Termite mound formation reduces the abundance and diversity of soil resistomes

Termites are pivotal ecosystem engineers in tropical and subtropical habitats, where they construct massive nests (‘mounds’) that substantially modify soil properties and promote nutrient cycling. Yet, little is known about the roles of termite nesting activity in regulating the spread of antimicrobial resistance (AMR), one of the major Global Health challenges. Here, we conducted a large-scale (> 1500 km) investigation in northern Australia and found distinct resistome profiles in termite mounds and bulk soils. By profiling a wide spectrum of ARGs, we found that the abundance and diversity of antibiotic resistance genes (ARGs) were significantly lower in termite mounds than in bulk soils (P < 0.001). The proportion of efflux pump ARGs was significantly lower in termite mound resistome than in bulk soil resistome (P < 0.001). The differences in resistome profiles between termite mounds and bulk soils may result from the changes in microbial interactions owing to the substantial increase in pH and nutrient availability induced by termite nesting activities. These findings advance our understanding of the profile of ARGs in termite mounds, which is a crucial step to evaluate the roles of soil faunal activity in regulating soil resistome under global environmental change.     

Termite cohabitation: the relative effect of biotic and abiotic factors on mound biodiversity

1. Termites are important ecosystem engineers that improve primary productivity in trees and animal diversity outside their mounds. However, their ecological relationship with the species nesting inside their mounds is poorly understood. 2. The presence of termite cohabitant colonies inside 145 Cornitermes cumulans mounds of known size and location was recorded. Using network‐theoretical methods in conjunction with a suite of statistical analyses, the relative influence of biotic and abiotic drivers of termite within‐mound diversity on the composition and species richness of the termite community was investigated, specifically builder presence and physical aspects of the mound. 3. We found that richness inside the mound increases with mound size, and the species similarity between mounds decreases with distance. The physical attributes (abiotic drivers) of termite mounds (size and relative distance to other mounds) are the strongest predictors of termite species richness and composition. The biotic driver (presence of a builder colony) has an important, though smaller, negative effect on within‐mound termite species richness. 4. The findings suggest that the termites' physical manipulation of their environment is an important driver of within‐mound community diversity. More generally, the approach taken here, using a combination of statistical and network‐theoretical methods, can be used to determine the relative importance of abiotic and biotic drivers of diversity in a wide range of communities of interacting species.     

Nutrient dynamics and plant assemblages of Macrotermes falciger mounds in a savanna ecosystem

Termites through mound construction and foraging activities contribute significantly to carbon and nutrient fluxes in nutrient-poor savannas. Despite this recognition, studies on the influence of termite mounds on carbon and nitrogen dynamics in sub-tropical savannas are limited. In this regard, we examined soil nutrient concentrations, organic carbon and nitrogen mineralization in incubation experiments in mounds of Macrotermes falciger and surrounding soils of sub-tropical savanna, northeast Zimbabwe. We also addressed whether termite mounds altered the plant community and if effects were similar across functional groups i.e. grasses, forbs or woody plants. Mound soils had significantly higher silt and clay content, pH and concentrations of calcium (Ca), magnesium (Mg), potassium (K), organic carbon (C), ammonium (NH₄⁺) and nitrate (NO₃⁻) than surrounding soils, with marginal differences in phosphorus (P) and sodium (Na) between mounds and matrix soils. Nutrient enrichment increased by a factor ranging from 1.5 for C, 4.9 for Mg up to 10.3 for Ca. Although C mineralization, nitrification and nitrification fraction were similar between mounds and matrix soils, nitrogen mineralization was elevated on mounds relative to surrounding matrix soils. As a result, termite mounds supported unique plant communities rich and abundant in woody species but less diverse in grasses and forbs than the surrounding savanna matrix in response to mound-induced shifts in soil parameters specifically increased clay content, drainage and water availability, nutrient status and base cation (mainly Ca, Mg and Na) concentration. In conclusion, by altering soil properties such as texture, moisture content and nutrient status, termite mounds can alter the structure and composition of sub-tropical savanna plant communities, and these results are consistent with findings in other savanna systems suggesting that increase in soil clay content, nutrient status and associated changes in the plant community assemblage may be a general property of mound building termites.     

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes

Despite the important roles of soil microbes, especially the most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter the stability and functions of the rare microbial biosphere remains unknown. We reciprocally transplanted field soils across a latitudinal gradient to simulate climate change and sampled the soils annually after harvesting the maize over the following 6 years (from 2005 to 2011). By sequencing microbial 16S ribosomal RNA gene amplicons, we found that changing climate regimes significantly altered the composition and dynamics of soil microbial communities. A continuous succession of the rare and abundant communities was observed. Rare microbial communities were more stable under changing climatic regimes, with lower variations in temporal dynamics, and higher stability and constancy of diversity. More nitrogen cycling genes were detected in the rare members than in the abundant members, including amoA, napA, nifH, nirK, nirS, norB and nrfA. Random forest analysis and receiver operating characteristics analysis showed that rare taxa may act as potential contributors to maize yield under changing climatics. The study indicates that the taxonomically and functionally diverse rare biosphere has the potential to increase functional redundancy and enhance the ability of soil communities to counteract environmental disturbances. With ongoing global climate change, exploring the succession process and functional changes of rare taxa may be important in elucidating the ecosystem stability and multifunctionality that are mediated by microbial communities.     

蚂蚁筑巢对西双版纳热带森林土壤微生物生物量碳及熵的影响

蚂蚁筑巢能够改变热带森林土壤理化环境,从而对土壤微生物生物量碳及熵的时空动态产生重要影响.本研究以西双版纳高檐蒲桃热带森林群落为对象,采用氯仿熏蒸法对蚂蚁巢地和非巢地土壤微生物生物量碳及熵时空动态进行测定.结果表明: 1)蚁巢地平均微生物生物量碳及熵(1.95 g·kg^-1,6.8%)显著高于非巢穴(1.76 g·kg^-1,5.1%);蚁巢地和非蚁巢地土壤微生物生物量碳呈单峰型时间变化趋势,而土壤微生物熵呈“V”型变化格局.2)蚁巢地和非巢地土壤微生物生物量碳及熵均具有明显的垂直变化:微生物生物量碳随土层加深显著降低,微生物熵则沿土层加深显著升高,但蚁巢微生物生物量碳及熵的垂直变化较非巢穴显著. 3)蚂蚁筑巢引起了巢内水分和温度的显著改变,进而影响土壤微生物生物量碳及熵的时空动态.土壤水分分别解释微生物生物量碳及熵的66%～83%和54%～69%,而土壤温度分别解释土壤微生物生物量碳及熵的71%～86%和67%～76%. 4)蚂蚁筑巢引起土壤理化性质变化对土壤微生物生物量碳和熵产生重要影响.蚁巢土壤微生物生物量碳与土壤有机碳、温度、全氮、含水率呈极显著正相关,与容重、硝态氮,水解氮呈显著正相关,与土壤pH呈极显著负相关;除土壤微生物熵与pH呈显著正相关外,与其他土壤理化指标均呈显著负相关.土壤总有机碳、全氮和温度对微生物生物量碳的贡献最大,而土壤总有机碳和全氮对微生物熵的负作用最小.因此,蚂蚁筑巢能够显著改变微生境(如土壤水分与温度)及土壤理化性质(如总有机碳及全氮),进而调控热带森林土壤微生物生物量碳及熵的时空动态.     

Temporal variability in soil microbial communities across land-use types

Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.     

Environmental Heterogeneity, Animal Disturbances, Microsite Characteristics, and Seedling Establishment in a Quercus havardii Community

In restoration experiments it is imperative to consider the study of mechanisms of how species are maintained and preserved in a system. This paper reports on the results of a field experiment examining the growth and survival of seedlings of Schizachyrium scoparium, a dominant perennial bunchgrass member of the Quercus havardii (sand shinnery oak) communities of semiarid western Texas, on mounds of displaced soil produced by Sylvilagus auduboni (rabbit). The central question posed is: does environmental heterogeneity created by small mammals influence seedling survival and growth? The specific questions addressed are: (1) Does seedling survival, growth, and nutrient uptake vary when grown on mounds, off-mound soils, and artificially created mounds?; (2) What is the influence of the microbial and litter components of mound soils on seedling survival?; and (3) In communities where animal disturbances create environmental heterogeneity and may impact seedling establishment, is it possible to artificially create mounds that could serve a similar function? Results show that characteristics of mound soils increase seedling survival, shoot and root biomass, root length, number of tillers, mycorrhizal infection, and nutrient uptake more in plants grown on mounds than off mounds. Both the microbial and litter components of mound soils are essential components of this effect. Artificial mounds generated from soils associated with the herbaceous community were more similar to intact rabbit mounds than artificial mounds generated from soils associated with the oaks. The results indicate that rabbits produce rich patches (both nutrient and microbial) favorable to the growth of seedlings of the dominant bunchgrass, and point to the potential importance of rabbit disturbances in shaping the dynamics of this plant community. Thus, rabbit-generated disturbances produce environmental heterogeneity in the sand shinnery oak community, similar to that produced by harvester ants in this community as shown by an earlier study. Small animal activity that results in soil displacement, and influences soil characteristics, may indirectly contribute to the persistence of certain plant species within a community. Thus, disturbances may well operate in semiarid communities to produce nutrient and microbe rich microsites which may function to maintain diversity.     

Differences between bacterial communities in the gut of a soil-feeding termite (Cubitermes niokoloensis) and its mounds

In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.     

Role of termites in the restoration of soils and plant richness on bowé in West Africa

Bowé (hardened ferricrete soils formed by erosion, drought or deforestation) are often associated with termite mounds, but little is known about these mounds and their role in the restoration of soils and plant biodiversity on bowé. This study examined termite mounds on bowé and their effects on soil depth and plant richness. Sixty-four sampling plots were laid out randomly on bowé sites with mounds and on adjacent bowé sites without mounds. The height and circumference of each mound were measured. Species inventories were made and soil depth measured in each plot. Linear mixed effects and generalised mixed effects models with Poisson error distribution were used to assess the variation in soil depth and plant species richness in mound and nonmound microsites. Two types of mounds (small vs. large) associated with different termite species were observed on bowé, with the small mounds being most common. Plots with either large or small mounds had deeper soils and higher plant richness than the adjacent plots without mounds. Conservation of termite mounds is important for restoring soils and plant richness on bowé, and termite mounds should be taken into consideration in biodiversity and soil management strategies for bowé.     

Geophagic termite mounds as one of the resources for African elephants in Ugalla Game Reserve,Western Tanzania

Knowledge of the distribution and nutrient values of key resources supporting the survival of wildlife species is integral for an effective conservation planning and management of the species. In the Miombo ecosystem of the Ugalla Game Reserve, African elephants (Loxodonta africana Blumenbach 1797), eat soil, that is geophagy, from certain termite mounds. We mapped that all the geophagic termite mounds are exclusively situated in the flood plain. To understand why soils from some termite mounds are eaten, we collected and analysed soil samples from 10 geophagic termite mounds, seven nongeophagic termite mounds and 13 samples from the surrounding flood plain. Percentage of clay content did not differ significantly among the soil samples. Soils from geophagic termite mounds were richer in mineral elements compared with other soil samples. The results demonstrate that the driver for geophagic behaviour is related to rich mineral element contents found in geophagic termite mounds made of the mineral‐enriching termites (Macrotermes). Thus, geophagic termite mounds play a role in elephant's dietary needs and possibly influence their movement patterns in Ugalla, as the elephants cannot obtain enough minerals from their feeds. Geophagic termite mounds should be protected from potential destructive land uses, such as airstrip construction.     

Historical forest disturbance mediates soil microbial community responses to drought

Despite the abundance of studies demonstrating the effects of drought on soil microbial communities, the role of land use legacies in mediating these drought effects is unclear. To assess historical land use influences on microbial drought responses, we conducted a drought-rewetting experiment in soils from two adjacent and currently forested watersheds with distinct land use histories: an undisturbed ‘reference’ site and a ‘disturbed’ site that was clear-cut and converted to agriculture ~60 years prior. We incubated intact soil cores at either constant moisture or under a drought-rewet treatment and characterized bacterial and fungal communities using amplicon sequencing throughout the experiment. Bacterial alpha diversity decreased following drought-rewetting while fungal diversity increased. Bacterial beta diversity also changed markedly following drought-rewetting, especially in historically disturbed soils, while fungal beta diversity exhibited little response. Additionally, bacterial beta diversity in disturbed soils recovered less from drought-rewetting compared with reference soils. Disturbed soil communities also exhibited notable reductions in nitrifying taxa, increases in putative r-selected bacteria, and reductions in network connectivity following drought-rewetting. Overall, our study reveals historical land use to be important in mediating responses of soil bacterial communities to drought, which will influence the ecosystem-scale trajectories of these environments under ongoing and future climate change.     

Effects of continuous cucumber cropping and alternative rotations under protected cultivation on soil microbial community diversity

The diversity of soil microbial communities as affected by continuous cucumber cropping and alternative rotations under protected cultivation were evaluated using community level physiological profiles (CLPP) and random amplified polymorphic DNA (RAPD) analysis. The soils were selected from six cucumber cropping systems, which cover two cropping practices (rotation and continuous cropping) and a wide spectrum for cucumber cropping history under protected cultivation. Shannon–Weaver index and multivariate analysis were performed to characterize variations in soil microbial communities. Both CLPP and RAPD techniques demonstrated that cropping systems and plastic-greenhouse cultivation could considerably affect soil microbial functional diversity and DNA sequence diversity. The open-field soil had the highest Shannon–Weaver index (3.27 for CLPP and 1.50 for RAPD), whereas the lowest value occurred in the 7-year continuous protected cultivation soil (3.27 for CLPP and 1.50 for RAPD). The results demonstrated that continuous plastic-greenhouse cultivation and management can cause the reduction in the species diversity of the biota. Higher Shannon–Weaver index and coefficients of DNA sequence similarity were found in soils under rotation than those under continuous cropping. Cluster analysis also indicated that microbial community profiles of continuous cultivation soils were different from profiles of rotation soils. The reduction in diversity of microbial communities found in continuous cultivation soils as compared with rotation soils might be due to the differences in the quantity, quality and distribution of soil organic matter. Section Editor: D. E. Crowley     

Differences between Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and Its Mounds

In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.     

Litter-forager termite mounds enhance the ectomycorrhizal symbiosis between Acacia holosericea A. Cunn. Ex G. Don and Scleroderma dictyosporum isolates

The hypothesis of the present study was that the termite mounds of Macrotermes subhyalinus (MS) (a litter-forager termite) were inhabited by a specific microflora that could enhance with the ectomycorrhizal fungal development. We tested the effect of this feeding group mound material on (i) the ectomycorrhization symbiosis between Acacia holosericea (an Australian Acacia introduced in the sahelian areas) and two ectomycorrhizal fungal isolates of Scleroderma dictyosporum (IR408 and IR412) in greenhouse conditions, (ii) the functional diversity of soil microflora and (iii) the diversity of fluorescent pseudomonads. The results showed that the termite mound amendment significantly increased the ectomycorrhizal expansion. MS mound amendment and ectomycorrhizal inoculation induced strong modifications of the soil functional microbial diversity by promoting the multiplication of carboxylic acid catabolizing microorganisms. The phylogenetic analysis showed that fluorescent pseudomonads mostly belong to the Pseudomonads monteillii species. One of these, P. monteillii isolate KR9, increased the ectomycorrhizal development between S. dictyosporum IR412 and A. holosericea. The occurrence of MS termite mounds could be involved in the expansion of ectomycorrhizal symbiosis and could be implicated in nutrient flow and local diversity.     

农牧交错带草地土壤剖面微生物总量、多样性和互作网络的垂直分布特征

【背景】草地土壤微生物是维持草地生态系统功能和稳定的关键要素之一,探寻微生物在土壤剖面的垂直分布特征和构建规律对于理解其在草地生态系统的作用至关重要。【目的】在80cm深的土壤剖面内,全面分析微生物的总量、多样性和物种间的相互作用网络表现出的垂直分布特征。【方法】基于内蒙古农牧交错带上典型草原土壤中原核微生物的定量和高通量测序数据,比较微生物的总量和多样性,使用分子生态网络方法(molecular ecological network approach,MENA)探究微生物相互作用网络的垂直变化。【结果】原核生物的总量和多样性随深度增加而逐渐降低,且群落结构变异沿土壤剖面逐渐增大。网络结构在表层最为复杂,微生物物种间联系紧密;随着深度的增加,微生物间紧密的关联会逐渐变稀疏,网络结构变得简单。此外,酸杆菌是当地土壤生态系统中的优势种群以及网络核心微生物物种,可能对土壤生态服务功能的稳定发挥具有重要的作用。【结论】原核微生物的总量、多样性和物种间的互作网络都表现出高度一致的垂直变化规律,即总量、多样性与深度成负相关,且其群落结构变异会逐渐扩大,同时微生物网络相关性会减弱。这些结果为我们提供了微生物动态变化的重要见解,对典型农牧交错带草地的生态保护具有一定的参考价值。     

生物炭对温室黄瓜不同连作年限土壤养分和微生物群落多样性的影响

以温室黄瓜连作6年和10年土壤添加质量比为5%生物炭为处理,以不添加生物炭为对照,采用桶栽的方法,研究了生物炭对不同年限连作土壤养分和微生物群落多样性的影响.结果表明: 与连作土壤相比,生物炭处理的连作6年土壤的黄瓜单株产量提高11.4%,连作10年土壤产量提高62.8%.施入生物炭显著降低了2种连作土壤容重,显著提高了有机质、速效磷含量、阳离子交换量(CEC)和pH;显著提高了土壤细菌数量和细菌/真菌,降低了真菌和尖孢镰刀菌数量,使土壤类型由真菌型向细菌型转变,尤其对连作10年土壤作用最为明显,土壤细菌和细菌/真菌分别是未处理的2.00和3.64倍,真菌和尖孢镰刀菌数量分别是未处理的54.8%和55.9%.土壤微生物群落碳源利用分析表明,10年连作土壤施入生物炭可显著提高土壤微生物活性、Shannon指数和均匀度指数,分别是未处理的1.50、2.14和1.31倍,同时显著提高了土壤微生物对糖类、氨基酸类、酚酸类和胺类碳源的利用强度,分别是未处理的1.62、1.81、1.74和1.93倍.相关性分析表明,土壤容重、速效磷含量、CEC和pH 4个指标对微生物群落变化的影响较显著.综上,生物炭通过对连作土壤理化性质及土壤微生物生态系统的改善,优化了黄瓜根区环境,促进了黄瓜产量的提高,缓解了温室黄瓜连作障碍.     

Dispersal alters soil microbial community response to drought

Microbial communities will experience novel climates in the future. Dispersal is now recognized as a driver of microbial diversity and function, but our understanding of how dispersal influences responses to novel climates is limited. We experimentally tested how the exclusion of aerially dispersed fungi and bacteria altered the compositional and functional response of soil microbial communities to drought. We manipulated dispersal and drought by collecting aerially deposited microbes after precipitation events and subjecting soil mesocosms to either filter-sterilized rain (no dispersal) or unfiltered rain (dispersal) and to either drought (25% ambient) or ambient rainfall for 6 months. We characterized community composition by sequencing 16S and ITS rRNA regions and function using community-level physiological profiles. Treatments without dispersal had lower soil microbial biomass and metabolic diversity but higher bacterial and fungal species richness. Dispersal also altered soil community response to drought; drought had a stronger effect on bacterial (but not fungal) community composition, and induced greater functional loss, when dispersal was present. Surprisingly, neither immigrants nor drought-tolerant taxa had higher abundance in dispersal treatments. We show experimentally that natural aerial dispersal rate alters soil microbial responses to disturbance. Changes in dispersal rates should be considered when predicting microbial responses to climate change.     

The effect of the soil-feeding termite Cubitermes niokoloensis on soil microbial activity in a semi-arid savanna in West Africa

Plant and Soil - Soil-feeding termite mounds are an important, highly specific soil microbial compartment in semi-arid savannas. The aim of this study was to determine the role of these mounds in...     

The bacterial biogeography of British soils

Despite recognition of the importance of soil bacteria to terrestrial ecosystem functioning there is little consensus on the factors regulating belowground biodiversity. Here we present a multi-scale spatial assessment of soil bacterial community profiles across Great Britain (> 1000 soil cores), and show the first landscape scale map of bacterial distributions across a nation. Bacterial diversity and community dissimilarities, assessed using terminal restriction fragment length polymorphism, were most strongly related to soil pH providing a large-scale confirmation of the role of pH in structuring bacterial taxa. However, while α diversity was positively related to pH, the converse was true for β diversity (between sample variance in α diversity). β diversity was found to be greatest in acidic soils, corresponding with greater environmental heterogeneity. Analyses of clone libraries revealed the pH effects were predominantly manifest at the level of broad bacterial taxonomic groups, with acidic soils being dominated by few taxa (notably the group 1 Acidobacteria and Alphaproteobacteria). We also noted significant correlations between bacterial communities and most other measured environmental variables (soil chemistry, aboveground features and climatic variables), together with significant spatial correlations at close distances. In particular, bacterial and plant communities were closely related signifying no strong evidence that soil bacteria are driven by different ecological processes to those governing higher organisms. We conclude that broad scale surveys are useful in identifying distinct soil biomes comprising reproducible communities of dominant taxa. Together these results provide a baseline ecological framework with which to pursue future research on both soil microbial function, and more explicit biome based assessments of the local ecological drivers of bacterial biodiversity.     

Rhizosphere shapes the associations between protistan predators and bacteria within microbiomes through the deterministic selection on bacterial communities

The assembly of bacterial communities in the rhizosphere is well-documented and plays a crucial role in supporting plant performance. However, we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rhizosphere selection. To address this, we examined bacterial and protistan taxa from 443 agricultural soil samples including bulk and rhizosphere soils. Our results presented distinct patterns of bacteria and protistan predators in rhizosphere microbiome assembly. Community assembly of protistan predators was determined by a stochastic process in the rhizosphere and the diversity of protistan predators was reduced in the rhizosphere compared to bulk soils, these may be attributed to the indirect impacts from the altered bacterial communities that showed deterministic process assembly in the rhizosphere. Interestingly, we observed that the plant rhizosphere facilitates more close interrelationships between protistan predators and bacterial communities, which might promote a healthy rhizosphere microbial community for plant growth. Overall, our findings indicate that the potential predator–prey relationships within the microbiome, mediated by plant rhizosphere, might contribute to plant performance in agricultural ecosystems.