Organic phosphorus availability shapes the diversity of phoD-harboring bacteria in agricultural soil

Soil Biology and Biochemistry, Год журнала: 2021, Номер 161, С. 108364 - 108364

Опубликована: Июль 26, 2021

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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Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks

Scientific Reports, Год журнала: 2023, Номер 13(1)

Опубликована: Фев. 16, 2023

Abstract Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects associations in aquatic ecosystems. A high degree clustering was observed modules, indicating densely connected neighbourhoods. Proteobacteria Bacteroidetes predominantly co-occurred with represented hubs most modules. Our results also indicated that species-specificity may be a characteristic microalgal associated microbiomes. Several previously known were recovered our network validating biologically meaningful inferred using this approach. range unknown recognised as co-occurrences Bacillariophyta uncultured Planctomycetes OM190 Deltaproteobacteria order NB1-j . Verrucomicrobia identified key associates due their frequent several taxa. Despite no clear taxonomic pattern, bacterial appeared functionally similar across different environments. To summarise, demonstrated hypothesis-generating framework guide more focused research on associations.

Язык: Английский

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Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics

The ISME Journal, Год журнала: 2024, Номер 18(1)

Опубликована: Янв. 1, 2024

Abstract Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, bacteria by partitioning low-concentration substrates though they compete for one simple, dominant substrate. We allowed ocean self-assemble leachates the brown seaweed Fucus vesiculosus and then analyzed competition among 10 taxonomically diverse isolates representing two distinct stages succession. All, but isolates, exhibited an average 90% ± 6% pairwise resource use, functional redundancy from same assembly stage was higher than between stages, leading us construct a simpler four-isolate community with each early late stages. found that, although short-term F. leachate dependent initial isolate ratios, long term, four leachate, albeit some strains at low abundance. therefore explored potential nonredundant use genomic content analysis RNA expression patterns. This revealed mainly differed peripheral metabolic pathways, such as ability degrade pyrimidine, leucine, tyrosine, well aromatic substrates. These results highlight importance fine-scale differences strategies supporting frequently observed coexistence large numbers rare organisms microbiomes.

Язык: Английский

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Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Фев. 3, 2025

Abstract Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal gradients have been shown to taxonomic dynamics microbiomes over time, little known about their impact on functional coupling between taxonomy function. Here, we demonstrate annually recurrent, structuring in a pelagic Arctic Ocean microbiome combining autonomous samplers situ sensors with long-read metagenomics SSU ribosomal metabarcoding. Specifically, identified five temporal modules whose succession within each annual cycle represents transition across different ecological states. For instance, Cand . Nitrosopumilus, Syndiniales, machinery oxidise ammonia reduce nitrite signatures early polar night, while late summer characterised Amylibacter sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans , also consistency wider during similar periods. Furthermore, genetic diversity functions time indicates that selection pressure acts heterogeneously seasons. By integrating taxonomic, information, our study provides insights into structured under pronounced changes understudied, yet rapidly changing marine

Язык: Английский

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Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling

The ISME Journal, Год журнала: 2018, Номер 12(10), С. 2417 - 2432

Опубликована: Июнь 13, 2018

Язык: Английский

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Patterns and processes of free‐living and particle‐associated bacterioplankton and archaeaplankton communities in a subtropical river‐bay system in South China

Limnology and Oceanography, Год журнала: 2019, Номер 65(S1)

Опубликована: Сен. 5, 2019

Abstract Free‐living and particle‐associated microbial communities play critical roles in nutrient cycles aquatic systems. However, little is known about their assembly process, function, interactions. Here, by using 16S rRNA gene amplicon sequencing of size‐fractionated samples collected during the wet dry seasons, we investigated processes co‐occurrence patterns bacterial archaeal Shenzhen River‐Bay system, South China. The showed specific distribution according to size fraction (free‐living vs. particle‐associated), habitat (river estuary), seasonality (wet season). Neutral modeling revealed that stochastic pattern was more pronounced for bacteria than archaea, although both deterministic significantly influenced communities. Homogeneous selection had a relatively higher importance structuring bacterioplankton free‐living fractions, while this process important archaeaplankton fractions. Aquatic community composition were most strongly associated with salinity water temperature. Network analysis each plankton connectivity intra‐bacteria, inter‐bacteria/archaea, intra‐archaea associations, accordingly, when nonlinear associations considered. These findings expand current understanding ecological mechanisms Archaea‐Bacteria interactions, underlying dynamics river‐bay system.

Язык: Английский

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Marine microbes in 4D — using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health

Current Opinion in Microbiology, Год журнала: 2018, Номер 43, С. 169 - 185

Опубликована: Фев. 21, 2018

Microbial observation is of high relevance in assessing marine phenomena scientific and societal concern including ocean productivity, harmful algal blooms, pathogen exposure. However, we have yet to realise its potential coherently comprehensively report on global status. The ability satellites monitor the distribution phytoplankton has transformed our appreciation microbes as foundation key ecosystem services; however, more in-depth understanding microbial dynamics needed fully assess natural anthropogenically induced variation ecosystems. While this first synthesis shows that notable efforts exist, vast regions such depths, open ocean, polar oceans, most Southern Hemisphere lack consistent observation. To secure a coordinated future for observing system, existing long-term must be better networked generate shared bioindicators Global Ocean's state health.

Язык: Английский

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Microbial Communities in the East and West Fram Strait During Sea Ice Melting Season

Frontiers in Marine Science, Год журнала: 2018, Номер 5

Опубликована: Ноя. 22, 2018

Climate models project that the Arctic Ocean may experience ice-free summers already in second half of this century. This have severe repercussions on phytoplankton bloom dynamics and associated cycling carbon surface waters. We currently lack baseline knowledge seasonal microbial communities, which is needed order to better estimate effects such changes ecosystem functioning. Here we present a comparative study polar summer communities (eastern) ice-covered (western) hydrographic regimes at LTER HAUSGARTEN Fram Strait, main gateway between North Atlantic Oceans. Based measured modeled biogeochemical parameters, tentatively identified two different states (i.e., stages) distinct regions. Using Illumina tag-sequencing, determined community composition both free-living particle-associated bacteria as well eukaryotes photic layer. Despite substantial horizontal mixing by eddies pelagic showed differences regimes, with proposed early spring (pre-bloom) western regime (with higher representation SAR11, SAR202, SAR406 eukaryotic MALVs) indicative late conditions (post-bloom) eastern Flavobacteria, Gammaproteobacteria heterotrophs). Co-occurrence networks revealed specific taxon-taxon associations bacterial taxa Our results suggest predicted sea-ice cover will strong impact potentially cycles region.

Язык: Английский

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