Peatland<i>Acidobacteria</i>with a dissimilatory sulfur metabolism

Hausmann, Bela; Pelikan, Claus; Herbold, Craig W.; Köstlbacher, Stephan; Albertsen, Mads; Eichorst, Stephanie A.; Rio, Tijana Glavina del; Huemer, Martin; Nielsen, Per Halkjær; Rattei, Thomas; Stingl, Ulrich; Tringe, Susannah G.; Trojan, Daniela; Wentrup, Cécilia; Woebken, Dagmar; Pester, Michael; Loy, Alexander

doi:10.1101/197269

Cited by 3 publications

(2 citation statements)

References 155 publications

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“…The N. marina genome also contains an alternative complex III (ACIII) module, which shares similarity with that from sulfur-reducing Acidobacteria [58]. (Table S5).…”

Section: Genome Analysismentioning

confidence: 99%

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

Bayer

Saito

McIlvin

et al. 2020

Preprint

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AbstractThe genus Nitrospira is the most widespread group of chemolithoautotrophic nitrite-oxidizing bacteria that thrive in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T represents the type genus and was isolated from the oceanic water column over 30 years ago, however, its genome has not yet been analyzed. Here, we analyzed the complete genome sequence of N. marina and performed select physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to combat oxidative, osmotic and UV-light induced stress and low dissolved pCO2, and is able to grow chemoorganotrophically on formate. We further investigated the metabolic response of N. marina to low (∼5.6 µM) O2 concentrations commonly encountered in marine environments with high nitrite concentrations. In response to O2-limited conditions, the abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high affinity cbb3-type terminal oxidase increased, suggesting a role in sustaining nitrite oxidation-driven autotrophy under O2 limitation. Additionally, a Cu/Zn-binding superoxide dismutase increased in abundance potentially protecting this putatively more O2-sensitive POR complex from oxidative damage. An increase in abundance of proteins involved in alternative energy metabolisms, including type 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides important insights into the metabolic diversity and niche differentiation of NOB in marine environments.

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“…The N. marina genome also contains an alternative complex III (ACIII) module, which shares similarity with that from sulfur-reducing Acidobacteria [58]. (Table S5).…”

Section: Genome Analysismentioning

confidence: 99%

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

Bayer

Saito

McIlvin

et al. 2020

Preprint

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“…Many of these functional traits are evolutionarily selected for in response to environmental conditions. In general, metagenomic studies of peatlands have been concentrated in the northern hemisphere, but have provided valuable insights into key functions and microbial populations involved in the biogeochemical cycles occurring in northern peat soils [17,23,25]. Metagenomic studies in tropical peatlands are rare and, to our knowledge, there is no published metagenomic study for peatlands found in the Amazon.…”

Section: Introductionmentioning

confidence: 99%

Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients

Pavia

Finn

Macedo‐Tafur

et al. 2022

Preprint

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The Pastaza-Maranon Foreland Basin (PMFB) holds the most extensive tropical peatland area in South America. PMFB peatlands store 7.07 Gt of organic carbon interacting with multiple microbial heterotrophic, methanogenic, and other oxic/anoxic respirations. Little is understood about the contribution of distinct microbial community members inhabiting tropical peatlands. Here, we studied the metagenomes of three geochemically distinct peatlands spanning minerotrophic, mixed, and ombrotrophic conditions. Using gene- and genome-centric approaches, we evaluate the functional potential of the underlying microbial communities. Abundance analyses shows significant differences in C, N, P, and S acquisition genes. Further, community interactions mediated by Toxin-antitoxin and CRISPR-Cas systems were enriched in oligotrophic soils, suggesting that non-metabolic interactions may exert additional controls in low nutrient environments. Similarly, we reconstructed 519 metagenome-assembled genomes spanning 28 phyla. Our analyses detail key differences across the nutrient gradient in the predicted microbial populations involved in degradation of organic matter, and the cycling of N and S. Notably, we observed differences in the nitrogen oxide (NO) reduction strategies between sites with high and low N2O fluxes and found phyla putatively capable of both NO and sulfate reduction. Our findings detail how gene abundances and microbial populations are influenced by geochemical differences in tropical peatlands.

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Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems

et al. 2018

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BackgroundMicroorganisms drive high rates of methanogenesis and carbon mineralization in wetland ecosystems. These signals are especially pronounced in the Prairie Pothole Region of North America, the tenth largest wetland ecosystem in the world. Sulfate reduction rates up to 22 μmol cm−3 day−1 have been measured in these wetland sediments, as well as methane fluxes up to 160 mg m−2 h−1—some of the highest emissions ever measured in North American wetlands. While pore waters from PPR wetlands are characterized by high concentrations of sulfur species and dissolved organic carbon, the constraints on microbial activity are poorly understood. Here, we utilized metagenomics to investigate candidate sulfate reducers and methanogens in this ecosystem and identify metabolic and viral controls on microbial activity.ResultsWe recovered 162 dsrA and 206 dsrD sequences from 18 sediment metagenomes and reconstructed 24 candidate sulfate reducer genomes assigned to seven phyla. These genomes encoded the potential for utilizing a wide variety of electron donors, such as methanol and other alcohols, methylamines, and glycine betaine. We also identified 37 mcrA sequences spanning five orders and recovered two putative methanogen genomes representing the most abundant taxa—Methanosaeta and Methanoregulaceae. However, given the abundance of Methanofollis-affiliated mcrA sequences, the detection of F420-dependent alcohol dehydrogenases, and millimolar concentrations of ethanol and 2-propanol in sediment pore fluids, we hypothesize that these alcohols may drive a significant fraction of methanogenesis in this ecosystem. Finally, extensive viral novelty was detected, with approximately 80% of viral populations being unclassified at any known taxonomic levels and absent from publicly available databases. Many of these viral populations were predicted to target dominant sulfate reducers and methanogens.ConclusionsOur results indicate that diversity is likely key to extremely high rates of methanogenesis and sulfate reduction observed in these wetlands. The inferred genomic diversity and metabolic versatility could result from dynamic environmental conditions, viral infections, and niche differentiation in the heterogeneous sediment matrix. These processes likely play an important role in modulating carbon and sulfur cycling in this ecosystem.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0522-4) contains supplementary material, which is available to authorized users.

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PeatlandAcidobacteriawith a dissimilatory sulfur metabolism

Cited by 3 publications

References 155 publications

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients

Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems

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