Embracing mountain microbiome and ecosystem functions under global change

New Phytologist, Journal Year: 2022, Volume and Issue: 234(6), P. 1987 - 2002

Published: Feb. 25, 2022

Mountains are pivotal to maintaining habitat heterogeneity, global biodiversity, ecosystem functions and services humans. They have provided classic model natural systems for plant animal diversity gradient studies over 250 years. In the recent decade, exploration of microorganisms on mountainsides has also achieved substantial progress. Here, we review literature microbial across taxonomic groups types mountains. Microbial community shows climatic zonation with orderly successions along elevational gradients, which largely consistent traditional hypotheses. However, patterns complicated species richness without general rules in terrestrial aquatic environments driven mainly by deterministic processes caused abiotic biotic factors. We see a major shift from documenting biodiversity towards identifying mechanisms that shape biogeographical how these vary under change inclusion novel ecological theories, frameworks approaches. thus propose key questions cutting-edge perspectives advance future research mountain biogeography focusing hypotheses, incorporating meta-ecosystem framework drivers, adapting recently developed approaches trait-based ecology manipulative field experiments, disentangling biodiversity-ecosystem functioning relationships finally modelling predicting their responses.

Language: Английский

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Extreme summers impact cropland and grassland soil microbiomes

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(10), P. 1589 - 1600

Published: July 7, 2023

The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond such disturbances. Here, metagenomics was used investigate effects future climate scenarios (+0.6 °C warming and altered precipitation) on during summers 2014-2019. Unexpectedly, Central Europe experienced heatwaves droughts 2018-2019, causing significant impacts structure, assembly, function microbiomes. Specifically, relative abundance Actinobacteria (bacteria), Eurotiales (fungi), Vilmaviridae (viruses) significantly increased in both cropland grassland. contribution homogeneous selection bacterial community assembly from 40.0% normal 51.9% summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), sporulation (spoIID, spoVK) were identified as potential contributors drought-enriched taxa, their expressions confirmed by metatranscriptomics 2022. impact further evident taxonomic profiles 721 recovered metagenome-assembled genomes (MAGs). Annotation contigs MAGs suggested that may have a competitive advantage due geosmin 2-methylisoborneol. Future caused similar pattern changes communities summers, but much lesser extent. Soil grassland showed greater resilience change than those cropland. Overall, this study provides comprehensive framework for understanding response

Language: Английский

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Niche differentiation of microbial community shapes vertical distribution of recalcitrant dissolved organic matter in deep-sea sediments

Environment International, Journal Year: 2023, Volume and Issue: 178, P. 108080 - 108080

Published: July 1, 2023

Sedimentary organic matter provides carbon substrates and energy sources for microorganisms, which drive benthic biogeochemical processes in turn modify the quantity quality of dissolved (DOM). However, molecular composition distribution DOM its interactions with microbes deep-sea sediments remain poorly understood. Here, relationship were analyzed samples collected from two sediment cores (∼40 cm below sea floor), at depths 1157 2253 m South China Sea. Results show that niche differentiation was observed on a fine scale different layers, Proteobacteria Nitrososphaeria dominating shallow (0-6 cm) Chloroflexi Bathyarchaeia prevailing deeper (6-40 cm), indicating correspondence microbial community both geographical isolation availability matter. An intimate link between further indicates that, mineralization fresh layer potentially resulted accumulation recalcitrant (RDOM), while relatively low abundance RDOM linked to anaerobic utilization layers. In addition, higher overlying water, as compared surface sediment, suggests might be source RDOM. These results emphasize close relation community, laying foundation understanding complex dynamics water column.

Language: Английский

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Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes

Science Advances, Journal Year: 2023, Volume and Issue: 9(5)

Published: Feb. 1, 2023

Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline lacustrine systems. An unbiased global assessment critical for understanding origins, dispersal mechanisms, ecosystem roles. Here, we leveraged continental-scale metagenomics document species systems remarkably low compared environments. We show uncultured AOA, "Candidatus Nitrosopumilus limneticus," ubiquitous genotypically static various large European lakes where it evolved 13 million years ago. find extensive proteome remodeling was innovation colonization AOA. These findings reveal adaptive mechanisms keystone has survived clonally millennia.

Language: Английский

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Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant on Earth, widely distributed in marine, terrestrial, geothermal ecosystems. However, genomic diversity, biogeography, evolutionary process of AOA populations subsurface environments vastly understudied compared to those marine soil systems. Here, we report a novel order Candidatus (Ca.) Nitrosomirales which forms sister lineage thermophilic Ca. Nitrosocaldales. Metagenomic 16S rRNA gene-read mapping demonstrates presence various groundwater their widespread distribution across range geothermal, habitats. Terrestrial show genetic capacity using formate as source reductant nitrate an alternative electron acceptor. appear have acquired key metabolic genes operons from other mesophilic via horizontal gene transfer, including encoding urease, nitrite reductase, V-type ATPase. The additional versatility conferred by functions may facilitated radiation into variety subsurface, environments. We also provide evidence that each four orders spans both terrestrial habitats, suggests more complex history for major lineages than previously proposed. Together, these findings establish robust phylogenomic framework new insights ecology adaptation this globally functional guild.

Language: Английский

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Niche Partitioning and Intraspecific Variation of Thaumarchaeota in Deep Ocean Sediments

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(1)

Published: Jan. 1, 2025

ABSTRACT Deep‐sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, ecology and evolutionary adaptations not well understood. Metagenomic analyses were conducted on samples various depths 750‐cm sediment core collected the Mariana Trench Challenger Deep. The abundance archaeal amoA generally decreased with depth, except for an unexpected peak midway through core. thaumarchaeotal metagenome‐assembled genomes classified into diverse phylogenetic clusters associated ‐NP‐γ, ‐NP‐θ, ‐NP‐δ ammonia‐oxidising non‐ammonia‐oxidising lineages. most abundant group was within which is usually found in coastal shallow habitats, indicating potential niche expansion marine to hadal environments. This benthic showed within‐species genomic variations compared previously identified Hadal water group, suggesting microdiversification along separation between Evolutionary benthic‐to‐pelagic transition included reduced genome size, loss motility/cell adhesion, altered energy metabolism, different mechanisms substrate acquisition regulation (e.g., ammonium). These findings offer new insights evolution demonstrate, first time, intraspecies‐level variation related benthic‐versus‐pelagic partitioning deep ocean.

Language: Английский

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Microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary responding to tidal fluctuation

Environmental Research, Journal Year: 2025, Volume and Issue: 274, P. 121363 - 121363

Published: March 9, 2025

Language: Английский

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Adaptive genetic traits in pelagic freshwater microbes

Environmental Microbiology, Journal Year: 2022, Volume and Issue: 25(3), P. 606 - 641

Published: Dec. 14, 2022

Abstract Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans can be broadly categorized in two groups: free‐living, specialized oligotrophs patch‐associated generalists or copiotrophs. In this review, we aim identify genomic traits that enable pelagic freshwater thrive their habitat. To do so, discuss main genetic differences marine are both dominated by difference sediment microbes, where copiotrophs more prevalent. We phylogenomically analysed a collection >7700 metagenome‐assembled genomes, classified habitat preferences on different taxonomic levels, compared metabolic freshwater, marine, microbes. Metabolic mainly associated with transport functions, environmental information processing, components electron chain, osmoregulation isoelectric point proteins. Several lineages known transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) underlying mechanisms process discussed review. Additionally, distribution, ecology make‐up most abundant prokaryotes described details separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, ‘ Ca . Patescibacteria’.

Language: Английский

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Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts biogeochemical cycles of carbon nitrogen. In contrast to these well-studied ammonia-oxidizing (AOA), deep-branching non-AOA within this class remain poorly characterized because a low number genome representatives. Here, we reconstructed 128 metagenome-assembled genomes from acid mine drainage hot spring sediment metagenomes. Comparative genomics revealed that extant functionally diverse, with capacity for fixation, monoxide oxidation, methanogenesis, respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested common ancestor was likely an aerobic thermophile. We further surmise functional differentiation primarily shaped by pH, temperature, acquisition carbon, nitrogen, sulfur metabolism. Our study provides more holistic less biased understanding diversity, ecology, deep evolution globally Nitrososphaeria.

Language: Английский

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Habitat Transition in the Evolution of Bacteria and Archaea

Annual Review of Microbiology, Journal Year: 2023, Volume and Issue: 77(1), P. 193 - 212

Published: April 26, 2023

Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics mechanisms these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review literature concerning transitions among a variety bacterial archaeal lineages, considering frequency migration events, potential environmental barriers, to new physicochemical conditions, including modification protein inventories other genomic characteristics. Cells dependent on microbial hosts, bacteria from Candidate Phyla Radiation, have undergone repeated sources into We compare their trajectories those both free-living cells-including Melainabacteria, Elusimicrobia, methanogenic archaea-and cellular endosymbionts bacteriophages, which made similar transitions. conclude by highlighting major related topics may be worthy future study.

Language: Английский

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