Extreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 16, 2023

Abstract Research in extreme environments has substantially expanded our understanding of the ecology and evolution life on Earth, but a major group organisms been largely overlooked: microbial eukaryotes (i.e., protists). In this Perspective, we summarize data from over 80 studies protists identify focal lineages that are significant interest for further study, including clades within Echinamoebida, Heterolobosea, Radiolaria, Haptophyta, Oomycota, Cryptophyta. We argue prime sampling targets to fill gaps eukaryotic tree increase ecology, metabolism, genome architecture, life.

Language: Английский

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Cultivation strategies for prokaryotes from extreme environments

iMeta, Journal Year: 2023, Volume and Issue: 2(3)

Published: June 12, 2023

Abstract The great majority of microorganisms are as‐yet‐uncultivated, mostly found in extreme environments. High‐throughput sequencing provides data‐rich genomes from single‐cell and metagenomic techniques, which has enabled researchers to obtain a glimpse the unexpected genetic diversity “microbial dark matter.” However, cultivating environments remains essential for dissecting utilizing functions extremophiles. Here, we provide straightforward protocol efficiently isolating prokaryotic different habitats (thermal, xeric, saline, alkaline, acidic, cryogenic environments), was established through previous successful work our long‐term experience extremophile resource mining. We propose common processes isolation at first then summarize multiple cultivation strategies recovering meanwhile specific tips that always overlooked but important. Furthermore, use multi‐omics‐guided microbial approaches culturing these as‐yet‐uncultivated two examples provided introduce how work. In summary, allows significantly improve efficiency pure cultures novel taxa, therefore paves way protection utilization resources

Language: Английский

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Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 14, 2024

Abstract Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, geological influences these Archaea not well understood. Here we explore genomic diversity in 152 metagenomes from 48 Tengchong, China, collected 2016 to 2021. Our dataset is comprised 2949 archaeal metagenome-assembled genomes spanning 12 phyla 392 newly identified species, which increases known species by ~48.6%. The structures potential functions communities strongly influenced temperature pH, with high-temperature acidic alkaline favoring abundance over Bacteria. Genome-resolved metagenomics metatranscriptomics provide insights into ecological niches their roles carbon, sulfur, nitrogen, hydrogen metabolism. Furthermore, our findings illustrate interplay competition cooperation among biogeochemical cycles, possibly arising overlapping functional metabolic handoffs. Taken together, study expands inhabiting provides a foundation for more incisive processes mediated ecosystems.

Language: Английский

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Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data

Advanced Biotechnology, Journal Year: 2024, Volume and Issue: 2(3)

Published: Aug. 5, 2024

Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions known extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying diversity, evolution, adaptation adversity. They also play critical roles in biogeochemical cycles. Additionally, extremophiles often produce novel bioactive compounds response corresponding challenging environments. Recent advances technologies, including genomic sequencing untargeted metabolomic analysis, significantly enhanced our understanding of ecology, genetic physiological characteristics The integration advanced multi-omics technologies into culture-dependent research has notably improved efficiency, providing valuable insights functions biosynthetic capacities vast untapped resources present substantial opportunities discovering natural products advancing knowledge ecology evolution. This review highlights current status on microbiomes, focusing ecological roles, isolation cultivation exploration their potential. Moreover, we emphasize importance potential more strain metabolites, would be boosted greatly by harnessing power data.

Language: Английский

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Acid Phosphatase-Driven Advancements in Peanut Growth and Microbial Community Dynamics in Phosphorus-Limited Soils

Journal of soil science and plant nutrition, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 6, 2025

Language: Английский

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Soil bacterial diversity correlates with precipitation and soil pH in long-term maize cropping systems

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: April 7, 2020

Abstract Unraveling the key drivers of bacterial community assembly in agricultural soils is pivotal for soil nutrient management and crop productivity. Presently, microbial structure remain unexplored maize cropping systems under complex variable environmental scenarios across large spatial scales. In this study, we conducted high-throughput 16S rRNA gene sequencing network analysis to identify major factors driving diversity co-occurrence patterns 21 field China. The results show that mean annual precipitation pH are shape communities soils. similarities significantly decreased with increasing geographic distance between different sites. differences turnover rates phyla indicate distinct dispersal capabilities groups, some abundant exhibited high capabilities. Aeromicrobium , Friedmanniella Saccharothrix Lamia Rhodococcus Skermanella Pedobacter were identified as keystone taxa. Based on node-level network-level topological features, members core microbiome more frequently found center ecosystem compared other This study highlights agro-ecosystems central ecological role maintaining web interactions.

Language: Английский

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Quantitative assessment of the environmental risks of geothermal energy: A review

Journal of Environmental Management, Journal Year: 2020, Volume and Issue: 276, P. 111287 - 111287

Published: Aug. 31, 2020

Language: Английский

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Microbial Functional Diversity Correlates with Species Diversity along a Temperature Gradient

mSystems, Journal Year: 2022, Volume and Issue: 7(1)

Published: Feb. 15, 2022

Microbial community diversity is often correlated with physical environmental stresses like acidity, salinity, and temperature. For example, species usually declines increasing temperature above 20°C. However, few studies have examined whether the genetic functional of metagenomes varies in a similar way as along stress gradients. Here, we investigated bacterial communities thermal spring sediments ranging from 21 to 88°C, representing 330 3,800 archaeal based on 16S rRNA gene amplicon analysis. Metagenomes were sequenced, Pfam abundances used proxy for metagenomic diversity. Significant decreases both observed temperatures. The relationship between followed power function steepest slopes high-temperature, low-diversity region gradient. Species additions simple thermophilic added many new Pfams, while complex mesophilic relatively fewer indicating that does not approach saturation rapidly does. Many Pfams appeared distinct ceilings 60 80°C. This study suggests limits taxonomic microbial communities, but quantitatively different manner. Lower at higher temperatures probably due two factors, including (i) absence enzymes adapted conditions, (ii) fact high-temperature are comprised smaller average genomes and, therefore, contain rare functions. IMPORTANCE Only recently ecologists begun assess how correlates factors pH, temperature, salinity. still, very number biochemical functions termed diversity, same factors. Our 18 sampled across wide gradient found reduced ways. Initially, increased sharply eventually plateaued, following function. pattern has been previously predicted theoretical models, our validates this field data. also presents unique overview distribution metabolic gradient, demonstrating "ceilings" which they no longer found.

Language: Английский

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Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: Feb. 17, 2023

Abstract Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) DPANN radiation characterized ultra-small cell genomes sizes, resulting in limited metabolic capacities probable dependency on other organisms to survive. We applied a multi-omics approach characterize the communities over wide range of aquifer groundwater chemistries. Results expand known global these unusual organisms, demonstrate geographical 11,000 subsurface-adapted Patescibacteria, Dependentiae archaea, indicate that prokaryotes with minimalistic metabolism characteristic feature terrestrial subsurface. Community composition activities were largely shaped water oxygen content, while site-specific relative abundance profiles driven combination physicochemistries (pH, nitrate-N, dissolved organic carbon). provide insights into activity evidence they major contributors community transcriptional activity. Ultra-small exhibited genetic flexibility respect transcriptionally distinct responses, proportionally greater transcription invested amino acid lipid signal transduction oxic groundwater, along differences taxa active. Those associated sediments differed from planktonic counterparts species activity, adaptations reflecting surface-associated lifestyle. Finally, results showed groups phylogenetically co-occurred strongly across sites, indicating shared preferences for conditions.

Language: Английский

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Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: March 22, 2023

Abstract Metagenomic studies on geothermal environments have been central in recent discoveries the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial features Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics mesocosm experiments. Detection methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide Mcr-encoding archaea inhabit differing physicochemical regimes across YNP. From three selected hot springs recovered twelve metagenome assembled genomes (MAGs) affiliated lineages cultured methanogens as well Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, Archaeoglobi. These MAGs encoded potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain oxidation. While represent minor fractions microbial community springs, experiments precursors resulted stimulation activity enrichment Methanosaeta Methanothermobacter uncultured including Korarchaeia, Nezhaarchaeia, We revealed that diverse metabolic to produce from different persist YNP can be enriched under conditions. This study highlights importance environmental laboratory-based expand our understanding their impact carbon transformations beyond.

Language: Английский

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