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.     

Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape

Background

The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.

Methodology/Principal Findings

Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.

Conclusions/Significance

Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.     

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms

Soils harbor large, diverse microbial communities critical for local and global ecosystem functioning that are controlled by multiple and poorly understood processes. In particular, while there is observational evidence of relationships between both biotic and abiotic conditions and microbial composition and diversity, there have been few experimental tests to determine the relative importance of these two sets of factors at local scales. Here, we report the results of a fully factorial experiment manipulating soil conditions and plant cover on old‐field mesocosms across a latitudinal gradient. The largest contributor to beta diversity was site‐to‐site variation, but, having corrected for that, we observed significant effects of both plant and soil treatments on microbial composition. Separate phyla were associated with each treatment type, and no interactions between soil and plant treatment were observed. Individual soil characteristics and biotic parameters were also associated with overall beta‐diversity patterns and phyla abundance. In contrast, soil microbial diversity was only associated with site and not experimental treatment. Overall, plant community treatment explained more variation than soil treatment, a result not previously appreciated because it is difficult to dissociate plant community composition and soil conditions in observational studies across gradients. This work highlights the need for more nuanced, multifactorial experiments in microbial ecology and in particular indicates a greater focus on relationships between plant composition and microbial composition during community assembly.     

贺兰山不同海拔典型植被带土壤微生物多样性

土壤微生物多样性在海拔梯度的分布格局研究近年来受到和植物动物一样的重视程度,但是干旱风沙区微生物多样性在海拔梯度上的多样性分布规律尚未揭示。本研究以处于干旱风沙区的贺兰山不同海拔的六个典型植被带（荒漠草原带、山地旱生灌丛带、温性针叶林带、针阔混交林带、寒温性针叶林带和亚高山草甸带）土壤为研究对象,利用Biolog微平板法和磷脂脂肪酸甲酯法(FAMEs)系统研究微生物多样性群落特征以及在不同植被带分布规律。结果表明：土壤微生物功能多样性随海拔增加发生变化,且微生物群落结构存在显著差异。Biolog分析显示土壤微生物群落代谢活性依次是：亚高山草甸>寒温性针叶林>针阔混交林>温性针叶林>山地旱生灌丛>荒漠草原,随海拔的升高土壤微生物群落物种丰富度指数（H）和均匀度指数（E）总体上均表现出增大的趋势,差异显著（P＜0.05）;FAMEs分析表明不同海拔的微生物区系发生了一定程度的变化,寒温性针叶林土壤微生物磷酸脂肪酸生物标记的数量和种类均最高,且细菌、真菌特征脂肪酸相对含量也最高;土壤微生物群落结构多样性次序是：寒温性针叶林带>针阔混交林带>温性针叶林带>亚高山草甸>山地旱生灌丛>荒漠草原。本研究结果表明贺兰山海拔梯度的微生物多样性分布规律不同于已有的植物多样性“中部膨胀”研究结果,这说明在高海拔地区有更多的适合该生境的微生物存在,这对维持干旱风沙区的生态系统功能稳定性具有重要意义。     

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere. This revised version was published online in August 2006 with corrections to the Cover Date.     

Relating belowground microbial composition to the taxonomic,phylogenetic, and functional trait distributions of trees in a tropical forest

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot‐level variability in belowground microbial communities.     

Land use is a determinant of plant pathogen alpha‐ but not beta‐diversity

Little is known about the diversity patterns of plant pathogens and how they change with land use at a broad scale. We employed DNA metabarcoding to describe the diversity and composition of putative plant pathogen communities in three substrates (soil, roots, and leaves) across five major land uses at a national scale. Almost all plant pathogen communities (fungi, oomycetes, and bacteria) showed strong responses to land use and substrate type. Land use category could explain up to 24% of the variance in composition between communities. Alpha‐diversity (richness) of plant pathogens was consistently lower in natural forests than in agricultural systems. In planted forests, there was also generally low pathogen alpha‐diversity in soil and roots, but alpha‐diversity in leaves was high compared with most other land uses. In contrast to alpha‐diversity, differences in within‐land use beta‐diversity of plant pathogens (the predictability of plant pathogen communities within land use) were subtle. Our results show that large‐scale patterns and distributions of putative plant pathogens can be determined using metabarcoding, allowing some of the first landscape level insights into these critically important communities.     

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes

The severe environmental stresses of the Arctic may have promoted unique soil bacterial communities compared with those found in lower latitude environments. Here, we present a comprehensive analysis of the biogeography of soil bacterial communities in the Arctic using a high resolution bar‐coded pyrosequencing technique. We also compared arctic soils with soils from a wide range of more temperate biomes to characterize variability in soil bacterial communities across the globe. We show that arctic soil bacterial community composition and diversity are structured according to local variation in soil pH rather than geographical proximity to neighboring sites, suggesting that local environmental heterogeneity is far more important than dispersal limitation in determining community‐level differences. Furthermore, bacterial community composition had similar levels of variability, richness and phylogenetic diversity within arctic soils as across soils from a wide range of lower latitudes, strongly suggesting a common diversity structure within soil bacterial communities around the globe. These results contrast with the well‐established latitudinal gradients in animal and plant diversity, suggesting that the controls on bacterial community distributions are fundamentally different from those observed for macro‐organisms and that our biome definitions are not useful for predicting variability in soil bacterial communities across the globe.     

Contrasting patterns and drivers of soil bacterial and fungal diversity across a mountain gradient

Microbial elevational diversity patterns have been extensively studied, but their shaping mechanisms remain to be explored. Here, we examined soil bacterial and fungal diversity and community compositions across a 3.4 km elevational gradient (consists of five elevations) on Mt. Kilimanjaro located in East Africa. Bacteria and fungi had different diversity patterns across this extensive mountain gradient—bacterial diversity had a U shaped pattern while fungal diversity monotonically decreased. Random forest analysis revealed that pH (12.61% importance) was the most important factor affecting bacterial diversity, whereas mean annual temperature (9.84% importance) had the largest impact on fungal diversity, which was consistent with results obtained from mixed-effects model. Meanwhile, the diversity patterns and drivers of those diversity patterns differ among taxonomic groups (phyla/classes) within bacterial or fungal communities. Taken together, our study demonstrated that bacterial and fungal diversity and community composition responded differently to climate and edaphic properties along an extensive mountain gradient, and suggests that the elevational diversity patterns across microbial groups are determined by distinct environmental variables. These findings enhanced our understanding of the formation and maintenance of microbial diversity along elevation, as well as microbial responses to climate change in montane ecosystems.     

上海大金山岛植被功能组成对草本植物、土壤动物和细菌多样性的影响

揭示植物群落对土壤动物和微生物多样性的上行调控效应有助于理解不同营养级生物多样性的维持机制。以往的研究主要集中在植物物种多样性对土壤动物和微生物多样性的影响,而关于植被功能组成自下而上的影响研究较少。以上海大金山岛13个植物群落为对象,在分析落叶木本植物占比与树木和草本物种多样性,以及土壤动物和细菌多样性的关系基础上,利用结构方程模型区分了落叶木本植物占比对土壤动物和细菌多样性的直接与间接影响效应。结果显示：落叶木本植物占比不仅分别对草本物种多样性和土壤动物多样性分别产生直接正效应和负效应（P<0.01;P<0.05）,也会通过草本物种的级联效应间接的降低地下土壤细菌多样性（P<0.10）。然而,木本植物多样性仅与草本物种多样性显著正关联（P<0.10）,与土壤动物和细菌多样性无显著关联（P>0.10）。该研究结果表明,相较于木本植物多样性,落叶植物占比在中亚热带北缘森林生态系统不同营养级生物多样性维持格局中扮演着更为重要的角色。     

Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development

The origins of the biological complexity and the factors that regulate the development of community composition, diversity and richness in soil remain largely unknown. To gain a better understanding of how bacterial communities change during soil ecosystem development, their composition and diversity in soils that developed over c. 77 000 years of intermittent aeolian deposition were studied. 16S rRNA gene clone libraries and fatty acid methyl ester (FAME) analyses were used to assess the diversity and composition of the communities. The bacterial community composition changed with soil age, and the overall diversity, richness and evenness of the communities increased as the soil habitat matured. When analysed using a multivariate Bray-Curtis ordination technique, the distribution of ribotypes showed an orderly pattern of bacterial community development that was clearly associated with soil and ecosystem development. Similarly, changes in the composition of the FAMEs across the chronosequence were associated with biomarkers for fungi, actinomycetes and Gram-positive bacteria. The development of the soil ecosystem promoted the development of distinctive microbial communities that were reminiscent of successional processes often evoked to describe change during the development of plant communities in terrestrial ecosystems.     

Nitrogen limitation and microbial diversity at the treeline

Tree growth limitation at treeline has mainly been studied in terms of carbon limitation while effects and mechanisms of potential nitrogen (N) limitation are barely known, especially in the southern hemisphere. We investigated how soil abiotic properties and microbial community structure and composition change from lower to upper sites within three vegetation belts (Nothofagus betuloides and N. pumilio forests, and alpine vegetation) across an elevation gradient (from 0 to 650 m a.s.l.) in Cordillera Darwin, southern Patagonia. Increasing elevation was associated with a decrease in soil N‐NH₄⁺ availability within the N. pumilio and the alpine vegetation belt. Within the alpine vegetation belt, a concurrent increase in the soil C:N ratio was associated with a shift from bacterial‐dominated in lower alpine sites to fungal‐dominated microbial communities in upper alpine sites. Lower forested belts (N. betuloides, N. pumilio) exhibited more complex patterns both in terms of soil properties and microbial communities. Overall, our results concur with recent findings from high‐latitude and altitude ecosystems showing decreased nutrient availability with elevation, leading to fungal‐dominated microbial communities. We suggest that growth limitation at treeline may result, in addition to proximal climatic parameters, from a competition between trees and soil microbial communities for limited soil inorganic N. At higher elevation, soil microbial communities could have comparably greater capacities to uptake soil N than trees, and the shift towards a fungal‐dominated community would favour N immobilization over N mineralization. Though evidences of altered nutrient dynamics in tree and alpine plant tissue with increasing altitude remain needed, we contend that the measured residual low amount of inorganic N available for trees in the soil could participate to the establishment limitation. Finally, our results suggest that responses of soil microbial communities to elevation could be influenced by functional properties of forest communities for instance through variations in litter quality.     

Global biogeography of highly diverse protistan communities in soil

Protists are ubiquitous members of soil microbial communities, but the structure of these communities, and the factors that influence their diversity, are poorly understood. We used barcoded pyrosequencing to survey comprehensively the diversity of soil protists from 40 sites across a broad geographic range that represent a variety of biome types, from tropical forests to deserts. In addition to taxa known to be dominant in soil, including Cercozoa and Ciliophora, we found high relative abundances of groups such as Apicomplexa and Dinophyceae that have not previously been recognized as being important components of soil microbial communities. Soil protistan communities were highly diverse, approaching the extreme diversity of their bacterial counterparts across the same sites. Like bacterial taxa, protistan taxa were not globally distributed, and the composition of these communities diverged considerably across large geographic distances. However, soil protistan and bacterial communities exhibit very different global-scale biogeographical patterns, with protistan communities strongly structured by climatic conditions that regulate annual soil moisture availability.     

Soil fertility shifts the relative importance of saprotrophic and mycorrhizal fungi for maintaining ecosystem stability

Soil microbial communities are essential for regulating the dynamics of plant productivity. However, how soil microbes mediate temporal stability of plant productivity at large scales across various soil fertility conditions remains unclear. Here, we combined a regional survey of 51 sites in the temperate grasslands of northern China with a global grassland survey of 120 sites to assess the potential roles of soil microbial diversity in regulating ecosystem stability. The temporal stability of plant productivity was quantified as the ratio of the mean normalized difference vegetation index to its standard deviation. Soil fungal diversity, but not bacterial diversity, was positively associated with ecosystem stability, and particular fungal functional groups determined ecosystem stability under contrasting conditions of soil fertility. The richness of soil fungal saprobes was positively correlated with ecosystem stability under high-fertility conditions, while a positive relationship was observed with the richness of mycorrhizal fungi under low-fertility conditions. These relationships were maintained after accounting for plant diversity and environmental factors. Our findings highlight the essential role of fungal diversity in maintaining stable grassland productivity, and suggest that future studies incorporating fungal functional groups into biodiversity–stability relationships will advance our understanding of their linkages under different fertility conditions.     

Contrasting elevational diversity patterns for soil bacteria between two ecosystems divided by the treeline

Above- and below-ground organisms are closely linked, but how elevational distribution pattern of soil microbes shifting across the treeline still remains unknown. Sampling of 140 plots with transect, we herein investigated soil bacterial distribution pattern from a temperate forest up to a subalpine meadow along an elevational gradient using Illumina sequencing. Our results revealed distinct elevational patterns of bacterial diversity above and below the treeline in responding to changes in soil conditions: a hollow elevational pattern in the forest (correlated with soil temperature, pH, and C:N ratio) and a significantly decreasing pattern in the meadow (correlated with soil pH, and available phosphorus). The bacterial community structure was also distinct between the forest and meadow, relating to soil pH in the forest and soil temperature in the meadow. Soil bacteria did not follow the distribution pattern of herb diversity, but bacterial community structure could be predicted by herb community composition. These results suggest that plant communities have an important influence on soil characteristics, and thus change the elevational distribution of soil bacteria. Our findings are useful for future assessments of climate change impacts on microbial community.     

Forest gene diversity is correlated with the composition and function of soil microbial communities

The growing field of community and ecosystem genetics indicates that plant genotype and genotypic variation are important for structuring communities and ecosystem processes. Little is known, however, regarding the effects of stand gene diversity on soil communities and processes under field conditions. Utilizing natural genetic variation occurring in Populus spp. hybrid zones, we tested the hypothesis that stand gene diversity structures soil microbial communities and influences soil nutrient pools. We found significant unimodal patterns relating gene diversity to soil microbial community composition, microbial exoenzyme activity of a carbon-acquiring enzyme, and availability of soil nitrogen. Multivariate analyses indicate that this pattern is due to the correlation between gene diversity, plant secondary chemistry, and the composition of the microbial community that impacts the availability of soil nitrogen. Together, these data from a natural system indicate that stand gene diversity may affect soil microbial communities and soil processes in ways similar to species diversity (i.e., unimodal patterns). Our results further demonstrate that the effects of plant genetic diversity on other organisms may be mediated by plant functional trait variation.     

Resource availability controls fungal diversity across a plant diversity gradient

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales.     

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.     

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high‐throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon–Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer.     

A Molecular Comparison of Plumage and Soil Bacteria Across Biogeographic,Ecological, and Taxonomic Scales

We used molecular methods to determine the microbial community of soil and avian plumage across biogeographic, ecological, and taxonomic scales. A total of 17 soil and 116 feather samples were collected from five avian species across multiple habitat types within one Neotropical and one temperate locality. Hypotheses regarding patterns of microbial composition relative to acquisition and dispersal of plumage bacteria in the ecosystem were tested by comparing microbial communities within and between soil and plumage. Samples from the plumage of American Redstarts (Setophaga ruticilla) were collected across both habitat types and geographic scales for intraspecific comparisons. The microbial diversity in avian plumage was moderately diverse and was dominated by Pseudomonas species. Despite a highly significant individual bird effect on microbial composition of the plumage, we detected significant biogeographic and type of habitat effects. Pseudomonas species were more abundant on the temperate site when all avian species were included in the analysis, and Bacillus subtilis and Xanthomonas groups were more abundant on the Neotropical site for redstarts alone. However, 16S rDNA sequence libraries were not significantly different between Jamaican and Maryland redstarts. Biogeographic and habitat effects were significant and more pronounced for soil samples indicating lower dispersal of soil microbiota. We detected a significant difference between soil and plumage microbial communities suggesting that soil plays a small role in plumage bacterial acquisition. Our results suggest bacterial communities on the plumage of birds are dynamic and may change at different stages in a bird’s annual cycle.