Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor DOI
Kathryn E. Appler, James P. Lingford, Xianzhe Gong

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 4, 2024

Abstract Asgard archaea were pivotal in the origin of complex cellular life. Hodarchaeales (Asgardarchaeota class Heimdallarchaeia) recently shown to be closest relatives eukaryotes. However, limited sampling these constrains our understanding their ecology and evolution 1–3 , including anticipated role eukaryogenesis. Here, we nearly double number Asgardarchaeota metagenome-assembled genomes (MAGs) 869, 136 new Heimdallarchaeia (49 Hodarchaeales) several novel lineages. Examining global distribution revealed Hodarcheales are primarily found coastal marine sediments. Detailed analysis metabolic capabilities guilds distinct from other Asgardarchaeota. These encode hallmarks aerobic eukaryotes, electron transport chain complexes (III IV), biosynthesis heme, response reactive oxygen species (ROS). The predicted structural architecture membrane-bound hydrogenases includes additional Complex-I-like subunits potentially increasing proton motive force ATP synthesis. CoxD, which regulates (ETC) Thus, key for respiration may have been present Asgard-eukaryotic ancestor. Moreover, that is a variety oxic environments. This expanded diversity reveals Archaea likely conferred energetic advantages during early stages eukaryogenesis, fueling complexity.

Language: Английский

Metagenomic and metatranscriptomic analyses reveal uncharted microbial constituents responsible for polyhydroxybutyrate biodegradation in coastal waters DOI Creative Commons
Kyohei Kuroda, Kyosuke Yamamoto, Rino Isshiki

et al.

Journal of Hazardous Materials, Journal Year: 2025, Volume and Issue: 487, P. 137202 - 137202

Published: Jan. 13, 2025

Language: Английский

Citations

2
Microbial manganese redox cycling drives co-removal of nitrate and ammonium DOI
Xuan Wang, Tianbiao Liu, Xiaowei Wang

et al.

Journal of Environmental Management, Journal Year: 2025, Volume and Issue: 375, P. 124095 - 124095

Published: Jan. 22, 2025

Language: Английский

Citations

1
Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode DOI Creative Commons
Daniel Tamarit, Stephan Köstlbacher, Kathryn E. Appler

et al.

Systematic and Applied Microbiology, Journal Year: 2024, Volume and Issue: 47(4), P. 126525 - 126525

Published: June 15, 2024

Asgardarchaeota, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest relatives of eukaryotes. Despite their prevalence in scientific literature, name Asgardarchaeota lacks nomenclatural validation. Here, we describe novel high-quality metagenome-assembled genome (MAG), AB3033_2

Language: Английский

Citations

7
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
Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution DOI Creative Commons
Daniel R. Colman, Lisa M. Keller,

Emilia Arteaga-Pozo

et al.

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

Published: Aug. 29, 2024

The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat life's origin. However, extent that contemporary thermophiles their habitats reflect those likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured 1022 metagenome-assembled-genomes (MAGs) generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park analysed alongside 444 MAGs 35 published metagenomes. We used these data to evaluate co-variation MAG taxonomy, metabolism, phylogeny as function hot spring geochemistry. found cohorts functions are discretely distributed across pH gradients different provinces. Acidic or circumneutral/alkaline harbor branched later enriched sulfur- arsenic-based O

Language: Английский

Citations

6
Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires DOI Creative Commons
Marie C. Schoelmerich, Lynn Ly, Jacob West-Roberts

et al.

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

Published: June 26, 2024

Abstract Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “ Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and reconstruct new genomes. 13 four near-complete linear share 40 genes that define a largely syntenous genome backbone. We use these conserved identify peatland soil delineate Borg phylogeny, revealing two major clades. Remarkably, encoding nanowire-like electron-transferring cytochromes cell surface proteins more highly expressed than those host Methanoperedens , indicating augment the activity in situ. reconstructed first 4.00 Mbp for is inferred be predicted its methylation motifs, which differ pervasive TC CC motifs Borgs. Thus, may enable distinguish their Very high ratios structural predictions suggest capable encapsulation. The findings clearly as distinct class ECE with shared genomic signatures, establish diversification common ancestor genetic inheritance, raise possibility periodic existence outside cells.

Language: Английский

Citations

5
Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns DOI Creative Commons
Raphael Eisenhofer, Antton Alberdi, Ben J. Woodcroft

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 17, 2024

Abstract Metagenomes often contain many reads derived from eukaryotes. However, there is usually no reliable method for estimating the prevalence of non-microbial in a metagenome, forcing analysis techniques to make often-faulty assumption that all are microbial. For instance, success metagenome-assembled genome (MAG) recovery efforts assessed by number mapped recovered MAGs, procedure which will underestimate true fidelity if eukaryotic present. Here we present “SingleM microbial_fraction” (SMF), scalable algorithm robustly estimates bacterial and archaeal average microbial size. SMF does not use reference data can be applied any Illumina metagenome. Based on SMF, propose “Domain-Adjusted Mapping Rate” (DAMR) as an improved metric assess metagenomes. We benchmark simulated real data, demonstrate how DAMRs guide recovery. Applying 136,284 publicly available metagenomes, report substantial variation fractions biome-specific patterns abundance, providing insights into microorganisms eukaryotes distributed across Earth. Finally, show amounts human host DNA sequence have been deposited public metagenome repositories, possibly counter ethical directives mandate screening these prior release. As adoption metagenomic sequencing continues grow, foresee being valuable tool appraisal efforts, global microorganism distribution.

Language: Английский

Citations

4
Rapid species-level metagenome profiling and containment estimation with sylph DOI Creative Commons
Jim Shaw, Yun William Yu

Nature Biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 8, 2024

Abstract Profiling metagenomes against databases allows for the detection and quantification of microorganisms, even at low abundances where assembly is not possible. We introduce sylph, a species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k -mer statistics, enabling ANI-based taxa detection. On Critical Assessment Metagenome Interpretation II (CAMI2) Marine dataset, sylph was most accurate profiling method seven tested. For multisample profiling, took >10-fold less central processing unit time compared to Kraken2 used 30-fold memory. Sylph’s ANI provided an orthogonal signal abundance, allowing metagenome-wide association study Parkinson disease (PD) 289,232 genomes while confirming known butyrate–PD associations strain level. Sylph <1 min 16 GB random-access memory profile 85,205 prokaryotic 2,917,516 viral genomes, detecting more sequences in human gut RefSeq. offers precise, efficient with estimation low-coverage genomes.

Language: Английский

Citations

4
Genome-resolved adaptation strategies of Rhodobacterales to changing conditions in the Chesapeake and Delaware Bays DOI Creative Commons

Mir Alvee Ahmed,

Barbara J. Campbell

Applied and Environmental Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

ABSTRACT The abundant and metabolically versatile aquatic bacterial order, Rhodobacterales , influences marine biogeochemical cycles. We assessed metagenome-assembled genome (MAG) abundance, estimated growth rates, potential expressed functions in the Chesapeake Delaware Bays, two important US estuaries. Phylogenomics of draft draft/closed genomes from this study others placed 46 nearly complete MAGs these bays into 11 genera, many were not well characterized. Their abundances varied between influenced by temperature, salinity, silicate phosphate concentrations. genera possessed unique shared genes for transporters, photoheterotrophy, complex carbon degradation, nitrogen, sulfur metabolism reflecting their seasonal differences abundance activity. Planktomarina genomospecies more ubiquitous than niche specialists, HIMB11, CPC320, LFER01, MED-G52. rates correlated to various factors including concentrations, cell density, light. Metatranscriptomic analysis four commonly revealed that aerobic anoxygenic photoheterotrophy-associated transcripts highly at night. These also differentially CO oxidation nutrient transport use different environmental conditions. Phosphate concentrations light penetration Bay likely contributed higher HIMB11 respectively, summer where they maintained ribosome prevented physiological gene expression constraints downregulating transporter compared Bay. Our highlights spatial temporal shifts estuarine within reflected through metabolisms, activity changes. IMPORTANCE In web global cycling, emerge as key players, exerting a profound influence dynamic While previous studies have primarily investigated organisms ecosystems, delves roles environments using combination metagenomic metatranscriptomic analyses. uncovered range generalists each exhibiting distinct patterns profiles. This diversity equips them with capacity thrive amidst varying conditions encountered habitats. Crucially, our findings illuminate adaptable nature revealing energy production pathways diverse resource management, especially during phytoplankton or algal blooms. Whether adopting free-living particle-attached existence, demonstrate remarkable flexibility metabolic strategies, underscoring pivotal role driving ecosystem dynamics ecosystems.

Language: Английский

Citations

0
Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities DOI Creative Commons
Matthew S. Schechter, Florian Trigodet, Iva Veseli

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 15, 2025

The increasing availability of microbial genomes is essential to gain insights into ecology and evolution that can propel biotechnological biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue from diverse habitats. However, ability explain how well a set account for diversity given environment remains challenging individual studies or biome-specific databases. Here we present EcoPhylo, computational workflow characterize phylogeography any gene family through integrated analyses metagenomes, our application this approach ribosomal proteins quantify phylogeny-aware rates across three biomes. Our findings show vary widely taxa biomes, single amplified genomes, metagenome-assembled isolate non-uniform yet quantifiable representation environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies conjunction with distribution patterns clades environments, providing means assess benchmark biome-level collections.

Language: Английский

Citations

0