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Data on soil microbial community distribution at large scales are limited despite the important information that could be drawn with regard to their function and the influence of environmental factors on nutrient cycling and ecosystem services. This study investigates the distribution of Archaea, Bacteria and Fungi as well as the dominant bacterial phyla ( Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes) , and classes of Proteobacteria ( Alpha- and Betaproteobacteria) across the Koiliaris watershed by qPCR and associate them with environmental variables. Predictive maps of microorganisms distribution at watershed scale were generated by co-kriging, using the most significant predictors. Our findings showed that 31-79% of the spatial variation in microbial taxa abundance could be explained by the parameters measured, with total organic carbon and pH being identified as the most important. Moreover, strong correlations were set between microbial groups and their inclusion on variance explanation improved the prediction power of the models. The spatial autocorrelation of microbial groups ranged from 309 to 2.226 m, and geographic distance, by itself, could explain a high proportion of their variation. Our findings shed light on the factors shaping microbial communities at a high taxonomic level and provide evidence for ecological coherence and syntrophic interactions at the watershed scale. [ABSTRACT FROM AUTHOR]

It is increasingly recognized that volatile organic compounds play an import role during interactions between soil microorganisms. Here, we examined the possible involvement of volatiles in the interaction of Collimonas bacteria with soil fungi. The genus Collimonas is known for its ability to grow at the expense of living fungi (mycophagy), and antifungal volatiles may contribute to the attack of fungi by these bacteria. We analyzed the composition of volatiles produced by Collimonas on agar under different nutrient conditions and studied the effect on fungal growth. The volatiles had a negative effect on the growth of a broad spectrum of fungal species. Collimonas bacteria did also produce volatiles in sand microcosms supplied with artificial root exudates. The production of volatiles in sand microcosms was enhanced by the presence of fungi. The overall picture that we get from our study is that antifungal volatiles produced by Collimonas could play an important role in realizing its mycophagous lifestyle. The current work is also interesting for understanding the ecological relevance of volatile production by soil bacteria in general as we found strong influences of root exudates composition and incubation conditions on the spectrum of volatiles produced. [ABSTRACT FROM AUTHOR]

There is growing evidence of a direct relationship between microbial community composition and function, which implies that distinct microbial communities vary in their functional properties. The aim of this study was to determine whether differences in initial substrate utilization between distinct microbial communities are due to the activities of certain microbial groups. We performed a short-term experiment with beech forest soils characterized by three different microbial communities (winter and summer community, and a community from a tree-girdling plot). We incubated these soils with different 13C-labelled substrates with or without inorganic N addition and analyzed microbial substrate utilization by 13C-phospholipid fatty acid ( PLFA) analysis. Our results revealed that the fate of labile C (glucose) was similar in the three microbial communities, despite differences in absolute substrate incorporation between the summer and winter community. The active microbial community involved in degradation of complex C substrates (cellulose, plant cell walls), however, differed between girdling and control plots and was strongly affected by inorganic N addition. Enhanced N availability strongly increased fungal degradation of cellulose and plant cell walls. Our results indicate that fungi, at least in the presence of a high N supply, are the main decomposers of polymeric C substrates. [ABSTRACT FROM AUTHOR]

Soil habitats contain vast numbers of microorganisms and harbor a large portion of the planet's biological diversity. Although high-throughput sequencing technologies continue to advance our appreciation of this remarkable phylogenetic and functional diversity, we still have only a rudimentary understanding of the forces that allow diverse microbial populations to coexist in soils. This conspicuous knowledge gap may be partially due the human perspective from which we tend to examine soilborne microorganisms. This review focusses on the highly heterogeneous soil matrix from the vantage point of individual bacteria. Methods describing micro-scale soil habitats and their inhabitants based on sieving, dissecting, and visualizing individual soil aggregates are discussed, as are microcosm-based experiments allowing the manipulation of key soil parameters. We identify how the spatial heterogeneity of soil could influence a number of ecological interactions promoting the evolution and maintenance of bacterial diversity. [ABSTRACT FROM AUTHOR]

The Po river plain lowland springs represent unique paradigms of managed environments. Their current locations used to be swamps that were drained 6-7 centuries ago, and they have been in constant use ever since. Our aims were to identify the effects of land use on the microbial communities of these soils, look for associated diversity drivers, and assess the applicability of ecology theories with respect to identified patterns. We screened the microbial diversity across a land use transect via high-throughput sequencing of partial 16 S r rRNA gene amplicons. Land use had a major effect on soil properties and microbial community structures. Total organic carbon and p H were major diversity drivers for Bacteria, and p H was important for Archaea. We identified the potential contribution of soil amendments to the indigenous microbial communities, and also gained insights into potential roles of taxa in the organic carbon turnover. Verrucomicrobia coincided with the higher values of the recalcitrant organic carbon. Actinobacteria and Acidobacteria correlated with the more labile organic carbon. Finally, the higher diversity found in the soils less enzymatically active and relatively poorer in nutrients, may be explained to an extent by niche-based theories such as the resource heterogeneity hypothesis and Connell's intermediate disturbance hypothesis. [ABSTRACT FROM AUTHOR]

Biological soil crusts (biocrusts) are common to drylands worldwide. We employed replicated, spatially nested sampling and 16 S r RNA gene sequencing to describe the soil microbial communities in three soils derived from different parent material (sandstone, shale, and gypsum). For each soil type, two depths (biocrusts, 0-1 cm; below-crust soils, 2-5 cm) and two horizontal spatial scales (15 cm and 5 m) were sampled. In all three soils, Cyanobacteria and Proteobacteria demonstrated significantly higher relative abundance in the biocrusts, while Chloroflexi and Archaea were significantly enriched in the below-crust soils. Biomass and diversity of the communities in biocrusts or below-crust soils did not differ with soil type. However, biocrusts on gypsum soil harbored significantly larger populations of Actinobacteria and Proteobacteria and lower populations of Cyanobacteria. Numerically dominant operational taxonomic units ( OTU; 97% sequence identity) in the biocrusts were conserved across the soil types, whereas two dominant OTUs in the below-crust sand and shale soils were not identified in the gypsum soil. The uniformity with which small-scale vertical community differences are maintained across larger horizontal spatial scales and soil types is a feature of dryland ecosystems that should be considered when designing management plans and determining the response of biocrusts to environmental disturbances. [ABSTRACT FROM AUTHOR]

The relationship between total and metabolically active soil microbial communities can change drastically with environment. In dry lands, water availability is a key factor limiting cells' activity. We surveyed the diversity of total and active Archaea and Bacteria in soils ranging from arid desert to Mediterranean forests. Thirty composited soil samples were retrieved from five sites along a precipitation gradient, collected from patches located between and under the dominant perennial plant at each site. Molecular fingerprinting was used to site-sort the communities according of their 16 S r RNA genes (total community) and their r RNA (active community) amplified by PCR or RT- PCR from directly extracted soil nucleic acids. The differences between soil samples were much higher in total rather than active microbial communities: differences in DNA fingerprints between sites were 1.2 and 2.5 times higher than RNA differences (for Archaea and Bacteria, respectively). Patch-type discrepancies between DNA fingerprints were on average 2.7-19.7 times greater than RNA differences. Moreover, RNA-based community patterns were highly correlated with soil moisture but did not necessarily follow spatial distribution pattern. Our results suggest that in water-limited environments, the spatial patterns obtained by the analysis of active communities are not as robust as those drawn from total communities. [ABSTRACT FROM AUTHOR]

Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16 S r RNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike. [ABSTRACT FROM AUTHOR]

Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet tropical soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh soils and incubated soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α-subunit ( amoA) gene. These relatively low pH soils appear to be dominated by ammonia-oxidizing archaea ( AOA), and AOA communities in the three soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet tropical soil AOA are tolerant of extended periods of anoxia. [ABSTRACT FROM AUTHOR]

Soil bacterial population dynamics were examined to assess patterns in microbial response to contamination by different petroleum mixtures with variation in n-alkane profiles or toxic constituents such as pentachlorophenol ( PCP). Three soil types from distinct areas of the United States ( Montana, Oregon, and Arizona) were used in controlled perturbation experiments containing crude oil, kerosene, diesel, or diesel plus PCP spiked with 14C-hexadecane or 14C-tridecane. After a 50-day incubation, 30-70% of added 14C-alkanes were mineralized to 14 CO2 in Montana and Oregon soils. In contrast, significantly lower mineralization was observed with diesel or kerosene (< 5%) compared to crude-oil treatment (~45%) in the Arizona soil. Different hydrocarbon mixtures selected both unique and common microbial populations across all three soils. Conversely, the contamination of different soils with the same mixture selected for distinct microbial populations. The most consistent genotype observed, a Rhodococcus-like population, was present in the Montana soil with all mixture types. The addition of PCP selected for PCP-tolerant alkane-degrading specialist populations. The results indicated that petroleum mixture type influenced hydrocarbon degradation rates and microbial population selection and that soil characteristics, especially organic content, could also be an important determinant of community responses to hydrocarbon perturbation. [ABSTRACT FROM AUTHOR]

We investigated soil streptomycete communities associated with four host plant species (two warm season C4 grasses: Andropogon gerardii, Schizachyrium scoparium and two legumes: Lespedeza capitata, Lupinus perennis), grown in plant communities varying in species richness. We used actinobacteria-selective PCR coupled with pyrosequencing to characterize streptomycete community composition and structure. The greatest pairwise distances between communities were observed in contrasts between monocultures of different plant species, indicating that plant species exert distinct selective effects on soil streptomycete populations. Increasing plant richness altered the composition and structure of streptomycete communities associated with each host plant species. Significant relationships between plant community characteristics, soil edaphic characteristics, and streptomycete community structure suggest that host plant effects on soil microbial communities may be mediated through changes to the soil environment. Co-occurring streptomycete taxa also shared consistent relationships with soil edaphic properties, providing further indication of the importance of habitat preference for taxon occurrence. Physical distance between sampling points had a significant influence on streptomycete community similarity. This work provides a detailed characterization of soil streptomycete populations across a field scale and in relation to plant host identity and plant community richness. [ABSTRACT FROM AUTHOR]

Aim This study evaluates the effect of surface application of dried Class A biosolids on microbial populations within copper mine tailings. Methods and Results Mine tailing sites were established at ASARCO Mission Mine close to Sahuarita Arizona. Site 1 ( December 1998) was amended with 248 tons ha−1 of Class A biosolids. Sites 2 ( December 2000) and 3 ( April 2006) were amended with 371 and 270 tons ha−1, respectively. Site D, a neighbouring native desert soil, acted as a control for the evaluation of soil microbial characteristics. Surface amendment of Class A biosolids showed a 4 log10 increase in heterotrophic plate counts (HPCs) compared to unamended tailings, with the increase being maintained for 10-year period. Microbial activities such as nitrification, sulphur oxidation and dehydrogenase activity were also sustained throughout the study period. 16S r RNA clone libraries obtained from community DNA suggest that mine tailings amended with biosolids achieve diversity and bacterial populations similar to native soil bacterial phyla, 10 years postapplication. Conclusion Addition of Class A biosolids to copper mine tailings in the desert south-west increased soil microbial numbers, activity and diversity relative to unamended mine tailings. Significance and Impact of the Study The amended tailings resulted in a functional soil with respect to microbial characteristics, which were sustainable over a 10-year period enabling the development of appropriate vegetation. [ABSTRACT FROM AUTHOR]

Arid and semi-arid ecosystems are often characterized by vegetation patchiness and variable availability of resources. Phospholipid fatty acid (PLFA) and 16S rRNA gene fragment analyses were used to compare the bulk soil microbial community structure at patchy arid and semi-arid landscapes. Multivariate analyses of the PLFA data and the 16S rRNA gene fragments were in agreement with each other, suggesting that the differences between bulk soil microbial communities were primarily related to shrub vs intershrub patches, irrespective of climatic or site differences. This suggests that the mere presence of a living shrub is the dominant driving factor for the differential adaptation of the microbial communities. Lipid markers suggested as indicators of Gram-positive bacteria were higher in soils under the shrub canopies, while markers suggested as indicators of cyanobacteria and anaerobic bacteria were elevated in the intershrub soils. Secondary differences between soil microbial communities were associated with intershrub characteristics and to a lesser extent with the shrub species. This study provides an insight into the multifaceted nature of the factors that shape the microbial community structure in patchy desert landscapes. It further suggests that these drivers not only act in concert but also in a way that is dependent on the aridity level. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizal (AM) fungi can enhance the rate of decomposition of organic material, and can acquire nitrogen (N) from organic sources, although they are not saprotrophs. These fungi may instead indirectly influence decomposition through interactions with other soil microorganisms. We investigated the impact of both AM hyphae and a bacterial filtrate on N capture by a host plant from sterilized organic material ( Lolium perenne shoots dual labelled with N and C), using compartmented microcosms. The addition of a bacterial filtrate considerably suppressed AM hyphal growth in the patch and reduced the root phosphorus content, demonstrating that bacterial populations can reduce symbiotic effectiveness. In contrast, AM hyphae had only a limited impact on bacterial community structure. Uptake of N greatly exceeded that of C, demonstrating that fungi acquired N in an inorganic form. We also examined the ability of AM fungi in gnotobiotic hairy root culture to acquire N directly from organic materials of varying complexities (glutamic acid, urea, bacterial lysate and L. perenne shoots). AM colonization did not enhance root N capture from these materials, although the bacterial lysate reduced both total AM colonization and arbuscule frequency. Collectively, these data demonstrate antagonistic interactions between AM fungi and bacteria that reflect resource competition for decomposition products. [ABSTRACT FROM AUTHOR]

Few studies have been conducted on adaptations of microbial communities to low and fluctuating temperatures using environmentally relevant conditions. In this study, six Himalayan and two temperate soils were selected as candidates for low-temperature/freeze-thaw (FT)-adapted and susceptible soils, respectively. Redundancy analysis with forward selection was used to create a model of environmental parameters explaining variability in the initial microbial abundance and 4 °C activities. The best predictor was soil carbon, explaining more than 74% of data variability ( P=0.002), despite significant differences in the soil characteristics and environmental history. We tested the hypothesis that the reproduced Himalayan FT fluctuations select physiologically similar communities in distinct soils. Microcosms were experimentally subjected to two separate 50 and 60 FT cycle (FTC) experiments. A significant decrease in abundance, 4 °C basal respiration and drastic rearrangements in community-level physiological profiles (CLPP) were observed in microcosms with temperate soils until 40 FTC. CLPP remained distinct from those of the Himalayan soils. Minor changes were observed in the Himalayan soils, confirming that microbial populations with physiological traits consistent with the noncontinuous permafrost conditions reside in the Himalayan soils, whereas the surviving temperate soil microorganisms actively adjusted to novel environmental conditions. [ABSTRACT FROM AUTHOR]

Exposure to pollution exerts strong selective pressure on microbial communities, which may affect their potential to adapt to current or future environmental challenges. In this microcosm study, we used DNA fingerprinting based on 16S rRNA genes to document the impact of high concentrations of benzene on two bacterial communities from a benzene-contaminated aquifer situated below a petrochemical plant (SIReN, UK). The two groundwaters harboured distinct aerobic benzene-degrading communities able to metabolize benzene to below detection levels (1 μg L−1). A benzene concentration of 100 mg L−1 caused a major shift from Betaproteobacteria to Actinobacteria, in particular Arthrobacter spp. A similar shift from Betaproteobacteria to Arthrobacter spp. and Rhodococcus erythropolis was observed in minimal medium (MM) inoculated with a third groundwater. These Gram-positive-dominated communities were able to grow on benzene at concentrations up to 600 mg L−1 in groundwater and up to 1000 mg L−1 in MM, concentrations that cause significant solvent stress to cellular systems. Therefore, Gram-positive bacteria were better competitors than Gram-negative organisms under experimental conditions of high benzene loads, which suggests that solvent-tolerant Gram-positive bacteria can play a role in the natural attenuation of benzene or the remediation of contaminated sites. [ABSTRACT FROM AUTHOR]

The long-term impacts of Cu- and Zn-rich sewage sludge additions on the structure of the microbial community in a field under pasture were investigated using a combination of multiplex-terminal restriction fragment length polymorphism (M-TRFLP) and T-RFLP profiling approaches. Changes in the community structure of bacteria, fungi, archaea and actinobacteria were observed in soils that had previously received Cu- (50–200 mg kg−1 soil) and Zn- (150–450 mg kg−1 soil) rich sewage sludge additions. Changes in the structure of all microbial groups measured were observed at Cu and Zn rates below the current EU guidelines (135 mg kg−1 Cu and 300 mg kg−1 Zn). The response of the fungal community, and to a lesser extent the bacterial and archaeal community, to Cu was dose dependent. The fungal community also showed a dose-dependent response to Zn, which was not observed in the other microbial groups assessed. Redundancy analysis demonstrated that individual terminal restriction fragments responded to both Cu and Zn and these may have potential as genetic markers of long-term metal effects in soil. [ABSTRACT FROM AUTHOR]

The key role of telluric microorganisms in pesticide degradation is well recognized but the possible relationships between the biodiversity of soil microbial communities and their functions still remain poorly documented. If microorganisms influence the fate of pesticides, pesticide application may reciprocally affect soil microorganisms. The objective of our work was to estimate the impact of 2,4-D application on the genetic structure of bacterial communities and the 2,4-D-degrading genetic potential in relation to 2,4-D mineralization. Experiments combined isotope measurements with molecular analyses. The impact of 2,4-D on soil bacterial populations was followed with ribosomal intergenic spacer analysis. The 2,4-D degrading genetic potential was estimated by real-time PCR targeted on tfdA sequences coding an enzyme specifically involved in 2,4-D mineralization. The genetic structure of bacterial communities was significantly modified in response to 2,4-D application, but only during the intense phase of 2,4-D biodegradation. This effect disappeared 7 days after the treatment. The 2,4-D degrading genetic potential increased rapidly following 2,4-D application. There was a concomitant increase between the tfdA copy number and the 14C microbial biomass. The maximum of tfdA sequences corresponded to the maximum rate of 2,4-D mineralization. In this soil, 2,4-D degrading microbial communities seem preferentially to use the tfd pathway to degrade 2,4-D. [ABSTRACT FROM AUTHOR]

Many experiments that measure the response of microbial communities to heavy metals increase metal concentrations abruptly in the soil. However, it is unclear whether abrupt additions mimic the gradual and often long-term accumulation of these metals in the environment where microbial populations may adapt. In a greenhouse experiment that lasted 26 months, we tested whether bacterial communities and soil respiration differed between soils that received an abrupt or a gradual addition of copper or no copper at all. Bacterial richness and other diversity indices were consistently lower in the abrupt treatment compared to the ambient treatment that received no copper. The abrupt addition of copper yielded different initial bacterial communities than the gradual addition; however, these communities appeared to converge once copper concentrations were approximately equal. Soil respiration in the abrupt treatment was initially suppressed but recovered after four months. Afterwards, respiration in both the gradual and abrupt treatments wavered between being below or equal to the ambient treatment. Overall, our study indicates that gradual and abrupt additions of copper can yield similar bacterial communities and respiration, but these responses may drastically vary until copper concentrations are equal. [ABSTRACT FROM AUTHOR]