New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient DOI Creative Commons
Miguel A. Cevallos, Mauro Degli Esposti

Microorganisms, Journal Year: 2022, Volume and Issue: 10(2), P. 455 - 455

Published: Feb. 16, 2022

We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding classification of an increasing number marine metagenome-assembled genomes (MAGs) that remain poorly defined their taxonomic position within Alphaproteobacteria. The traditional NCBI taxonomy increasingly complemented by Genome Taxonomy Database (GTDB), but two taxonomies differ considerably especially from ocean metagenomes. analyzed Alphaproteobacteria lineages most common environments, using integrated approaches phylogenomics and functional profiling metabolic features define aerobic metabolism. Using protein markers such as NuoL, largest membrane subunit complex I, we have identified new clades specific to niches with steep oxygen gradients (oxycline). These relatives among MAGs found anoxic strata Lake Tanganyika together lineage distinct either Rhodospirillales or Sneathiellales. characterized particular 'oxycline' clade. Our analysis also reveals clues ancestry mitochondria, likely evolved oxycline environments.

Language: Английский

A phylogenomic framework for charting the diversity and evolution of giant viruses DOI Creative Commons
Frank O. Aylward, Mohammad Moniruzzaman, Anh D. Ha

et al.

PLoS Biology, Journal Year: 2021, Volume and Issue: 19(10), P. e3001430 - e3001430

Published: Oct. 27, 2021

Large DNA viruses of the phylum Nucleocytoviricota have recently emerged as important members ecosystems around globe that challenge traditional views viral complexity. Numerous this cannot be classified within established families been reported, and there is presently a strong need for robust phylogenomic taxonomic framework these viruses. Here, we report comprehensive analysis Nucleocytoviricota, present set giant virus orthologous groups (GVOGs) together with benchmarked reference phylogeny, delineate hierarchical taxonomy phylum. We show majority diversity can partitioned into 6 orders, 32 families, 344 genera, substantially expanding number currently recognized ranks integrate our results has adopted all to establish unifying study diversity, evolution, environmental distribution.

Language: Английский

Citations

143
Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean DOI Creative Commons
Tom O. Delmont, Morgan Gaïa, Damien Daniel Hinsinger

et al.

Cell Genomics, Journal Year: 2022, Volume and Issue: 2(5), P. 100123 - 100123

Published: April 28, 2022

Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation culture collections limits our understanding of the evolutionary history genomic underpinnings ecosystems. Here, we used 280 billion

Language: Английский

Citations

137
An estimate of the deepest branches of the tree of life from ancient vertically evolving genes DOI Creative Commons
Edmund R. R. Moody, Tara Mahendrarajah, Nina Dombrowski

et al.

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Feb. 22, 2022

Core gene phylogenies provide a window into early evolution, but different sets and analytical methods have yielded substantially views of the tree life. Trees inferred from small set universal core genes typically supported long branch separating archaeal bacterial domains. By contrast, recent analyses broader non-ribosomal suggested that Archaea may be less divergent Bacteria, estimates inter-domain distance are inflated due to accelerated evolution ribosomal proteins along branch. Resolving this debate is key determining diversity domains, shape life, our understanding course cellular evolution. Here, we investigate evolutionary history marker debate. We show reduced Archaea-Bacteria (AB) length result transfers hidden paralogy in expanded set. analysis broad range manually curated datasets an evenly sampled 700 Bacteria reveals current likely underestimate AB substitutional saturation poor model fit; best-performing phylogenetic markers tend support longer lengths; lengths statistically indistinguishable. Furthermore, phylogeny 27 highest-ranked recovers clade DPANN at base places Candidate Phyla Radiation (CPR) within as sister group Chloroflexota.

Language: Английский

Citations

67
ATP synthase evolution on a cross-braced dated tree of life DOI Creative Commons
Tara Mahendrarajah, Edmund R. R. Moody, Dominik Schrempf

et al.

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

Published: Nov. 17, 2023

Abstract The timing of early cellular evolution, from the divergence Archaea and Bacteria to origin eukaryotes, is poorly constrained. ATP synthase complex thought have originated prior Last Universal Common Ancestor (LUCA) analyses genes, together with ribosomes, played a key role in inferring rooting tree life. We reconstruct evolutionary history synthases using an expanded taxon sampling set develop phylogenetic cross-bracing approach, constraining equivalent speciation nodes be contemporaneous, based on imprint endosymbioses ancient gene duplications. This approach results highly resolved, dated species establishes absolute timeline for evolution. Our show that into F- A/V-type lineages was very event evolution dating back more than 4 Ga, potentially predating diversification Bacteria. cross-braced, life also provides insight recent transitions including eukaryogenesis, showing eukaryotic nuclear mitochondrial diverged their closest archaeal (2.67-2.19 Ga) bacterial (2.58-2.12 relatives at approximately same time, slightly longer stem-lineage.

Language: Английский

Citations

41
Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota DOI Creative Commons
Timothy D’Angelo, Jacqueline Goordial, Melody R. Lindsay

et al.

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(6), P. 891 - 902

Published: April 3, 2023

Abstract The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important biogeochemical industrial processes. These are common inhabitants of marine terrestrial subsurface environments contain members capable diverse physiologies in addition nitrite oxidation complete ammonia oxidation. Here, we use phylogenomics gene-based analysis with ancestral state reconstruction gene-tree–species-tree reconciliation methods investigate the life histories these two phyla. We find that basal clades both primarily inhabit environments. genomes appear smaller more densely coded than later-branching clades. extant share many traits inferred be present respective ancestors, including hydrogen, one-carbon, sulfur-based metabolisms. Later-branching groups, namely frequently studied classes Nitrospiria Nitrospinia, characterized by genome expansions driven either de novo origination or laterally transferred genes encode functions expanding metabolic repertoire. include gene clusters perform most well known for. Our analyses support replicated evolutionary bacterial phyla, modern representing a genomic repository for coding potential traits.

Language: Английский

Citations

33
Valid publication of names of two domains and seven kingdoms of prokaryotes DOI
Markus Göker, Aharon Oren

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2024, Volume and Issue: 74(1)

Published: Jan. 22, 2024

The International Code of Nomenclature Prokaryotes (ICNP) now includes the categories domain and kingdom. For purpose valid publication their names under ICNP, we consider here two known domains, ‘ Bacteria ’ Archaea ’, as well a number taxa suitable for rank kingdom, based on previous phylogenetic taxonomic studies. It is proposed to subdivide into kingdoms Bacillati , Fusobacteriati Pseudomonadati Thermotogati . This arrangement reflects contemporary hypotheses proposals cell wall structure, including ‘diderms’ vs. ‘monoderms’, Gracilicutes Firmicutes Negibacteria Unibacteria Hydrobacteria Terrabacteria Hydrobacterida Terrabacterida ’. include Methanobacteriati Nanobdellati Thermoproteati reflecting division Euryarchaeota ‘DPANN superphylum’ ‘TACK superphylum’.

Language: Английский

Citations

14
The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA DOI
Patrick Forterre

Journal of Molecular Evolution, Journal Year: 2024, Volume and Issue: 92(5), P. 550 - 583

Published: Aug. 19, 2024

Language: Английский

Citations

8
Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales DOI Creative Commons
Carolina A. Martínez-Gutiérrez, Frank O. Aylward

PLoS Genetics, Journal Year: 2022, Volume and Issue: 18(5), P. e1010220 - e1010220

Published: May 23, 2022

The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over last few decades. Although preferential loss genes observed prokaryotes is explained through deletional bias, factors promoting preventing fixation such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider potential bias introduced by shared ancestry many lineages, which critical when using species as data points because dependence residuals. In study, we investigated distributions across a broad diversity to evaluate if trait phylogenetically conserved at phylogenetic scales. After model fit, Pagel’s lambda indicated strong signal data, suggesting diversification influenced histories. We used generalized least-squares analysis (PGLS) test whether phylogeny influences predictability from dN/dS ratios 16S copy number, two variables previously linked size. These results confirm failure account for history can lead biased interpretations predictors. Overall, our indicate although rapidly gain lose genetic material transfers deletions, respectively, still be recovered scales should taken into inferring drivers evolution.

Language: Английский

Citations

35
Deep-branching acetogens in serpentinized subsurface fluids of Oman DOI Creative Commons
Daniel R. Colman, E. Kraus, Patrick H. Thieringer

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(42)

Published: Oct. 10, 2022

Little is known of acetogens in contemporary serpentinizing systems, despite widely supported theories that serpentinite-hosted environments the first life on Earth via acetogenesis. To address this knowledge gap, genome-resolved metagenomics was applied to subsurface fracture water communities from an area active serpentinization Samail Ophiolite, Sultanate Oman. Two deeply branching putative bacterial acetogen types were identified belonging Acetothermia (hereafter, I and II) exhibited distinct distributions among waters with lower higher water–rock reaction (i.e., influence), respectively. Metabolic reconstructions revealed contrasting core metabolic pathways type II Acetothermia, including acetogenic pathway components (e.g., bacterial- vs. archaeal-like carbon monoxide dehydrogenases [CODH], respectively), hydrogen use drive acetogenesis, chemiosmotic potential generation respiratory (type I) or canonical ferredoxin-based complexes II). Notably, allow for serpentinization-derived substrates implicate them as key primary producers hyperalkaline serpentinite environments. Phylogenomic analyses indicate 1) CODH genomes those other serpentinite-associated Bacteria derive a rooted horizontal transfer origin archaeal methanogens 2) are earliest evolving lineages. The discovery dominant early-branching largest near-surface formation provides insight into physiological traits likely facilitated rock-supported flourish primitive possibly rocky planets undergoing serpentinization.

Language: Английский

Citations

32
Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics DOI Creative Commons
Joanne Boden,

Juntao Zhong,

R. Anderson

et al.

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

Published: May 2, 2024

Abstract Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations the Precambrian ocean, during life’s origin and early evolution, vary over several orders magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, their bioavailability on Earth remains unknown. Here, we reconstruct phylogenomic record life find that transporting genes ( pnas ) evolved Paleoarchean (ca. 3.6-3.2 Ga) are consistent with above modern levels > 3 µM). The first gene optimized for low pstS ; <1 µM) appeared around same time or Mesoarchean depending reconstruction method. Most enzymatic pathways metabolising emerged expanded across tree later. This includes phosphonate-catabolising CP-lyases, phosphite-oxidising hypophosphite-oxidising pathways. CP-lyases particularly abundant dissolved below 0.1 µM. Our results thus indicate at least local regions declining through Archean, possibly linked phosphate-scavenging Fe(III), which limited productivity. However, did not become widely used until after Paleoproterozoic Great Oxidation Event (2.3 Ga), expansion biosphere time.

Language: Английский

Citations

6