Diversity and spatial patterns in plant and animal communities are well documented as a positive-power law of a taxa-area relationship (TAR). At present little is known whether this also applies to soil microbial communities and whether long-term fertilization has an influence on the underlying microbial diversity. To test the effects of long-term fertilization on above-ground botanical diversity and below-ground microbial diversity, a nested sampling approach on Park Grass plots (12d& 11/2c) of Rothamsted Reseach in United Kingdom, both at ~;; pH 5 but with plant diversities of between 42 and 13 respectively were used. GeoChip 3.0, covering approximately 57, 000 gene sequences of 292 gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, was used to determine the gene area relationships for both functional and phylogenetic groups and the relationship to plant diversity. Our analysis indicated that the microbial communities were separated by different plant diversity based on DCA. The soil microbial diversity was in accord with plant diversity. Soil microbial community exhibited different z value with different plant diversity, z = 0.0449 with higher plant diversity and z = 0.0583 with lower plant diversity (P< 0.0001). These results suggest that …

Biodiversity and its responses to environmental changes is a central issue in ecology, and for society. Almost all microbial biodiversity researches focus on species richness and abundance but ignore the interactions among different microbial species/populations. However, determining the interactions and their relationships to environmental changes in microbial communities is a grand challenge, primarily due to the lack of information on the network structure among different microbial species/populations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene networks (fEGNs) is developed with the high throughput functional gene array hybridization data from the grassland microbial communities in a long-term FACE (Free Air CO2 Enrichment) experiment. Both fEGNs under elevated CO2 (eCO2) and ambient CO2 (aCO2) possessed general characteristics of many complex systems such as scale-free, small-world, modular and hierarchical. However, the topological structure of the fEGNs is distinctly different between eCO2 and aCO2, suggesting that eCO2 dramatically altered the interactions among different microbial functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen dynamics, and plant productivity, indicating the potential importance of network interactions in ecosystem functioning. Elucidating network interactions in microbial communities and their responses to environmental changes are …

The role of tetraheme cytochrome c3 (CycA) in the metabolism of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was investigated by deletion of the cycA gene using a marker-exchange deletion strategy. A highly abundant periplasmic cytochrome, CycA has the important function of transferring electrons from periplasmic hydrogenases (Hyd, Hyn, Hys) to transmembrane complexes which transport the electrons to the cytoplasm where sulfate is reduced. Previous studies have indicated that during its interaction with periplasmic hydrogenases, CycA is also involved in the reduction of toxic metals. Growth of the cycA mutant strain on lactate as the electron donor and sulfate as the terminal electron acceptor showed that, despite its abundance, CycA is not essential for DvH growth. However, the rate of growth of the mutant strain was significantly lower, and the extent of growth less, than rates and extents of growth of the wild type and complement strains on lactate/sulfate medium. This indicates that a portion of the electrons generated from cytoplasmic lactate oxidation are transported by CycA for energy production, possibly in a hydrogen cycling mechanism employed to generate ATP. Failure of the mutant strain to grow on either formate or H2, with sulfate or sulfite as electron acceptors, further …

While more and more studies are being conducted on the effects of global warming, little is known regarding the response of metabolic change of whole soil microbial communities to this phenomenon. In this study, functional gene changes at the mRNA level were analyzed by our new developed GeoChip 3.0. Soil samples were taken from a long-term climate warming experiment site, which has been conducted for ~;;8 years at the Kessler Farm Field Laboratory, a 137.6-ha farm located in the Central Redbed Plains, in McClain County, Oklahoma. The experiment uses a paired factorial design with warming as the primary factor nested with clipping as a secondary factor. An infrared heater was used to simulate global warming, and clipping was used to mimic mowing hay. Twelve 2m x 2m plots were divided into six pairs of warmed and control plots. The heater generates a constant output of ~;;100 Watts m-2 to approximately 2 oC increase in soil temperature above the ambient plots, which is at the low range of the projected climate warming by IPCC. Soil whole microbial communities? mRNA was extracted, amplified, labeled and hybridized with our GeoChip 3.0, a functional gene array covering genes involved in N, C, P, and …

Multiple sets of chemotaxis genes including three cheA homologs were identified in the genome sequence of the anaerobic bacterium Desulfovibrio vulgaris Hildenborough. Each CheA is a histidine kinase (HK) and part of a two component signal transduction system. Knock out mutants in the three cheA genes were created using single cross-over homologous recombination insertion. We studied the phenotypes of the cheA mutants in detail and discovered that ?cheA-3 has a non swarming/swimming phenotype both in the soft agar plates and Palleroni chamber assays. CheA-3 shows similarity to the Shewanella oneidensis CheA-3 and the Vibrio cholerae CheA-2 that are responsible for chemotaxis in the respective organisms. We did not find any morphological or structural differences between the three Delta cheA mutants and the wild type cells in electron microscopy. Our results from these studies are presented.

Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possess an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ~;;87 intergenic, while ~;;140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenic …

D. vulgaris Hildenborough has 72 response regulators. The Desulfovibrio are sulfate reducing bacteria that are important in the sulfur and carbon cycles in anoxic habitats. Its large number of two componenent systems are probably critical to its ability to sense and respond to its environment. Our goal is to map these RRs to the genes they regulate using a DNA-affinity-purification-chip (DAP-chip) protocol. First target determined usuing EMSA. A positive target was determined for as many RRs as possible using EMSA. Targets were selected based on gene proximity, regulon predictions and/or predicted sigma54 dependent promoters. qPCR was used to ensure that the target was enriched from sheared genomic DNA before proceeding to the DAP-chip.

In environments where the amount of the inorganic electron acceptors (oxygen, nitrate, sulfate, sulfur oroxidized metal ions (Fe3+;Mn4+) is insufficient for complete breakdown of organic matter, methane is formed as the major reduced end product. In such methanogenic environments organic acids are degraded by syntrophic associations of fermenting, acetogenic bacteria (e.g., sulfate-reducing bacteria (SRB) as"secondary fermenters") and methanogenic archaea. In these consortia, the conversion of lactate to acetate, CO2 and methane depends on the cooperating activities of both metabolically distinct microbial groups that are tightly linked by the need to maintain the exchanged metabolites (hydrogenandformate) at very low concentrations.

The environmentally relevant Desulfovibrio species are sulfate-reducing bacteria that are of interest in the bioremediation of heavy metal contaminated water. Among these, the genome of D. vulgaris Hildenborough encodes a large number of two component systems consisting of 72 putative response regulators (RR) and 64 putative histidinekinases (HK), the majority of which are uncharacterized. We classified the D. vulgaris Hildenborough RRs based on their output domains and compared the distribution of RRs in other sequenced Desulfovibrio species. We have successfully purified most RRs and several HKs as His-tagged proteins. We performed phospho-transfer experiments to verify relationships between cognate pairs of HK and RR, and we have also mapped a few non-cognate HK-RR pairs. Presented here are our discoveries from the Desulfovibrio RR categorization and results from the in vitro studies using purified His tagged D. vulgaris HKs and RRs.

Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we …

A 15 h ozonation was performed on bioremediated soil to remove recalcitrant residual oil. To monitor the survival of indigenous microorganisms in the soil during in-situ chemical oxidation(ISCO) culturing and a functional genearray, GeoChip, was used to examine the functional genes and structure of the microbial community during ozonation (0h, 2h, 4h, 6h, 10hand15h). Breakthrough ozonation decreased the population of cultivable heterotrophic bacteria by about 3 orders of magnitude. The total functional gene abundance and diversity decreased during ozonation, as the number of functional genes was reduced by 48percent after 15 h. However, functional genes were evenly distributed during ozonation as judged by the Shannon-Weaver Evenness index. A sharp decrease in gene number was observed in the first 6 h of ozonation followed by a slower decrease in the next 9 h, which was consistent with microbial populations measured by a culture based method. Functional genes involved in carbon, nitrogen, phosphors and sulfur cycling, metal resistance and organic remediation were detected in all samples. Though the pattern of gene categories detected was similar for all time points, hierarchica lcluster of all functional genes and major functional categories all showed a time-serial pattern. Bacteria, archaea and fungi decreased by 96.1percent, 95.1percent …

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Effective environmental management of DOE sites requires reliable prediction of reactive transport phenomena. A central issue in prediction of subsurface reactive transport is the impact of multiscale physical, chemical, and biological heterogeneity. Heterogeneity manifests itself through incomplete mixing of reactants at scales below those at which concentrations are explicitly defined (i.e., the numerical grid scale). This results in a mismatch between simulated reaction processes (formulated in terms of average concentrations) and actual processes (controlled by local concentrations). At the field scale, this results in apparent scale-dependence of model parameters and inability to utilize laboratory parameters in field models. Accordingly, most field modeling efforts are restricted to empirical estimation of model parameters by fitting to field observations, which renders extrapolation of model predictions beyond fitted conditions unreliable. The objective of this project is to develop a theoretical and computational framework for (1) connecting models of coupled reactive transport from pore-scale processes to field-scale bioremediation through a hierarchy of models that maintain crucial information from the smaller scales at the larger scales; and (2) quantifying the uncertainty that is introduced by both the upscaling process and uncertainty in physical parameters. One of the challenges of addressing scale-dependent effects of coupled processes in …

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The Environmental Molecular Sciences laboratory (EMSL) is a national scientific user facility operated by the Pacific Northwest National Laboratory (PNNL) for the U.S. Department of Energy's Office of Biological and Environmental Research. Located in Richland, Washington, EMSL offers researchers a comprehensive array of cutting-edge capabilities unmatched anywhere else in the world and access to the expertise of over 300 resident users--all at one location. EMSL's resources are available on a peer-reviewed proposal basis and are offered at no cost if research results are shared in the open literature. Researchers are encouraged to submit a proposal centered around one of EMSL's four Science Themes, which represent growing areas of research: (1) Geochemistry/Biogeochemistry and Subsurface Science; (2) Atmospheric Aerosol Chemistry; (3) Biological Interactions and Dynamics; and (4) Science of Interfacial Phenomena. To learn more about EMSL, visit www.emsl.pnl.gov.

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This paper examines three models used to estimate the maximum power (P{sub m}) of PV modules when the irradiance and PV cell temperature are known: (1) the power temperature coefficient model, (2) the PVFORM model, and (3) the bilinear interpolation model. A variation of the power temperature coefficient model is also presented that improved model accuracy. For modeling values of P{sub m}, an 'effective' plane-of-array (POA) irradiance (E{sub e}) and the PV cell temperature (T) are used as model inputs. Using E{sub e} essentially removes the effects of variations in solar spectrum and reflectance losses, and permits the influence of irradiance and temperature on model performance for P{sub m} to be more easily studied. Eq. 1 is used to determine E{sub e} from T and the PV module's measured short-circuit current (I{sub sc}). Zero subscripts denote performance at Standard Reporting Conditions (SRC).

This poster describes the Changes in Microbial Community Structure During Biostimulation for Uranium Reduction at Different Levels of Resolution

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