However, at Bruntland Burn cryogenic and equilibration methods gave similar results for peaty soils, and reasonable agreement with xylem water. Extraction focusing on small-scale moisture isotope dynamics at the root – soil interface may be needed, including scalable methods to explore the phase change/mycorrhizal mechanisms suggested above. Our findings, based on bulk soil field measurements, underline the major difficulties associated with relating potential water sources to plant water stable isotope compositions. Even under controlled laboratory conditions, Orlowski et al. could not confidently link relate the soil water to root crown isotopic compositions, but reported similar 2 H depletion as we found in Dandelions growing on sandy soils.Differences between angiosperms vs gymnosperms: A clear finding of our study is that the extracted xylem waters of angiosperms and gymnosperms have a very different isotopic composition at most sites, with gymnosperms generally showing a greater degree of fractionation. In this regard, several hypotheses could be tested. Firstly, root networks and root-mycorrhizal networks of different species may be able to access different pore sizes. For example, gymnosperms may have greater potential to mobilize water that has undergone some fractionation during the interactions among water, gas, and solid phases of the soil. Secondly, storage and mixing of water within plant tissues may be greater in softwood gymnosperms, as suggested in recent modelling work . The generally slower metabolism and transpiration rates for gymnosperms might exacerbate this mechanism. InTherestingly, Amin et al. showed little difference between angiosperms and gymnosperm xylem waters for cold and temperate environments in their meta-analysis, plastic planters wholesale whereas angiosperms in arid regions were offset in δ2 H compared to gymnosperms.
We sampled xylem water in conjunction with soil water at five well-instrumented sites across northern cold landscapes. At all sites except Krycklan, water sources of angiosperms could be associated with soil water. At all sites except Dry Creek, the sources of water uptake by gymnosperms were much less easily explained. Whereas the isotopic composition of xylem water for angiosperms generally overlapped that of soil water for a range of antecedent periods, overlap did not occur for gymnosperms . This suggests that the xylem water of angiosperms was influenced by the isotopic composition of water retained in the soil weeks or months prior to plant sampling, whereas gymnosperms generally did not exhibit such a memory effect. The isotopic offset between soil and xylem samples was generally greatest during the growing season for the wetter sites . However, at the drier two sites xylem and soil water isotopes tended to be similar, showing the effects of evaporation. We attribute this dry site anomaly to the relatively rare occurrence of mobile water during the growing season. There simply are not many choices of water sources form plants in dry areas, so soil water and xylem water trend towards similarity, and typically have a strong evaporation signal. Our study also raised questions that will need to be addressed in future research: Which biophysical processes at the root – soil interface contribute to isotopic fractionation in uptake that affects the composition of xylem water? What are the internal dynamics of water storage, mixing and release within vegetation and how does this relate to the degree of synchronicity between phenology and soil water availability? What reservoirs are sampled during cryogenic extraction – only xylem water or does this include water from other plant cells? And finally, why are angiosperms and gymnosperms at the same sites so isotopically different? Addressing some or all of these questions will contribute to our understanding of soil-plant-atmosphere interactions in northern landscapes.Understanding the mechanisms of adaptive evolution in pathogenic bacteria is central to long-term disease control.
One major focus of research into adaptive bacterial evolution has been lateral gene transfer , usually defined as the transfer of genes across species boundaries . Until recently, discussions of LGT focused on the transfer of novel genes, as exemplified by the discovery of the plasmid-mediated transfer across species of the genes coding for penicillin resistance ; however, with the increasing availability of genomic sequence data, it has become apparent that the transfer of homologous gene copies is also widespread . These two kinds of exchange, the transfer of novel genes or novel alleles, are fundamentally different. The acquisition of novel genes can result in the acquisition of a completely new trait that has already been refined in other taxa by natural selection . It can determine critical traits such as virulence, antibiotic resistance, and ecological niche , even though most of the material transferred appears to be evolutionarily transient . In contrast the acquisition of novel alleles is analogous to the effect of sexual reproduction in eukaryotes: it increases the genetic variance that natural selection can act on but does not, in itself, result in a qualitative change in the ecology of the recipient . Due to these fundamental differences, we favor reserving the term “LGT” for the transfer of novel genes, using the term “interspecific” or “intersubspecific homologous recombination” for the transfer of alleles; however, both processes, if successful, lead to genetic “introgression,” a term commonly used to describe the spread of genetic material across taxonomic boundaries in plants and animals and now increasingly used to describe the analogous process in bacteria . Homologous recombination is almost ubiquitous among bacteria, although the degree to which it occurs varies widely among species . It involves the replacement of a stretch of DNA sequence in one individual’s genome by a homologous sequence from another individual of the same species following any of the 3 mechanisms of DNA transfer . It typically involves short pieces of DNA . Given the prevalence of homologous recombination, it is generally assumed that it is beneficial, in some cases enabling bacteria to enhance their resistance to antibiotics and avoid host defenses or perhaps promoting adaptation to novel environments . Analogy with the assumed benefits maintaining sexual recombination in metazoans strongly supports this view. Documenting the adaptive benefit of homologous recombination in bacteria has proved difficult. This is to be expected even if the benefits are large and common. Homologous recombination typically falls off rapidly with genetic distance , so a well-established population will usually reflect the mixing of relatively similar alleles. This mixing can be easily detected by the lack of clonality between genes and quantified using evolutionary models ; however, detection of recombination breaks within genes is more problematic. The approaches currently used have very limited power; although the introgression test has improved this situation . Another approach is to test loci sequenced from 2 or more taxa and use the genetic partitioning program STRUCTURE . Alleles that cannot be confidently allocated to one or more of the taxa are likely to be mosaics generated by recombination . To link recombination to adaptive change, it is useful to study a system in which recombination is limited, recognizable, plastic plant pot and likely to lead to novel adaptation. Arnold et al. recently made an inTheresting link between the acquisition of novel adaptations in bacteria via LGT and that via hybridization in metazoans. Excellent examples of how interspecific introgression can result in adaptation to new environments in higher plants are given in the work of Rieseberg and colleagues on the effects of introgression in sunflower species . However, it is not only metazoans that hybridize: bacterial homologous recombination can sometimes result in interspecific introgression . Interspecific hybridization of this kind is likely to be relatively rare, suggesting that the ideal study system is one with a significant frequency of homologous recombination between well-defined groups within a species . This level of study appears most likely to provide valuable insights into recombination-related adaptive change in pathogens. For example, Didelot et al. showed that two human-pathogenic forms of Salmonella enterica are relatively dissimilar across about 75% of their genomes but show marked convergence across the rest.
They concluded that this similarity reflects adaptation to the human host, driven by homologous recombination and selection. Similarly, Sheppard et al. proposed that human activity has probably led to an increase in recombination between Campylobacter jejuni and Campylobacter coli and may have also created novel environments that have favored the evolution of hybrids. Another species in which homologous recombination between closely related but distinct taxa has been documented is the plantpathogenic bacterium Xylella fastidiosa . X. fastidiosa is a xylem-limited bacterium that is transmitted by xylem-feeding insects, typically leafhoppers, and is divided into four subspecies: fastidiosa, sandyi, multiplex, and pauca . These subspecies have diverged genetically by 1 to 3%, apparently due to their geographical isolation over about the last 20,000 to 50,000 years . This isolation has now broken down, due presumably to human activity . The cooccurrence of the previously allopatric subspecies has resulted in intersubspecific homologous recombination , recombination that can be detected relatively easily due to the preexisting genetic divergence of the subspecies . Consistent with these observations, recent experimental work has confirmed that X. fastidiosa is transformationally competent and that some isolates carry a conjugative plasmid . X. fastidiosa is known to infect a wide range of hosts, causing scorch and dwarfing diseases . In citrus, it causes citrus variegated chlorosis , a disease restricted to South America, and in grapevines in the United States and Central America, it causes Pierce’s disease. In the United States, it also causes disease in almond, apricot, plum, peach, alfalfa, pecan, and blueberry. However, individual X. fastidiosa strains are not generalists. The different subspecies infect a characteristic and largely nonoverlapping range of plant hosts, and even within subspecies, different genotypes show differences in host specificity . For example, in the South American X. fastidiosa subsp. pauca, citrus isolates do not typically grow in coffee and vice versa , and in X. fastidiosa subsp. multiplex, Nunney et al. found associations between the genotype and host plant. In their study of X. fastidiosa subsp. multiplex, Nunney et al. used the multilocus sequence typing protocol of Yuan et al. to categorize 143 isolates. The MLST protocol is valuable for gaining insight into the evolutionary history and genetic diversity of taxa . MLST groups isolates into sequence types , where each ST defines a unique set of alleles across the loci used . Based on 8 loci, 31 of these isolates were identified as IHR forms , and 2 isolates were considered “intermediate” , while the remaining 110 non-IHR isolates showed no evidence of introgression. The IHR and intermediate types together were considered to define the “recombinant” group of X. fastidiosa subsp. multiplex isolates . Most were observed more than once, and 5 were found in two different U.S. states or districts . The analysis of Nunney et al. was focused on the evolution and host range ofX. fastidiosa subsp. multiplex. For this purpose, it was necessary to identify and exclude isolates whose recent evolution was influenced by intersubspecific recombination. As such, once the 23 non-IHR STswere identified, there was no further analysis of the remaining recombinant group STs. In particular, no evidence was presented for classifying some alleles as atypical of X. fastidiosa subsp. multiplex beyond the observation that they were never found in the non-IHR group . Nunney et al. did observe one intriguing pattern when they compared their results to those of Parker et al. . Of the 143 isolates, 13 were also used in the study by Parker et al. , in which typing was based on a different set of 9 loci. Unexpectedly, these 13 isolates maintained the same grouping with the IHR and non-IHR types corresponding, respectively, to the clade A and clade B groupings . This highly statistically significant concordance strongly suggested that IHR is not distributed randomly across all X. fastidiosa subsp. multiplex isolates but instead is restricted to a small subset, while the remainder is little influenced by IHR. However, Parker et al. failed to find evidence of intersubspecific recombination within any of the X. fastidiosa subsp. multiplex isolates, despite applying a series of 9 tests designed to detect recombination contained within the RDP4 program and the PHI program . This result presented a strong argument against our hypothesis that clade A members cluster because they are recombinant types carrying alleles derived from IHR . Here we reexamined the sequence data obtained in their study by using the more sensitive introgression test to determine if their tests missed evidence of IHR and, if so, whether it was confined to clade A.