scholarly journals Comparison of Water Sampling between Environmental DNA Metabarcoding and Conventional Microscopic Identification: A Case Study in Gwangyang Bay, South Korea

2019 ◽  
Vol 9 (16) ◽  
pp. 3272
Author(s):  
Kim ◽  
Park ◽  
Jo ◽  
Kwak
Keyword(s):  
South Korea ◽  
Community Composition ◽  
Late Summer ◽  
Environmental Dna ◽  
Ecological Monitoring ◽  
Data Sampling ◽  
Biological Communities ◽  
Microscopic Identification ◽  
Gwangyang Bay ◽  
Study Sites

Our study focuses on methodological comparison of plankton community composition in relation to ecological monitoring and assessment with data sampling. Recently, along with the advancement of monitoring techniques, metabarcoding has been widely used in the context of environmental DNA (eDNA). We examine the applicability of eDNA metabarcoding for effective monitoring and assessment of community composition, compared with conventional observation using microscopic identification in a coastal ecosystem, Gwangynag Bay in South Korea. Our analysis is based primarily on two surveys at a total of 15 study sites in early and late summer (June and September) of the year 2018. The results of our study demonstrate the similarity and dissimilarity of biological communities in composition, richness and diversity between eDNA metabarcoding and conventional microscopic identification. It is found that, overall, eDNA metabarcoding appears to provide a wider variety of species composition, while conventional microscopic identification depicts more distinct plankton communities in sites. Finally, we suggest that eDNA metabarcoding is a practically useful method and can be potentially considered as a valuable alternative for biological monitoring and diversity assessments.

scholarly journals Spatial distribution of environmental DNA in a nearshore marine habitat

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3044 ◽  
Author(s):  
James L. O’Donnell ◽  
Ryan P. Kelly ◽  
Andrew Olaf Shelton ◽  
Jameal F. Samhouri ◽  
Natalie C. Lowell ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Pcr Primers ◽  
Ecological Monitoring ◽  
Life History Stage ◽  
Illumina Platform ◽  
Marine Habitat ◽  
Biological Communities ◽  
Marine Surface

In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.

scholarly journals Ethanol eDNA Reveals Unique Community Composition of Aquatic Macroinvertebrates Compared to Bulk Tissue Metabarcoding in a Biomonitoring Sampling Scheme

Diversity ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 34
Author(s):  
Sadhna Fiona Persaud ◽  
Karl Cottenie ◽  
Jennifer Erin Gleason
Keyword(s):  
Land Use ◽  
Community Composition ◽  
Agricultural Land ◽  
Environmental Dna ◽  
Ecological Condition ◽  
Freshwater Ecosystems ◽  
Aquatic Macroinvertebrates ◽  
Biological Communities ◽  
Non Destructive ◽  
Bulk Tissue

Freshwater ecosystems provide essential ecosystem services and support biodiversity; however, their water quality and biological communities are influenced by adjacent agricultural land use. Aquatic macroinvertebrates are commonly used as bioindicators of stream conditions in freshwater biomonitoring programs. Sorting benthic samples for molecular identification is a time-consuming process, and this study investigates the potential of ethanol-collected environmental DNA (eDNA) for metabarcoding macroinvertebrates, especially for common bioindicator groups. The objective of this study was to compare macroinvertebrate composition between paired bulk tissue and ethanol eDNA samples, as eDNA could provide a less time-consuming and non-destructive method of sampling macroinvertebrates. We collected benthic samples from streams in Ontario, Canada, and found that community composition varied greatly between sampling methods and that few taxa were shared between paired tissue and ethanol samples, suggesting that ethanol eDNA is not an acceptable substitute. It is unclear why we did not detect all the organisms that were preserved in the ethanol, or the origin of the DNA we did detect. Furthermore, we also detected no difference in community composition for bioindicator taxa due to surrounding land use or water chemistry, suggesting sites were similar in ecological condition.

scholarly journals Spatial distribution of environmental DNA in a nearshore marine habitat

2016 ◽  
Author(s):  
James L O'Donnell ◽  
Ryan P Kelly ◽  
Andrew Olaf Shelton ◽  
Jameal F Samhouri ◽  
Natalie C Lowell ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Massively Parallel Sequencing ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Ecological Monitoring ◽  
Life History Stage ◽  
Marine Habitat ◽  
Biological Communities ◽  
The Face ◽  
Marine Surface

In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to 4 kilometers from shore. Using massively parallel sequencing of 16S amplicons, we identified a diverse community of metazoans and quantified their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.

scholarly journals Spatial distribution of environmental DNA in a nearshore marine habitat

2016 ◽  
Author(s):  
James L O'Donnell ◽  
Ryan P Kelly ◽  
Andrew Olaf Shelton ◽  
Jameal F Samhouri ◽  
Natalie C Lowell ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Massively Parallel Sequencing ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Ecological Monitoring ◽  
Life History Stage ◽  
Marine Habitat ◽  
Biological Communities ◽  
The Face ◽  
Marine Surface

In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to 4 kilometers from shore. Using massively parallel sequencing of 16S amplicons, we identified a diverse community of metazoans and quantified their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.

Taxonomic survey compared to ecological sampling: are the results consistent for woodland epiphytes?

2017 ◽  
Vol 49 (2) ◽  
pp. 141-155 ◽  
Author(s):  
C. J. ELLIS ◽  
B. J. COPPINS
Keyword(s):  
Species Richness ◽  
Community Composition ◽  
Statistical Treatment ◽  
Ecological Monitoring ◽  
Conservation Strategy ◽  
Habitat Dynamics ◽  
Study Sites ◽  
Ecological Sampling ◽  
A Site ◽  
High Degree

AbstractField survey by a taxonomist or specialist biologist (‘taxonomic survey’) provides a comprehensive inventory of species in a habitat. Common and conspicuous species are rapidly recorded and search effort can be targeted to inconspicuous or rare species. However, the subjective nature of taxonomic survey limits its usefulness in ecological monitoring and analysis. In contrast, ‘ecological sampling’, focused on the standardized use of repeated sub-units such as quadrats, is designed to quantify the observational error of results, allowing for more robust statistical treatment. Nevertheless, the spatial extent of recording will be lower during ecological sampling, and rarities might be missed. Despite their differences, these two approaches are often assumed to be congruent for decision making. Taxonomic survey is commonly used to identify priority sites for conservation (including species-rich sites, or those with many rare/threatened species) while ecological sampling is used to design conservation strategy by relating species richness or composition to habitat dynamics. If these contrasting approaches are indeed congruent, then trends in species richness and community composition, detected by ecological sampling, will mirror the results of taxonomic survey so that management confidently protects the attributes for which a site was prioritized. This study performed both taxonomic survey and ecological sampling for lichen epiphytes in 13 woodland study sites in Scotland. To understand the procedure of taxonomic survey, fieldwork by a professional taxonomist was structured by effort into 15-minute time intervals. As expected, taxonomic survey discovered more species per site, while ecological sampling (allowing a measure of species frequency) resolved greater variation in community composition. However, the patterns of richness and species composition obtained from the different methods were correlated, suggesting an overall high degree of congruence in identifying and then managing priority sites. Furthermore, when exploring the taxonomic survey in detail, we found that a minimum effort of 45 minutes was required to accurately determine species richness differences among contrasting woodland sites.

Polychlorinated biphenyls (PCBs) in a benthic ecosystem in Gwangyang Bay, South Korea

2011 ◽  
Vol 62 (12) ◽  
pp. 2863-2868 ◽  
Author(s):  
Sang Hee Hong ◽  
Narayanan Kannan ◽  
Un Hyuk Yim ◽  
Jin-Woo Choi ◽  
Won Joon Shim
Keyword(s):  
South Korea ◽  
Polychlorinated Biphenyls ◽  
Gwangyang Bay

Autumnal nutrient transfers by retranslocation, leaching, and litter fall in a chestnut oak forest in southern Illinois

1982 ◽  
Vol 12 (1) ◽  
pp. 40-51 ◽  
Author(s):  
Nancy L. Ostman ◽  
George T. Weaver
Keyword(s):  
Late Summer ◽  
Dry Weight ◽  
Litter Fall ◽  
Leaf Color ◽  
Southern Illinois ◽  
Foliar Concentrations ◽  
Important Means ◽  
Study Sites ◽  
Free Falling ◽  
Leaf Dry Weight

Retranslocation from leaves was investigated as a means of retaining nutrients in stands of Quercusprinus L. on two sites in southern Illinois, where wind rapidly moves litter downslope. Foliage samples were collected from late summer until leaf fall to describe the trends of leaf dry weight and nutrient concentration (N, K, P, Ca) changes. Free-falling rain and throughfall were collected to estimate foliar leaching. Foliar concentrations of N, K, and P decreased markedly during senescence while Ca concentrations increased. The pattern of concentration change was unique for each element, and the change in N concentration was closely correlated with change in leaf color. For the study sites as a whole, leaf dry weight decreased to 70% of the original value. Of 84.2 kg N/ha in green foliage, only 22.6% was returned to the site as litter. The canopy gained 0.3 kg N/ha (0.4%) from rainfall. The 78.5% N unaccounted for is attributed to retranslocation. Similarly, from 51.4 kg K/ha; 8.2, P; and 47.8, Ca in green foliage, 9.8, 1.3, and 3.3%, respectively, were removed by leaching; 27.4, 43.7, and 85.1% were returned to the site in litter. The remaining 63.0% K, 55.0% P, and 11.5% Ca unaccounted for is attributed to retranslocation. Retranslocation and leaching of nutrients was greater on the site of higher quality. But on both sites it appears that retranslocation is an important means of retaining and conserving N, K, and P countering the effect of annual litter removal.

scholarly journals Benthic estuarine communities' contribution to bioturbation under the experimental effect of marine heatwaves

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Dolbeth ◽  
O. Babe ◽  
D. A. Costa ◽  
A. P. Mucha ◽  
P. G. Cardoso ◽  
...  
Keyword(s):  
Community Composition ◽  
Ecosystem Functioning ◽  
Structural Changes ◽  
Nutrient Release ◽  
Biological Communities ◽  
Thermal Change ◽  
Composition And Structure ◽  
Temperature Ranges ◽  
Negative Impacts ◽  
Heat Extremes

AbstractMarine heatwaves are increasing worldwide, with several negative impacts on biological communities and ecosystems. This 24-day study tested heatwaves' effect with distinct duration and recovery periods on benthic estuarine communities' diversity and contribution to ecosystem functioning experimentally. The communities were obtained from a temperate estuary, usually subjected to high daily thermal amplitudes. Our goal was to understand the communities' response to the thermal change, including the community descriptors and behavioural changes expected during heat extremes. We measured community composition and structural changes and the bioturbation process and nutrient release as ecosystem functioning measurements. Overall, our findings highlight the potential tolerance of studied estuarine species to the temperature ranges tested in the study, as community composition and structure were similar, independently of the warming effect. We detected a slight trend for bioturbation and nutrient release increase in the communities under warming, yet these responses were not consistent with the heatwaves exposure duration. Overall, we conclude on the complexity of estuarine communities’ contribution to functioning under warming, and the importance of scalable experiments with benthic organisms' responses to climate variability, accommodating longer time scales and replication. Such an approach would set more efficient expectations towards climate change mitigation or adaptation in temperate estuarine ecosystems.

scholarly journals Environmental DNA as a tool for ecological monitoring of fungal communities

2017 ◽  
Vol 74 (5) ◽  
pp. 442-448
Author(s):  
V.M. Pomohaybo ◽  
◽  
Ya.M. Makarenko ◽  
Keyword(s):  
Environmental Dna ◽  
Ecological Monitoring ◽  
Fungal Communities

scholarly journals Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

2021 ◽  
Vol 12 ◽  
Author(s):  
Larissa Frühe ◽  
Verena Dully ◽  
Dominik Forster ◽  
Nigel B. Keeley ◽  
Olivier Laroche ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Environmental Dna ◽  
Community Diversity ◽  
Rrna Gene ◽  
Local Conditions ◽  
Global Trends ◽  
Bacterial Taxon ◽  
Metabolic Properties

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

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