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ABSTRACT “Candidatus Bathyarchaeia” is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 Ca. Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot spring sediments in Tibet and Yunnan, China. Phylogenetic analysis revealed all MAGs of Ca. Bathyarchaeia can be classified into 7 orders and 15 families. Among them, 4 families have been first discovered in the present study, significantly expanding the known diversity of Ca. Bathyarchaeia. Comparative genomics demonstrated Ca. Bathyarchaeia MAGs from thermal habitats to encode a large variety of genes related to carbohydrate degradation, which are likely a metabolic adaptation of these organisms to a lifestyle at high temperatures. At least two families are potential methanogens/alkanotrophs, indicating a potential for the catalysis of short-chain hydrocarbons. Three MAGs from Family-7.3 are identified as alkanotrophs due to the detection of an Mcr complex. Family-2 contains the largest number of genes relevant to alkyl-CoM transformation, indicating the potential for methylotrophic methanogenesis, although their evolutionary history suggests the ancestor of Ca. Bathyarchaeia was unable to metabolize alkanes. Subsequent lineages have acquired the ability via horizontal gene transfer. Overall, our study significantly expands our knowledge and understanding of the metabolic capabilities, habitat adaptations, and evolution of Ca. Bathyarchaeia in thermal environments. IMPORTANCE Ca. Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems. In this study, we uncovered the metabolic capabilities and ecological role of Ca. Bathyarchaeia in hot springs and give a comprehensive comparative analysis between thermal and nonthermal habitats to reveal the thermal adaptability of Ca. Bathyarchaeia. Also, we attempt to determine the evolutionary history of methane/alkane metabolism in Ca. Bathyarchaeia, since it appears to be the first archaea beyond Euryarchaeota which contains the mcrABG genes. The reclassification of Ca. Bathyarchaeia and significant genomic differences among different lineages largely expand our knowledge on these cosmopolitan archaea, which will be beneficial in guiding the future studies.

Abstract: Here we report the genome sequence of Acinetobacter venetianus VE-C3, a strain isolated from the Venice Lagoon and known to be able to degrade n-alkanes. Post sequencing analyses revealed that this strain is relatively distantly related to the other Acinetobacter strains completely sequenced so far as shown by phylogenetic analysis and pangenome analysis (1285 genes shared with all the other Acinetobacter genomes sequenced so far). A. venetianus VE-C3 possesses a wide range of determinants whose molecular functions are probably related to the survival in a strongly impacted ecological niche. Among them, genes probably involved in the metabolism of long-chain n-alkanes and in the resistance to toxic metals (e.g. arsenic, cadmium, cobalt and zinc) were found. Genes belonging to these processes were found both on the chromosome and on plasmids. Also, our analysis documented one of the possible genetic bases underlying the strategy adopted by A. venetianus VE-C3 for the adhesion to oil fuel droplets, which could account for the differences existing in this process with other A. venetianus strains. Finally, the presence of a number of DNA mobilization-related genes (i.e. transposases, integrases, resolvases) strongly suggests an important role played by horizontal gene transfer in shaping the genome of A. venetianus VE-C3 and in its adaptation to its special ecological niche. [Copyright &y& Elsevier]

The induction of the enzyme activities involved in butane metabolism in Pseudomonas butanovora was characterized. P. butanovora was grown on butane or its metabolites, both singly and in mixtures with other growth substrates. Cells grown in each of the butane metabolites readily consumed the growth substrate and downstream metabolites, but consumed the upstream butane metabolites more slowly. Upstream activities in the butane metabolism could be induced by downstream metabolites, but to much lower levels than with the primary substrate. The induction of butane oxidation was not repressed when P. butanovora was grown or incubated in a mixture of butane and 1-butanol, butyraldehyde or butyrate. However, no induction of butane consumption was observed in a mixture of butane and lactate, which is indicative of catabolite repression. In lactate-grown cells that were rid of the growth substrate and incubated with butane and acetylene (to inactivate newly formed butane monooxygenase), the consumption of butane, 1-butanol and butyraldehyde consumption was not induced. The overall results suggest an independent regulatory mechanism for each of the enzyme activities in butane metabolism. In addition, a low, constitutive butane oxidation was observed in cells grown on substrates other than butane metabolites. [ABSTRACT FROM AUTHOR]

" Candidatus Bathyarchaeia" is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 Ca . Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot spring sediments in Tibet and Yunnan, China. Phylogenetic analysis revealed all MAGs of Ca . Bathyarchaeia can be classified into 7 orders and 15 families. Among them, 4 families have been first discovered in the present study, significantly expanding the known diversity of Ca . Bathyarchaeia. Comparative genomics demonstrated Ca . Bathyarchaeia MAGs from thermal habitats to encode a large variety of genes related to carbohydrate degradation, which are likely a metabolic adaptation of these organisms to a lifestyle at high temperatures. At least two families are potential methanogens/alkanotrophs, indicating a potential for the catalysis of short-chain hydrocarbons. Three MAGs from Family-7.3 are identified as alkanotrophs due to the detection of an Mcr complex. Family-2 contains the largest number of genes relevant to alkyl-CoM transformation, indicating the potential for methylotrophic methanogenesis, although their evolutionary history suggests the ancestor of Ca . Bathyarchaeia was unable to metabolize alkanes. Subsequent lineages have acquired the ability via horizontal gene transfer. Overall, our study significantly expands our knowledge and understanding of the metabolic capabilities, habitat adaptations, and evolution of Ca . Bathyarchaeia in thermal environments. IMPORTANCE Ca . Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems. In this study, we uncovered the metabolic capabilities and ecological role of Ca . Bathyarchaeia. Also, we attempt to determine the evolutionary history of methane/alkane metabolism in Ca . Bathyarchaeia. Also, we attempt to determine the evolutionary history of methane/alkane metabolism in Ca . Bathyarchaeia, since it appears to be the first archaea beyond Euryarchaeota which contains the mcrABG genes. The reclassification of Ca . Bathyarchaeia and significant genomic differences among different lineages largely expand our knowledge on these cosmopolitan archaea, which will be beneficial in guiding the future studies.