Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks

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

Published: Sept. 17, 2024

Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and complementarity networks. We apply this approach temperature gradient hot spring, unraveling the interplay between thermal stress cooperation. Our analysis reveals an increase in frequency of with rising temperatures. Amino acids, coenzyme A derivatives, carbohydrates emerge as key exchange metabolites, forming foundation for syntrophic which commensalistic take greater proportion than mutualistic ones. These exchanges are most prevalent phylogenetically distant species, especially archaea-bacteria collaborations, crucial adaptation harsh environments. Furthermore, identify significant positive correlation basal metabolite genome size disparity, potentially signifying means streamlined leverage cooperation metabolically richer partners. This phenomenon is also confirmed another composting system has similar wide range fluctuations. provides feasible way decipher mechanisms underlying microbial interactions, our findings suggested environmental regulates cooperative strategies thermophiles, while dependencies have been hardwired into their during co-evolutions.

Language: Английский

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Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Feb. 18, 2022

Abstract The SKY hot spring is a unique site filled with thick layer of plant litter. With the advancement next-generation sequencing, it now possible to mine many new biocatalyst sequences. In this study, we aimed (i) identify metataxonomic prokaryotes and eukaryotes in microbial mats using 16S 18S rRNA markers, (ii) explore carbohydrate degrading enzymes (CAZymes) that have high potential for future applications. Green mat, predominantly photosynthetic bacteria, was attached submerged or floating leaves At head, sediment mixture consisted debris, brownish-reddish gelatinous pale tan biofilm, grey-white filament biofilm. population head had higher percentage archaea hyperthermophiles than green mat. Concurrently, cataloged nearly 10,000 sequences CAZymes both brown biofilms shotgun metagenomic sequencing approach. These include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α- l -arabinofuranosidase, other CAZymes. conclusion, work elucidated due its rich lignocellulosic material, often absent springs. data collected from study serves as repository thermostable macromolecules, particular families glycoside hydrolases.

Language: Английский

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Bacterial community structure in geothermal springs on the northern edge of Qinghai-Tibet plateau

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 31, 2023

Introduction: In order to reveal the composition of subsurface hydrothermal bacterial community in zones magmatic tectonics and their response heat storage environments. Methods: this study, we performed hydrochemical analysis regional sequencing 16S rRNA microbial V4-V5 region 7 Pleistocene Lower Neogene hot water samples from Gonghe basin. Results: Two geothermal spring reservoirs study area were found be alkaline reducing environments with a mean temperature 24.83°C 69.28°C, respectively, major type hydrochemistry was SO 4 -Cl·Na. The structure microorganisms both types geologic thermal primarily controlled by temperature, environment intensity, hydrogeochemical processes. Only 195 ASVs shared across different environments, dominant genera recent temperate springs Thermus Hydrogenobacter , being typical thermophiles. correlation showed that overall level relative abundance relied on high slightly environment. Nearly all top species (53.99% total abundance) positively correlated pH, whereas they negatively ORP (oxidation–reduction potential), nitrate, bromine ions. Discussion: general, bacteria groundwater sensitive also relationship geochemical processes, such as gypsum dissolution, mineral oxidation, etc.

Language: Английский

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Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: April 9, 2024

Abstract Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate microbial biomass at these sites. Little is known about host-virus interactions environments. We analyzed virus community associated with algal mats three neighboring habitats (creek, endolithic, soil) Lemonade Creek, Yellowstone National Park (YNP), USA. find despite proximity, each habitat houses a unique collection of viruses, giant Megaviricetes, dominant all three. The early branching phylogenetic position genes encoded on metagenome assembled genomes (vMAGs) suggests YNP lineages are ancient origin and not due to multiple invasions from mesophilic habitats. existence genomic footprints adaptation thermophily vMAGs consistent this idea. geothermal sites originated ca. 1.5 Bya therefore relevant understanding biotic Earth.

Language: Английский

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Harmful and beneficial properties of cyanotoxins: Two sides of the same coin

Biotechnology Advances, Journal Year: 2023, Volume and Issue: 68, P. 108235 - 108235

Published: Aug. 10, 2023

Cyanotoxins are by definition "harmful agents" produced cyanobacteria. Their toxicity has been extensively studied and reviewed over the years. have commonly classified, based on their poisonous effects mammals, into three main classes, neurotoxins, hepatotoxins dermatotoxins, and, considering chemical features, mainly identified as peptides, alkaloids lipopolysaccharides. Here we propose a broader subdivision of cyanotoxins eight distinct taking account molecular structures, biosynthesis modes action: alkaloids, non-ribosomal polyketides, non-protein amino acids, indole organophosphates, lipopeptides lipoglycans. For each class, structures primary mechanisms representative reported. Despite powerful biological activities, only recently scientists considered biotechnological potential cyanotoxins, applications both in medical industrial settings, even if few these reached biotech market. In this perspective, discuss uses anticancer, antimicrobial, biocidal agents, common for cytotoxic compounds. Furthermore, action, describe peculiar bioactivities several cyanotoxin such local anaesthetics, antithrombotics, neuroplasticity promoters, immunomodulating antifouling agents. review, aim to stimulate research beneficial roles which require interdisciplinary cooperation facilitate discovery innovative biotechnologies.

Language: Английский

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Biotechnological Exploitation of Cyanobacteria and Microalgae for Bioactive Compounds

Published: Jan. 1, 2025

Language: Английский

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Distribution and Genomic Variation of Thermophilic Cyanobacteria in Diverse Microbial Mats at the Upper Temperature Limits of Photosynthesis

mSystems, Journal Year: 2022, Volume and Issue: 7(5)

Published: Aug. 18, 2022

Thermophilic cyanobacteria have been extensively studied in Yellowstone National Park (YNP) hot springs, particularly during decades of work on the thick laminated mats Octopus and Mushroom springs. However, focused studies outside these two springs lacking, especially regarding how physical chemical parameters along with community morphology influence genomic makeup organisms. Here, we used a metagenomic approach to examine existing at upper temperature limit photosynthesis. We examined 15 alkaline spring samples across six geographic areas YNP, all various morphology. recovered 22 metagenome-assembled genomes (MAGs) belonging thermophilic cyanobacteria, notably an uncultured Synechococcus-like taxon from setting photosynthesis, 73°C, addition Gloeomargarita. Furthermore, found that three distinct groups MAGs different ranges vary their makeup. very-high-temperature (up 73°C) lack key nitrogen metabolism genes implicated cellular stress responses diverge other MAGs. Across measured, was primary determinant taxonomic cyanobacterial total Fe, morphology, biogeography played additional role distribution abundance upper-temperature-limit-adapted These findings expand our understanding diversity YNP provide basis for interrogation understudied cyanobacteria. IMPORTANCE Oxygenic photosynthesis arose early microbial evolution-approximately 2.5 3.5 billion years ago-and entirely reshaped biological Earth. despite span time which has refined, it is strictly limited temperatures below barrier many processes able overcome. above 56°C circumneutral pH. Hot (YNP), large temperatures, pH, geochemistry, natural laboratory study within. While decades, vast majority within same geyser basin, both containing similar morphologies. Thus, drivers adaptations limits variety environmental understudied. Our new insights into content range samples.

Language: Английский

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Genome-scale identification and comparative analysis of transcription factors in thermophilic cyanobacteria

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Jan. 9, 2024

Abstract Background The transcription factors (TFs) in thermophilic cyanobacteria might represent a uniquely evolved gene repertoire light of the strong selective pressure caused by hostile habitats. Understanding molecular composition TF genes will facilitate further studies regarding verifying their exact biochemical functions and genetic engineering. However, limited information is available on TFs cyanobacteria. Herein, thorough investigation comparative analysis were performed to gain insights into 22 Results results suggested fascinating diversity among these thermophiles. abundance type diversified genomes. identified are speculated play various roles biological regulations. Further evolutionary genomic analyses revealed that HGT may be associated with plasticity Thermostichus Thermosynechococcus strains. Comparative also indicated different pattern between thermophiles corresponding mesophilic reference Moreover, unique putatively involved regulations, mainly as responses ambient changes, facilitating survive hot springs. Conclusion findings herein shed fundamental knowledge for research broad potential regulations environmental fluctuations.

Language: Английский

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Genomic and phenotypic characterization of Thermosynechococcus-like strains reveals eight species within the genus Thermosynechococcus and a novel genus Parathermosynechococcus gen. nov.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 197, P. 108094 - 108094

Published: May 8, 2024

Language: Английский

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Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias

Acta Biochimica Polonica, Journal Year: 2025, Volume and Issue: 71

Published: Jan. 8, 2025

Members of the families Thermosynechococcaceae and Thermostichaceae are well-known unicellular thermophilic cyanobacteria a non-thermophilic genus Pseudocalidococcus was newly classified into former. Analysis codon usage bias (CUB) cyanobacterial species inhabiting different thermal non-thermal niches will benefit understanding their genetic evolutionary characteristics. Herein, CUB context patterns protein-coding genes were systematically analyzed compared between members two families. Overall, nucleotide composition indices found to differ thermophiles non-thermophiles. The showed higher G/C content in base tended end with Correlation analysis indicated significant associations indices. results effective number codons, parity-rule 2, neutral correspondence analyses that mutational pressure natural selection primarily account for these species, but primary driving forces exhibit variation among genera. Moreover, optimal codons identified based on relative synonymous values genera even within In addition, pattern revealed specificity sequence start stop Intriguingly, clustering appeared be more related thermotolerance than phylogenomic relationships. conclusion, this study facilitates characteristics sources evolution surveyed clades provides insights adaptation environments.

Language: Английский

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