Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms

The ISME Journal, Journal Year: 2020, Volume and Issue: 14(6), P. 1369 - 1383

Published: Feb. 19, 2020

Massive releases of organic substrates during marine algal blooms trigger growth many clades heterotrophic bacteria. Algal polysaccharides represent the most diverse and structurally complex class these substrates, yet their role in shaping microbial community composition is poorly understood. We investigated, whether polysaccharide utilization capabilities contribute to niche differentiation Polaribacter spp. (class Flavobacteriia; known include relevant polysaccharide-degraders) that were abundant 2009-2012 spring southern North Sea. identified six distinct using phylogenetic phylogenomic analyses, quantified abundances via fluorescence situ hybridization, compared metagenome-assembled genomes, assessed gene expression metaproteomics. Four with niches dominating. 2-a comprised typical first responders featuring small genomes limited capacities. 3-a only 2010 possessed a sulfated α-glucoronomannan degradation potential. 3-b responded late had capacity utilize xylan. 1-a featured high numbers glycan genes particularly following Chattonella algae blooms. These results support hypothesis sympatric occupy Sea

Language: Английский

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Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: Jan. 21, 2020

Ecological differentiation between strains of bacterial species is shaped by genomic and metabolic variability. However, connecting genotypes to ecological niches remains a major challenge. Here, we linked geno- phenotypes contextualizing pangenomic, exometabolomic physiological evidence in twelve the marine bacterium Alteromonas macleodii, illuminating adaptive strategies carbon metabolism, microbial interactions, cellular communication iron acquisition. In A. macleodii strain MIT1002, secretion amino acids unique capacity for phenol degradation may promote associations with Prochlorococcus cyanobacteria. Strain 83-1 three novel Pacific isolates, featuring clonal genomes despite originating from distant locations, have profound abilities algal polysaccharide utilization but without detrimental implications Ecklonia macroalgae. Degradation toluene xylene, mediated via plasmid syntenic terrestrial Pseudomonas, was EZ55. Benzoate EC673 related chromosomal gene cluster shared mediterranea EC615, underlining that mobile genetic elements drive adaptations. Furthermore, revealed strain-specific production siderophores homoserine lactones, nutrient acquisition communication. Phenotypic variability corresponded different competitiveness co-culture geographic distribution, indicating linkages intraspecific diversity, interactions biogeography. The finding "ecological microdiversity" helps understanding widespread occurrence contributes interpretation niche specialization, population ecology biogeochemical roles.

Language: Английский

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North Sea spring bloom-associated Gammaproteobacteria fill diverse heterotrophic niches

Environmental Microbiome, Journal Year: 2021, Volume and Issue: 16(1)

Published: Aug. 17, 2021

Abstract Background The planktonic bacterial community associated with spring phytoplankton blooms in the North Sea is responsible for a large amount of carbon turnover an environment characterised by high primary productivity. Individual clades belonging to Gammaproteobacteria have shown similar population dynamics Bacteroidetes species , and are thus assumed fill competing ecological niches. Previous studies generated numbers metagenome assembled genomes metaproteomes from these environments, which can be readily mined identify populations performing potentially important ecosystem functions. In this study we attempt catalogue bloom-associated far attracted less attention than sympatric Alphaproteobacteria . Methods We annotated 120 non-redundant species-representative gammaproteobacterial bloom sampling campaigns covering four years 2010–2012 2016 using combination Prokka PfamScan, further confirmation via BLAST against NCBI-NR. also matched gene annotations 20 previously published those periods plus 2009. Results Metagenome clear capacity polysaccharide degradation dedicated clusters carbohydrate active enzymes were among most abundant during blooms. Many lacked clearly identifiable predicted substrates, although abundantly expressed loci uptake molecules identified metaproteomes. While larger biopolymers, sources reduced following algal blooms, likely main energy source, some specialised smaller organic compounds. Their substrates range amino acids, monosaccharides, DMSP, expected, such as terpenoids, aromatics biphenyls, well many ‘unknowns’. particular uncover much greater breadth apparent methylotrophic capability heretofore identified, present several order level without cultivated representatives. Conclusions Large today publicly available, containing wealth accessible information. Here variety metabolisms interest, include diverse potential heterotrophic niches Features here could fertile ground future experimental studies.

Language: Английский

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Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome

The ISME Journal, Journal Year: 2021, Volume and Issue: 16(3), P. 666 - 675

Published: Sept. 15, 2021

Abstract Glacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which clades ecologically successful in these nor understand potentially underlying mechanisms. Ecologically should be more prevalent across GFSs compared to other clades, reflected as clade-wise distinctly low phylogenetic turnover. However, methods assess such patterns currently missing. Here developed applied a novel analytical framework, “phyloscore analysis”, identify with lower spatial turnover than sediment twenty New Zealand. These constituted up 44% 64% community α-diversity abundance, respectively. Furthermore, both their abundance increased chlorophyll decreased, corroborating ecological success habitats largely devoid primary production. also contained elevated levels putative microdiversity others, could explain high prevalence GFSs. This hitherto unknown may threatened glaciers shrink, urging towards further genomic functional exploration microbiome.

Language: Английский

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Estuarine gradients dictate spatiotemporal variations of microbiome networks in the Chesapeake Bay

Environmental Microbiome, Journal Year: 2021, Volume and Issue: 16(1)

Published: Nov. 27, 2021

Abstract Background Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially those long residence time such as the Chesapeake Bay (CB). However, it is unclear how taxa cooccurr inter-taxa networks respond to environmental gradients estuaries. Results Here, we constructed co-occurrence on prokaryotic communities CB, which included seasonal samples from seven stations along salinity for three consecutive years. Our results showed that spatiotemporal of planktonic microbiomes promoted differentiations characteristics stability CB estuary. Prokaryotic exhibited a clear pattern where microbes were more closely connected during warm season compared associations cold season. In addition, stable lower (ocean side) than upper (freshwater side). Multivariate regression tree (MRT) analysis piecewise structural equation modeling (SEM) indicated temperature, total suspended substances nutrient availability, particulate carbon Chl , affected distribution groups, Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, Verrucomicrobia. Interestingly, abundant groups (such SAR11, Saprospiraceae Actinomarinaceae), rare including OM60 (NOR5) clade (Gammaproteobacteria), Micrococcales (Actinobacteria), NS11-12 marine group (Bacteroidetes) contributed greatly Bay. Modularity cluster structures varied spatiotemporally, provided valuable insights into ‘small world’ (a interconnected species), network stability, habitat partitioning/preferences. Conclusion shed light alter ecosystem, well their adaptability disturbances complexity stability.

Language: Английский

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