The whole-plant N2 fixation potential was calculated by multiplying the total dry nodule biomass of each plant and the N2 fixation potential, which had been normalized to dry nodule biomass. To understand how plant effects were related to CNM concentration-dependent agglomeration in moist soils, the short- and long-term stabilities of CNMs were studied in soil water extracts. Briefly, control soil was weighed into separate 50 mL centrifuge tubes with 1:5 w/v Nanopure water . The centrifuge tubes were sealed securely and shaken horizontally on a shaker for 3 h . The extract was centrifuged to separate large solids, and the supernatant was decanted. The supernatant was vacuum filtered through a 0.22 μm membrane filter , and the filtrate was collected as the final soil extract and stored prior to use. A CNM stock solution was prepared by weighing dry CNM powder into the filtered soil extract, then mixing by brief sonication using a Branson 1510 bath sonicator . Aliquots of the dispersed CNM stock solution were further diluted by the filtered soil extract to yield a final lower concentration of 10 mg L−1. These two CNM concentrations were chosen for comparing the effect of lower versus higher CNM concentrations on CNM agglomeration in moist soil; both concentrations are relevant to the CNM doses used in the plant exposure experiment . The CNM suspensions were bathsonicated immediately before use in static agglomeration and sedimentation studies, hydroponic nft channel which were performed over a long time period . The changes of CNM hydrodynamic diameter and derived count rate with time were measured using dynamic light scattering in a Zetasizer NanoZS90 . DLS measurements were made every 15 s for the first 12 h, then daily from 1 to 7 d, and finally weekly until 56 d.
Meanwhile, dynamic CNM sedimentation in the soil extract was monitored by measuring the suspension absorbance at 600 nm using a UV-1800 spectrophotometer . Sedimentation patterns were inferred from the time course of normalized suspension absorbance at 600 nm . The UV-1800 spectrophotometer was zeroed using Nanopure water. The absorbance of the filtered soil extract alone was monitored over time as well, to confirm there was no interfering absorbance from the soil extract in the CNM suspensions. The zeta potential and electrophoretic mobility of the filtered soil extract and of 10 mg L−1 CNMs were also obtained using the Zetasizer NanoZS90. For either DLS, absorbance, ζ potential, or EPM, at least three replicate measurements were performed. Environmental scanning electron microscopy was performed to visualize the agglomerate morphologies of 10 and 300 mg L−1 CNMs in the soil extract, against a clean quartz sand substrate. Specimens were prepared by dispensing approximately 100 μL of the CNM suspensions onto clean quartz sand overlaying a 10 mm stainless steel conical-well Peltier stub. Imaging was by an FEI Co. XL30 field emission gun microscope , operated at 15 kV accelerating voltage, in a 3.5-torr chamber pressure with a gaseous secondary electron detector in environmental mode. Data are shown as the mean ± SE . For each CNM type, one-way analysis of variance with Tukey’s or Games-Howell post hoc multiple comparisons was used to determine significant differences between treatments . Homogeneity of variance was tested with Levene’s test. To explore dose–response relationships, correlations were performed between plant growth and end point metrics with soil CNM concentrations, using both two-tailed linear and power regression models. Correlation analyses were conducted both with and without the control data. Statistical analyses were performed using Microsoft Excel 2013, IBM SPSS Statistics 23, and SigmaPlot 12.3.P. vulgaris is characterized by a particular evolutionary history.
Recent analyses based on sequence data presented clear evidence of the Mesoamerican origin of common bean, which was most likely located in México . The expansion of this species to South America resulted in the development of two ecogeographic distinct genetic pools with partial reproductive isolation . After the formation of these genetic pools -between 500,000 and 100,000 years ago – domestication took place, independently in the Mesoamerican and the southern Andean regions of the American continent . Genome analysis of BAT93 and G19833 , P. vulgaris sequenced model genotypes, has initially revealed interesting differences, for example between their genome size and number of annotated genes . The common bean is the most important legume for human consumption. In less favored countries from Latin America and Africa, common bean are staple crops serving as the primary source of protein in the diet. Soil acidity in these tropical regions is a major constraint for crop productivity, usually resulting in a combination of nutrient deficiency and metal toxicity . In acidic soils, aluminum toxicity is the primary factor of growth restriction, resulting in the inhibition of root growth and function, as well as in the increased risk of plants to perish of drought and mineral deficiencies, thus decreasing crop production . High Al levels mainly affect roots causing an arrest of the growth of the principal and lateral roots . In Arabidopsis, the regulation of root growth is modulated by an ABC transporter‐like protein, annotated as ALUMINUM SENSITIVE PROTEIN 3 , which is localized in the tonoplast, suggesting a role in Al vacuolar sequestration . The LOW PHOSPHATE ROOT 1 ferroxidase, an ALS3– downstream protein of the phosphate-deficiency signaling pathway, is involved in root growth inhibition, by modulating iron homeostasis and ROS accumulation in root apical meristem and elongation zone . In root cells, AlT can affect multiple areas, as the plasma membrane, the cell wall and symplastic components .
Common bean is known to be highly sensitive to AlT but this sensitivity is genotype-dependent . In 2010, the evaluation of the root morphological traits related to AlT of 36 P. vulgaris genotypes revealed that Andean genotypes were more resistant to Al than Mesoamerican ones . Mendoza-Soto et al. reported that Mesoamerican common-bean plants subjected to high Al levels for short periods showed decreased root length as well as characteristic symptoms of AlT, such as ROS accumulation, callose deposition, lipoperoxidation and cell death in roots. Along other regulators, plant response to metal toxicity involves also microRNAs as part of the regulatory mechanisms. These molecules are a class of non-coding small RNAs of about 21 nucleotides in length, regulating gene expression at post-transcriptional level, guided by sequence complementarity, inducing cleavage or translational inhibition of the corresponding target transcript . The relevance of miRNA regulation in heavy metal tolerance is well documented; it has been demonstrated that heavy metal-responsive miRNAs show differential expression according to the toxicity level. Target genes of these miRNAs generally encode transcription factors that transcriptionally regulate networks relevant for the response to heavy metals. Additionally these encode transcripts for proteins that participate in metal absorption and transport, protein folding, antioxidant system, phytohormone signaling, or miRNA biogenesis and feedback regulation . High-throughput small RNA sequencing analyses have identified miRNAs that respond to AlT in roots of different plants species, however their function in response to AlT is largely unknown. Some of the target genes cleaved by AlT-responsive miRNAs encode disease resistance proteins, transcription factors or auxin signaling proteins . Our previous research indicated that P. vulgaris is no exception to this phenomenon. We identified common-bean miRNAs that respond to Al, these include conserved miRNAs that are Al-responsive in other plant species -i.e. miR319, miR390, miR393- and also miR1511 . miRNAs from the miR1511 family have been identified in non-legume plants like strawberry and poplar tree ,nft growing system although in the latter its nature as a miRNA has been discussed as it has been considered as part of a retrotransposon . Regarding legumes, miR1511 has been identified in Medicago truncatula and soybean . Also, miR1511 was identified in Mesoamerican common-bean cultivars, being more abundant in flowers and roots . However, this miRNA was not identified when analyzing the Andean G19833 reference genome . Genetic variation in MIR1511 has been reported in a comparative genotyping analysis of different Asian accession of domesticated soybean as well as its wild type progenitor Glycine soja. While sequences of mature miR1511 and miR1511* were found in G. max accessions, the sequences of annual wild G. soja showed insertion/deletion in the stem-loop region of MIR1511 that included complete or partial deletions of mature miR1511 sequence . Updated research indicates that the miR1511 target gene is not conserved in the different plants where it has been identified. In strawberry, the miR1511 targets an LTR retrotransposon gene .
Inconsistencies about the nature of miR1511 target gene also hold for legume species. For instance, different targets have been proposed for soybean ranging from genes coding for proteins involved in the regulation of nitrogen metabolism to proteins relevant in plant cell development . While in other species such as M. truncatula target genes have been searched but have not been identified. The SP1L1 transcript has been proposed as the common-bean miR1511 target , however despite several efforts from our and other groups this prediction could not be experimentally validated. These results suggested a species-specific selection of the corresponding target thus it was essential to experimentally validate the nature and possible function of the miR1511 target gene in common bean. Recent analyses led us to predict an ABC-2-type transporter-related gene, annotated as Aluminum Sensitive Protein 3 , as the target for miR1511. In this work we present its experimental validation. In addition, we genotyped MIR1511 in ecogeographically different common-bean cultivars and investigated the role of miR1511 and its corresponding target in the regulation of plant response to AlT. The comparison of MIR1511 sequence from BAT93 vs. G19833 P. vulgaris reference sequences showed a 58-bp deletion in the G19833 genotype. Such deletion comprised around 57% of pre-miR1511 sequence and included 7-bp and 10-bp of mature and star miR1511, respectively . To explore this phenomenon at a larger scale within the Phaseolus genus, we analyzed Genotyping-By-Sequencing data from 87 genotypes originated from a single genetic population , called non-admixed genotypes. These included genotypes from three Phaseolus species and different populations of wild P. vulgaris: three populations from the Mesoamerican , one from the Andean , and one from the Northern Peru–Ecuador gene pools . All the genotypes belonging to the Andean gene pool and part of the Mesoamerican genotypes displayed a truncated MIR1511, in contrast to the Northern Peru– Ecuador genotypes and the other Phaseolus species that presented a complete version of the MIR1511 in their genome. A population clustering of P. vulgaris genotypes confirmed these results and showed that in the three Mesoamerican populations only a part of the MW1 cluster presented the MIR1511 deletion . Predicted target genes for P. vulgaris miR1511 include SP1L1-like and isopentyl-diphosphate delta-isomerase , previously reported , and a protein with unknown function and the Aluminum Sensitive Protein 3 , from our recent bio-informatic analysis. From these predicted targets, ALS3 is the only one possibly related to AlT, as reported for Arabidopsis , and showing an adequate binding-site penalty score , thus the 5’RLM-RACE assay was used to experimentally validate the ALS3 mRNA cleavage site. As shown in Figure 3a, a significant number independently cloned transcripts mapped to the predicted site of cleavage, between the nucleotides at positions 457 and 458 of the transcript, which corresponds to position 9 and 10 of the predicted miR1511 binding site, thus confirming a miR1511-induced degradation. The other two degradation events mapped to 7 nucleotides upstream and 17 nucleotides downstream of the miRNA-associated degradation site, suggesting random degradation. An additional action of miR1511 to induce translation inhibition of ALS3 mRNA in common bean, cannot be excluded. miR1511 target genes differ among plant species . In order to evaluate the specificity of the miR1511/ALS3 regulatory node in common bean, we analyzed the miR1511/ALS3 binding site sequence alignment from eight model plant species, including five legumes, which contain a precursor gene of miR1511 in their genome . Because of the deletion in MIR1511 from the G19833 genotype, we used the mature miR1511 and the corresponding ALS3 binding site sequences from the BAT93 Mesoamerican genotype, as representative of P. vulgaris. Among plant species analyzed, P. vulgaris was the only one that showed a binding-site penalty score lower than 5, corresponding to a score recommended to consider a small RNA-target binding as probably functional. For other species, the high penalty scores, ranging from 7.5 to 9, indicate a very low probability for the existence of a functional miR1511/ALS3 regulatory node .