Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 818, P. 151783 - 151783

Published: Nov. 19, 2021

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification whole communities within a targeted group) is revolutionizing the field aquatic biomonitoring. To date, most studies aiming to assess ecological status ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, has also been applied soft sediment samples, mainly assessing microbial or meiofaunal biota. Compared classical methodologies based manual sorting morphological benthic taxa, offers potentially important advantages environmental quality sediments. The methods protocols utilized can vary considerably among studies, standardization efforts are needed improve their robustness, comparability use regulatory frameworks. Here, we review available information with focus sampling, preservation, extraction steps. We discuss challenges specific analysis, including variety different sources states its persistence in sediment. This paper aims identify good-practice strategies facilitate method harmonization routine future monitoring.

Language: Английский

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Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective

Microbiology Research, Journal Year: 2022, Volume and Issue: 13(3), P. 418 - 465

Published: July 1, 2022

There is a real consensus that new antibiotics are urgently needed and the best chance for combating antibiotic resistance. The phylum Actinobacteria one of main producers antibiotics, with recent paradigm shift whereby rare actinomycetes have been increasingly targeted as source secondary metabolites discovery antibiotics. However, this review shows genus Streptomyces still largest current producer innovative metabolites. Between January 2015 December 2020, significantly high number novel spp. isolated from different environments, including extreme symbionts, terrestrial soils, sediments also marine mainly invertebrates sediments. This highlights 135 species during 6-year period 108 environment 27 sources. A brief summary pre-treatment methods used successful isolation some discussed, well biological activities total 279 recorded 121 which exhibit diverse activity. greatest originated terrestrial-sourced

Language: Английский

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Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Science Advances, Journal Year: 2022, Volume and Issue: 8(5)

Published: Feb. 4, 2022

Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) abyssal and lower bathyal surficial sediments euphotic aphotic ocean pelagic layers distinguish plankton diversity in material. Based 1685 samples collected throughout world ocean, show that DOS is at threefold realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These communities spatially structured basins particulate organic carbon (POC) flux upper ocean. Plankton reaching originates species, maximal deposition high latitudes. Its seafloor signature predicts variations POC export surface reveals previously overlooked taxa may drive biological pump.

Language: Английский

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Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: May 10, 2022

The deep sea harbors the majority of microbial biomass in ocean and is a key site for organic matter (OM) remineralization storage biosphere. Microbial metabolism greatly controlled by generally depleted but periodically fluctuating supply OM. Currently, little known about metabolic potentials dominant deep-sea microbes to cope with variable OM inputs, especially those living hadal trenches-the deepest part ocean.In this study, we report first extensive examination sediment Chloroflexi, phylum trenches global ocean. In total, 62 metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived sediments Mariana Trench. These MAGs represent six novel species, four genera, one family, order within classes Anaerolineae Dehalococcoidia. Fragment recruitment showed that these are globally distributed waters surface sediments, transcriptomic analysis indicated their situ activities. Metabolic reconstruction Chloroflexi mainly had heterotrophic lifestyle, potential degrade wide range carbon, sulfur, halogenated compounds. Our results revealed time harbor pathways complete hydrolytic or oxidative degradation various recalcitrant OM, including aromatic compounds (e.g., benzoate), polyaromatic hydrocarbons fluorene), polychlorobiphenyl 4-chlorobiphenyl), organochlorine chloroalkanes, chlorocyclohexane). Moreover, organisms synthesize energy trehalose) regulatory modules respond changes nutrient conditions. traits suggest may follow "feast-or-famine" strategy, i.e., preferentially consume labile store intracellularly under OM-rich conditions, utilize stored survival OM-limited condition.This study expands current knowledge on strategies deep-ocean Chlorolfexi highlights significance halogen cycles. plasticity likely provides advantages heterogenic inputs Video Abstract.

Language: Английский

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Marine natural products

Natural Product Reports, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

A comprehensive review of 1220 new MNPs including a novel sex inducing pheromone from the diatom Seminavis robusta .

Language: Английский

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Typhoon-induced turbulence redistributed microplastics in coastal areas and reformed plastisphere community

Water Research, Journal Year: 2021, Volume and Issue: 204, P. 117580 - 117580

Published: Aug. 19, 2021

Language: Английский

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Characteristics of microbial community composition and its relationship with carbon, nitrogen and sulfur in sediments

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 795, P. 148848 - 148848

Published: July 3, 2021

Language: Английский

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Sulfur Biogeochemical Cycle of Marine Sediments

Geochemical Perspectives, Journal Year: 2021, Volume and Issue: unknown, P. 145 - 307

Published: Oct. 1, 2021

Complex interactions between microbial communities and geochemical processes drive the major element cycles control function of marine sediments as a dynamic reservoir organic matter. Sulfate reduction is globally dominant pathway anaerobic mineralisation main source sulfide. The effective re-oxidation this sulfide at direct or indirect expense oxygen prerequisite for aerobic life on our planet. Although largely hidden beneath oxic sediment surface, sulfur cycle therefore critical Earth’s redox state. This Geochemical Perspectives begins with brief primer description my own scientific journey through nearly fifty years studies geochemistry microbiology. Among objectives these were to quantify identify behind them. Radiotracers in combination chemical analyses have thereby been used extensively laboratory experiments, supported by diverse molecular microbiological methods. following sections discuss sulfate reduction, oxidation disproportionation inorganic intermediates, especially elemental thiosulfate. experimental approaches enable analysis how environmental factors such substrate concentration temperature affect process rates concurrent cryptic cycle. energy chemolithotrophic bacteria, including fascinating big bacteria cable supports their dark CO2 fixation, which produces new biomass. During burial aging sediments, predominant change cascade reactions, rate matter degradation drops continuously over many orders magnitude. pathways age turnover are discussed. In deep methanic zone, only few percent entire remains, provides small boost methane oxidation. stable isotopes provide an additional tool understand diagenetic processes, whereby isotope fractionation open system diagenesis generate differential diffusion flux isotopes. relation carbon seabed contribution methane, paper discusses global budget role different depth regions ocean – from coast sea. published estimates parameters evaluated compared. Finally, looks future perspectives respect gaps current understanding need further studies.

Language: Английский

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Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(12), P. 2800 - 2816

Published: May 8, 2021

Microbial abundance and community composition in marine sediments have been widely explored. However, high-resolution vertical changes of benthic microbial diversity co-occurrence patterns are poorly described. The ecological contributions abundant rare species also remain largely unknown. Here, by analysing populations at 14 depth layers 10 subseafloor sediment cores (water 1,250-3,530 m) obtained the South China Sea, we provided profiles β-diversity influenced subcommunities different abundance. These 134 samples were clustered into four groups according to (1-2, 6-10, 30-90 190-790 cm) with obvious shifts compositions. succession microorganisms was consistent redox zonation terrestrial inputs. Partitioning showed extremely high replacement between deep surface layer, indicating selection-induced loss dispersal dormant cells spores. By contrast, for horizontal β-diversity, richness became increasingly significant sediments. Accompanying this profile clear association pattern, being less connected deeper layers, probably reflecting reduced syntrophic interactions. Rare accounted an indispensable proportion network, tended form complex "small worlds." subcommunity responded differently various environmental factors compared subcommunity. Our findings expand current knowledge on their patterns, emphasizing potential roles species.

Language: Английский

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An excavate root for the eukaryote tree of life

Science Advances, Journal Year: 2023, Volume and Issue: 9(17)

Published: April 28, 2023

Much of the higher-order phylogeny eukaryotes is well resolved, but root remains elusive. We assembled a dataset 183 eukaryotic proteins archaeal ancestry to test this root. The resulting identifies four lineages currently classified as "Excavata" branching separately at base tree. Thus, Parabasalia appear first major branch followed sequentially by Fornicata, Preaxostyla, and Discoba. All excavate points receive full statistical support from analyses with commonly used evolutionary models, protein structure partition model that we introduce here, various controls for deep artifacts. absence aerobic mitochondria in Parabasalia, Preaxostyla suggests modern arose under anoxic conditions, probably much earlier than expected, without benefit mitochondrial respiration.

Language: Английский

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