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Huang X, Li H, Shenkar N, Zhan A. Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions. RNA (NEW YORK, N.Y.) 2023; 29:675-690. [PMID: 36810233 PMCID: PMC10159005 DOI: 10.1261/rna.079319.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 02/01/2023] [Indexed: 05/06/2023]
Abstract
Rapid plastic response to environmental changes, which involves extremely complex underlying mechanisms, is crucial for organismal survival during many ecological and evolutionary processes such as those in global change and biological invasions. Gene expression is among the most studied molecular plasticity, while co- or posttranscriptional mechanisms are still largely unexplored. Using a model invasive ascidian Ciona savignyi, we studied multidimensional short-term plasticity in response to hyper- and hyposalinity stresses, covering the physiological adjustment, gene expression, alternative splicing (AS), and alternative polyadenylation (APA) regulations. Our results demonstrated that rapid plastic response varied with environmental context, timescales, and molecular regulatory levels. Gene expression, AS, and APA regulations independently acted on different gene sets and corresponding biological functions, highlighting their nonredundant roles in rapid environmental adaptation. Stress-induced gene expression changes illustrated the use of a strategy of accumulating free amino acids under high salinity and losing/reducing them during low salinity to maintain the osmotic homoeostasis. Genes with more exons were inclined to use AS regulations, and isoform switches in functional genes such as SLC2a5 and Cyb5r3 resulted in enhanced transporting activities by up-regulating the isoforms with more transmembrane regions. The extensive 3'-untranslated region (3'UTR) shortening through APA was induced by both salinity stresses, and APA regulation predominated transcriptomic changes at some stages of stress response. The findings here provide evidence for complex plastic mechanisms to environmental changes, and thereby highlight the importance of systemically integrating different levels of regulatory mechanisms in studying initial plasticity in evolutionary trajectories.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing 100085, China
| | - Hanxi Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801 Tel-Aviv, Israel
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel-Aviv, Israel
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
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2
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Duarte S, Vieira PE, Lavrador AS, Costa FO. Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141729. [PMID: 32889465 DOI: 10.1016/j.scitotenv.2020.141729] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and regions of the globe, seeking the best approach for detecting the broadest range of species, while minimizing the chances of a false positive or negative detection.
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Affiliation(s)
- Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana S Lavrador
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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3
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Dexter E, Bollens SM. Zooplankton invasions in the early 21st century: a global survey of recent studies and recommendations for future research. HYDROBIOLOGIA 2020; 847:309-319. [PMID: 32435070 PMCID: PMC7223066 DOI: 10.1007/s10750-019-04096-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/24/2019] [Accepted: 10/02/2019] [Indexed: 05/13/2023]
Abstract
We present a comprehensive survey of the scientific literature pertaining to non-indigenous and invasive zooplankton published across the first decades of the twenty-first century (i.e., 2000-2018). We provide a concise summary of the manner in which the scientific community has allocated its efforts to this issue in recent decades, and to illuminate trends that emerge from the literature. Our search yielded 620 publications encompassing 139 invasive zooplankton species, with invasive zooplankton reported from every region of the planet-including the Arctic and Antarctic. Most taxa were reported in a small number of publications, with the majority being mentioned in only a single paper. In contrast, approximately half of the surveyed publications concerned just four species: Bythotrephes longimanus, Mnemioposis leidyi, Cercopagis pengoi, and Daphnia lumholtzi. Our survey reveals strong geographic patterns among the literature, with most publications arising from economically developed western nations. We found that the majority of publications pertained to holoplanktonic organisms from freshwater habitats, especially from the North American Great Lakes. Based on these results, we present several recommendations for future research topics that may hold considerable opportunity for growth in our understanding of the invasion process.
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Affiliation(s)
- Eric Dexter
- School of the Environment, Washington State University, 14204 NE Salmon Creek Avenue, Vancouver, WA 98686-9600 USA
- Present Address: Department of Environmental Sciences, The University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Stephen M. Bollens
- School of the Environment, School of Biological Sciences, Washington State University, 14204 NE Salmon Creek Avenue, Vancouver, WA 98686-9600 USA
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Lin Y, Zhan A, Hernandez MR, Paolucci E, MacIsaac HJ, Briski E. Can chlorination of ballast water reduce biological invasions? J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Yaping Lin
- GEOMAR Helmholtz‐Zentrum für Ozeanforschung Kiel Kiel Germany
- Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Aibin Zhan
- Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Marco R. Hernandez
- Great Lakes Institute for Environmental Research University of Windsor Windsor ON Canada
| | - Esteban Paolucci
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” and Consejo Nacional de Investigaciones Cientı́ficas y Técnicas Buenos Aires Argentina
| | - Hugh J. MacIsaac
- Great Lakes Institute for Environmental Research University of Windsor Windsor ON Canada
- School of Ecology and Environmental Sciences Yunnan University Kunming China
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Rey A, Carney KJ, Quinones LE, Pagenkopp Lohan KM, Ruiz GM, Basurko OC, Rodríguez-Ezpeleta N. Environmental DNA Metabarcoding: A Promising Tool for Ballast Water Monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11849-11859. [PMID: 31545591 DOI: 10.1021/acs.est.9b01855] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nonindigenous species are introduced worldwide with ballast water (BW). To prevent further introductions, oceanic BW exchange and BW treatment systems are utilized, but their performance needs to be evaluated. To that aim, characterizing BW communities is essential but usually relies on exhaustive sampling and morphological taxonomic identification, which does not always allow fine-scale taxonomic resolution. Through the analysis of BW samples from 11 vessels arriving to the Chesapeake Bay (USA), we evaluated the potential of environmental DNA (eDNA) metabarcoding for BW monitoring by assessing whether the impact of BW management type could be identified, analyzing the influence of BW sampling access locations on communities, and comparing the accuracy of eDNA for taxonomic assignment and identification of nonindigenous taxa. We found that (1) different sampling access locations of the same tank resulted in different communities, (2) communities from treated and exchanged BW differ, (3) signals of source port and of ocean exchange are observed, (4) eDNA metabarcoding results in more diversity than morphological taxonomy, and (5) the nonindigenous copepod Oithona davisae, not reported before in the Chesapeake Bay, is detected. Overall, this study highlights the potential of eDNA metabarcoding for BW monitoring, but more comprehensive sampling will be needed to optimize the approach.
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Affiliation(s)
- Anaïs Rey
- Marine Research Division , AZTI , Sukarrieta , Spain
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Darling JA, Martinson J, Gong Y, Okum S, Pilgrim E, Lohan KMP, Carney KJ, Ruiz GM. Ballast Water Exchange and Invasion Risk Posed by Intracoastal Vessel Traffic: An Evaluation Using High Throughput Sequencing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:9926-9936. [PMID: 30059206 PMCID: PMC6944436 DOI: 10.1021/acs.est.8b02108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ballast water remains a potent vector of non-native aquatic species introductions, despite increased global efforts to reduce risk of ballast water mediated invasions. This is particularly true of intracoastal vessel traffic, whose characteristics may limit the feasibility and efficacy of management through ballast water exchange (BWE). Here we utilize high throughput sequencing (HTS) to assess biological communities associated with ballast water being delivered to Valdez, Alaska from multiple source ports along the Pacific Coast of the United States. Our analyses indicate that BWE has a significant but modest effect on ballast water assemblages. Although overall richness was not reduced with exchange, we detected losses of some common benthic coastal taxa (e.g., decapods, mollusks, bryozoans, cnidaria) and gains of open ocean taxa (e.g., certain copepods, diatoms, and dinoflagellates), including some potentially toxic species. HTS-based metabarcoding identified significantly differentiated biodiversity signatures from individual source ports; this signal persisted, though weakened, in vessels undergoing BWE, indicating incomplete faunal turnover associated with management. Our analysis also enabled identification of taxa that may be of particular concern if established in Alaskan waters. While these results reveal a clear effect of BWE on diversity in intracoastal transit, they also indicate continued introduction risk of non-native and harmful taxa.
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Affiliation(s)
- John A Darling
- United States Environmental Protection Agency , National Exposure Research Laboratory , Research Triangle Park , North Carolina 27711 , United States
| | - John Martinson
- United States Environmental Protection Agency , National Exposure Research Laboratory , Research Triangle Park , North Carolina 27711 , United States
| | - Yunguo Gong
- United States Environmental Protection Agency , Cincinnati , Ohio 45220 , United States
| | - Sara Okum
- United States Environmental Protection Agency , Cincinnati , Ohio 45220 , United States
| | - Erik Pilgrim
- United States Environmental Protection Agency , National Exposure Research Laboratory , Research Triangle Park , North Carolina 27711 , United States
| | | | - Katharine J Carney
- Smithsonian Environmental Research Center , Edgewater , Maryland 21037 United States
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center , Edgewater , Maryland 21037 United States
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Selwyn JD, Johnson JE, Downey-Wall AM, Bynum AM, Hamner RM, Hogan JD, Bird CE. Simulations indicate that scores of lionfish ( Pterois volitans) colonized the Atlantic Ocean. PeerJ 2018; 5:e3996. [PMID: 29302383 PMCID: PMC5740958 DOI: 10.7717/peerj.3996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/13/2017] [Indexed: 11/20/2022] Open
Abstract
The invasion of the western Atlantic Ocean by the Indo-Pacific red lionfish (Pterois volitans) has had devastating consequences for marine ecosystems. Estimating the number of colonizing lionfish can be useful in identifying the introduction pathway and can inform policy decisions aimed at preventing similar invasions. It is well-established that at least ten lionfish were initially introduced. However, that estimate has not faced probabilistic scrutiny and is based solely on the number of haplotypes in the maternally-inherited mitochondrial control region. To rigorously estimate the number of lionfish that were introduced, we used a forward-time, Wright-Fisher, population genetic model in concert with a demographic, life-history model to simulate the invasion across a range of source population sizes and colonizing population fecundities. Assuming a balanced sex ratio and no Allee effects, the simulations indicate that the Atlantic population was founded by 118 (54–514, 95% HPD) lionfish from the Indo-Pacific, the Caribbean by 84 (22–328, 95% HPD) lionfish from the Atlantic, and the Gulf of Mexico by at least 114 (no upper bound on 95% HPD) lionfish from the Caribbean. Increasing the size, and therefore diversity, of the Indo-Pacific source population and fecundity of the founding population caused the number of colonists to decrease, but with rapidly diminishing returns. When the simulation was parameterized to minimize the number of colonists (high θ and relative fecundity), 96 (48–216, 95% HPD) colonists were most likely. In a more realistic scenario with Allee effects (e.g., 50% reduction in fecundity) plaguing the colonists, the most likely number of lionfish increased to 272 (106–950, 95% HPD). These results, in combination with other published data, support the hypothesis that lionfish were introduced to the Atlantic via the aquarium trade, rather than shipping. When building the model employed here, we made assumptions that minimize the number of colonists, such as the lionfish being introduced in a single event. While we conservatively modelled the introduction pathway as a single release of lionfish in one location, it is more likely that a combination of smaller and larger releases from a variety of aquarium trade stakeholders occurred near Miami, Florida, which could have led to even larger numbers of colonists than simulated here. Efforts to prevent future invasions via the aquarium trade should focus on the education of stakeholders and the prohibition of release, with adequate rewards for compliance and penalties for violations.
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Affiliation(s)
- Jason D Selwyn
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - John E Johnson
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Alan M Downey-Wall
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America.,Marine Science Center, Northeastern University, Nahant, MA, United States of America
| | - Adam M Bynum
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Rebecca M Hamner
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - J Derek Hogan
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Christopher E Bird
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America.,Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States of America
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8
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Johansson ML, Chaganti SR, Simard N, Howland K, Winkler G, Rochon A, Laget F, Tremblay P, Heath DD, MacIsaac HJ. Attenuation and modification of the ballast water microbial community during voyages into the Canadian Arctic. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Mattias L. Johansson
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor ON Canada
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor ON Canada
| | - Nathalie Simard
- Maurice Lamontagne Institute; Fisheries and Oceans Canada; Mont-Joli QC Canada
| | - Kimberly Howland
- Central & Arctic Region; Fisheries and Oceans Canada; Winnipeg MB Canada
| | - Gesche Winkler
- Institut des Sciences de la Mer; Université du Québec à Rimouski; Rimouski QC Canada
| | - André Rochon
- Institut des Sciences de la Mer; Université du Québec à Rimouski; Rimouski QC Canada
| | - Frederic Laget
- Institut des Sciences de la Mer; Université du Québec à Rimouski; Rimouski QC Canada
| | - Pascal Tremblay
- Institut des Sciences de la Mer; Université du Québec à Rimouski; Rimouski QC Canada
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor ON Canada
| | - Hugh J. MacIsaac
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor ON Canada
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