A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments

Seasonal and Zonal Succession of Bacterial Communities in North Sea Salt Marsh Sediments

Benthic microbial communities of intertidal zones perform important biogeochemical processes and provide accessible nutrients for higher organisms. To unravel the ecosystem services of salt marsh microbial communities, we analyzed bacterial diversity and metabolic potential along the land–sea transition zone on seasonal scales on the German North Sea Island of Spiekeroog. Analysis of bacterial community was based on amplicon sequencing of 16S rRNA genes and –transcripts. Insights into potential community function were obtained by applying the gene prediction tool tax4fun2. We found that spatial variation of community composition was greater than seasonal variations. Alphaproteobacteria (15%), Gammaproteobacteria (17%) and Planctomycetes (11%) were the most abundant phyla across all samples. Differences between the DNA-based resident and RNA-based active communities were most pronounced within the Planctomycetes (17% and 5%) and Cyanobacteriia (3% and 12%). Seasonal differences were seen in higher abundance of Gammaproteobacteria in March 2015 (25%) and a cyanobacterial summer bloom, accounting for up to 70% of the active community. Taxonomy-based prediction of function showed increasing potentials for nitrification, assimilatory nitrate and sulfate reduction from sea to land, while the denitrification and dissimilatory sulfate reduction increased towards the sea. In conclusion, seasonal differences mainly occurred by blooming of individual taxa, while the overall community composition strongly corresponded to locations. Shifts in their metabolism could drive the salt marsh’s function, e.g., as a potential nitrogen sink.

Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function

Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.

Increasing Inundation Frequencies Enhance the Stochastic Process and Network Complexity of the Soil Archaeal Community in Coastal Wetlands

Coastal wetlands are experiencing frequent flooding because of global climate changes, such as the rising sea level. Despite the key role of archaea in soil biogeochemical cycles, the assembly processes and co-occurrence patterns of archaeal communities in coastal wetlands in response to increasing inundation frequencies remain elusive. In this study, we established an in situ mesocosm with an inundation frequency gradient to investigate the response of soil archaeal community toward increasing inundation frequencies in monocultures of Spartina alterniflora and a mangrove species, Kandelia obovata Both neutral community model and null model analyses suggested that stochastic processes are dominant in governing the archaeal community assembly and that the stochastic processes are enhanced with increasing inundation frequencies. Increasing inundation frequencies significantly increased the community niche width. Moreover, archaeal community in S. alterniflora soil displayed lower niche overlap and higher stochasticity than in K. obovata soil. Co-occurrence network analysis revealed that the network complexity increases with increase in the inundation frequencies. Soil water content is the most decisive factor influencing the archaeal communities. Overall, we found that increasing inundation frequencies enhance the stochastic processes and network complexity of the soil archaeal community in coastal wetlands. This study could enhance our understanding on the response of soil archaeal communities in coastal wetlands toward global change.IMPORTANCE Coastal wetlands, subjected to regular disturbances by periodic tides, are highly productive and important in the regulation of climate change. However, the assembly mechanisms and co-occurrence patterns of soil archaeal communities in coastal areas remain poorly known, especially for their responses to increasing inundation frequencies. In this study, we aimed at unraveling these uncertainties by studying typical estuarine ecosystems in southern China. We show that increasing inundation frequencies enhance the stochastic processes and network complexity of the soil archaeal community. This study offers a new path for an improved understanding of archaeal community assembly and species coexistence in coastal environments, with a special focus on the role of inundation frequency.

Dramatic change of bacterial assembly process and co-occurrence pattern in Spartina alterniflora salt marsh along an inundation frequency gradient

Exotic Spartina alterniflora has become widely distributed along most of the coastlines in China in a wide range of inundation frequencies. However, the assembly processes and co-occurrence patterns of the bacterial community in S. alterniflora wetlands under different inundation frequencies remain elusive. In this study, an in-situ mesocosm was established to investigate the changes in soil bacterial community. We found that soil water content was the most decisive factor in influencing the bacterial community. Balanced variation, rather than abundance gradients, accounted for the major shifts in bacterial communities and was significantly and positively correlated with the changes in water content, suggesting that species substitution was facilitated by the increased water content. Deterministic processes were dominant in community assembly, and a large degree of change in water content increased variable selection. Co-occurrence network revealed that increasing water content significantly decreased the average degree and the relative abundance of keystone species, resulting in a network with less complexity. Structural equation modelling suggests that increasing inundation frequency has strong impacts on bacterial community, primarily by altering water content, network degree, and the relative abundance of keystone species. Overall, our results illustrate that increasing inundation frequency significantly influences the bacterial community assembly processes and co-occurrence patterns.

Strong associations between plant genotypes and bacterial communities in a natural salt marsh

Although microbial communities have been shown to vary among plant genotypes in a number of experiments in terrestrial ecosystems, relatively little is known about this relationship under natural conditions and outside of select model systems. We reasoned that a salt marsh ecosystem, which is characterized by twice‐daily flooding by tides, would serve as a particularly conservative test of the strength of plant–microbial associations, given the high degree of abiotic regulation of microbial community assembly resulting from alternating periods of inundation and exposure. Within a salt marsh in the northeastern United States, we characterized genotypes of the foundational plant Spartina alterniflora using microsatellite markers, and bacterial metagenomes within marsh soil based on pyrosequencing. We found significant differences in bacterial community composition and diversity between bulk and rhizosphere soil, and that the structure of rhizosphere communities varied depending on the growth form of, and genetic variation within, the foundational plant S. alterniflora. Our results indicate that there are strong plant–microbial associations within a natural salt marsh, thereby contributing to a growing body of evidence for a relationship between plant genotypes and microbial communities from terrestrial ecosystems and suggest that principles of community genetics apply to this wetland type.

Bacterial Community Structure at the Microscale in Two Different Soils

The spatial distributions of bacteria in the soil matrix have a role in ecosystem function, for example, at the small scale, through gene transfer or xenobiotic degradation. Soil bacterial biogeography has been evidenced at the large scale, but data are scarce at the small scale. The objective of this work was to determine the spatial pattern of bacterial diversity, in spatially referenced microsamples, in order to define bacterial community spatial traits. Two soils with different physical structures, moderately aggregated (La Côte St André (LCSA)) or poorly aggregated (La Dombes (LD)), were studied. The spatial distribution of bacteria was studied in microsamples (diameter 3 mm) along 10- and 20-cm transects, with a taxonomic microarray. 16S rRNA gene sequencing was used to further study the spatial characteristics of the microbial communities in LD soil. The frequency-occupancy plot, in the LCSA and LD soils, using microarray and sequencing data, followed Hanski's core-satellite theory. The frequency-occupancy distribution plots obtained in two different soils showed bimodality and indicated that the microscale spatial distributions were different, particularly core taxa percentage. Core taxa are widespread and abundant, while satellite taxa are restricted in their distribution. The spread of satellite taxa was at a distance range larger than 5 cm, whereas the core taxa were distributed in a distance range less than 3 mm. Besides, there was a positive abundancy-occupancy relationship at this fine scale. It may be interesting to further evaluate the role of the different bacterial spatial distributions at the fine scale on soil function.

Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250–2000 μm) and micro-aggregates (53–250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.

The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond

The detection of biomarkers plays a central role in our effort to establish whether there is, or was, life beyond Earth. In this review, we address the importance of considering mineralogy in relation to the selection of locations and biomarker detection methodologies with characteristics most promising for exploration. We review relevant mineral-biomarker and mineral-microbe interactions. The local mineralogy on a particular planet reflects its past and current environmental conditions and allows a habitability assessment by comparison with life under extreme conditions on Earth. The type of mineral significantly influences the potential abundances and types of biomarkers and microorganisms containing these biomarkers. The strong adsorptive power of some minerals aids in the preservation of biomarkers and may have been important in the origin of life. On the other hand, this strong adsorption as well as oxidizing properties of minerals can interfere with efficient extraction and detection of biomarkers. Differences in mechanisms of adsorption and in properties of minerals and biomarkers suggest that it will be difficult to design a single extraction procedure for a wide range of biomarkers. While on Mars samples can be used for direct detection of biomarkers such as nucleic acids, amino acids, and lipids, on other planetary bodies remote spectrometric detection of biosignatures has to be relied upon. The interpretation of spectral signatures of photosynthesis can also be affected by local mineralogy. We identify current gaps in our knowledge and indicate how they may be filled to improve the chances of detecting biomarkers on Mars and beyond.

Spatial scales of interactions among bacteria and between bacteria and the leaf surface

Microbial life on plant leaves is characterized by a multitude of interactions between leaf colonizers and their environment. While the existence of many of these interactions has been confirmed, their spatial scale or reach often remained unknown. In this study, we applied spatial point pattern analysis to 244 distribution patterns of Pantoea agglomerans and Pseudomonas syringae on bean leaves. The results showed that bacterial colonizers of leaves interact with their environment at different spatial scales. Interactions among bacteria were often confined to small spatial scales up to 5-20 μm, compared to interactions between bacteria and leaf surface structures such as trichomes which could be observed in excess of 100 μm. Spatial point-pattern analyses prove a comprehensive tool to determine the different spatial scales of bacterial interactions on plant leaves and will help microbiologists to better understand the interplay between these interactions.

Bacterial community response to petroleum contamination and nutrient addition in sediments from a temperate salt marsh

Microbial communities play an important role in the biodegradation of organic pollutants in sediments, including hydrocarbons. The aim of this study was to evaluate the response of temperate salt marsh microbial communities to petroleum contamination, in terms of community structure, abundance and capacity to degrade hydrocarbons. Sediments un-colonized and colonized (rhizosediments) by Juncus maritimus, Phragmites australis and Triglochin striata were collected in a temperate estuary (Lima, NW Portugal), spiked with petroleum under variable nutritional conditions, and incubated for 15 days. Results showed that plant speciation emerged as the major factor for shaping the rhizosphere community structure, overriding the petroleum influence. Moreover, when exposed to petroleum contamination, the distinct salt marsh microbial communities responded similarly with (i) increased abundance, (ii) changes in structure, and (iii) decreased diversity. Communities, particularly those associated to J. maritimus and P. australis roots displayed a potential to degrade petroleum hydrocarbons, with degradation percentages between 15% and 41%, depending on sediment type and nutritional conditions. In conclusion, distinct salt marsh microbial communities responded similarly to petroleum contamination, but presented different pace, nutritional requirements, and potential for its biodegradation, which should be taken into account when developing bioremediation strategies.

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.

Diversity of prokaryotes associated with soils around coal-fire gas vents in MaNasi county of Xinjiang, China

Bacterial and archaeal diversity in surface soils of three coal-fire vents was investigated by T-RFLP analysis and clone libraries of 16S rRNA genes. Soil analysis showed that underground coal fires significantly influenced soil pH, moisture and NO(3) (-) content but had little effect on other elements, organic matter and available nutrients. Hierarchical cluster analysis showed that bacterial community patterns in the soils were very similar, but abundance varied with geographic distance. A clone library from one soil showed that the bacterial community was mainly composed of Firmicutes, Proteobacteria, Acidobacteria, Bacteroidetes, Planctomycetes, Actinobacteria, and unidentified groups. Of these, Firmicutes was the most abundant, accounting for 71.4 % of the clones, and was mainly represented by the genera Bacillus and Paenibacillus. Archaeal phylotypes were closely related to uncultivated species of the phyla Crenarchaeota (97.9 % of clones) and Thaumarchaeota (2.1 %). About 28 % of archaeal phylotypes were associated with ammonia oxidization, especially phylotypes that were highly related to a novel, ammonia-oxidizing isolate from the phylum Thaumarchaeota. These results suggested that microbial communities in the soils were diverse and might contain a large number of novel cultivable species with the potential to assimilate materials by heterotrophic metabolism at high temperature.

Factors driving potential ammonia oxidation in Canadian arctic ecosystems: does spatial scale matter?

Ammonia oxidation is a major process in nitrogen cycling, and it plays a key role in nitrogen limited soil ecosystems such as those in the arctic. Although mm-scale spatial dependency of ammonia oxidizers has been investigated, little is known about the field-scale spatial dependency of aerobic ammonia oxidation processes and ammonia-oxidizing archaeal and bacterial communities, particularly in arctic soils. The purpose of this study was to explore the drivers of ammonia oxidation at the field scale in cryosols (soils with permafrost within 1 m of the surface). We measured aerobic ammonia oxidation potential (both autotrophic and heterotrophic) and functional gene abundance (bacterial amoA and archaeal amoA) in 279 soil samples collected from three arctic ecosystems. The variability associated with quantifying genes was substantially less than the spatial variability observed in these soils, suggesting that molecular methods can be used reliably evaluate spatial dependency in arctic ecosystems. Ammonia-oxidizing archaeal and bacterial communities and aerobic ammonia oxidation were spatially autocorrelated. Gene abundances were spatially structured within 4 m, whereas biochemical processes were structured within 40 m. Ammonia oxidation was driven at small scales (<1m) by moisture and total organic carbon, whereas gene abundance and other edaphic factors drove ammonia oxidation at medium (1 to 10 m) and large (10 to 100 m) scales. In these arctic soils heterotrophs contributed between 29 and 47% of total ammonia oxidation potential. The spatial scale for aerobic ammonia oxidation genes differed from potential ammonia oxidation, suggesting that in arctic ecosystems edaphic, rather than genetic, factors are an important control on ammonia oxidation.

Spatial uncoupling of biodegradation, soil respiration, and PAH concentration in a creosote contaminated soil

Hotspots and coldspots of concentration and biodegradation of polycyclic aromatic hydrocarbons (PAHs) marginally overlapped at the 0.5-100 m scale in a creosote contaminated soil in southern Sweden, suggesting that concentration and biodegradation had little spatial co-variation. Biodegradation was substantial and its spatial variability considerable and highly irregular, but it had no spatial autocorrelation. The soil concentration of PAHs explained only 20-30% of the variance of their biodegradation. Soil respiration was spatially autocorrelated. The spatial uncoupling between biodegradation and soil respiration seemed to be governed by the aging of PAHs in the soil, since biodegradation of added 13C phenanthrene covaried with both soil respiration and microbial biomass. The latter two were also correlated with high concentrations of phospholipid fatty acids (PLFAs) that are common in gram-negative bacteria. However, several of the hotspots of biodegradation coincided with hotspots for the distribution of a PLFA indicative of fungal biomass.

Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities and the ecosystem services they provide. In the most comprehensive analysis of spatial patterns of microbial communities to date, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites in Burgundy, a 31,500 km(2) region of France, using a 16 × 16 km(2) sampling grid. At each sampling site, the abundance of total bacteria, crenarchaea, nitrate reducers, denitrifiers- and ammonia oxidizers were estimated by quantitative PCR and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time, and soil physico-chemical properties to the spatial distribution of the different communities were analyzed by canonical variation partitioning. Our results indicate that 43-85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of microbial communities at the landscape scale. The present study highlights the potential of a spatially explicit approach for microbial ecology to identify the overarching factors driving the spatial heterogeneity of microbial communities even at the landscape scale.

Negative effects of sample pooling on PCR-based estimates of soil microbial richness and community structure

In this study, we examined the effect of various pooling strategies on the characterization of soil microbial community composition and phylotype richness estimates. Automated ribosomal intergenic spacer analysis (ARISA) profiles were determined from soil samples that were (i) unpooled (extracted and amplified individually), (ii) pooled prior to PCR amplification, or (iii) pooled prior to DNA extraction. Regression analyses suggest that the less even the soil microbial community (i.e., low Shannon equitability, E(H)), the greater was the impact of either pooling strategy on microbial detection (R(2) = 0.766). For example, at a tropical rainforest site, which had the most uneven fungal (E(H) of 0.597) and bacterial communities (E(H) of 0.822), the unpooled procedure detected an additional 67 fungal and 115 bacterial phylotypes relative to either of the pooled procedures. Phylotype rarity, resulting in missed detection upon pooling, differed between the fungal and bacterial communities. Fungi were typified by locally abundant but spatially rare phylotypes, and the bacteria were typified by locally rare but spatially ubiquitous phylotypes. As a result, pooling differentially influenced plot comparisons, leading to an increase in similarity for the bacterial community and a decrease in the fungal community. In conclusion, although pooling reduces sample numbers and variability, it could mask a significant portion of the detectable microbial community, particularly for fungi due to their higher spatial heterogeneity.

Spatial structure in soil chemical and microbiological properties in an upland grassland

We characterised the spatial structure of soil microbial communities in an unimproved grazed upland grassland in the Scottish Borders. A range of soil chemical parameters, cultivable microbes, protozoa, nematodes, phospholipid fatty acid (PLFA) profiles, community-level physiological profiles (CLPP), intra-radical arbuscular mycorrhizal community structure, and eubacterial, actinomycete, pseudomonad and ammonia-oxidiser 16S rRNA gene profiles, assessed by denaturing gradient gel electrophoresis (DGGE) were quantified. The botanical composition of the vegetation associated with each soil sample was also determined. Geostatistical analysis of the data revealed a gamut of spatial dependency with diverse semivariograms being apparent, ranging from pure nugget, linear and non-linear forms. Spatial autocorrelation generally accounted for 40-60% of the total variance of those properties where such autocorrelation was apparent, but accounted for 97% in the case of nitrate-N. Geostatistical ranges extending from approximately 0.6-6 m were detected, dispersed throughout both chemical and biological properties. CLPP data tended to be associated with ranges greater than 4.5 m. There was no relationship between physical distance in the field and genetic similarity based on DGGE profiles. However, analysis of samples taken as close as 1 cm apart within a subset of cores suggested some spatial dependency in community DNA-DGGE parameters below an 8 cm scale. Spatial correlation between the properties was generally weak, with some exceptions such as between microbial biomass C and total N and C. There was evidence for scale-dependence in the relationships between properties. PLFA and CLPP profiling showed some association with vegetation composition, but DGGE profiling did not. There was considerably stronger association between notional sheep urine patches, denoted by soil nutrient status, and many of the properties. These data demonstrate extreme spatial variation in community-level microbiological properties in upland grasslands, and that despite considerable numeric ranges in the majority of properties, overarching controlling factors were not apparent.

Spatial heterogeneity of methanotrophs: a geostatistical analysis of pmoA-based T-RFLP patterns in a paddy soil

Despite numerous studies on methanotrophs, virtually nothing is known about their spatial heterogeneity in nature. These patterns, however, have strong influences on the interpretations made from analysing microbial processes and community structure. Here we report the first use of geostatistics to analyse the spatial heterogeneity of methanotrophs in a rice field soil (Vercelli, Italy). We used the gene encoding the particulate methane monooxygenase, pmoA, for terminal restriction fragment length polymorphism (T-RFLP) analysis. The profiles obtained were compared using a pseudo-variogram analysis to study autocorrelation as a function of distance. We demonstrated that there was no large-scale spatial structure at this study site, but a micro-scale spatial structure could not be excluded. A species accumulation curve with all terminal restriction fragments revealed that even 75 samples were insufficient to cover the diversity of methanotrophs in a rice field. However, a species accumulation curve of methanotrophs defined as operational taxonomic units validated from a clone library with 90% coverage demonstrated saturation after approximately 15 samples. The results of this study have consequences for studying the diversity and function of methanotrophs. In this agroecosystem population structure showed no spatial pattern implying that both a systematic and random sampling design would be adequate.

Fine scale patterns in microbial extracellular enzyme activity during leaf litter decomposition in a stream and its floodplain

Microorganisms mediate the decomposition of leaf-litter through the release of extracellular enzymes. The surfaces of decomposing leaves are both chemically and physically heterogeneous, and spatial patterns in microbial enzyme activity on the litter surface should provide insights into fine-scale patterns of leaf-litter decomposition. Platanus occidentalis leaves were collected from the floodplain of a third-order stream in northern Mississippi, enclosed in individual litter bags, and placed in the stream channel and in the floodplain. Replicate leaves were collected approximately monthly over a 9-month period and assayed for spatial variation in microbial extracellular enzyme activity and rates of organic matter (OM) decomposition. Spatial variation in enzyme activity was measured by sampling 96 small discs (5-mm diameter) cut from each leaf. Discs were assayed for the activity of enzymes involved in lignin (oxidative enzymes) and cellulose (beta-glucosidase, cellobiohydrolase) degradation. Rates of OM loss were greater in the stream than the floodplain. Activities of all enzymes displayed high variability in both environments, with severalfold differences across individual leaves, and replicate leaves varied greatly in their distribution of activities. Geostatistical analysis revealed no clear patterns in spatial distribution of activity over time or among replicates, and replicate leaves were highly variable. These results show that fine-scale spatial heterogeneity occurs on decomposing leaves, but the level of spatial variability varies among individual leaves at the measured spatial scales. This study is the first to use geostatistical analyses to analyze landscape patterns of microbial activity on decomposing leaf litter and in conjunction with studies of the microbial community composition and/or substrate characteristics, should provide key insights into the function of these processes.

Salt marsh sediment bacteria: their distribution and response to external nutrient inputs

A primary focus among microbial ecologists in recent years has been to understand controls on the distribution of microorganisms in various habitats. Much less attention has been paid to the way that environmental disturbance interacts with processes that regulate bacterial community composition. We determined how human disturbance affected the distribution and community structure of salt marsh sediment bacteria by using denaturing gradient gel electrophoresis of 16S rRNA in five different habitats in each of four salt marshes located in northeastern Massachusetts, USA. Two of the four marsh creeks were experimentally enriched 15 x above background by the addition of nitrogen and phosphorus fertilizers for two or more growing seasons. Our results indicate that extrinsic factors acting at broad scales do not influence the distribution of salt marsh sediment bacteria. Intrinsic factors, controlled by local-scale environmental heterogeneity, do play a role in structuring these sediment microbial communities, although nutrient enrichment did not have a consequential effect on the microbial community in most marsh habitats. Only in one habitat, a region of the marsh creek wall that is heavily colonized by filamentous algae, did we see any effect of fertilization on the microbial community structure. When similar habitats were compared among marshes, there was considerable convergence in the microbial community composition during the growing season. Environmental factors that correlated best with microbial community composition varied with habitat, suggesting that habitat-specific intrinsic forces are primarily responsible for maintaining microbial diversity in salt marsh sediments.

Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer

Heterogeneity in eukaryotic and bacteria community structure in surface and subsurface sediment samples downgradient of the Banisveld landfill (The Netherlands) was studied using a culturing-independent molecular approach. Along a transect covering the part of the aquifer most polluted by landfill leachate, sediment was sampled at 1-m depth intervals, until a depth of 5.5 m, at four distances from the landfill. Two drillings were placed in a nearby clean area as a reference. Denaturing gradient gel electrophoresis banding patterns revealed high bacterial and eukaryotic diversity and complex community structures. Bacteria and eukaryotic community profiles in polluted samples grouped different from those in clean samples. Bacteria community profiles in surface samples clustered together and separately from subsurface community profiles. Subsurface bacteria profiles clustered in a location-specific manner. Eukaryotic community structure did not significantly relate to distance from the landfill or depth. No significant spatial autocorrelation of bacteria or eukaryotic communities was observed over 1-m depth intervals per sampling location. Spatial heterogeneity in sediment-associated bacterial communities appears to be much larger than in groundwater. We discuss how on the one hand, spatial heterogeneity may complicate the assessment of microbial community structure and functioning, while on the other it may provide better opportunities for natural attenuation.

Biodegradation in contaminated aquifers: incorporating microbial/molecular methods

In order to evaluate natural attenuation in contaminated aquifers, there has been a recent recognition that a multidisciplinary approach, incorporating microbial and molecular methods, is required. Observed decreases in contaminant mass and identified footprints of biogeochemical reactions are often used as evidence of intrinsic bioremediation, but characterizing the structure and function of the microbial populations at contaminated sites is needed. In this paper, we review the experimental approaches and microbial methods that are available as tools to evaluate the controls on microbially mediated degradation processes in contaminated aquifers. We discuss the emerging technologies used in biogeochemical studies and present a synthesis of recent studies that serve as models of integrating microbiological approaches with more traditional geochemical and hydrogeologic approaches in order to address important biogeochemical questions about contaminant fate.

Relationships between sediment microbial communities and pollutants in two California salt marshes

Salt marshes are important ecosystems whose plant and microbial communities can alter terrestrially derived pollutants prior to coastal water discharge. However, knowledge regarding relationships between anthropogenic pollutant levels and salt marsh microbial communities is limited, and salt marshes on the West Coast of the United States are rarely examined. In this study, we investigated the relationships between microbial community composition and 24 pollutants (20 metals and 4 organics) in two California salt marshes. Multivariate ordination techniques were used to assess how bacterial community composition, as determined by terminal restriction fragment length polymorphism and phospholipid fatty acid analyses, was related to pollution. Sea urchin embryo toxicity measurements and plant tissue metabolite profiles were considered two other biometrics of pollution. Spatial effects were strongly manifested across marshes and across channel elevations within marshes. Utilizing partial canonical correspondence analysis, an ordination technique new to microbial ecology, we found that several metals were strongly associated with microbial community composition after accounting for spatial effects. The major patterns in plant metabolite profiles were consistent with patterns across microbial community profiles, but sea urchin embryo assays, which are commonly used to evaluate ecological toxicity, had no identifiable relationships with pollution. Whereas salt marshes are generally dynamic and complex habitats, microbial communities in these marshes appear to be relatively sensitive indicators of toxic pollutants.

Does disturbance and restoration of alpine grassland soils affect the genetic structure and diversity of bacterial and N2-fixing populations?

Responses of bacterial communities to disturbance and restoration processes were investigated on alpine grassland soil. Bulk soil, rhizosphere soil and two soil separates, i.e. sand-size (2000-200 microm) and silt-size (50-2 microm) were sampled from undisturbed grassland soil to soil under restoration for 1 month, 1 year, 4 years and 13 years after disturbance. Automated ribosomal intergenic spacer analysis (ARISA) and restriction fragment length polymorphism (RFLP) of nifH gene pools were used to assay genetic structure of the bacterial communities and N2-fixing guild. According to the distribution of ARISA band length in bacterial phyla, the dominance of ARISA bands below 400 bp showed that Gram-positive bacteria would be predominant in the studied grassland soil when not disturbed. Disturbance affected the genetic structure of bacterial community and of N2-fixing guild in relation to their location within the selected habitats. Shifts in IGS and nifH profiles of bulk soil metagenome were larger than those observed from sand-size- and silt-size-fractions, accounting for 40-50% of the variance in the profiles. Restoration of the genetic structure of telluric bacteria community and N2-fixing populations was found to be influenced by the spatial heterogeneity of the soil and niche diversification. Particular bacterial genetic structure within distinct habitats were evidenced and must be defined as subdivisions of the meta-community of bulk soil. Scale of soil microbial diversity/stability relationships is discussed with special attention to disconnected bacterial habitat compared with whole soil with multiple niches.

Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant-induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes.

Microbial biogeography: putting microorganisms on the map

We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.

Bacterial activity, community structure, and centimeter-scale spatial heterogeneity in contaminated soil

In an anthropogenically disturbed soil (88% sand, 8% silt, 4% clay), 150-mg samples were studied to examine the fine-scale relationship of bacterial activity and community structure to heavy metal contaminants. The soils had been contaminated for over 40 years with aromatic solvents, Pb, and Cr. Samples from distances of <1, 5, 15, and 50 cm over a depth range of 40-90 cm underwent a sequential analysis to determine metabolic potential (from 14C glucose mineralization), bacterial community structure [using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)], and total extractable Pb and Cr levels. Metabolic potential varied by as much as 10,000-fold in samples <1 cm apart; log-log plots of metal concentration and microbial metabolic potential showed no correlation with each other. Overall, metal concentrations ranged from 9 to 29,000 mg kg(-1) for Pb and from 3 to 8500 mg kg(-1) for Cr with small zones of high contamination present. All regions exhibited variable metal concentrations, with some soil samples having 30-fold differences in metal concentration in sites <1 cm apart. Geostatistical analysis revealed a strong spatial dependence for all three parameters tested (metabolic activity, Pb, and Cr levels) with a range up to 30 cm. Kriging maps showed that in zones of high metal, the corresponding metabolic activity was low suggesting that metals negatively impacted the microbial community. PCR-DGGE analysis revealed that diverse communities were present in the soils with a random distribution of phylotypes throughout the sampling zones. These results suggest the presence of spatially isolated microbial communities within the soil profile.

The effect of sample size in studies of soil microbial community structure

Replicate soil samples of 0.01, 0.1, 0.25, 1.0 and 10.0 g were taken from a single, large, homogenized sample from a field maintained as continuous meadow. The samples were processed for direct enumeration of bacterial cells and community structure assays by DGGE analysis of PCR-amplified 16S-rDNA fragments from whole community extracts. The goal was to determine the sample size or size range that produced the most consistent results (i.e., mean values) and the lowest variance. Enumeration data were analyzed by ANOVA, and the community composition fingerprints were analyzed by discriminant analysis (DA). Acceptable results were obtained for sample sizes from 0.1 to 1.0 g for both enumeration and community fingerprinting, but the size that yielded the best results for both measures was 0.25 g. The results suggest that for well homogenized silt loam soils with moderate organic matter concentrations, this sample size should produce high quality consistent results. For soils that differ in organic concentrations or clay content, a reconnaissance survey similar to the present examination is recommended.

A multivariate statistical approach to spatial representation of groundwater contamination using hydrochemistry and microbial community profiles

Managers of landfill sites are faced with enormous challenges when attempting to detect and delineate leachate plumes with a limited number of monitoring wells, assess spatial and temporal trends for hundreds of contaminants, and design long-term monitoring (LTM) strategies. Subsurface microbial ecology is a unique source of data that has been historically underutilized in LTM groundwater designs. This paper provides a methodology for utilizing qualitative and quantitative information (specifically, multiple water quality measurements and genome-based data) from a landfill leachate contaminated aquifer in Banisveld, The Netherlands, to improve the estimation of parameters of concern. We used a principal component analysis (PCA) to reduce nonindependent hydrochemistry data, Bacteria and Archaea community profiles from 16S rDNA denaturing gradient gel electrophoresis (DGGE), into six statistically independent variables, representing the majority of the original dataset variances. The PCA scores grouped samples based on the degree or class of contamination and were similar over considerable horizontal distances. Incorporation of the principal component scores with traditional subsurface information using cokriging improved the understanding of the contaminated area by reducing error variances and increasing detection efficiency. Combining these multiple types of data (e.g., genome-based information, hydrochemistry, borings) may be extremely useful at landfill or other LTM sites for designing cost-effective strategies to detect and monitor contaminants.

Brood size modifications affect plumage bacterial assemblages of European starlings

During reproduction, birds face trade-offs between time and energy devoted to parental effort and traits associated with self-maintenance. We manipulated brood sizes to investigate the effects of such trade-offs on feather bacterial densities and the structure of bacterial assemblages on feathers in adult European starlings, Sturnus vulgaris, and in vitro feather degradation. As predicted by a trade-off between parental effort and self-maintenance, we found that birds with enlarged broods had more free-living bacteria on their feathers than birds with reduced broods. Furthermore, we found a significant interaction between brood manipulation and original brood size on free-living bacterial densities suggesting that the trade-off is mediated by the adults' initial reproductive investment. In contrast, brood size manipulations had no significant effect on densities of attached bacteria. Using ribosomal intergenic spacer analysis (RISA), we demonstrated that brood manipulations significantly modified the structure (band pattern) of feather-degrading bacterial assemblages, but had no significant effect on their richness (number of bands) or the in vitro feather degradation. In vitro feather degradation varied in relation to the premanipulation brood size and positively with the richness of the feather degrading bacterial community. Besides brood manipulation effect, we found that ecological factors and individual traits, such as the age, the nest location or the capture date, shaped bacterial assemblages and feather degradation capacities.

Distribution of microbial communities associated with the dominant high marsh plants and sediments of the United States East Coast

Microbial communities in the sediment and associated with the dominant type of standing dead plant were collected from the high marsh zones of 10 sites along the eastern coast of the United States from Maine to Florida. Microbial community composition was examined using T-RFLP, and bacterial and fungal abundance was determined microscopically. Within the sediment, community composition was strongly correlated with latitude, indicating that biogeographical factors are important determinants of sediment community composition, whereas abundance was positively and strongly correlated with sediment organic matter content. A strong biogeographical effect was observed for both bacterial and fungal abundance on standing dead plants, but there was no clear relationship between community composition and latitude. Microbial community composition was more similar among plants of the same type (i.e., related plant species) suggesting that plant type (i.e., substrate quality) is primarily responsible for the determining community composition on standing dead plants.

Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field

To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties.