Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction DOI Creative Commons
Sophie A. Simon, Katharina Schmidt,

Lea Griesdorn

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 16, 2023

Abstract Background While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies short-reads often result incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing increasingly been used as long reads greatly improve the assembly quality MAGs, recommended DNA quantity usually exceeds recoverable amount samples. Here, we evaluated lower-than-recommended quantities for library preparation by determining quality, community composition, recovery MAGs. Results We generated 27 metagenomes using commercially available ZYMO mock varied input from 1000 ng (the minimum) down to 1 eight steps. The remained stable across all levels. read mapping accuracy, which reflects how well match a known reference genome, was consistently high libraries. relative abundance species levels 50 ng. High-quality MAGs (> 95% completeness, ≤ 5% contamination) could be recovered 35 material. When combined with publicly Illumina community, low improved hybrid assemblies. Conclusion Our results show that can substantially reduced without any adverse effects genome still bolster when short-read data. posit presented herein will enable studies low-biomass environments, enhancing microbiome understanding.

Language: Английский

Asgard archaea modulate potential methanogenesis substrates in wetland soil DOI Creative Commons
Luis E. Valentin-Alvarado, Kathryn E. Appler, Valerie De Anda

et al.

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

Published: July 31, 2024

Abstract The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions soil ecosystems remain unknown. Of particular interest archaeal to methane cycling wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new lineage, genome Freyarchaeia, predicted metabolism situ. Metatranscriptomics reveals expression genes [NiFe]-hydrogenases, pyruvate oxidation carbon fixation via the Wood-Ljungdahl pathway. Also expressed encoding enzymes amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification carbohydrate breakdown acetate formate. Overall, include non-methanogenic acetogens, highlighting potential role terrestrial environments.

Language: Английский

Citations

6
Non-negligible roles of archaea in coastal carbon biogeochemical cycling DOI Open Access
Xinxu Zhang, Cui‐Jing Zhang, Yang Liu

et al.

Trends in Microbiology, Journal Year: 2022, Volume and Issue: 31(6), P. 586 - 600

Published: Dec. 23, 2022

Language: Английский

Citations

25
Archaeal virus entry and egress DOI Creative Commons
Bastiaan P. Kuiper, Anna M C Schöntag, Hanna M. Oksanen

et al.

microLife, Journal Year: 2024, Volume and Issue: 5

Published: Jan. 1, 2024

Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these enter exit their host cells. Research on archaeal has lately made significant progress due to advances in genetic tools imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, steady output newly identified viral receptors egress offered first insight into how interact with cell envelope. As more entry unravelled, patterns starting emerge. This helps better understand interactions between envelope compare infection strategies other domains life. Here, we provide an overview developments field egress, shedding light onto most elusive part virosphere.

Language: Английский

Citations

5
Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses DOI Creative Commons
Apoorva Prabhu, Julian Zaugg, Cheong Xin Chan

et al.

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

Published: Jan. 1, 2025

ABSTRACT Viruses infecting archaea play significant ecological roles in marine ecosystems through host infection and lysis, yet they have remained an underexplored component of the virosphere. In this study, we recovered 451 archaeal viruses from a subtropical estuary, identifying 63 that are associated with dominant order Poseidoniales (Marine Group II Archaea). Phylogenetic analyses subset complete nearly‐complete viral genomes assigned these to Magrovirales , lineage viruses, identified novel group distinct . Utilising demarcation criteria established for classification tailed propose two families within Magrovirales: Apasviridae (magrovirus A), comprising genera Agnivirus Savitrvirus, Krittikaviridae E) encompassing genus Velanvirus. Additionally, new order, named Adrikavirales, which includes Vyasavirus. Our detailed genomic characterisation lineages revealed genes involved assembly egress, such as those responsible creating holin rafts lyse cell membranes, feature predominantly known bacteriophages. Furthermore, broad spectrum auxiliary metabolic genes, suggesting can modulate metabolism. Collectively, our findings substantially enhance current understanding diversity functional potential viruses.

Language: Английский

Citations

0
Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components DOI Creative Commons
Changhai Duan, Yang Liu, Ying Liu

et al.

ISME Communications, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. Here we report 56 metagenome-assembled genomes viruses identified metagenomes from different environments. Gene sharing network phylogenomic analyses led to the proposal four virus families, including realms Duplodnaviria Adnaviria, archaea-specific spindle-shaped viruses. Genomic uncovered diverse CRISPR elements these Viruses proposed family "Fuxiviridae" harbor an atypical Type IV-B CRISPR-Cas system Cas4 protein that might interfere with host immunity. "Chiyouviridae" encode Cas2-like endonuclease two mini-CRISPR arrays, one repeat identical array, potentially allowing recruit adaptation machinery acquire spacers could contribute competition other mobile genetic or inhibit defenses. These findings present outline virome offer glimpse into their counter-defense mechanisms.

Language: Английский

Citations

3
Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere DOI Creative Commons
Anja Spang, Tara Mahendrarajah, Pierre Offre

et al.

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(6)

Published: Feb. 25, 2022

Abstract The tree of life (TOL) is a powerful framework to depict the evolutionary history cellular organisms through time, from our microbial origins diversification multicellular eukaryotes that shape visible biosphere today. During past decades, perception TOL has fundamentally changed, in part, due profound methodological advances, which allowed more objective approach studying organismal and viral diversity led discovery major new branches as well lineages. Phylogenetic comparative genomics analyses these data have, among others, revolutionized understanding deep roots life, origin eukaryotic cell, diversity, origin, viruses. In this review, we provide an overview some recent discoveries on their viruses discuss variety complementary techniques consider crucial for making further progress its interconnection with virosphere.

Language: Английский

Citations

15
The expanding Asgard archaea and their elusive relationships with Eukarya DOI Creative Commons
Violette Da Cunha, Morgan Gaïa, Patrick Forterre

et al.

mLife, Journal Year: 2022, Volume and Issue: 1(1), P. 3 - 12

Published: March 1, 2022

Abstract The discovery of Asgard archaea and the exploration their diversity over last 6 years have deeply impacted scientific community working on eukaryogenesis, rejuvenating an intense debate topology universal tree life (uTol). Here, we discuss how this is by two recent publications that expand number lineages eukaryotic signature proteins (ESPs). We some main difficulties can impair phylogenetic reconstructions uTol suggest about its not settled. notably hypothesize existence horizontal gene transfers between ancestral Asgards proto‐eukaryotes could result in observed abnormal behaviors ESPs marker proteins. This hypothesis relevant regardless scenario considered regarding eukaryogenesis. It implies were already diversified before common ancestor shared same biotopes with proto‐eukaryotes. might be still living symbiosis today modern Eukarya.

Language: Английский

Citations

15
Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis DOI Creative Commons

Michael Jüttner,

Sébastien Ferreira-Cerca

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(4)

Published: March 8, 2022

Abstract Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an been greatly fueled by culture-independent metagenomics analyses. However, outcome some these studies their biological implications, such as origin eukaryotic lineage from recently discovered archaeal Asgard superphylum, is debated. The sequences ribosomal constituents are amongst most used phylogenetic markers. functional consequences underlying analysed sequence putative implications essentially not taken into consideration. Here, we propose to exploit additional hallmarks ribosome biogenesis help disentangle competing hypotheses. Using selected examples, multiple origins halophily in archaea or relationship between Eukaryotes, illustrate discuss how function-aware framework can contribute refining our phylogeny cells.

Language: Английский

Citations

14
A metagenomic catalogue of the ruminant gut archaeome DOI Creative Commons
Jiandui Mi, Xiaoping Jing,

Chouxian Ma

et al.

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

Published: Nov. 7, 2024

While the ruminant gut archaeome regulates microbiota and hydrogen balance, it is also a major producer of greenhouse gas methane. However, diversity within gastrointestinal tract (GIT) animals worldwide remains largely underexplored. Here, we construct catalogue 998 unique archaeal genomes recovered from GITs ruminants, utilizing 2270 metagenomic samples across 10 different species. Most (669/998 = 67.03%) belong to Methanobacteriaceae Methanomethylophilaceae (198/998 19.84%). We recover 47/279 previously undescribed at strain level with completeness >80% contamination <5%. investigate biogeography various ruminants demonstrate that compositional similarities vary significantly by breed location. The contains 42,691 protein clusters, clustering methanogenic pathway analysis reveal strain- host-specific dependencies among animals. find archaea potentially carry antibiotic metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, complex viromes. Overall, this substantial repository for recourses, providing potential advancing our understanding ecology discovering strategies regulate methane production in ruminants. employing 2,270 species, authors archaeome, comprised nonredundant genomes, expanding knowledge on Archaea compositions, diversity, functions

Language: Английский

Citations

2
Asgard archaea modulate potential methanogenesis substrates in wetland soil DOI Creative Commons
Luis E. Valentin-Alvarado, Kathryn E. Appler, Valerie De Anda

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 22, 2023

Abstract The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions soil ecosystems unknown. Of particular interest archaeal to methane cycling wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new lineage, the first genome Freyarchaeia, defined metabolism situ . Metatranscriptomics highlights high expression [NiFe]-hydrogenases, pyruvate oxidation carbon fixation via Wood-Ljungdahl pathway genes. Also highly expressed genes encoding enzymes amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification glycerol carbohydrate breakdown acetate formate. Overall, predicted be non-methanogenic acetogens, likely impacting reservoirs substrates production terrestrial ecosystems. One-Sentence Summary Complete archaea, coupled with metatranscriptomic data, indicate consumption compounds that known serve as wetlands.

Language: Английский

Citations

6