Earth’s most needed uncultivated aquatic prokaryotes DOI Open Access
Sophie A. Simon,

Vera Aschmann,

Annika Behrendt

et al.

Published: June 24, 2024

Aquatic ecosystems house a significant fraction of Earth’s biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth metabolic potential residing in uncultivated Bacteria Archaea, cultivation microorganisms is required to study their physiology via systems, confirm predicted biochemical pathways, exploit biotechnological potential, accurately appraise nutrient turnover. Over past two decades, limitations culture-independent investigations highlighted importance bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after lineages aquatic Archaea with global ecological impact. In addition fulfilling critical roles carbon, nitrogen, sulfur cycling, many organisms are thought partake key symbiotic relationships. This review highlights vital contributions uncultured microbes ecosystems, from lakes groundwater surfaces depths oceans will guide current future initiatives tasked cultivating our planet’s elusive, consequential microflora.

Language: Английский

Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China DOI Creative Commons
Shao‐Ming Gao, David Páez-Espino, Jintian Li

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: May 2, 2022

Abstract Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses natural settings. Yet, our knowledge viral biogeographic patterns and corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China examine biogeography this extreme environment. The results demonstrate that prokaryotic communities dictate taxonomic functional diversity, abundance structure, whereas other factors especially latitude mean annual temperature also impact populations functions. In silico predictions highlight lineage-specific virus-host ratios richness-dependent interaction structure. Further analyses reveal important roles conditions horizontal gene transfers shaping auxiliary metabolic genes potentially involved phosphorus assimilation. Our findings underscore importance both abiotic biotic predicting dynamics AMD sediments.

Language: Английский

Citations

69
Virus-associated organosulfur metabolism in human and environmental systems DOI Creative Commons
Kristopher Kieft, Adam M. Breister, Phil Huss

et al.

Cell Reports, Journal Year: 2021, Volume and Issue: 36(5), P. 109471 - 109471

Published: Aug. 1, 2021

Viruses influence the fate of nutrients and human health by killing microorganisms altering metabolic processes. Organosulfur metabolism biologically derived hydrogen sulfide play dynamic roles in manifestation diseases, infrastructure degradation, essential biological Although microbial organosulfur is well studied, role viruses unknown. Here, we report discovery 39 gene families involved encoded 3,749 from diverse ecosystems, including microbiomes. The infect organisms all three domains life. Six encode for enzymes that degrade compounds into sulfide, whereas others manipulate may production. We show viral genes key enzymatic domains, are translated protein, maintained after recombination, provides a fitness advantage to viruses. Our results reveal as drivers with important implications environmental health.

Language: Английский

Citations

66
Three families of Asgard archaeal viruses identified in metagenome-assembled genomes DOI
Sofia Medvedeva, Jiarui Sun, Natalya Yutin

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 962 - 973

Published: June 27, 2022

Language: Английский

Citations

38
Recent insights into aquatic viruses: Emerging and reemerging pathogens, molecular features, biological effects, and novel investigative approaches DOI Creative Commons

Qi-Ya Zhang,

Fei Ke, Lang Gui

et al.

Water Biology and Security, Journal Year: 2022, Volume and Issue: 1(4), P. 100062 - 100062

Published: July 31, 2022

Aquatic viruses are naturally present in the aquatic environment and number of is staggering. Various multicellular organisms ecosystems may be infected, cross-species transmitted, manipulated, killed by viruses, which can lead to cascading ecological effects. The unicellular alter interactions between host individuals, essential effecting or maintaining dynamics microbial communities, horizontal gene transfer, biodiversity, modulating processes globally. Meanwhile, hosts also impact viral abundance diversity. Microbial diversity drives multifunctionality ecosystems, while shape complex communities crucial for ecosystem functioning. This review focuses on molecular, genetic, evolutionary, ecosystemic advances related emerging reemerging presents contexts, novel tools, investigative approaches pertaining study virology, discusses mechanisms affect ecosystems. paper provides an efficient broadly-based blueprint improving understanding viruses.

Language: Английский

Citations

36
Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut DOI Creative Commons
Ran Li, Yongming Wang, Han Hu

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Dec. 29, 2022

Abstract The human gut microbiome has been extensively explored, while the archaeal viruses remain largely unknown. Here, we present a comprehensive analysis of from metagenomes and existing virus collections using CRISPR spacer viral signature-based approach. This results in 1279 species, which, 95.2% infect Methanobrevibacteria_A , 56.5% shared high identity (>95%) with proviruses, 37.2% have host range across 55.7% are highly prevalent population (>1%). A methanogenic virus-specific gene for pseudomurein endoisopeptidase (PeiW) frequently occurs sequences ( n = 150). Analysis 33 Caudoviricetes complete genome often discovers genes integrase 29; mazE 10) regulating lysogenic-lytic cycle, implying dominance temperate virome. Together, our work uncovers unexplored diversity viruses, revealing novel facet microbiome.

Language: Английский

Citations

36
A predicted CRISPR-mediated symbiosis between uncultivated archaea DOI
Sarah P. Esser, Janina Rahlff, Weishu Zhao

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(9), P. 1619 - 1633

Published: July 27, 2023

Language: Английский

Citations

11
Diverse viruses of marine archaea discovered using metagenomics DOI
Yifan Zhou, Liang Zhou, Shuling Yan

et al.

Environmental Microbiology, Journal Year: 2022, Volume and Issue: 25(2), P. 367 - 382

Published: Nov. 17, 2022

Abstract During the past decade, metagenomics became a method of choice for discovery novel viruses. However, host assignment uncultured viruses remains challenging, especially archaeal viruses, which are grossly undersampled compared to bacteria and eukaryotes. Here, we assessed utility CRISPR spacer targeting, tRNA gene matching homology searches viral signature proteins, such as major capsid hosts validated these approaches on metaviromes from Yangshan Harbor (YSH). We report 35 new genomes could be confidently assigned representing diverse lineages marine archaea. show that YSH virome is highly diverse, with some enriching previously described virus groups, magroviruses Marine Group II Archaea (Poseidoniales), others groups Metagenomic recruitment Tara Oceans datasets demonstrated presence Poseidoniales Nitrososphaeria in global oceans, but also revealed endemic YSH‐specific lineages. Furthermore, our results highlight relationship between soil thaumarchaeal propose three families within class Caudoviricetes classification five complete predicted replicate Nitrososphaeria, two ecologically important widespread groups. This study illustrates exploring provides insights into diversity, distribution evolution

Language: Английский

Citations

17
The smallest in the deepest: the enigmatic role of viruses in the deep biosphere DOI Creative Commons
Lanlan Cai, Markus G. Weinbauer, Le Xie

et al.

National Science Review, Journal Year: 2023, Volume and Issue: 10(4)

Published: Jan. 10, 2023

It is commonly recognized that viruses control the composition, metabolism, and evolutionary trajectories of prokaryotic communities, with resulting vital feedback on ecosystem functioning nutrient cycling in a wide range ecosystems. Although deep biosphere has been estimated to be largest reservoir for their hosts, biology ecology therein remain poorly understood. The virosphere an enigmatic field study which many critical questions are still answered. Is simply repository deeply preserved, non-functioning virus particles? Or infectious agents can readily infect suitable hosts subsequently shape microbial populations cycling? Can cellular content released by viral lysis, even organic structures virions themselves, serve as source bioavailable nutrients activity other ecosystems? In this review, we synthesize our current knowledge seek identify topics potential substantial discoveries future.

Language: Английский

Citations

9
Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica DOI
Janina Rahlff, Till L. V. Bornemann, Anna Lopatina

et al.

Applied and Environmental Microbiology, Journal Year: 2022, Volume and Issue: 88(10)

Published: May 2, 2022

Host-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands kilometers across Antarctic continent, which functions as an extraterrestrial analogue because its harsh environmental conditions. Due presence these bacteria carrying genome-integrated prophages on space-related equipment and potential for host-associated demonstrated here, our work has implications planetary protection, a discipline astrobiology interested preventing contamination celestial bodies with alien biomolecules or forms life.

Language: Английский

Citations

11
Continental scientific drilling and microbiology: (extremely) low biomass in bedrock of central Sweden DOI Creative Commons
George Westmeijer, Cristina Escudero, Claudia Bergin

et al.

Biogeosciences, Journal Year: 2024, Volume and Issue: 21(2), P. 591 - 604

Published: Jan. 26, 2024

Abstract. Scientific drilling expeditions offer a unique opportunity to characterize microbial communities in the subsurface that have long been isolated from surface. With biomass being low general, biological contamination fluid, sample processing, or molecular work is major concern. To address this, characterization of contaminant populations fluid and negative extraction controls are essential for assessing evaluating such sequencing data. Here, rock cores down 2250 m depth, groundwater-bearing fractures, were sampled DNA using broad genomic approach. However, even after removing potential present notorious contaminants abundant mainly affiliated with bacterial order Burkholderiales. These microorganisms likely originated reagents used isolating despite stringent quality standards during work. The detection strictly anaerobic sulfate reducers as Candidatus Desulforudis audaxviator suggested presence autochthonous deep biosphere taxa sequenced libraries, yet these clades represented only minor fraction sequence counts (< 0.1 %), hindering further ecological interpretations. described methods findings emphasize importance can support experimental design future microbiological studies conjunction continental operations.

Language: Английский

Citations

2