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See detailMechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.
Laloo, Andrew E.; Wei, Justin; Wang, Dongbo et al

in Environmental science & technology (2018), 52(9), 5386-5397

Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of ... [more ▼]

Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of wastewater treatment processes (WWTPs), nitrite-oxidizing bacteria (NOB) are more susceptible to FNA compared to ammonia-oxidizing bacteria (AOB). This selective inhibition of NOB over AOB in WWTPs bypasses nitrate production and improves the efficiency and costs of the nitrogen removal process in both the activated sludge and anaerobic ammonium oxidation (Anammox) system. However, the molecular mechanisms governing this atypical tolerance of AOB to FNA have yet to be understood. Herein we investigate the varying effects of the antimicrobial FNA on activated sludge containing AOB and NOB using an integrated metagenomics and label-free quantitative sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) metaproteomic approach. The Nitrosomonas genus of AOB, on exposure to FNA, maintains internal homeostasis by upregulating a number of known oxidative stress enzymes, such as pteridine reductase and dihydrolipoyl dehydrogenase. Denitrifying enzymes were upregulated on exposure to FNA, suggesting the detoxification of nitrite to nitric oxide. Interestingly, proteins involved in stress response mechanisms, such as DNA and protein repair enzymes, phage prevention proteins, and iron transport proteins, were upregulated on exposure to FNA. In addition enzymes involved in energy generation were also upregulated on exposure to FNA. The total proteins specifically derived from the NOB genus Nitrobacter was low and, as such, did not allow for the elucidation of the response mechanism to FNA exposure. These findings give us an understanding of the adaptive mechanisms of tolerance within the AOB Nitrosomonas to the biocidal agent FNA. [less ▲]

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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 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 (The) (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 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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