DNA barcoding, an effective tool for species identification: a review

Molecular Biology Reports, Год журнала: 2022, Номер 50(1), С. 761 - 775

Опубликована: Окт. 29, 2022

Язык: Английский

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From webs, loops, shunts, and pumps to microbial multitasking: Evolving concepts of marine microbial ecology, the mixoplankton paradigm, and implications for a future ocean

Limnology and Oceanography, Год журнала: 2022, Номер 67(3), С. 585 - 597

Опубликована: Янв. 21, 2022

Abstract Emerging knowledge of mixoplankton—ubiquitous microbes that employ phototrophy and phagotrophy synergistically in one cell—reshapes our the flow materials energy, with wide‐reaching impacts on marine productivity, biodiversity, sustainability. Conceptual models microbial interactions have evolved from food‐chains, where carbon‐fixing phytoplankton are conceived as being grazed solely by zooplankton that, turn, support fisheries higher trophic levels, to webs, loops, shunts, about abundance, activity, roles organisms—as well complexity their interactions—has increased. In a future world, plankton depend single strategy for acquiring nutrition (photo‐autotrophy or phago‐heterotrophy) may be disadvantaged increasing temperatures ocean acidification impacting vital rates, thermal stratification decreasing water column nutrient exchange, anthropogenic pollution shifting amounts, forms, proportions nutrients. These conditions can lead stoichiometric imbalances promote mixoplanktonic species an likelihood harmful blooms. Such changes composition alters interconnectivity oceanic direct consequences biogeochemical cycling, dynamics, ecosystem services. Here, implications mixoplankton paradigm relative traditional concepts oceanography globally‐changing, anthropogenically‐impacted world explored.

Язык: Английский

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The Mixoplankton Database (MDB): Diversity of photo‐phago‐trophic plankton in form, function, and distribution across the global ocean

Journal of Eukaryotic Microbiology, Год журнала: 2023, Номер 70(4)

Опубликована: Фев. 27, 2023

Protist plankton are major members of open-water marine food webs. Traditionally divided between phototrophic phytoplankton and phagotrophic zooplankton, recent research shows many actually combine phototrophy phagotrophy in the one cell; these protists "mixoplankton." Under mixoplankton paradigm, "phytoplankton" incapable (diatoms being exemplars), while "zooplankton" phototrophy. This revision restructures webs, from regional to global levels. Here, we present first comprehensive database mixoplankton, bringing together extant knowledge identity, allometry, physiology, trophic interactivity organisms. (MDB) will aid researchers that confront difficulties characterizing life traits protist plankton, it benefit modelers needing better appreciate ecology organisms with their complex functional allometric predator-prey interactions. The MDB also identifies gaps, including need understand, for different types, sources nutrition (use nitrate, prey nutritional states), obtain vital rates (e.g. growth, photosynthesis, ingestion, factors affecting photo' vs. phago' -trophy). It is now possible revisit re-classify protistan databases forms so as clarify roles ecosystems.

Язык: Английский

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Swarm v3: towards tera-scale amplicon clustering

Bioinformatics, Год журнала: 2021, Номер 38(1), С. 267 - 269

Опубликована: Июль 1, 2021

Abstract Motivation Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) are free of arbitrary global thresholds. Here, present swarm v3 to address issues contemporary datasets growing towards tera-byte sizes. Results When compared with previous versions, has modernized C++ source code, reduced memory footprint by up 50%, optimized CPU-usage and multithreading (more than 7 times faster default parameters), it been extensively tested for its robustness logic. Availability implementation Source code binaries available at https://github.com/torognes/swarm. Supplementary information data Bioinformatics online.

Язык: Английский

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Composition and spatial-temporal dynamics of phytoplankton community shaped by environmental selection and interactions in the Jiaozhou Bay

Water Research, Год журнала: 2022, Номер 218, С. 118488 - 118488

Опубликована: Апрель 22, 2022

Язык: Английский

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Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias

Metabarcoding and Metagenomics, Год журнала: 2022, Номер 6

Опубликована: Авг. 15, 2022

Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and more cost-efficient less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene the most widely used marker for groups’ species’ detection classification within eukaryotic microorganisms. These datasets have commonly relied acquisition of organismal abundances directly from number DNA sequences (i.e. reads). Besides inherent technical biases metabarcoding, largely varying copy numbers (GCN) among protists (ranging tens to thousands) one important biological species quantification. In this work, we present a correction factor (CF) four planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous flagellated cells. On basis theoretical assumption that ‘1 read’ equivalent GCN’, GCN median values per plankton group calculate corrected cell biomass relative abundances. The species-specific absolute were obtained various studies published literature. We contributed development database proposed by previous authors. To assess efficiency compared morphological (in biomass) 15 surface water samples collected Belgian Coastal Zone. Results showed application over results enables us significantly improve estimates cells, but not Bacillariophyta. This likely due large biovolume plasticity diatoms corresponding genome size numbers. C-biomass abundance estimations amplicon reads only improved Dinoflagellata Ciliophora. method still facing related low assessed. Nevertheless, increase may lead refinement factor.

Язык: Английский

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metaPR²: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists

Molecular Ecology Resources, Год журнала: 2022, Номер 22(8), С. 3188 - 3201

Опубликована: Июнь 28, 2022

In recent years, metabarcoding has become the method of choice for investigating composition and assembly microbial eukaryotic communities. The number environmental data sets published increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, rarely available a usable format. Clustered sequences reported as operational taxonomic units (OTUs) with different similarity levels or more recently amplicon variants (ASVs). This hampers comparative studies between environments sets, example examining biogeographical patterns specific groups/species, well analysing genetic microdiversity within these groups. Here, we present newly-assembled database 18S rRNA metabarcodes that annotated PR2 reference database. database, called metaPR2 , contains 41 corresponding to than 4000 samples 90,000 ASVs. which is accessible through both web-based interface (https://shiny.metapr2.org) an R package, should prove useful all researchers working on protist diversity variety systems.

Язык: Английский

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Interactions between soil protists and pollutants: An unsolved puzzle

Journal of Hazardous Materials, Год журнала: 2022, Номер 429, С. 128297 - 128297

Опубликована: Янв. 19, 2022

Язык: Английский

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Role of Syndiniales parasites in depth-specific networks and carbon flux in the oligotrophic ocean

ISME Communications, Год журнала: 2024, Номер 4(1)

Опубликована: Янв. 1, 2024

Microbial associations that result in phytoplankton mortality are important for carbon transport the ocean. This includes parasitism, which microbial food webs is dominated by marine alveolate group, Syndiniales. Parasites expected to contribute recycling via host lysis; however, knowledge on dynamics and correlation export remain unclear limit inclusion of parasitism biogeochemical models. We analyzed a 4-year 18S rRNA gene metabarcoding dataset (2016-19), performing network analysis 12 discrete depths (1-1000 m) determine Syndiniales-host seasonally oligotrophic Sargasso Sea. Analogous water column sediment trap data were included define environmental drivers Syndiniales their with particulate flux (150 m). accounted 48-74% edges, most often associated Dinophyceae Arthropoda (mainly copepods) at surface Rhizaria (Polycystinea, Acantharea, RAD-B) aphotic zone. only eukaryote group be significantly (and negatively) correlated flux, indicating contribution attenuation remineralization. Examination amplicons revealed range depth patterns, including specific ecological niches vertical connection among subset (19%) community, latter implying sinking parasites (infected hosts or spores) particles. Our findings elevate critical role systems reveal potential use as biomarkers export.

Язык: Английский

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Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding

Frontiers in Marine Science, Год журнала: 2021, Номер 8

Опубликована: Май 25, 2021

The abyssal seafloor is a mosaic of highly diverse habitats that represent the least known marine ecosystems on Earth. Some regions enriched in natural resources, such as polymetallic nodules Clarion-Clipperton Zone (CCZ), attract much interest because their huge commercial potential. Since nodule mining will be destructive, baseline data are necessary to measure its impact benthic communities. Hence, we conducted an environmental DNA and RNA metabarcoding survey CCZ biodiversity targeting microbial meiofaunal eukaryotes component deep-sea benthos. We analyzed two 18S rRNA gene with focus Foraminifera (37F) metazoans (V1V2), sequenced from 310 surface-sediment samples other regions. Our results confirm unknown biodiversity. Over 60% foraminiferal almost third eukaryotic operational taxonomic units (OTUs) could not assigned taxon. Benthic more common than dominated by clades only surveys. most striking uniqueness areas, both datasets being characterized high number OTUs exclusive CCZ, well greater beta diversity compared alpha correlated water depth terrain complexity. Topography was important at local scale, communities stations located depressions heterogeneous those slopes. This result eDNA accumulation, justifying interim use eRNA for accurate biomonitoring descriptions support previous findings consolidate our general understanding ecosystems, but also provide resource inviting further taxon-specific large-scale modeling studies. foresee useful efforts consider small taxa, it must validated based ground truthing or experimental

Язык: Английский

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