Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament

MacGregor, Barbara J.; Biddle, Jennifer F.; Harbort, Christopher J.; Matthysse, Ann G.; Teske, Andreas

doi:10.1016/j.margen.2013.08.001

Cited by 32 publications

(72 citation statements)

References 83 publications

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“…Many genes for the enzymes constituting the tricarboxylic acid cycle have been identified in other members of the family Beggiatoaceae, but some of the genes are missing from their draft genomes (MacGregor et al, 2013a). In the genome of T. ingrica, a full set of genes for tricarboxylic acid cycle enzymes was identified.…”

Section: Carbon Metabolismmentioning

confidence: 99%

“…Some bacteria harboring the ProU system can cope with increased environmental osmolarity by accumulating glycine betaine (Lucht and Bremer, 1994). A full set of genes for this system is also present in the genome of Orange Guaymas, obtained from marine sediment under the influence of hydrothermal fluid in the Guaymas Basin (MacGregor et al, 2013a). It was suggested that the habitat of Orange Guaymas is exposed to large fluctuation of temperature (McKay et al, 2012), presumably because of changes in supply of the hot water.…”

Section: Phosphorus Metabolismmentioning

confidence: 99%

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Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence

et al. 2014

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Large sulfur-oxidizing bacteria, which accumulate a high concentration of nitrate, are important constituents of aquatic sediment ecosystems. No representative of this group has been isolated in pure culture, and only fragmented draft genome sequences are available for these microorganisms. In this study, we successfully reconstituted the genome of Thioploca ingrica from metagenomic sequences, thereby generating the first complete genome sequence from this group. The Thioploca samples for the metagenomic analysis were obtained from a freshwater lake in Japan. A PCR-free paired-end library was constructed from the DNA extracted from the samples and was sequenced on the Illumina MiSeq platform. By closing gaps within and between the scaffolds, we obtained a circular chromosome and a plasmid-like element. The reconstituted chromosome was 4.8 Mbp in length with a 41.2% GC content. A sulfur oxidation pathway identical to that suggested for the closest relatives of Thioploca was deduced from the reconstituted genome. A full set of genes required for respiratory nitrate reduction to dinitrogen gas was also identified. We further performed a proteomic analysis of the Thioploca sample and detected many enzymes/proteins involved in sulfur oxidation, nitrate respiration and inorganic carbon fixation as major components of the protein extracts from the sample, suggesting that these metabolic activities are strongly associated with the physiology of T. ingrica in lake sediment.

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Section: Carbon Metabolismmentioning

confidence: 99%

Section: Phosphorus Metabolismmentioning

confidence: 99%

Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence

et al. 2014

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“…We identified Beggiatoaceae sequences with PhymmBL (40), using a confidence score cutoff of 0.65 (as determined by simulated taxonomic classification [see below; see also Fig. S1 in the supplemental material]) and a custom database amended with contigs from the following draft genomes: Beggiatoa alba B18LD (NCBI BioProject number 62137), "Beggiatoa orange Guaymas" (41,42), "Beggiatoa PS" and "Beggiatoa SS" (43), Thioploca araucae Tha-CCL (NCBI BioProject number 19383), and an unpublished Thiomargarita nelsonii genome. The taxonomic composition of the mRNA subset was determined by PhymmBL classification of a subset of 31 conserved universal phylogenetic marker genes (44).…”

Section: Methodsmentioning

confidence: 99%

“…The two longest contigs in the Beggiatoaceae bin are most similar to a recently characterized octaheme cytochrome that was proposed to be involved in the reduction of nitrogenous compounds in vacuolated marine Beggiatoa ("Ca. Maribeggiatoa") (41,42). This Beggiatoa protein, BOGUAY_0691, was found to have nitrite reductase, hydroxylamine oxidase, and hydrazine oxidase properties in vitro (42).…”

Section: Observations Of Cold Seeps and Large Sulfur-oxidizing Bacteriamentioning

confidence: 99%

“…This Beggiatoa protein, BOGUAY_0691, was found to have nitrite reductase, hydroxylamine oxidase, and hydrazine oxidase properties in vitro (42). Although its physiological role remains uncertain, MacGregor et al (41,42) argued that the latter two functions are unlikely and that BOGUAY_0691 probably serves as a nitrite reductase in vivo. Indeed, its expression under anoxic, sulfidic conditions in our incubation experiments is further evidence for its involvement in reductive rather than oxidative dissimilatory N metabolism.…”

Section: Observations Of Cold Seeps and Large Sulfur-oxidizing Bacteriamentioning

confidence: 99%

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Metatranscriptomic Analysis of Diminutive Thiomargarita-Like Bacteria (“Candidatus Thiopilula” spp.) from Abyssal Cold Seeps of the Barbados Accretionary Prism

Jones

Flood

Bailey

2015

Appl Environ Microbiol

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Large sulfur-oxidizing bacteria in the family Beggiatoaceae are important players in the global sulfur cycle. This group contains members of the well-known genera Beggiatoa, Thioploca, and Thiomargarita but also recently identified and relatively unknown candidate taxa, including "Candidatus Thiopilula" spp. and "Ca. Thiophysa" spp. We discovered a population of "Ca. Thiopilula" spp. colonizing cold seeps near Barbados at a ϳ4.7-km water depth. The Barbados population consists of spherical cells that are morphologically similar to Thiomargarita spp., with elemental sulfur inclusions and a central vacuole, but have much smaller cell diameters (5 to 40 m). Metatranscriptomic analysis revealed that when exposed to anoxic sulfidic conditions, Barbados "Ca. Thiopilula" organisms expressed genes for the oxidation of elemental sulfur and the reduction of nitrogenous compounds, consistent with their vacuolated morphology and intracellular sulfur storage capability. Metatranscriptomic analysis further revealed that anaerobic methane-oxidizing and sulfate-reducing organisms were active in the sediment, which likely provided reduced sulfur substrates for "Ca. Thiopilula" and other sulfur-oxidizing microorganisms in the community. The novel observations of "Ca. Thiopilula" and associated organisms reported here expand our knowledge of the globally distributed and ecologically successful Beggiatoaceae group and thus offer insight into the composition and ecology of deep cold seep microbial communities.T he family Beggiatoaceae contains the sulfur-oxidizing genera Beggiatoa, Thioploca, and Thiomargarita, including the largest known bacterium, Thiomargarita namibiensis, which can have cell diameters of Ͼ750 m (1, 2). Certain members of the Beggiatoaceae store nitrate in a large central vacuole, which supplies an electron acceptor to fuel anaerobic sulfur oxidation when oxygen is unavailable (2-4). As sulfide-oxidizing lithotrophs, members of the Beggiatoaceae thrive in diverse sulfidic environments (5, 6). Biomats constructed by these microorganisms are a conspicuous feature at oxygen minimum zones, hydrocarbon seeps, hydrothermal vents, and whale falls (see reference 7 and references therein), where they fill important roles in the global carbon and sulfur cycles. For example, the Beggiatoaceae are often primary producers in sulfidic marine sediments, where they act to conserve some of the potential energy present in sulfide that is produced during the anaerobic remineralization of organic carbon. As much as 80 to 95% of the sulfide produced during sulfate reduction escapes burial and is reoxidized, and much of this reoxidation occurs in the shallow sediment zone (8, 9). In addition to catalyzing important sulfur and nitrogen transformations, marine representatives of the Beggiatoaceae may even contribute to phosphate mineral formation (10-12). Furthermore, because of their large size and morphological complexity, Beggiatoa-and Thiomargarita-like cells have been identified in the fossil record and offer clues to microbial sul...

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Guaymas Basin, a Hydrothermal Hydrocarbon Seep Ecosystem

Teske

2020

Springer Oceanography

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Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament

Cited by 32 publications

References 83 publications

Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence

Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence

Metatranscriptomic Analysis of Diminutive Thiomargarita-Like Bacteria (“Candidatus Thiopilula” spp.) from Abyssal Cold Seeps of the Barbados Accretionary Prism

Guaymas Basin, a Hydrothermal Hydrocarbon Seep Ecosystem

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