scholarly journals Environmental DNA biomonitoring revealed species diversity of Cnidarian and Poriferan across Jakarta Bay and Seribu Islands National Park

2021 ◽  
Author(s):  
Ismail Maqbul ◽  
Farrahdiba Yossan Fahrezi ◽  
Ersya Nurul A Bakhri ◽  
Indri Verawati ◽  
Lalu M Iqbal Sani ◽  
...  
Keyword(s):  
Invasive Species ◽  
Introduced Species ◽  
National Park ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Ecological Research ◽  
Negative Consequences ◽  
Approach Method ◽  
Broad Approach ◽  
Conservation Method

Abstract Indonesia, as a country having a unique sea lane known as the Indonesian Archipelagic Sea Lanes (ASLs), has become one of the busiest countries in the world with varied shipping activities. These actions have the ability to facilitate the transmission of species (bio-invasion). Until recently, the number of global introduced species has increased, with negative consequences for environment and the economy. Environmental DNA (eDNA) approaches for detecting the presence of invasive species are currently receiving a lot of interest as a broad approach method in ecological research. As a result, the study used the eDNA technique to compare the quantity and variety of introduced species from the Cnidaria and Porifera Phyla, as well as to characterize their invasiveness status and possible presence in the waters of Jakarta Bay. Based on data from the inside Zone of National Park (ZI) and Outside Zone of National Park (ZO), the biological community composition, richness, and diversity were assessed (ZO). The mBrave workflow generated a total of 14,275 reads from high-throughput sequencing of amplicons from two zones, with 8,917 reads in ZI and 5,358 reads in ZO. Blackfordia virginica , Cordylophora caspia , and Ectopleura crocea were among the imported species included in the invasive category, with E. crocea having the highest abundance and being detected in both zones, with a total of 1300 reads, consisting of 1253 reads in ZI and 47 reads in ZO. Based on the findings, the eDNA methodology can be used as a biomonitoring and conservation method for invasive species.

scholarly journals Environmental DNA detection of endangered and invasive species in Kejimkujik National Park and Historic Site

Genome ◽  
2020 ◽  
Author(s):  
Tzitziki Loeza-Quintana ◽  
Steven Crookes ◽  
Pei Yuan Li ◽  
Darrin P Reid ◽  
Matthew Smith ◽  
...  
Keyword(s):  
Invasive Species ◽  
Water Samples ◽  
National Park ◽  
Sampling Site ◽  
Environmental Dna ◽  
Smallmouth Bass ◽  
Historic Site ◽  
Blanding's Turtle ◽  
Kejimkujik National Park ◽  
Blanding’S Turtle

The use of environmental DNA (eDNA) allows the early detection of aquatic species at low densities (e.g. elusive and invasive species), which otherwise could be challenging to monitor using conventional techniques. Here, we assess the ability of eDNA sampling to detect the presence/absence of one species-at-risk (Blanding’s Turtle) and two invasive species (Chain Pickerel and Smallmouth Bass) in Kejimkujik National Park and National Historic site, Nova Scotia, where the aquatic system is highly acidic and rich in organic compounds. Five replicates of 1L water samples were taken per sampling site. Water filtration and eDNA extractions were performed on-site, while qPCR reactions were performed in the laboratory using species-specific assays. Samples were treated with an inhibition removal kit and analyzed pre- and post-inhibition removal. Despite the low pH and PCR inhibitors in water samples, our results showed positive eDNA detections in almost all expected positive sites (except in one site for Blanding’s Turtle). Detections of the target species were also observed at sites where their presence was previously unknown. Our study supports the advantage of eDNA to monitor species at low densities, revealing new distributions or recently invaded areas. We also demonstrate how eDNA can directly instruct management strategies in Kejimkujik.

scholarly journals Effective removal of the American bullfrog (Lithobates catesbeianus) on a landscape level: long term monitoring and removal efforts in Yosemite Valley, Yosemite National Park

2019 ◽  
Vol 22 (2) ◽  
pp. 617-626 ◽  
Author(s):  
Colleen Kamoroff ◽  
Ninette Daniele ◽  
Robert L. Grasso ◽  
Rebecca Rising ◽  
Travis Espinoza ◽  
...  
Keyword(s):  
Invasive Species ◽  
National Parks ◽  
National Park ◽  
Environmental Dna ◽  
Freshwater Ecosystems ◽  
Yosemite National Park ◽  
American Bullfrog ◽  
Yosemite Valley ◽  
Park Service ◽  
Landscape Level

Abstract Invasive alien species are a major threat to freshwater ecosystems, and American bullfrogs are among the world’s 100 most prominent aquatic invasive species causing negative direct and indirect effect on native aquatic fauna worldwide. Bullfrogs were intentionally introduced into Yosemite Valley, Yosemite National Park in the 1950s where they became well established in the subsequent years. Starting in 2005, the National Park Service (NPS) began bullfrog removal, targeting various life stages using hand, net, and spear techniques. Starting in 2015, the NPS conducted environmental DNA (eDNA) surveys and deployed audio recordings devices to ensure adequate detection of bullfrogs. During the first year of cencerted effort in the Valley in 2005, the NPS removed 86% of all recorded bullfrog. The subsequent decade was spent searching for individuals with lower return on effort. In 2012, the NPS removed the last observed signs of bullfrog breeding, and the last observed bullfrog in 2019. Following removal of the breeding bullfrog population, the NPS began restoration projects for species of special concern. The NPS introduced the federally threatened California red-legged frogs (Rana draytonii) into Yosemite Valley beginning in 2016. This is the first published successful eradication of bullfrogs on a landscape level. National Parks and Monuments often provide refuges for imperiled wildlife and should be managed to remove invasive species. Our work highlights effective bullfrog removal is obtainable and can lead to local recovery of endangered species.

Active and passive environmental DNA surveillance of aquatic invasive species

2016 ◽  
Vol 73 (1) ◽  
pp. 76-83 ◽  
Author(s):  
Megan Simmons ◽  
Andrew Tucker ◽  
W. Lindsay Chadderton ◽  
Christopher L. Jerde ◽  
Andrew R. Mahon
Keyword(s):  
Invasive Species ◽  
Active Surveillance ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Single Species ◽  
Bighead Carp ◽  
Passive Surveillance ◽  
Molecular Surveillance ◽  
River Watershed ◽  
Channa Argus

Environmental DNA (eDNA) is useful for delimiting species ranges in aquatic systems, whereby water samples are screened for the presence of DNA from a single species. However, DNA from many species is collected in every sample, and high-throughput sequencing approaches allow for more passive surveillance where a community of species is identified. In this study, we use active (targeted) and passive molecular surveillance approaches to detect species in the Muskingum River Watershed in Ohio, USA. The presence of bighead carp (Hypophthalmichthys nobilis) eDNA in the Muskingum River Watershed was confirmed with active surveillance using digital droplet polymerase chain reaction (ddPCR). The passive surveillance method detected the presence of eDNA from northern snakehead (Channa argus), which was further confirmed with active ddPCR. Whereas active surveillance may be more sensitive to detecting rare DNA, passive surveillance has the capability of detecting unexpected invasive species. Deploying both active and passive surveillance approaches with the same eDNA samples is beneficial for invasive species management.

scholarly journals Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions

NeoBiota ◽  
2021 ◽  
Vol 66 ◽  
pp. 117-159
Author(s):  
Sheena M. Feist ◽  
Richard F. Lance
Keyword(s):  
Invasive Species ◽  
Zebra Mussel ◽  
High Throughput Sequencing ◽  
Freshwater Mussel ◽  
Environmental Dna ◽  
Zebra Mussels ◽  
Aquatic Invasive Species ◽  
Quagga Mussel ◽  
Future Directions ◽  
Dreissena Rostriformis Bugensis

Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts involved in the development of various assays for use in multiple different technologies (e.g. quantitative PCR, high-throughput sequencing and loop-mediated isothermal amplification) and sampling scenarios. We discuss important discoveries made along the way, including novel revelations involving environmental RNA (eRNA), as well as the advantages and limitations of available methods and instrumentation. In closing, we highlight critical remaining gaps, where further investigation could lead to advancements in dreissenid monitoring capacity.

scholarly journals Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Correlation Coefficients ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Absolute Quantification ◽  
Taqman Probe ◽  
Individual Species ◽  
Natural Environments ◽  
Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

2021 ◽  
pp. 1-10
Author(s):  
Micheline Carvalho-Silva ◽  
Luiz Henrique Rosa ◽  
Otávio H.B. Pinto ◽  
Thamar Holanda Da Silva ◽  
Diego Knop Henriques ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Crater Lake ◽  
Environmental Dna ◽  
Food Sources ◽  
South Shetland Islands ◽  
Deception Island ◽  
Shetland Islands ◽  
Operational Taxonomic Units ◽  
First Time ◽  
Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

scholarly journals Diet composition of the invasive red-whiskered bulbul Pycnonotus jocosus in Mauritius

2010 ◽  
Vol 26 (3) ◽  
pp. 347-350 ◽  
Author(s):  
Jannie Fries Linnebjerg ◽  
Dennis M. Hansen ◽  
Nancy Bunbury ◽  
Jens M. Olesen
Keyword(s):  
Invasive Species ◽  
Introduced Species ◽  
Native Species ◽  
Diet Composition ◽  
Ecological Perspective ◽  
Positive Interactions ◽  
Invasional Meltdown ◽  
Ecological Processes ◽  
Successful Establishment ◽  
The Impact

Disruption of ecosystems is one of the biggest threats posed by invasive species (Mack et al. 2000). Thus, one of the most important challenges is to understand the impact of exotic species on native species and habitats (e.g. Jones 2008). The probability that entire ‘invasive communities’ will develop increases as more species establish in new areas (Bourgeois et al. 2005). For example, introduced species may act in concert, facilitating one another's invasion, and increasing the likelihood of successful establishment, spread and impact. Simberloff & Von Holle (1999) introduced the term ‘invasional meltdown’ for this process, which has received widespread attention since (e.g. O'Dowd 2003, Richardson et al. 2000, Simberloff 2006). Positive interactions among introduced species are relatively common, but few have been studied in detail (Traveset & Richardson 2006). Examples include introduced insects and birds that pollinate and disperse exotic plants, thereby facilitating the spread of these species into non-invaded habitats (Goulson 2003, Mandon-Dalger et al. 2004, Simberloff & Von Holle 1999). From a more general ecological perspective, the study of interactions involving introduced and invasive species can contribute to our knowledge of ecological processes – for example, community assembly and indirect interactions.

scholarly journals Small mammals of the Addo Elephant National Park

Koedoe ◽  
1975 ◽  
Vol 18 (1) ◽  
Author(s):  
P. Swanepoel
Keyword(s):  
Introduced Species ◽  
Small Mammals ◽  
National Park ◽  
Sex Ratios ◽  
Rattus Rattus ◽  
Reproductive Activity ◽  
Body Measurements ◽  
Suricata Suricatta ◽  
Rhabdomys Pumilio ◽  
Mus Minutoides

A survey of the small mammals of the Addo Elephant National Park resulted in a checklist, as well as information on relative numbers, distribution within the Park, reproductive activity, sex ratios, and body measurements. Forty mammals species occur in the Park, while three re-introduced species probably do not occur any longer. Of the 40 species 28 are considered small mammals comprising 13 rodent, eight carnivore, two shrew, two bat, one primate and one lagomorph species, as well as the aardvark: Crociduraflavescens, C. cyanea infumata, Rousettus aegyptiacus, Eptesicus capensis, Cercopithecus pygerythrus, Canis mesomelas, Ictonyx striatus, Poecilogale albinucha, Genetta sp., Herpestes pulverulentus, Suricata suricatta, Proteles cristatus, Felis caracal, Orycteropus afer, Lepus saxatilis, Cryptomys hottentotus, Hystrix africae-australis, Pedetes capensis, Graphiurus murinus, Aethomys namaquensis, Praomys natalensis, Rhabdomys pumilio, Mus minutoides, Rattus rattus, Saccostomys campestris, Desmodillus auricularis, Otomys irroratus and 0. unisulcatus.

scholarly journals High prevalence and diversity of beta-lactamase-encoding bacteria in cryosoils and ancient permafrost

2021 ◽  
Author(s):  
Sofia Rigou ◽  
Eugene Christo-Foroux ◽  
Sebastien Santini ◽  
Artemiy Goncharov ◽  
Jens Strauss ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Genome ◽  
Environmental Dna ◽  
Single Copy ◽  
The Arctic ◽  
Human Society ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
Arctic Regions ◽  
Global Threat

Background: Antimicrobial resistance is one of the major challenges affecting public health. It is mostly due to the continuous emergence of extended-spectrum beta-lactamase from various environments followed by their rapid dissemination and selection in clinical settings. The warming of Earth' s climate is the other global threat facing human society, in particular with the Arctic regions experiencing a twice faster warming than the global average and permafrost affected by widespread thawing. A potentially dreadful combination of these two threats would be the release and dispersion of harmful microbes that have remained confined to largely uninhabited Arctic regions, or are stored dormant in permafrost. Methods: Environmental DNA was isolated from 12 soil samples from various Arctic and subarctic pristine regions in Siberia (Yakutia and Kamchatka), including 9 permafrost samples collected at various depths. The large datasets obtained from high throughput sequencing was assembled in contigs and their protein-gene contents predicted. We used exhaustive similarity searches to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. In addition, we specifically identified beta-lactamase genes and their prevalence per bacterial genome estimated through the detection of two universal single copy genes. Findings: A total of 9.217 1011 bp were exploited, leading to a total of 525,313 contigs at least 5kb in size. The DNA content of the various samples was found to be highly variable, not strictly correlated with the depth or radio-carbon-based deposit age, and most likely linked to the global density of microbes trapped in the corresponding permafrost layers. Bacteria account for more than 90% of the contigs in most samples, followed by Eukaryotes and Archaea (always lower than 10%). Viruses represented less than 2% of all contigs in all samples. The taxonomic profiles of surface cryosoils and deep permafrost samples exhibited a high diversity, including between permafrost samples originating from various depths in the same borehole. In all samples, bacterial contigs carrying different beta-lactamases from class A to D were identified. Interpretation: No clear common taxonomic feature could be found shared by surface cryosoils or ancient permafrost layers. However, most samples (9/12) exhibited a high frequency of beta-lactamase genes, with an estimated average close to 1 copy/bacterial genome. In addition to the well-documented reactivation of infectious ancient pathogens (bacteria, viruses, protozoa), we show now that global warming could contribute to the emergence of new antibiotic resistances through the mobilization by contemporary bacteria of ancient DNA released from thawing permafrost.

scholarly journals The pig of the Lençóis Maranhenses, first record of wild boar (Sus scrofa) in Maranhão State, Brazil

Check List ◽  
2019 ◽  
Vol 15 (4) ◽  
pp. 1-1
Author(s):  
Gilberto Nepomuceno Salvador ◽  
Nathali Garcia Ristau ◽  
Isabel Sanches da Silva ◽  
André Nunes
Keyword(s):  
Invasive Species ◽  
Wild Boar ◽  
Sus Scrofa ◽  
Native Species ◽  
National Park ◽  
First Record ◽  
Negative Effects ◽  
The World

The wild boar is one of the most dangerous invasive species. It is widespread in the world, including records for many Brazilian states. However, there is a lack of record from Maranh&atilde;o state. In the present study, we reported a population of wild boar inside the Len&ccedil;&oacute;is Maranhenses National Park, in Barrerinhas county, State of Maranh&atilde;o. We discuss about the negative effects of this introduction on native species, including a record of predation by wild boar in nests of endangered turtles.

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