Community conservatism is widespread throughout microbial phyla and environments DOI Creative Commons
Lukas Malfertheiner, Janko Tackmann, João F. Matias Rodrigues

et al.

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

Published: Nov. 7, 2024

Abstract Evolution gives rise to various long-term phenomena, including Phylogenetic signal, which describes the tendency of related biological taxa resemble each other in morphology and function. Related tend also live similar ecological niches – this trend is termed Niche conservatism . Both concepts are widely used understand crucial aspects evolu1on specia1on well-established animals plants. The extension these microorganisms however challenging thus far only assumed. Here, we hypothesize that two closely microbial species, if indeed both their niche, should be found samples with community compositions. We propose “community conservatism” refer this, leverage a database millions hundreds thousands pairs assess relatedness similarity communities they occupy. Our findings reveal can observed globally all environments phyla tested, varying extents. Ecologically specialized show stronger signal than generalists, discerned over nearly taxonomic ranks. Analyzing shows promise advance our understanding evolution, speciation, mechanisms governing assembly microorganisms. Furthermore, it reintegrate parameters into Operational Taxonomic Unit delimitation.

Language: Английский

Predicting microbial growth conditions from amino acid composition DOI Creative Commons
Tyler P. Barnum,

Alexander Crits‐Christoph,

Michael Molla

et al.

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

Published: March 22, 2024

The ability to grow a microbe in the laboratory enables reproducible study and engineering of its genetics. Unfortunately, majority microbes tree life remain uncultivated because effort required identify culturing conditions. Predictions viable growth conditions guide experimental testing would be highly desirable. While carbon energy sources can computationally predicted with annotated genes, it is harder predict other requirements for such as oxygen, temperature, salinity, pH. Here, we developed genome-based computational models capable predicting oxygen tolerance (92% balanced accuracy), optimum temperature (R2=0.73), salinity (R2=0.81) pH (R2=0.48) novel taxonomic microbial families without requiring functional gene annotations. Using genome sequences 15,596 bacteria archaea, found that amino acid frequencies are predictive requirements. As little two acids 88% accuracy. cellular localization proteins compute improved prediction (R2 increase 0.36). Because these do not rely on presence or absence specific they applied incomplete genomes, 10% completeness. We our all 85,205 species sequenced archaea enriched thermophiles, anaerobes, acidophiles. Finally, 3,349 environmental samples metagenome-assembled genomes showed individual within community have differing This work guides identification constraints cultivation diverse microbes.

Language: Английский

Citations

12
Persistence selection between simulated biogeochemical cycle variants for their distinct effects on the Earth system DOI Creative Commons
Richard Boyle, Edmund R. R. Moody, Gunnar Babcock

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(7)

Published: Feb. 12, 2025

The average long-term impact of Darwinian evolution on Earth’s habitability remains extremely uncertain. Recent attempts to reconcile this uncertainty by “Darwinizing” nonreplicating biogeochemical processes subject persistence-based selection conform with the historicity geochemical record but lack mechanistic clarity. Here, we present a theoretical framework showing how: 1) A “cycle-biota-variant” (CBV) can be defined non-arbitrarily as one biologically facilitated pathway for net recycling an essential element, plus genotypes driving relevant interconversion reactions. 2) Distinct CBVs individuated if they have climatic or side effects that feed-back relative persistence. 3) separation spatial/temporal scales between dynamics such and those conventional introduce degree randomness into relationship their Earth system properties, loosely analogous biochemical causes evolutionary genetic mutation. 4) Threshold behavior in climate feedback accentuate biotic impacts lead CBV-level “competitive exclusion”. 5) persistence is observationally distinguishable from genotype-level strong covariance “internal” CBV properties (genotypes reactions) “external” effects, which argue fitness traits under selection. These factors cannot circumvent basic fact local natural will often favor phenotypes ultimately destabilize large-scale geochemical/climatic properties. However, claim our results nevertheless demonstrate coherence persistence-selection non-replicating life–environment interaction patterns therefore broad applicability.

Language: Английский

Citations

1
A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism DOI Creative Commons
Felix J. Elling, Fabien Pierrel,

Sophie-Carole Chobert

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(8)

Published: Feb. 20, 2025

The dominant organisms in modern oxic ecosystems rely on respiratory quinones with high redox potential (HPQs) for electron transport aerobic respiration and photosynthesis. diversification of quinones, from low (LPQ) anaerobes to HPQs aerobes, is assumed have followed Earth's surface oxygenation ~2.3 billion years ago. However, the evolutionary origins remain unresolved. Here, we characterize structure biosynthetic pathway an ancestral HPQ, methyl-plastoquinone (mPQ), that unique bacteria phylum Nitrospirota. mPQ structurally related two previously known HPQs, plastoquinone Cyanobacteriota/chloroplasts ubiquinone Pseudomonadota/mitochondria, respectively. We demonstrate a common origin three HPQ pathways predates emergence Nitrospirota, Cyanobacteriota, Pseudomonadota. An evolved ≥ 3.4 ago extinct lineage was laterally transferred these phyla ~2.5 3.2 show Cyanobacteriota Pseudomonadota were ancestrally thus propose metabolism using significantly oxygenation. Two later obtained by eukaryotes through endosymbiosis forming chloroplasts mitochondria, enabling their rise dominance ecosystems.

Language: Английский

Citations

1
An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota DOI Creative Commons

Ella McReynolds,

Mostafa S. Elshahed, Noha H. Youssef

et al.

Microbial Genomics, Journal Year: 2025, Volume and Issue: 11(1)

Published: Jan. 29, 2025

Members of the phylum Acidobacteriota inhabit a wide range ecosystems including soils. We analysed global patterns distribution and habitat preferences various lineages across major (soil, engineered, host-associated, marine, non-marine saline alkaline terrestrial non-soil ecosystems) in 248 559 publicly available metagenomic datasets. Classes Terriglobia , Vicinamibacteria Blastocatellia Thermoanaerobaculia were highly ubiquitous showed clear preference to soil over habitats, while classes Aminicenantia Holophagae habitats. However, specific observed, most generalists rather than specialists, with genomic and/or fragments recovered from habitats at levels taxonomic resolution. Comparative analysis 1930 genomes strongly indicates that phylogenetic affiliation plays more important role which genome was shaping characteristics metabolic capacities . The observed lack strong specialization habitat-transition-driven lineage evolution suggest ready cross-colonization between posit such capacity is key successful establishment as component microbiomes post-ecosystem disturbance events or during pedogenesis.

Language: Английский

Citations

0
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution DOI Creative Commons
Tom A. Williams, Adrián Davín, Lénárd L. Szánthó

et al.

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

Published: Jan. 1, 2024

In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along species tree explain differences between them via evolutionary events including duplications, transfers, losses. Here, we describe provides natural framework genome evolution highlight applications ancestral content inference, the rooting of trees, insights into metabolic ecological transitions they yield. Reconciliation analyses have elucidated diverse lineages, from Chlamydiae Asgard archaea, shedding light on adaptation, host-microbe interactions, symbiotic relationships. However, there are many opportunities broader application in microbiology. Continuing improvements make models more realistic scalable, integration metadata such habitat, pH, temperature, oxygen use offer enormous potential understanding rich tapestry life.

Language: Английский

Citations

3
An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota DOI

Ella McReynolds,

Mostafa S. Elshahed, Noha H. Youssef

et al.

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

Published: July 5, 2024

Abstract Members of the phylum Acidobacteriota inhabit a wide range ecosystems including soils. We analyzed global patterns distribution and habitat preferences various lineages across major (soil, engineered, host-associated, marine, non-marine saline alkaline, terrestrial non-soil ecosystem) in 248,559 publicly available metagenomic datasets. Classes Terriglobia, Vicinamibacteria, Blastocatellia, Thermoanaerobaculia were highly ubiquitous showed clear preference to soil over habitats, class Polarisedimenticolia comparable ubiquity between while classes Aminicenantia Holophagae habitats. However, specific observed, most generalists rather than specialists, with genomic and/or fragments recovered from habitats at levels taxonomic resolution. Comparative analysis 1930 genomes strongly indicates that phylogenetic affiliation plays more important role which genome was shaping characteristics metabolic capacities . The observed lack strong specialization transition driven lineage evolution suggest ready cross colonization posit such capacity is key successful establishment as component microbiomes post ecosystem disturbance events or during pedogenesis.

Language: Английский

Citations

0
A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism DOI Creative Commons
Felix J. Elling, Fabien Pierrel,

Sophie-Carole Chobert

et al.

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

Published: July 27, 2024

The dominant organisms in modern oxic ecosystems rely on respiratory quinones with high redox potential (HPQs) for electron transport aerobic respiration and photosynthesis. diversification of quinones, from low anaerobes to HPQs aerobes, is assumed have followed Earth's surface oxygenation ~2.3 billion years ago. However, the evolutionary origins remain unresolved. Here, we reconstruct biosynthetic pathway a novel HPQ, methyl-plastoquinone, that unique bacteria phylum Nitrospirota. We demonstrate three extant HPQ pathways, Nitrospirota, Cyanobacteriota, Pseudomonadota, share common origin predates emergence these phyla. show metabolism using ancestral Cyanobacteriota Pseudomonadota significantly oxygenation.

Language: Английский

Citations

0
Community conservatism is widespread throughout microbial phyla and environments DOI Creative Commons
Lukas Malfertheiner, Janko Tackmann, João F. Matias Rodrigues

et al.

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

Published: Nov. 7, 2024

Abstract Evolution gives rise to various long-term phenomena, including Phylogenetic signal, which describes the tendency of related biological taxa resemble each other in morphology and function. Related tend also live similar ecological niches – this trend is termed Niche conservatism . Both concepts are widely used understand crucial aspects evolu1on specia1on well-established animals plants. The extension these microorganisms however challenging thus far only assumed. Here, we hypothesize that two closely microbial species, if indeed both their niche, should be found samples with community compositions. We propose “community conservatism” refer this, leverage a database millions hundreds thousands pairs assess relatedness similarity communities they occupy. Our findings reveal can observed globally all environments phyla tested, varying extents. Ecologically specialized show stronger signal than generalists, discerned over nearly taxonomic ranks. Analyzing shows promise advance our understanding evolution, speciation, mechanisms governing assembly microorganisms. Furthermore, it reintegrate parameters into Operational Taxonomic Unit delimitation.

Language: Английский

Citations

0