Metagenomic and metaproteomic analyses of Accumulibacter phosphatis‐enriched floccular and granular biofilm

Barr, Jeremy J.; Dutilh, Bas E.; Skennerton, Connor T.; Fukushima, Toshikazu; Hastie, Marcus L.; Gorman, Jeffrey J.; Tyson, Gene W.; Bond, Philip L.

doi:10.1111/1462-2920.13019

Cited by 53 publications

(35 citation statements)

References 86 publications

(123 reference statements)

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“…Only 32 proteins (3% of all identified proteins) showed significant fold changes, with P values of Ͻ0.05 (see Table S3 in the supplemental material). In comparison to other metaproteomic studies, where 10 to 15% of all identified proteins were significantly regulated (35,36), the number of regulated proteins in this study is distinctly small and implies a stable metaproteome profile of the rhizospheric community. Remarkably, more than 20% of these significantly regulated proteins were involved in PHA metabolism or the glyoxylate cycle and were also previously identified (25) (Fig.…”

Section: Resultscontrasting

confidence: 84%

Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism

Lünsmann

Kappelmeyer

Taubert

et al. 2016

Appl Environ Microbiol

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Constructed wetlands (CWs) are successfully applied for the treatment of waters contaminated with aromatic compounds. In these systems, plants provide oxygen and root exudates to the rhizosphere and thereby stimulate microbial degradation processes. Root exudation of oxygen and organic compounds depends on photosynthetic activity and thus may show day-night fluctuations. While diurnal changes in CW effluent composition have been observed, information on respective fluctuations of bacterial activity are scarce. We investigated microbial processes in a CW model system treating toluene-contaminated water which showed diurnal oscillations of oxygen concentrations using metaproteomics. Quantitative real-time PCR was applied to assess diurnal expression patterns of genes involved in aerobic and anaerobic toluene degradation. We observed stable aerobic toluene turnover by Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis was upregulated in these bacteria during the day, suggesting that they additionally feed on organic root exudates while reutilizing the stored carbon compounds during the night via the glyoxylate cycle. Although mRNA copies encoding the anaerobic enzyme benzylsuccinate synthase (bssA) were relatively abundant and increased slightly at night, the corresponding protein could not be detected in the CW model system. Our study provides insights into diurnal patterns of microbial processes occurring in the rhizosphere of an aquatic ecosystem. IMPORTANCEConstructed wetlands are a well-established and cost-efficient option for the bioremediation of contaminated waters. While it is commonly accepted knowledge that the function of CWs is determined by the interplay of plants and microorganisms, the detailed molecular processes are considered a black box. Here, we used a well-characterized CW model system treating toluenecontaminated water to investigate the microbial processes influenced by diurnal plant root exudation. Our results indicated stable aerobic toluene degradation by members of the Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis in these bacteria was higher during the day, suggesting that they additionally fed on organic root exudates and reutilized the stored carbon compounds during the night. Our study illuminates microbial processes occurring in the rhizosphere of an aquatic ecosystem. C onstructed wetlands (CWs) are well-established treatment systems for the bioremediation of contaminated waters (1), including industrial effluents originating from petroleum refineries and their associated contaminated sites (2, 3). Aromatic hydrocarbons present in those wastewaters can effectively be removed in CWs (4-7), largely driven by the interplay of plant physiology and microbial degradation processes in the rhizosphere (8, 9). As in any planted habitat, the rhizosphere of CWs is a complex environment with increased abundance and activity of microorganisms compared to those in the surrounding zones (10). It is shaped by the roots and plant-derived exu...

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Section: Resultscontrasting

confidence: 84%

Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism

Lünsmann

Kappelmeyer

Taubert

et al. 2016

Appl Environ Microbiol

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“…Here, isocitrate dehydrogenase was found NADP + dependent. This is consistent with the observation that most acetate consumers will use this conversion to produce NADPH for their anabolism (72) and confirms the protein annotation found in (64). Since PHA accumulation is now known to be NADH-preferring and without another sink of NADPH, the latter might accumulate anaerobically and thereby inhibit the isocitrate dehydrogenase reaction.…”

Section: Discussionsupporting

confidence: 92%

“…The discussion will be based on the observed high PAO enrichment of mainly Ca . Accumulibacter phosphatis clade I. Consequently, extrapolations of these results to Accumulibacter clade II or GAOs are speculative until further validation using respective environments for enrichments (10, 47, 61–64).…”

Section: Discussionmentioning

confidence: 96%

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Revealing metabolic flexibility ofCandidatusAccumulibacter phosphatis through redox cofactor analysis and metabolic network modeling

Silva

Olavarría

Gomes

et al. 2018

Preprint

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23Environmental fluctuations in the availability of nutrients lead to intricate 24 metabolic strategies. Candidatus Accumulibacter phosphatis, a polyphosphate 25 accumulating organism (PAO) responsible for enhanced biological phosphorus 26 removal (EBPR) from wastewater treatment systems, is prevalent in 27 aerobic/anaerobic environments. While the overall metabolic traits of these 28 bacteria are well described, the inexistence of isolates has led to controversial 29 conclusions on the metabolic pathways used. 30Here, we experimentally determined the redox cofactor preference of 31 different oxidoreductases in the central carbon metabolism of a highly enriched 32 Ca. A. phosphatis culture. Remarkably, we observed that the acetoacetyl-CoA 33 reductase engaged in polyhydroxyalkanoates (PHA) synthesis is NADH-34 preferring instead of the generally assumed NADPH dependency. Based on 35 previously published meta-omics data and the results of enzymatic assays, a 36 reduced central carbon metabolic network was constructed and used for 37 simulating different metabolic operating modes. In particular, scenarios with 38 different acetate-to-glycogen consumption ratios were simulated. For a high 39 ratio (i.e. more acetate), a polyphosphate-based metabolism arises as optimal 40 with a metabolic flux through the glyoxylate shunt. In case of a low acetate-to-41 glycogen ratio, glycolysis is used in combination with reductive branch of the 42 TCA cycle. Thus, optimal metabolic flux strategies will depend on the 43 environment (acetate uptake) and on intracellular storage compounds 44 availability (polyphosphate/glycogen). 45 This metabolic flexibility is enabled by the NADH-driven PHA synthesis. It 46 allows for maintaining metabolic activity under varying environmental substrate 47 3 conditions, with high carbon conservation and lower energetic costs compared 48 to NADPH dependent PHA synthesis. Such (flexible) metabolic redox coupling 49 can explain PAOs' competitiveness under oxygen-fluctuating environments. 50 IMPORTANCE 51 Here we demonstrate how microbial metabolism can adjust to a wide range 52 of environmental conditions. Such flexibility generates a selective advantage 53 under fluctuating environmental conditions. It can also explain the different 54 observations reported in PAO literature, including the capacity of Ca. 55Accumulibacter phosphatis to act like glycogen accumulating organisms 56 (GAO). These observations stem from slightly different experimental conditions 57 and controversy only arises when one assumes metabolism can only operate 58 in one single mode. Furthermore, we also show how the study of metabolic 59 strategies is possible when combining -omics data with functional assays and 60 modeling. Genomic information can only provide the potential of a 61 microorganism. The environmental context and other complementary 62 approaches are still needed to study and predict the functional application of 63 such metabolic potential. 64

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“…Recently, mass spectrometry based metaproteomic approaches are attracting particular attention for discovering microbial functions in mixed culture systems (Barr et al, 2015;Mosier et al, 2015;de Almeida et al, 2016;Salerno et al, 2016). mRNA levels can respond rapidly and sensitively to environmental conditions changes, while changes in protein abundances can be comparatively much slower (Zhu et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Evidence of differential adaptation to decreased temperature by anammox bacteria

Lin

Wang

et al. 2018

Environmental Microbiology

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Low temperature is recognized as one of the major barriers for the application of the anaerobic ammonium oxidation (anammox) process to treat mainstream wastewater. Studies are yet to reveal the underlying biological limitations and molecular mechanisms associated with the inhibition of low temperature on the anammox process. In this study, metaproteomics was used to examine proteome modulation patterns of the anammox community occurring at different temperatures. The anammox community remarkably altered their proteomes when the temperature decreased from 35 °C to 20 °C. This was especially for proteins involved in energy conversion, transcription and translation and inorganic ion transport. However, at 15 °C the anammox activities became distinctly inhibited, and there was evidence of energy limitations and severe stress in Candidatus Kuenenia and to a lesser degree in Candidatus Brocadia. Candidatus Jettenia exhibited more changes in its proteome at 15 °C. From the proteomes, at the lower temperatures there was evidence of stress caused by toxic nitrogen compounds or reactive oxygen species in the anammox bacteria. Hydroxylamine oxidoreductase (HAO)-like proteins and an oxidative stress response protein (a catalase) were in high abundance to potentially ameliorate these inhibitory effects. This study offers metaproteomic insight into the anammox community-based physiological response to decreasing temperatures.

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Metagenomic and metaproteomic analyses of Accumulibacter phosphatis‐enriched floccular and granular biofilm

Cited by 53 publications

References 86 publications

Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism

Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism

Revealing metabolic flexibility ofCandidatusAccumulibacter phosphatis through redox cofactor analysis and metabolic network modeling

Evidence of differential adaptation to decreased temperature by anammox bacteria

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