Genetic diversity of Rhizobium present in nodules of Phaseolus vulgaris L. cultivated in two soils of the central region in Chile

Although Phaseolus vulgaris L. is native from the Americas and is currently cultured in diverse areas, very little is known about the diversity of symbiotic nitrogen fixing Rhizobium (mycrosymbiont) in many of those cultures. Therefore, the aim of this study was to assess the genetic diversity of Rhizobium present in nodules of P. vulgaris in the central region of Chile. A method to extract DNA from surface-sterilized nodules was applied to two populations of the same seed variety grown in different fields. The 16S rRNA and nifH genes were amplified directly from the DNA extracted. DGGE analysis and clone libraries showed a restricted genetic diversity of the microsymbiotic populations that nodulate P. vulgaris. Both molecular markers revealed the presence of a microsymbiont closely related to Rhizobium etli in all the plants from the soils studied, indicating that the populations of Rhizobium sp. nodulating P. vulgaris in the central region of Chile displayed an extremely low genetic diversity. The level of genetic diversity in microsymbiont populations in plants grown in soils with different origin suggested that other factors rather than the indigenous soil rhizobial populations play a major role in the selection of the symbiotic partner in P. vulgaris.     

The genetic diversity of Rhizobium leguminosarum bv. viciae in cultivated soils of the eastern Canadian prairie

Soil populations of Rhizobium leguminosarum bv. viciae (Rlv) that are infective and symbiotically effective on pea (Pisum sativum L.) have recently been shown to be quite widespread in agricultural soils of the eastern Canadian prairie. Here we report on studies carried out to assess the genetic diversity amongst these endemic Rlv strains and to attempt to determine if the endemic strains arose from previously used commercial rhizobial inoculants. Isolates of Rlv were collected from nodules of uninoculated pea plants from 20 sites across southern Manitoba and analyzed by plasmid profiling and PCR-RFLP of the 16S-23S rDNA internally transcribed spacer (ITS) region. Of 214 field isolates analyzed, 67 different plasmid profiles were identified, indicating a relatively high degree of variability among the isolates. Plasmid profiling of isolates from proximal nodules (near the base of the stem) and distal nodules (on lateral roots further from the root crown) from individual plants from one site suggested that the endemic strains were quite competitive relative to a commercial inoculant, occupying 78% of the proximal nodules and 96% of the distal nodules. PCR-RFLP of the 16S-23S rDNA ITS also suggested a relatively high degree of genetic variability among the field isolates. Analysis of the PCR-RFLP patterns of 15 selected isolates by UPGMA indicated two clusters of three field isolates each, with simple matching coefficients (SMCs) ≥0.95. However, to group all field isolates together, the SMC has to be reduced to 0.70. Regarding the origin of the endemic Rlv strains, there were few occurrences of the plasmid profiles of field isolates being identical to the profiles of inoculant Rlv strains commonly used in the region. Likewise, the plasmid profiles of isolates from nodules of wild Lathyrus plants located near some of the sites were all different from those of the field isolates. However, comparison of PCR-RFLP patterns suggested an influence of some inoculant strains on the chromosomal composition of some of the field isolates with SMCs of ≥0.92. Overall, plasmid profiles and PCR-RFLP patterns of the isolates from endemic Rlv populations from across southern Manitoba indicate a relatively high degree of genetic diversity among both plasmid and chromosomal components of endemic strains, but also suggest some influence of chromosomal information from previously used inoculant strains on the endemic soil strains.     

Survival and plasmid stability of rhizobia introduced into a contaminated soil

The behaviour of Rhizobium strains introduced separately into soil from a contaminated site with high concentrations of heavy metals (mainly Zn and Hg), and the role of plasmids in the ecology of these rhizobia strains were studied. Six Rhizobium leguminosarum biovar trifolii strains, from different sources and with different plasmid contents, were selected. Two of them were isolated from nodules of subterranean clover plants (Trifolium subterraneum) grown in the contaminated soil and four were from an uncontaminated soil. After inoculation with approximately 10⁷ cells g⁻¹ soil, of each strain, survival and plasmid stability were assessed over a period of 12-18 months. Differences in survival of Rhizobium strains were only detected more than 12 months after inoculation. After 18 months it was clear that survival in contaminated soil was greatest in the two strains originally isolated from that contaminated soil, and also by two of the strains originally isolated from uncontaminated soil. The latter two strains were also the only ones that showed changes in their plasmid profiles. The remaining isolates had the lowest populations, and their plasmid profiles were unchanged and similar to the parent strains.     

Restricted gene flow in the clonal hepatic Trichocolea tomentella in fragmented landscapes

We studied the genetic diversity, gene flow and population structure among 18 populations of the clonal bryophyte Trichocolea tomentella located in Finland, Lithuania, the UK and Canada using DNA fingerprinting methods. T. tomentella is a habitat-limited, unisexual hepatic, which occupies spring and mesic habitats in woodland. The relatively small populations are increasingly fragmented with a high risk for extinction for extrinsic reasons. The presence of relatively high levels of genetic diversity regardless of population size highlights the role of even small remnant populations as important sources of genetic diversity in T. tomentella. The long-term accumulation of genotypes and somatic mutations may explain the observed levels of diversity. Gene flow among populations seems to be infrequent indicating dispersal limitation also on the relatively small spatial scale. Colonization within populations is not affected by isolation by distance suggesting the occurrence of random short-range dispersal of detached vegetative fragments. The population structure study confirmed the low mortality rates of shoots indicating a long life span of the clones in favourable conditions. Efficient ramet production by branching is likely to operate against interspecific competition. To conclude, T. tomentella appears to persist well in undisturbed habitats due to clonal regeneration, although restricted dispersal capacity is likely to prevent successful (re-)colonization in the potential habitat patches of recovering forest landscapes. The implications of the results for conservation are introduced.     

Global analysis of Coffea canephora Pierre ex Froehner (Rubiaceae) from the Guineo-Congolese region reveals impacts from climatic refuges and migration effects

As the second species used for commercial coffee, evaluation of Coffea canephora Pierre ex Froehner population genetics is a challenging task for coffee breeding. This study examined the pattern of genetic variability and genetic relationships of cultivated and wild populations of C. canephora sampled across the Guineo-Congolese region of Africa and some improved populations maintained in field genebanks. A total of 293 individuals, sampled from 17 populations, were genotyped with 39 nuclear microsatellite markers. Genetic diversity and structure were investigated with both a model-based and a graphical approach; isolation by distance was also tested. Relationships between the diversity clusters are discussed with regard to differentiation due to several glacial refuges during the Last Glacial Maximum (LGM). High genetic diversity within C. canephora is confirmed with a mean number of alleles of 11.85 per marker, a mean gene diversity of 0.72 and a mean observed heterozygosity of 0.36. An overall structure of two main groups (Guinean and Congolese) subdivided in six subgroups (2 for the Guinean and 4 for the Congolese) was found, including one described for the first time in the Guinean group. A fine structure within the Guinean group was also newly detected. Genetic structure of C. canephora appears to be consistent with its geographic repartition at the continent scale. Structure of diversity was found in accordance with localizations of refuge zones during LGM and migration from this period. Results from this genetic structure study raise our capabilities to better manage and use the collections of genetics resources for breeding purposes. Those results will be used in future association studies to optimize the number of genotypes to be phenotyped.     

Rapid identification and discrimination among Egyptian genotypes of Rhizobium leguminosarum bv. viciae and Sinorhizobium meliloti nodulating faba bean (Vicia faba L.) by analysis of nodC, ARDRA, and rDNA sequence analysis

Twenty-eight Rhizobium strains were isolated from the root nodules of faba bean (Vicia faba L.) collected from 11 governorates in Egypt. A majority of these strains (57%) were identified as Rhizobium leguminosarum bv. viciae (Rlv) based on analysis of a nodC gene fragment amplified using specific primers for these faba bean symbionts. The strains were characterized using a polyphasic approach, including nodulation pattern, tolerance to environmental stresses, and genetic diversity based on amplified ribosomal DNA-restriction analysis (ARDRA) of both 16S and 23S rDNA. Analysis of tolerance to environmental stresses revealed that some of these strains can survive in the presence of 1% NaCl and a majority of them survived well at 37 °C. ARDRA indicated that the strains could be divided into six 16S rDNA genotypes and five 23S rDNA genotypes. Sequence analysis of 16S rDNA indicated that 57% were Rlv, two strains were Rhizobium etli, one strain was taxonomically related to Rhizobium rubi, and a group of strains were most closely related to Sinorhizobium meliloti. Results of these studies indicate that genetically diverse rhizobial strains are capable of forming N₂-fixing symbiotic associations with faba bean and PCR done using nodC primers allows for the rapid identification of V. faba symbionts.     

Comparing the historic olive trees (Olea europaea L.) of Santa Cruz Island with contemporaneous trees in the Santa Barbara, CA area: a case study of diversity and structure in an introduced agricultural species conserved in situ

Historic populations of crop species outside their centers of origin and diversity, like the domestic olive (Olea europaea L.) in North America, are genetic resources for contemporary agriculture, including genotypes that could be readily evaluated for, and may be adapted to, local conditions. The primary goal of this study was to describe the diversity and structure of several significant, adjacent, contemporaneous historic olive plantings in central coastal California, USA with reference to the USDA ex situ Olea europaea germplasm, and test the hypothesis that physical and chronological proximity are predictive of genetic similarity in those trees. The groups studied using 14 SSR markers were dominated by a limited number of genotypes represented in the USDA collection, but also four unique cultivar genotypes not in that collection. Historical socioeconomic networks appear to have had an important influence on the source and kind of material planted. This is the first study of historic olive trees conserved in situ in North America and provides the basis for a larger regional study integrating genetic, historical and geographic data to describe the structure and diversity of remaining historic olive plantings in California.     

The domestication and dispersal of the cultivated ramie (Boehmeria nivea (L.) Gaud. in Freyc.) determined by nuclear SSR marker analysis

Ramie (Boehmeria nivea) was domesticated in China. However, the geographic region of domestication is not exactly known. Genetic diversity and population structure of ramie and their wild relatives were assessed using microsatellite markers. The 8 microsatellite primers revealed 96 alleles in 50 ramie populations, with an average of 10.25 alleles per locus. Cultivated ramie gene pool harbors approximately 82.9 % of the SSR diversity presented in wild B. nivea var. nivea. It is suggested that ramie has experienced a relatively moderate domestication bottleneck. The distribution of genetic diversity shows that genetic diversity is relatively high in populations along the Yangtze River compared to the peripheral ones. The scatter plots of principal coordinates analysis indicated that there are three well-supported varieties in B. nivea. The NJ tree and the distribution of genetic diversity showed that ramie has been domesticated in the middle and lower regions of the Yangtze valley, and populations in Sichuan province have been introduced from this region, forming naturalized populations.     

Bio-indicators to assess impacts of heavy metals in land-applied sewage sludge

Soils from a pastoral farm that had received large amounts of heavy metal contaminated sewage sludge 6-10 years previously were investigated to determine the impact of heavy metals on Rhizobium. The 8 ha application area was originally divided into five different-sized blocks (blocks 1-5), which received sludge at different times between 1991 and 1994. The response of a lux biosensor based on R. leguminosarum bv. trifolii (Rhizotox-C), was compared with more traditional techniques for measuring the presence of effective strains of Rhizobium (MPN) and nitrogen fixation (δ¹⁵N natural abundance). Although population size (MPNs), nitrogen fixation and biosensor response varied between treatment blocks, linear regression analysis determined that this block effect could not be directly linked to soil heavy metal concentrations, but was probably due to biological, physical, chemical and environmental compounding factors at the site. In this type of uncontrolled field application, the lux bioassay may provide the most useful information as it measures toxicity to any microorganism exposed to the soil solution, for example, the free living rhizobia.     

Spatial Distribution of Genetic Diversity in Wild Populations of Phaseolus vulgarisL. from Guanajuato and Michoacán, Méexico

The diversity, genetic structure, and genetic flow of wild populations of Phaseolus vulgaris L. within its Mesoamerican area of domestication, were analyzed by means of morphological and inter-simple sequence repeat molecular markers. Overall, 89% of the loci studied were polymorphic, 35% in the least diverse population and 65% in the most diverse. Genetic diversity in the populations was high, between h = 0.14 and 0.29, as was the maximum distance between populations (D = 0.3). Between 40% and 45% of the diversity was explained by the differences among populations, indicating that a large number of populations is necessary to represent the wild gene pool in the germplasm collections. We found uniformity in allele frequencies among the populations, suggesting presence of outcrossing. We did not find correlation between genetic and geographic distances, but the dendrogram topology suggests geographical isolation due to the mountainous topography. Negative correlations were observed between the coefficient of variation of seed size and the distance between wild populations and fields . We obtained a highly negative correlation between percentage of polymorphic loci and distance to the nearest crop field, which also suggests gene flow from the domesticated populations. These observations suggest that genetic flow is taking place from domesticated toward wild populations and that the farmer, through his agricultural activities, could be influencing the magnitude and the characteristics of the gene flow, and along with this, the differentiation of wild populations. New approaches should be established for conservation in situ and maintaining bio-safety, given the risk of introducing genotypes from the Andes and transgenic varieties and causing genetic assimilation.     

Chickpea rhizobium populations: Survey of influence of season,soil depth and cropping pattern

Chickpea Rhizobium populations in soil samples from research stations and farmers' fields in different geographic regions of India ranged from <10 to > 10⁴ rhizobia g⁻¹ soil. Fields on research stations with a known history of chickpea cropping had more rhizobia (calc. 10³ to 10⁵ rhizobia g^1&#x0304; soil) than the majority of farmers' fields (calc. < 10 to 10³ rhizobia g⁻¹ soil). In the absence of chickpea in the cropping pattern, soils generally had < 10² rhizobia g^1&#x0304; and crops in such fields nodulated poorly. However, poor nodulation was also observed when populations of rhizobia were high, indicating that other factors were also important for nodulation. There was no obvious consistent correlation of Rhizobium population with pH, electrical conductivity and nitrate-nitrogen status of the soil.Rhizobium populations declined with soil depth and were highest (about 10⁴ rhizobia g⁻¹ soil) in the top 30 cm of the profile and lowest, but still present (calc. 10³–10³ rhizobia g'1 soil), at 90–120 cm—a depth where no nodules are found. Populations fluctuated most in the top 5 cm, being reduced during periods of high soil temperature in summer and recovering after rains. Rhizobium populations were at a maximum after chickpea but survived well under pigeonpea, groundnut and maize. When rice followed an inoculated chickpea crop, there was about a 100-fold decrease in the Rhizobium population.     

Spatial demographic and genetic consequences of harvesting within populations of the terrestrial orchid Cymbidium goeringii

Populations of many orchids, especially terrestrial species, have been rapidly decreasing due to mass collection by plant sellers and enthusiasts. Given the presumably negative demographic and genetic consequences, such anthropogenic activity should be taken into consideration for predicting ecological and evolutionary dynamics and for planning conservation strategies. To determine how recent human disturbance alters spatial demographic and population genetic processes, populations of the terrestrial orchid Cymbidium goeringii located in South Korea were examined to quantify the spatial distributions of individuals and genotypes with respect to three levels of disturbance: “disturbed” (four populations), “putatively disturbed” (two), and “undisturbed” (two). Undisturbed and putatively disturbed populations were found to possess significantly positive spatial clustering of individuals over a range of spatial scales. In contrast, disturbed populations exhibited little or no spatial aggregation, consistent with the selective removal of plants by collectors from higher density areas within these populations. Although overall genetic differentiation among populations was moderate and significant (F_ST = 0.082), levels of genetic diversity within populations were similar despite the different disturbance histories (mean H_e = 0.257-0.324). Spatial genetic autocorrelation analyses revealed that the undisturbed populations exhibited significant declines in kinship (F_ij) with distance, that mean kinship at interplant distances of ?4-6 m was significantly greater than zero and between plants ?0.5 m apart was in the range expected for first cousins to half-sibs. In contrast, only one putatively disturbed and one disturbed population exhibited significant declines in kinship with distance. These differences between disturbed versus putatively disturbed and undisturbed populations in the spatial distribution of individuals and genetic variation likely reflect the consequences of mass collections. Since these differences (and reduced population density) have important implications for future ecological and evolutionary trajectories, conservation managers of endangered terrestrial orchids may want to analyze the spatial distribution of individuals and their genotypes to infer whether a population with few individuals represents a natural state or the likely outcome of mass collection.     

Low levels of genetic variation among southern peripheral populations of the threatened herb, Leontice microrhyncha (Berberidaceae) in Korea

Levels of genetic variation and intrapopulation genetic structures of Leontice microrhyncha S. Moore (Berberidaceae) were assessed for six populations in South Korea, representing the southern most range of a species found in Northeast China and the Korean peninsula. Detected genetic diversity (H_es) was very low (0.024) and F_IS values showed large heterozygote deficiencies. The small percentage of polymorphic loci and numbers of alleles per locus suggest that L. microrhyncha has a history of severe or long-lasting population bottlenecks that have eroded genetic diversity. This study suggests that the Korean population appears to consist of two historically isolated and independently evolving populations. It seems likely that these groups have been isolated and unstable for a significant period of time. However, the effects of recent habitat fragmentation on the historically disjunct and fragmented population system found in L. microrhyncha were not those predicted from the lack of significant relationships between population-level patterns of genetic variation and population sizes. Most non-unique genotypes were shared by most individuals and the lower level of diversity, high levels of inbreeding and population differentiation as well as high rate of seed production indicated that this species is autogamous and self-compatible and probably largely selfing. Therefore, to preserve extant genetic variation, all populations must be protected across the small geographic range of the species to retain both allelic and genotypic diversity.     

Genotypic characterisation of rhizobia nodulating Vicia faba from the soils of Jordan: a comparison with UK isolates

Seven isolates of Rhizobium leguminosarum bv. viciae (Rlv) that nodulate faba beans (Vicia faba) from six sites in Jordan were characterised for chromosomal (glnII) and symbiotic (nodD-F) genotypes using polymerase chain reaction-restriction fragment length polymorphism and sequencing methods. The results were compared to those obtained in a previous UK study, to determine whether or not the UK field population are indigenous or if they were dispersed during the radiation of V. faba domestication. All seven Jordanian isolates displayed novel chromosomal and symbiotic genotypes not identified in the UK population.     

ISSR analysis shows low genetic diversity versus high genetic differentiation for giant bamboo, Dendrocalamus giganteus (Poaceae: Bambusoideae), in China populations

Dendrocalamus giganteus Munro is a high-value woody bamboo widely grown in Southeast Asia and China’s Yunnan Province. We investigated its genetic diversity in Yunnan as a prelude to considering effective breeding programs and the protection of germplasm resources. Inter-simple sequence repeat (ISSR) markers were used to assess the genetic structure and differentiation of seven populations. Seven ISSR primers generated 140 bands, of which 124 were polymorphic (88.57%). Genetic diversity within populations was relatively low, averaging 11.33% polymorphic bands (PPB), while diversity was considerably higher among populations, with PPB = 88.57%. Greater genetic differentiation was detected among populations (G _ST = 0.8474). We grouped these seven populations into two clusters within an UPGMA dendrogram—one comprised the Xinping and Shiping populations from central Yunnan, the other included the remaining five populations. Mantel tests indicated no significant correlation between genetic and geographic distances among populations. Breeding system characteristics, genetic drift, and limited gene flow (N _m = 0.0901) might be important factors for explaining this differentiation. Based on the overall high genetic diversity and differentiation among D. giganteus populations in Yunnan, we suggest the implementation of in situ conservation measures for all populations and sufficient sampling for ex situ conservation collections.     

Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest

Tropical rainforests are becoming increasingly fragmented and understanding the genetic consequences of fragmentation is crucial for conservation of their flora and fauna. We examined populations of the toad Rhinella ornata, a species endemic to Atlantic Coastal Forest in Brazil, and compared genetic diversity among small and medium forest fragments that were either isolated or connected to large forest areas by corridors. Genetic differentiation, as measured by F_ST, was not related to geographic distance among study sites and the size of the fragments did not significantly alter patterns of genetic connectivity. However, population genetic diversity was positively related to fragment size, thus haplotype diversity was lowest in the smallest fragments, likely due to decreases in population sizes. Spatial analyses of genetic discontinuities among groups of populations showed a higher proportion of barriers to gene flow among small and medium fragments than between populations in continuous forest. Our results underscore that even species with relatively high dispersal capacities may, over time, suffer the negative genetic effects of fragmentation, possibly leading to reduced fitness of population and cases of localized extinction.     

Genetic diversity of resident soil rhizobia isolated from nodules of distinct hairy vetch (Vicia villosa Roth) genotypes

Hairy vetch (Vicia villosa Roth, HV) is widely grown as a legume cover crop throughout the U.S.A., with biological nitrogen fixation (BNF) through symbiosis with Rhizobium leguminosarum biovar viciae (Rlv) being one of the most sought after benefits of its cultivation. This study determined if HV cultivation history and plant genotype affect genetic diversity of resident Rlv. Soil samples were collected from within farmers’ fields at Graham, Cedar Grove and Ivanhoe sites in North Carolina and pairs of genetically similar hairy vetch genotypes used as trap hosts. A total of 519 Rlv strains were isolated from six paired field soils, three with and three without histories of HV cultivation. A total of 46 strains failed to PCR-amplify the nifH gene; however nodC PCR amplification of these nifH-negative strains resulted in amplification of 22 of the strains. Repetitive element polymerase chain reaction (rep-PCR) with BOX-A1R primer and redundancy analysis showed rhizobial diversity to vary greatly within and between fields, with over 30 BOX banding patterns obtained across the six fields. Cluster analysis of BOX-PCR banding patterns resulted in 36 genetic groups of Rlv at a similarity level of 70%, with 15 of the isolates from fields with HV history not belonging to any of the clusters. Site was found to be the main driver of isolate diversity overall, explaining 57%, of the total variation among rhizobia occupying HV nodules, followed by history of hairy vetch cultivation. Evidence of a HV host genotype influence on the populations of rhizobia that infect hairy vetch was also observed, with plant genotype explaining 12.7% of the variation among all isolates. Our results show that second to site, HV cultivation history was the most important driver of rhizobial nodule community structure and increases the genetic diversity of resident Rlv in soils.     

Heavy metal toxicity in Rhizobium leguminosarum biovar viciae isolated from soils subjected to different sources of heavy-metal contamination: Effects on protein expression

Heavy metals adversely influence microorganisms, affecting their growth, morphology and activities. Metals also can exert a selective pressure on the organisms, resulting in microbial populations with higher tolerance to metals. Given the importance of legumes in animal and human consumption and their use in maintaining soil fertility, some attention has been given to the effects that heavy metals exert on Rhizobium isolates. In this context, Rhizobium leguminosarum biovar viciae was isolated from areas with different heavy metal contents and their tolerances were compared. Alterations in the protein pool of Rhizobium populations were also evaluated. Physicochemical parameters were determined and heavy metal concentrations in soils were analysed by ICP-AES. Isolates were screened for their tolerance in YEM media supplemented with different heavy metals (Zn, Pb, Co, Cd, Ni, Cr). Proteins were extracted and separated by SDS-PAGE. EI₁ and EI₂ (engineering industries) soils presented the highest metal concentration, and were therefore the most polluted soils. Isolates showed different growth responses to heavy metals. C (control soil) and M (mines) isolates were less tolerant than EI₁, EI₂ and CI (chemical industries) isolates. Metals influenced their protein profiles, most of the alterations corresponding to decreases in polypeptide expression. However, in tolerant isolates these alterations corresponding basically to increases, as occurred in CI isolates.This work suggests that there is a relationship between Rhizobium's tolerance, heavy metal soil contamination and alterations in protein pool. As a result, the analysis of protein alterations seems to be a good indicator to estimate the level of stress imposed on Rhizobium populations submitted to heavy-metal contamination.     

Geographic distance and amorphous iron affect the abundance and distribution of <Emphasis Type="Italic">Geobacteraceae</Emphasis> in paddy soils in China

Purpose

Geobacteraceae are important dissimilatory Fe (III)-reducing microorganisms, influencing the cycling of metals, nutrients as well as the degradation of organic contaminants. However, little is known about their distribution, diversity, and abundance of Geobacteraceae and the effects of environment factors and geographic distance on the distribution and diversity of Geobacteraceae in paddy soils remain unclear. Therefore, the objectives of this study were to investigate the distribution, diversity, and abundance of Geobacteraceae in paddy soils and to determine key factors in shaping the Geobacteraceae distribution, environmental factors, geographic distance, or both and to quantify their contribution to Geobacteraceae variation.

Materials and methods

Illumina sequencing and quantitative real-time PCR using a primer set targeting 16S rRNA genes of bacteria affiliated with the family Geobacteraceae were employed to measure the community composition, diversity, and abundance patterns of 16S rRNA genes of Geobacteraceae in 16 samples collected from north to south of China. MRT, Mantel test, and VPA were used to analyze the relationship between communities of Geobacteraceae and environmental factors and geographic distance.

Results and discussion

Quantitative PCR showed that the abundance of 16S rRNA genes of Geobacteraceae ranged from (1.20?±?0.18)?×?10⁸ to 1.13?×?10⁹?±?2.25?×?10⁸ copies per gram of soil (dry weight) across different types of soils. Illumina sequencing results showed Geobacter was the dominant genus within the family of Geobacteraceae. Multivariate regression tree (MRT) analysis showed that soil amorphous iron contributed more (22.46 %) to the variation of dominant species of Geobacteraceae than other examined soil chemical factors such as pH (14.52 %), ammonium (5.12 %), and dissolved organic carbon (4.74 %). Additionally, more geographically distant sites harbored less similar communities. Variance partitioning analysis (VPA) showed that geographic distance contributed more to the variation of Geobacteraceae than any other factor, although the environmental factors explained more variation when combined. So, we detected the uneven distribution of Geobacteraceae in paddy soils of China and demonstrated that Geobacteraceae community composition was strongly associated with geographic distance and soil chemical factors including aFe, pH, Fe, DOC, C:N, and NO₃ ^?-N. These results greatly expand the knowledge of the distribution of Geobacteraceae in environments, particularly in terrestrial ecosystems.

Conclusions

Our results showed that geographic distance and amorphous iron played important roles in shaping Geobacteraceae community composition and revealed that both geographic distance and soil properties governed Geobacteraceae biogeography in paddy soils. Our findings will be critical in facilitating the prediction of element cycling by incorporating information on functional microbial communities into current biogeochemical models.

     

Genetic Diversity in Tunisian Ceratonia siliqua L. (Caesalpinioideae) Natural Populations

The last two centuries witnessed the human-caused fragmentation of Tunisian Ceratonia siliqua L. (Caesalpinoideae) populations which were often represented by scattered individuals. Seventeen populations growing in four bioclimatic zones: sub-humid, upper semi-arid, mean semi-arid and lower semi-arid zones, were sampled for allozyme diversity to assess their genetic diversity and structuration using eight isozymes revealed by starch gel electrophoresis. The species showed high diversity within populations. The average number of alleles per polymorphic locus was 1.98, the percentage of polymorphic loci was 83.4% and the mean observed heterozygosity (Ho) and expected heterozygosity (He) under Hardy–Weinberg equilibrium were respectively 0.247 and 0.316. A substantial level of inbreeding within populations induced by Wahlund effect, was observed (F_IS = 0.231). High diversity resulted from the great number of genotypes in the ancestral population before fragmentation, favoured by the outbreeding of the species. High differentiation and low gene flow were detected among populations (F_ST = 0.200) and among pairs of ecological zones (0.113< F_ST <0.198). However, the differentiation coefficient of the four zones was low (F_ST = 0.085) and similar to the average F_ST for forest trees. Population structuration depends on geographic distance between sites rather than bioclimate, indicating that structuration has occurred slowly and that climatic conditions have had little effect. Nei's genetic distances (D) between populations were low and ranged from 0.004 to 0.201. Mean D value for all population was 0.087. The UPGMA clustering established for all populations through Nei's genetic distances did not clearly show that, for the majority of populations, grouping had resulted from ecological factors or geographic location. The substantial differentiation and the high genetic similarities between populations indicate that populations have been recently isolated as a result of anthropic pressure. In-situ conservation strategies must first focus on populations with a high level of genetic diversity and rare alleles. Appropriate conservation action should take account of bioclimatic zones. Ex-situ preservation should be based on a maximum number of individuals collected within populations in each ecological group and their propagation in different bioclimates by means of cuttings.