scholarly journals High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem

2021 ◽  
Vol 8 ◽  
Author(s):  
Raquel Ríos-Castro ◽  
Alejandro Romero ◽  
Raquel Aranguren ◽  
Alberto Pallavicini ◽  
Elisa Banchi ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Coastal Upwelling ◽  
Marine Ecosystem ◽  
Environmental Dna ◽  
Functional Roles ◽  
Molecular Approaches ◽  
Eukaryotic Microorganisms ◽  
Causative Agents ◽  
Veterinary Importance ◽  
Water Fractions

The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.

scholarly journals Global diversity and biogeography of the Zostera marina mycobiome

2021 ◽  
Author(s):  
Cassandra L. Ettinger ◽  
Laura E. Vann ◽  
Jonathan A. Eisen
Keyword(s):  
Fungal Community ◽  
Community Assembly ◽  
Zostera Marina ◽  
High Throughput Sequencing ◽  
Marine Fungi ◽  
Marine Ecosystem ◽  
Fungal Community Composition ◽  
Functional Roles ◽  
Functional Guilds ◽  
The Many

Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens or endophytes in global ecosystems. Here we characterize the distribution of fungi associated with the seagrass, Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S ribosomal RNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested amplicon sequence variants (ASVs) were plant-selected or dispersal-limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak, but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The Z. marina core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp. and Saccharomyces sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds, that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses. Importance Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass, Zostera marina, across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases, that general knowledge of seagrass-associated fungi and marine fungi generally is lacking. This work serves as an important foundational step towards future work investigating the functional ramifications of fungi in the marine ecosystem.

scholarly journals Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

2017 ◽  
Author(s):  
Masayuki Ushio ◽  
Hiroaki Murakami ◽  
Reiji Masuda ◽  
Tetsuya Sado ◽  
Masaki Miya ◽  
...  
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Marine Ecosystem ◽  
Internal Standard ◽  
Environmental Dna ◽  
Illumina Miseq ◽  
Pcr Inhibition ◽  
Copy Numbers ◽  
Quantitative Monitoring ◽  
Monitoring Of Biodiversity

Effective ecosystem conservation and resource management require quantitative monitoring of biodiversity, including accurate descriptions of species composition and temporal variations of species abundance. Therefore, quantitative monitoring of biodiversity has been performed for many ecosystems, but it is often time- and effort-consuming and costly. Recent studies have shown that environmental DNA (eDNA), which is released to the environment from macro-organisms living in a habitat, contains information about species identity and abundance. Thus, analyzing eDNA would be a promising approach for more efficient biodiversity monitoring. In the present study, we added internal standard DNAs (i.e., known amounts of short DNA fragments from fish species that have never been observed in a sampling area) to eDNA samples, which were collected weekly from a coastal marine ecosystem in Maizuru-Bay, Kyoto, Japan (from April 2015 to March 2016), and performed metabarcoding analysis using Illumina MiSeq to simultaneously identify fish species and quantify fish eDNA copy numbers. A correction equation was obtained for each sample using the relationship between the number of sequence reads and the added amount of the standard DNAs, and this equation was used to estimate the copy numbers from the sequence reads of non-standard fish eDNA. The calculated copy numbers showed significant positive correlation with those determined by quantitative PCR, suggesting that eDNA metabarcoding with standard DNA enabled useful quantification of eDNA. Furthermore, for samples that show a high level of PCR inhibition, our method might allow more accurate quantification than qPCR because the correction equations generated using internal standard DNAs would include the effect of PCR inhibition. A single run of Illumina MiSeq produced > 70 quantitative fish eDNA time series in our study, showing that our method could contribute to more efficient and quantitative monitoring of biodiversity.

scholarly journals Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9821 ◽  
Author(s):  
Monika K. Reczuga ◽  
Christophe Victor William Seppey ◽  
Matthieu Mulot ◽  
Vincent E.J. Jassey ◽  
Alexandre Buttler ◽  
...  
Keyword(s):  
High Throughput ◽  
Ecosystem Functioning ◽  
High Throughput Sequencing ◽  
Ecosystem Respiration ◽  
Carbon Sources ◽  
Environmental Dna ◽  
Severe Drought ◽  
Food Web Interactions ◽  
Eukaryotic Diversity ◽  
Eukaryotic Microorganisms

Current projections suggest that climate warming will be accompanied by more frequent and severe drought events. Peatlands store ca. one third of the world’s soil organic carbon. Warming and drought may cause peatlands to become carbon sources through stimulation of microbial activity increasing ecosystem respiration, with positive feedback effect on global warming. Micro-eukaryotes play a key role in the carbon cycle through food web interactions and therefore, alterations in their community structure and diversity may affect ecosystem functioning and could reflect these changes. We assessed the diversity and community composition of Sphagnum-associated eukaryotic microorganisms inhabiting peatlands and their response to experimental drought and warming using high throughput sequencing of environmental DNA. Under drier conditions, micro-eukaryotic diversity decreased, the relative abundance of autotrophs increased and that of osmotrophs (including Fungi and Peronosporomycetes) decreased. Furthermore, we identified climate change indicators that could be used as early indicators of change in peatland microbial communities and ecosystem functioning. The changes we observed indicate a shift towards a more “terrestrial” community in response to drought, in line with observed changes in the functioning of the ecosystem.

scholarly journals Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Correlation Coefficients ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Absolute Quantification ◽  
Taqman Probe ◽  
Individual Species ◽  
Natural Environments ◽  
Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

2021 ◽  
pp. 1-10
Author(s):  
Micheline Carvalho-Silva ◽  
Luiz Henrique Rosa ◽  
Otávio H.B. Pinto ◽  
Thamar Holanda Da Silva ◽  
Diego Knop Henriques ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Crater Lake ◽  
Environmental Dna ◽  
Food Sources ◽  
South Shetland Islands ◽  
Deception Island ◽  
Shetland Islands ◽  
Operational Taxonomic Units ◽  
First Time ◽  
Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

scholarly journals Phytoplankton blooms on the western shelf of Tasmania: evidence of a highly productive ecosystem

Ocean Science ◽  
2015 ◽  
Vol 11 (1) ◽  
pp. 1-11 ◽  
Author(s):  
J. Kämpf
Keyword(s):  
Satellite Data ◽  
Coastal Upwelling ◽  
Phytoplankton Bloom ◽  
Hot Spot ◽  
Marine Ecosystem ◽  
Austral Summer ◽  
Phytoplankton Blooms ◽  
Study Region ◽  
Upwelling System ◽  
Fluorescence Line

Abstract. Satellite-derived chlorophyll a data using the standard NASA-OC3 (ocean colour) algorithm are strongly biased by coloured dissolved organic matter and suspended sediment of river discharges, which is a particular problem for the western Tasmanian shelf. This work reconstructs phytoplankton blooms in the study region using a quadratic regression between OC3 data and chlorophyll fluorescence based on the fluorescence line height (FLH) data. This regression is derived from satellite data of the nearby Bonney upwelling region, which is devoid of river influences. To this end, analyses of 10 years of MODIS-aqua satellite data reveal the existence of a highly productive ecosystem on the western Tasmanian shelf. The region normally experiences two phytoplankton blooms per annum. The first bloom occurs during late austral summer months as a consequence of upwelling-favourable coastal winds. Hence, the western Tasmanian shelf forms a previously unknown upwelling centre of the regional upwelling system, known as Great South Australian Coastal Upwelling System. The second phytoplankton bloom is a classical spring bloom also developing in the adjacent Tasman Sea. The author postulates that this region forms another important biological hot spot for the regional marine ecosystem.

scholarly journals Plankton blooms in vortices: the role of biological and hydrodynamic timescales

2007 ◽  
Vol 14 (4) ◽  
pp. 443-454 ◽  
Author(s):  
M. Sandulescu ◽  
C. López ◽  
E. Hernández-García ◽  
U. Feudel
Keyword(s):  
Coastal Upwelling ◽  
Marine Ecosystem ◽  
Coupled System ◽  
Component Model ◽  
Residence Times ◽  
Key Factors ◽  
Mesoscale Structures

Abstract. We study the interplay of hydrodynamic mesoscale structures and the growth of plankton in the wake of an island, and its interaction with a coastal upwelling. Our focus is on a mechanism for the emergence of localized plankton blooms in vortices. Using a coupled system of a kinematic flow mimicking the mesoscale structures behind the island and a simple three component model for the marine ecosystem, we show that the long residence times of nutrients and plankton in the vicinity of the island and the confinement of plankton within vortices are key factors for the appearance of localized plankton blooms.

scholarly journals High prevalence and diversity of beta-lactamase-encoding bacteria in cryosoils and ancient permafrost

2021 ◽  
Author(s):  
Sofia Rigou ◽  
Eugene Christo-Foroux ◽  
Sebastien Santini ◽  
Artemiy Goncharov ◽  
Jens Strauss ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Genome ◽  
Environmental Dna ◽  
Single Copy ◽  
The Arctic ◽  
Human Society ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
Arctic Regions ◽  
Global Threat

Background: Antimicrobial resistance is one of the major challenges affecting public health. It is mostly due to the continuous emergence of extended-spectrum beta-lactamase from various environments followed by their rapid dissemination and selection in clinical settings. The warming of Earth' s climate is the other global threat facing human society, in particular with the Arctic regions experiencing a twice faster warming than the global average and permafrost affected by widespread thawing. A potentially dreadful combination of these two threats would be the release and dispersion of harmful microbes that have remained confined to largely uninhabited Arctic regions, or are stored dormant in permafrost. Methods: Environmental DNA was isolated from 12 soil samples from various Arctic and subarctic pristine regions in Siberia (Yakutia and Kamchatka), including 9 permafrost samples collected at various depths. The large datasets obtained from high throughput sequencing was assembled in contigs and their protein-gene contents predicted. We used exhaustive similarity searches to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. In addition, we specifically identified beta-lactamase genes and their prevalence per bacterial genome estimated through the detection of two universal single copy genes. Findings: A total of 9.217 1011 bp were exploited, leading to a total of 525,313 contigs at least 5kb in size. The DNA content of the various samples was found to be highly variable, not strictly correlated with the depth or radio-carbon-based deposit age, and most likely linked to the global density of microbes trapped in the corresponding permafrost layers. Bacteria account for more than 90% of the contigs in most samples, followed by Eukaryotes and Archaea (always lower than 10%). Viruses represented less than 2% of all contigs in all samples. The taxonomic profiles of surface cryosoils and deep permafrost samples exhibited a high diversity, including between permafrost samples originating from various depths in the same borehole. In all samples, bacterial contigs carrying different beta-lactamases from class A to D were identified. Interpretation: No clear common taxonomic feature could be found shared by surface cryosoils or ancient permafrost layers. However, most samples (9/12) exhibited a high frequency of beta-lactamase genes, with an estimated average close to 1 copy/bacterial genome. In addition to the well-documented reactivation of infectious ancient pathogens (bacteria, viruses, protozoa), we show now that global warming could contribute to the emergence of new antibiotic resistances through the mobilization by contemporary bacteria of ancient DNA released from thawing permafrost.

scholarly journals External forcing mechanisms controlling the North Atlantic coastal upwelling regime during the mid-Holocene

Geology ◽  
2020 ◽  
Author(s):  
Armand Hernández ◽  
Mário Cachão ◽  
Pedro Sousa ◽  
Ricardo M. Trigo ◽  
Jürg Luterbacher ◽  
...  
Keyword(s):  
North Atlantic ◽  
Coastal Upwelling ◽  
Marine Ecosystem ◽  
External Forcing ◽  
The North ◽  
New Findings ◽  
The North Atlantic ◽  
Eastern North Atlantic ◽  
Forcing Mechanisms ◽  
The Impact

Nearshore upwelling along the eastern North Atlantic margin regulates regional marine ecosystem productivity and thus impacts blue economies. While most global circulation models show an increase in the intensity and duration of seasonal upwelling at high latitudes under future human-induced warmer conditions, projections for the North Atlantic are still ambiguous. Due to the low temporal resolution of coastal upwelling records, little is known about the impact of natural forcing mechanisms on upwelling variability. Here, we present a microfossil-based proxy record and modeling simulations for the warmest period of the Holocene (ca. 9–5 ka) to estimate the contribution of the natural variability in North Atlantic upwelling via atmospheric and oceanic dynamics. We found that more frequent high-pressure conditions in the eastern North Atlantic associated with solar activity and orbital parameters triggered upwelling variations at multidecadal and millennial time scales, respectively. Our new findings offer insights into the role of external forcing mechanisms in upwelling changes before the Anthropocene, which must be considered when producing future projections of midlatitude upwelling activity.

Inter-decadal variations of surface winds off Peruvian coast

2021 ◽  
Author(s):  
Sadegh Yari ◽  
Volker Mohrholz
Keyword(s):  
Coastal Upwelling ◽  
Marine Ecosystem ◽  
Wind Forcing ◽  
Trade Wind ◽  
Positive Anomaly ◽  
Peruvian Coast ◽  
Wide Range ◽  
Decadal Variations ◽  
Interannual Fluctuations

&lt;p&gt;The Peruvian upwelling system (PUS) is the most productive marine ecosystem among the Eastern Boundary upwelling Systems (EBUS). The trade wind system drives a nearly continuous upwelling which is subjected to variations on a wide range of times scales. The wind forced upwelling controls crucially the nutrient supply to the euphotic surface layer and thus, the overall productivity of the system.&lt;/p&gt;&lt;p&gt;Using long term data from ERA5 (1979-2019) the wind forcing in the PUS was analyzed to obtain information about long term trends in the mean state and its variability.&lt;/p&gt;&lt;p&gt;Beside the strong annual cycle, the wind forcing is dominated by interannual and a long term interdecadal oscillation.&lt;/p&gt;&lt;p&gt;The interannual fluctuations with a period of 2-5 years are related to the known events of El Ni&amp;#241;o and La Ni&amp;#241;a. The wind anomaly shows a good correlation with Oceanic Ni&amp;#241;o Index (ONI). Interdecadal variation of wind depict a main period of 15-20 years whit negative anomaly values from 1979 to 1996, and positive anomaly values for 1996-2014. These long term variations can be attributed to the Interdecadal Pacific Oscillations (IPO). The spatial distribution of wind stress along the Peruvian coast is not uniform. The highest values are observed in Lima-Marcona area (12&amp;#186;-15.4&amp;#186; S) while it decreases sharply southward and gradually northward. Additionally the coastal upwelling area is modulated locally by the coupling of wind and SST.&lt;/p&gt;

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