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See detailMicrobial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles
Wilmes, Paul UL; Bond, Philip L.

in Current Opinion in Microbiology (2009), 12(3), 310-317

Molecular techniques are providing unprecedented insights into the organismal and functional make-up of natural microbial consortia. Apart from nucleic acid based approaches, community proteomics has the ... [more ▼]

Molecular techniques are providing unprecedented insights into the organismal and functional make-up of natural microbial consortia. Apart from nucleic acid based approaches, community proteomics has the potential to provide a high-resolution representation of genotypic and phenotypic traits of distinct community members. With the recent availability of extensive genomic sequences from different microbial ecosystems, community proteomics has thus far been applied to activated sludge, acid mine drainage biofilms, freshwater and seawater, soil, symbiotic communities, and gut microbiota. Although these studies differ considerably in the depth of coverage of their respective protein complements, they highlight the power of community proteomics in providing a conclusive link between community composition, physilogy, function, interaction, ecology, and evolution. [less ▲]

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See detailThe dynamic genetic repertoire of microbial communities
Wilmes, Paul UL; Simmons, Sheri; Denef, Vincent J. et al

in FEMS Microbiology Reviews (2009), 33(1), 109-132

Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as ... [more ▼]

Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus-host dynamics in generating and shaping within-population diversity. [less ▲]

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See detailNatural acidophilic biofilm communities reflect distinct organismal and functional organization
Wilmes, Paul UL; Remis, Jonathan P.; Hwang, Mona et al

in ISME Journal (2009), 3(2), 266-270

Pellicle biofilms colonize the air-solution interface of underground acid mine drainage (AMD) streams and pools within the Richmond Mine (Iron Mountain, Redding, CA, USA). They exhibit relatively low ... [more ▼]

Pellicle biofilms colonize the air-solution interface of underground acid mine drainage (AMD) streams and pools within the Richmond Mine (Iron Mountain, Redding, CA, USA). They exhibit relatively low species richness and, consequently, represent good model systems to study natural microbial community structure. Fluorescence in situ hybridization combined with epifluorescent microscopy and transmission electron microscopy revealed spatially and temporally defined microbial assemblages. Leptospirillum group II dominates the earliest developmental stages of stream pellicles. With increasing biofilm maturity, the proportion of archaea increases in conjunction with the appearance of eukaryotes. In contrast, mature pool pellicles are stratified with a densely packed bottom layer of Leptospirillum group II, a less dense top layer composed mainly of archaea and no eukarya. Immunohistochemical detection of Leptospirillum group II cytochrome 579 indicates a high abundance of this protein at the interface of the biofilm with the AMD solution. Consequently, community architecture, which most likely develops in response to chemical gradients across the biofilm, is reflected at the functional gene expression level. [less ▲]

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See detailOrganismal and functional partitioning within natural microbial communities
Wilmes, Paul UL

Scientific Conference (2008, August)

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See detailMetaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment
Wilmes, Paul UL; Wexler, Margaret; Bond, Philip L.

in PLoS ONE (2008), 3(3), 1-2

Background: Through identification of highly expressed proteins from a mixed culture activated sludge system this study provides functional evidence of microbial transformations important for enhanced ... [more ▼]

Background: Through identification of highly expressed proteins from a mixed culture activated sludge system this study provides functional evidence of microbial transformations important for enhanced biological phosphorus removal (EBPR). Methodology/Principal Findings: A laboratory-scale sequencing batch reactor was successfully operated for different levels of EBPR, removing around 25, 40 and 55 mg/l P. The microbial communities were dominated by the uncultured polyphosphate-accumulating organism "Candidatus Accumulibacter phosphatis''. When EBPR failed, the sludge was dominated by tetrad-forming alpha-Proteobacteria. Representative and reproducible 2D gel protein separations were obtained for all sludge samples. 638 protein spots were matched across gels generated from the phosphate removing sludges. 111 of these were excised and 46 proteins were identified using recently available sludge metagenomic sequences. Many of these closely match proteins from "Candidatus Accumulibacter phosphatis'' and could be directly linked to the EBPR process. They included enzymes involved in energy generation, polyhydroxyalkanoate synthesis, glycolysis, gluconeogenesis, glycogen synthesis, glyoxylate/TCA cycle, fatty acid beta oxidation, fatty acid synthesis and phosphate transport. Several proteins involved in cellular stress response were detected. Conclusions/Significance: Importantly, this study provides direct evidence linking the metabolic activities of "Accumulibacter'' to the chemical transformations observed in EBPR. Finally, the results are discussed in relation to current EBPR metabolic models. [less ▲]

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See detailCommunity proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal
Wilmes, Paul UL; Andersson, Anders F.; Lefsrud, Mark G. et al

in ISME Journal (2008), 2(8), 853-864

Enhanced biological phosphorus removal (EBPR) selects for polyphosphate accumulating microorganisms to achieve phosphate removal from wastewater. We used high-resolution community proteomics to identify ... [more ▼]

Enhanced biological phosphorus removal (EBPR) selects for polyphosphate accumulating microorganisms to achieve phosphate removal from wastewater. We used high-resolution community proteomics to identify key metabolic pathways in 'Candidatus Accumulibacter phosphatis' (A. phosphatis)-mediated EBPR and to evaluate the contributions of co-existing strains within the dominant population. Overall, 702 proteins from the A. phosphatis population were identified. Results highlight the importance of denitrification, fatty acid cycling and the glyoxylate bypass in EBPR. Strong similarity in protein profiles under anaerobic and aerobic conditions was uncovered (only 3% of A. phosphatis-associated proteins exhibited statistically significant abundance differences). By comprehensive genome-wide alignment of 13 930 orthologous proteins, we uncovered substantial differences in protein abundance for enzyme variants involved in both core-metabolism and EBPR-specific pathways among the A. phosphatis population. These findings suggest an essential role for genetic diversity in maintaining the stable performance of EBPR systems and, hence, demonstrate the power of integrated cultivation-independent genomics and proteomics for the analysis of complex biotechnological systems. [less ▲]

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See detailNatural microbial assemblages reflect distinct organismal and functional partitioning
Wilmes, Paul UL

Scientific Conference (2007, December)

Detailed reference viewed: 39 (0 UL)
See detailEnvironmental proteomics, a new window on microbial community function
Wilmes, Paul UL

Scientific Conference (2006, July)

Detailed reference viewed: 39 (0 UL)
See detailMetaproteomic investigations of enhanced biological phosphorus removal in activated sludge
Wilmes, Paul UL

Scientific Conference (2006, June)

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See detailMetaproteomics: studying functional gene expression in microbial ecosystems
Wilmes, Paul UL

Scientific Conference (2006)

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See detailTowards exposure of elusive metabolic mixed-culture processes: the application of metaproteomic analyses to activated sludge
Wilmes, Paul UL; Bond, P. L.

in Water Science & Technology (2006), 54(1), 217-226

4th IWA Activated Sludge Population Dynamics Conference (ASPD4) Location: Gold Coast, AUSTRALIA Date: JUL 17-20, 2005 Sponsor(s): IWA Specialist Grp Activated Sudge Populat Dynam; Adv Wastewater ... [more ▼]

4th IWA Activated Sludge Population Dynamics Conference (ASPD4) Location: Gold Coast, AUSTRALIA Date: JUL 17-20, 2005 Sponsor(s): IWA Specialist Grp Activated Sudge Populat Dynam; Adv Wastewater management Ctr; Australian Water Assoc Abstract: Protein expression is a direct reflection of specific microbial activities in any ecosystem. In order to assess protein expression in mixed microbial communities, the feasibility of applying proteomic techniques to activated sludge samples has recently been demonstrated. We report the application of metaproteomics to two activated sludges from a laboratory-scale sequencing batch reactor with dissimilar phosphorus removal performances. Fluorescence in situ hybridization (FISH) revealed that the sludge with good enhanced biological phosphorus removal performance (EBPR) was dominated by Betaproteobacteria (65% of EUBMIX binding cells) and gave positive signals for the Rhodocyclus-type PAO specific probe (59%). The non-EBPR sludge was dominated by tetrad-forming Alphaproteobacteria (75%). With regard to the proteomic investigation, 630 individual protein spots were matched across the replicate groups of the anaerobic and aerobic phases of the EBPR sludge with 9.4% of all spots being statistically different between the two phases. The non-EBPR metaproteomic maps exhibited 590 matched spots with 14.7% statistical differences between the two phases. Overall, the non-EBPR sludge expressed around 30% more significant differences than the EBPR sludge. The comparison of protein expression in the two sludges showed that their metaproteomes were substantially different and this was reflected in their microbial community structures and metabolic transformations. [less ▲]

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See detailMetaproteomics: studying functional gene expression in microbial ecosystems
Wilmes, Paul UL; Bond, P. L.

in Trends in Microbiology (2006), 14(2), 92-97

The recent availability of extensive metagenomic sequences from various environmental microbial communities has extended the postgenomic era to the field of environmental microbiology. Although still ... [more ▼]

The recent availability of extensive metagenomic sequences from various environmental microbial communities has extended the postgenomic era to the field of environmental microbiology. Although still restricted to a small number of studies, metaproteomic investigations have revealed interesting aspects of functional gene expression within microbial habitats that contain limited microbial diversity. These studies highlight the potential of proteomics for the study of microbial consortia. However, the application of proteomic investigations to complex microbial assemblages such as seawater and soil still presents considerable challenges. Nonetheless, metaproteomics will enhance the understanding of the microbial world and link microbial community composition to function. [less ▲]

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See detailMetaproteomics: studying functional gene expression in microbial ecosystems
Wilmes, Paul UL

Scientific Conference (2005, September)

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See detailThe metaproteome: dynamic function of a complex microbial system
Wilmes, Paul UL

Scientific Conference (2005, January)

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See detailMetaproteomic investigations of enhanced biological phosphorus removal in activated sludge
Wilmes, Paul UL

Scientific Conference (2004, July)

Detailed reference viewed: 40 (0 UL)
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See detailThe application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms
Wilmes, Paul UL; Bond, P. L.

in Environmental Microbiology (2004), 6(9), 911-920

In the post-genomic era, the focus of numerous researchers has moved to studying the functional products of gene expression. In microbiology, these 'omic' approaches have largely been limited to pure ... [more ▼]

In the post-genomic era, the focus of numerous researchers has moved to studying the functional products of gene expression. In microbiology, these 'omic' approaches have largely been limited to pure cultures of microorganisms. Consequently, they do not provide information on gene expression in a complex mixture of microorganisms as found in the environment. Our method enabled the successful extraction and purification of the entire proteome from a laboratory-scale activated sludge system optimized for enhanced biological phosphorus removal, its separation by two-dimensional polyacrylamide gel electrophoresis and the mapping of this metaproteome. Highly expressed protein spots were excised and identified using quadrupole time-of-flight mass spectrometry with de novo peptide sequencing. The proteins isolated were putatively identified as an outer membrane protein (porin), an acetyl coenzyme A acetyltransferase and a protein component of an ABC-type branched-chain amino acid transport system. These proteins possibly stem from the dominant and uncultured Rhodocyclus-type polyphosphate-accumulating organism in the activated sludge. We propose the term 'metaproteomics' for the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time. [less ▲]

Detailed reference viewed: 144 (2 UL)