Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan

Nature Microbiology, Год журнала: 2020, Номер 5(8), С. 1026 - 1039

Опубликована: Май 25, 2020

Язык: Английский

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In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes

The ISME Journal, Год журнала: 2019, Номер 13(11), С. 2800 - 2816

Опубликована: Июль 17, 2019

Abstract We investigated Bacteroidetes during spring algae blooms in the southern North Sea 2010–2012 using a time series of 38 deeply sequenced metagenomes. Initial partitioning yielded 6455 bins, from which we extracted 3101 metagenome-assembled genomes (MAGs) including 1286 MAGs covering ~120 mostly uncultivated species. identified 13 dominant, recurrent clades carrying restricted set conserved polysaccharide utilization loci (PULs) that likely mediate bulk bacteroidetal algal degradation. The majority PULs were predicted to target diatom storage laminarin, alpha-glucans, alpha-mannose-rich substrates, and sulfated xylans. Metaproteomics at 14 selected points revealed expression SusC-like proteins targeting all these substrates. Analyses abundant key players their PUL repertoires over furthermore suggested fewer simpler polysaccharides dominated early bloom stages, more complex became available as progressed.

Язык: Английский

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Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations

The ISME Journal, Год журнала: 2018, Номер 13(2), С. 388 - 401

Опубликована: Сен. 25, 2018

Язык: Английский

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Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Янв. 11, 2019

Abstract Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around world, evidence supports photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with remineralization high molecular weight organic matter. Divided between two clades, distinct ecological patterns that are not understood based on limited number available genomes. Here, I present comparative genomic analysis 250 genomes, providing comprehensive investigation these mesophilic archaea. This identifies 17 subclades including nine previously lacked reference metabolic potential distribution genera reveals roles environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean mesopelagic proteorhodopsins, common all other subclades.

Язык: Английский

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Environmental vulnerability of the global ocean epipelagic plankton community interactome

Science Advances, Год журнала: 2021, Номер 7(35)

Опубликована: Авг. 27, 2021

A global photic-ocean plankton ecological network predicts distinct vulnerabilities to environmental change across marine biomes.

Язык: Английский

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Benchmarking microbial growth rate predictions from metagenomes

The ISME Journal, Год журнала: 2020, Номер 15(1), С. 183 - 195

Опубликована: Сен. 16, 2020

Growth rates are central to understanding microbial interactions and community dynamics. Metagenomic growth estimators have been developed, specifically codon usage bias (CUB) for maximum "peak-to-trough ratio" (PTR) in situ rates. Both were originally tested with pure cultures, but natural populations more heterogeneous, especially individual cell histories pertinent PTR. To test these methods, we compared predictors observed of freshly collected marine prokaryotes unamended seawater. We prefiltered diluted samples remove grazers greatly reduce virus infection, so net approximated gross growth. sampled over 44 h abundances metagenomes, generating 101 metagenome-assembled genomes (MAGs), including Actinobacteria, Verrucomicrobia, SAR406, MGII archaea, etc. tracked each MAG population by cell-abundance-normalized read recruitment, finding 0 5.99 per day, the first reported several groups, used as benchmarks. PTR, calculated three rarely correlated (r ~-0.26-0.08), except rapidly growing γ-Proteobacteria ~0.63-0.92), while CUB moderately well = 0.57). This suggests that current PTR approaches poorly predict actual most bacterial populations, can be from genomic characteristics.

Язык: Английский

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Seasonal niche differentiation among closely related marine bacteria

The ISME Journal, Год журнала: 2021, Номер 16(1), С. 178 - 189

Опубликована: Июль 20, 2021

Abstract Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of bacteria a coastal oligotrophic series station, tested how similar temporal niche closely related taxa is, and what are environmental parameters modulating their patterns. We further explored conserved is at higher taxonomic levels. The community presented recurrent patterns seasonality for 297 out 6825 amplicon sequence variants (ASVs), which constituted almost half total relative (47%). For certain genera, similarity decreased as nucleotide divergence 16S rRNA gene increased, pattern compatible with selection through filtering. Additionally, observed evidence differentiation within various genera seen by distinct taxa. At broader levels, coherent trends did not exist class level, while order family ranks depended on that existed genus level. This study identifies coexistence some bacterial groups others environment subjected to strong seasonality.

Язык: Английский

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Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom

The ISME Journal, Год журнала: 2021, Номер 15(8), С. 2336 - 2350

Опубликована: Март 1, 2021

Abstract Algal blooms produce large quantities of organic matter that is subsequently remineralised by bacterial heterotrophs. Polysaccharide a primary component algal biomass. It has been hypothesised individual heterotrophic niches during are in part determined the available polysaccharide substrates present. Measurement expression TonB-dependent transporters, often specific for uptake, might serve as proxy assessing consumption over time. To investigate this, we present here high-resolution metaproteomic and metagenomic datasets from bacterioplankton 2016 spring phytoplankton bloom at Helgoland island southern North Sea, profiles transporters bloom, which demonstrate importance both Gammaproteobacteria Bacteroidetes degraders polysaccharide. were most highly expressed protein class, split approximately evenly between Bacteroidetes, totalling on average 16.7% all detected proteins bloom. About 93% these predicted to take up matter, about 12% target class. Most significantly, observed change substrate specificities time, was not reflected corresponding data. From conclude cell wall-related compounds containing fucose, mannose, xylose mostly utilised later stages, whereas glucose-based storage molecules including laminarin, glycogen, starch used throughout. Quantification could therefore be key understanding marine carbon cycling.

Язык: Английский

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Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S

Environmental Microbiology, Год журнала: 2021, Номер 23(6), С. 3240 - 3250

Опубликована: Май 3, 2021

Summary Universal primers for SSU rRNA genes allow profiling of natural communities by simultaneously amplifying templates from Bacteria, Archaea, and Eukaryota in a single PCR reaction. Despite the potential to show relative abundance all genes, universal are rarely used, due various concerns including amplicon length variation its effect on bioinformatic pipelines. We thus developed 16S 18S mock pipeline validate this approach. Using these mocks, we that (515Y/926R) outperformed eukaryote‐specific V4 observed versus expected correlations (slope = 0.88 vs. 0.67–0.79), community members with mismatches primer were strongly underestimated (threefold eightfold). field samples, both yielded similar beta‐diversity patterns (Mantel test, p < 0.001) but differences proportions many rarer taxa. To test biases, mixed (16S + 18S) before found twofold underestimation sequences sequencing bias. Correcting underestimation, estimate that, Southern California samples (1.2–80 μm), there averages 35% 18S, 28% chloroplast 16S, 37% prokaryote genes. These data demonstrate generate comprehensive microbiome profiles.

Язык: Английский

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A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Molecular Ecology Resources, Год журнала: 2022, Номер 23(1), С. 16 - 40

Опубликована: Фев. 2, 2022

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs the entire Earth System. Their members are found among prokaryotes (cyanobacteria) multiple eukaryotic lineages containing chloroplasts. Genetic surveys phytoplankton communities generally consist PCR amplification bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted environmental samples. However, our appreciation abundance or biomass is limited by PCR-amplification biases, gene copy number variations across taxa, fact that do not provide insights into metabolic traits such as photosynthesis. Here, we targeted photosynthetic psbO metagenomes to circumvent these limitations: method PCR-free, universally exclusively present in eukaryotes, mainly one per genome. We applied validated this new strategy with size-fractionated marine samples collected Tara Oceans, showed improved correlations flow cytometry microscopy than when based genes. Furthermore, revealed unexpected features ecology ecosystems, high picocyanobacterial aggregates symbionts ocean, decrease relative phototrophs towards larger size classes dinoflagellates. To facilitate incorporation molecular-based surveys, compiled a curated database >18,000 unique sequences. Overall, appears be promising evaluations communities.

Язык: Английский

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