Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities

Frontiers in Microbiology, Год журнала: 2021, Номер 12

Опубликована: Фев. 16, 2021

Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as their horizontal, vertical, and temporal turnover. Yet, recent studies showed that marine ecosystem harbors unique microbial community members adapted harsh environmental conditions, such near-freezing temperatures extreme seasonality. The gene for small ribosomal subunit (16S rRNA) is commonly used study taxonomic composition natural environment. Several primer sets this marker have been extensively tested across various sample sets, but these typically originated from low-latitude environments. An explicit evaluation primer-set performances representing currently lacking. To select a suitable set studying microbiomes habitats (sea ice, surface water, snow, deep ocean basin, deep-sea sediment), we conducted performance between two widely targeting different hypervariable regions 16S rRNA (V3-V4 V4-V5). We observed both were highly similar total down genus rank, which was also confirmed independently by subgroup-specific catalyzed reporter deposition-fluorescence

Язык: Английский

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Phytoplankton composition from sPACE: Requirements, opportunities, and challenges

Remote Sensing of Environment, Год журнала: 2024, Номер 302, С. 113964 - 113964

Опубликована: Янв. 10, 2024

Ocean color satellites have provided a synoptic view of global phytoplankton for over 25 years through near surface measurements the concentration chlorophyll a. While remote sensing ocean has revolutionized our understanding and their role in oceanic freshwater ecosystems, it is important to consider both total biomass changes community composition order fully understand dynamics aquatic ecosystems. With upcoming launch NASA's Plankton, Aerosol, Clouds, Ecosystem (PACE) mission, we will be entering into new era hyperspectral data, with it, increased capabilities monitor diversity from space. In this paper, analyze needs user community, review existing approaches detecting situ space, highlight benefits that PACE mission bring. Using three-pronged approach, challenges gaps addressed by going forward, while offering vision what look like "eyes" PACE.

Язык: Английский

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Relative Influence of Plastic Debris Size and Shape, Chemical Composition and Phytoplankton-Bacteria Interactions in Driving Seawater Plastisphere Abundance, Diversity and Activity

Frontiers in Microbiology, Год журнала: 2021, Номер 11

Опубликована: Янв. 13, 2021

The thin film of life that inhabits all plastics in the oceans, so-called “plastisphere,” has multiple effects on fate and impacts plastic marine environment. Here, we aimed to evaluate relative influence size, shape, chemical composition, environmental changes such as a phytoplankton bloom shaping plastisphere abundance, diversity activity. Polyethylene (PE) polylactide acid (PLA) together with glass controls forms meso-debris (18 mm diameter) large-microplastics (LMP; 3 diameter), well small-microplastics (SMP) 100 μm diameter spherical or irregular shapes were immerged seawater during 2 months. Results bacterial abundance (confocal microscopy) (16S rRNA Illumina sequencing) indicated three classical biofilm colonization phases (primo-colonization after days; growing phase 10 maturation 30 days) not influenced by size shape materials, even when diatom ( Pseudo-nitzschia sp.) occurred first month incubation. However, had an effect activity H leucine incorporation). Bacterial communities associated material fraction showed highest compared other sizes. A mature developed within days types, higher glass, distinct assemblages detected each type. event great impact resulting drastic change Our results relatively low diversity, activity, composition presence bloom.

Язык: Английский

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Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys

mSystems, Год журнала: 2021, Номер 6(3)

Опубликована: Июнь 11, 2021

PCR amplification and sequencing of marker genes are a low-cost technique for monitoring prokaryotic eukaryotic microbial communities across space time but will work optimally only if environmental organisms match primer sequences exactly. In this study, we evaluated how well primers globally distributed short-read oceanic metagenomes.

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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Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series

ISME Communications, Год журнала: 2022, Номер 2(1)

Опубликована: Апрель 13, 2022

Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth multiple years. Here, characterized microbes at the San-Pedro Ocean Time series (2005-2018), using SSU rRNA gene sequencing from two size fractions (0.2-1 1-80 μm), with a universal primer set that amplifies both eukaryotes, allowing direct comparisons of single analyses. The 16S + 18S composition small fraction was mostly prokaryotic (>92%) as expected, but large unexpectedly contained 46-93% genes. Prokaryotes showed opposite vertical patterns; peaked mid-depth, protistan surface. Temporal beta-diversity indicated prokaryote communities were much more stable than protists. Although changed monthly, average community stayed remarkably steady 14 years, showing high resilience. Additionally, particle-associated diverse smaller free-living ones, especially deeper depths, contributed by abundant SAR11 clade II. Eukaryotic strongly correlated not reflecting physical associations result strongest interactions, including symbioses, parasitism, decomposer relationships.

Язык: Английский

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Selection, drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean

The ISME Journal, Год журнала: 2022, Номер 16(12), С. 2653 - 2665

Опубликована: Сен. 17, 2022

Abstract Despite accumulating data on microbial biogeographic patterns in terrestrial and aquatic environments, we still lack a comprehensive understanding of how these establish, particular ocean basins. Here show the relative significance ecological mechanisms selection, dispersal drift for shaping composition communities Pacific Ocean over transect 12,400 km between subantarctic subarctic regions. In epipelagic, homogeneous selection contributes 50–60% least to three mechanism assembly prokaryotic whereas upper mesopelagic, is relatively most important particle-associated subcommunities. Temperature limitation community assembly. The both was inverted with increasing temperature difference along transect. For eukaryotes >8 µm, also at two epipelagic depths all other predominant. As species interactions are essential structuring further analyzed co-occurrence-based metrics assess These interaction-adjusted indices explained much better variations as function abiotic biotic variables than compositional or phylogenetic distance measures like Bray–Curtis UniFrac. Our analyses understand processes layers largest they adapt effectively perform global biogeochemical processes. Similar principles presumably act upon

Язык: Английский

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Effects of tire wear particles on freshwater bacterial-fungal community dynamics and subsequent elemental cycles using microcosms

Journal of Hazardous Materials, Год журнала: 2025, Номер 487, С. 137062 - 137062

Опубликована: Янв. 5, 2025

Ecological impacts of tire wear particles (TWPs) on microbial communities and biogeochemical cycles in freshwater remain largely unknown. Here, we conducted a microcosm experiment to investigate interactions between the overlying water sediment without with TWPs addition rural vs. urban lake system. Our results revealed degree change community diversity is higher than that following addition. For bacterial communities, changed their composition water, but only little sediment. fungal both sediments. Furthermore, increased network complexity bacteria-bacteria, fungi-fungi bacteria-fungi system reduced it one. In contrast, presence did not significantly among lakes. Isotope labeling analysis uncovered based short-term (6 hours) incubation experiment, carbon nor nitrogen cycling water. Yet, certain changes could be observed, especially long-term (1 month), indicating pollution has potential impact elemental thus ecosystem functions by altering communities. provide new insights into TWPs-induced ecological effects microorganisms consequences

Язык: Английский

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Effects of phytoplankton, viral communities, and warming on free-living and particle-associated marine prokaryotic community structure

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Дек. 23, 2022

Abstract Free-living and particle-associated marine prokaryotes have physiological, genomic, phylogenetic differences, yet factors influencing their temporal dynamics remain poorly constrained. In this study, we quantify the entire microbial community composition monthly over several years, including viruses, prokaryotes, phytoplankton, total protists, from San-Pedro Ocean Time-series using ribosomal RNA sequencing viral metagenomics. Canonical analyses show that in addition to physicochemical factors, double-stranded DNA is strongest factor predicting free-living explaining 28% of variability, whereas phytoplankton (via chloroplast 16S rRNA) with 31% variability. Unexpectedly, protist explains little Our findings suggest biotic interactions are significant determinants relative importance specific varies depending on lifestyles. Also, warming influenced prokaryotic community, which largely remained oligotrophic summer-like throughout 2014–15, cyanobacterial populations shifting cold-water ecotypes warm-water ecotypes.

Язык: Английский

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Primer selection impacts the evaluation of microecological patterns in environmental microbiomes

iMeta, Год журнала: 2023, Номер 2(4)

Опубликована: Сен. 17, 2023

This study revealed that primer selection substantially influences the taxonomic and predicted functional composition characterization of microecological patterns, which was not alleviated by close-reference clustering. Biases were relatively consistent across different habitats in community profiling but patterns. These biases could be attributed to multiple aspects, including taxa specificity, regional hypervariability, amplification efficiency.

Язык: Английский

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