Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria

Iino, Takao; Mori, Koji; Uchino, Yuichi; Nakagawa, Tatsunori; Harayama, Shigeaki; Suzuki, Ken‐ichiro

doi:10.1099/ijs.0.012484-0

Cited by 244 publications

(152 citation statements)

References 41 publications

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“…Although it was previously expected to be a chlorophototroph because all other known Chlorobiales spp. are photolithoautotrophs , the recent discovery of a non-phototrophic member of the Chlorobi, Ignavibacterium album (Iino et al, 2009), made this assumption questionable. These findings about its photosynthesis genes being highly transcribed strongly suggest that Chlorobiales spp.…”

Section: Solid-3 Sequencing and Transcription Of Photosynthesis Genesmentioning

confidence: 99%

Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat

et al. 2011

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The phototrophic microbial mat community of Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, was studied by metatranscriptomic methods. RNA was extracted from mat specimens collected at four timepoints during light-to-dark and dark-to-light transitions in one diel cycle, and these RNA samples were analyzed by both pyrosequencing and SOLiD technologies. Pyrosequencing was used to assess the community composition, which showed that B84% of the rRNA was derived from members of four kingdoms Cyanobacteria, Chloroflexi, Chlorobi and Acidobacteria. Transcription of photosynthesis-related genes conclusively demonstrated the phototrophic nature of two newly discovered populations; these organisms, which were discovered through metagenomics, are currently uncultured and previously undescribed members of Chloroflexi and Chlorobi. Data sets produced by SOLiD sequencing of complementary DNA provided 4100-fold greater sequence coverage. The much greater sequencing depth allowed transcripts to be detected from B15 000 genes and could be used to demonstrate statistically significant differential transcription of thousands of genes. Temporal differences for in situ transcription patterns of photosynthesis-related genes suggested that the six types of chlorophototrophs in the mats may use different strategies for maximizing their solar-energy capture, usage and growth. On the basis of both temporal pattern and transcript abundance, intra-guild gene expression differences were also detected for two populations of the oxygenic photosynthesis guild. This study showed that, when community-relevant genomes and metagenomes are available, SOLiD sequencing technology can be used for metatranscriptomic analyses, and the results suggested that this method can potentially reveal new insights into the ecophysiology of this model microbial community.

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Section: Solid-3 Sequencing and Transcription Of Photosynthesis Genesmentioning

confidence: 99%

Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat

et al. 2011

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“…Hence, either there is a very rapid microbial turnover of methane, which would result in low in situ concentrations, or oxidation of 13 C-and 14 C-depleted organic carbon seems a more plausible explanation, one that is further supported by the molecular data. Indeed, bacteria of the family Ignavibacteriaceae, a major group in Group 3 wells, are chemoorganotrophs growing on carbohydrate fermentation (Iino et al, 2010).…”

Section: Biogeochemical Processes Affecting Group 3 Wellsmentioning

confidence: 99%

Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages

Nowak

Schwab

Lazar

et al. 2017

Hydrol. Earth Syst. Sci.

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Abstract. Isotopes of dissolved inorganic carbon (DIC) are used to indicate both transit times and biogeochemical evolution of groundwaters. These signals can be complicated in carbonate aquifers, as both abiotic (i.e., carbonate equilibria) and biotic factors influence the δ 13 C and 14 C of DIC. We applied a novel graphical method for tracking changes in the δ 13 C and 14 C of DIC in two distinct aquifer complexes identified in the Hainich Critical Zone Exploratory (CZE), a platform to study how water transport links surface and shallow groundwaters in limestone and marlstone rocks in central Germany. For more quantitative estimates of contributions of different biotic and abiotic carbon sources to the DIC pool, we used the NETPATH geochemical modeling program, which accounts for changes in dissolved ions in addition to C isotopes.Although water residence times in the Hainich CZE aquifers based on hydrogeology are relatively short (years or less), DIC isotopes in the shallow, mostly anoxic, aquifer assemblage (HTU) were depleted in 14 C compared to a deeper, oxic, aquifer complex (HTL). Carbon isotopes and chemical changes in the deeper HTL wells could be explained by interaction of recharge waters equilibrated with post-bomb 14 C sources with carbonates. However, oxygen depletion and δ 13 C and 14 C values of DIC below those expected from the processes of carbonate equilibrium alone indicate considerably different biogeochemical evolution of waters in the upper aquifer assemblage (HTU wells). Changes in 14 C and 13 C in the upper aquifer complexes result from a number of biotic and abiotic processes, including oxidation of 14 C-depleted OM derived from recycled microbial carbon and sedimentary organic matter as well as water-rock interactions. The microbial pathways inferred from DIC isotope shifts and changes in water chemistry in the HTU wells were supported by comparison with in situ microbial community structure based on 16S rRNA analyses.Our findings demonstrate the large variation in the importance of biotic as well as abiotic controls on 13 C and 14 C of DIC in closely related aquifer assemblages. Further, they support the importance of subsurface-derived carbon sources like DIC for chemolithoautotrophic microorganisms as well as rock-derived organic matter for supporting heterotrophic groundwater microbial communities and indicate that even shallow aquifers have microbial communities that use a variety of subsurface-derived carbon sources.

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“…Over the last ten years, a few thermophilic members of these groups and others have been isolated and described as axenic cultures (e.g. [9][10][11][12][13]); however, most of the diversity within them remains to be explored. Recent advancements in metagenomics and single-cell genomics have provided access to the genomes of yet-uncultivated thermophiles, enabling insight into their evolution, cell biology, and possible metabolic and ecological functions.…”

Section: Introductionmentioning

confidence: 99%