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PubMed2006

Effect of methamidophos and urea application on microbial communities in soils as determined by microbial biomass and community level physiological profiles.

In this study, we evaluated the effect of the application by two agrochemicals, methamidophos (O,S-dimethyl phosphoroamidothioate) and urea, on microbial diversity in soil, using the combined approaches of soil microbial biomass analysis and community level physiological profiles (CLPPs). The results showed that both a low and a high level of methamidophos application (CS2 and CS3) and urea application (CS4) significantly decreased microbial biomass C (Cmic) by 41-83% compared with the control (CS1). The soil organic C (Corg) values of CS3 and CS4 were significantly higher and lower by 24% and 14%, respectively, than that of CS1. Similarly to Cmic, the values of Cmic/Corg of the three applied soils which decreased were lower by 31-84% than that of CS1. In contrast, the respiration activity of the three applied soils were significantly higher than the control. Agrochemical application also significantly increased the soil total of N and P (Ntol and Ptol) and decreased the Corg/Ntol and Corg/Ptol values. The CLPPs results showed that the AWCD (average well color development) of the three applied soils were significantly higher than that of CS1 during the incubation period. Substrate richness, Shannon and Simpson indices of microbial communities under chemical stresses, increased significantly. In addition, the CFU (colony-forming unit) numbers of methamidophos metabolized bacteria in CS2 and CS3 also increased significantly by 86.1% and 188.9% compared with that of CS1. The combined results suggest that agrochemicals reduce microbial biomass and enhance functional diversities of soil microbial communities; meanwhile, some species of bacteria may be enriched in soils under methamidophos stress.

Biomass↗
PubMed2001

CMEIAS: A Computer-Aided System for the Image Analysis of Bacterial Morphotypes in Microbial Communities.

A major challenge in microbial ecology is to develop reliable and facile methods of computer-assisted microscopy that can analyze digital images of complex microbial communities at single cell resolution, and compute useful quantitative characteristics of their organization and structure without cultivation. Here we describe a computer-aided interactive system to analyze the high degree of morphological diversity in growing microbial communities revealed by phase-contrast microscopy. The system, called "CMEIAS" (Center for Microbial Ecology Image Analysis System) consists of several custom plug-ins for UTHSCSA ImageTool, a free downloadable image analysis program operating on a personal computer in a Windows NT environment. CMEIAS uses various measurement features and two object classifiers to extract size and shape measurements of segmented, digital images of microorganisms and classify them into their appropriate morphotype. The first object classifier uses a single measurement feature to analyze relatively simple communities containing only a few morphotypes (e.g., regular rods, cocci, filaments). A second new hierarchical tree classifier uses an optimized subset of multiple measurement features to analyze significantly more complex communities containing greater morphological diversity than ever before possible. This CMEIAS shape classifier automatically categorizes each cell into one of 11 predominant bacterial morphotypes, including cocci, spirals, curved rods, U-shaped rods, regular straight rods, unbranched filaments, ellipsoids, clubs, rods with extended prostheca, rudimentary branched rods, and branched filaments. The training and testing images for development and evaluation of the CMEIAS classifier were obtained from 1,937 phase-contrast grayscale digital images of various diverse communities. The CMEIAS shape classifier had an accuracy of 96.0% on a training set of 1,471 cells and 97.0% on a test set of 4,270 cells representing all 11 bacterial morphotype classes, indicating that accurate classification of rich morphological diversity in microbial communities is now possible. An interactive edit feature was added to address the main sources of error in automatic shape classification, enabling the operator to inspect the assigned morphotype of each bacterium based on visual recognition of its distinctive pseudocolor, reassign it to another morphotype class if necessary, and add up to five other morphotypes to the classification scheme. The shape classifier reports on the number and types of different morphotypes present and the abundance among each of them, thus providing the data needed to compute the morphological diversity within the microbial community. An example of how CMEIAS can augment the analysis of microbial community structure is illustrated by studies of morphological diversity as an indicator of dynamic ecological succession following a nutrient shift-up perturbation in two continuously fed, anaerobic bioreactors with morphologically distinct start communities. Various steps to minimize the limitations of computer-assisted microscopy to classify bacterial morphotypes using CMEIAS are described. In summary, CMEIAS is an accurate, robust, flexible semiautomatic computing tool that can significantly enhance the ability to quantitate bacterial morphotype diversity and should serve as a useful adjunct to the analysis of microbial community structure. This first version of CMEIAS will be released as free, downloadable plug-ins so it can provide wide application in studies of microbial ecology.

Journal Article↗
PubMed2006

The influence of tropical plant diversity and composition on soil microbial communities.

There is growing interest in understanding the linkages between above- and belowground communities, and very little is known about these linkages in tropical systems. Using an experimental site at La Selva Biological Station, Costa Rica, we examined whether plant diversity, plant community composition, and season influenced microbial communities. We also determined whether soil characteristics were related to differences in microbial communities. Phospholipid fatty acid (PLFA) composition revealed that microbial community composition differed across a plant diversity gradient (plots contained 1, 3, 5, or over 25 species). Plant species identity also was a factor influencing microbial community composition; PLFA composition significantly varied among monocultures, and among three-species combinations that differed in plant species composition. Differences among treatments within each of these comparisons were apparent in all four sampling dates of the study. There was no consistent shift in microbial community composition between wet and dry seasons, although we did see significant changes over time. Of all measured soil characteristics, soil C/N was most often associated with changes in microbial community composition across treatment groups. Our findings provide evidence for human alteration of soil microbial communities via the alteration of plant community composition and diversity and that such changes are mediated in part by changes in soil carbon quality.

Bacteria↗
PubMed2004

Soil water content and organic carbon availability are major determinants of soil microbial community composition.

Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (-C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.

Agriculture↗
PubMed2002

Extensive profiling of a complex microbial community by high-throughput sequencing.

Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned cpn60 sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned cpn60 sequences from the four libraries were sequenced. Among the 1,125 cloned cpn60 sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.

Animals↗
PubMed2003

Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities.

Little is known about how the structure of microbial communities impacts carbon cycling or how soil microbial community composition mediates plant effects on C-decomposition processes. We examined the degradation of four (13)C-labeled compounds (starch, xylose, vanillin, and pine litter), quantified rates of associated enzyme activities, and identified microbial groups utilizing the (13)C-labeled substrates in soils under oaks and in adjacent open grasslands. By quantifying increases in non-(13)C-labeled carbon in microbial biomarkers, we were also able to identify functional groups responsible for the metabolism of indigenous soil organic matter. Although microbial community composition differed between oak and grassland soils, the microbial groups responsible for starch, xylose, and vanillin degradation, as defined by (13)C-PLFA, did not differ significantly between oak and grassland soils. Microbial groups responsible for pine litter and SOM-C degradation did differ between the two soils. Enhanced degradation of SOM resulting from substrate addition (priming) was greater in grassland soils, particularly in response to pine litter addition; under these conditions, fungal and Gram+ biomarkers showed more incorporation of SOM-C than did Gram- biomarkers. In contrast, the oak soil microbial community primarily incorporated C from the added substrates. More (13)C (from both simple and recalcitrant sources) was incorporated into the Gram- biomarkers than Gram+ biomarkers despite the fact that the Gram+ group generally comprised a greater portion of the bacterial biomass than did markers for the Gram- group. These experiments begin to identify components of the soil microbial community responsible for decomposition of different types of C-substrates. The results demonstrate that the presence of distinctly different plant communities did not alter the microbial community profile responsible for decomposition of relatively labile C-substrates but did alter the profiles of microbial communities responsible for decomposition of the more recalcitrant substrates, pine litter and indigenous soil organic matter.

Benzaldehydes↗
PubMed2006

Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils.

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA). Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function.

Bacteria↗
PubMed2006

Response of microbial community composition and function to soil climate change.

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying (13)C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes.

Bacteria↗
PubMed2025

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.

MOTIVATION: Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level and other methods such as quantitative polymerase chain reaction (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes. RESULTS: Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy and efficiency than other tools utilizing shotgun metagenomic sequencing reads. We demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. AVAILABILITY AND IMPLEMENTATION: Software is available at GitHub and implemented in C, R, and Bash. Software is supported on Linux and MacOS, with packages available on Bioconda or as a Docker container. The source code at the time of publication is also available on figshare at the doi: 10.6084/m9.figshare.29420780.

Mice↗
PubMed2004

Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community.

A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO(3)(-)-N mg of mixed-liquor volatile suspended solids (MLVSS)(-1) h(-1) to a steady-state value of 0.06 mg of NO(3)(-)-N mg of MLVSS(-1) h(-1) over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [(13)C]methanol to biomark the DNA of the denitrifiers. The extracted [(13)C]DNA and [(12)C]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [(13)C]DNA clone library was closely related to those of the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96 to 97% sequence identities), while the most abundant clone groups in the [(12)C]DNA clone library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera Hyphomicrobium and Paracoccus or the Saprospiraceae clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [(14)C]methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.

Autoradiography↗
PubMed2002

Adaption of a fragment analysis technique to an automated high-throughput multicapillary electrophoresis device for the precise qualitative and quantitative characterization of microbial communities.

The analysis of microbial communities is of increasing importance in life sciences and bioengineering. Traditional techniques of investigations like culture or cloning methods suffer from many disadvantages. They are unable to give a complete qualitative and quantitative view of the total amount of microorganisms themselves, their interactions among each other and with their environment. Obviously, the determination of static or dynamic balances among microorganisms is of fast growing interest. The generation of species specific and fluorescently labeled 16S ribosomal DNA (rDNA) fragments by the terminal restriction fragment length polymorphism (T-RFLP) technique is a suitable tool to overcome the problems other methods have. For the separation of these fragments polyacrylamide gel sequencers are preferred as compared to capillary sequencers using linear polymers until now because of their higher electrophoretic resolution and therefore sizing accuracy. But modern capillary sequencers, especially multicapillary sequencers, offer an advanced grade of automation and an increased throughput necessary for the investigation of complex communities in long-time studies. Therefore, we adapted a T-RFLP technique to an automated high-throughput multicapillary electrophoresis device (ABI 3100 Genetic Analysis) with regard to a precise qualitative and quantitative characterization of microbial communities.

Bacteria↗
PubMed2000

Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis.

Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses. html) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5' terminus of the user-specified primer to the 3' terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with terminal restriction fragment length polymorphisms.

Bacteria↗
PubMed2002

Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis.

Analysis of microbial community structure in complex environmental samples using nucleic acid techniques requires efficient unbiased DNA extraction procedures; however, humic acids and other contaminants complicate the isolation of PCR-amplifiable DNA from compost and other organic-rich samples. In this study, combinations of DNA extraction and purification methods were compared based on DNA yield, humic acid contamination, PCR amplifiability, and microbial community structure assessed by terminal restriction fragment length polymorphisms (TRFLP) of amplified 16S rRNA genes. DNA yield and humic acid contamination, determined by A230, varied significantly between extraction methods. Humic acid contamination of DNA obtained from compost decreased with increasing salt concentration in the lysis buffer. DNA purified by gel permeation chromatography (Sepharose 4B columns) gave satisfactory PCR amplification with universal eubacterial 16S rRNA gene primers only when A260/A280 ratios exceeded 1.5. DNA purified with affinity chromatography (hydroxyapatite columns), and showing A260/A280 ratios as high as 1.8, did not show consistently satisfactory PCR amplification using the same 16S rRNA primers. Almost all DNA samples purified by agarose gel electrophoresis showed satisfactory PCR amplification. Principal components analysis (PCA) of TRFLP patterns differentiated compost types based on the presence/absence of peaks and on the height of the peaks, but differences in TRFLP patterns were not appreciable between extraction methods that yielded relatively pure DNA. High levels of humic acid contamination in extracted DNA resulted in TRFLP patterns that were not consistent and introduced a bias towards lower estimates of diversity.

Bacteria↗
PubMed2005

A quantitative assay for linking microbial community function and structure of a naphthalene-degrading microbial consortium.

A comprehensive culture-independent assay, called Q-FAST, was developed for concurrent identification and quantification of active microorganisms involved a specific function in a given microbial community. The development of Q-FAST was achieved by integrating the concept of stable isotope probing technique into a new quantitative fingerprinting assay called real-time-t-RFLP for microbial community structure analysis. The Q-FAST was successfully validated by using a three-member artificial microbial community containing a known naphthalene-utilizing bacterium (Pseudomonas putida G7) and two nonnaphthalene-degrading bacteria (Escherichia coli and Bacillus thuringiensis). The application of Q-FAST to identify and quantify a guild of naphthalene-utilizing microorganisms in soils revealed the involvement of eight members, with six members relating to several phylogenetic groups of eubacteria (three in beta-proteobacteria, two in gamma-proteobacteria, and one in genera Intrasporangium of Gram-positive bacteria) and two members showing no close phylogenetic affiliation to any known bacterial sequences deposited in GenBank. The quantity of three members belonging to beta-proteobacteria accounted for 34% of total 16S rDNA copies measured from the "heavier" fraction of DNA that was contributed from the DNA of microorganisms capable of incorporating 13C-labeled naphthalene into their genetic biomarkers. The other five members composed 66% of total 16S rDNA copies of active naphthalene-utilizing populations measured. Offering a powerful tool for studying microbial ecology, Q-FAST thus opens a new avenue for deeper exploration of microbial-mediated processes, mainly the quantitative relationship between microbial diversity and microbial activity in a given environment.

Bacillus thuringiensis↗
PubMed2003

Diversity and dynamics of microbial communities in soils from agro-ecosystems.

Soil microbial communities are integrally involved in biogeochemical cycles and their activities are crucial to the productivity of terrestrial ecosystems. Despite the importance of soil microorganisms, little is known about the distribution of microorganisms in the soil or the manner in which microbial community structure responds to changes in land management. We investigated the structure of microbial communities in the soil over two years in a series of replicated plots, that included, cultivated fields, fields abandoned from cultivation and fields with no history of cultivation. Microbial community structure was examined by monitoring the relative abundance of ribosomal RNA (rRNA) from seven of the most common bacterial groups in soil (the Alpha and Beta Proteobacteria, Actinobacteria, Cytophagales, Planctomycetes, Verrucomicrobia and the Acidobacteria) and the Eukarya. These data reveal that soil microbial communities are dynamic, capable of significant change at temporal scales relative to seasonal events. However, despite temporal change in microbial community structure, the rRNA relative abundance of particular microbial groups is affected by the local environment such that recognizable patterns of community structure exist in relation to field management.

Agriculture↗
PubMed2005

Effects of microbial community diversity on the survival of Pseudomonas aeruginosa in the wheat rhizosphere.

Ecological theory suggests that microbial communities with greater microbial diversity would be less susceptible to invasion by potential opportunistic pathogens. We investigated whether the survival of the opportunistic pathogen Pseudomonas aeruginosa in the wheat rhizosphere would be affected by the presence of natural and constructed microbial communities of various diversity levels. Three levels of microbial community diversity were derived from wheat roots by a dilution/extinction approach. These wheat rhizosphere inocula, as well as a gnotobiotic microbial community consisting of seven culturable wheat rhizobacterial isolates, were introduced into the nutrient solution of hydroponically grown wheat plants on the day of planting. Phenotypic characterization of the culturable microbial communities on R2A medium, Shannon microbial diversity index, community-level physiological profiles, and terminal restriction fragment length polymorphisms were used to assess the varying microbial diversity levels. At day 7 the roots were invaded with P. aeruginosa and the number of P. aeruginosa colony forming units per root were measured at day 14. The average number of surviving P. aeruginosa cells was 3.52, 4.90, 7.18, 6.65 log(10) cfu/root in the high, medium, low, and gnotobiotic microbial community diversity level treatments, respectively. The invasibility of the rhizosphere communities by P. aeruginosa was inversely related to the level of diversity from the dilution extinction gradient. The gnotobiotic community did not confer protection against P. aeruginosa invasion. Although these data indicate that invasibility is inversely related to diversity, further study is needed to both reproduce these findings and define the specific mechanisms of the diversity effect.

Biodiversity↗
PubMed2006

Root controls on soil microbial community structure in forest soils.

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0-10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.

Plant Roots↗
PubMed2006

Modeling taxa-abundance distributions in microbial communities using environmental sequence data.

We show that inferring the taxa-abundance distribution of a microbial community from small environmental samples alone is difficult. The difficulty stems from the disparity in scale between the number of genetic sequences that can be characterized and the number of individuals in communities that microbial ecologists aspire to describe. One solution is to calibrate and validate a mathematical model of microbial community assembly using the small samples and use the model to extrapolate to the taxa-abundance distribution for the population that is deemed to constitute a community. We demonstrate this approach by using a simple neutral community assembly model in which random immigrations, births, and deaths determine the relative abundance of taxa in a community. In doing so, we further develop a neutral theory to produce a taxa-abundance distribution for large communities that are typical of microbial communities. In addition, we highlight that the sampling uncertainties conspire to make the immigration rate calibrated on the basis of small samples very much higher than the true immigration rate. This scale dependence of model parameters is not unique to neutral theories; it is a generic problem in ecology that is particularly acute in microbial ecology. We argue that to overcome this, so that microbial ecologists can characterize large microbial communities from small samples, mathematical models that encapsulate sampling effects are required.

Biodiversity↗