A field ecologist's guide to environmental DNA sampling in freshwater environments

2020 ◽  
Vol 40 (4) ◽  
pp. 641-651
Author(s):  
Emily F. McColl-Gausden ◽  
Andrew R. Weeks ◽  
Reid Tingley
Keyword(s):  
Environmental Samples ◽  
Environmental Dna ◽  
Single Species ◽  
Freshwater Ecosystems ◽  
False Positives ◽  
Imperfect Detection ◽  
Occupancy Detection ◽  
Multiple Species ◽  
Methodological Considerations ◽  
Species Occupancy

Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an emerging survey technique that has the potential to transform biodiversity monitoring in freshwater ecosystems. We provide a brief overview of the primary methodological aspects of eDNA sampling that ecologists should consider before taking environmental samples in the field. We outline five key methodological considerations: (i) targeting single species vs multiple species; (ii) where and when to sample; (iii) how much water to collect; (iv) how many samples to take; and (v) recognising potential sources of false positives. The need to account for false negatives and false positives in eDNA surveys, and the power of species occupancy detection models in accounting for imperfect detection, is also discussed.

scholarly journals Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: a case study using coastal marine eDNA

2019 ◽  
Author(s):  
Beverly McClenaghan ◽  
Zacchaeus G. Compson ◽  
Mehrdad Hajibabaei
Keyword(s):  
Model Comparison ◽  
Environmental Dna ◽  
Model Assessment ◽  
Occupancy Models ◽  
Ecological Inference ◽  
Biodiversity Data ◽  
Imperfect Detection ◽  
Coastal Marine ◽  
Species Occupancy

AbstractEnvironmental DNA (eDNA) metabarcoding is an increasingly popular method for rapid biodiversity assessment. As with any ecological survey, false negatives can arise during sampling and, if unaccounted for, lead to biased results and potentially misdiagnosed environmental assessments. We developed a multi-scale, multi-species occupancy model for the analysis of community biodiversity data resulting from eDNA metabarcoding; this model accounts for imperfect detection and additional sources of environmental and experimental variation. We present methods for model assessment and model comparison and demonstrate how these tools improve the inferential power of eDNA metabarcoding data using a case study in a coastal, marine environment. Using occupancy models to account for factors often overlooked in the analysis of eDNA metabarcoding data will dramatically improve ecological inference, sampling design, and methodologies, empowering practitioners with an approach to wield the high-resolution biodiversity data of next-generation sequencing platforms.

scholarly journals Best practices on the differential expression analysis of multi-species RNA-seq

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Matthew Chung ◽  
Vincent M. Bruno ◽  
David A. Rasko ◽  
Christina A. Cuomo ◽  
José F. Muñoz ◽  
...  
Keyword(s):  
Best Practices ◽  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Single Species ◽  
Rna Seq ◽  
Species Analysis ◽  
Differential Gene ◽  
Multiple Species ◽  
Downstream Analysis

AbstractAdvances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.

scholarly journals Evaluating Coexistence of Fish Species with Coastal Cutthroat Trout in Low Order Streams of Western Oregon and Washington, USA

Fishes ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 4
Author(s):  
Kyle D. Martens ◽  
Jason Dunham
Keyword(s):  
Pacific Northwest ◽  
Species Interactions ◽  
Coho Salmon ◽  
Cutthroat Trout ◽  
Single Species ◽  
The Pacific ◽  
Small Streams ◽  
Coastal Cutthroat Trout ◽  
Multiple Species ◽  
Low Order

When multiple species of fish coexist there are a host of potential ways through which they may interact, yet there is often a strong focus on studies of single species without considering these interactions. For example, many studies of forestry–stream interactions in the Pacific Northwest have focused solely on the most prevalent species: Coastal cutthroat trout. To examine the potential for interactions of other fishes with coastal cutthroat trout, we conducted an analysis of 281 sites in low order streams located on Washington’s Olympic Peninsula and along the central Oregon coast. Coastal cutthroat trout and juvenile coho salmon were the most commonly found salmonid species within these streams and exhibited positive associations with each other for both presence and density. Steelhead were negatively associated with the presence of coastal cutthroat trout as well as with coho salmon and sculpins (Cottidae). Coastal cutthroat trout most frequently shared streams with juvenile coho salmon. For densities of these co-occurring species, associations between these two species were relatively weak compared to the strong influences of physical stream conditions (size and gradient), suggesting that physical conditions may have more of an influence on density than species interactions. Collectively, our analysis, along with a review of findings from prior field and laboratory studies, suggests that the net effect of interactions between coastal cutthroat trout and coho salmon do not appear to inhibit their presence or densities in small streams along the Pacific Northwest.

scholarly journals Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mark D. Johnson ◽  
Mohamed Fokar ◽  
Robert D. Cox ◽  
Matthew A. Barnes
Keyword(s):  
Plant Community ◽  
Plant Communities ◽  
Traditional Method ◽  
Environmental Dna ◽  
Single Species ◽  
Community Survey ◽  
Sampling Effort ◽  
Sampling Campaign ◽  
Dna Metabarcoding ◽  
Human Health Impacts

Abstract Background Airborne environmental DNA (eDNA) research is an emerging field that focuses on the detection of species from their genetic remnants in the air. The majority of studies into airborne eDNA of plants has until now either focused on single species detection, specifically only pollen, or human health impacts, with no previous studies surveying an entire plant community through metabarcoding. We therefore conducted an airborne eDNA metabarcoding survey and compared the results to a traditional plant community survey. Results Over the course of a year, we conducted two traditional transect-based visual plant surveys alongside an airborne eDNA sampling campaign on a short-grass rangeland. We found that airborne eDNA detected more species than the traditional surveying method, although the types of species detected varied based on the method used. Airborne eDNA detected more grasses and forbs with less showy flowers, while the traditional method detected fewer grasses but also detected rarer forbs with large showy flowers. Additionally, we found the airborne eDNA metabarcoding survey required less sampling effort in terms of the time needed to conduct a survey and was able to detect more invasive species than the traditional method. Conclusions Overall, we have demonstrated that airborne eDNA can act as a sensitive and efficient plant community surveying method. Airborne eDNA surveillance has the potential to revolutionize the way plant communities are monitored in general, track changes in plant communities due to climate change and disturbances, and assist with the monitoring of invasive and endangered species.

scholarly journals Practical Considerations for Implementing Species Distribution Essential Biodiversity Variables

2021 ◽  
Vol 5 ◽  
Author(s):  
Robin Boyd ◽  
Nick Isaac ◽  
Robert Cooke ◽  
Francesca Mancini ◽  
Tom August ◽  
...  
Keyword(s):  
Species Distribution ◽  
Biodiversity Indicators ◽  
The United Kingdom ◽  
Occupancy Detection ◽  
Essential Biodiversity Variables ◽  
The Uk ◽  
Species Occupancy ◽  
Very High ◽  
The Ideal

Species Distribution Essential Biodiversity Variables (SD EBVs; Pereira et al. 2013, Kissling et al. 2017, Jetz et al. 2019) are defined as measurements or estimates of species’ occupancy along the axes of space, time and taxonomy. In the “ideal” case, additional stipulations have been proposed: occupancy should be characterized contiguously along each axis at grain sizes relevant to policy and process (i.e., fine scale); and the SD EBV should be global in extent, or at least span the entirety of the focal taxa’s geographical range (Jetz et al. 2019). These stipulations set the bar very high and, unsurprisingly, most operational SD EBVs fall short of these ideal criteria. In this presentation, I will discuss the major challenges associated with developing the idealized SD EBV. I will demonstrate these challenges using an operational SD EBV spanning ~6000 species in the United Kingdom (UK) over the period 1970 to 2019 as a case study (Outhwaite et al. 2019). In short, this data product comprises annual estimates of occupancy for each species in all sampled 1 km cells across the UK; these are derived from opportunistically-collected species occurrence data using occupancy-detection models (Kéry et al. 2010). Having discussed which of the “ideal” criteria the case study satisfies, I will then touch on what are, in my view, two underappreciated challenges when constructing SD EBVs: dealing with sampling biases in the underlying data and the difficulty in evaluating the extent to which they bias the final product. These challenges should be addressed as a matter of urgency, as SD EBVs are increasingly applied in important settings such as underpinning national and international biodiversity indicators (see e.g., https://geobon.org/ebvs/indicators/).

Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment

2021 ◽  
Author(s):  
Sakcham Bairoliya ◽  
Jonas Koh Zhi Xiang ◽  
Bin Cao
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Environmental Samples ◽  
Environmental Dna ◽  
Extracellular Dna ◽  
Biodiversity Assessment ◽  
Microbial Biodiversity ◽  
Technical Details ◽  
The Impact

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

scholarly journals Labour sharing promotes coexistence in atrazine degrading bacterial communities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Loren Billet ◽  
Marion Devers ◽  
Nadine Rouard ◽  
Fabrice Martin-Laurent ◽  
Aymé Spor
Keyword(s):  
Bacterial Communities ◽  
Gene Loss ◽  
Bacterial Species ◽  
Single Species ◽  
Microbial Consortia ◽  
The Public ◽  
Herbicide Atrazine ◽  
Set Up ◽  
Multiple Species ◽  
Isolated Species

AbstractMicrobial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.

scholarly journals Two new frog species (Microhylidae: Cophixalus) from the Australian Wet Tropics region, and redescription of Cophixalus ornatus

Zootaxa ◽  
2012 ◽  
Vol 3271 (1) ◽  
pp. 1 ◽  
Author(s):  
CONRAD J. HOSKIN
Keyword(s):  
Single Species ◽  
Biological Species ◽  
Tropical Rainforests ◽  
Genetic Lineages ◽  
North East ◽  
The North ◽  
Mating Call ◽  
The Family ◽  
Wet Tropics ◽  
Multiple Species

In Australia the frog family Microhylidae is largely restricted to tropical rainforests of the Wet Tropics region in the north-east of the country, but in that region the family is diverse. Only one species, Cophixalus ornatus, is widespread in the WetTropics but there has been suspicion that it may comprise multiple species. A recent study (Hoskin et al. 2011) assessedgenetic and phenotypic variation across the range of C. ornatus, finding three deeply divergent genetic lineages that differin mating call and some aspects of morphology. Two of these lineages abutt in the central Wet Tropics and in that areahybridization was found to be very limited despite sympatry at high densities. Based on multiple lines of data, Hoskin etal. (2011) concluded that the three genetic lineages represent biological species. The taxonomy of these three lineages isresolved here. I describe two new species, Cophixalus australis sp. nov. and Cophixalus hinchinbrookensis sp. nov., andredescribe C. ornatus. The three species are not distinguishable based on any single morphological or call trait and arebest identified by genetics or locality. The distributions of the three species are largely allopatric. Cophixalus ornatus isfound in rainforest in the northern Wet Tropics, C. australis sp. nov. occurs in rainforest and adjacent wet sclerophyllforests in the central and southern Wet Tropics, and C. hinchinbrookensis sp. nov. inhabits rainforest and montane heathon Hinchinbrook Island. All three species are common. Cophixalus australis sp. nov. contains three genetic subgroupsthat are considered a single species based on phenotypic similarity and high levels of hybridization at contact zones. Thedescription of Cophixalus australis sp. nov. and Cophixalus hinchinbrookensis sp. nov. brings the number of Australian Cophixalus species to 18, 15 of which are restricted to the Wet Tropics region.

scholarly journals Monitoring spawning migrations of potamodromous fish species via eDNA

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bettina Thalinger ◽  
Elisabeth Wolf ◽  
Michael Traugott ◽  
Josef Wanzenböck
Keyword(s):  
Fish Species ◽  
Anthropogenic Impacts ◽  
Environmental Dna ◽  
Signal Strength ◽  
Digital Pcr ◽  
Freshwater Ecosystems ◽  
Non Invasive ◽  
River Stretch ◽  
Daily Discharge ◽  
Invasive Techniques

Abstract Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.

Predicting fish species richness and habitat relationships using Bayesian hierarchical multispecies occupancy models

2020 ◽  
Vol 77 (3) ◽  
pp. 602-610
Author(s):  
Shannon White ◽  
Evan Faulk ◽  
Caleb Tzilkowski ◽  
Andrew Weber ◽  
Matthew Marshall ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Community ◽  
Fish Assemblages ◽  
Similar Species ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Modeling Framework ◽  
Bayesian Hierarchical ◽  
Recreation Area ◽  
Species Occupancy

Understanding how stream fishes respond to changes in habitat availability is complicated by low occurrence rates of many species, which in turn reduces the ability to quantify species–habitat relationships and account for imperfect detection in estimates of species richness. Multispecies occupancy models have been used sparingly in the analysis of fisheries data, but address the aforementioned deficiencies by allowing information to be shared among ecologically similar species, thereby enabling species–habitat relationships to be estimated for entire fish communities, including rare species. Here, we highlight the utility of hierarchical multispecies occupancy models for the analysis of fish community data and demonstrate the modeling framework on a stream fish community dataset collected in the Delaware Water Gap National Recreation Area, USA. In particular, we demonstrate the ability of the modeling framework to make inferences at the species-, guild-, and community-levels, thereby making it a powerful tool for understanding and predicting how environmental variables influence species occupancy probabilities and structure fish assemblages.

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