scholarly journals eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Eva Garcia-Vazquez ◽  
Oriane Georges ◽  
Sara Fernandez ◽  
Alba Ardura
Keyword(s):  
High Throughput Sequencing ◽  
Fish Larvae ◽  
Early Stage ◽  
Zooplankton Community ◽  
Coi Gene ◽  
Fish Diet ◽  
Commercial Fish ◽  
Tropical Waters ◽  
Small Water ◽  
Sampling Protocols

AbstractZooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the “missing biomass”) is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.

scholarly journals Faunistic survey of the zooplankton community in an oligotrophic sinkhole, Cenote Azul (Quintana Roo, Mexico), using different sampling methods, and documented with DNA barcodes

2018 ◽  
Author(s):  
Lucia Montes-Ortiz ◽  
Manuel Elias-Gutierrez
Keyword(s):  
Dna Barcoding ◽  
High Throughput Sequencing ◽  
Sampling Methods ◽  
Fish Larvae ◽  
Zooplankton Community ◽  
Quintana Roo ◽  
Essential Difference ◽  
Dna Barcodes ◽  
Light Traps ◽  
Freshwater System

This study is the first faunistic inventory of a zooplankton community from an open, karstic and oligotrophic aquatic sinkhole in the south of the Yucatan Peninsula (Mexico), we describe the richness of the zooplankton collected with the combination of plankton nets and light traps of our own design, using morphological and molecular characters to identify the species and demonstrate the effectiveness of only one set of primers to sequence all taxa. Recently, it has been demonstrated that different sampling methods can increase the number of zooplankton species from tropical and temperate systems dramatically. These more effective methods together with DNA barcoding can give a new and more realistic picture of the species dwelling in a freshwater system. In total, we sequenced 268 specimens, and the list of species known in this sinkhole increased from 13 to 77 taxa, with a projection of 87 in total, including cladocerans, copepods, ostracods, fish larvae, tadpoles, rotifers, chironomids, water mites, among others. From the 77 taxa identified by us, 72 BINS (Barcode Index Numbers, equivalent to putative species) were assigned by the BOLD Database (boldsystems.org), and 30 of them are new records for both, BOLD and GenBank (www.ncbi.nlm.nih.gov). There was an essential difference in the number of taxa collected with the plankton nets and the light traps. Only 23 taxa were registered in the nets, representing between 28 and 29% of the total richness, while 67 were present in the light traps representing 87% of the species found. From these, 46 taxa were exclusive to this sampling method. Light traps are an effective method for rapid evaluation of zooplankton. In the future, combining DNA barcoding and high-throughput sequencing methods with more  efficient collecting will enable us to perform quick and precise biomonitoring of any aquatic ecosystem, enabling the detection of changes in zooplankton composition resulting from climate change and anthropogenic disturbances. Nevertheless, as a first step it is fundamental to establish a baseline of DNA barcodes for the species in these ecosystems.

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 724-737 ◽  
Author(s):  
Mamoon M.D. Al-Rshaidat ◽  
Allison Snider ◽  
Sydney Rosebraugh ◽  
Amanda M. Devine ◽  
Thomas D. Devine ◽  
...  
Keyword(s):  
Coral Reefs ◽  
Red Sea ◽  
High Throughput Sequencing ◽  
Reference Sequence ◽  
Coi Gene ◽  
Gulf Of Aqaba ◽  
Dna Barcodes ◽  
Sampling Protocols ◽  
Animal Phyla ◽  
Northern Red Sea

High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm – 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.

scholarly journals Diversity of dinoflagellate assemblages in coastal temperate and offshore tropical waters of Australia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Tahnee Manning ◽  
Arjun Venkatesh Thilagaraj ◽  
Dmitri Mouradov ◽  
Richard Piola ◽  
Clare Grandison ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
High Throughput ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Marine Phytoplankton ◽  
Tropical Waters ◽  
Total Sequence ◽  
Phytoplankton Communities

Abstract Background Dinoflagellates are a ubiquitous and ecologically important component of marine phytoplankton communities, with particularly notable species including those associated with harmful algal blooms (HABs) and those that bioluminesce. High-throughput sequencing offers a novel approach compared to traditional microscopy for determining species assemblages and distributions of dinoflagellates, which are poorly known especially in Australian waters. Results We assessed the composition of dinoflagellate assemblages in two Australian locations: coastal temperate Port Phillip Bay and offshore tropical waters of Davies Reef (Great Barrier Reef). These locations differ in certain environmental parameters reflecting latitude as well as possible anthropogenic influences. Molecular taxonomic assessment revealed more species than traditional microscopy, and it showed statistically significant differences in dinoflagellate assemblages between locations. Bioluminescent species and known associates of HABs were present at both sites. Dinoflagellates in both areas were mainly represented by the order Gymnodiniales (66%—82% of total sequence reads). In the warm waters of Davies Reef, Gymnodiniales were equally represented by the two superclades, Gymnodiniales sensu stricto (33%) and Gyrodinium (34%). In contrast, in cooler waters of Port Phillip Bay, Gymnodiniales was mainly represented by Gyrodinium (82%). In both locations, bioluminescent dinoflagellates represented up to 0.24% of the total sequence reads, with Protoperidinium the most abundant genus. HAB-related species, mainly represented by Gyrodinium, were more abundant in Port Phillip Bay (up to 47%) than at Davies Reef (28%), potentially reflecting anthropogenic influence from highly populated and industrial areas surrounding the bay. The entire assemblage of dinoflagellates, as well as the subsets of HAB and bioluminescent species, were strongly correlated with water quality parameters (R2 = 0.56–0.92). Significant predictors differed between the subsets: HAB assemblages were explained by salinity, temperature, dissolved oxygen, and total dissolved solids; whereas, bioluminescent assemblages were explained only by salinity and dissolved oxygen, and had greater variability. Conclusion High-throughput sequencing and genotyping revealed greater diversity of dinoflagellate assemblages than previously known in both subtropical and temperate Australian waters. Significant correlations of assemblage structure with environmental variables suggest the potential for explaining the distribution and composition of both HAB species and bioluminescent species.

Calibration of the zooplankton community size spectrum as an indicator of change in Canadian Shield lakes

2019 ◽  
Vol 76 (12) ◽  
pp. 2268-2287
Author(s):  
Lauren Emily Barth ◽  
Brian John Shuter ◽  
William Gary Sprules ◽  
Charles Kenneth Minns ◽  
James Anthony Rusak
Keyword(s):  
Zooplankton Community ◽  
Canadian Shield ◽  
Rate Of Change ◽  
Crustacean Zooplankton ◽  
Size Spectrum ◽  
Community Size ◽  
Mean Values ◽  
Sampling Protocols ◽  
Stable Characteristic ◽  
Shield Lakes

Developing the crustacean zooplankton community size spectrum into an indicator of change in lakes requires quantification of the natural variability in the size spectrum related to broad-scale seasonal, annual, and spatial factors. Characterizing seasonal patterns of variation in the size spectrum is necessary so that monitoring programs can be designed to minimize the masking effects that seasonal processes can have on detecting longer-term temporal change. We used a random effects model to measure monthly, annual, and interlake variability in the slope (i.e., relative abundance of small and large organisms) and centered height (i.e., total abundance) of the crustacean zooplankton normalized abundance size spectrum from 1981 to 2011 among eight Canadian Shield lakes. Consistent with theoretical predictions, the slope was a relatively stable characteristic of the zooplankton community compared with the height, which varied significantly among lakes. We identified a seasonal signal in height and slope and used a mixed effects model to characterize the linear rate of change from May to October; there was an overall decline in height and an overall increase in slope. Seasonal variance was greater than annual variance for both the height and the slope, suggesting that long-term monitoring of lakes and interlake comparisons using zooplankton size spectra should be based on temporally standardized sampling protocols that minimize the effects of seasonal processes. We recommend sampling the zooplankton community in midsummer because this results in size spectrum estimates close to seasonal mean values.

scholarly journals Culturing embryonic cells from the parthenogenetic clonal marble crayfish (Marmorkrebs) Procambarus virginalis Lyko, 2017 (Decapoda: Astacidea: Cambaridae)

2019 ◽  
Vol 39 (6) ◽  
pp. 758-763
Author(s):  
Heriberto Deleon ◽  
Juan Garcia ◽  
Dionn Carlo Silva ◽  
Oscar Quintanilla ◽  
Zen Faulkes ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Early Stage ◽  
Model Organism ◽  
Coi Gene ◽  
Embryonic Cells ◽  
Oxidase Subunit ◽  
Marbled Crayfish

Abstract The parthenogenetic marbled crayfish, or Marmorkrebs (Procambarus virginalis Lyko 2017), is an emerging model organism. We describe a method to isolate cells from early-stage embryos and culture them in vitro. The identity of the cells was confirmed by sequencing the cytochrome c oxidase subunit I (COI) gene. This technique can be applied for use in the manipulation of embryonic parthenogenetic crayfish cells.

Temporal patterns in distributions of tropical fish larvae on the North West Shelf of Australia

2004 ◽  
Vol 55 (5) ◽  
pp. 473 ◽  
Author(s):  
A. Sampey ◽  
M. G. Meekan ◽  
J. H. Carleton ◽  
A. D. McKinnon ◽  
M. I. McCormick
Keyword(s):  
Southern Oscillation ◽  
Fish Larvae ◽  
Early Stage ◽  
Larval Survival ◽  
Zooplankton Biomass ◽  
Tropical Fish ◽  
North West ◽  
Larval Fishes ◽  
The North ◽  
Abundance And Diversity

Information on the temporal distributions of tropical fish larvae is scarce. Early stage larval fishes were sampled using towed bongo plankton nets at sites on the southern North West Shelf of Australia (21°49′S, 114°14′E), between October and February of 1997/98 and 1998/99. The first summer was characterised by El Niño–Southern Oscillation-driven upwelling and high primary productivity, whereas in the second summer water temperatures were warmer and primary production was lower. Benthic percoid shorefishes dominated surface assemblages in both summers and this pattern may be typical of tropical shelf environments.The abundance and diversity of larval fishes were lowest in October and increased from November through to February. Assemblages displayed weak cross-shelf patterns, with a few taxa being more abundant at inshore sites (e.g. monacanthids), whereas others were more abundant offshore (e.g. scombrids). Although the composition of assemblages remained relatively consistent, many taxa (e.g. pomacentrids and carangids) showed differences in abundance between summers. Multivariate analyses found no relationships between abundance patterns of larval fishes and biophysical variables, such as temperature, salinity, and zooplankton biomass. Thus, seasonal changes in abundance may reflect differences in the spawning activities of adult fishes and/or larval survival.

scholarly journals Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuka Torii ◽  
Kazuhiro Horiba ◽  
Satoshi Hayano ◽  
Taichi Kato ◽  
Takako Suzuki ◽  
...  
Keyword(s):  
Kawasaki Disease ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Early Stage ◽  
Rna Virus ◽  
Systemic Vasculitis ◽  
Human Herpesvirus ◽  
Acute Stage ◽  
Serum Samples

Abstract Background Kawasaki disease (KD) is an idiopathic systemic vasculitis that predominantly damages coronary arteries in children. Various pathogens have been investigated as triggers for KD, but no definitive causative pathogen has been determined. As KD is diagnosed by symptoms, several days are needed for diagnosis. Therefore, at the time of diagnosis of KD, the pathogen of the trigger may already be diminished. The aim of this study was to explore comprehensive pathogens in the sera at the acute stage of KD using high-throughput sequencing (HTS). Methods Sera of 12 patients at an extremely early stage of KD and 12 controls were investigated. DNA and RNA sequences were read separately using HTS. Sequence data were imported into the home-brew meta-genomic analysis pipeline, PATHDET, to identify the pathogen sequences. Results No RNA virus reads were detected in any KD case except for that of equine infectious anemia, which is known as a contaminant of commercial reverse transcriptase. Concerning DNA viruses, human herpesvirus 6B (HHV-6B, two cases) and Anelloviridae (eight cases) were detected among KD cases as well as controls. Multiple bacterial reads were obtained from KD and controls. Bacteria of the genera Acinetobacter, Pseudomonas, Delfita, Roseomonas, and Rhodocyclaceae appeared to be more common in KD sera than in the controls. Conclusion No single pathogen was identified in serum samples of patients at the acute phase of KD. With multiple bacteria detected in the serum samples, it is difficult to exclude the possibility of contamination; however, it is possible that these bacteria might stimulate the immune system and induce KD.

scholarly journals Abiotic parameters and planktonic community of an earthen fish pond with continuous water flow

2019 ◽  
Vol 31 ◽  
Author(s):  
Lúcia Helena Sipaúba-Tavares ◽  
Rodrigo Ney Millan ◽  
Érica Camargo Oliveira Capitano ◽  
Bruno Scardoelli-Truzzi
Keyword(s):  
Water Flow ◽  
Zooplankton Community ◽  
Information Criterion ◽  
Sampling Period ◽  
Plankton Community ◽  
Dominant Group ◽  
Small Water ◽  
Management Protocol ◽  
Thermotolerant Coliforms ◽  
Zooplankton Communities

Abstract Aim Limnological conditions, phytoplankton and zooplankton communities in a fishpond highly affected by management during the dry and rainy seasons are investigated. Methods Water samples were analyzed for physicochemical parameters; soil samples were analyzed for macro- and micro-nutrients, phytoplankton and zooplankton communities, at four sites, during eight months in the rainy and dry seasons. Distance-based linear model (DISTLM) was applied with Akaike Information Criterion (AIC), where the influence of environmental variables in the variation of phytoplankton and zooplankton composition could be assessed and the best model could be selected. Results The multiparameter test revealed that variables pH, TSS and TP better explain the composition of the biotic community (AICc = 45.6; R2 = 0.80). Chlorophyceae was the dominant group with 32 taxa, or rather, 75-85% of total phytoplankton, with high density at 2,365-4,180 ind.L-1 during the sampling period. Rotifera was the most abundant group in the zooplankton community during the two seasons, except at IW2 during the dry season, when Copepoda had a higher density, namely, 52% of total zooplankton community at this site. Conclusions The contribution of allochthonous material to the fishpond during the two seasons mainly consists of macro- and micro-nutrients and thermotolerant coliforms that influenced the plankton community and enhanced high Cyanobacteria density in the rainy season. Plankton community in the studied pond was characteristic of small water bodies. Management protocol in places with continuous water flow according to the region may be an important tool to optimize and to avoid risks in fish production.

scholarly journals Early Stage Root-Associated Fungi Show a High Temporal Turnover, but Are Independent of Beech Progeny

2020 ◽  
Vol 8 (2) ◽  
pp. 210 ◽  
Author(s):  
Kezia Goldmann ◽  
Silke Ammerschubert ◽  
Rodica Pena ◽  
Andrea Polle ◽  
Bin-Wei Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Early Stage ◽  
European Beech ◽  
Fungal Species ◽  
Fungal Communities ◽  
Transplant Experiment ◽  
Fungal Community Structure ◽  
Temporal Turnover ◽  
One Year ◽  
The Impact

The relationship between trees and root-associated fungal communities is complex. By specific root deposits and other signal cues, different tree species are able to attract divergent sets of fungal species. Plant intraspecific differences can lead to variable fungal patterns in the root’s proximity. Therefore, within the Beech Transplant Experiment, we analyzed the impact of three different European beech ecotypes on the fungal communities in roots and the surrounding rhizosphere soil at two time points. Beech nuts were collected in three German sites in 2011. After one year, seedlings of the different progenies were out-planted on one site and eventually re-sampled in 2014 and 2017. We applied high-throughput sequencing of the fungal ITS2 to determine the correlation between tree progeny, a possible home-field advantage, plant development and root-associated fungal guilds under field conditions. Our result showed no effect of beech progeny on either fungal OTU richness or fungal community structure. However, over time the fungal OTU richness in roots increased and the fungal communities changed significantly, also in rhizosphere. In both plant compartments, the fungal communities displayed a high temporal turnover, indicating a permanent development and functional adaption of the root mycobiome of young beeches.

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