Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies

Chen, Dai-Di; Tian, Yongsheng; Jiao, Jian‐Yu; Zhang, Xiaotong; Zhang, Yongguang; Dong, Zhou-Yan; Xiong, Mengjie; Xiao, Min; Shu, Wen‐Sheng; Li, Wenjun

doi:10.1007/s00792-019-01150-3

Cited by 12 publications

(13 citation statements)

References 99 publications

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“…10), corroborating the preference of these classes for high-salinity niches (Zhang et al, 2019). Extreme halophiles accumulate intracytoplasmic KCl to regulate their osmotic potential, which constrains them to be obligate halophiles and limits their dispersal (Chen et al, 2020;Shameer, 2016;Vaidya et al, 2018). Salinity (EC) decreased significantly from Bo1 to Bo2 (Fig.…”

Section: Geochemistry-dependent Microbial Community Assembly In the E...supporting

confidence: 60%

Contrasted microbial community colonization of a bauxite residue deposit marked by a complex geochemical context

Macías-Pérez

Levard

Barakat

et al. 2022

Journal of Hazardous Materials

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Section: Geochemistry-dependent Microbial Community Assembly In the E...supporting

confidence: 60%

Contrasted microbial community colonization of a bauxite residue deposit marked by a complex geochemical context

Macías-Pérez

Levard

Barakat

et al. 2022

Journal of Hazardous Materials

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“…Both soil microbiomes included specialist taxa adapted to survival in saline and dry environments. Adaptations include the production of: (1) endogenous compatible solutes by Nitriliruptoraceae ( Chen et al, 2020 ) that include small organic molecules such as sugars and amino-acids, involved in cell protection against osmotic pressure and desiccation ( Vargas et al, 2006 ); and (2) biopolymers like polyhydroxyalkanoates (PHA) by Rubrobacter which are considered extremolytes ( Kourilova et al, 2021 ). PHAs not only serve as a reserve of carbon, energy, and nitrogen for cell survival during starvation ( Vargas et al, 2006 ), but also contribute to the organic matter associated with dead cell debris ( Jansson and Hofmockel, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Hyperarid soil microbial community response to simulated rainfall

Demergasso,

Neilson,

Tebes-Cayo

et al. 2023

Front. Microbiol.

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The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to ex situ simulated rainfall (5% g water/g dry soil for 4 weeks) without nutrient amendment. We conducted replicated microcosm experiments with surface soils from two previously well-characterized AD hyperarid locations near Yungay at 1242 and 1609 masl (YUN1242 and YUN1609) with distinct microbial community compositions and average soil relative humidity levels of 21 and 17%, respectively. The bacterial and archaeal response to soil wetting was evaluated by 16S rRNA gene qPCR, and amplicon sequencing. Initial YUN1242 bacterial and archaeal 16S rRNA gene copy numbers were significantly higher than for YUN1609. Over the next 4 weeks, qPCR results showed significant increases in viable bacterial abundance, whereas archaeal abundance decreased. Both communities were dominated by 10 prokaryotic phyla (Actinobacteriota, Proteobacteria, Chloroflexota, Gemmatimonadota, Firmicutes, Bacteroidota, Planctomycetota, Nitrospirota, Cyanobacteriota, and Crenarchaeota) but there were significant site differences in the relative abundances of Gemmatimonadota and Chloroflexota, and specific actinobacterial orders. The response to simulated rainfall was distinct for the two communities. The actinobacterial taxa in the YUN1242 community showed rapid changes while the same taxa in the YUN1609 community remained relatively stable until day 30. Analysis of inferred function of the YUN1242 microbiome response implied an increase in the relative abundance of known spore-forming taxa with the capacity for mixotrophy at the expense of more oligotrophic taxa, whereas the YUN1609 community retained a stable profile of oligotrophic, facultative chemolithoautotrophic and mixotrophic taxa. These results indicate that bacterial communities in extreme hyperarid soils have the capacity for growth in response to simulated rainfall; however, historic variations in long-term hyperaridity exposure produce communities with distinct putative metabolic capacities.

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“…glossodoripedis KCTC 12842 T . The glutathione-gated potassium efux systems and mechanosensitive channels play a major role in the release of cytoplasmic ions and solutes to reduce turgor pressure [21]. The phylogenomic tree based on the whole genome sequences of strain CAU 1612 T and six related species of the genus Sneathiella supported the data obtained from the 16S rRNA gene analysis ().…”

Section: Phylogenomic Analysismentioning

confidence: 71%

Sneathiella sedimenti sp. nov., isolated from marine sediment

Lee

Weerawongwiwat

Kim

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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A novel bacterium, designated CAU 1612T, was isolated from coastal sediment sampled in the Republic of Korea. Cells of the strain were Gram-stain-negative, rod-shaped and motile. Optimum growth occurred at 30 °C, at pH 7.0 and with 1.0 % (w/v) NaCl. Based on 16S rRNA gene sequences, phylogenetic analysis revealed that strain CAU 1612T belonged to the genus Sneathiella and showed highest similarity to ‘Sneathiella litorea’ JCM 33810T (98.5 %), followed by Sneathiella chungangensis KCTC 32476T (97.7 %), Sneathiella aquimaris KCTC 12842T (96.0 %), Sneathiella chinensis LMG 23452T (95.5 %), Sneathiella limimaris KCTC 52846T (95.5 %) and Sneathiella glossodoripedis KCTC 12842T (95.4 %). The average nucleotide identity and digital DNA–DNA hybridization values of strain CAU 1612T were estimated to be 68.5–81.7 % and ≤23.7 %, respectively, to members of the genus Sneathiella . The DNA G+C content was 54.1 mol%. The major cellular fatty acids (>10 %) were C16:0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major menaquinone was Q-10 and the predominant polar lipids were phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. On the basis of taxonomic evidence, strain CAU 1612T represents a novel species, for which the name Sneathiella sedimenti sp. nov. is proposed. The type strain is CAU 1612T (=KCTC 82427T=MCCC 1K06082T).

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Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies

Cited by 12 publications

References 99 publications

Contrasted microbial community colonization of a bauxite residue deposit marked by a complex geochemical context

Contrasted microbial community colonization of a bauxite residue deposit marked by a complex geochemical context

Hyperarid soil microbial community response to simulated rainfall

Sneathiella sedimenti sp. nov., isolated from marine sediment

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