Effect of on-field inoculation of Phaseolus vulgaris with rhizobia on soil bacterial communities

The aim of this study was to assess the impact of inoculation of Phaseolus vulgaris with two indigenous rhizobia strains on plant growth promotion, nitrogen turnover processes, richness and structure of the Rhizobiaceae and total bacterial communities in the bulk soil. Both strains used induced a significant increase in nodulation and grain yield. Analysis of bulk soil fertility showed positive, negative and strain-dependent effects of inoculation on nitrate, phosphorus and ammonium, respectively. Terminal-restriction fragment length polymorphism profiling demonstrated that inoculation significantly increased the phylotype richness of the bacterial communities. No significant difference in richness between the strains used and no additive effect of co-inoculation were observed. However, differences between both inoculants and a clear additive effect of co-inoculation on heterogeneity were found. This work gives original insights into the effect of rhizobial inoculation outside the restricted rhizospheric area. Effects on bacterial structure and diversity are clearly sensed in the neighbourhood of 25 cm and in a limited time course. Both Alpha- and Gammaproteobacteria, together with Firmicutes and Actinobacteria, were enhanced by inoculation, No evidence of terminal-restriction fragment inhibition was found. However, it remains to be answered how the impact on taxonomic groups can be related to effects on functional capabilities of soil microbial communities.     

Responses of soil microbial catabolic diversity to arbuscular mycorrhizal inoculation and soil disinfection

Although it is usually admitted that arbuscular mycorrhizal (AM) fungi are key components in soil bio-functioning, little is known on the response of microbial functional diversity to AM inoculation. The aims of the present study were to determine the influence of Glomus intraradices inoculum densities on plant growth and soil microflora functional diversity in autoclaved soil or non-disinfected soil. Microbial diversity of soil treatments was assessed by measuring the patterns of in situ catabolic potential of microbial communities. The soil disinfection increased sorghum growth, but lowered catabolic evenness (4.8) compared to that recorded in the non-disinfected soil (6.5). G. intraradices inoculation induced a higher plant growth in the autoclaved soil than in the non-disinfected soil. This AM effect was positively related to inoculum density. Catabolic evenness and richness were positively correlated with the number of inoculated AM propagules in the autoclaved soil, but negatively correlated in the non-disinfected soil. In addition, after soil disinfection and AM inoculation, these microbial functionality indicators had higher values than in the autoclaved or in the non-disinfected soil without AM inoculation. These results are discussed in relation to the ecological influence of AM inoculation, with selected fungal strains and their associated microflora on native soil microbial activity.     

Phenotypic and genotypic characteristics of Acacia senegal (L.) Willd. root-nodulating bacteria isolated from soils in the dryland part of Senegal

Aims:  We characterized phenotypically and genotypically root-nodulating bacteria associated with Acacia senegal (L.) Willd. isolated from the soils surrounding A. senegal trees in the dry land area of Senegal.
Methods and Results:  The phenotypical and genotypical characterizations we carried out showed a high diversity of A. senegal root-nodulating bacteria. Phenotypic patterns showed adaptations of the rhizobial strains to many environmental stresses such as heat, drought, and salinity. Twelve molecular groups were distinguished by profiles obtained using polymerase chain reaction/restriction fragment length polymorphism techniques from intergenic spacer region rDNA. The highest genetic diversity was found around the A. senegal rhizosphere. Therefore, A. senegal seemed to have a positive influence on occurrence and genotypical diversity of rhizobial populations. Rhizobial isolates obtained in this study belonged phylogenetically to the genera Mesorhizobium and Rhizobium .
Conclusions:  Our results provided information about the genetic diversity of the rhizobial strains associated with A. senegal and suggested the adaptability of natural rhizobial populations to major ecological environmental stress within these soil environments.
Significance and Impact of the Study:  These results suggested a potential selection of compatible and well adapted strains under stress conditions as inoculants for successful A. senegal growth in arid lands.     

Microbial phylotype composition and diversity predicts plant productivity and plant–soil feedbacks

The relationship between ecological variation and microbial genetic composition is critical to understanding microbial influence on community and ecosystem function. In glasshouse trials using nine native legume species and 40 rhizobial strains, we find that bacterial rRNA phylotype accounts for 68% of amoung isolate variability in symbiotic effectiveness and 79% of host specificity in growth response. We also find that rhizobial phylotype diversity and composition of soils collected from a geographical breadth of sites explains the growth responses of two acacia species. Positive soil microbial feedback between the two acacia hosts was largely driven by changes in diversity of rhizobia. Greater rhizobial diversity accumulated in association with the less responsive host species, Acacia salicina, and negatively affected the growth of the more responsive Acacia stenophylla. Together, this work demonstrates correspondence of phylotype with microbial function, and demonstrates that the dynamics of rhizobia on host species can feed back on plant population performance.     

Changes in soil diversity and global activities following invasions of the exotic invasive plant, Amaranthus viridis L., decrease the growth of native sahelian Acacia species

The objectives of this study were to determine whether the invasive plant Amaranthus viridis influenced soil microbial and chemical properties and to assess the consequences of these modifications on native plant growth. The experiment was conducted in Senegal at two sites: one invaded by A. viridis and the other covered by other plant species. Soil nutrient contents as well as microbial community density, diversity and functions were measured. Additionally, five sahelian Acacia species were grown in (1) soil disinfected or not collected from both sites, (2) uninvaded soil exposed to an A. viridis plant aqueous extract and (3) soil collected from invaded and uninvaded sites and inoculated or not with the arbuscular mycorrhizal (AM) fungus Glomus intraradices . The results showed that the invasion of A. viridis increased soil nutrient availability, bacterial abundance and microbial activities. In contrast, AM fungi and rhizobial development and the growth of Acacia species were severely reduced in A. viridis -invaded soil. Amaranthus viridis aqueous extract also exhibited an inhibitory effect on rhizobial growth, indicating an antibacterial activity of this plant extract. However, the inoculation of G. intraradices was highly beneficial to the growth and nodulation of Acacia species. These results highlight the role of AM symbiosis in the processes involved in plant coexistence and in ecosystem management programs that target preservation of native plant diversity.     

Arbuscular mycorrhizal symbiosis can counterbalance the negative influence of the exotic tree species Eucalyptus camaldulensis on the structure and functioning of soil microbial communities in a sahelian soil

The hypothesis of the present study was that bacterial communities would differentiate under Eucalyptus camaldulensis and that an enhancement of arbuscular mycorrhizal (AM) density would minimize this exotic plant species effect. Treatments consisted of control plants, preplanting fertilizer application and AM inoculation. After 4 months of culture in autoclaved soil, E. camaldulensis seedlings were either harvested for growth measurement or transferred into containers filled with the same soil but not sterilized. Other containers were kept without E. camaldulensis seedlings. After 12 months, effects of fertilizer amendment and AM inoculation were measured on the growth of Eucalyptus seedlings and on soil microbial communities. The results clearly show that this plant species significantly modified the soil bacterial community. Both community structure (assessed by denaturing gradient gel electrophoresis profiles) and function (assessed by substrate-induced respiration responses including soil catabolic evenness) were significantly affected. Such changes in the bacterial structure and function were accompanied by disturbances in the composition of the herbaceous plant species layer. These results highlight the role of AM symbiosis in the processes involved in soil bio-functioning and plant coexistence and in afforestation programmes with exotic tree species that target preservation of native plant diversity.     

Water Content Differences Have Stronger Effects than Plant Functional Groups on Soil Bacteria in a Steppe Ecosystem

Many investigations across natural and artificial plant diversity gradients have reported that both soil physicochemical factors and plant community composition affect soil microbial communities. To test the effect of plant diversity loss on soil bacterial communities, we conducted a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia (China). We found that the number and composition type of plant functional groups had no effect on bacterial diversity and community composition, or on the relative abundance of major taxa. In contrast, bacterial community patterns were significantly structured by soil water content differences among plots. Our results support researches that suggest that water availability is the key factor structuring soil bacterial communities in this semi-arid ecosystem.     

垃圾堆肥复合菌剂对干旱胁迫下草坪植物生理生态特性的影响

从生活垃圾堆肥中提取有益微生物菌种,配成不同浓度的复合微生物菌剂（CM）,施入草坪基质,研究了复合微生物菌剂对干旱胁迫下草坪植物生理生态特性的影响。结果表明：在干旱胁迫下,接种过复合微生物菌剂的草坪植物叶片的丙二醛（MDA）含量显著低于未接种菌剂的对照,超氧化物歧化酶（SOD）、过氧化物酶（POD）、过氧化氢酶（CAT）活性显著高于对照。不同草坪植物品种生理生态特性在接种CM后对干旱胁迫的响应程度不同。即高羊茅（Festuca arundinacea L.）,当接种200倍稀释液的菌剂,叶片SOD、POD和CAT活性达到最大,分别是对照的8.13、1.53和2.46倍;而黑麦草（Lolium perenne L.）则当接种100倍稀释液的菌剂,POD和CAT活性分别高出对照64.4%和56.1%,而SOD活性是对照的6.50倍。和对照相比,各接种菌剂处理的脯氨酸（Pro）含量、可溶性蛋白含量明显降低,离体叶片持水力却保持了较高的水平。上述结果表明,接种复合微生物菌剂后,植物能够通过自身的保护酶活性和渗透调节物质含量来减轻干旱伤害,维持植物体的正常生理代谢功能,从而有效缓解干旱胁迫对草坪植物的伤害,提高草坪植物的抗旱性,为干旱环境草坪植物的建植提供依据。     

Legacy of prior host and soil selection on rhizobial fitness in planta

Measuring selection acting on microbial populations in natural or even seminatural environments is challenging because many microbial populations experience variable selection. The majority of rhizobial bacteria are found in the soil. However, they also live symbiotically inside nodules of legume hosts and each nodule can release thousands of daughter cells back into the soil. We tested how past selection (i.e., legacies) by two plant genotypes and by the soil alone affected selection and genetic diversity within a population of 101 strains of Ensifer meliloti. We also identified allelic variants most strongly associated with soil‐ and host‐dependent fitness. In addition to imposing direct selection on rhizobia populations, soil and host environments had lasting effects across host generations. Host presence and genotype during the legacy period explained 22% and 12% of the variance in the strain composition of nodule communities in the second cohort, respectively. Although strains with high host fitness in the legacy cohort tended to be enriched in the second cohort, the diversity of the strain community was greater when the second cohort was preceded by host rather than soil legacies. Our results indicate the potential importance of soil selection driving the evolution of these plant‐associated microbes.     

羊草基因型数目与氮添加对土壤微生物群落的交互影响

物种多样性(或同一物种遗传多样性)减少和氮富集都是影响陆地生态系统进程的主要因素,它们之间的交互作用是否对土壤微生物群落产生显著影响已成为研究者关心的主要科学问题。研究羊草基因型数目(1、2、4三种基因型数目组合)和氮添加(无氮添加、低氮添加和高氮添加3种水平)对土壤微生物群落的总磷脂脂肪酸(PLFA,Phospholipid Fatty Acid)含量、细菌PLFA生物标记含量、真菌PLFA生物标记含量、真菌/细菌比、以及基于每个PLFA生物标记相对含量百分比所得微生物群落的Shannon-Wiener多样性指数和Simpson优势度指数的影响。结果表明:氮添加对细菌PLFA生物标记含量,以及土壤微生物PLFA生物标记的Shannon-Wiener多样性指数和Simpson优势度指数具有显著影响(P0.05);基因型数目对所测变量无显著影响(P0.05),但基因型数目和氮添加的交互作用对细菌PLFA生物标记含量和真菌/细菌比具有显著影响(P0.05)。研究结果为全球变化背景下氮沉降及重要物种种群数量减少对土壤微生物群落的影响提供了科学数据,为合理解释群落动态变化提供了数据支持。     

Effects of plant species richness and evenness on soil microbial community diversity and function

Understanding the links between plant diversity and soil communities is critical to disentangling the mechanisms by which plant communities modulate ecosystem function. Experimental plant communities varying in species richness, evenness, and density were established using a response surface design and soil community properties including bacterial and archaeal abundance, richness, and evenness were measured. The potential to perform a representative soil ecosystem function, oxidation of ammonium to nitrite, was measured via archaeal and bacterial amoA genes. Structural equation modeling was used to explore the direct and indirect effects of the plant community on soil diversity and potential function. Plant communities influenced archaea and bacteria via different pathways. Species richness and evenness had significant direct effects on soil microbial community structure, but the mechanisms driving these effects did not include either root biomass or the pools of carbon and nitrogen available to the soil microbial community. Species richness had direct positive effects on archaeal amoA prevalence, but only indirect impacts on bacterial communities through modulation of plant evenness. Increased plant evenness increased bacterial abundance which in turn increased bacterial amoA abundance. These results suggest that plant community evenness may have a strong impact on some aspects of soil ecosystem function. We show that a more even plant community increased bacterial abundance, which then increased the potential for bacterial nitrification. A more even plant community also increased total dissolved nitrogen in the soil, which decreased the potential for archaeal nitrification. The role of plant evenness in structuring the soil community suggests mechanisms including complementarity in root exudate profiles or root foraging patterns.     

盐城滨海滩涂湿地典型植物群落土壤微生物组成与结构特征

土壤微生物是生态系统维持正常结构与功能的重要组成部分,为探究盐城滩涂典型湿地土壤微生物群落结构特征,以江苏盐城滩涂互花米草、藨草、盐地碱蓬、芦苇及淤泥质光滩5种典型群落为对象,采用16S rRNA高通量测序技术分析0—10 cm(表层)、10—30 cm(中层)、30—60 cm(深层)土壤微生物多样性及群落结构。结果表明：(1)几种植物群落间,土壤微生物群落结构差异较大,主要体现在细菌群落结构的差异性,古菌群落结构差异相对较小。光滩与植物群落间,在土壤细菌种类及相对丰度上差异相对较大,互花米草群落与本土植物群落间,在微生物群落的细菌种类组成上存在较大差异;藨草群落土壤表层微生物群落结构与互花米草群落相似,深层与盐地碱蓬、芦苇群落相似。(2)同一群落不同层次土壤微生物群落结构相似,差异小于不同群落间土壤微生物群落的结构差异性;不同群落对应层次间,表深层土壤中五种群落土壤微生物多样性存在显著差异,中层土壤中五种群落微生物多样性差异不显著。总体上,植物群落类型对土壤微生物群落结构的影响大于土壤深度;与本土植物群落相比,互花米草群落土壤主要优势门微生物种类差异较小,但部分优势门微生物相对丰度...     

Symbiotic characterization and diversity of rhizobia associated with native and introduced acacias in arid and semi-arid regions in Algeria

The diversity of rhizobia associated with introduced and native Acacia species in Algeria was investigated from soil samples collected across seven districts distributed in arid and semi-arid zones. The in vitro tolerances of rhizobial strains to NaCl and high temperature in pure culture varied greatly regardless of their geographical and host plant origins but were not correlated with the corresponding edaphoclimatic characteristics of the sampling sites, as clearly demonstrated by principal component analysis. Based on 16S rRNA gene sequence comparisons, the 48 new strains isolated were ranked into 10 phylogenetic groups representing five bacterial genera, namely, Ensifer, Mesorhizobium, Rhizobium, Bradyrhizobium, and Ochrobactrum. Acacia saligna, an introduced species, appeared as the most promiscuous host because it was efficiently nodulated with the widest diversity of rhizobia taxa including both fast-growing ones, Rhizobium, Ensifer, and Mesorhizobium, and slow-growing Bradyrhizobium. The five other Acacia species studied were associated with fast-growing bacterial taxa exclusively. No difference in efficiency was found between bacterial taxa isolated from a given Acacia species. The tolerances of strains to salinity and temperature remains to be tested in symbiosis with their host plants to select the most adapted Acacia sp.-LNB taxa associations for further revegetation programs.     

The legacy of bacterial invasions on soil native communities

Soil microbial communities are often not resistant to the impact caused by microbial invasions, both in terms of structure and functionality, but it remains unclear whether these changes persist over time. Here, we used three strains of Escherichia coli O157:H7 (E. coli O157:H7), a species used for modelling bacterial invasions, to evaluate the resilience of the bacterial communities from four Chinese soils to invasion. The impact of E. coli O157:H7 strains on soil native communities was tracked for 120 days by analysing bacterial community composition as well as their metabolic potential. We showed that soil native communities were not resistant to invasion, as demonstrated by a decline in bacterial diversity and shifts in bacterial composition in all treatments. The resilience of native bacterial communities (diversity and composition) was inversely correlated with invader's persistence in soils (R² = 0.487, p < 0.001). Microbial invasions also impacted the functionality of the soil communities (niche breadth and community niche), the degree of resilience being dependent on soil or native community diversity. Collectively, our results indicate that bacteria invasions can potentially leave a footprint in the structure and functionality of soil communities, indicating the need of assessing the legacy of introducing exotic species in soil environments.     

Microbial Nonlinear Response to a Precipitation Gradient in the Northeastern Tibetan Plateau

The response of soil microbes to global warming, especially their response to precipitation, remains poorly known. The Tibetan Plateau is very sensitive to climate change. In particular, the northeastern margin of the Tibetan Plateau is an interesting area to test the response of soil microbial communities to precipitation, as there is a distinct gradient in annual precipitation from east to west. We collected soil samples along a precipitation gradient in arid and semi-arid areas of the northeastern Tibetan Plateau. Phospholipid fatty acid (PLFA) technology was used to analyze the microbial community structure and total microbial biomass. With declining precipitation, bacterial biomass decreased significantly, whereas fungal biomass did not show an obvious trend; this result indicates that bacteria are more sensitive to mean annual precipitation (MAP). Overall, the biomass of Gram-negative (G^?) bacteria represented up to 82% of the total bacterial biomass. In the high (260–394 mm yr^?1) MAP areas, bacterial biomass was mainly concentrated at the surface and decreased with increasing soil depth (0–40 cm). In contrast, in the low (36–260 mm yr^?1) MAP areas, bacterial biomass was mainly concentrated in the deep soils. The mean annual precipitation was strongly correlated with soil microbial community in space, with microbial communities in the 0–10-cm soil depth most affected by precipitation. Groundwater may impact microbial communities in the 20–40-cm soil depth of this arid and semiarid region. The clustering of the microbial communities was significantly grouped according to the MAP gradient, revealing that MAP is a major driving force of microbial communities in this arid and semi-arid area. The decline in MAP led to a shift in the structure of the microbial community and an overall reduction in microbial biomass.     

Relative roles of niche and neutral processes on turnover of plant,fungal and bacterial communities in arid and semi-arid areas at the regional scale

The mechanisms that determine the spatial structure of macroscopic and microbial communities and how they respond to environmental changes are central themes that have been explored in ecological research. However, little is known about the relative roles and importance of neutral and niche-related factors in the assemblage of bacterial, fungal, and plant communities. Here partial Mantel, null model, and variation partitioning analysis were used to compare mechanisms driving the beta diversity of bacteria, fungi and plant communities at the regional scale in arid and semi-arid areas. Denaturing gradient gel electrophoresis (PCR-DGGE) was used to evaluate the distribution pattern of microbial communities, and vegetation survey were conducted to evaluate the characteristics of plant communities. We found that bacterial, fungal, and plant communities were strongly influenced by niche processes at the regional scale in arid and semi-arid areas. Bacteria had a stronger habitat association, indicating community assembly is strongly affected by niche processes. Fungi, with their body size between plants and bacteria, had moderate environment correlation, and plants had less environment association than fungi or bacteria, which suggests that body size may determine the association between organism and environment. We concluded that the pivotal niche process, environmental filtering, weakened with increasing body size, and it should be considered when we evaluate the relative roles of deterministic and stochastic processes in community assemblage.     

Comparison among bacterial communities present in arenized and adjacent areas subjected to different soil management regimes

Aims

The aims of this work were to characterize the soil bacterial communities in an arenized area in southern Brazil subjected to different management regimes through cultivation-dependent and cultivation-independent methods and to evaluate the potential of selected plant growth-promoting (PGP) bacteria to improve the growth of native Lupinus albescens plants.

Methods

Bulk soil samples from an arenized site and rhizospheric soil and roots of L. albescens grown in this arenized site as well as samples from soils of the same region outside of the arenized area and rhizospheric soil and roots of L. albescens grown in non-arenized sites were evaluated. Phosphate solubilization, indolic compound and siderophore production abilities of the isolates were screened and compared. Some isolates were selected for in vivo plant growth promotion in greenhouse experiment.

Results

The samples from the arenized area presented less microbial biomass and less diverse bacterial communities compared with those from non-arenized areas. The PGP characteristics produced by the bacterial isolates showed differences among arenized and non arenized areas. A growth chamber experiment with L. albescens showed that phosphate-insoluble conditions coupled with bacterial inoculation resulted in the best PGP effect.

Conclusions

Culture-dependent and culture-independent methods showed converging results regarding diversity indices and the rhizospheric environments increased bacterial diversity and biomass when compared to bulk soils. The PGP traits analyzed in this work were affected by environmental conditions.     

Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices

Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.     

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty‐five 1 m² plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.     

Microbial diversity and community structure in Fynbos soil

The Fynbos biome in South Africa is renowned for its high plant diversity and the conservation of this area is particularly important for the region. This is especially true in the case of endangered vegetation types on the lowlands such as Sand Fynbos, of which only small fragments remain. The question is thus whether the diversity of the above‐ground flora is mirrored in the below‐ground microbial communities. In order to determine the relationship of the above‐ and below‐ground communities, the soil community composition of both fungal and bacterial groups in Sand Fynbos was characterized over space and time. A molecular approach was used based on the isolation of total soil genomic DNA and automated ribosomal intergenic spacer analysis of bacterial and fungal communities. Soil from four different sites was compared to resolve the microbial diversity of eubacterial and fungal groups on a local (alpha diversity) scale as well as a landscape scale (beta diversity). The community structures from different sites were compared and found to exhibit strong spatial patterns which remained stable over time. The plant community data were compared with the fungal and the bacterial communities. We concluded that the microbial communities in the Sand Fynbos are highly diverse and closely linked to the above‐ground floral communities.