Microbial diversity in extreme environments

Shu, Wen‐Sheng; Huang, Li-Nan

doi:10.1038/s41579-021-00648-y

Cited by 290 publications

(149 citation statements)

References 204 publications

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“…On the other hand, Uritskiy, et al 9 reported an increase in the relative abundance of Bacteroidetes in halite nodules at Salar Grande with increasing water availability after a rainfall. The observed trends recapitulate the changes in community structure observed elsewhere along salinity gradients, with haloarchaea dominating at the highest salinities (lower water content), while the relative abundance of Bacteroidetes remains practically unchanged 48,49 .…”

Section: Discussionsupporting

confidence: 74%

Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert

Perez-Fernandez

Wilburn

Dávila

et al. 2022

Preprint

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The adaptation mechanisms of microbial communities to natural perturbations remain relatively unexplored, particularly in extreme environments. The extremophilic communities of halite (NaCl) nodules from the hyper-arid core of the Atacama Desert are self-sustained and represent a unique opportunity to study functional adaptations and community dynamics with changing environmental conditions. We transplanted halite nodules to different sites in the desert and investigated how their taxonomic, cellular, and biochemical changes correlated with water availability, using environmental data modeling and metagenomic analyses. Salt-in strategists, mainly represented by haloarchaea, significantly increased in relative abundance at sites characterized by extreme dryness, multiple wet/dry cycles, and colder conditions. The functional analysis of metagenome-assembled genomes (MAGs) revealed site-specific enrichments in archaeal MAGs encoding for the uptake of various compatible solutes and for glycerol utilization. These findings suggest that opportunistic salt-in strategists took over the halite communities at the driest sites. They most likely benefited from metabolites newly released in the environment by the death of microorganisms least adapted to the new conditions. The observed changes were consistent with the need to maximize cellular bioenergetics when confronted with lower water availability and higher salinity, providing valuable information on microbial community adaptations and resilience to climate change.

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Section: Discussionsupporting

confidence: 74%

Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert

Perez-Fernandez

Wilburn

Dávila

et al. 2022

Preprint

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“…The maximum‐likelihood inferences of the phylogeny based on both the tacka60 and tacka120 marker gene sets showed a confident placement of Korarchaeota as the basal branch to other TACK archaea and as a sister group to Asgard archaea as depicted in Figure 1D but with additional Asgard archaeal lineages. Such evolution position of Korarchaeota is following several recent studies about archaeal/universal Tree of Life 4−7 . Considering the most ancient lineage within TACK archaea so far, Korarchaeota might play a transitional role in the evolution and diversification between TACK and Asgard archaea.…”

Section: Figurementioning

confidence: 66%

The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea

Liu

2022

mLife

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Impact statementThe applications of marker gene concatenation have been advanced to resolve the key questions in the Tree of Life. However, the interphylum evolutionary relationship between Korarchaeota of TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) and Asgard archaea remains uncertain. We applied a marker gene ranking procedure to examine their evolutionary history. Our updated trees showed confident placements of (1) Korarchaeota as the basal branch to other TACK archaea and as a sister group to Asgard archaea; (2) Njordarchaeota at basal branch to Korarchaeota instead of within Asgard archaea. They highlight the importance of evaluating marker genes for phylogeny inference of the Archaea domain.

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“…Over the past 20 years, both the taxonomic and the functional profiles of microbial communities from both local and large-scale regions (e.g., Tara Oceans [12], Earth Microbiome [13]) are being accumulated at a higher and higher rate. Extreme environments, i.e., areas with high salinity, low pH, etc., are being studied, providing us with unprecedented insight [14]. Both amplicon and shotgun metagenomics studies have played a crucial part in this development.…”

Section: Introductionmentioning

confidence: 99%

PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

et al. 2022

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To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO’s capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes.

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Microbial diversity in extreme environments

Cited by 290 publications

References 204 publications

Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert

Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert

The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea

PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

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