Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.

Dodsworth, Jeremy A.; Gevorkian, Jonathan; Despujos, Fairuz; Cole, Jesse; Murugapiran, Senthil K.; Hong, Ming; Li, Wen Jun; Zhang, Gengxin; Dohnálková, Alice; Hedlund, Brian P.

doi:10.1099/ijs.0.055855-0

Cited by 65 publications

(72 citation statements)

References 44 publications

(60 reference statements)

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“…The most abundant bacterial 16S rRNA gene transcript OTU in RSW communities (maximum 72.9% of total sequences at site RSW3) exhibited 91% sequence identity to the thermophilic and heterotrophic microaerophile Thermoflexus hugenholtzii (Dodsworth et al., ) within the order Chloroflexi (Figure ). The next most abundant OTU in these communities (56% total sequences at site RSW4) exhibited 93% sequence identity to the cyanobacterium Cyanothece sp.…”

Section: Resultsmentioning

confidence: 99%

“…Based on sequencing of transcripts of 16S rRNA genes from sediments and physiological inferences, populations putatively involved in H 2 oxidation in RSW include OTUs related to Thermoflexus hugenholtzii and Thermofilum sp. 1807‐2 (members of the orders Thermoflexales and Thermoproteales, respectively) (Dodsworth et al., ; Huber, Huber, & Stetter, ). Thermoflexus hugenholtzii is a facultative anaerobe and its genome encodes for at least one [NiFe]‐hydrogenase, which is classified as a Group 3c enzyme (Greening et al., ).…”

Section: Discussionmentioning

confidence: 99%

“…It is unclear whether T. hugenholtzii can reduce

{SO}_{4}^{2 -}

as its characterization did not include an examination of

{SO}_{4}^{2 -}

as a potential electron acceptor. That said, genes for the

{SO}_{4}^{2 -}

dissimilatory reduction pathway were not detected in the genome of T. hugenholtzii (Dodsworth et al., ). Nonetheless, it is still possible that the organism affiliated with T. hugenholtzii can respire

{SO}_{4}^{2 -}

given that the 16S rRNA gene transcripts obtained from RSW were only 91% identical to T. hugenholtzii .…”

Section: Discussionmentioning

confidence: 99%

“…Nonetheless, it is still possible that the organism affiliated with T. hugenholtzii can respire

{SO}_{4}^{2 -}

given that the 16S rRNA gene transcripts obtained from RSW were only 91% identical to T. hugenholtzii . Additionally, given that there is currently only one cultivated representative from this order (Dodsworth et al., ), known physiological diversity within this order may be limited. Thermofilum spp.…”

Section: Discussionmentioning

confidence: 99%

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Subsurface processes influence oxidant availability and chemoautotrophic hydrogen metabolism in Yellowstone hot springs

et al. 2018

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The geochemistry of hot springs and the availability of oxidants capable of supporting microbial metabolisms are influenced by subsurface processes including the separation of hydrothermal fluids into vapor and liquid phases. Here, we characterized the influence of geochemical variation and oxidant availability on the abundance, composition, and activity of hydrogen (H )-dependent chemoautotrophs along the outflow channels of two-paired hot springs in Yellowstone National Park. The hydrothermal fluid at Roadside East (RSE; 82.4°C, pH 3.0) is acidic due to vapor-phase input while the fluid at Roadside West (RSW; 68.1°C, pH 7.0) is circumneutral due to liquid-phase input. Most chemotrophic communities exhibited net rates of H oxidation, consistent with H support of primary productivity, with one chemotrophic community exhibiting a net rate of H production. Abundant H -oxidizing chemoautotrophs were supported by reduction in oxygen, elemental sulfur, sulfate, and nitrate in RSW and oxygen and ferric iron in RSE; O utilizing hydrogenotrophs increased in abundance down both outflow channels. Sequencing of 16S rRNA transcripts or genes from native sediments and dilution series incubations, respectively, suggests that members of the archaeal orders Sulfolobales, Desulfurococcales, and Thermoproteales are likely responsible for H oxidation in RSE, whereas members of the bacterial order Thermoflexales and the archaeal order Thermoproteales are likely responsible for H oxidation in RSW. These observations suggest that subsurface processes strongly influence spring chemistry and oxidant availability, which in turn select for unique assemblages of H oxidizing microorganisms. Therefore, these data point to the role of oxidant availability in shaping the ecology and evolution of hydrogenotrophic organisms.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…It is unclear whether T. hugenholtzii can reduce

{SO}_{4}^{2 -}

as its characterization did not include an examination of

{SO}_{4}^{2 -}

as a potential electron acceptor. That said, genes for the

{SO}_{4}^{2 -}

{SO}_{4}^{2 -}

given that the 16S rRNA gene transcripts obtained from RSW were only 91% identical to T. hugenholtzii .…”

Section: Discussionmentioning

confidence: 99%

“…Nonetheless, it is still possible that the organism affiliated with T. hugenholtzii can respire

{SO}_{4}^{2 -}

Section: Discussionmentioning

confidence: 99%

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Subsurface processes influence oxidant availability and chemoautotrophic hydrogen metabolism in Yellowstone hot springs

et al. 2018

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“…S1 in the supplemental material) from the GBS Calescamantes SAG coassembly. SAGs and isolate genomes representing other abundant populations in GBS included Calescamantes (JGI_2527291514), "Fervidibacteria" (JGI_0000001-G10), a novel crenarchaeota, "Geoarchaeota" (JGI_AAA471-L13), "Aigarchaeota" (JGI_2264867219), and the Thermoflexus hugenholtzii strain JAD2 draft genome (JGI_2140918011) (31). This approach provides multiple points of reference during training of the MLP algorithm.…”

Section: Methodsmentioning

confidence: 99%

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

Becraft

Dodsworth

Murugapiran

et al. 2016

Appl Environ Microbiol

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The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This "microbial dark matter" represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum "Calescamantes" (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O 2 , or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs.T he vast majority of the diversity of microbial life on Earth remains undiscovered; the core metabolisms of yet-uncultivated species, interguild interactions within natural and managed ecosystems, and the contributions of microbial populations to the geochemistry of the environment remain poorly understood (1, 2). There are currently over 60 bacterial and archaeal phylumlevel groups that have been observed through the use of 16S rRNA gene sequencing and phylogenetics, with over half containing no cultivated representatives (3). This so-called microbial dark matter comprises a substantial proportion of the tree of life and of microbial communities that likely play significant roles in biogeochemical cycles in a variety of environments (4-9).Metagenomic analyses of low-diversity microbial communities have yielded robust, near-complete genomic assemblies representative of the abundant populations, expanding the knowledge of the metabolic potential of predominant organisms in these ecosystems (10-14). Nucleotide word frequencies calculated from metagenomic contiguous assembled sequences (contigs) have been used to separate population-specific clusters, or "bins," from the community DNA pool (15-17), which has greatly advanced our understanding of the genomic diversity in natural environments and how populations differ between chemically distinct environments and along environmental gradients (18,19). Even using modern sequencing techniques, ...

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T hermoflexia

Dodsworth¹

2018

Bergey's Manual of Systematics of Archaea and Bacteria

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Thermoflexia (Ther.mo.fle'xi.a. N.L. n. Thermoflexus type genus of the order; L. suff. ‐ ia ending to denote a class; N.L. neut. pl. n. Thermoflexia the class of the genus Thermoflexus ). Chloroflexi / Thermoflexia Thermophilic. Cells form curved or bent filaments. 16S rRNA gene sequences are phylogenetically affiliated with members of the order Thermoflexales to the exclusion of other classes in the phylum Chloroflexi . Found in both terrestrial geothermal and marine hydrothermal environments. Currently, the class is represented by a single isolate, Thermoflexus hugenholtzii JAD2 T .

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Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.

Cited by 65 publications

References 44 publications

Subsurface processes influence oxidant availability and chemoautotrophic hydrogen metabolism in Yellowstone hot springs

Subsurface processes influence oxidant availability and chemoautotrophic hydrogen metabolism in Yellowstone hot springs

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

T hermoflexia

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