina Abrams which was likely one of citrus thrips more common native host plants in southern California and northwestern Mexico prior to the introduction of citrus. In the SJV of California, S. citri has recently broadened its known host range and become a significant pest of high-bush blueberries . Scirtothrips citri was not known in Florida until 1986 where it was first detected in grape surveys . A collaborator was aware that in Florida, S. citri is not often collected from or abundant in several crops it is notorious for attacking in other regions of the Americas , but it is the most common thrips species he has collected from native vegetation and weeds. Species identifications from slide-mounted specimens can be unreliable or inconsistent and alternative or additional methods of identification may be necessary. Morphological identification suggests that S. citri is present in California, Arizona and Florida, but given that it is not a pest on several crops one might expect in Florida, further investigation is necessary to determine if S. citri is actually a cryptic species complex. The development of molecular genetic techniques , predominantly analysis of mitochondrial DNA , has significantly contributed to an understanding of natural genetic diversity and speciation . Genetic markers offer additional methods of species determination and delineation, especially when coupled with morphological identifications . These approaches are especially useful in groups that demonstrate a mixture of diverse ecological traits coupled with a conserved morphology. Given the distribution of S. citri in major citrus growing regions of North America and the level of its pest status in those regions, re-evaluation of morphological and molecular identifications was deemed necessary. The goals of this work were to investigate the haplotypic variation among S. citri populations based on phylogenetic analysis of the mitochondrial and ribosomal DNA, and to identify possible cryptic species complexes within the Scirtothrips attacking citrus. The collection records for all specimens used in this study are listed in Table 1. Specimens were collected from various parts of California, Arizona, Texas, Florida , Mexico, Nicaragua and Turkey. Specimens from Turkey were included in this analysis as it is an under-represented area of the world and at the time of collection from citrus, the collector believed the specimens to be citrus thrips. Specimens were collected into 95% ethanol by beating the live thrips onto a white piece of paper, touching a clean 5/0 Princeton paint brush into the ethanol filled collection vial, touching the ethanol imbibed paint brush tip to the live insect so that the insect stuck to the paint brush tip and then depositing it passively into the collection vial. After collection, all specimens were stored at -20°C until analysis. Some of the collections contained Frankliniella occidentalis and Neohydatothrips burungae but these collected groups were not included in our analysis.spinetoram and this may result in reduced E. hibisci mortality. Growers should be aware of the data presented herein when deciding upon a pesticide rotation management plan, which reduces avocado thrips resistance evolution. Each of the four recommended products have different features with respect to the efficacy of thrips control, concurrent control of avocado mite pests, and persistence of impacts on predaceous mites and other natural enemies . Thrips were removed from ethanol and allowed to air dry on filter paper for 2 min.

The upper and lower parts of the Plexiglas sandwich were solid and between the lower base and test arena a piece a piece of filter paper was placed to allow moisture exchange and to extend the life of the leaf during the bio-assay. Airflow through the test arena was provided through two holes drilled through the center cell layer directly opposite one another, with fine-mesh screening melted onto the interior of the test arena to prevent escape. The Plexiglas sandwich was held together with four binder clips positioned such that the airflow was not covered. Once dry, the leaves were placed on the filter paper in Munger cells and the respective thrips species was added. The lid was placed on the cell but leaving the cell arena exposed, so that once the thrips were added, the cells could be closed quickly. Female and late second-instar avocado thrips and citrusthrips were then placed on treated leaves of their respective host plants inside the Munger cell. Control leaves for both species were treated with a mixture of the same suspension ingredients minus the protein. Bioassays were conducted concurrently in the following manner for both species: adult female thrips were placed on leaves coated with activated or inactivated forms of both Cyt1A and Cry11A, immature thrips were also placed on leaves coated with activated or inactivated forms of both Cyt1A and Cry11A, and all combinations for adults and immature thrips were carried out along with the corresponding control cells. The Munger cells were closed and placed in an environmental chamber at 28ºC, 55% RH,raspberry container and long daylight conditions . Each cell was carefully removed daily and the filter paper doused with water to prevent leaf desiccation. The bio-assay was replicated on two separate dates .

A minimum of 10 individuals was placed into each Munger cell and thrips were checked daily for eight days to assess mortality. Post seven days, the integrity of the leaves was questionable and in all but one bio-assay, mortality was observed before seven days; thus data were analyzed using day 7 mortality. Six strains of B. bassiana were obtained from the USDA-ARS Western Integrated Cropping Systems Research Unit located in Shafter, CA. GHA is the commercially available strain found in the field formulation of B. bassiana, Mycotrol O and the greenhouse formulation BotaniGard ES, and each of the other five strains were obtained via isolation from soils in Kern County by USDA-ARS collaborators in 2000. They were stored at – 80ºC. Culture methods for the thrips experiments were similar to those described previously for Lygus hesperus Knight bio-assays and were conducted by collaborators from USDA-ARS, Shafter, CA. Briefly, isolates were grown on SDAY media, or Sabouraud’s dextrose agar plus yeast extract . The conidia were harvested from culture plates after 10–14 days incubation by scraping with a sterile rubber policeman into a 0.01% solution of Silwet L- 77 . The conidia were then enumerated with a hemocytometer. For preservation and storage, glycerol was added to the conidial suspension and stored in aliquots of 2 × 108 in a 2 ml solution at −80°C until needed for bio-assays. Conidial viability was assessed following incubation for 16 h in potato dextrose broth just prior to use in experiments. Viability was determined by adding a sample of approximately 107 conidia to 20 ml potato dextrose broth and incubating ca. 16 h in a rotary shaker at 28°C.

Conidia germination was examined under a compound microscope at 400× and scored as viable if the germ tube was at least twice the length of the conidium. Percentage viability was measured on 250 conidia of each isolate. All bio-assays were conducted on the basis of the number of viable conidia measured after thawing and the desired concentrations were formulated by serial dilution. The strain from Mycotrol was isolated and cultured exactly as above to eliminate possible effects of production methods and formulation ingredients on insecticidal activity. Glycerol was not removed prior to using the conidia in bio-assays. All six B. bassiana strains were suspended in 0.01% Silwet in a de-ionized water solution and evaluated on the same date at four concentrations for each thrips species. The control consisted of 0.01% Silwet in de-ionized water solution. Each of the 25 treatments was evaluated using five Munger cells , which contained a minimum of ten adult female thrips. These bio-assays were repeated on 10 dates with both species tested simultaneously on each date . Groups of thrips were anesthetized by exposure to CO2 for 15-30 sec, and each strain was administered to the dorsum of the abdomen of each knocked out thrips quickly and carefully in a 1µl drop with a Burkard Hand Microapplicator over filter paper. The droplet spread the length of the thrips immediately and the thrips was then deposited, still knocked out, onto the leaf tissue in the Munger cell. Once a minimum of 10 treated thrips were added, Munger cells were closed and sealed with binder clips and placed in an environmental chamber at 28ºC, 55% RH, and long daylight conditions . Each cell was checked daily for seven days to observe infection by the fungus. Each cell was carefully removed daily and the filter paper doused with water to prevent leaf desiccation. Individuals infected with B. bassiana were defined as those whose natural activity was retarded and/or showed arrestment and subsequently produced mycelia, which was confirmed post bio-assay.

Mortality caused by mycosis was confirmed on the basis of visual observation and then crushing individuals to reveal the presence of mycelial growth. When mycelial growth was not apparent, crushed individual thrips were placed on potato-dextrose agar plates for 5 days and then re-examined for the presence of mycelial growth. Data were analyzed after Abbott’s correction for control mortality using log-probit analysis with PROC PROBIT on SAS 9.2 and using the Raymond Statistics package . The purpose of the probit analysis was strictly for gross strain comparison. Probit analysis was used to estimate the LC50 and LC95 levels, confidence intervals, and χ 2 values for each strains. Lethal concentrations with overlapping 95% confidence intervals were not considered significantly different. The daily check data were analyzed as non-cumulative counts per day via the Survival Distribution Function on SAS 9.2 , where observation time represented the probability that the experimental unit from the population would have a lifetime exceeding that time with the variables strain and concentration. Assessments for each variable by species were done with Log-rank and Wilcoxon tests and multiple comparisons for the log-rank test were adjusted by using Tukey-Kramer method. Data were then plotted as estimates of the survivor function for the different strains separately for each species. Bacillus thuringiensis israelensis produces two groups of toxic proteins, the Cry and Cyt toxins that have different modes of action. In this investigation, results with Cyt1A and Cry11A were disappointing as both activated and inactivated forms of both proteins showed little effect against adult and second instar citrus thrips and avocado thrips. To our knowledge, there have been no reports of Bt endotoxins with activity against Thysanoptera, although Cyt1Aa was found to be toxic to the non-target species Chrysomela scripta Fabricius . Many hypothesize that because thrips feed with a punch and suck method, rather than direct chewing and mastication of leaf tissues, they do not receive toxic amounts of the Bt proteins . Alternatively, they may not possess the proper binding receptors for the Bt proteins tested to date and thus, no pore can be formed in the midgut lining and the Bt proteins are excreted . The literature indicates the latter hypothesis is more likely based on findings from life table parameters where development, fecundity,growing raspberries in container and adult longevity or relative abundance are not significantly different from thrips reared on Bt positive versus Bt negative corn, cotton, or potato plants. The aforementioned studies were not specifically looking at Bt effects on thrips nor were the Bti toxins tested here involved in previous studies involving thrips. The combinations of proteins used in this study were, to date, unique pairings with thrips. It is indeed possible that there are no Bt endotoxins currently available that cause mortality to Thysanoptera. The LC50 with strain GHA was 8.61 x 104 conidia/ ml and was two orders of magnitude lower than for the other five B. bassiana strains tested . GHA also gave the only statistically valid dose-response values in probit analysis, and provided the only data that fit the probit model. The other B. bassiana strains failed to provide a linear relationship based on their p-values , i.e. the probit regression lines were of poor quality, except for GHA. Therefore, data were evaluated based on line slopes as is commonly seen in the scientific literature with other biological agents where data lines are not straight and do not fit the model . Strains 1741ss, SFBb1, S44ss, and NI1ss showed a flat dose-response between concentrations, did not fit the model, and LC50’sranged from 2.7 x 106 – 9.6 x 108 . Assessment of Beauveria strain while adjusting for concentration, in both Logrank and Wilcoxon tests showed that strain and concentration had a highly significant effect on the infection rate. Multiple comparisons for the Logrank test to assess the strain effect while adjusting for the concentration differences showed that strains 1741ss, S44ss, 3769ss, and NI1ss infection rates were not distinct from one another.

Strain GHA and SFBb1 had infection rates different from each other as well, and GHA had the fastest infection rate and SFBb1 showed the slowest kill rate . The Survival Distribution Function analysis coupled with the probit analysis clearly shows that GHA would be the best strain choice for citrus thrips control. Results with avocado thrips. The LC50 for strain GHA was 2.2 x 106 conidia / ml and was similar to that obtained with the other five B. bassiana strains tested . Again, because a strong linear response was not observed, the performance between strains was rated based upon the LC50 and relative linearity of the response. Based on overlap of confidence intervals, there were no significant differences between any of the strain LC50’s or LC95’s . Assessment of Beauveria strains while adjusting for the concentration, using both Log-rank and Wilcoxon analysis showed that strain did not have an effect on the infection rate. The multiple comparisons for the Log-rank test to assess the strain effect while adjusting for the concentration differences showed infection rates for all 5 strains were not distinct from one another . The Survival Distribution Function analysis coupled with probit analysis indicated there was no one best strain to select for avocado thrips management. Citrus thrips were more susceptible to Beauveria than avocado thrips; citrus thrips LC values were much lower for the most active strain, GHA, indicating that significantly lower dosages of strain GHA were required to infect and kill citrus thrips compared with avocado thrips. The overall survival analysis results showed a similar pattern to the results of the probit analysis; GHA had the fastest infection rate and SFBb1 had the slowest rate . Infection rates for the other three strain’s fit in between the rates for GHA and SFBb1, and 1741ss, S44ss, 3769ss, and NI1ss infection rates were not separable. This low dosage association and having the fastest infection rate suggest GHA is the best candidate for field-testing among the strains examined. Except for the worst performing strain, SFBb1, the performance of all of the strains with avocado thrips were similar. The LC50 value for citrus thrips was 8.6 x 104 conidia/ml, which may suggest economical feasibility in some cases, e.g., for use on organic products. The maximum recommended field application rate is 5.0 x 1012 conidia/ha. Therefore, 8.6 x 1011 conidia/ha of GHA is needed based on the estimated LC50 of 86 conidia/µl and this amount is reasonable to obtain in a field setting. Conducting the same analysis for avocado thrips control using GHA, with an LC50 of 2.2 x 106 , 2.2 x 1013 conidia/ha would be required. This is 4.4 times greater than the standard field use rate of GHA. We hypothesize that differences in susceptibility between citrus and avocado thrips may be due to the different habitats in which they evolved.

These treatments are provided visually in Figure 1.In the second experiment, individual grapes from different cluster positions were collected from two cultivars grown in a commercial vineyard in Oakville, CA in 2017. Cabernet Sauvignon grapevines and Petit Verdot grapevines were 21 and 9-years old, respectively. The exposure of each individual grape was estimated with fish-eye lens photography from the grape perspective pointing the zenith. The images were processed in R . After applying a thresholding condition to the blue channel of all images, they were converted into binary pixels . Thus, the percent of binary pixels capturing the sky was used to calculate the percentage of canopy porosity as reported previously . Then, those berries were collected at harvest, and their flavonoid content was analyzed with reversed-phase high performance liquid chromatography.The experiment was conducted in 2019 in Oakville, CA with row orientation NW-SE. The vineyard was spaced 2 m × 2.4 m with Cabernet Sauvignon grapevines on 110R root stock. The grapevines were trained to a vertically shoot-positioned system with a cordon height 96 cm above vineyard floor, trained to a bilateral cordon, and pruned to 1-bud spurs. Plants were irrigated weekly with 2-drip emitters per vine, with the capacity to deliver 3.8 L of water per hour. The experiment was designed as a randomized complete block with three canopy management practices: removal of 5 to 6 basal leaves on the NE side ; thinned to 24 shoots per vine ; and a combination of LR and ST and an untreated control ,square plant pots with four replicates each consisting in 5 grapevines, 3 of which were sampled and the 2 on distal ends were treated as border plants.

The ST and LR treatments were applied on 11 June 2019. Harvest commenced when the berry TSS reached to ca. 24°Brix on 23 September . The sampling time points were as follows: 2 weeks before veraison , veraison , 2 weeks after veraison , 3 weeks after veraison , 5 weeks after veraison , and harvest , were chosen to cover the response of the berry metabolism to cultural practices and the concomitant increase in exposure.Leaf area index was measured on 21 June to characterize grapevine canopy growth and converted into leaf area on by a smartphone based program, VitiCanopy, coupled with an iOS system . The gap fraction threshold was set to 0.75, extinction coefficient was set to 0.7, and sub-divisions were 25. A “selfie-stick” was used for an easy access to place the device about 75 cm underneath the canopy. The device was positioned with the maximum length of the screen being perpendicular to the cordon, and the cordon being in the middle of the screen according to previous work . In each experimental unit, three images were taken to capture half canopy of each vine, and analyzed by the software. The relationship between leaf dry mass and area was determined on a sub-sample of leaves of different sizes using a leaf area meter . Total leaf area was calculated by defoliating one grapevine per treatment replicate after harvest and using the regressive relationship between leaf dry mass and leaf area. At harvest, clusters were manually removed, counted, and weighed on a top-loading balance. Leaf area to fruit ratio was calculated by dividing leaf area with crop weight. Dormant pruning weight was collected during the dormant season ; and crop load was calculated as the ratio between yield per vine and the pruning mass of each vine. Labor operations costs and gross income per hectare were calculated based on yield and net returns per hectare and methods presented elsewhere . Anthocyanin productivity was calculated as reported by Cook et al. .

At each sampling point and experiment, 55 berries were randomly collected from the middle of each treatment-replicate and kept on ice until they were measured. Berries were weighed, and mean berry mass was determined as the average mass of the counted berries. These berries were used to determine the total soluble solids , the pH, and the titratable acidity . TSS was measured as °Brix, with a digital refractometer . The juice pH and TA was determined with an autotitrator using sodium hydroxide to titrate to an end point of pH 8.3, and it was expressed as g•L−1 of tartaric acid.For each sampling point in each experiment, 20 berries were collected, gently peeled, and berry skins were freeze-dried . Dried tissues were ground with a tissue lyser . Fifty mg of the resultant powder was extracted in methanol: water: 7 M hydrochloric acid to simultaneously determine flavonol and anthocyanin concentration and profile as previously described Martınez-Lüscher et al. . Briefly, extracts were filtered and analyzed using an Agilent 1260 series reversedphase high performance liquid chromatography system coupled to a diode array detector. Separation was performed on a reversed-phase C18 column LiChrospher® 100, 250 mm × 4 mm with a 5-µm particle size and a 4-mm guard column of the same material at 25°C with elution at 0.5 ml per minute. The mobile phase was designed to avoid co-elution of anthocyanins and flavonols consisted in a constant 5% of acetic acid and the following gradient of acetonitrile in water: 0 min 8%, at 25 min 12.2%, at 35 min 16.9, at 70 min 35.7%, 65% between 70 and 75 min, and 8% between 80 and 90 min. The identification of flavonoid compounds was conducted by determining the peak area of the absorbance at 280, 365, and 520 nm for flavan-3-ols, flavonols and anthocyanins, respectively. Identification of individual flavan-3-ols, anthocyanins, and flavonols were made by comparison of the commercial standard retention times found in the literature. Commercial standards of epicatechin, malvidin-3-O-glucoside, and quercetin-3-Oglucoside were used for the quantification of flavan-3-ols, anthocyanins, and flavonols, respectively.

The determination of proanthocyanidins was performed using an Agilent HPLC-DAD after an acid catalysis in the presence of excess phloroglucinol , with minor modifications described in Martınez-Lüscher et al. .The 3-isobutyl-2-methoxypyrazine was quantified by a stable isotope dilution assay using headspace solid phase microextraction coupled to a gas chromatograph and a mass spectrometer as described Chapman et al. and Koch et al. with some modifications. Briefly, 20 berries per treatment-replicate from Experiment 3 were randomly collected from the clusters of three vines in the middle of each treatment-replicate on both side of the canopy, by cutting the pedicel with a pair of scissors and frozen at −80°C until analysis. Pedicels were removed by hand and berries were placed in 50 ml conical tubes. 10 ml of pure water and 100 ml of deuterated IBMP isotope were added into the tube. Then, samples were ground with a tissue homogenizer Power Gen 1800D and centrifuged at 3000 rpm for 10 min. 10 ml of the supernatant was pipetted into 20 ml SPME vials containing 3 g of sodium chloride.Statistical analyses were carried out using the R-Studio version 3.6.1 for Windows. All data were subjected to Shapiro-Wilk’snormality test . Correlations between variables were calculated with the Pearson’s test by using the same software. Segmented regression analysis was used to determine the point of inflection the in the relationship between increasing exposure and the berry skin anthocyanin and flavonol content with “segmented” 0.5-0.3 R package . Data were normally distributed and, subsequently, were submitted to an analysis of variance to assess the statistical differences between the treatments applied in each experiment performed. Means ± standard errors were calculated, and when the F value was significant , a Duncan’s new multiple range post hoc test was executed using “agricolae” 1.2-8 R package . When data were not normally distributed, a Kruskal-Wallis test was conducted. Percentage data were transformed according to the suggestion of the most likelihood test,plastic pots for planting into arcsine root square before ANOVA or Kruskal-Wallis tests.The growing season of 2017 was warmer and drier compared to the reference data for the same period within the last 20 years . Thereby, average daily temperature was 4°C higher and rainfall was 18 mm less. Grape berry mass differed significantly depending on the degree of exposure . Overexposed berries were the smallest due to overexposure resulting in dehydration thereby reducing berry mass. Neither total soluble solids nor titratable acidity changed regardless of the degree of exposure to which berries were subjected. However, the juice pH of the Exp+ Deg+ and Exp+ Deg++ berry must was greater compared to Exp− and Exp+ Deg− berries. Berry skin flavonoid content and composition were also affected by the degree of exposure . The berry anthocyanin content of Exp− was similar to Exp+ Deg−. However, overexposed berries resulted in berry anthocyanin content that was 70% and 90% lower when compared to the Exp− berries. Grape berry exposure to solar radiation not only affected the anthocyanin content but also modified the ratio between the tri- and di-substituted anthocyanins leading to a less stable profile in all treatments with exposed berries. Likewise, berry skin flavonol content and composition were strongly affected by the degree of exposure to solar radiation. Therefore, in Exp+ Deg− flavonol content was two-fold greater than Exp−, albeit they abruptly decreased in overexposed grapes where flavonol content was 25% and 50% lower when compared to Exp− berries. Furthermore, in overexposed berries the proportion of kaempferol and quercetin significantly increased while the proportion of myricetin decreased. Regarding proanthocyanidins in berries, mild exposure did not affect their content in Exp+ Deg− compared to Exp− berries.

However, greater solar exposure decreased proanthocyanidin content in berries but to a lesser extent compared to Exp−. Finally, the content of flavan-3-ols was severely reduced in Exp+ Deg++ berries .The analyses performed on single berries from two varieties confirmed the obtained response in anthocyanins and flavonols in Cabernet Sauvignon . Thus, exposure affected the accumulation/degradation of these flavonoids. Exposed berries from the East side of the canopy decreased 8%and 36% of the anthocyanin content in Cabernet Sauvignon and Petit Verdot, respectively. Thus, Petit Verdot seemed to be more sensitive to higher level of solar exposure and degraded anthocyanins. Overexposed berries of Cabernet Sauvignon resulted in an 87% decrease of the berry skin anthocyanins when compared to the interior berries . Berry skin anthocyanins and increasing exposure showed a significant trend below the 22% of kaempferol . Conversely, analysis of the segmented regression on Petit Verdot berries did not show a clear trend below the 3.2% of Kaempferol and after the point of inflection, anthocyanins started to degrade . Regarding flavonol content, no differences were observed between cultivars . Conversely, when exposure increased to ca. 60% the content of flavonols in exposed berries of both canopy sides and in both cultivars; the overexposed berries had the lowest flavonol content . Thus, our data revealed a strong positive relationship between the berry skin flavonols and the percentage of kaempferol until 8.6% of kaempferol proportion for Cabernet Sauvignon and 7.2% Petit Verdot . However, beyond these thresholds, flavonols started to degrade, and there was an indirect relationship between the flavonol content and the percentage of kaempferol for both cultivars, this relationship being significant only for Cabernet Sauvignon .The weather conditions during the execution of this experiment were highlighted by greater maximum daily temperatures when compared to the reference period . This was more prominent during the driest months . Moreover, global solar radiation received at the experimental site was to ca. 200 W m−2 greater than the total solar radiation recorded within the reference period . The combinatory effect of LR and LT treatments caused a 58% reduction of LAI and a 45% increase of canopy porosity . However, neither leaf area nor pruning mass showed significant differences between treatments. On the other hand, yield components were mostly affected by the shoot thinning treatments . Thus, shoot thinned vines showed lower number of clusters, yield, and Ravaz Index , and increased leaf area to fruit ratio per vine as expected. The extent of yield reductions was 55% and 47% for ST and LRST vines, respectively . Berry mass was not significantly affected by canopy management practices during the berry ripening although vines subjected to LRST tended to result in smaller berries . The most influential effects observed on berry chemistry were due to shoot thinning treatments . Therefore, shoot thinned vines had greater total soluble solids and lower titratable acidity from mid-ripening to harvest. However, no significant effect was observed on the must pH . Shoot thinned grapevines had higher anthocyanin content at veraison . However, we did not measure any changes to anthocyanin content at harvest as affected by the canopy management practices applied.

For instance, to measure the relative strength of automatic associations between the BII bipolar dimensions of cultural harmony and cultural blendedness with self-related words, participants were asked to complete the following tasks. During one block of trials, participants had to categorize “self” words with words that depict the “Harmony” concept pole of the BII dimension on one side and “other” words with words that represent the “Conflict” concept pole of the BII dimension on the other side. In a second block of trials, “self” words shared the same response as the “Conflict” pole of the BII dimension and “other” words shared the same response option as the “Harmony” pole of the BII dimension. The second IAT followed the same logic in that participants had to discriminate between words that represent the “Blended vs. Distance” dimension of BII, paired with words that differentiate between “self vs. other” concept pair. In total, participants completed seven blocks of trials. Each block included 20 practice trials and 40 test trials. The order of blocks was randomized across participants. For each bicultural participant, the software randomly determined the order in which the seven blocks were completed. This procedure limits the influence of order effects on the obtained results. Explicit measures. After completing the two IATs,square plastic planter participants filled out the battery of acculturation and outcome measures described in Study 1. The implicit measures were administered first. The opposite order might have produced more noise in the implicit data due to fatigue. Please see Study 1 for a description of the explicit measures .

Data screening of test trials showed an overall error rate of 5.6% and a mean response latency of 901 ms for the IAT that assessed the conflict versus harmony dimension of BII. Furthermore, there was an overall error rate of 8.1% and a mean response latency of 919 ms for the IAT that assessed the blendedness versus distance dimension of BII. For the experimental condition, data screening of test trials showed an error rate of 5.5% and a mean response latency of 934 ms for the IAT that assessed the conflict versus harmony dimension of BII. There was an overall error rate of 7.2% and a mean response latency of 954 ms for the IAT that assessed the blendedness versus distance dimension of BII. For the control condition, there was an overall error rate of 5.7% and a mean response latency of 866 ms for the IAT that assessed the conflict versus harmony dimension of BII. Finally, there was an overall error rate of 9.1% and a mean response latency of 881 ms for the IAT that assessed the blendedness versus distance dimension of BII. Taken together, these results suggest that participants had little trouble completing the IATs. Similarly to Study 1, any outliers of extremely fast or slow responses were noted and excluded during data screening. Based on the criterion developed by Greenwald et al. , there were a total of 6 participants eliminated from the study. See Study 1 for how the IAT D effect is calculated. In Study 2, for the Harmony vs. Conflict IAT, a positive score indicated that the Self + Harmony association was stronger than the Self+ Conflict association. A negative score indicated that the Self + Conflict association was stronger than the Self+ Harmony association. Forthe Blendedness vs. Distance IAT, a positive score indicated that the Self + Blendeness association was stronger than the Self+ Distance association. A negative score indicated that the Self + Distance association was stronger than the Self+ Blendedness association.

Two one-sample t-tests were performed in order to examine if the two IAT D means differ from 0 . For the Harmony versus Conflict IAT, results indicated that the sample mean of .396 was significantly greater than 0, t=9.60, p<.001. This result suggested that overall participants implicitly identified more strongly with being a harmonious bicultural relative to being a conflicted bicultural. For the Blendedness versus Distance IAT, results indicated that the sample mean of .270 was significantly greater than 0, t=7.95, p<.001. This result suggested that overall participants implicitly identified strongly with being a blended bicultural compared to being a distant bicultural. Finally, a paired sample t-test was performed to examine the difference between these two groups and results suggested there to be a significant difference between the harmony vs. conflict IAT and blendedness vs. distance IAT, t=2.20, p=.024. This result suggested that Mexican American participants implicitly showed a stronger self-attachment to harmony relative to self + blendedness association. An independent sample t-test was performed to examine if there was a difference in IAT D effect between the experimental and control conditions for both dimensions ofBII. Results indicated that for the harmony versus conflict dimension of BII, there was no significant difference in the IAT D effect between the control condition and experimental conditions, t=.645, p=.520. For the blendedness versus distance dimension of BII, there was no significant difference in the IAT D effect between the control and experimental conditions, t=1.38, p=.171. A second independent sample t-test was performed to examine if there was a difference in the explicit BII scores between the experimental and control conditions for both dimensions of BII. Similarly to the implicit measures, results indicated that for the harmony versus conflict dimension of BII, there was no significant difference in the explicit scores between the control condition and experimental conditions, t=.113, p=.910.

For the blendedness versus distance dimension of BII, there was no significant difference in the explicit scores between the control condition and experimental conditions, t=1.16, p=.248. Taken together, these results suggested that the manipulation did not work. First, correlation analyses were performed to examine the overall pattern among the two IATs . Results indicated that there was no significant relationship between the Harmony vs. Conflict IAT and the Blendedness vs. Distance IAT , r=-.07, p=.46. Next correlational analyses were performed to examine the relation between explicit BII measures and both IATs. Overall, results showed that there was only one significant correlation between the implicit harmony versus conflict BII dimension and explicit BII dimension of blendedness versus distance . This result suggested that the more Mexican American participants explicitly selfidentified as being a blended bicultural, the less they implicit self-identified as being a harmonious bicultural. The rest of the results indicated that there were no other significant relationships among the other three pairings: implicit and explicit conflict versus harmony dimension of BII , implicit and explicit blendedness versus harmony dimension of BII , and the implicit blendedness versus distance BII dimension with the explicit BII dimension of harmony versus conflict . Even though the experimental manipulation did not work, the aforementioned relationships were examined separately for the experimental and control conditions. Reason being is that these correlations will help to explain the discrepancy in the results in the general discussion section. Results indicated that there was no significant relationship between the harmony vs. conflict IAT and the blendedness vs. distance IAT for both the experimental and control groups . Next correlational analyses were performed to examine the relation between explicit BII measures and both IATs. Similarly to the overall pattern of results, for the control group, there was a significant correlation between the implicit harmony versus conflict BII dimension and explicit BII dimension of blendedness versus distance . This result was consistent with the overall correlation; however, the association was stronger. In regards to the experimental group,square plastic plant pot there was no significant correlation between implicit harmony versus conflict BII dimension and explicit BII dimension of blendedness versus distance . The rest of the results indicated that there were no other significant relationships among the other three pairings for both the experimental and control groups . To further explore the validity of the implicit BII measure, additional correlations were run to assess the overall relationship between the two IATs and a battery of explicit acculturation and outcome measures. Interesting enough, there were no significant correlations between the implicit BII measures and the battery of explicit acculturation and outcomes measures with the exception of two correlations. Results indicated a marginal correlation between implicit BII dimension of blendedness versus distance and the explicit acculturation strategy measure of separation and explicit U.S. Identification . These correlations suggested that the more Mexican American participants implicitly self-identified as being a blended bicultural, the less they explicitly endoresd the separation strategy and identified with U.S. culture. The same correlations were also run separately for both the experimental and control groups. Results indicated the same pattern of correlations found in the overall correlation patterns, however differed by either the experimental or control groups . Overall, these correlational analyses indicated that there is little to no relationship between the implicit BII measure and the battery of acculturation and outcome measures including the explicit BII measure. Participants were categorized into two groups based on their explicit BII scores. First, participants received two BII scores for blendedness and harmony. A median split was performed on the two BII scores in order to determine the high versus low groups for each BII dimension. For both BII dimensions, the median score was 4.0. Any participant that scored below the median was categorized as being a conflicted or distant bicultural, whereas any participant that scored at the median or higher was categorized as being a harmonious or blended bicultural.

Based upon these categorization criteria, results from the explicit data indicated that 51% of participants were categorized as high blendedness and 57% were categorized as high harmony, while 49% were categorized as low blendedness and 43% were categorized as low harmony. Participants were then categorized into two groups based on their implicit IAT D scores for comparison purposes. First, participants received two implicit IAT D scores for blendedness and harmony. A median split was performed on the two implicit IAT D scores in order to determine the high versus low groups for each BII dimension. For the harmony vs. conflict dimension of BII, the median score was .459. For the blendedness vs. distance dimension of BII, the median score was .263. Any participant that scored below the median scores of each BII dimension was categorized as being a conflicted or distant bicultural, whereas any participant that scored at the median or higher of each BII dimension was categorized as being a harmonious or blended bicultural. Based upon these categorization criteria, results from the implicit data indicated that 52% of participants were categorized as high blendedness and 51% were categorized as high harmony, while 48% were categorized as low blendedness and 49% were categorized as low harmony. Upon comparing the categorizations based upon the explicit and implicit data, results indicated that the categorizations for high versus low blendedness were roughly identical. However, categorization results based on the explicit and implicit data showed some discrepancy between the high versus low harmony groups. These results indicated that the Mexican American participants tend to assess their blended bicultural identities at both levels of awareness with little variation; however tend to assess their harmonious bicultural identities across two levels of awareness with a little more variation. To further examine the validity of the implicit BII measures, four independent sample tests were performed to examine the overall differences between explicit high and low blendedness and harmony groups on the two IAT measures . Results indicated that there was a significant difference between the explicit high and low blendedness groups on the harmony versus conflict IAT measure, t=-2.23, p=.027. This result suggested that Mexican American participants who explicitly selfidentified as being high in blendedness, implicitly self-identified weaker with harmony compared to those explicitly low in blendedness. Results further indicated that there was no significant difference between the explicit high and low blendedness groups on the blendedness versus distance IAT measure, t=1.31, p=.194. Results for the high versus low explicit harmony groups showed that there was no significant difference between the high and low harmony groups on the harmony versus conflict IAT measure, t=-.526, p=.600. Results further indicated that there was no significant difference between the explicit high and low harmony groups on the blendedness versus distance IAT measure, t=-1.75, p=.083. For the experimental condition, results showed that that there was no significant difference between explicit high and low blendedness and harmony groups on the two IAT measures .

Technical improvements for this project include developing a stronger data augmentation technique. Instead of using the set transform method which artificially augments the data set, using another package that can actually create the separate images and add them to the data set instead would be interesting to see how it would perform. More Hyper-parameter fine-tuning could be done such as exploring the learning rate and adding an optimizer. More Epochs should be tested in order to see how the model will perform over a greater period of time. Another idea is to explore more the Training-Validation-Testing splits chosen for the data. Exploring the performance between different splits could show how to better improve the classification model. To achieve our expected agricultural need of feeding 10 billion people by 2050, we must prioritize minimizing crop loss wherever possible. More research is needed to help develop more tools to assist crop growers with preventing crop loss. The study “Mobile phone use is associated with higher smallholder agricultural productivity in Tanzania, East Africa” by Amy Quandt et al. looks into the relationship crop growers have with their cell phones as agricultural tools to help increase crop yields. “A key result is the positive association between phone use for agricultural activities and self-reported agricultural yields” . Cell phones are increasing accessibility to technological tools that help with agriculture. These technologies for assisting with crop loss will not only be utilized by commercial crop growers or the average hobbyist and enthusiast as well. Whether crop growers use a ViT image classification model or a convolutional neural network image classification model, or another type of machine learning architecture is used,25 liter plant pot more research is needed to help develop tools to assist crop growers worldwide in eradicating crop loss everywhere!

Variation in bitter taste sensitivity has long been recognized as an important determinant of diet and health. By shaping behaviors such as diet choice and smoking habits, it exerts downstream effects on health measures such as body mass index, cardiovascular function, hormonal processes, and possibly even cancer susceptibility . Much interest stems from the fact that bitter sensitivity varies profoundly from person to person and is highly heritable . This has spurred efforts to detect gene mutations shaping responses to specific compounds, with the aim of better understanding the mechanistic underpinnings of taste–health connections. A consistent finding as these efforts have progressed is that mutations in TAS2R genes, which encode G protein-coupled receptors controlling the initial stages of the bitter perception process, are major contributors . This issue of Chemical Senses features a new study of TAS2R38, which is famous for its role in shaping PTC sensitivity . Here, Risso et al. investigate associations between mutations in TAS2R38 and taste responses to fruit from a little known tree found in southeast Asia, Antidesma bunius. Risso et al. ask, does variation in TAS2R38 predict bitter taste perception of A. bunius fruit, as it does in PTC? The short answer is, yes. However, the association is the opposite of PTC’s: mutations associated with high PTC sensitivity are associated with low A. bunius sensitivity and, conversely, mutations associated with low PTC sensitivity are associated with high A. bunius sensitivity. The pattern is striking, and it is more than a novelty. It bears on our understanding of not just PTC and A. bunius perception, but bitter perception in general. Though little known outside the region, A. bunius is a familiar sight in south and southeast Asia, and into the Malay archipelago, the Philippines, Borneo, Papua New Guinea, and most regions of Melanesia and Micronesia. A. bunius goes by many common names, most commonly bignay or bignai, Chinese laurel, salamander tree, or variants of these .

It is a leafed evergreen with characteristics similar to those of oak, with a large central trunk and limbs branching above, and heights reaching 30 m . It is frequently cultivated as an ornamental due to its attractive appearance, ability to provide shade, and yield of edible fruit. A. bunius fruit is small , round, consists of a single seed surrounded by a thin layer of pulp, and grows in clusters like grapes . The fruits ripen at different rates, giving maturing clusters a striking appearance with white, red, and black berries. A. bunius fruit is generally not eaten raw due to its sourness and astringency, but it is a popular ingredient in sweetened, cooked, or fermented products such as jellies, juices, and wine. A. bunius tea, another popular product, is derived from the tree’s bark.Henkin and Gillis evaluated subjects’ responses to 2 solutions: PTC at saturation in water and juice pressed from A. bunius fruits. Subjects’ responses to PTC were consistent with previous studies, with 68% of subjects reporting bitterness and 32% reporting no taste . Patterns of response to A. bunius were different, with 15% of subjects being responders and 85% being non-responders. Strikingly, responses to PTC and A. bunius were negatively associated. Of the 115 PTC responders, none were A. bunius responders; however, of the 25 A. bunius responders, none were PTC responders. Henkin and Gillis concluded from this that bitter perception of PTC and A. bunius are mediated by related factors, probably on a genetic level, although the specific mechanism accounting for this remained speculative. Risso et al.’s new study capitalizes on current understanding of the molecular genetics of bitter perception to revisit the A. bunius puzzle. It is now firmly established that the inheritance of PTC sensitivity is controlled principally by 2 alleles at a single locus, TAS2R38 . Thus, it seemed likely that these might account for the patterns observed by Henkin and Gillis. To find out, Risso et al. frst replicated Henkin and Gillis’ earlier taste tests. Perception was ascertained in subjects evaluating 2 solutions: PTC and A. bunius juice. Risso et al. then went farther, obtaining DNA sequences from TAS2R38 in subjects. These allowed, for the frst time, a test of whether the specific mechanism underlying variability in PTC perception also accounts for variation in A. bunius perception.

Risso et al.’s results are consistent with those of Henkin and Gillis and shed new light on the mechanisms underlying the PTC/A. bunius relationship. Risso et al. found that taste responses to PTC are indeed predictive of responses to A. bunius: only 11% of PTC responders were A. bunius responders, whereas 16% of A. bunius responders were PTC responders. Thus, there is an unambiguous inverse relationship between sensitivity to PTC and sensitivity to A. bunius. Risso et al.’s data further show that variation in TAS2R38 does show an association with A. bunius sensitivity, and it is strong. More than 30% of Risso et al.’s subjects harbored the TAS2R38-PAV/PAV genotype, yet none were A. bunius responders; conversely, 100% of A. bunius responders harbored TAS2R38-AVI. These results are consistent with the longstanding hypothesis that perception of both PTC and A. bunius is mediated by alleles of TAS2R38, with PAV conferring PTC sensitivity and AVI conferring A. bunius sensitivity. They are also consistent with computational structure-function analyses suggesting that the A262V mutation causes a shift in ligand specificity, but does not disable the receptor . Thus, the simplest explanation for Risso et al.’s findings is that A. bunius harbors an agonist compound specific to AVI, much as PTC is an agonist of PAV, and homozygotes can only perceive one compound or the other while heterozygotes can perceive both . Although the findings of Henkin and Gillis and Risso et al. only pertain directly to perception of PTC and A. bunius, they have implications for bitter perception in general. Most TAS2Rs are responsive to multiple substances, and it is already known that PAV mediates responses not just to PTC, but to a constellation of related compounds as well . If AVI is a functional receptor,black plastic plant pots it would be remarkable if were mediating responses to just a single compound found in relatively obscure plant. What is it mediating responses to? The obvious strategy for answering this question is to take the approach of and systematically test AVI for responses to libraries of compounds in vitro. A sensible starting point would be to focus on compounds already known to be present in A. bunius, which are receiving attention for their bio-active properties . Evidence that both of TAS2R38’s common alleles contribute to bitter responses also raises the prospect that similar patterns occur in other TAS2Rs. TAS2R genes are highly diverse, harboring signifcantly more variation than average for the human genome . In a study analyzing genetic diversity in all known TAS2R genes in 55 subjects, Kim et al. found an average of 6 coding haplotypes per locus. In larger sample, found that TAS2R38 alone has >20 coding haplotypes. If divergent functionality among TAS2R alleles is the norm rather than the exception, or even merely common, it would point to the presence of major phenotypic variation arising from effectively unlimited combinatorial diversity. An additional point made by Risso et al. is that evidence for functionality of AVI provides an explanation for signatures of balancing natural selection at TAS2R38. If PAV enables perception of one set of compounds, and AVI enables perception of another, then heterozygotes should be able to perceive both. This could provide a selective advantage to heterozygotes, resulting in the maintenance of both alleles human populations. Evidence that AVI is functional also explains an intriguing but little discussed aspect of variation in TAS2R38, which is that while coding variants of AVI do exist, they are found only at low frequencies, and no profound mutations such as premature stop codons or frame shifts have been reported on the AVI background .

Both of these observations are consistent with the AVI sequence being conserved by selective processes, which could only occur if it has some type of function. It is crucial to recognize that while the simplest explanation for Risso et al.’s findings is that AVI is a functional receptor, it is not the only mechanism through which AVI might mediate taste responses to A. bunius. A compelling alternative is protein–protein interaction. Protein–protein interactions such as heterodimerization are ubiquitous among members of the GPCR super family, and frequently alter the function of the participating molecules . Indeed, the human umami and sweet receptors are both GPCR heterodimers: TAS1R1+TAS1R3 and TAS1R2+TAS1R3, respectively . One explanation for the association of AVI with A. bunius perception is that AVI interacts with a second TAS2R, forming a heterodimer responsive to A. bunius constituents. In this scenario, AVI would be functional, but as a cofactor rather than a receptor. Support for this possibility comes from computational and experimental evidence that the A/V and V/I mutations abolish TAS2R38’s activation by ligands, but do not have major effects on the protein’s overall structure . Thus, while the present findings suggest that AVI is acting as a receptor for constituents of A. bunius, they do not demonstrate it defnitively. Isolating AVI’s function will require identifcation of the specific compounds involved and establishing their interactions. The possibility that the AVI allele is mediating responses to unknown substances suggests that caution should be taken in efforts to understand associations between TAS2R variation and responses to complex aspects of diet and other orosensation driven behaviors. In particular, it raises questions about the directionality and strength of genotype–phenotype associations. In the case of TAS2R38, the prevailing focus is currently on the fact that genotype predicts high, medium, and low sensitivity to known agonists, such as goitrogens found in cruciferous vegetables. The new findings raise the question of whether sensitivity to some unknown compound is commensurately increasing, and whether it might be an equally important driver of observed associations. Both could even occur simultaneously, which could weaken or obscure associations. Dissecting such effects, even if just to rule them out, will require substantial effort from all chemosensory perspectives: molecular, psychophysical, and behavioral.Tomatoes may suffer some leaf burn and early stunting but rapidly outgrow these problems and soon surpass plants grown over bare soil. Eggplant tends to be more sensitive and may suffer prolonged injury. We have observed no problems with any cucurbits grown over metalized mulches. Plants, particularly cucurbits, grown over metalized mulches may be more susceptible to frost injury in the late fall. More widespread adoption of the use of UV-reflective plastic mulches in California has not occurred largely because of added costs associated with their use and disposal and a general lack of familiarity with production techniques required for their successful use.

These results highlight the power and accuracy of diploid Mendelian exclusion analysis methods for pedigree authentication , intellectual property protection, and quality control monitoring of germplasm and nursery stock collections in octoploid strawberry using subgenome-specific DNA markers. The application of these approaches was straightforward because of the simplicity and accuracy of subgenome-specific genotyping approaches in octoploid strawberry populations . The development and robustness of SNP genotyping platforms has facilitated the application of standard diploid genetic theory and methods in octoploid strawberry, including the exclusion analysis methods applied in the present study . The power and accuracy of these methods were rigorously tested and affirmed in a court of law where DNA forensic evidence was pivotal in proving the theft of University of California intellectual property by the defendants in a 2017 case in US District Court for the Northern District of California captioned The Regents of the University of California v California Berry Cultivars, LLC, Shaw, and Larson . The DNA forensic approaches and evidence applied in that case are documented in a publicly available expert report identified by case number 3:16- cv-02477 .We estimated that 80-90% of the individuals in the California and Cosmopolitan pedigree networks were extinct . Using SNP array-genotyped individuals preserved in public germplasm collections as anchor points, we searched for evidence that the allelic diversity transmitted by extinct founders had been “lost.” This is a difficult question to answer with certainty; however, the findings reported here,drainage pot combined with the findings of Hardigan et al. , suggest that genetic diversity has been exceptionally well preserved in domesticated populations.

Using SNA and PCAs of H, we did not observe structural features in sociograms or PCA plots that were indicative of the loss of novel ancestral genetic diversity . The kinship or numerator relationship matrix was estimated for the entire pedigree of genotyped and ungenotyped individuals . For the present study, 1,495 historically important and geographically diverse UCD and USDA F. ananassa individuals were genotyped with high-density SNP arrays . The genomic relationship matrix was estimated for the genotyped individuals and combined with the A matrix to estimate the H matrix for the entire pedigree . The global H matrix was partitioned as needed for subsequent analyses . PCAs of the H matrices yielded two-dimensional visualizations of genetic relationships that were remarkably similar in shape and structure to sociograms for the California and Cosmopolitan populations . We observed distinctive differences in the shapes and structures of the sociograms and PCA plots between the populations . The pattern in the Cosmopolitan population was a characteristic of pervasive admixture among individuals across geographies . We observed a strong chronological trend in the California population but not in Cosmopolitan population . We observed a mid-twentieth-century bottleneck in the California population , in addition to a bottleneck pinpointed to approximately 1987-1993 when the California population became closed. We discovered that 48 founders contributed 100% of the allelic diversity to the California population from 1987 onward . Hardigan et al. showed that even though nucleotide diversity had been progressively reduced by bottlenecks and selection, a significant nucleotide diversity has persisted in the California population but was found to be unevenly distributed across the genome.Our genealogy search did not uncover pedigree records for F. ananassa cultivars developed between 1714 and 1775, the 61-year period following the initial migration of F. chiloensis ecotypes from Chile to Europe .

The scarcity of pedigree records from the eighteenth century was anticipated because the interspecific hybrid origin of F. ananassa was not discovered until the mid-1700s . “Madame Moutot” was the only cultivar in the database with ancestry that could bedirectly traced to one of the putative original wild octoploid progenitors of the earliest F. ananassa hybrids that emerged in France in the early 1700s . Although the genealogy primarily covers the past 200 years of domestication and breeding , ascendants in the pedigree of the cultivar “Madame Moutot” traced to “Chili de Plougastel” , a putative clone of one of the original F. chiloensis subsp. chiloensis plants imported from Chile to France by the explorer Ame´de´e-Franc¸ois Fre´zier . These plants were carried aboard the French frigate “St. Joseph,” delivered by Fre´zier to Brest, France , and shared with Antoine Laurent de Jussieu, a botanist at the Jardin des plantes de Paris. According to de Lambertye , the Fre´zier clone was widely disseminated and cultivated in Plougastel near Brest and interplanted with F. virginiana . Hence, some of the earliest spontaneous hybrids between F. chiloensis and F. virginiana undoubtedly arose in the strawberry fields of Brittany in the early 1700s . The French naturalist Bernard de Jussieu, the brother of Antoine Laurent de Jussieu and a mentor of Antoine Duchesne—“the father of the modern strawberry”—brought clones of the original Fre´zier F. chiloensis plants to the Jardins du Chaˆ teau de Versailles where Duchesne unraveled the interspecific hybrid origin of F.  ananassa . The next earliest F. chiloensis founders appear to be a California ecotype identified in German breeding records from the mid-1800s and an anonymous ecotype in the pedigree of the French cultivar “La Constante” from 1855 . The origins and identities of the earliest F. virginiana founders of F.  ananassa remain a mystery because their migrations from North America to Europe in the early 1600s and subsequent intracontinental migrations were not well documented . The oldest F. virginiana individuals identified in historic documents and pedigree records were “Large Early Scarlet” , “Old Scarlet” , and “Hudson Bay” , all extinct .

We identified 30 anonymous F. virginiana and 76 anonymous F. chiloensis founders in the pedigree records. These individuals were assigned unique alphanumerical aliases to facilitate the reconstruction of the genealogy; e.g., FV22 is the alias for an anonymous F. virginiana founder and FC71 is the alias for an anonymous F. chiloensis founder in the pedigree of “Madame Moutot” .Once the interspecific hybrid origin of F.  ananassa became widely known , domestication began in earnest with extensive intra- and interspecific hybridization, artificial selection, and intra- and intercontinental migration . These forces shaped the genetic structure of the F.  ananassa populations that emerged in Europe and North America, and ultimately migrated around the globe . Over the next 250 years, horticulturalists and plant breeders repeatedly tapped into the wild reservoir of genetic diversity, especially wild octoploid taxa native to North America . There are numerous narrative accounts of what transpired, especially in Europe, North America, and California , but none have painted a holistic picture of the complicated wild ancestry and dynamic forces that shaped genetic diversity in F.  ananassa. We identified 1,438 founders in the genealogy of cultivated strawberry . Here and elsewhere, “founders” are individuals with unknown parents, whereas “ancestors” are ascendants that may or may not be founders . The terminal nodes in the pedigree networks are either founders or the youngest descendants in a pedigree . Of the 1,438 founders, 267 were wild species and 1,171 were F.  ananassa individuals . Because the F.  ananassa founders are either interspecific hybrids or descendants of interspecific hybrids, the number of wild species founders could exceed 268. One of the challenges we had with estimating the number of wild species founders was the anonymity of ecotypes that were used as parents before breeders began carefully documenting pedigrees . We could not rule out that some of the anonymous wild species founders in the pedigree records might have been clones of the same individuals, drainage planter pot which means that the estimated number of wild species founders reported here could be inflated. As interspecific hybridization with wild founders became less important and intraspecific hybridization became more important in strawberry breeding, the proportional GC of wild founders to the gene pool of cultivated strawberry decreased . This seems paradoxical because 100% of the alleles found in F.  ananassa were inherited from wild founders, but increasingly flowed through F.  ananassa descendants over time—wild octoploids numerically only constituted 14% of the founders we identified . Several trends emerged from our analyses of genetic relationships and founder contributions. First, inbreeding has steadily increased over time as a consequence of population bottlenecks and directional selection . Second, the California population was significantly more inbred than the Cosmopolitan population . These results were consistent with the findings of Hardigan et al. from genome-wide analyses of DNA variants and population structure. They found selective sweeps on several chromosomes in the California population, which was shown to be unique and bottle necked. Finally, the relative number of founder equivalents has decreased over time, consistent with the increase in inbreeding over time .

The primary gene pool of cultivated strawberry is comprised of eight cross-compatible, interfertile octoploid taxa: F. chiloensis subsp. chiloensis, F. chiloensis subsp. lucida, F. chiloensis subsp. pacifica, F. chiloensis subsp. sandwicensis, F. virginiana subsp. virginiana, F. virginiana subsp. glauca, F. virginiana subsp. grayana, and F. virginiana subsp. platypetala , seven of which were found in pedigree records . The only primary gene pool taxon not found in the pedigree records was F. virginiana subsp. grayana. We identified 112 F. chiloensis, 65 F. virginiana, and 1,171 F. ananassa founders, which constituted 95% of the founders and were estimated to have contributed 99% of the allelic diversity to global, California, and Cosmopolitan F.  ananassa populations . Even though wild species from the secondary gene pool constituted 6% of the founders and 30% of the wild species founders identified in pedigree records, they were estimated to have contributed < 0:1% of the allelic diversity in the global F.  ananassa population . While the assignment of F. chiloensis and F. virginiana subspecies to the primary gene pool was unequivocal and uncontroversial, the assignment of non-octoploid Fragaria and Potentilla species to secondary or tertiary gene pools, as per the definitions of Harlan and de Wet , was tenuous because evidence for the inheritance of alleles from exotic donors among inter-ploidy hybrid offspring with cultivated strawberry was not always clear from genealogical and breeding records. We lumped the non-octoploid Fragaria and Potentilla into the secondary gene pool solely because they were recorded as ancestors of F.  ananassa individuals , which implied that interspecific, intergeneric, and inter-ploidy hybrid descendants inherited alleles transmitted by secondary gene pool donors. However, the genetic proof was not always clear or available. One or more of the species assigned to the secondary gene pool might belong in the tertiary gene pool , a distinction of negligible practical importance. The secondary gene pool founders in the genealogy were nearly always parents of orphans or other isolated individuals in short dead-end pedigrees that have not materially contributed allelic diversity to important cultivated strawberry populations or cultivars. The exotic founders have included decaploid F.  vescana and pentaploid F.  bringhurstii individuals . Although cited as important genetic resources for strawberry breeding , the secondary gene pool species have had a limited utility because of the range of biological challenges one encounters when attempting to introgress alleles from exotic donors through interspecific, intergeneric, and inter-ploidy hybrids, e.g., reproductive and recombination barriers, ploidy differences, meiotic abnormalities, and hybrid sterility . Genetic variation in the secondary gene pool has not been needed to drive genetic gains or solve problems in strawberry breeding. As highlighted earlier, Hardigan et al. showed that genetic diversity is massive in the primary gene pool and has not been eroded by domestication and breeding on a global scale, even though it has been significantly reduced and restructured in certain populations, e.g., the California population. The profound changes and restructuring in the California population over time, as previously noted, were clearly evident in the sociograms and PCAs of the pedigree–genomic relationship matrices . Because the California population has been the source of numerous historically and commercially important cultivars, we hypothesize that intense selection and population bottlenecks have purged a high frequency of unfavorable alleles compared to many other populations, thereby yielding an elite population with lower genetic diversity than the highly admixed Cosmopolitan population .We used coancestry, betweenness-centrality , and out-degree statistics to estimate the GC of founders and non-founders to genetic variation within a population and identify the most prominent and important ancestors in the genealogy of cultivated strawberry . For founders, GC was estimated by the mean coancestry or MK between each founder and cultivars within a focal population .

More comprehensive human intervention studies will be essential in the future to provide insight into the potential influence of dietary polyphenols and their aromatic bacterial metabolites on intestinal microbial communities and their activities.Probiotics are defined as viable microorganisms that, when consumed in sufficient amounts, confer a health benefit on the host.To date, most of the commonly used probiotics are limited to strains of certain Lactobacillus and Bifidobacterium species . Survival during passage through the GI tract is generally considered as the essential feature for probiotics to preserve their active functions in the colon. Indeed, the probiotic strains must overcome biological barriers, including resisting gastric and bile acid secretion and tolerating intestinal lysozyme and toxic metabolites produced during digestion . Various studies found that at least a fraction of probiotic bacteria can be detected in stool for between 1 and 3 weeks after consumption . Probiotic Lactobacillus strains were also found to adapt for survival in the gut and possess gut-inducible genes that are responsive at different sites in the intestine. Interestingly, provision of the probiotic Lactobacillus plantarum to mice fed a Westernstyle diet and to humans resulted in similar gene expression profiles of this strain.As probiotics are delivered via various food vehicles, the complex food matrix should also be viewed as an important factor that may alter the probiotic activity in the gut. To date,pots with drainage holes only a few animal and clinical studies have addressed the functional roles of food on probiotic-conferred health benefits.

The mechanisms of probiotic effects on health are only partially understood but likely function either directly through interactions with host intestinal epithelial and immune cells or indirectly by modulating the indigenous intestinal microbiota. In regard to the latter, several studies have concluded that probiotic consumption does not result in global modifications of the intestinal microbiota in healthy individuals.However, probiotics might confer modest but significant changes to the functional activities of local intestinal bacterial populations. When examined at the meta-transcriptional level, intake of a probiotic fermented milk was associated with the upregulation of microbial genes corresponding to plant polysaccharide metabolism.Similarly, administration of probiotics was shown to induce crosstalk between the probiotics from the diet and the individual bacterial species in the gut and might induce competition for limited substrates that results in fluctuations tof the metabolic profile of the host.The gut microbiome of healthy adults is highly resilient , where the stable native microbiota prohibits the succession of microbes from the diet.In addition, the effect of probiotics on the gut microbiome appears to differ depending on host phenotypes such as age, health status, and chronic conditions. For example, the infant gut microbiome is highly diverse and dynamically changes during development and therefore may be easily influenced by the consumption of probiotics . In individuals with irritable bowel syndrome , probiotic consumption resulted in an increase in the numbers of Bacteroidetes in the intestine.Moreover, intake of two Lactobacillus strains by diet-induced obese mice altered microbial composition and decreased expression of inflammatory genes in the adipose tissue while increasing levels of fatty acid oxidation in the liver.Further studies are needed to investigate the effects of assorted probiotic supplements on the gut microbiome with respect to various host life stages and phenotypes.The premise behind substituting sugar with artificial sweeteners is to maintain the palatability of food at the same time as lowering energy intake.

However, a sufficiently high ingestion of non/low-digestible sugar substitutes stimulates the growth of gut microbiota and can induce transitory diarrhea in humans.In particular, the great proportion of non/low digestible sugar substitutes that reach the distal intestine are subject to fermentation by the colonic microbiota, offering approximately 2 kcal/g of energy.Although discovering and characterizing these compounds within foods is relatively new, it is of interest to note that many of these food ingredients are common in our daily diet. For example, the disaccharide alcohol maltitol is considered a common replacement for sucrose. Urinary and fecal excretions of sorbitol and maltitol after 24 h in conventional rats were shown to be minimal compared with germ-free rats.Likewise, maltitol consumption significantly increased production of SCFAs in addition to nine tested fecal microbes after a 6 week trial, including bifidobacteria, Bacteroides, Clostridium, lactobacilli, eubacteria, Atopobium, Fusobacterium prausnizii, Ruminococcus flavefaciens, and R. bromii. A 12 week administration of Splenda, composed of 1.1% of the artificial sweetener sucralose, increased fecal pH and reduced the amount of fecal bifidobacteria, lactobacilli, Bacteroides, clostridia, and total aerobic bacteria in a rat,whereas isomalt, a widely used low-energy sweetener, was considered to be bifidogenic in a human study.Overall, artificial sweetener fermentation by gut microbiota remains either unexplored or poorly documented, some of which are highlighted in a review by Payne et al.Azo compounds are widely used as coloring agents in foods, beverages, and food packaging.In addition, azo polymer coatings have been specifically designed for colon-selective drug delivery due to the presence of pH-sensitive monomers and azo cross-linking agents in the hydrogel structure. Indeed, azo dyes can be metabolized under anaerobic conditions by intestinal microbial processes and, as a result, produce the reductive cleavage products aromatic amines .

The majority of the toxic effects of azo dyes are exerted through aromatic amines produced by their colonic degradation.Raffi et al. reported that isolated intestinal bacteria in an anaerobic culture system were able to decolorize the dyes in the supernatant, suggesting that some of the azoreductase activities are extracellularly released.Xu et al. demonstrated a variable degree of efficiency in the reduction of Sudan azo dyes and Para Red by 35 prevalent human intestinal microbes in vitro.In contrast, Sudan azo dyes and their metabolites selectively inhibit the growth of some human intestinal microorganisms,which may suggest a potential impact on gut microbiome after long-term exposure. In summary, although there are tantalizing glimpses into the effect of azo dyes on microbes in vitro, more data from animal and human studies are keenly awaited.In the colon, sulfur is present in either inorganic form or organic form .The human GI tract poorly absorbs sulfate, and there is little sulfatase activity in the mucosa of the GI tract; therefore, free sulfate in the colon is likely to be of dietary origin.Dietary sulfate drives the activity of sulfate-reducing bacteria that couple oxidative phosphorylation with reduction of sulfate to produce sulfide.The total inorganic sulfur intake is much higher in the Western diet in comparison to a typical African rural diet.Highly processed foods that are high in sulfate include bread, soy flour, dried fruits, and brassicas, as well as sausage, beers, ciders, and wines.Sulfur-containing amino acids such as cysteine can be found in dietary protein and are a source of sulfur for colonic sulfate-reducing bacteria Desulfovibrio desulfuricans. Native Americans who consume a diet high in resistant starch and low in animal products harbor significantly distinct sulfate-reducing bacterial populations and more diverse and different methanogenic archaea than Americans consuming a typical Western diet.Substrate competition for hydrogen among methanogenic archaea, sulfate-reducing bacteria, acetogenic bacteria, and otherspecies likely occurs in the colon.Because hydrogen is an essential component for the survival of colonic methanogens, removal of the substrate terminates methanogenesis. Given an adequate supply of sulfate, sulfate-reducing bacteria that are more abundant in the right colon out compete methanogenic archaea for H2 due to their higher substrate affinity to produce hydrogen sulfide ,an end-product of dissimilatory sulfate reduction.As a result, the mucosal microbiome may be shaped in part through the availability of toxic sulfide compounds and the differential susceptibility of mucosalistic microbes to the toxins.Furthermore, the activity of methanogenic bacteria can also be disrupted by bile acids.In brief, methane production was thought to occur only when sulfate-reducing bacteria were not active.If sulfate is limited and hydrogen is in relative excess, methanogenic bacteria or perhaps acetogenic bacteria will become essential.Therefore, the levels of sulfate present in the colon are critical for determining which bacterial group gains a better survival advantage.Many people consume alcoholic beverages; however,drainage pot few studies exist on the effect of alcohol consumption on the gut microbiome of healthy individuals. For individuals who consume alcohol to excess, abnormal gut microbiota and bacterial overgrowth can potentially initiate or worsen alcoholinduced impaired gut barrier function and contribute to endotoxemia in patients with alcoholic fatty liver disease.

Yan et al. demonstrated a 3 week acute effect following alcohol administration in mice that resulted in bacterial overgrowth, as well as an expansion of Bacteroidetes and Verrucomicrobia bacteria while decreasing Firmicutes, with no difference observed after only 1 day or 1 weekChronic alcohol consumption induces changes in gut community profiles. For example, daily alcohol consumption for 10 weeks in a rat alters the colonic mucosa-associated bacterial microbiota fingerprint pattern.Similarly, chronic ethanol feeding for 8 weeks increased fecal pH and decreased abundance of both Bacteriodetes and Firmicutes phyla with a remarkable expansion of Proteobacteria and Actinobacteria phyla in mice.In a human trial, chronic alcohol consumption resulted in the alteration of the mucosa-associated colonic bacterial composition in a subset of alcoholics, with lower median abundances of Bacteroides and higher Proteobacteria. Furthermore, measurement of serum endotoxin suggests a change in microbial function, rather than abundance, which may lead to increased levels of gut-derived pro-inflammatory factors in chronic alcohol consumption. It is noted that the inability to detect clear differences between alcoholics with and without liver disease suggests that chronic alcohol consumption, rather than the disease physiology, is the most important event that appears to alter microbiota composition.It is now well established that host diet alters the gut microbiome. Changes in the gut microbiota composition are also considered an important factor in health and disease. Dietary assessment has provided us with a window to discover a way to reconfigure the gut microbiome. In this regard, the nutritional manipulation of the gut microbiome serves as a basis for formulating therapeutic approaches that are feasible and acceptable to the general population as a promising way to promote health in the era of personalized nutrition and medicine. Understanding the impact of foods and nutrients on host− microbe coevolution supports the essential role of a mutualistic relationship for intestinal homeostasis, but there remain challenges for nutritionists and scientific investigators alike to determine the “ideal” diet. This review collectively maintains the emerging view that diet supports a specific bacterial community structure and further suggests that a suboptimal dietary composition/quality may promote the development of diseases through introducing intestinal microbial dysbiosis. Major shifts in intestinal microbial composition are often observed when dietary differences between groups are extreme. Only a few population-wide studies are available to date, but some of them support a role of food diversity as a potential mechanism for altering gut microbial diversity. Although it is difficult to determine the causality of observed fecal microbiota shift with respect to many lifelong changes, generally, an adequate control over influential factors is important for the success of clinical studies to eliminate the drastic effects of unnecessary confounding variables. Many of the studies reviewed here rely on the assumption of equivalence between the term “fecal microbiome” and “intestinal microbiome”. Further studies are necessary to elucidate more clearly the exact impact of the selection of different diets on qualitative changes in the gut microbiota. Some nutrients that have been studied, such as dietary fiber, are a possible option for the maintenance of intestinal homeostasis and improvement of gut health, whereas others may contribute an opposite effect. Therefore, future research must be focused on looking to improve the effectiveness of diets with an underlying long-term “targeted approach” that allows improvement of intestinal microbial composition and functional activities. In other instances, when dietary differences are small and on a short time scale, gut microbiota changes are not as obvious, but that is not to say that changes do not occur. An alteration of the gut microbiota at lower taxonomic levels is still likely to have important functional consequences for the host. Notably, gut microbiota varies dramatically from individual to individual in lower taxonomic levels. Even small dietary changes may have impacts on the gut microbiota and altered metabolic activities in the microbial profile that are not easily detected by the phylogenetic/taxonomic methods. Metabolic alterations induced by diet may result in varying the microbial capability of synthesizing substances in the intestinal tract. It appears that measurement of bacterial enzyme activities may be a more sensitive indicator of diet induced changes in the gut microbiota than taxonomic-based methods.