Analysis of Soil Whole- and Inner-Microaggregate Bacterial Communities

Although soil structure largely determines energy flows and the distribution and composition of soil microhabitats, little is known about how microbial community composition is influenced by soil structural characteristics and organic matter compartmentalization dynamics. A UV irradiation-based procedure was developed to specifically isolate inner-microaggregate microbial communities, thus providing the means to analyze these communities in relation to their environment. Whole- and inner-microaggregate fractions of undisturbed soil and soils reclaimed after disturbance by surface coal mining were analyzed using 16S rDNA terminal restriction fragment polymorphism (T-RFLP) and sequence analyses to determine salient bacterial community structural characteristics. We hypothesized that inner-microaggregate environments select for definable microbial communities and that, due to their sequestered environment, inner-microaggregate communities would not be significantly impacted by disturbance. However, T-RFLP analysis indicated distinct differences between bacterial populations of inner-microaggregates of undisturbed and reclaimed soils. While both undisturbed and reclaimed inner-microaggregate bacterial communities were found dominated by Actinobacteria, undisturbed soils contained only Actinobacteridae, while in inner-microaggregates of reclaimed soils Rubrobacteridae predominate. Spatial stratification of division-level lineages within microaggregates was also evidenced, with Proteobacteria clones being prevalent in libraries derived from whole microaggregates. The fractionation methods employed in this study therefore represent a valuable tool for defining relationships between biodiversity and soil structure.     

Effect of Bacillus mesonae H20-5 Treatment on Rhizospheric Bacterial Community of Tomato Plants under Salinity Stress

Plant growth-promoting bacteria improve plant growth under abiotic stress conditions. However, their effects on microbial succession in the rhizosphere are poorly understood. In this study, the inoculants of Bacillus mesonae strain H20-5 were administered to tomato plants grown in soils with different salinity levels (EC of 2, 4, and 6 dS/m). The bacterial communities in the bulk and rhizosphere soils were examined 14 days after H20-5 treatment using Illumina MiSeq sequencing of the bacterial 16S rRNA gene. Although the abundance of H20-5 rapidly decreased in the bulk and rhizosphere soils, a shift in the bacterial community was observed following H20-5 treatment. The variation in bacterial communities due to H20-5 treatment was higher in the rhizosphere than in the bulk soils. Additionally, the bacterial species richness and diversity were greater in the H20-5 treated rhizosphere than in the control. The composition and structure of the bacterial communities varied with soil salinity levels, and those in the H20-5 treated rhizosphere soil were clustered. The members of Actinobacteria genera, including Kineosporia, Virgisporangium, Actinoplanes, Gaiella, Blastococcus, and Solirubrobacter, were enriched in the H20-5 treated rhizosphere soils. The microbial co-occurrence network of the bacterial community in the H20-5 treated rhizosphere soils had more modules and keystone taxa compared to the control. These findings revealed that the strain H20-5 induced systemic tolerance in tomato plants and influenced the diversity, composition, structure, and network of bacterial communities. The bacterial community in the H20-5 treated rhizosphere soils also appeared to be relatively stable to soil salinity changes.     

Vertical profiles of microbial communities in perfluoroalkyl substance-contaminated soils

Poly- and perfluoroalkyl compounds (PFASs) are ubiquitous in the environment, but their influences on microbial community remain poorly known. The present study investigated the depth-related changes of archaeal and bacterial communities in PFAS-contaminated soils. The abundance and structure of microbial community were characterized using quantitative PCR and high-throughput sequencing, respectively. Microbial abundance changed considerably with soil depth. The richness and diversity of both bacterial and archaeal communities increased with soil depth. At each depth, bacterial community was more abundant and had higher richness and diversity than archaeal community. The structure of either bacterial or archaeal community displayed distinct vertical variations. Moreover, a higher content of perfluorooctane sulfonate (PFOS) could have a negative impact on bacterial richness and diversity. The rise of soil organic carbon content could increase bacterial abundance but lower the richness and diversity of both bacterial and archaeal communities. In addition, Proteobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Acidobacteria were the major bacterial groups, while Thaumarchaeota, Euryarchaeota, and unclassified Archaea dominated in soil archaeal communities. PFASs could influence soil microbial community.     

Soil fungal community variation by large-scale reclamation in Sanjiang plain,China

Large-scale marshland reclamation can cause substantial changes to the soil fungal community by disturbances associated with the growth of crop plants and by the addition of fertilizers and pesticides. In this study, high-throughput sequencing of the fungal-specific internal transcribed spacer (ITS) gene region was used to identify fungal taxa. We analyzed the variation in soil fungi diversity and community composition in marshland, paddy, and farmland corn soils, and investigated the relationship between soil fungal community composition and soil physicochemical characteristics to quantify the effect of large-scale reclamation on marshland soil environment in the Sanjiang Plain, northeast China. Marshland soil contained most of the 1997 operational taxonomic units (OTUs) found across all sites (1241), while paddy soil had only 614 OTUs and farmland corn soil 817 OTUs. All reclaimed lands presented a decline in richness and diversity of soil fungi at the OTU level, and soil fungal richness was significantly different between marshland and reclaimed sites (P < 0.05), although it did not differ significantly between marshland and farmland corn sites. Additionally, soil fungal community composition showed different trends and structure after the reclamation. One-way analysis of variance showed Basidiomycota, Zygomycota, Glomeromycota, and Chytridiomycota composition differed significantly between marshland and reclaimed sites (P < 0.05). Nine dominant genera (relative abundance >1.5% in at least one site) and many unclassified genera showed significant variation between marshland and reclaimed sites, including Blumeria, Tomentella, Peziza, Hypholoma, Zopfiella, Mrakia, and Fusarium. Soil fungal community composition and diversity were affected by soil moisture, pH, total carbon (C), available nitrogen (N), soil organic carbon, soil dissolved organic carbon, and C/N (the ratio of total carbon to total nitrogen). The present results contribute to understanding the fungal community in marshland ecosystems, and the role of environmental variability as a predictor of fungal community composition.     

鄱阳湖湿地不同土地利用方式下土壤微生物群落功能多样性

于2011年5月分别采集鄱阳湖围垦92、48a和38a的水稻田,退田还湖25a的退耕地以及自然湿地共5个样地的表层土壤,利用Biolog-ECO板技术对土壤微生物群落的单一碳源利用情况进行了测定,并结合群落指数和主成分分析(PCA)对培养72 h土壤微生物群落功能多样性变化进行了分析。结果表明:退耕地和自然湿地土壤微生物群落利用31种碳源的能力较强,来自不同围垦年限的土壤微生物群落利用碳源能力均较弱;且随围垦时间的增长,土壤微生物对碳源的利用能力呈降低的趋势。自然湿地、退耕地与围垦92、38a样地土壤之间存在显著的微生物功能多样性差异;围垦对土壤微生物代谢糖类、羧酸类、氨基酸类物质的影响最为明显。结果提示,围垦改变了湿地土壤微生物群落结构,退田还湖有助于湿地土壤微生物群落结构的恢复。     

The effects of different vegetation restoration patterns on soil bacterial diversity for sandy land in Hulunbeier

Grassland desertification seriously threatens sustainable economic and social development. Much attention has been paid to the control of grassland desertification, and even to the restoration and reconstruction of the grassland. Vegetation restoration is considered to be a very effective solution. Soil sustains an immense diversity of microbes, and the characteristics of soil microbial communities are sensitive indicators of soil. It is important to understand the relationship between vegetation and soil microbial diversity during the restoration process. Soil microbial, which is the main index to evaluate soil quality, plays a significant role in ecosystem and soil microbial diversity is the important one of global diversity. Exploring the effects of different vegetation patterns on soil microbial diversity can provide scientific bases and technical support for systemic and impersonal assessment of the best vegetation restoration patterns, as well as the vegetation restoration and reconstruction of Hulunbeier sandy land. Based on PCR–DGGE technology, a case study was carried out to investigate the effects of five different vegetation restoration patterns on soil microbial functional diversity after 4 years in sandy land in Hulunbeier, China. The five vegetation restoration patterns included mono-cultivar planting of Agropyron cristatum (UA), mono-cultivar planting of Hedysarum fruticosum (UH), mono-cultivar planting of Caragana korshinskii (UC), mixed-cultivar planting of Agropyron cristatum and Hedysarum fruticosum (AC) and mixed-cultivar planting of Agropyron cristatum, Hedysarum fruticosum, Caragana korshinskii and Elymus nutans (ACHE). Completely degraded sandy land was used as control.The results indicated that the vegetation restoration increased the genetic diversity of soil bacterial community obviously, and the structure of soil bacterial community was changed. The results of phylogenetic analysis suggested that the bacterial community in Hulunbeier sandy land mainly attributed to Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria. The dominant groups were Proteobacteria and Bacteroidetes. The effects of different vegetation type on soil bacterial community structures were different.     

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...     

Long-term effect of re-vegetation on the microbial community of a severely eroded soil in sub-tropical China

The long-term (18 years) effects of re-vegetating eroded soil on soil microbial biomass, community structure and diversity were investigated in a forest soil derived from Quaternary clay in the Red Soil Ecological Experimental Station of the Chinese Academy of Sciences. Large areas of land in this region of China have been subjected to severe soil erosion, characterised by the removal of the fertile surface soil and even the exposure of parental rock in some areas due to a combination of deforestation and heavy rainfall. The effects of planting eroded or uneroded soil with Pinus massoniana, Cinnamomum camphora or Lespedeza bicolor on the soil microbial community and chemical properties were assessed. Total soil microbial community DNA was extracted and bacterial 16 S rRNA gene fragments were amplified by PCR and analysed by terminal restriction fragment length polymorphism (T-RFLP). Microbial biomass carbon (C_mic) was measured by chloroform fumigation-extraction. Following the restoration there were significant increases in both C_mic and bacterial diversity (Shannon index), and significant changes in bacterial community structure. Erosion factors were significant only in minor dimensions suggesting that the restoration had been largely successful in terms of bacterial community structure. Compared with uneroded soil, C_mic recovered in L. bicolor and P. massoniana restored eroded plots and was significantly greater under these tree species than C. camphora, although soils in C. camphora restored plots displayed the highest bacterial diversity. The recovery of microbial biomass and diversity in the eroded plots was, to large extent, accompanied by the development of the same bacterial community structure as in the uneroded plots with erosion having relatively little effect on bacterial community structure.     

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

It is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, with Proteobacteria as the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, with Proteobacteria, Bacteroidetes, and Verrucomicrobia as the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.     

Changes of Soil Bacterial Diversity as a Consequence of Agricultural Land Use in a Semi-Arid Ecosystem

Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years) of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE) analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes) correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.     

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils.     

不同森林恢复类型对土壤微生物群落的影响

为了评价不同森林恢复类型与方式对南方红壤丘陵区退化生态系统土壤微生物群落的影响,借助氯仿熏蒸法、平板涂抹法和BIOLOG检测法,比较研究了4种森林恢复类型土壤微生物的群落特征．结果表明,4种森林恢复类型土壤微生物生物量碳、细菌数量差异显著,2项指标均以天然次生林土壤最高,人工林次之,荒地最差;碳源平均颜色变化率(AWCD法)和微生物代谢多样性指数(丰富度和多样性)在5种植被类型的土壤中也有明显差异,其趋势与微生物量碳、细菌数量基本相同;天然次生林土壤微生物群落利用碳源的整体能力和功能多样性比人工林和荒地强．相关分析表明,0～20和20～40cm土壤微生物的代谢多样性与根系生物量紧密相关(r=0．933,P<0．05;r=0．925,P<0．05)．自然恢复更有利于改善土壤微生物的结构和功能．     

不同生境黑果枸杞根际与非根际土壤微生物群落多样性

研究典型生境黑果枸杞根际与非根际土壤微生物群落多样性及其与土壤理化性质间的关系,为进一步研究黑果枸杞抗逆性提供理论数据。采集新疆精河县艾比湖地区(EB)盐碱地、乌苏市(WS)路旁荒地、五家渠市(WQ)人工林带的黑果枸杞根际与非根际土壤,利用Illumina-MiSeq高通量测序技术分析细菌和真菌群落组成和多样性。结果表明:根际土壤细菌多样性高于非根际土壤(WQ除外),而根际真菌多样性低于非根际土壤。WQ非根际土壤细菌和真菌多样性均高于EB和WS;根际细菌多样性排序为EBWSWQ,根际真菌多样性排序为WSEBWQ。根际土壤优势细菌门依次是变形菌门、拟杆菌门、放线菌门、酸杆菌门,真菌优势门为子囊菌门、担子菌门。根际土壤细菌变形菌门、拟杆菌门、酸杆菌门的相对丰度高于非根际土壤,而厚壁菌在根际土壤中的丰度显著降低,真菌优势门丰度在根际土和非根际土中的变化趋势因地区而异; Haliea、Gp10、Pelagibius、Microbulbifer、假单胞菌属、Thioprofundum、Deferrisoma是根际土壤细菌优势属;多孢子菌属、支顶孢属、Corollospora、Cochlonema是根际真菌优势属。细菌、真菌优势类群(门、属)的组成以及丰富度存在地区间差异,厚壁菌门在EB地区的丰富度显著高于含盐量较低的WS、WQ;盐碱生境EB中根际土壤嗜盐细菌的丰度高于非盐碱生境(WQ、WS),如盐单胞菌属、动性球菌属、Geminicoccu、Pelagibius、Gracilimonas、Salinimicrobium等。小囊菌属是EB根际真菌的最优势属,Melanoleuca是WQ和WS的最优势属,地孔菌属、Xenobotrytis、Brachyconidiellopsis、多孢子菌属等在EB根际土壤中的丰度显著高于WQ和WS。非盐碱生境(WS和WQ)的微生物群落之间的相似性较高,并且高于与盐碱环境(EB)之间的相似性,表明土壤含盐量对微生物群落组成丰度具有重要的影响。     

Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits

This study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (P < 0.05). At Hillside, communities in surface soils (0.03- to 0.2-m depth) differed significantly with landform and land use (P < 0.05). Communities in deeper soils (>0.2 m) differed significantly with lithology and mineral deposit (P < 0.05). Across both sites, elevated metal contents in soils overlying mineral deposits were selective for a range of bacterial taxa, most importantly Acidobacteria, Bacilli, Betaproteobacteria, and Epsilonproteobacteria. In conclusion, long-term geogenic factors can be just as important as land use in determining soil microbial community diversity.     

Influence of geogenic factors on microbial communities in metallogenic Australian soils

Links between microbial community assemblages and geogenic factors were assessed in 187 soil samples collected from four metal-rich provinces across Australia. Field-fresh soils and soils incubated with soluble Au(III) complexes were analysed using three-domain multiplex-terminal restriction fragment length polymorphism, and phylogenetic (PhyloChip) and functional (GeoChip) microarrays. Geogenic factors of soils were determined using lithological-, geomorphological- and soil-mapping combined with analyses of 51 geochemical parameters. Microbial communities differed significantly between landforms, soil horizons, lithologies and also with the occurrence of underlying Au deposits. The strongest responses to these factors, and to amendment with soluble Au(III) complexes, was observed in bacterial communities. PhyloChip analyses revealed a greater abundance and diversity of Alphaproteobacteria (especially Sphingomonas spp.), and Firmicutes (Bacillus spp.) in Au-containing and Au(III)-amended soils. Analyses of potential function (GeoChip) revealed higher abundances of metal-resistance genes in metal-rich soils. For example, genes that hybridised with metal-resistance genes copA, chrA and czcA of a prevalent aurophillic bacterium, Cupriavidus metallidurans CH34, occurred only in auriferous soils. These data help establish key links between geogenic factors and the phylogeny and function within soil microbial communities. In particular, the landform, which is a crucial factor in determining soil geochemistry, strongly affected microbial community structures.     

Responses of Bacterial Communities to Simulated Climate Changes in Alpine Meadow Soil of the Qinghai-Tibet Plateau

The soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, microbial responses to climate warming or cooling remain poorly understood, limiting our ability to predict the consequences of future climate changes. To address this issue, it is critical to identify microbes sensitive to climate change and key driving factors shifting microbial communities. In this study, alpine soil transplant experiments were conducted downward or upward along an elevation gradient between 3,200 and 3,800 m in the Qinghai-Tibet plateau to simulate climate warming or cooling. After a 2-year soil transplant experiment, soil bacterial communities were analyzed by pyrosequencing of 16S rRNA gene amplicons. The results showed that the transplanted soil bacterial communities became more similar to those in their destination sites and more different from those in their “home” sites. Warming led to increases in the relative abundances in Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria and decreases in Acidobacteria, Betaproteobacteria, and Deltaproteobacteria, while cooling had opposite effects on bacterial communities (symmetric response). Soil temperature and plant biomass contributed significantly to shaping the bacterial community structure. Overall, climate warming or cooling shifted the soil bacterial community structure mainly through species sorting, and such a shift might correlate to important biogeochemical processes such as greenhouse gas emissions. This study provides new insights into our understanding of soil bacterial community responses to climate warming and cooling.     

Size, activity and catabolic diversity of the soil microbial biomass in a wetland complex invaded by reed canary grass

Reed canary grass (Phalaris arundinacea, L.) invasion of wetlands is an ecological issue that has received attention, but its impact on soil microbial diversity is not well documented. The present study assessed the size (substrate-induced respiration), catabolic diversity (CLPP, community level physiological profiles) and composition (selective inhibition) of the soil microbial community in invaded (>95% P. arundinacea cover) and in non-invaded areas of a wetland occupied by native species grown either as a mixed assemblage (22 species) or as quasi-monotypic stands of Scirpus cyperinus (74% cover). The study also tested the hypothesis that decomposition of lignin- and phenolics-rich plant tissues would be fastest in soils exhibiting high catabolic diversity. Results showed that soil respiration, microbial biomass and diversity were significantly higher (P?<?0.03; 1.5 to 3 fold) in P. arundinacea-invaded soils than in soils supporting native plant species. Fungal to bacterial ratios were also higher in invaded (0.6) than in non-invaded (0.4) plots. Further, canonical discriminant analysis of CLPP data showed distinct communities of soil decomposers associated with each plant community. However, these differences in microbial attributes had no effect on decomposition of plant biomass which was primarily controlled by its chemical composition. While P. arundinacea invasion has substantially reduced plant diversity, this study found no parallel decline in the size and diversity of the soil microbial community in the invaded areas.     

Soil bacterial diversity in degraded and restored lands of Northeast Brazil

Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.     

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance.     

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R² = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.The biogeographical patterns exhibited by microbial communities have been examined in a wide range of environments, and studies focusing on microbial biogeography continue to be published at a rapid pace. We know that microbial community diversity and composition can vary considerably across space, and this variation is theorized to be linked to changes in a number of biotic or abiotic factors (22, 36, 41). There are numerous overarching reasons for this interest in understanding microbial biogeography. For example, comparing microbial patterns to those commonly observed in plant and animal taxa is of intense theoretical interest (22, 25). From a more practical standpoint, studies of microbial biogeography can often provide key insights into the physiologies, environmental tolerances, and ecological strategies of microbial taxa, particularly those difficult-to-culture taxa that often dominate in natural environments. However, perhaps the most important rationale for studying microbial biogeography is the most basic one: microbes are diverse, ubiquitous, and abundant, yet their biogeographical patterns and the factors driving these spatial patterns often remain poorly understood.No single biogeographical pattern is shared by all microorganisms, just as there is no single biogeographical pattern followed by all “macrobial” (i.e., plant and animal) communities (31). The specific biogeographical patterns exhibited by microorganisms are variable and highly dependent on a number of factors, including the taxonomic group in question (29), the degree of phylogenetic resolution at which the communities are examined (e.g., Pseudomonas) (7), and the spatial scale of the study (40). However, some common patterns emerge if we specifically examine the biogeography of soil microorganisms. In particular, the structure and diversity of soil bacterial communities have been found to be closely related to soil environmental characteristics (5, 37, 47), and soil pH is often correlated with the observed biogeographical patterns (19, 24). However, due to the paucity of detailed and comprehensive studies of soil bacterial biogeography, particularly across larger spatial scales, our understanding of soil microbial biogeography remains incomplete.Previous studies of soil bacterial biogeography have focused on either surveying a few soils in detail or surveying a larger number of soils by techniques that offer less detailed phylogenetic information. For example, a few recent studies used pyrosequencing or Sanger sequencing-based techniques to deeply survey the diversity and composition of the bacterial communities within a single soil or a few soils (1, 14, 20, 39, 42). Such studies are valuable in that they provide our best assessments of overall bacterial diversity and community structure and the relative abundances of specific bacterial taxa within soils. However, because such studies often examine only a limited number of soils, they do not allow for robust assessment of biogeographical patterns and the factors that may drive these patterns. Other studies have examined bacterial communities across a larger number of soils, using more limited techniques, such as fingerprinting methods that offer little specific phylogenetic information on bacterial community structure or techniques that describe communities at very coarse levels of taxonomic resolution (18, 19). A comprehensive assessment of the biogeographical patterns exhibited by soil bacterial communities requires both depth (individual communities surveyed at a reasonable level of phylogenetic detail) and breadth (examining a sufficiently large number of samples to assess spatial patterns). With the recent development of the bar-coded pyrosequencing technique (23), we need not sacrifice depth for breadth, or vice versa. This was demonstrated in several recent studies (2, 12, 17, 28) that used bar-coded pyrosequencing to simultaneously analyze relatively large numbers of individual samples, surveying the bacterial community in each sample to an extent that would be difficult (or prohibitively expensive) using standard cloning and Sanger sequencing techniques.Here we apply the bar-coded pyrosequencing technique to examine the structure and diversity of bacterial communities in 88 soils collected from across North and South America. This work expands on a previous fingerprinting-based survey of bacterial communities across a similar set of soils (19), using the pyrosequencing technique to extend the analyses and to answer the following questions. Which taxa are most abundant in soil? How does the phylogenetic structure of bacterial communities vary across the continental scale? Which environmental factors best predict bacterial community structure and diversity? Are some soil bacterial phyla more diverse than others?