Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in “
            <i>Candidatus</i>
            Bathyarchaeia”

Qi, Yanling; Evans, Paul N.; Li, Yuxian; Rao, Yang-Zhi; Qu, Yan-Ni; Tan, Sha; Jiao, Jian‐Yu; Chen, Ya-Ting; Hedlund, Brian P.; Shu, Wen‐Sheng; Hua, Zheng-Shuang; Li, Wenjun

doi:10.1128/msystems.00252-21

Cited by 33 publications

(53 citation statements)

References 92 publications

(115 reference statements)

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“…This suggests that Thermocrinis -affiliated bacteria may not have nitrogen fixation ability in some hot springs. This phenomenon can be explained by the fact that some Thermocrinis species living in YNP hot springs may obtain nifH gene from coexisting diazotrophs such as Hydrogenobacter through horizontal gene transfer that was speculated to occur among diazotrophs ( Koirala and Brözel, 2021 ) or prokaryotes in hot springs ( Zhu et al, 2019 ; Li et al, 2021 ; Qi et al, 2021 ). In addition, there was one unique Aquificae -related nifH gene lineage in Japan hot springs ( Figure 3 ), but those related nifH gene sequences have stop codons in their amino acid sequences ( Nishihara et al, 2018b ), indicating they are pseudogenes.…”

Section: Discussionmentioning

confidence: 99%

nifH gene expression and diversity in geothermal springs of Tengchong, China

et al. 2022

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Terrestrial hot springs have been suggested to harbor diverse diazotrophic lineages by using DNA-based nifH gene phylogenetic analysis. However, only a small amount of diazotrophs were ever confirmed to perform nitrogen fixation. In order to explore the compositions of active diazotrophic populations in hot springs, the in situ expression and diversity of nifH and 16S rRNA genes were investigated in the sediments of hot springs (pH 4.3-9.1; temperature 34-84°C) in Tengchong, China, by using high-throughput sequencing. The results showed that active diazotrophs were diverse in the studied Tengchong hot springs. The main active diazotrophs in high-temperature hot springs were affiliated with Aquificae, while those in low-temperature hot springs belonged to Cyanobacteria and Nitrospirae. Such dominance of Aquificae and Nitrospirae of diazotrophs has not been reported in other ecosystems. This suggests that hot springs may harbor unique active diazotrophs in comparison with other type of ecosystems. Furthermore, there were significant differences in the phylogenetic lineages of diazotrophs between hot springs of Tengchong and other regions, indicating that diazotrophs have geographical distribution patterns. Statistical analysis suggests that the expression and distribution of nifH gene were influenced by temperature and concentrations of ammonia and sulfur seem in Tengchong hot springs. These findings avail us to understand element cycling mediated by diazotrophs in hot spring ecosystems.

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Section: Discussionmentioning

confidence: 99%

nifH gene expression and diversity in geothermal springs of Tengchong, China

et al. 2022

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“…Helarchaeota species encodes the complete set of enzymes allowing these archaea to perform methanogenesis or alkanotrophy under some conditions. 86 − 89 , 91 The alkane oxidation would rely on an association with sulfate-reducing bacteria. 92 …”

Section: Discovery and Diversity Of Coenzyme M-dependent Alkanotrophi...mentioning

confidence: 99%

“…Helarchaeota species encodes the complete set of enzymes allowing these archaea to perform methanogenesis or alkanotrophy under some conditions. [86][87][88][89]91 The alkane oxidation would rely on an association with sulfate-reducing bacteria. 92 In the mentioned methanogens and alkanotrophs, the alkane chemistry is supposed to be performed by ACRs.…”

Section: T H Imentioning

confidence: 99%

“…Bathyarchaeota phylum contain an incomplete methanogenesis/alkanotrophic pathway while the genome of some Ca . Helarchaeota species encodes the complete set of enzymes allowing these archaea to perform methanogenesis or alkanotrophy under some conditions. − , The alkane oxidation would rely on an association with sulfate-reducing bacteria …”

Section: Discovery and Diversity Of Coenzyme M-dependent Alkanotrophi...mentioning

confidence: 99%

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A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea

Lemaire

Wagner

2022

Biochemistry

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Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO 2 by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.

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“…Comparative genomic analysis is an effective approach to illuminate the evolution and habitat adaptation mechanism of microorganisms ( 14 – 16 ) and the diverse metabolic capabilities of strains within the same species isolated from different habitats ( 17 ). Five Clostridium beijerinckii strains were isolated from pit mud, and comparative genomics of these strains and C. beijerinckii from other habitats showed that hundreds of genes were shared only by strains isolated from pit mud ( 18 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of Clostridium in an Artificial Ecosystem for Liquor Production

et al. 2022

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Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in “ Candidatus Bathyarchaeia”

Abstract: Ca . Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems.

Cited by 33 publications

References 92 publications

nifH gene expression and diversity in geothermal springs of Tengchong, China

nifH gene expression and diversity in geothermal springs of Tengchong, China

A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea

Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of Clostridium in an Artificial Ecosystem for Liquor Production

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