Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment

Abstract Background Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris–microbe associations. Results Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences. Conclusion These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents.

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Unraveling Fe(II)-oxidizing mechanisms in a facultative Fe(II) oxidizer Sideroxydans lithotrophicus ES-1 via culturing, transcriptomics, and RT-qPCR

10.1101/2021.08.18.456919 ◽

2021 ◽

Author(s):

Nanqing Zhou ◽

Jessica L. Keffer ◽

Shawn W. Polson ◽

Clara S Chan

Keyword(s):

Gene Expression ◽

Carbon Fixation ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Sulfur Oxidation ◽

Complex Iii ◽

Initial Growth ◽

Gene Expression Response ◽

Oxidase Gene ◽

Thiosulfate Oxidation

Sideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or thiosulfate oxidation, in contrast to most other neutrophilic Fe(II)-oxidizing bacteria (FeOB) isolates. This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with RT-qPCR. We explored the long-term gene expression response at different growth phases (over days-week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II) even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO2 is an important electron sink for Fe(II) oxidation.

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Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and “Candidatus Thiothrix anitrata” sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation

Frontiers in Microbiology ◽

10.3389/fmicb.2021.760289 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nikolai V. Ravin ◽

Tatyana S. Rudenko ◽

Dmitry D. Smolyakov ◽

Alexey V. Beletsky ◽

Andrey L. Rakitin ◽

...

Keyword(s):

Core Genome ◽

Carbon Fixation ◽

Tricarboxylic Acid Cycle ◽

Sulfur Metabolism ◽

Sulfide Oxidation ◽

Calvin Cycle ◽

Sulfur Oxidation ◽

Rrna Gene ◽

Reduced Sulfur Compounds ◽

Hybridization Data

Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.

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Niche Partitioning in the Rimicaris Exoculata Holobiont: The Case of the First Symbiotic Zetaproteobacteria

10.21203/rs.3.rs-136571/v1 ◽

2020 ◽

Author(s):

Marie-Anne Cambon-Bonavita ◽

Johanne Aubé ◽

Valérie Cueff-Gauchard ◽

Julie Reveillaud

Keyword(s):

Hydrothermal Vents ◽

Carbon Fixation ◽

Iron Sulfide ◽

Hydrogen Oxidation ◽

Niche Partitioning ◽

Sulfur Oxidation ◽

Single Copy ◽

Rimicaris Exoculata ◽

Invertebrate Animals ◽

Close Relatives

Abstract Background Mutualistic symbioses between invertebrate animals and chemosynthetic bacteria are the basis of life in hydrothermal vent ecosystems. The shrimp Rimicaris exoculata , which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax, including the dominant Campylobacteria , Desulfobulbia (formerly Deltaproteobacteria ), Alpha proteobacteria , Gammaproteobacteria and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria . This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens in three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris –microbe associations. Results Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria , Desulfobulbia , Thiotrichaceae as well as some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences. Conclusion These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents.

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Bioleaching of Pyrite by Iron-Oxidizing Acidophiles under the Influence of Reactive Oxygen Species

Solid State Phenomena ◽

10.4028/www.scientific.net/ssp.262.372 ◽

2017 ◽

Vol 262 ◽

pp. 372-375

Author(s):

Dieu Huynh ◽

Sören Bellenberg ◽

Mario Vera Véliz ◽

Ansgar Poetsch ◽

Wolfgang Sand

Keyword(s):

Reactive Oxygen Species ◽

Biofilm Formation ◽

Carbon Fixation ◽

Iron Oxidation ◽

Reactive Oxygen ◽

Sulfur Oxidation ◽

Oxygen Species ◽

Proteomics Analysis ◽

Iron Dissolution ◽

Grain Sizes

After 24h of exposure to acidic media, pyrite generates reactive oxygen species (ROS). Freshly-crushed pyrite with grain sizes between 50-100 μm at a 5 % (w/v), pulp density generated 0.17 ± 0.01 mM H2O2, while 10% pyrite generated 0.29 ± 0.01 mM and 30 % pyrite generated approximately 0.83 ± 0.06 mM. These levels of H2O2 inhibit iron oxidation in iron-grown cells of AcidithiobacillusferrooxidansT but not in pyrite-grown cells. ROS originating from pyrite, which was incubated for 24 h in acidic medium, prohibited pyrite dissolution by iron-grown cells, while pyrite-grown cells were adapted to these concentrations of ROS. Periodical addition of 100 μM H2O2 to pyrite cultures inoculated with pyrite-grown cells did not lower iron dissolution as it was observed with iron-grown cells. By high throughput proteomics analysis, an increased expression of proteins related to oxidative stress management, iron-and sulfur oxidation systems, carbon fixation and biofilm formation was observed in biofilm cells grown on pyrite compared to iron-grown cells.

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Anaerobic sulfur oxidation underlies adaptation of a chemosynthetic symbiont to oxic-anoxic interfaces

10.1101/2020.03.17.994798 ◽

2020 ◽

Author(s):

Gabriela F. Paredes ◽

Tobias Viehboeck ◽

Raymond Lee ◽

Marton Palatinszky ◽

Michaela A. Mausz ◽

...

Keyword(s):

Carbon Fixation ◽

Isotope Labeling ◽

Sulfur Oxidation ◽

Carbon And Nitrogen ◽

Marine Habitats ◽

Cofactor Biosynthesis ◽

Stress Related Genes ◽

Effect Of Oxygen ◽

Chemoautotrophic Bacteria ◽

Anaerobic Sulfur Oxidation

AbstractChemosynthetic symbioses occur worldwide in marine habitats. However, physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by monocultures of thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. Here, by applying omics, Raman microspectroscopy and stable isotope labeling, we investigated the effect of oxygen on the metabolism of Candidatus Thiosymbion oneisti. Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation, the assimilation of organic carbon and polyhydroxyalkanoate (PHA) biosynthesis, as well as nitrogen fixation and urea utilization were upregulated in oxic conditions. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin and cofactor biosynthesis genes likely necessary to withstand its deleterious effects.Based on this first global physiological study of a chemosynthetic ectosymbiont, we propose that, in anoxic sediment, it proliferates by utilizing nitrate to oxidize reduced sulfur, whereas in superficial sediment it exploits aerobic respiration to facilitate assimilation of carbon and nitrogen to survive oxidative stress. Both anaerobic sulfur oxidation and its decoupling from carbon fixation represent unprecedented adaptations among chemosynthetic symbionts.

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Reconciling a Model of Core Metabolism with Growth Yield Predicts Biochemical Mechanisms and Efficiency for a Versatile Chemoautotroph

10.1101/717884 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jesse McNichol ◽

Stefan M. Sievert

Keyword(s):

Comparative Genomics ◽

Energy Conservation ◽

Carbon Fixation ◽

Tricarboxylic Acid Cycle ◽

Conceptual Modeling ◽

Growth Yield ◽

Sulfur Oxidation ◽

Growth Efficiency ◽

Biochemical Mechanisms ◽

Core Metabolism

AbstractObligately chemoautotrophic Campylobacteria dominate productivity in dark, sulfidic, and oxygen-depleted environments. However, biochemical mechanisms underlying their growth remain poorly known, limiting understanding of their physiology, ecology, and biogeochemical impact. In this study, we used comparative genomics, conceptual modeling of core metabolism, and chemostat growth yields to derive a model of energy conservation consistent with experimental data for the versatile chemoautotroph Sulfurimonas denitrificans. Our model rests on three core mechanisms: Firstly, to allow electrogenic sulfur-based denitrification, we predict that the campylobacterial-type sulfur oxidation enzyme complex must donate electrons to the membrane quinone pool, possibly via a sulfide:quinone oxidoreductase. Secondly, to account for the unexpectedly low growth efficiency of aerobic sulfur oxidation compared to denitrification, we posit the high-affinity campylobacterial-type cbb3 cytochrome c oxidase has a relatively low H+/e− of 1, likely due to a lack of proton pumping under physiological conditions. Thirdly, we hypothesize that reductant for carbon fixation by the reverse tricarboxylic acid cycle is produced by a non-canonical complex I that reduces both ferredoxin and NAD(P)H. This complex is conserved among related Campylobacteria and may have allowed for the radiation of organisms like S. denitrificans into sulfur-rich environments that became available after the great oxidation event. Our theoretical model has two major implications. Firstly, it sets the stage for future experimental work by providing testable hypotheses about the physiology, biochemistry, and evolution of chemoautotrophic Campylobacteria. Secondly, it provides constraints on the carbon fixation potential of chemoautotrophic Campylobacteria in sulfidic environments worldwide by predicting theoretical ranges of chemosynthetic growth efficiency.SignificanceChemoautotrophic Campylobacteria are abundant in many low-oxygen, high-sulfide environments where they contribute significantly to dark carbon fixation. Although the overall redox reactions they catalyze are known, the specific biochemical mechanisms that support their growth are mostly unknown. Our study combines conceptual modeling of core metabolic pathways, comparative genomics, and measurements of physiological growth yield in a chemostat to infer the most likely mechanisms of chemoautotrophic energy conservation in the model organism Sulfurimonas denitrificans. The hypotheses proposed herein are novel, experimentally falsifiable, and will guide future biochemical, physiological, and environmental modelling studies. Ultimately, investigating the core mechanisms of energy conservation will help us better understand the evolution and physiological diversification of chemoautotrophic Campylobacteria and their role in modern ecosystems.

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Genome-reconstruction for eukaryotes from complex natural microbial communities

10.1101/171355 ◽

2017 ◽

Cited By ~ 4

Author(s):

Patrick T. West ◽

Alexander J. Probst ◽

Igor V. Grigoriev ◽

Brian C. Thomas ◽

Jillian F. Banfield

Keyword(s):

Organic Carbon ◽

Microbial Communities ◽

Environmental Samples ◽

Carbon Fixation ◽

Sulfur Oxidation ◽

Metabolic Potential ◽

Microbial Eukaryotes ◽

Sequence Identification ◽

Ecosystem Studies ◽

Almost All

AbstractMicrobial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a kmer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.

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Niche Partitioning in the Rimicaris Exoculata Holobiont: The Case of the First Symbiotic Zetaproteobacteria

10.21203/rs.3.rs-33129/v1 ◽

2020 ◽

Author(s):

Marie-Anne Cambon-Bonavita ◽

Johanne Aubé ◽

Valérie Cueff-Gauchard ◽

Julie Reveillaud

Keyword(s):

Hydrothermal Vents ◽

Carbon Fixation ◽

Iron Sulfide ◽

Hydrogen Oxidation ◽

Niche Partitioning ◽

Extraction Procedure ◽

Sulfur Oxidation ◽

Rimicaris Exoculata ◽

Invertebrate Animals ◽

Close Relatives

Abstract BackgroundMutualistic symbioses between invertebrate animals and chemosynthetic bacteria are at the basis of Life in hydrothermal vent ecosystems. The shrimp Rimicaris exoculata, which dominates animal fauna along the Mid Atlantic Ridge, houses in its cephalothorax a complex bacterial community including Campylobacteria, Gamma- Delta- and some recently discovered iron oxyhydroxides-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane and hydrogen as energy sources. Here, we used a DNA extraction procedure adapted to recalcitrant embedded bacteria and generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic community. We aimed reconstructing symbiotic genomes from specimen collected in three geochemically contrasted vent fields, TAG, Rainbow and Snake Pit to unravel the specificity, variability and adaptation of host-microbes associations.ResultsUsing these data we were able to reconstruct 49 high quality metagenome-assembled genomes (MAGs) from TAG and Rainbow vents fields. Most critically, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (ANI < 77% from the closest relative Ghiorsea bivora isolated from TAG and <88% between each other), suggesting potential novel species. Genes for CBB carbon fixation, iron and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and quorum sensing as well as multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts that co-exist in a single shrimp at both basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further insights into the seemingly functional redundancy between those epibionts revealed important differences. ConclusionThese data highlight microniche partitioning in the Rimicaris holobiont and confirm recent works that show functional diversity enables multiple symbiont strains to coexist in animals from hydrothermal vents.

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Draft Genome Sequence of a Psychrotolerant Sulfur-Oxidizing Bacterium, Sulfuricella denitrificans skB26, and Proteomic Insights into Cold Adaptation

Applied and Environmental Microbiology ◽

10.1128/aem.01349-12 ◽

2012 ◽

Vol 78 (18) ◽

pp. 6545-6549 ◽

Cited By ~ 27

Author(s):

Tomohiro Watanabe ◽

Hisaya Kojima ◽

Manabu Fukui

Keyword(s):

Genome Sequence ◽

Cold Adaptation ◽

Ribosomal Proteins ◽

Carbon Fixation ◽

Draft Genome ◽

Sulfur Oxidation ◽

Draft Genome Sequence ◽

Trna Genes ◽

Rna Helicases ◽

Content Type

ABSTRACTExcept for several conspicuous cases, very little is known about sulfur oxidizers living in natural freshwater environments.Sulfuricella denitrificansskB26 is a psychrotolerant sulfur oxidizer recently isolated from a freshwater lake as a representative of a new genus in the classBetaproteobacteria. In this study, an approximately 3.2-Mb draft genome sequence of strain skB26 was obtained. In the draft genome, consisting of 23 contigs, a single rRNA operon, 43 tRNA genes, and 3,133 coding sequences were identified. The identified genes include those required for sulfur oxidation, denitrification, and carbon fixation. Comparative proteomic analysis was conducted to assess cold adaptation mechanisms of this organism. From cells grown at 22°C and 5°C, proteins were extracted for analysis by nano-liquid chromatography–electrospray ionization–tandem mass spectrometry. In the cells cultured at 5°C, relative abundances of ribosomal proteins, cold shock proteins, and DEAD/DEAH box RNA helicases were increased in comparison to those at 22°C. These results suggest that maintenance of proper translation is critical for growth under low-temperature conditions, similar to the case for other cold-adapted prokaryotes.

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