Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

Valdéz-Moreno, Martha; Ivanova, Natalia V.; Elías‐Gutiérrez, Manuel; Pedersen, Stephanie; Bessonov, Kyrylo

doi:10.1371/journal.pone.0215505

Cited by 54 publications

(45 citation statements)

References 72 publications

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“…This is likely because most invasions have been documented in temperate regions (particularly North America, Europe, and Australia), and less so in tropical Asia and Africa [ 83 ]. Thus, many biological invasions in the tropics may have been overlooked and gone undocumented as suggested by recent detections of potentially invasive species in tropical lentic ecosystems (e.g., [ 102 , 103 ]) using eDNA techniques, which have so far been more widely employed in temperate freshwater habitats [ 104 ]. Considering the importance of climate match, the effects of such geographical bias would be especially pronounced for tropical species.…”

Section: Discussionmentioning

confidence: 99%

Invasive species trait-based risk assessment for non-native freshwater fishes in a tropical city basin in Southeast Asia

2021

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Biological invasions have created detrimental impacts in freshwater ecosystems. As non-native freshwater species include economically beneficial, but also harmful, species, trait-based risk assessments can be used to identify and prevent the import of potentially invasive species. Freshwater fishes are one of the most evaluated freshwater taxa to date. However, such assessments have mostly been done in sub-temperate to temperate regions, with a general lack of such research in the tropics. In view of this knowledge gap, this study aims to determine if a different set of traits are associated with successful establishment of non-native fishes within the tropics. In tropical Southeast Asia, Singapore represents a suitable model site to perform an invasive species trait-based risk assessment for the tropical region given its susceptibility to the introduction and establishment of non-native freshwater fishes and lack of stringent fish import regulation. A quantitative trait-based risk assessment was performed using random forest to determine the relative importance of species attributes associated with the successful establishment of introduced freshwater fishes in Singapore. Species having a match in climate, prior invasion success, lower absolute fecundity, higher trophic level, and involvement in the aquarium trade were found to have higher establishment likelihood (as opposed to native distributional range and maximum size being among the commonly identified predictors in subtropical/temperate trait-based risk assessments). To minimize invasive risk, incoming freshwater fishes could be screened in future for such traits, allowing lists of prohibited or regulated species to be updated. The findings could also potentially benefit the development of invasive species action plans and inform management decisions in the Southeast Asian region. Considering a geographical bias in terms of having relatively less documentation of biological invasions in the tropics, particularly Asia, this study highlights the need to perform more of such risk assessments in other parts of the tropics.

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Section: Discussionmentioning

confidence: 99%

Invasive species trait-based risk assessment for non-native freshwater fishes in a tropical city basin in Southeast Asia

2021

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“…Environmental DNA metabarcoding has been hailed as a promising tool for biodiversity assessment and monitoring worldwide, in both marine and freshwater ecosystems (Bohmann et al, 2014; Boussarie et al, 2018; Deiner et al, 2017; Hänfling et al, 2016; Pont et al, 2018; Thomsen & Willerslev, 2015). This method relies on obtaining the DNA shed by organisms in the surrounding environment (e.g., water, soil), amplifying it with primers targeting the taxonomic spectrum of interest, and high‐throughput sequencing it to reconstruct community composition (Bohmann et al, 2014; Handley et al, 2018; Valdez‐Moreno et al, 2018; Valentini et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river

et al. 2019

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Environmental DNA (eDNA) has rapidly emerged as a promising biodiversity monitoring technique, proving to be a sensitive and cost‐effective method for species detection. Despite the increasing popularity of eDNA, several questions regarding its limitations remain to be addressed. We investigated the effect of sampling medium and time, and preservation methods, on fish detection performance based on eDNA metabarcoding of neotropical freshwater samples. Water and sediment samples were collected from 11 sites along the Jequitinhonha River, Southeastern Brazil; sediment samples were stored in ethanol, while the same amounts of water per sample (3 L) were stored in a cool box with ice, as well as by adding the cationic surfactant benzalkonium chloride (BAC). Sediment and water samples yielded a similar amount of fish MOTUs (237 vs. 239 in the first sampling event, and 153 vs. 142 in the second sampling event). Water stored in ice provided better results than those preserved in BAC (239 and 142 vs. 194 and 71 MOTUs). While documenting the effectiveness of eDNA surveys as practical tools for fish biodiversity monitoring in poorly accessible areas, we showed that keeping water samples cooled results in greater eDNA recovery and taxon detection than by adding cationic surfactants (BAC) as sample preservatives. Furthermore, by comparing two sets of samples collected from the same locations at a 3‐week interval, we highlight the importance of conducting multiple sampling events when attempting to recover a realistic picture of fish assemblages in lotic systems.

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“…The following bioinformatics workflow was used to process NGS data: Cutadapt (v1.8.1) was used to trim primer sequences; Sickle (v1.33) was used for filtering (less than 200 bp were discarded) and Uclust (v1.2.22q) was used to cluster OTUs with 99% identity and minimum read depth of 10. Local BLAST 2.2.29+ algorithm was utilized to match resulting OTUs to custom reference library database for 16S generated from available BOLD records DS-ECCSTAGE dataset in BOLD; BLAST output results were parsed using custom built python script [51] OTUBLASTParser.py (available at https://gitlab.com/biodiversity/OTUExtractorFromBLASToutput): with the following 16S Identity Filter (Species 99%, Genus 97%, Family 95%, Order 90%); matches were concatenated using custom script ConcatenatorResults.py (available at https://gitlab.com/biodiversity/OTUExtractorFromBLASToutput), exported to Excel, and further processed in Tableau software 10.2 (min coverage 10).…”

Section: Methodsmentioning

confidence: 99%

Rapid assessment of phytoplankton assemblages using Next Generation Sequencing – Barcode of Life database: a widely applicable toolkit to monitor biodiversity and harmful algal blooms (HABs)

Ivanova

Watson

Comte

et al. 2019

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19Harmful algal blooms have important implications for the health, functioning and services of aquatic 20 ecosystems. Our ability to detect and monitor these events is often challenged by the lack of rapid and 21 cost-effective methods to identify bloom-forming organisms and their potential for toxin production, 22 samples, which match commercial kit performance and offer a cost-efficient solution for large scale 34 ecological assessments of harmful blooms while giving benefits of reproducibility and increased 35 accessibility. Our bioinformatics pipeline was designed to handle low taxonomic resolution for 36 problematic genera of cyanobacteria such as the Anabaena-Aphanizomenon-Dolichospermum species 37 complex, two clusters of Anabaena (I and II), Planktothrix and Microcystis. This newly developed HAB-38 ID toolset was further validated by applying it to assess cyanobacterial and algal composition in field 39 samples from waterbodies with recurrent HABs events. 40 41 construction of a reference BOLD database for algal and cyanobacterial 16S ribosomal RNA, using 93 isolates from the Great Lakes and other regions; 2) optimization of Polymerase Chain Reaction (PCR) 94 primers and DNA extraction protocols; 3) validation of the NGS method on mock communities generated 95 from known cyanobacterial and algal cultures; 4) application of the HAB-ID tool to environmental 96 samples and comparison of its performance with traditional microscopy. 97 98 Fig 1. Project phasesfrom initial optimization to high-throughput analysis of environmental 99 samples 100 101 Material and methods 102 Ethics statement 103 Environmental samples were collected from permanent Environment and Climate Change 104 Canada (ECCC) survey stations in Lakes Erie, St. Clair and Winnipeg. No specific permissions 105were required for the sampling stations/activities because the sampling stations were not 106 privately owned or protected. This study did not involve endangered or protected species.

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Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

Cited by 54 publications

References 72 publications

Invasive species trait-based risk assessment for non-native freshwater fishes in a tropical city basin in Southeast Asia

Invasive species trait-based risk assessment for non-native freshwater fishes in a tropical city basin in Southeast Asia

Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river

Rapid assessment of phytoplankton assemblages using Next Generation Sequencing – Barcode of Life database: a widely applicable toolkit to monitor biodiversity and harmful algal blooms (HABs)

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