Recurrent patterns of microdiversity in a temperate coastal marine environment

The ISME Journal, Journal Year: 2017, Volume and Issue: 12(1), P. 237 - 252

Published: Oct. 24, 2017

Abstract Temperate coastal marine environments are replete with complex biotic and abiotic interactions that amplified during spring summer phytoplankton blooms. During these events, heterotrophic bacterioplankton respond to successional releases of dissolved organic matter as algal cells lysed. Annual seasonal shifts in the community composition free-living follow broadly predictable patterns, but whether similar communities each year bloom disturbance events remains unknown owing a lack data sets, employing high-frequency sampling over multiple years. We capture fine-scale microdiversity weekly using high-resolution method discriminate 16S ribosomal RNA gene amplicons >99% identical. Furthermore, we used 2 complete years facilitate identification recurrent sub-networks co-varying microbes. demonstrate despite inter-annual variation blooms dynamism coastal–oceanic transition zone, patterns both non-bloom conditions. Sub-networks co-occurring microbes identified reveal correlation structures between members appear quite stable seasonally driven response oligotrophic eutrophic

Language: Английский

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Estimating intraspecific genetic diversity from community DNA metabarcoding data

PeerJ, Journal Year: 2018, Volume and Issue: 6, P. e4644 - e4644

Published: April 9, 2018

DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput instruments are fairly common, usually requiring reads be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity the process. While Cytochrome c oxidase subunit I (COI) haplotype limited resolving it nevertheless often useful e.g. a phylogeographic context, helping formulate hypotheses taxon distribution and dispersal.This study combines sequence denoising strategies, normally applied microbial research, with additional abundance-based filtering extract from freshwater macroinvertebrate datasets. This novel approach was added R package "JAMP" can COI amplicon We tested our haplotyping method by (i) single-species mock community composed of 31 individuals 15 different haplotypes spanning three orders magnitude biomass (ii) 18 monitoring samples each amplified four primer sets two PCR replicates.We detected all single specimens relaxed settings. up 480 unexpected remained both replicates. Rigorous removes most haplotypes, but also discard expected mainly small specimens. In samples, 177-200 OTUs, containing an average 2.40-3.30 per OTU. The derived showed population structures that were consistent between replicates similar pairs resolution depended length. A closer look at abundant taxa dataset revealed various genetic patterns, stonefly Taeniopteryx nebulosa caddisfly Hydropsyche pellucidula distinct north-south cline respect distribution, while beetle Oulimnius tuberculatus isopod Asellus aquaticus displayed no clear pattern differed diversity.We developed strategy infer bulk invertebrate data. It needs stressed this point metabarcoding-informed not capable capturing full present such due variation specimen size, bias loss variants low abundance. Nevertheless, high number recovered, identifying potentially isolated populations further more detailed investigation. we currently lacking large-scale datasets fully take advantage new approach, holds great promise biomonitoring efforts only seek about underlying diversity.

Language: Английский

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The microbial rare biosphere: current concepts, methods and ecological principles

FEMS Microbiology Ecology, Journal Year: 2020, Volume and Issue: 97(1)

Published: Nov. 6, 2020

ABSTRACT Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack integrative view key taxa, functions and metabolic activity which make-up this communal pool, usually referred as ‘rare biosphere’, across domains life. In context, review examines rare biosphere its broader sense, providing historical perspective on representative studies enabled bridge concept from macroecology ecology. It then addresses our current knowledge prokaryotic biosphere, covers emerging insights into ecology, taxonomy evolution microeukaryotic, viral host-associated communities. We also recent methodological advances provide a synthetic overview how fits different conceptual models used explain community assembly mechanisms, composition function.

Language: Английский

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Are We Overestimating Protistan Diversity in Nature?

Trends in Microbiology, Journal Year: 2018, Volume and Issue: 27(3), P. 197 - 205

Published: Nov. 16, 2018

Language: Английский

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Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column

The ISME Journal, Journal Year: 2020, Volume and Issue: 14(5), P. 1304 - 1315

Published: Feb. 14, 2020

Abstract Microbial communities are critical to ecosystem dynamics and biogeochemical cycling in the open oceans. Viruses essential elements of these communities, influencing productivity, diversity, evolution cellular hosts. To further explore natural history ecology open-ocean viruses, we surveyed spatiotemporal double-stranded DNA (dsDNA) viruses both virioplankton bacterioplankton size fractions North Pacific Subtropical Gyre, one largest biomes on planet. Assembly clustering viral genomes revealed a peak diversity at base euphotic zone, where virus populations host species richness reached their maxima. Simultaneous characterization extracellular intracellular suggested depth-specific reproductive strategies. In particular, analyses indicated elevated lytic interactions mixed layer, more temporally variable temperate phage increased lysogeny mesopelagic ocean. Furthermore, depth variability auxiliary metabolic genes habitat-specific strategies for influence light-energy, nitrogen, phosphorus acquisition during infection. Most were persistent over several years this environment 95% nucleic acid identity level. total, our distributional patterns diverse water column.

Language: Английский

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Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

eLife, Journal Year: 2020, Volume and Issue: 9

Published: June 17, 2020

Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological evolutionary factors. New strategies needed for ample representation rare taxa slow-growers that often outcompeted by fast-growers experiments. Here we describe a microfluidic platform anaerobically isolates cultivates microbial cells millions picoliter droplets automatically sorts them based on colony density enhance slow-growing organisms. We applied our strategy fecal microbiota transplant (FMT) donor stool using multiple growth media, found significant increase taxonomic richness larger clinically relevant among droplet-grown compared conventional plates. Furthermore, screening the FMT antibiotic resistance revealed 21 populations evaded detection plate-based assessment resistance. Our method improves cultivation-based surveys diverse microbiomes gain deeper insights into functioning lifestyles.

Language: Английский

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Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: March 12, 2019

Abstract Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent viruses. Many studies assemble new viral genomes and diversity using marker genes from free Here we use cellular metatranscriptomics to active community-wide infections. Recruitment contigs allows tracking infection dynamics over time space. Our assemblies represent populations, but appear biased towards low taxa. Tracking relatives published T4-like cyanophages pelagiphages reveals high genomic continuity. We determine potential hosts matching with abundance particular Finally, quantify the relative contribution cyanobacteria viruses photosystem-II psbA (reaction center) expression our sites. show sometimes >50% all cyanobacterial+viral is origin, highlighting photosynthesis oxygen production.

Language: Английский

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Microbial generalist or specialist: Intraspecific variation and dormancy potential matter

Molecular Ecology, Journal Year: 2021, Volume and Issue: 31(1), P. 161 - 173

Published: Oct. 9, 2021

Abstract Microbial generalists and specialists coexist in the soil environment while having distinctive impacts on microbial community dynamics. In ecology, underlying mechanisms as to why a species is generalist or specialist remain ambiguous. Herein, we collected soils across national scale identified bacterial according niche breadth at level (OTU level), single‐nucleotide differences each were measured investigate intraspecific variation (at zero‐radius OTU level). Compared with that of specialists, was much higher, which ensured their wider lower variability. The higher asynchrony different preferences conspecific individuals dormancy potential within further contributed stability varying environments. Besides, less controlled by environmental filtering, indicated stronger signature stochastic processes assembly, had diversification transition rates allowed them adapt changes greater extent than specialists. Overall, this study provides new comprehensive understanding rules assembly evolutionary roles It also highlights importance species.

Language: 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, Journal Year: 2021, Volume and Issue: 23(6), P. 3240 - 3250

Published: May 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.

Language: Английский

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Building plumbing influences the microdiversity and community assembly of the drinking water microbiome.

Water Research, Journal Year: 2025, Volume and Issue: 276, P. 123244 - 123244

Published: Feb. 6, 2025

Language: Английский

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