Comparative environmental RNA and DNA metabarcoding analysis of river algae and arthropods for ecological surveys and water quality assessment

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Nov. 18, 2022

Environmental DNA (eDNA) metabarcoding is widely used for species analysis, while the use of environmental RNA (eRNA) more limited. We conducted comparative eDNA/eRNA algae and arthropods (aquatic insects) in water samples from Naka River, Japan, to evaluate their potential biological monitoring quality assessment. Both methods detected various arthropod species; however, compositions were remarkably different those traditional field surveys (TFSs), indicating low sensitivity. For algae, composition derived eDNA eRNA was equivalent. While TFSs focus on attached analysis theoretically detects both planktonic algae. A recently expanded genomic database aquatic insects significantly contributed sensitivity positive predictivity arthropods. lower than that eDNA, higher. The terrestrial indicated extremely high or read numbers when compared with suggesting could be an effective indicator false positives. Arthropod enabled estimates TFSs. thus biodiversity provide insights ecological surveys.

Language: Английский

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Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 290(1999)

Published: May 30, 2023

Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to aged that has long since been released from individual is more likely be detected at site further away its source. In order address issue, this manuscript focuses on state eDNA, proposing new methodologies estimate age eDNA: (1) damage rate, (2) particle size distribution, (3) viable cell-derived eDNA. addition, also shorter persistence environmental RNA (eRNA) compared highlighting application eRNA nucleic acid ratio for assessing genetic materials water. Although substantial research essential support feasibility these methodologies, incorporating time-scale information into would update current analysis, improve accuracy reliability eDNA-based monitoring, refine as useful monitoring tool ecology, fisheries various sciences.

Language: Английский

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Evaluating eDNA and eRNA metabarcoding for aquatic biodiversity assessment: From bacteria to vertebrates

Environmental Science and Ecotechnology, Journal Year: 2024, Volume and Issue: 21, P. 100441 - 100441

Published: June 12, 2024

The monitoring and management of aquatic ecosystems depend on precise estimates biodiversity. Metabarcoding analyses environmental nucleic acids (eNAs), including DNA (eDNA) RNA (eRNA), have garnered attention for their cost-effective non-invasive biomonitoring capabilities. However, the accuracy biodiversity obtained through eNAs can vary among different organismal groups. Here we evaluate performance eDNA eRNA metabarcoding across nine groups, ranging from bacteria to terrestrial vertebrates, in three cross-sections Yangtze River, China. We observe robust complementarity between data. relative detectability was notably influenced by major taxonomic groups sizes, with providing more signals larger organisms. Both exhibited similar cross-sectional longitudinal patterns. organisms declined metabarcoding, possibly due differential release decay or sizes. While underscoring potential large river biomonitoring, emphasize need interpretation versus This highlights importance careful method selection studies.

Language: Английский

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Environmental RNA applications and their associated gene targets for management and conservation

Environmental DNA, Journal Year: 2022, Volume and Issue: 5(2), P. 227 - 239

Published: Dec. 26, 2022

Abstract Environmental DNA (eDNA) analysis is now a widely‐used tool to non‐invasively monitor variety of organisms. However, eDNA applications are limited with respect gaining information on population demography and the status individuals within population. Although in its infancy, environmental RNA (eRNA) has potential reveal about populations that may be important for conservation or management decisions. Using gene databases current literature, we synthesized products useful eRNA targets samples focusing model organisms Danio rerio (zebrafish), Xenopus laevis (African clawed frog), X. tropicalis (Western frog). We suggested appropriate must expressed tissues thought contribute samples, exclusively upregulated by at least 2‐fold portions (e.g., single age class), relevant application monitoring. categorized 127 total based their applications: distinguishing quantifying living communities, determining structure, sex ratios, assessing health. There many uncertainties limitations need addressed before can an established method including understanding ecology eRNA, methods assay specificity, applying what know from other species. see immense utility gathering population‐level serving as managers near future.

Language: Английский

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Lung microbiome and transcriptome reveal mechanisms underlying PM2.5 induced pulmonary fibrosis

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 831, P. 154974 - 154974

Published: April 2, 2022

Language: Английский

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Effects of Temperature on the Timeliness of eDNA/eRNA: A Case Study of Fenneropenaeus chinensis

Water, Journal Year: 2022, Volume and Issue: 14(7), P. 1155 - 1155

Published: April 3, 2022

Environmental DNA (eDNA) technology has been successfully applied to detect organisms in various aquatic ecosystems. However, eDNA proven exist for a long time environmental samples. The timeliness of detection results largely depends on the rate molecular degradation. RNA (eRNA) is considered an excellent complementary tool because most researchers believe that degrades faster than vitro, while, best our knowledge, number published articles related eRNA very limited. To address important knowledge gap, this study focused response mechanism degradation water temperature change as compared with eDNA. Changes concentration and mitochondrial cytochrome c oxidase subunit 1 (COI) gene from Fenneropenaeuschinensis were detected at four temperatures (10, 15, 20 25 °C). showed increased increase temperature. constants ranged 0.011 0.486 h−1 8 383 h changed slightly 0.190 0.379 11 22 eRNA. better stability under maintained low temperatures. These provide answers questions whether rates are fast or slow. Furthermore, may suggest potential superiority over promote further future research.

Language: Английский

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Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?

Molecular Ecology, Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 4, 2023

Abstract To safeguard biodiversity in a changing climate, taxonomic information about species turnover and insights into the health of organisms are required. Environmental DNA approaches increasingly used for identification, but cannot provide functional insights. Transcriptomic methods reveal physiological states macroorganisms, currently species‐specific require tissue sampling or animal sacrifice, making community‐wide assessments challenging. Here, we test whether broad (expression level transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra‐organismal macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well phytoplankton prey microorganism colonizers to control (20°C) heat stress (28°C) conditions 7 days. sequenced eRNA tank water (after complete removal ) tissue, enabling comparisons organismal RNA‐based gene expression profiles. Both types detected similar responses . Using eRNA, identified 32 genes differentially expressed following stress. Of these, 17 were also exhibited levels relative RNA. In addition response, consisting distinct profiles 121 across eight taxa. Our study demonstrates that transcriptomics based on noninvasively changes, potential implications biomonitoring trophic chain.

Language: Английский

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A review of new and existing non-extractive techniques for monitoring marine protected areas

Frontiers in Marine Science, Journal Year: 2023, Volume and Issue: 10

Published: July 19, 2023

Ocean biodiversity loss is being driven by several anthropogenic threats and significant efforts are required to halt losses promote healthy marine ecosystems. The establishment of a network Marine Protected Areas (MPAs) can help restrict damaging activities have been recognised as potential solution aid conservation. When managed correctly they deliver both ecological socio-economic benefits. In recent times, MPA designations increased rapidly while many countries set future targets for the decades ahead. An integral element management adequate monitoring that collects data assess if conservation objectives achieved. Data acquired vary widely techniques employed collect such data. Ideally, non-destructive non-invasive methods preferred prevent damage habitats species, though this may rule out number traditional extractive sampling approaches dredges trawls. Moreover, advances in ocean observation technologies enable collection large amounts at high resolutions, automated processing beginning make analyses more logistically feasible less time-consuming. Therefore, developments existing new emerging led diverse array options when choosing implement an programme. Here, we present review non-extractive which be applied monitoring. We summarise their capabilities, applications, advantages, limitations possible developments. intended managers researchers determining suitability available based on requirements site conditions.

Language: Английский

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When are environmental DNA early detections of invasive species actionable?

Journal of Environmental Management, Journal Year: 2023, Volume and Issue: 343, P. 118216 - 118216

Published: May 27, 2023

Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an rapid response program because positive detections are not always indicative of eventual infestation. We used a structured decision making (SDM) framework evaluate appropriate actions hypothetical aquatic plant in Sebago Lake (Maine, USA). The were juxtaposed recent study that similar SDM approach mussels Jordanelle Reservoir (Utah, found actionable the plant's invasion potential was spatially constrained and current management activities provided acceptable levels mitigation. In Reservoir, due high analyses supported contain invasion. divergent outcomes two case studies related unique attributes habitats species, highlighting utility when considering monitoring program. use these present general set heuristics can be efficiently applied scenarios other instances associated indeterminant detections, especially there is imperative make decisions as quickly possible.

Language: Английский

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Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture

PeerJ, Journal Year: 2023, Volume and Issue: 11, P. e15201 - e15201

Published: May 16, 2023

Background Aquacultured animals are reared in water hosting various microorganisms with which they close relationships during their whole lifecycle as some of these can be involved host’s health or physiology. In aquaculture hatcheries, understanding the interactions existing between natural seawater microbiota, rearing larval stage and status, may allow establishment microbial proxies to monitor ecosystems. Indeed, could help define optimal microbiota for shrimp development ultimately management. Methods this context, we monitored daily composition active a hatchery Pacific blue Penaeus stylirostris. Two distinct conditions were analyzed; one antibiotics added without antibiotics. During rearing, healthy larvae high survival rate unhealthy mortality observed. Using HiSeq sequencing V4 region 16S rRNA gene coupled zootechnical statistical analysis, aimed distinguish taxa related rates at given stage. Results We highlight that is highly dynamic whatever rate. A clear distinction shown harboring heathy versus However, it hard untangle effects antibiotic addition death on water. Various specific except zoea good Comparing communities those lagoon, appears many originally detected seawater. This highlights great importance lagoon microbiota. Considering several genera: Nautella, Leisingera, Ruegerira , Alconivorax Marinobacter Tenacibaculum beneficial may, water, overcome r-strategist and/or putative pathogens. Members genera might also act probiotics larvae. Marivita Aestuariicocccus, HIMB11 Nioella appeared unfavorable associated upcoming occurring mortalities. All biomarkers larvae, used early routine detection then first days manage select

Language: Английский

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