Selfish bacteria are active throughout the water column of the ocean

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: Feb. 4, 2023

Heterotrophic bacteria in the ocean invest carbon, nitrogen, and energy extracellular enzymes to hydrolyze large substrates smaller sizes suitable for uptake. Since hydrolysis products produced outside of a cell may be lost diffusion, return on this investment is uncertain. Selfish change odds their favor by binding, partially hydrolyzing, transporting polysaccharides into periplasmic space without loss products. We expected selfish most common upper ocean, where phytoplankton produce abundant fresh organic matter, including complex polysaccharides. We, therefore, sampled water western North Atlantic Ocean at four depths from three stations differing physiochemical conditions; these also differed considerably microbial community composition. To our surprise, we found that are throughout column greater than 5500 m. uptake as strategy thus appears geographically-and phylogenetically-widespread. processing require highly sensitive substrate structure, activities might not reflected measurements relying only low molecular weight substrates. Moreover, even bottom supply structurally-intact polysaccharides, therefore enzymatic investment, must sufficient maintain organisms.

Language: Английский

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Bacterial communities in temperate and polar coastal sands are seasonally stable

ISME Communications, Journal Year: 2021, Volume and Issue: 1(1)

Published: June 28, 2021

Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine terrestrial origin, thus, acting as centers transformation. At high temporal resolution, we accessed the variability benthic bacterial communities over two annual cycles at Helgoland (North Sea), compared it with seasonality in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable both, temperate polar sediments on level cell counts 16S rRNA-based taxonomy. Actinobacteriota uncultured Actinomarinales Microtrichales were a major group, 8 ± 1% total reads (Helgoland) 31 6% (Svalbard). Their activity (frequency dividing cells 28%) situ numbers >10% microbes Svalbard suggest key heterotrophs carbon mineralization. Even though sampling sites showed no phytodetritus-driven changes structure, they harbored significantly different (p < 0.0001, r = 0.963). The stability is stark contrast to dynamic succession typical coastal waters, suggesting that pelagic respond phytoplankton productivity very differently.

Language: Английский

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Extracellular Polymeric Substances Drive Symbiotic Interactions in Bacterial‒Microalgal Consortia

Microbial Ecology, Journal Year: 2021, Volume and Issue: 83(3), P. 596 - 607

Published: June 16, 2021

Language: Английский

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Linkages Among Dissolved Organic Matter Export, Dissolved Metabolites, and Associated Microbial Community Structure Response in the Northwestern Sargasso Sea on a Seasonal Scale

Frontiers in Microbiology, Journal Year: 2022, Volume and Issue: 13

Published: March 8, 2022

Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter as deep 300 m, providing a unique model system examine (DOM) its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical parameters collected northwestern Sea, including bulk (DOC), total amino acids (TDAA), metabolites, bacterial abundance production, community structure, assess fate DOM microbes on seasonal time-scale in 2016–2017. dynamics at Bermuda Atlantic Time-series Study site followed general trend DOC accumulation during stratified periods downward flux mixing. Changes acid concentrations compositions provide useful indices diagenetic alteration DOM. TDAA degradation increased mesopelagic zone mixing, indicating relatively less diagenetically altered (i.e., more labile) During subset such acids, vitamins, benzoic was produced or lost. change were accompanied growth response specific lineages SAR11, SAR202, SAR86 clades, Acidimicrobiales , Flavobacteria shortly following Complementary biogeochemistry measurements revealed changes composition state, highlighting quantity quality ocean.

Language: Английский

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Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic

ISME Communications, Journal Year: 2023, Volume and Issue: 3(1)

Published: Dec. 1, 2023

Carbohydrates are chemically and structurally diverse, represent a substantial fraction of marine organic matter key substrates for heterotrophic microbes. Studies on carbohydrate utilisation by microbes have been centred phytoplankton blooms in temperate regions, while far less is known from high-latitude waters during later seasonal stages. Here, we combine glycan microarrays analytical chromatography with metagenomics metatranscriptomics to show the spatial heterogeneity distribution potential Atlantic Arctic. The composition abundance monomers structures POM varied location depth. Complex fucose-containing sulfated polysaccharides, accumulate ocean, were consistently detected, more labile β-1,3-glucan exhibited patchy distribution. Through 'omics analysis, identify variations transcription degradation-related genes across samples at community population level. populations contributing most taxonomically related those as primary responders degraders ecosystems, such NS4 Marine Group Formosa. unique profiles these suggest distinct substrate potentials, predicted targets corresponding identified same sampling sites. By combining cutting-edge technologies protocols, provide insights into component carbon cycle Arctic late summer present high-quality dataset that will be great value future comparative analyses.

Language: Английский

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Polymeric carbohydrates utilization separates microbiomes into niches: insights into the diversity of microbial carbohydrate-active enzymes in the inner shelf of the Pearl River Estuary, China

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: June 21, 2023

Polymeric carbohydrates are abundant and their recycling by microbes is a key process of the ocean carbon cycle. A deeper analysis carbohydrate-active enzymes (CAZymes) can offer window into mechanisms microbial communities to degrade in ocean. In this study, metagenomic genes encoding CAZymes sugar transporter systems were predicted assess glycan niches functional potentials utilization inner shelf Pearl River Estuary (PRE). The gene compositions significantly different between free-living (0.2–3 μm, FL) particle-associated (&gt;3 PA) bacteria water column surface sediments, reflecting niche separation on size fraction selective degradation depth. Proteobacteria Bacteroidota had highest abundance width genes, respectively. At genus level, Alteromonas (Gammaproteobacteria) exhibited greatest marked high periplasmic protein TonB members major facilitator superfamily (MFS). increasing contribution transporters for bottom contrasted metabolism tightly related with particulate (pectin, alginate, starch, lignin-cellulose, chitin, peptidoglycan) rather than ambient-water DOC. Candidatus Pelagibacter (Alphaproteobacteria) narrow was primarily preferred nitrogen-containing carbohydrates, while ABC (ATP binding cassette) supported scavenging mode carbohydrate assimilation. Planctomycetota, Verrucomicrobiota, similar potential consumption main component transparent exopolymer particles (sulfated fucose rhamnose containing polysaccharide sulfated-N-glycan), developing considerable overlap among these taxa. most as well widest bacterial taxa implied roles organic utilization, degree composition importantly influenced coastal waters PRE. These findings expand current understanding biotransformation, underlying size-fractionated near estuarine system.

Language: Английский

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Taxonomic and functional stability overrules seasonality in polar benthic microbiomes

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

Published: Jan. 1, 2024

Abstract Coastal shelf sediments are hot spots of organic matter mineralization. They receive up to 50% primary production, which, in higher latitudes, is strongly seasonal. Polar and temperate benthic bacterial communities, however, show a stable composition based on comparative 16S rRNA gene sequencing despite different microbial activity levels. Here, we aimed resolve this contradiction by identifying seasonal changes at the functional level, particular with respect algal polysaccharide degradation genes, combining metagenomics, metatranscriptomics, glycan analysis sandy surface from Isfjorden, Svalbard. Gene expressions diverse carbohydrate-active enzymes changed between winter spring. For example, β-1,3-glucosidases (e.g. GH30, GH17, GH16) degrading laminarin, an energy storage molecule algae, were elevated spring, while related α-glucan expressed both seasons maxima GH63, GH13_18, GH15). Also, expression GH23 involved peptidoglycan was prevalent, which line recycling biomass. Sugar extractions bulk low concentrations during but spring samples, glucose constituting largest fraction measured monosaccharides (84% ± 14%). In porewater, ~18-fold than overlying seawater (1107 484 vs. 62 101 μg C l−1) depleted glucose. Our data indicate that communities digest transform labile parts photosynthesis-derived particulate likely release more stable, glucose-depleted residual glycans unknown structures, quantities, residence times into ocean, thus modulating marine coastal waters.

Language: Английский

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Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group

The ISME Journal, Journal Year: 2022, Volume and Issue: 16(6), P. 1570 - 1582

Published: Feb. 15, 2022

Abstract Niche concept is a core tenet of ecology that has recently been applied in marine microbial research to describe the partitioning taxa based either on adaptations specific conditions across environments or specialised substrates. In this study, we combine spatiotemporal dynamics and predicted substrate utilisation species-level niche within NS5 Marine Group. Despite representing one most abundant flavobacterial clades from world’s oceans, our knowledge their phylogenetic diversity ecological functions limited. Using novel database-derived 16S rRNA gene ribosomal protein sequences, delineate into 35 distinct clusters, contained four candidate genera. One species, “Arcticimaribacter forsetii AHE01FL”, includes cultured isolate, for which provide complete genome sequence—the first an NS5—along with morphological insights using transmission electron microscopy. Assessing species’ spatial distribution Tara Oceans dataset, identify depth as key influencing factor, 32 species preferring surface waters, well patterns relation temperature, oxygen salinity. Each harbours unique substrate-degradation potential along substrates conserved at genus-level, e.g. alginate NS5_F. Successional were observed three time-series likely driven by adaptations. We propose mainly abiotic factors, define space, availability drive species-specific temporal dynamics.

Language: Английский

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Pulsed inputs of high molecular weight organic matter shift the mechanisms of substrate utilisation in marine bacterial communities

Environmental Microbiology, Journal Year: 2024, Volume and Issue: 26(2)

Published: Jan. 22, 2024

Abstract Heterotrophic bacteria hydrolyze high molecular weight (HMW) organic matter extracellularly prior to uptake, resulting in diffusive loss of hydrolysis products. An alternative ‘selfish’ uptake mechanism that minimises this has recently been found be common the ocean. We investigated how HMW addition affects these two processing mechanisms surface and bottom waters at three stations North Atlantic Ocean. A pulse increased cell numbers, as well rate spectrum extracellular enzymatic activities both depths. The effects on selfish were more differentiated: Gulf Stream productive south Newfoundland, structurally simple polysaccharides upon addition. number taking up complex polysaccharides, however, was largely unchanged. In contrast, oligotrophic gyre, despite external rates, unchanged, irrespective polysaccharide structure. deep (> 4000 m), substrates processed only by bacteria. Mechanisms substrate processing—and extent which products are released environment—depend structural complexity resident bacterial community.

Language: Английский

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Strong Effects of Increased Hydrostatic Pressure on Polysaccharide‐Hydrolyzing Enzyme Activities in Coastal Seawater and Sediments

Journal of Geophysical Research Biogeosciences, Journal Year: 2025, Volume and Issue: 130(2)

Published: Feb. 1, 2025

Abstract Heterotrophic microorganisms are responsible for transforming and respiring a substantial fraction of the organic matter produced by phytoplankton in surface ocean. Much this is composed polysaccharides, high‐molecular weight (HMW) sugars. To initiate degradation must produce extracellular enzymes right structural specificity to hydrolyze these complex structures. date, most measurements enzyme activities made at situ temperatures, but atmospheric pressure. However, previous studies have shown that hydrostatic pressure can impact functionality enzymes. Since deep sea communities may be seeded microbes from shallow waters, we aimed determine if affects performance coastal waters. extent which enzymatic microbial affected pressure, quantified seven polysaccharides under pressures ranging 0.1 MPa (atmospheric) 40 (equivalent 4,000 m). Enzyme pelagic were inhibited with increased while benthic more resistant Addition HMW resulted freely‐dissolved (<0.2 μm) strongly suggesting pressure‐resistant cell‐surface attached. Because inhibition varied polysaccharide, surmise complexity polysaccharide—and therefore number distinct required hydrolysis—is likely closely associated inhibition.

Language: Английский

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