A Two-Species Test of the Hypothesis That Spatial Isolation Influences Microbial Diversity in Soil

The hypothesis that spatial isolation is a key determinant of microbial community structure in soils was evaluated by examining the competitive dynamics of two species growing on a single resource in a uniform sand matrix under varied moisture content. One species dominated the community under highly connected, saturated treatments, suggesting that these conditions allow competitive interactions to structure the community. As moisture content decreased, however, the less competitive species became established in the community. This effect was most pronounced at a matric water potential of -0.14 MPa where estimates of final population density and species fitness were equal. A second but more closely related species pair exhibited a similar response to decreasing moisture, suggesting that the effects of spatial isolation we observed are not simply a species-pair-specific phenomenon. These findings indicate that spatial isolation, created by low moisture content, plays an important role in structuring soil microbial communities.     

Soil Stoichiometry Mediates Links Between Tree Functional Diversity and Soil Microbial Diversity in a Temperate Forest

Ecosystems - Interactions between plants and soil microbial communities underpin soil processes and forest ecosystem function, but the links between tree diversity and soil microbial diversity are...     

Soil Microbial Diversity in the Vicinity of Desert Shrubs

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0–10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon–Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.     

Microbial Diversity and Community Structure in Two Different Agricultural Soil Communities

Abstract In this study, two different agricultural soils were investigated: one organic soil and one sandy soil, from Stend (south of Bergen), Norway. The sandy soil was a field frequently tilled and subjected to crop rotations. The organic soil was permanent grazing land, infrequently tilled. Our objective was to compare the diversity of the cultivable bacteria with the diversity of the total bacterial population in soil. About 200 bacteria, randomly isolated by standard procedures, were investigated. The diversity of the cultivable bacteria was described at phenotypic, phylogenetic, and genetic levels by applying phenotypical testing (Biolog) and molecular methods, such as amplified rDNA restriction analysis (ARDRA); hybridization to oligonucleotide probes; and REP-PCR. The total bacterial diversity was determined by reassociation analysis of DNA isolated from the bacterial fraction of environmental samples, combined with ARDRA and DGGE analysis. The relationship between the diversity of cultivated bacteria and the total bacteria was elucidated. Organic soil exhibited a higher diversity for all analyses performed than the sandy soil. Analysis of cultivable bacteria resulted in different resolution levels and revealed a high biodiversity within the population of cultured isolates. The difference between the two agricultural soils was significantly higher when the total bacterial population was analyzed than when the cultivable population was. Thus, analysis of microbial diversity must ultimately embrace the entire microbial community DNA, rather than DNA from cultivable bacteria.     

Soil Microbial Abundance and Diversity Along a Low Precipitation Gradient

The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while ∼2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (∼9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem.     

Microbial Diversity of Septic Tank Effluent and a Soil Biomat

Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.On-site wastewater treatment systems serve approximately 22 million homes throughout the United States (39), resulting in ∼15 billion liters of wastewater, typically treated in septic tanks (Fig. ​(Fig.1A),1A), being discharged into the environment daily (8). Septic tank effluent (STE) is normally discharged into subsurface trenches or beds (i.e., soil treatment units [STU]) (40), where many pathogenic bacteria, viruses, and nutrients are removed, transformed, or destroyed.Open in a separate windowFIG. 1.Shown are typical on-site wastewater system components (A), a chamber system with an open infiltrative architecture (B), and a stone-and-pipe system with a gravel-laden infiltrative surface architecture (C). (Adapted with permission from Infiltrator Systems, Inc.)Within the STU, a complex ecosystem referred to as a biomat evolves over time at and near the soil infiltrative surface in response to STE application (5, 6, 32). This region (1 to 2 cm in thickness) becomes dark in color and has high organic matter accumulation, high water content, and high microbial densities. The biomat may be important from a purification perspective (42); however, excessive soil pore clogging can be detrimental to long-term hydraulic functioning.Biomat formation and potential soil clogging appear to be dependent on several factors: wastewater composition and loading rate (18, 31, 32, 38), soil characteristics (23), microorganisms (2, 11, 14, 24, 29, 33), temperature (17), and wastewater application method (17). Although it is believed that microorganisms are involved, research examining the microbial community of the biomat is limited and until recently has focused only on using plating techniques to determine bacterial numbers (27, 29). Few researchers have attempted to characterize the microbial community found in the biomat (3, 29, 41). In this study, traditional culturing techniques and a molecular approach (see “Methods” in the supplemental material) were used to explore the diversity of microbes found in domestic STE and the biomat that developed in the STU in a sandy loam soil.The biomat that developed within an Ascalon sandy loam soil as a result of STE infiltration over a period of 30 months was characterized using 16S rRNA gene sequence analysis and culturing techniques (37). The microbial communities were analyzed by using STE and biomat samples from two different pilot-scale infiltration units for STE; one (MP10) had an open architecture above the soil infiltrative surface (Fig. ​(Fig.1B),1B), and one (MP9) had gravel aggregate sitting on the soil infiltrative surface (Fig. ​(Fig.1C).1C). For use as a negative control, samples of sandy loam soil were also collected from an infiltration unit at the same site that received clean tap water and had an open architecture. Biomat samples were taken at two depth intervals, 0.0 to 0.5 cm and 0.5 to 1.0 cm from test units MP10 and MP9, and the control sample was taken from 0.0 to 0.5 cm. At the time of sampling, the three infiltration units had received STE or tap water for 30 months.A total of 447 bacterial 16S rRNA gene sequences were generated from samples of the STE and the biomat (two STE units and a tap water unit). This number likely represents a great undersampling of these environments; however, these sequences are sufficient to provide insight into the microbial community phylotype composition. Although “universal” (i.e., all three phylogenetic domains amplified) PCR primers 515F and 1391R (19) were used, only organisms from the bacterial domain were detected. As in a previous study of a biomat (3) and other studies of soil microbial communities (9, 28), Proteobacteria sequences dominated the biomat samples, but Bacteroidetes and Acidobacteria sequences were also found in significant abundance (Fig. ​(Fig.2).2). The control community was comprised mainly of sequences from Proteobacteria, Acidobacteria, and Actinobacteria, with a distribution similar to that of the biomat. However, only 31% of sequences at the family level were shared between the 0.0- to 0.5-cm-depth samples of each biomat and the control. Furthermore, 95% of the operational taxonomic units (OTUs) found in the control sample were not found in any other sample analyzed in this study.Open in a separate windowFIG. 2.Bacterial phylum diversity based on rRNA gene clone libraries and the Ribosomal Database Project classification (7). MP9A, gravel-laden architecture test unit (0.5 cm); MP9B, gravel-laden architecture test unit (1.0 cm); MP10A, open architecture test unit (0.5 cm); MP10B, open architecture test unit (1.0 cm); STE; Control, negative control infiltrative surface architecture; and Summary, a compilation of the sequences of all clones used in this study and examined in all environments. Percentages are based on the total number of clones within each sample.The lack of shared sequences suggests that the nutrient-rich STE fosters the growth of a different soil microbial community. The composition of the effluent applied (clean water versus STE) appears to lead to distinct microbial communities, based on the relatively low percentage of shared OTUs. Additionally, scanning electron micrographs of both biomat and control soil samples were strikingly different, supporting the differences observed by molecular comparative methods (see Fig. S1 in the supplemental material).The STE library was also dominated by proteobacteria (81%), but the class distribution differed considerably from both the control and biomat (see Fig. S2 in the supplemental material). Epsilonproteobacteria (from the genera Sulfurospirillum, Arcobacter, and Sulfurimonas) species represented the dominant subphyla in the STE sample but were absent from all other samples. None of the OTUs found in STE were found in the biomat samples, suggesting that the microbial community of the biomat originates in the soil rather than from the influx of organisms entering the soil in STE. This also may indicate limited survival or the possibility that they are outcompeted by indigenous soil microbes. Species of both the Sulfurospirillum and Sulfurimonas genera have also been found in aquatic environments (13, 16) and contaminated sediments (22). Sequences of Arcobacter spp., aerotolerant gram-negative spiral-shaped bacteria, were the most dominant found in STE. Arcobacter spp. have been found in mangrove sediments (21) and activated sludge (34) and have been associated with human and animal diarrhea (1, 20, 36). The lack of Arcobacter spp. in any of the biomat samples indicates a rapid die-off or predation at the soil infiltrative surface or the possibility that they are vastly outnumbered in this environment and were not detected by the sequencing performed.There was far less overall phylogenetic diversity in STE than in the biomat samples (see Table S1 in the supplemental material). The phylum distribution in the STE is similar to that of the human gut, which contains some of the highest cell densities of any ecosystem (43); however, diversity at the phylum level is among the lowest (15). Studies have shown that the human gut and feces are dominated by Bacteroidetes (30%) and Firmicutes (30%) species (4, 10). The lack of sequences grouping with Firmicutes spp. in this study suggests that they may not survive the septic tank environment. Not surprisingly, Escherichia coli sequences were not detected in this study, as these bacteria represent less than 0.1% of the species found in the colon (10, 35).The amount of fecal coliforms and E. coli bacteria was reduced by a minimum of 90% and 85%, respectively, from the STE to the biomat. Similar to results of previous studies (12, 25, 26, 30), culturable heterotrophic bacteria, fecal coliforms, and E. coli bacteria decreased with the increase in depth (1 to 10 cm) in both of the STE test units. The number of heterotrophic bacteria was 3 to 5 orders of magnitude greater in all samples than counts for fecal coliforms and E. coli. At all depths, the number of fecal coliforms and E. coli were greater in test unit MP10 than in MP9; this may be due in part to differences between open versus gravel-laden infiltration surfaces, with the gravel architecture of MP9 being more conducive to the formation of a water-treating biomat.Further analysis may determine the roles that microbes play in the treatment of organic and inorganic pollutants in the biomat. Ultimately, understanding the microbial community will allow engineers to implement on-site systems that control the rate of biomat formation and thus keep clogging and subsequent failure to a minimum. This improved design and operation would help to protect the underlying groundwater.     

Post-Fire Spatial Patterns of Soil Nitrogen Mineralization and Microbial Abundance

Stand-replacing fires influence soil nitrogen availability and microbial community composition, which may in turn mediate post-fire successional dynamics and nutrient cycling. However, fires create patchiness at both local and landscape scales and do not result in consistent patterns of ecological dynamics. The objectives of this study were to (1) quantify the spatial structure of microbial communities in forest stands recently affected by stand-replacing fire and (2) determine whether microbial variables aid predictions of in situ net nitrogen mineralization rates in recently burned stands. The study was conducted in lodgepole pine (Pinus contorta var. latifolia) and Engelmann spruce/subalpine fir (Picea engelmannii/Abies lasiocarpa) forest stands that burned during summer 2000 in Greater Yellowstone (Wyoming, USA). Using a fully probabilistic spatial process model and Bayesian kriging, the spatial structure of microbial lipid abundance and fungi-to-bacteria ratios were found to be spatially structured within plots two years following fire (for most plots, autocorrelation range varied from 1.5 to 10.5 m). Congruence of spatial patterns among microbial variables, in situ net N mineralization, and cover variables was evident. Stepwise regression resulted in significant models of in situ net N mineralization and included variables describing fungal and bacterial abundance, although explained variance was low (R²<0.29). Unraveling complex spatial patterns of nutrient cycling and the biotic factors that regulate it remains challenging but is critical for explaining post-fire ecosystem function, especially in Greater Yellowstone, which is projected to experience increased fire frequencies by mid 21^st Century.     

Microbial Diversity and PAH Catabolic Genes Tracking Spatial Heterogeneity of PAH Concentrations

We analyzed the within-site spatial heterogeneity of microbial community diversity, polyaromatic hydrocarbon (PAH) catabolic genotypes, and physiochemical soil properties at a creosote contaminated site. Genetic diversity and community structure were evaluated from an analysis of denaturant gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified sequences of 16S rRNA gene. The potential PAH degradation capability was determined from PCR amplification of a suit of aromatic dioxygenase genes. Microbial diversity, evenness, and PAH genotypes were patchily distributed, and hot and cold spots of their distribution coincided with hot and cold spots of the PAH distribution. The analyses revealed a positive covariation between microbial diversity, biomass, evenness, and PAH concentration, implying that the creosote contamination at this site promotes diversity and abundance. Three patchily distributed PAH-degrading genotypes, NAH, phnA, and pdo1, were identified, and their abundances were positively correlated with the PAH concentration and the fraction of soil organic carbon. The covariation of the PAH concentration with the number and spatial distribution of catabolic genotypes suggests that a field site capacity to degrade PAHs may vary with the extent of contamination.     

用于微生物多样性分析的棉田土壤总DNA的提取

目的：探讨适用于微生物多样性研究的棉田土壤微生物总DNA提取方法。方法：采用4种方法提取不同连作和轮作处理的棉田土壤微生物总DNA,比较其纯度、产率、片段大小,并应用ARDRA技术验证其质量。结果：其中3种方法均可获得23kb的DNA片段,但不同方法提取的DNA的产率和纯度上有明显差异。改良CTAB-SDS法提取的DNA完整性好,得率为24.20μg.g-1干土,纯化后A260/A280和A260/A230为分别为1.80和1.70,纯化回收率可达70.1%,完全适用于后续的PCR分析。结论：采用该法提取棉田土壤总DNA简便而高效。对该法提取获得的棉田土壤微生物总DNA进行ARDRA和DGGE分析,所得图谱能较全面地反映不同处理间微生物多样性及群落结构的差别,为不同栽培体系下棉田土壤微生物的分子生态学研究提供了基础。     

Factors Controlling Soil Microbial Biomass and Bacterial Diversity and Community Composition in a Cold Desert Ecosystem: Role of Geographic Scale

Understanding controls over the distribution of soil bacteria is a fundamental step toward describing soil ecosystems, understanding their functional capabilities, and predicting their responses to environmental change. This study investigated the controls on the biomass, species richness, and community structure and composition of soil bacterial communities in the McMurdo Dry Valleys, Antarctica, at local and regional scales. The goals of the study were to describe the relationships between abiotic characteristics and soil bacteria in this unique, microbially dominated environment, and to test the scale dependence of these relationships in a low complexity ecosystem. Samples were collected from dry mineral soils associated with snow patches, which are a significant source of water in this desert environment, at six sites located in the major basins of the Taylor and Wright Valleys. Samples were analyzed for a suite of characteristics including soil moisture, pH, electrical conductivity, soil organic matter, major nutrients and ions, microbial biomass, 16 S rRNA gene richness, and bacterial community structure and composition. Snow patches created local biogeochemical gradients while inter-basin comparisons encompassed landscape scale gradients enabling comparisons of microbial controls at two distinct spatial scales. At the organic carbon rich, mesic, low elevation sites Acidobacteria and Actinobacteria were prevalent, while Firmicutes and Proteobacteria were dominant at the high elevation, low moisture and biomass sites. Microbial parameters were significantly related with soil water content and edaphic characteristics including soil pH, organic matter, and sulfate. However, the magnitude and even the direction of these relationships varied across basins and the application of mixed effects models revealed evidence of significant contextual effects at local and regional scales. The results highlight the importance of the geographic scale of sampling when determining the controls on soil microbial community characteristics.     

Geochemical Influence on Diversity and Microbial Processes in High Temperature Oil Reservoirs

The diversity of thermophilic microbial assemblages detected within two neighboring high temperature petroleum formations was shown to closely parallel the different geochemical regimes existing in each. A high percentage of archaeal 16S rRNA gene sequences, related to thermophilic aceticlastic and hydrogenotrophic methanogens, were detected in the natural gas producing Rincon Formation. In contrast, rRNA gene libraries from the highly sulfidogenic Monterey Formation contained primarily sulfur-utilizing and fermentative archaea and bacteria. In addition to the variations in microbial community structure, microbial activities measured in microcosm experiments using high temperature production fluids from oil-bearing formations also demonstrated fundamental differences in the terminal respiratory and redox processes. Provided with the same suite of basic energy substrates, production fluids from the South Elwood Rincon Formation actively generated methane, while thermophilic microflora within the Monterey production fluids were dominated by hydrogen sulfide producing microorganisms. In both cases, molecular hydrogen appeared to play a central role in the stimulation of carbon and sulfur cycling in these systems. In methanogenic production fluids, the addition of sulfur compounds induced a rapid shift in the terminal electron accepting process, stimulating hydrogen sulfide formation and illustrating the metabolic versatility of the subsurface thermophilic assemblage. The high similarity between microbial community structure and activity corresponding with the prevalent geochemical conditions observed in deep subsurface petroleum reservoirs suggests that the resident microflora have adapted to the subsurface physicochemical conditions and may actively influence the geochemical environment in situ.     

番茄根际微生物种群动态变化及多样性

采用盆栽试验的方法对番茄根际主要微生物种群在不同生育期的动态变化进行了跟踪研究.结果表明,在番茄整个生育期内,可培养细菌数量在初花期和初果期时最多;放线菌数量从苗期到末期逐渐减少;真菌数量逐渐增多.番茄对细菌根际效应明显.DGGE图谱显示不同生育期番茄根际均具有较高的细菌多样性.根际细菌种类和数量在初花期发生较为显著的变化,初果期根际群落多样性指数(H)和物种丰度(S)值都达到最高,微生物最丰富,是筛选拮抗菌的较好时期.     

Association of Host and Microbial Species Diversity across Spatial Scales in Desert Rodent Communities

Relationships between host and microbial diversity have important ecological and applied implications. Theory predicts that these relationships will depend on the spatio-temporal scale of the analysis and the niche breadth of the organisms in question, but representative data on host-microbial community assemblage in nature is lacking. We employed a natural gradient of rodent species richness and quantified bacterial communities in rodent blood at several hierarchical spatial scales to test the hypothesis that associations between host and microbial species diversity will be positive in communities dominated by organisms with broad niches sampled at large scales. Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. These communities exhibited positive correlations between host diversity, microbial diversity and the likelihood for rare pathogens at the regional scale but not at finer scales. These findings demonstrate how microbial diversity is affected by host diversity at different spatial scales and suggest that the relationships between host diversity and overall disease risk are not always negative, as the dilution hypothesis predicts.     

辣椒青枯病罹病与健康植株根际土壤微生物群落多样性研究

系统研究和分析辣椒青枯病常发地发病与健康植株土壤微生物群落结构特征,为辣椒青枯病的绿色防治提供理论依据.基于16SrDNA基因高通量测序技术,对辣椒青枯病发病和健康植株根际土壤微生物群落结构和组成进行分析,同时采用biologyeco平板培养技术研究其土壤微生物群落代谢多样性和功能多样性的特征.结果表明,辣椒青枯病发病和健康植株根际土壤微生物群落组成之间存在显著差异,辣椒青枯病发病土壤的OTU为4566个,辣椒青枯病健康土壤的OTU为4167个.依据OTU所属细菌物种信息对土壤细菌群落结构进行分析,变形菌门在发病和健康土壤中均为优势细菌类群,其次为放线菌门类群.其中健康植株根际土壤中芽单胞菌门(Gemmatimonadetes)、装甲菌门(Armatimonadetes)的相对丰度比发病植株的分别高出了4.37,3.87倍,而发病植株根际土壤中厚壁菌门(Firmicutes)的相对丰度比健康植株的高出了3.87倍.辣椒青枯病发病土壤和健康土壤的土壤微生物代谢多样性也存在显著差异,同时,健康土壤中其微生物群落代谢得到显著增强,特别是对酚类化合物的利用显著增多,对辣椒抗病性存在显著的影响.研究表明,辣椒青枯病发病和健康植株根际土壤微生物群落组成和结构之间存在显著差异,并且健康土壤的微生物群落对酚类化合物的利用显著增强.     

Spatial and Temporal Biogeography of Soil Microbial Communities in Arid and Semiarid Regions

Microbial communities in soils may change in accordance with distance, season, climate, soil texture and other environmental parameters. Microbial diversity patterns have been extensively surveyed in temperate regions, but few such studies attempted to address them with respect to spatial and temporal scales and their correlations to environmental factors, especially in arid ecosystems. In order to fill this gap on a regional scale, the molecular fingerprints and abundance of three taxonomic groups – Bacteria, α-Proteobacteria and Actinobacteria – were sampled from soils 0.5–100 km apart in arid, semi-arid, dry Mediterranean and shoreline Mediterranean regions in Israel. Additionally, on a local scale, the molecular fingerprints of three taxonomic groups – Bacteria, Archaea and Fungi – were sampled from soils 1 cm–500 m apart in the semi-arid region, in both summer and winter. Fingerprints of the Bacteria differentiated between all regions (P<0.02), while those of the α-Proteobacteria differentiated between some of the regions (0.01<P<0.09), and actinobacterial fingerprints were similar among all regions (P>0.05). Locally, fingerprints of archaea and fungi did not display distance-decay relationships (P>0.13), that is, the dissimilarity between communities did not increase with geographic distance. Neither was this phenomenon evident in bacterial samples in summer (P>0.24); in winter, however, differences between bacterial communities significantly increased as the geographic distances between them grew (P<0.01). Microbial community structures, as well as microbial abundance, were both significantly correlated to precipitation and soil characteristics: texture, organic matter and water content (R²>0.60, P<0.01). We conclude that on the whole, microbial biogeography in arid and semi-arid soils in Israel is determined more by specific environmental factors than geographic distances and spatial distribution patterns.