Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’

Hedlund, Brian P.; Murugapiran, Senthil K.; Alba, T. W.; Levy, Asaf; Dodsworth, Jeremy A.; Goertz, Gisele Braga; Ivanova, Natalia; Woyke, Tanja

doi:10.1016/j.mib.2015.06.008

Cited by 48 publications

(47 citation statements)

References 73 publications

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“…Hot springs are attractive environments for studying cellulose decomposition because they continue to be a source of unexplored genetic diversity [20,21], and the environmental conditions often mirror the pretreatment of lignocellulosic biomass before conversion to biofuels [22]. The hot spring sample used in the current study was collected from a pool in the GBS Geothermal Field.…”

Section: Capturing and Characterizing The Cellulose-bound Populationsmentioning

confidence: 99%

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

et al. 2019

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Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven singlecell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus 'Cellulosimonas argentiregionis'. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function.

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Section: Capturing and Characterizing The Cellulose-bound Populationsmentioning

confidence: 99%

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

et al. 2019

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“…These thermophilic specialists include but are not limited to members of the bacterial phyla Aquificae, Thermi, Thermotogae, Thermodesulfobacteria, and Dictyoglomi and thermophilic Crenarchaeota and Euryarchaeota. Many thermal systems also host abundant populations of yet-uncultivated "microbial dark matter" lineages of Bacteria and Archaea; for example, a meta-analysis of 16S rRNA gene censuses in terrestrial geothermal systems globally estimated high relative abundances of yet-uncultivated phyla ( x ¼ 16:1%), classes ( x ¼ 34:0%), orders ( x ¼ 42:1%), and families ( x ¼ 46:9%) (89).…”

Section: Diversity Of Moderately and Extremely Thermophilic Microorgamentioning

confidence: 99%

Life in High-Temperature Environments

Hedlund

Thomas

Dodsworth

et al. 2015

Manual of Environmental Microbiology

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“…Candidatus applies both to the organism as well as the potential new lineage. This allows us to combine environmentally derived genome sequence taxonomic classification with currently accepted nomenclature standards, as proposed by Hedlund et al (2015). In this study, we use full genome sequencing and metabolic reconstruction to elucidate the probable ecological importance of this newly identified candidate lineage.…”

Section: Introductionmentioning

confidence: 99%

Genomic Description of ‘Candidatus Abyssubacteria,’ a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes

2018

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The subsurface biosphere is a massive repository of fixed carbon, harboring approximately 90% of Earth’s microbial biomass. These microbial communities drive transformations central to Earth’s biogeochemical cycles. However, there is still much we do not understand about how complex subterranean microbial communities survive and how they interact with these cycles. Recent metagenomic investigation of deeply circulating terrestrial subsurface fluids revealed the presence of several novel lineages of bacteria. In one particular example, phylogenomic analyses do not converge on any one previously identified taxon; here we describe the first full genomic sequences of a new bacterial lineage within the candidate phylum Hydrogenedentes, ‘Candidatus Abyssubacteria.’ A global survey revealed that members of this proposed lineage are widely distributed in both marine and terrestrial subsurface environments, but their physiological and ecological roles have remained unexplored. Two high quality metagenome assembled genomes (SURF_5: 97%, 4%; SURF_17: 91% and 4% completeness and contamination, respectively) were reconstructed from fluids collected 1.5 kilometers below surface in the former Homestake gold mine—now the Sanford Underground Research Facility (SURF)—in Lead, South Dakota, United States. Metabolic reconstruction suggests versatile metabolic capability, including possible nitrogen reduction, sulfite oxidation, sulfate reduction and homoacetogenesis. This first glimpse into the metabolic capabilities of these cosmopolitan bacteria suggests that they are involved in key geochemical processes, including sulfur, nitrogen, and carbon cycling, and that they are adapted to survival in the dark, often anoxic, subsurface biosphere.

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Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’

Cited by 48 publications

References 73 publications

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

Life in High-Temperature Environments

Genomic Description of ‘Candidatus Abyssubacteria,’ a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes

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