scholarly journals Comparison of materials for rapid passive collection of environmental DNA

2021 ◽  
Author(s):  
Cindy Bessey ◽  
Yuan Gao ◽  
Yen Truong ◽  
Haylea Miller ◽  
Simon Jarman ◽  
...  
Keyword(s):  
Species Richness ◽  
Sampling Method ◽  
Electrospun Nanofibers ◽  
Environmental Dna ◽  
Aquatic Systems ◽  
Biological Surveys ◽  
Biological Matter ◽  
Cotton Fibres ◽  
Hemp Fibres ◽  
Template Dna

Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive, efficient, and requires minimal equipment, making it suited to high density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3 million litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibers and 1% chitosan, cotton fibres, hemp fibres and sponge with either zeolite or active carbon) for intervals between five and 1080 minutes. We show that for most materials, with as little as five minutes submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 to 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19-32). Using scanning electron microscopy, we visualised biological matter adhered to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. Environmental DNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost and time-sensitive biological surveys, and where access to equipment is limited.

scholarly journals Comparison of materials for rapid passive collection of environmental DNA

2021 ◽  
Author(s):  
Cindy Bessey ◽  
Yuan Gao ◽  
Yen Bach Truong ◽  
Haylea Miller ◽  
Simon Neil Jarman ◽  
...  
Keyword(s):  
Species Richness ◽  
Sampling Method ◽  
Electrospun Nanofibers ◽  
Environmental Dna ◽  
Aquatic Systems ◽  
Biological Surveys ◽  
Biological Matter ◽  
Cotton Fibres ◽  
Hemp Fibres ◽  
Template Dna

Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive, efficient, and requires minimal equipment, making it suited to high density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3 million litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibers and 1% chitosan, cotton fibres, hemp fibres and sponge with either zeolite or active carbon) for intervals between five and 1080 minutes. We show that for most materials, with as little as five minutes submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 to 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19-32). Using scanning electron microscopy, we visualised biological matter adhered to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. Environmental DNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost and time-sensitive biological surveys, and where access to equipment is limited.

scholarly journals Designing environmental DNA surveys in complex aquatic systems: Backpack sampling for rare amphibians in Sierra Nevada meadows

2020 ◽  
Vol 30 (10) ◽  
pp. 1975-1987 ◽  
Author(s):  
Karen L. Pope ◽  
Caren S. Goldberg ◽  
Nicolette L. Nelson ◽  
Adam K. Cummings ◽  
Travis Seaborn ◽  
...  
Keyword(s):  
Sierra Nevada ◽  
Environmental Dna ◽  
Aquatic Systems ◽  
Sierra Nevada Meadows

scholarly journals Communities of Fungi in Black Cherry Stumps and Effects of Herbicide

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1126
Author(s):  
Robert Korzeniewicz ◽  
Marlena Baranowska ◽  
Hanna Kwaśna ◽  
Gniewko Niedbała ◽  
Jolanta Behnke-Borowczyk
Keyword(s):  
Species Richness ◽  
Environmental Dna ◽  
Bioinformatic Analysis ◽  
Diversity Indices ◽  
Fungal Species ◽  
Fungal Communities ◽  
Reference Sequence ◽  
Deciduous Tree ◽  
Black Cherry ◽  
5.8S Rdna

So far, there have been no studies on fungal communities in Prunus serotina (black cherry) wood. Our objectives were to characterize fungal communities from P. serotina wood and to evaluate effects of glyphosate (Glifocyd 360 SL) used on P. serotina stumps on abundance, species richness and diversity of those communities. In August 2016, in the Podanin Forest District, stumps of black cherry trees left after felling were treated with the herbicide. Control stumps were treated with water. Wood discs were cut from the surface of the stumps in May and July–August 2017. Eight treatment combinations (2 herbicide treatments × 2 disc sizes × 2 sample times) were tested. Sub-samples were pooled and ground in an acryogenic mill. Environmental DNA was extracted with a Plant Genomic DNA Purification Kit. The ITS1, 5.8S rDNA region was used to identify fungal species, using primers ITS1FI2 5′-GAACCWGCGGARGGATCA-3′ and 5.8S 5′-CGCTGCGTT CTTCATCG-3′. The amplicons were sequenced using the Illumina system. The results were subjected to bioinformatic analysis. Sequences were compared with reference sequences from the NCBI database using the BLASTn 2.8.0 algorithm. Abundance of fungi was defined as the number of Operational Taxonomic Units (OTUs), and diversity as the number of species in a sample. Differences between the number of OTUs and taxa were analyzed using the chi-squared test (χ2). Diversity in microbial communities was compared using diversity indices. A total of 54,644 OTUs were obtained. Culturable fungi produced 49,808 OTUs (91.15%), fungi not known from culture had 2571 OTUs (4.70%), non-fungal organisms had 1333 (2.44%) and organisms with no reference sequence in NCBI, 934 OTUs (1.71%). The total number of taxa ranged from 120 to 319. Fungi in stump wood were significantly more abundant in July–August than in May, in stumps >5 cm diameter than in stumps <5 cm diameter, in glyphosate-treated than in untreated stumps when sampled in May, and in untreated than in glyphosate-treated stumps when sampled in July–August. Species richness was significantly greater in July–August than in May, and in stumps >5 cm diameter than in stumps <5 cm diameter, either treated or untreated, depending on size. Herbicides can therefore affect the abundance and diversity of fungal communities in deciduous tree wood. The greater frequency of Ascomycota in herbicide-treated than in untreated stumps indicates their greater tolerance of glyphosate.

Molluscs Diversity in Coastal Ecosystem of South Biak, Papua

2017 ◽  
Vol 2 (1) ◽  
pp. 25 ◽  
Author(s):  
Ludi Parwadani Aji ◽  
Andriani Widyastuti
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Sampling Method ◽  
Diversity Index ◽  
Similarity Index ◽  
Coastal Areas ◽  
Seagrass Beds ◽  
Simpson Index ◽  
Transect Line ◽  
Evenness Index

Coastal areas of Biak Island consist of three major ecosystems: the mangrove, seagrass beds, and coral reefs where a variety of molluscs live. Mollusc diversity in South Biak waters was investigated in September 2011. The observation was conducted at 4 locations, i.e. Paray, Ambroben, Yenures, and Sorido with 2 stations at each location. The study aimed to obtain information on the diversity and community structure of the benthic molluscs (gastropods and bivalves) on the coastal areas of South Biak waters. Sampling method applied was quadrate-transect line in intertidal areas from inshore to offshore. The molluscs (epifauna and infauna) found inside the quadrate-transect were counted and identified. The result showed high benthic mollusc diversity with a total of 94 species, consisting of 75 species of gastropods and 19 species of bivalves. The most widespread gastropod found in all stations was Nassarius sp., while for bivalves was Tellina sp. The highest value of diversity index (H) was 2.96 found in Paray 1 and the lowest was 0.58 in Yenures 1. The Evenness index (E) and Simpson index (D) ranged from 0.27 to 0.96 and from 0.06 to 0.72 respectively. Species richness (d) ranged from 2.89 to 6.84 and similarity index from 3.90 to 42.40.  

scholarly journals An environmental DNA sampling method for aye-ayes from their feeding traces

2018 ◽  
Vol 8 (18) ◽  
pp. 9229-9240 ◽  
Author(s):  
Megan L. Aylward ◽  
Alexis P. Sullivan ◽  
George H. Perry ◽  
Steig E. Johnson ◽  
Edward E. Louis
Keyword(s):  
Sampling Method ◽  
Environmental Dna ◽  
Dna Sampling

scholarly journals Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering

2017 ◽  
Vol 74 (9) ◽  
pp. 1362-1374 ◽  
Author(s):  
Nathan T. Evans ◽  
Yiyuan Li ◽  
Mark A. Renshaw ◽  
Brett P. Olds ◽  
Kristy Deiner ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Species Richness ◽  
Spatial Resolution ◽  
Spatial Patterns ◽  
Water Body ◽  
Fish Community ◽  
Sampling Design ◽  
Environmental Dna ◽  
Body Type ◽  
Multiple Samples

Species richness is a metric of biodiversity that represents the number of species present in a community. Traditional fisheries assessments that rely on capture of organisms often underestimate true species richness. Environmental DNA (eDNA) metabarcoding is an alternative tool that infers species richness by collecting and sequencing DNA present in the ecosystem. Our objective was to determine how spatial distribution of samples and “bioinformatic stringency” affected eDNA-metabarcoding estimates of species richness compared with capture-based estimates in a 2.2 ha reservoir. When bioinformatic criteria required species to be detected only in a single sample, eDNA metabarcoding detected all species captured with traditional methods plus an additional 11 noncaptured species. However, when we required species to be detected with multiple markers and in multiple samples, eDNA metabarcoding detected only seven of the captured species. Our analysis of the spatial patterns of species detection indicated that eDNA was distributed relatively homogeneously throughout the reservoir, except near the inflowing stream. We suggest that interpretation of eDNA metabarcoding data must consider the potential effects of water body type, spatial resolution, and bioinformatic stringency.

scholarly journals The role of microhabitats in structuring cave invertebrate communities in Guatemala

2020 ◽  
Vol 49 (2) ◽  
pp. 161-169
Author(s):  
Gabrielle Pacheco ◽  
◽  
Marconi Souza Silva ◽  
Enio Cano ◽  
Rodrigo L. Ferreira ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Invertebrate Community ◽  
Biological Surveys ◽  
Trophic Resources ◽  
Main Driver ◽  
Broad Variety ◽  
Substrate Heterogeneity ◽  
Invertebrate Community Structure

Several studies have tried to elucidate the main environmental features driving invertebrate community structure in cave environments. They found that many factors influence the community structure, but rarely focused on how substrate types and heterogeneity might shape these communities. Therefore, the objective of this study was to assess which substrate features and whether or not substrate heterogeneity determines the invertebrate community structure (species richness and composition) in a set of limestone caves in Guatemala. We hypothesized that the troglobitic fauna responds differently to habitat structure regarding species richness and composition than non-troglobitic fauna because they are more specialized to live in subterranean habitats. Using 30 m2 transects, the invertebrate fauna was collected and the substrate features were measured. The results showed that community responded to the presence of guano, cobbles, boulders, and substrate heterogeneity. The positive relationship between non-troglobitic species composition with the presence of guano reinforces the importance of food resources for structuring invertebrate cave communities in Guatemalan caves. Furthermore, the troglobitic species responded to different substrate features when compared to non-troglobitic species. For them, instead of the presence of organic matter, a higher variety of abiotic microhabitats seem to be the main driver for species diversity within a cave. The high specialization level of troglobitic organisms might be the reason why they respond differently to environmental conditions. The findings of this study highlight the importance of biological surveys for understanding cave biodiversity and give insights on how this biodiversity might be distributed within a cave. Conservation measures should keep in mind the target organisms and if such measures aim to protect a broad variety of organisms, then one should aim to preserve as many microhabitats and trophic resources as possible.

scholarly journals eDNAir: proof of concept that animal DNA can be collected from air sampling

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11030
Author(s):  
Elizabeth L. Clare ◽  
Chloe K. Economou ◽  
Chris G. Faulkes ◽  
James D. Gilbert ◽  
Frances Bennett ◽  
...  
Keyword(s):  
Sampling Methods ◽  
Air Sampling ◽  
Research Programme ◽  
Environmental Dna ◽  
Aquatic Systems ◽  
Ecological Research ◽  
Proof Of Concept ◽  
Confined Space ◽  
Substantial Interest

Environmental DNA (eDNA) is one of the fastest developing tools for species biomonitoring and ecological research. However, despite substantial interest from research, commercial and regulatory sectors, it has remained primarily a tool for aquatic systems with a small amount of work in substances such as soil, snow and rain. Here we demonstrate that eDNA can be collected from air and used to identify mammals. Our proof of concept successfully demonstrated that eDNA sampled from air contained mixed templates which reflect the species known to be present within a confined space and that this material can be accessed using existing sampling methods. We anticipate this demonstration will initiate a much larger research programme in terrestrial airDNA sampling and that this may rapidly advance biomonitoring approaches. Lastly, we outline these and potential related applications we expect to benefit from this development.

On the Effectiveness of Hand Collection to Complement Baits When Studying Ant Vertical Stratification in Tropical Rainforests

Sociobiology ◽  
2020 ◽  
Vol 67 (2) ◽  
pp. 213
Author(s):  
Reuber Antoniazzi ◽  
Diana Ahuatzin ◽  
Jaime Pelayo-Martínez ◽  
Liliana Ortiz-Lozada ◽  
Maurice Leponce ◽  
...  
Keyword(s):  
Species Richness ◽  
Species Composition ◽  
Forest Floor ◽  
Sampling Method ◽  
Tropical Rainforest ◽  
Sampling Methods ◽  
Search Time ◽  
Tropical Rainforests ◽  
Additional Advantage ◽  
Key Factor

Choosing an appropriate sampling method to study ants is a key factor since distinct sampling methods can capture distinct ant fauna and, therefore, leading to bias in the interpretation and conclusion of the patterns observed. Despite it is well known that the ant fauna is vertically stratified, some of the sampling methods cannot be used throughout the whole vertical stratum (e.g., fogging and Winkler extractor). Here we compared the complementarity of hand collecting and baiting (with tuna or honey) in ant surveys focused on the stratification of the ant fauna in a tropical rainforest in Mexico. We found a total of 44 ant species, belonging to 17 genera and five subfamilies. The three sampling methods were clearly complementary at both the forest floor and canopy levels, even with as little as 10 minutes of search time for hand collecting. The ant species composition differed among sampling methods at both vertical strata. Hand collecting yielded higher ant species richness and more exclusive species than either bait at both vertical strata, but both tuna and honey baits also led to the detection of some (though fewer) exclusive ant species. The combination of hand collecting, tuna, and honey baits should thus be considered complementary tools for ant inventories, since using the two methods together yielded more complete inventories at both vertical strata. An additional advantage is that both methods can be used in both strata, ensuring that data in different vertical strata are comparable and allowing more reliable comparisons among these different habitats.

scholarly journals Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

2021 ◽  
Vol 288 (1949) ◽  
Author(s):  
Emilie Boulanger ◽  
Nicolas Loiseau ◽  
Alice Valentini ◽  
Véronique Arnal ◽  
Pierre Boissery ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Species ◽  
Fish Assemblages ◽  
Marine Reserves ◽  
Marked Change ◽  
Environmental Dna ◽  
Biodiversity Loss ◽  
Conclusive Evidence ◽  
Anthropogenic Pressure ◽  
Local Species Richness

Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.

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