Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions

The ISME Journal, Год журнала: 2019, Номер 13(12), С. 2969 - 2983

Опубликована: Авг. 16, 2019

Язык: Английский

---

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

---

Microbial assembly, interaction, functioning, activity and diversification: a review derived from community compositional data

Marine Life Science & Technology, Год журнала: 2019, Номер 1(1), С. 112 - 128

Опубликована: Сен. 30, 2019

Abstract Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge studies on marine microbial community composition using high-throughput sequencing methods. Extensive mining of the compositional data has provided exciting new insights into ecology from a number perspectives. Both deterministic and stochastic processes contribute to assembly but their relative importance structuring subcommunities, that are categorized by traits such as abundance, functional type activity, differs. Through correlation-based network analysis, significant progress been made unraveling co-occurrence patterns dynamics response environmental changes. Prediction functioning, based data, is receiving increasing attention, closely related microbes often share similar ecological diversity exhibits correlations functioning. functioning likely executed not whole community, rather active fraction which can be inferred marker gene transcription level members. Furthermore, huge amount significantly expanded tree life illuminated phylogenetic divergence evolutionary history. This review summarizes important findings assembly, interaction, activity diversification, highlighting interacting different aspects, derived data.

Язык: Английский

---

Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms

The ISME Journal, Год журнала: 2021, Номер 16(3), С. 630 - 641

Опубликована: Сен. 7, 2021

Abstract Marine algae annually sequester petagrams of carbon dioxide into polysaccharides, which are a central metabolic fuel for marine cycling. Diatom microalgae produce sulfated polysaccharides containing methyl pentoses that challenging to degrade bacteria compared other monomers, implicating these sugars as potential sink. Free-living occurring in phytoplankton blooms specialise on consuming microalgal sugars, fucose and rhamnose remain unknown. Here, genomic proteomic data indicate small, coccoid, free-living Verrucomicrobiota consumption during spring algal the North Sea. cell abundance was coupled with bloom onset accounted up 8% bacterioplankton. Glycoside hydrolases, sulfatases, bacterial microcompartments, critical proteins fucosylated were actively expressed consecutive events. These specialised pathways assigned novel discrete candidate species Akkermansiaceae Puniceicoccaceae families, we here describe Candidatus Mariakkermansia forsetii Fucivorax forsetii. Moreover, our results suggest could determine fate complex consumed blooms. Thus sequestration organic matter via pentose likely depend activity populations.

Язык: Английский

---

Unifying the known and unknown microbial coding sequence space

eLife, Год журнала: 2022, Номер 11

Опубликована: Март 31, 2022

Genes of unknown function are among the biggest challenges in molecular biology, especially microbial systems, where 40-60% predicted genes unknown. Despite previous attempts, systematic approaches to include fraction into analytical workflows still lacking. Here, we present a conceptual framework, its translation computational workflow AGNOSTOS and demonstration on how can bridge known-unknown gap genomes metagenomes. By analyzing 415,971,742 from 1749 metagenomes 28,941 bacterial archaeal genomes, quantify extent fraction, diversity, relevance across multiple organisms environments. The sequence space is exceptionally diverse, phylogenetically more conserved than known predominantly taxonomically restricted at species level. From 71 M identified be function, compiled collection 283,874 lineage-specific for

Язык: Английский

---

Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides

Microbiome, Год журнала: 2024, Номер 12(1)

Опубликована: Фев. 20, 2024

Abstract Background Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists considerable proportions polysaccharides, substantial parts which are rapidly remineralized by heterotrophic bacteria. We analyzed diversity, activity, functional potential such polysaccharide-degrading bacteria different size fractions diverse spring bloom at Helgoland Roads (southern North Sea) high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, metaproteome analyses. Results Prominent active 0.2–3 µm free-living clades comprised Aurantivirga , “Formosa”, Cd . Prosiliicoccus, NS4, NS5, Amylibacter Planktomarina SAR11 Ia, SAR92, SAR86, whereas BD1-7, Stappiaceae Nitrincolaceae Methylophagaceae Sulfitobacter NS9, Polaribacter Lentimonas CL500-3, Algibacter Glaciecola dominated 3–10 > 10 particles. Particle-attached were more exhibited dynamic adaptive shifts over time terms taxonomic composition repertoires encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes obtained, including 152 particle-attached bacteria, 100 novel for sampling site with 76 representing new species. Compared to they featured on average larger higher polysaccharide utilization loci. The latter predicted target broader spectrum substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) less complex structural, or secreted xylans, cellulose, pectins). particular, poorly soluble was widespread among abundant Conclusions represented only 1% all bloom-associated yet our data suggest that many played gatekeeping solubilization subsequent degradation numerous important classes algal glycans. diversity niches is determining factor proportion can be generally short-lived events.

Язык: Английский

---

Root and mycorrhizal nutrient acquisition strategies in the succession of subtropical forests under N and P limitation

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Янв. 2, 2025

Nutrient limitation is a universal phenomenon in terrestrial ecosystems. Root and mycorrhizal are critical to plant nutrient absorption nutrient-limited However, how they modified by N P limitations with advancing vegetation successions karst forests remains poorly understood. The present study compared the diversity indices, composition, co-occurrence network of arbuscular fungi (AMF) between grassland, shrubland, shrub-tree forest, tree forest subtropical forests, as well soil nutrients fine root functional traits (e.g., specific length (SRL), area (SRA), diameter, biomass, contents). roots contents increased succession, whereas SRL SRA decreased. Network complexity Richness Chao1 indices AMF from grassland but decreased forest. were positively related their diameter nutrients, composition negatively correlated SRA. Moreover, these two parameters increase nutrients. variations mainly explained interactions traits, other three stages. Additionally, interactive explanation shrubland Our results indicated that strategy might be main acquisition under co-limitation. In contrast, one when an individual subject or strategies generally mutualistic, enhances

Язык: Английский

---

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

---

Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms

The ISME Journal, Год журнала: 2018, Номер 12(12), С. 2894 - 2906

Опубликована: Июль 30, 2018

Abstract Polysaccharide degradation by heterotrophic microbes is a key process within Earth’s carbon cycle. Here, we use environmental proteomics and metagenomics in combination with cultivation experiments biochemical characterizations to investigate the molecular details of situ polysaccharide mechanisms during microalgal blooms. For this, laminarin as model polysaccharide. Laminarin ubiquitous marine storage polymer microalgae particularly abundant phytoplankton In this study, show that highly specialized bacterial strains Bacteroidetes phylum repeatedly reached high abundances North Sea algal blooms dominated turnover. These genomically streamlined bacteria genus Formosa have an expanded set hydrolases transporters belonged most proteins samples. vitro cultured isolates allowed us determine functions expressed enzymes confirm their role utilization. It shown consumption spp. paralleled enhanced uptake diatom-derived peptides. This study reveals genome reduction, enzyme fusions, transporters, expansion well tight coupling nitrogen metabolism provide tools, which make so competitive

Язык: Английский

---

Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes

Molecular Ecology, Год журнала: 2020, Номер 30(13), С. 2988 - 3006

Опубликована: Апрель 14, 2020

Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive more efficient bioassessments methodologies. One promising approach is integration DNA metabarcoding in environmental monitoring. A critical step this process inference ecological quality (EQ) status from identified molecular bioindicator signatures that mirror classification based standard macroinvertebrate surveys. The most approaches to infer EQ biotic indices (BI) are supervised machine learning (SML) calculation indicator values (IndVal). In study we compared performance both using metabarcodes bacteria ciliates as bioindicators obtained 152 samples collected seven Norwegian salmon farms. Results macroinvertebrate-monitoring same were used reference compare accuracy approaches. First, SML outperformed IndVal eDNA metabarcodes. Random Forest (RF) algorithm appeared be sensitive noisy data (a typical feature massive sequence sets) uneven coverage across classes compliance monitoring scheme) a widely method IndVals for BI. Second, allowed accurate assessment than ciliate For implementation into routine programmes assess around aquaculture cages, therefore recommend bacterial combination with classify categories signatures.

Язык: Английский

---