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Zhang Y, Qiu Y, Liu K, Zhong W, Yang J, Altermatt F, Zhang X. Evaluating eDNA and eRNA metabarcoding for aquatic biodiversity assessment: From bacteria to vertebrates. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100441. [PMID: 39027464 PMCID: PMC11254946 DOI: 10.1016/j.ese.2024.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
The monitoring and management of aquatic ecosystems depend on precise estimates of biodiversity. Metabarcoding analyses of environmental nucleic acids (eNAs), including environmental DNA (eDNA) and environmental RNA (eRNA), have garnered attention for their cost-effective and non-invasive biomonitoring capabilities. However, the accuracy of biodiversity estimates obtained through eNAs can vary among different organismal groups. Here we evaluate the performance of eDNA and eRNA metabarcoding across nine organismal groups, ranging from bacteria to terrestrial vertebrates, in three cross-sections of the Yangtze River, China. We observe robust complementarity between eDNA and eRNA data. The relative detectability of eNAs was notably influenced by major taxonomic groups and organismal sizes, with eDNA providing more robust signals for larger organisms. Both eDNA and eRNA exhibited similar cross-sectional and longitudinal patterns. However, the detectability of larger organisms declined in eRNA metabarcoding, possibly due to differential RNA release and decay among different organismal groups or sizes. While underscoring the potential of eDNA and eRNA in large river biomonitoring, we emphasize the need for differential interpretation of eDNA versus eRNA data. This highlights the importance of careful method selection and interpretation in biomonitoring studies.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Yu Qiu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenjun Zhong
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
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Lu S, Zeng H, Xiong F, Yao M, He S. Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1368-1384. [PMID: 38512561 DOI: 10.1007/s11427-023-2493-5] [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: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 03/23/2024]
Abstract
Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.
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Affiliation(s)
- Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Balard A, Baltazar-Soares M, Eizaguirre C, Heckwolf MJ. An epigenetic toolbox for conservation biologists. Evol Appl 2024; 17:e13699. [PMID: 38832081 PMCID: PMC11146150 DOI: 10.1111/eva.13699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Ongoing climatic shifts and increasing anthropogenic pressures demand an efficient delineation of conservation units and accurate predictions of populations' resilience and adaptive potential. Molecular tools involving DNA sequencing are nowadays routinely used for these purposes. Yet, most of the existing tools focusing on sequence-level information have shortcomings in detecting signals of short-term ecological relevance. Epigenetic modifications carry valuable information to better link individuals, populations, and species to their environment. Here, we discuss a series of epigenetic monitoring tools that can be directly applied to various conservation contexts, complementing already existing molecular monitoring frameworks. Focusing on DNA sequence-based methods (e.g. DNA methylation, for which the applications are readily available), we demonstrate how (a) the identification of epi-biomarkers associated with age or infection can facilitate the determination of an individual's health status in wild populations; (b) whole epigenome analyses can identify signatures of selection linked to environmental conditions and facilitate estimating the adaptive potential of populations; and (c) epi-eDNA (epigenetic environmental DNA), an epigenetic-based conservation tool, presents a non-invasive sampling method to monitor biological information beyond the mere presence of individuals. Overall, our framework refines conservation strategies, ensuring a comprehensive understanding of species' adaptive potential and persistence on ecologically relevant timescales.
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Affiliation(s)
- Alice Balard
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | | | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - Melanie J Heckwolf
- Department of Ecology Leibniz Centre for Tropical Marine Research Bremen Germany
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Bell KL, Campos M, Hoffmann BD, Encinas-Viso F, Hunter GC, Webber BL. Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171810. [PMID: 38513869 DOI: 10.1016/j.scitotenv.2024.171810] [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: 12/21/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.
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Affiliation(s)
- Karen L Bell
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Mariana Campos
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Francisco Encinas-Viso
- CSIRO Centre of Australian National Biodiversity Research, Black Mountain, Australian Capital Territory 2601, Australia
| | - Gavin C Hunter
- CSIRO Health & Biosecurity, Black Mountain, Australian Capital Territory 2601, Australia
| | - Bruce L Webber
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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5
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Parsley MB, Goldberg CS. Environmental RNA can distinguish life stages in amphibian populations. Mol Ecol Resour 2024; 24:e13857. [PMID: 37593778 DOI: 10.1111/1755-0998.13857] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/19/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
Applications of environmental DNA (eDNA) analysis methods for biomonitoring have grown exponentially over the last decade and provide a wealth of new information on the distribution of species. However, eDNA methods have limited application for estimating population-level metrics. Environmental RNA (eRNA) has the potential to address ecological questions by gathering population demographic information from environmental media but may be challenging to detect and analyze. We developed gene-specific eRNA assays targeting keratin-associated genes in two focal species, American bullfrogs (Lithobates catesbeianus) and tiger salamanders (Ambystoma mavortium) to answer an important question in amphibian management: whether species detections represent breeding populations versus transitory adults. We performed an extensive laboratory validation with amphibians housed across development stages, where we collected 95 and 127 environmental samples for bullfrogs and salamanders, respectively. Both assays were highly specific to the larval stage and amplified with high sensitivity (90% in bullfrog and 88.4% in tiger salamander samples). We then applied our validated assays to multiple natural systems. When larvae were present, we found 74.1% overall detection in bullfrog field samples and 70.8% and 48.5% overall detection in field samples from ponds with A. macrodactylum and A. californiense larvae, correlating with eDNA detection rates. When only adults were present, we did not detect larvae-specific eRNA in A. macrodactylum ponds, despite high eDNA detection rates. Although much work is ahead for optimizing assay design, sampling and filtering methods, we demonstrate that eRNA can successfully be used to discern life stages with direct application for ecology and conservation management.
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Affiliation(s)
- Meghan B Parsley
- School of the Environment, Washington State University, Pullman, Washington, USA
| | - Caren S Goldberg
- School of the Environment, Washington State University, Pullman, Washington, USA
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6
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Schenekar T, Baxter J, Phukuntsi MA, Sedlmayr I, Weckworth B, Mwale M. Optimizing waterborne eDNA capture from waterholes in savanna systems under remote field conditions. Mol Ecol Resour 2024; 24:e13942. [PMID: 38390664 DOI: 10.1111/1755-0998.13942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Environmental DNA (eDNA) is used for biodiversity assessments in a variety of ecosystems across the globe, whereby different eDNA concentration, preservation and extraction methods can outperform others depending on the sampling conditions and environment. Tropical and subtropical ecosystems in Africa are among the less studied systems concerning eDNA-based monitoring. Waterholes in arid parts of southern Africa represent important agglomeration points for terrestrial mammals, and the eDNA shed into such waterbodies provides a powerful source of information for monitoring mammalian biodiversity in the surrounding area. However, the applied methods for eDNA sampling, preservation and filtering in different freshwater systems vary greatly, and rigorous protocol testing in African freshwater systems is still lacking. This study represents the first attempt to examine variations in eDNA concentration, preservation and extraction methods under remote field conditions using waterborne eDNA in a savanna system. Collected samples were heavily affected by microalgal and bacterial growth, impeding eDNA capture and PCR success. We demonstrate clear effects of the methodological choices, which also depend on the state of eDNA. A preliminary metabarcoding run showed little taxonomic overlap in mammal species detection between two metabarcoding primers tested. We recommend water filtering (using filters with pore sizes >1 μm) over centrifugation for eDNA concentration, Longmire's solution for ambient temperature sample preservation and Qiagen's DNeasy PowerSoil Pro Kit for DNA extraction of these inhibitor-prone samples. Furthermore, at least two independent metabarcoding markers should be utilized in order to maximize species detections in metabarcoding studies.
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Affiliation(s)
| | - Janine Baxter
- South African National Biodiversity Institute, National Zoological Gardens, Pretoria, South Africa
| | - Metlholo Andries Phukuntsi
- South African National Biodiversity Institute, National Zoological Gardens, Pretoria, South Africa
- South African Environmental Observation Network, Egagasini Node, South African Environmental Observation Network, Cape Town, South Africa
| | | | | | - Monica Mwale
- South African National Biodiversity Institute, National Zoological Gardens, Pretoria, South Africa
- NRF-South African Institute for Aquatic Biodiversity, Makhanda (Grahamstown), South Africa
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7
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Hechler RM, Cristescu ME. Revealing population demographics with environmental RNA. Mol Ecol Resour 2024; 24:e13951. [PMID: 38501157 DOI: 10.1111/1755-0998.13951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/06/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
The analyses of environmental DNA (eDNA) and environmental RNA (eRNA) released by organisms into their surrounding environment (water, soil and air) have emerged as powerful tools for monitoring biodiversity. While eDNA has been widely adopted for the non-invasive detection of species and characterization of community composition, the utilization of eRNA is still in its infancy. Due to its functional nature, eRNA holds intriguing potential for biodiversity monitoring offering new avenues of research beyond species detection. For example, conspecifics that are almost genetically identical can exhibit distinct transcriptomic differences depending on their life stage. In this issue of Molecular Ecology Resources, Parsley and Goldberg (2024) demonstrate, through a lab-validated field study, that eRNA can be used to detect distinct life stages of amphibians. This study elegantly demonstrates that eRNA can be used not only to detect invasive or endangered species but also to reveal population demographic information important for guiding effective conservation strategies.
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8
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Yonago T, Kawakami T, Kasai A. Linkage between spatiotemporal distribution of environmental DNA and phenological activity in an amphidromous fish, ayu Plecoglossus altivelis altivelis, in a river located in its northernmost distributional area. JOURNAL OF FISH BIOLOGY 2024; 104:1468-1482. [PMID: 38369621 DOI: 10.1111/jfb.15687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024]
Abstract
Environmental DNA (eDNA) is a promising tool for the continuous monitoring of fish ecology and diversity. However, its potential for describing the phenological activity of fish has rarely been examined. This study aimed to elucidate a linkage between the spatiotemporal distribution of eDNA and the phenology of an amphidromous fish, ayu Plecoglossus altivelis altivelis, in a river in Hokkaido, Japan, which is its northernmost distributional area. A significant positive correlation between eDNA concentration and catch per unit effort of P. a. altivelis in the river confirmed the use of eDNA as a surrogate for the abundance of P. a. altivelis. eDNA of P. a. altivelis was first detected in late April on a sandy beach adjacent to the river mouth. Subsequent to its first detection at the lowest site in the river in early May, eDNA spread throughout the river, indicating the upstream migration of P. a. altivelis. Spawning activity was also represented by a rapid increase in eDNA concentration and its surge at night in the lowest reaches of the river during September and October. These results suggest that upstream migration and spawning primarily commenced when the water temperature reached 10°C and decreased below 20°C, respectively. This observation is consistent with the behavioral responses observed in P. a. altivelis populations from other regions of Japan. Consequently, this study demonstrated that eDNA distribution was closely linked to the phenological activity of P. a. altivelis and that eDNA is a powerful tool for studying the phenology of migratory fishes.
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Affiliation(s)
- Takuma Yonago
- Division of Marine Bioresource and Environmental Science, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Tatsuya Kawakami
- Division of Marine Bioresource and Environmental Science, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Akihide Kasai
- Division of Marine Bioresource and Environmental Science, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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da Silva LP, Mata VA, Lopes PB, Pinho CJ, Chaves C, Correia E, Pinto J, Heleno RH, Timoteo S, Beja P. Dietary metabarcoding reveals the simplification of bird-pest interaction networks across a gradient of agricultural cover. Mol Ecol 2024; 33:e17324. [PMID: 38506491 DOI: 10.1111/mec.17324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024]
Abstract
Agriculture is vital for supporting human populations, but its intensification often leads to landscape homogenization and a decline in non-provisioning ecosystem services. Ecological intensification and multifunctional landscapes are suggested as nature-based alternatives to intensive agriculture, using ecological processes like natural pest regulation to maximize food production. Birds are recognized for their role in increasing crop yields by consuming invertebrate pests in several agroecosystems. However, the understanding of how bird species, their traits and agricultural land cover influence the structure of bird-pest interactions remains limited. We sampled bird-pest interactions monthly for 1 year, at four sites within a multifunctional landscape, following a gradient of increasing agricultural land cover. We analysed 2583 droppings of 55 bird species with DNA metabarcoding and detected 225 pest species in 1139 samples of 42 bird species. As expected, bird-pest interactions were highly variable across bird species. Dietary pest richness was lower in the fully agricultural site, while predation frequency remained consistent across the agricultural land cover gradient. Network analysis revealed a reduction in the complexity of bird-pest interactions as agricultural coverage increased. Bird species abundance affected the bird's contribution to the network structure more than any of the bird traits analysed (weight, phenology, invertebrate frequency in diet and foraging strata), with more common birds being more important to network structure. Overall, our results show that increasing agricultural land cover increases the homogenization of bird-pest interactions. This shows the importance of maintaining natural patches within agricultural landscapes for biodiversity conservation and enhanced biocontrol.
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Affiliation(s)
- Luis P da Silva
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Vanessa A Mata
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Pedro B Lopes
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Catarina J Pinho
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Catia Chaves
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Edna Correia
- Departamento de Biologia Animal, Centro de Estudos Do Ambiente e Do Mar, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Joana Pinto
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Ruben H Heleno
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, University of Coimbra, Coimbra, Portugal
| | - Sergio Timoteo
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, University of Coimbra, Coimbra, Portugal
| | - Pedro Beja
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Institute of Agronomy, University of Lisbon, Lisbon, Portugal
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10
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Jo TS. Larger particle size distribution of environmental RNA compared to environmental DNA: a case study targeting the mitochondrial cytochrome b gene in zebrafish (Danio rerio) using experimental aquariums. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:18. [PMID: 38502308 DOI: 10.1007/s00114-024-01904-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
Environmental RNA (eRNA) analysis is conventionally expected to infer physiological information about organisms within their ecosystems, whereas environmental DNA (eDNA) analysis only infers their presence and abundance. Despite the promise of eRNA application, basic research on eRNA characteristics and dynamics is limited. The present study conducted aquarium experiments using zebrafish (Danio rerio) to estimate the particle size distribution (PSD) of eRNA in order to better understand the persistence state of eRNA particles. Rearing water samples were sequentially filtered using different pore-size filters, and the resulting size-fractioned mitochondrial cytochrome b (CytB) eDNA and eRNA data were modeled with the Weibull complementary cumulative distribution function (CCDF) to estimate the parameters characterizing the PSDs. It was revealed that the scale parameter (α) was significantly higher (i.e., the mean particle size was larger) for eRNA than eDNA, while the shape parameter (β) was not significantly different between them. This result supports the hypothesis that most eRNA particles are likely in a protected, intra-cellular state, which mitigates eRNA degradation in water. Moreover, these findings also imply the heterogeneous dispersion of eRNA relative to eDNA and suggest an efficient method of eRNA collection using a larger pore-size filter. Further studies on the characteristics and dynamics of eRNA particles should be pursued in the future.
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Affiliation(s)
- Toshiaki S Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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11
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Jo TS, Matsuda N, Hirohara T, Yamanaka H. Comparative evaluation for the performance of environmental DNA and RNA analyses targeting mitochondrial and nuclear genes from ayu (Plecoglossus altivelis). ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:374. [PMID: 38491297 DOI: 10.1007/s10661-024-12535-z] [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: 11/16/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Environmental DNA and RNA (eDNA and eRNA; collectively eNA) analyses have the potential for non-invasive and cost-efficient biomonitoring compared with traditional capture-based surveys. Although various types of eNA particles, including not only mitochondrial eDNA but also nuclear eDNA and their transcripts, are present in the water, performances of eNA detection and quantification have not yet been evaluated sufficiently across multiple mitochondrial and nuclear genes. We conducted a tank experiment with ayu (Plecoglossus altivelis) to compare the detection sensitivity, yields per water sample, and quantification variability between replicates of each type of eNAs. The assay targeting the multi-copy nuclear gene exhibited a higher sensitivity than the assay targeting the mitochondrial gene, and both the target eDNA and eRNA concentrations per water sample were higher for the nuclear gene. On the contrary, variation in eRNA quantifications per sample does not necessarily correspond to that in eDNA, and the intra-sample quantification variability (represented as the CVs between PCR replicates) tended to be larger for eRNA than eDNA. Our results suggested that, even if suitable to the sensitive detection of species occurrence, the use of eRNA particularly derived from multi-copy nuclear gene may not be necessarily appropriate for the reliable assessment of species abundance. The findings in this study would help optimize eNA analyses for making biomonitoring and stock assessment in aquatic environments more efficient and reliable.
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Affiliation(s)
- Toshiaki S Jo
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan.
| | - Nao Matsuda
- Shiga Prefectural Fisheries Experiment Station, 2138-3, Hassaka-cho, Hikone City, Shiga, 522-0057, Japan
| | - Takaya Hirohara
- Graduate School of Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan
- KANSO TECHNOS CO., LTD., Azuchimachi 1-3-5, Chuo-ku, Osaka, 541-0052, Japan
| | - Hiroki Yamanaka
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan
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12
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Rishan ST, Kline RJ, Rahman MS. New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11406-11427. [PMID: 38183542 DOI: 10.1007/s11356-023-31776-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Ecosystems are multifaceted and complex systems and understanding their composition is crucial for the implementation of efficient conservation and management. Conventional approaches to biodiversity surveys can have limitations in detecting the complete range of species present. In contrast, the study of environmental RNA (eRNA) offers a non-invasive and comprehensive method for monitoring and evaluating biodiversity across different ecosystems. Similar to eDNA, the examination of genetic material found in environmental samples can identify and measure many species, including ones that pose challenges to traditional methods. However, eRNA is degraded quickly and therefore shows promise in detection of living organisms closer to their actual location than eDNA methods. This method provides a comprehensive perspective on the well-being of ecosystems, facilitating the development of focused conservation approaches to save at-risk species and uphold ecological equilibrium. Furthermore, eRNA has been recognized as a valuable method for the identification of COVID-19 in the environment, besides its established uses in biodiversity protection. The SARS-CoV-2 virus, which is accountable for the worldwide epidemic, releases RNA particles into the surrounding environment via human waste, providing insights into the feasibility of detecting it in wastewater and other samples taken from the environment. In this article, we critically reviewed the recent research activities that use the eRNA method, including its utilization in biodiversity conservation, ecological surveillance, and ecotoxicological monitoring as well as its innovative potential in identifying COVID-19. Through this review, the reader can understand the recent developments, prospects, and challenges of eRNA research in ecosystem management and biodiversity conservation.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
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13
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Cunningham SW, Tessler M, Johnson-Rosemond J, Whittaker IS, Brugler MR. Environmental DNA Isolation, Validation, and Preservation Methods. Methods Mol Biol 2024; 2744:171-180. [PMID: 38683318 DOI: 10.1007/978-1-0716-3581-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Environmental DNA (eDNA) workflows contain many familiar molecular-lab techniques, but also employ several unique methodologies. When working with eDNA, it is essential to avoid contamination from the point of collection through preservation and select a meaningful negative control. As eDNA can be obtained from a variety of samples and habitats (e.g., soil, water, air, or tissue), protocols will vary depending on usage. Samples may require additional steps to dilute, block, or remove inhibitors or physically break up samples or filters. Thereafter, standard DNA isolation techniques (kit-based or phenol:chloroform:isoamyl [PCI]) are employed. Once DNA is extracted, it is typically quantified using a fluorometer. Yields vary greatly, but are important to know prior to amplification of the gene(s) of interest. Long-term storage of both the sampled material and the extracted DNA is encouraged, as it provides a backup for spilled/contaminated samples, lost data, reanalysis, and future studies using newer technology. Storage in a freezer is often ideal; however, some storage buffers (e.g., Longmires) require that filters or swabs are kept at room temperature to prevent precipitation of buffer-related solutes. These baseline methods for eDNA isolation, validation, and preservation are detailed in this protocol chapter. In addition, we outline a cost-effective, homebrew extraction protocol optimized to extract eDNA.
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Affiliation(s)
- Seth W Cunningham
- Department of Biological Sciences, Fordham University, Bronx, NY, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Michael Tessler
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Department of Biology, St. Francis College, Brooklyn, NY, USA
| | | | - Iesha S Whittaker
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
| | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
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14
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Takeda-Nishikawa K, Palanichamy R, Miyazato N, Suzuki T. What samples are suitable for monitoring antimicrobial-resistant genes? Using NGS technology, a comparison between eDNA and mrDNA analysis from environmental water. Front Microbiol 2023; 14:954783. [PMID: 38179449 PMCID: PMC10765985 DOI: 10.3389/fmicb.2023.954783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/14/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction The rise in antimicrobial resistance (AMR) that is affecting humans, animals, and the environment, compromises the human immune system and represents a significant threat to public health. Regarding the impact on water sanitation, the risk that antimicrobial-resistant genes (ARGs) and antimicrobial-resistant bacteria in surface water in cities pose to human health remains unclear. To determine the prevalence of AMR in environmental surface water in Japan, we used DNA sequencing techniques on environmental water DNA (eDNA) and the DNA of multidrug-resistant bacteria (mrDNA). Methods The eDNA was extracted from four surface water samples obtained from the Tokyo area and subjected to high- throughput next-generation DNA sequencing using Illumina-derived shotgun metagenome analysis. The sequence data were analyzed using the AmrPlusPlus pipeline and the MEGARes database. Multidrug-resistant bacteria were isolated using a culture-based method from water samples and were screened by antimicrobial susceptibility testing (for tetracycline, ampicillin-sulbactam, amikacin, levofloxacin, imipenem, and clarithromycin). Of the 284 isolates, 22 were identified as multidrug-resistant bacteria. The mrDNA was sequenced using the Oxford nanopore MinION system and analyzed by NanoARG, a web service for detecting and contextualizing ARGs. Results and discussion The results from eDNA and mrDNA revealed that ARGs encoding beta-lactams and multidrug resistance, including multidrug efflux pump genes, were frequently detected in surface water samples. However, mrDNA also revealed many sequence reads from multidrug-resistant bacteria, as well as nonspecific ARGs, whereas eDNA revealed specific ARGs such as pathogenic OXA-type and New Delhi metallo (NDM)-beta-lactamase ARGs. Conclusion To estimate potential AMR pollution, our findings suggested that eDNA is preferable for detecting pathogen ARGs.
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Affiliation(s)
| | - Rajaguru Palanichamy
- Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur, India
| | - Naoki Miyazato
- National Institute of Technology (KOSEN), Gunma College, Maebashi, Japan
| | - Takayoshi Suzuki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Japan
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15
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Collins G, Schneider C, Boštjančić LL, Burkhardt U, Christian A, Decker P, Ebersberger I, Hohberg K, Lecompte O, Merges D, Muelbaier H, Romahn J, Römbke J, Rutz C, Schmelz R, Schmidt A, Theissinger K, Veres R, Lehmitz R, Pfenninger M, Bálint M. The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution. Commun Biol 2023; 6:1241. [PMID: 38066075 PMCID: PMC10709333 DOI: 10.1038/s42003-023-05621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.
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Affiliation(s)
- Gemma Collins
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ljudevit Luka Boštjančić
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | | | - Axel Christian
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Peter Decker
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ingo Ebersberger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Karin Hohberg
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | - Dominik Merges
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hannah Muelbaier
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Juliane Romahn
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbH, Flörsheim, Germany
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | | | - Alexandra Schmidt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Kathrin Theissinger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | - Robert Veres
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Ricarda Lehmitz
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Johannes Gutenberg University, Mainz, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.
- Department of Insect Biotechnology, Justus-Liebig University, Gießen, Germany.
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16
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Ip YCA, Chang JJM, Tun KPP, Meier R, Huang D. Multispecies environmental DNA metabarcoding sheds light on annual coral spawning events. Mol Ecol 2023; 32:6474-6488. [PMID: 35852023 DOI: 10.1111/mec.16621] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 06/27/2022] [Accepted: 07/14/2022] [Indexed: 11/28/2022]
Abstract
Synchronous multispecific coral spawning generally occurs annually and forms an integral part of the coral life cycle. Apart from spawning times and species participation, however, much else remains unknown. Here, we applied environmental DNA (eDNA) metabarcoding to study two tropical reef sites of contrasting coral cover before, during and after coral spawning. Using coral-ITS2 and vertebrate-12S markers, we evaluated eDNA as an alternative monitoring tool by assessing its capabilities in detecting spawning species and tracking relative abundances of coral and fish eDNA. Over 3 years, elevated eDNA coral signals during the event (proportional read increase of up to five-fold) were observed, detecting a total of 38 coral and 133 fish species with all but one of the coral species visually observed to be spawning. This is also the first demonstration that eDNA metabarcoding can be used to infer the diurnal partitioning of night- and day-time spawning, spawning in coral species overlooked by visual surveys, and the associated changes in fish trophic structures as an indicator of spawning events. Our study paves the way for applied quantitative eDNA metabarcoding approaches to better study ephemeral and important biological events.
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Affiliation(s)
- Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
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17
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Edmunds PJ. Coral recruitment: patterns and processes determining the dynamics of coral populations. Biol Rev Camb Philos Soc 2023; 98:1862-1886. [PMID: 37340617 DOI: 10.1111/brv.12987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/22/2023]
Abstract
Coral recruitment describes the addition of new individuals to populations, and it is one of the most fundamental demographic processes contributing to population size. As many coral reefs around the world have experienced large declines in coral cover and abundance, there has been great interest in understanding the factors causing coral recruitment to vary and the conditions under which it can support community resilience. While progress in these areas is being facilitated by technological and scientific advances, one of the best tools to quantify recruitment remains the humble settlement tile, variants of which have been in use for over a century. Here I review the biology and ecology of coral recruits and the recruitment process, largely as resolved through the use of settlement tiles, by: (i) defining how the terms 'recruit' and 'recruitment' have been used, and explaining why loose terminology has impeded scientific advancement; (ii) describing how coral recruitment is measured and why settlement tiles have value for this purpose; (iii) summarizing previous efforts to review quantitative analyses of coral recruitment; (iv) describing advances from hypothesis-driven studies in determining how refuges, seawater flow, and grazers can modulate coral recruitment; (v) reviewing the biology of small corals (i.e. recruits) to understand better how they respond to environmental conditions; and (vi) updating a quantitative compilation of coral recruitment studies extending from 1974 to present, thus revealing long-term global declines in density of recruits, juxtaposed with apparent resilience to coral bleaching. Finally, I review future directions in the study of coral recruitment, and highlight the need to expand studies to deliver taxonomic resolution, and explain why time series of settlement tile deployments are likely to remain pivotal in quantifying coral recruitment.
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Affiliation(s)
- Peter J Edmunds
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA, 91330-8303, USA
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18
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Jo TS. Validating post-enrichment steps in environmental RNA analysis for improving its availability from water samples. Funct Integr Genomics 2023; 23:338. [PMID: 37975936 DOI: 10.1007/s10142-023-01269-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Environmental RNA (eRNA) analysis is expected to inclusively provide the physiological information of a population and community without individual sampling, having the potential for the improved monitoring of biodiversity and ecosystem function. Protocol development for maximizing eRNA availability is crucial to interpret its detection and quantification results with high accuracy and reliability, but the methodological validation and improvement of eRNA collection and processing methods are scarce. In this study, the technical steps after eRNA extraction, including genomic DNA (gDNA) removal and reverse transcription, were focused on and their performances were compared by zebrafish (Danio rerio) aquarium experiments. Additionally, this study also focused on the eRNA quantification variabilities between replicates and compared them between the PCR and sample levels. Results showed that (i) there was a trade-off between gDNA removal approaches and eRNA yields and an excess gDNA removal could lead to the false-negative eRNA detection, (ii) the use of the gene-specific primers for reverse transcription could increase the eRNA yields for multiple mitochondrial and nuclear genes compared with the random hexamer primers, and (iii) the coefficient of variation (CV) values of eRNA quantifications between PCR replicates were substantially lower for those between samples. Including the study, further knowledge for the sensitive and precise detection of macro-organismal eRNA should be needed for increasing the reliability and robustness of eRNA-based biomonitoring.
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Affiliation(s)
- Toshiaki S Jo
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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19
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Chatterjee A, Zhang K, Parker KM. Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16086-16096. [PMID: 37811805 DOI: 10.1021/acs.est.3c05019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.
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Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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20
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Hechler RM, Yates MC, Chain FJJ, Cristescu ME. Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms? Mol Ecol 2023. [PMID: 37792902 DOI: 10.1111/mec.17152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
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 are increasingly used for species identification, but cannot provide functional insights. Transcriptomic methods reveal the physiological states of macroorganisms, but are currently species-specific and require tissue sampling or animal sacrifice, making community-wide assessments challenging. Here, we test whether broad functional information (expression level of the transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra-organismal RNA from macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well as phytoplankton prey and microorganism colonizers to control (20°C) and heat stress (28°C) conditions for 7 days. We sequenced eRNA from tank water (after complete removal of Daphnia) as well as RNA from Daphnia tissue, enabling comparisons of extra-organismal and organismal RNA-based gene expression profiles. Both RNA types detected similar heat stress responses of Daphnia. Using eRNA, we identified 32 Daphnia genes to be differentially expressed following heat stress. Of these, 17 were also differentially expressed and exhibited similar levels of relative expression in organismal RNA. In addition to the extra-organismal Daphnia response, eRNA detected community-wide heat stress responses consisting of distinct functional profiles and 121 differentially expressed genes across eight taxa. Our study demonstrates that environmental transcriptomics based on extra-organismal eRNA can noninvasively reveal gene expression responses of macroorganisms following environmental changes, with broad potential implications for the biomonitoring of health across the trophic chain.
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Affiliation(s)
- Robert M Hechler
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Matthew C Yates
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
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21
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Jo TS. Methodological considerations for aqueous environmental RNA collection, preservation, and extraction. ANAL SCI 2023; 39:1711-1718. [PMID: 37326949 DOI: 10.1007/s44211-023-00382-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Environmental RNA (eRNA) analysis is expected to infer species' physiological information (health status, developmental stage, and environmental stress response) and their distribution and composition more correctly than environmental DNA (eDNA) analysis. With the prospect of such eRNA applications, there is an increasing need for technological development for efficient eRNA detection because of its physicochemical instability. The present study conducted a series of aquarium experiments using zebrafish (Danio rerio) and validated the methodologies for capture, preservation, and extraction of eRNA in a water sample. In the eRNA extraction experiment, an approximately 1.5-fold increase in lysis buffer volume resulted in a more than sixfold increase in target eRNA concentration. In the eRNA capture experiment, although GF/F and GF/A filters yielded similar eRNA concentrations, a GF/A filter may be capable of passing through more volume of water samples and consequently collecting more eRNA particles, given the time required for water filtration. In the eRNA preservation experiment, the use of RNA stabilization reagent (RNAlater) allowed for stably preserving target eRNA on a filter sample at - 20 and even 4 °C for 6 days at least. Altogether, the findings enable the improvement of eRNA availability from the field and easily preserve eRNA samples without deep-freezing, which will contribute to the refinement of eRNA analysis for biological and physiological monitoring in aquatic ecosystems.
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Affiliation(s)
- Toshiaki S Jo
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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22
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Hulme PE, Beggs JR, Binny RN, Bray JP, Cogger N, Dhami MK, Finlay-Smits SC, French NP, Grant A, Hewitt CL, Jones EE, Lester PJ, Lockhart PJ. Emerging advances in biosecurity to underpin human, animal, plant, and ecosystem health. iScience 2023; 26:107462. [PMID: 37636074 PMCID: PMC10450416 DOI: 10.1016/j.isci.2023.107462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
One Biosecurity is an interdisciplinary approach to policy and research that builds on the interconnections between human, animal, plant, and ecosystem health to effectively prevent and mitigate the impacts of invasive alien species. To support this approach requires that key cross-sectoral research innovations be identified and prioritized. Following an interdisciplinary horizon scan for emerging research that underpins One Biosecurity, four major interlinked advances were identified: implementation of new surveillance technologies adopting state-of-the-art sensors connected to the Internet of Things, deployable handheld molecular and genomic tracing tools, the incorporation of wellbeing and diverse human values into biosecurity decision-making, and sophisticated socio-environmental models and data capture. The relevance and applicability of these innovations to address threats from pathogens, pests, and weeds in both terrestrial and aquatic ecosystems emphasize the opportunity to build critical mass around interdisciplinary teams at a global scale that can rapidly advance science solutions targeting biosecurity threats.
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Affiliation(s)
- Philip E. Hulme
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Jacqueline R. Beggs
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Rachelle N. Binny
- Manaaki Whenua - Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Jonathan P. Bray
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Naomi Cogger
- Tāwharau Ora, School of Veterinary Science, Massey University, Palmerston North 4472, New Zealand
| | - Manpreet K. Dhami
- Manaaki Whenua - Landcare Research, PO Box 69040, Lincoln, New Zealand
| | | | - Nigel P. French
- Tāwharau Ora, School of Veterinary Science, Massey University, Palmerston North 4472, New Zealand
| | - Andrea Grant
- Scion, 10 Kyle Street, Riccarton, Christchurch 8011, New Zealand
| | - Chad L. Hewitt
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Eirian E. Jones
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Phil J. Lester
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Peter J. Lockhart
- School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand
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Douchet P, Gourbal B, Loker ES, Rey O. Schistosoma transmission: scaling-up competence from hosts to ecosystems. Trends Parasitol 2023; 39:563-574. [PMID: 37120369 PMCID: PMC10880732 DOI: 10.1016/j.pt.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/01/2023]
Abstract
In a One-Health context, it is urgent to establish the links between environmental degradation, biodiversity loss, and the circulation of pathogens. Here we review and literally draw a general vision of aquatic environmental factors that interface with Schistosoma species, agents of schistosomiasis, and ultimately modulate their transmission at the ecosystem scale. From this synthesis, we introduce the concept of ecosystem competence defined as 'the propensity of an ecosystem to amplify or mitigate an incoming quantity of a given pathogen that can be ultimately transmitted to their definitive hosts'. Ecosystem competence integrates all mechanisms at the ecosystem scale underlying the transmission risk of a given pathogen and offers a promising measure for operationalizing the One-Health concept.
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Affiliation(s)
- Philippe Douchet
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France
| | - Benjamin Gourbal
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France
| | - Eric S Loker
- Center for Evolutionary and Theoretical Immunology (CETI), Parasite Division - Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Olivier Rey
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.
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24
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Jo TS. Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis. Proc Biol Sci 2023; 290:20230979. [PMID: 37253423 PMCID: PMC10229230 DOI: 10.1098/rspb.2023.0979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences.
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Affiliation(s)
- Toshiaki S. Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
- Ryukoku Center for Biodiversity Science, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga 520-2194, Japan
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga 520-2194, Japan
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25
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Qiu S, Ooi JLS, Chen W, Poong SW, Zhang H, He W, Su S, Luo H, Hu W, Affendi YA, Du J, Loh KH. Heterogeneity of Fish Taxonomic and Functional Diversity Evaluated by eDNA and Gillnet along a Mangrove-Seagrass-Coral Reef Continuum. Animals (Basel) 2023; 13:1777. [PMID: 37889697 PMCID: PMC10251956 DOI: 10.3390/ani13111777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 10/07/2023] Open
Abstract
The effective and reliable monitoring of fish communities is important for the management and protection of marine ecosystems. Environmental DNA (eDNA) metabarcoding is a relatively new method that has been widely used in recent years, while traditional sampling via fish catching (i.e., gillnets) is one of the most common and reliable fish monitoring methods used to date. We compared the taxonomic and functional diversity of fish detected within a mangrove-seagrass-coral reef continuum using both survey methods. One liter seawater and gillnet samples were collected in August 2021 from mangrove forests, seagrass meadows and coral reef habitats (n = 3 each) in Hainan, China. Surveys using eDNA and gillnets identified 139 genera belonging to 66 families and 58 genera belonging to 42 families, respectively. Regardless of the survey method, fish detected in mangrove, seagrass and coral reef habitats were heterogeneous in their communities; however, the shared species between habitats suggest some degree of connectivity. There were no significant differences between habitats in terms of taxonomic and functional diversity, but a higher taxonomic diversity was detected using eDNA. Both methods were able to distinguish fish assemblages between different habitats; however, gillnet surveys performed better than eDNA surveys for distinguishing mangrove from seagrass assemblages. Therefore, the concurrent use of eDNA and gillnet survey methods provides a more comprehensive approach to understanding the heterogeneity of fish taxonomic and functional diversity along mangrove-seagrass-coral reef continuums.
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Affiliation(s)
- Shuting Qiu
- Institute of Ocean and Earth Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Jillian Lean Sim Ooi
- Department of Geography, Faculty of Arts and Social Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Weilin Chen
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Sze-Wan Poong
- Institute of Ocean and Earth Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Han Zhang
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Weiyi He
- Institute of Ocean and Earth Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Shangke Su
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Hao Luo
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Wenjia Hu
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yang Amri Affendi
- Institute of Ocean and Earth Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Jianguo Du
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- Faculty of Marine Biology, Xiamen Ocean Vocational College, Xiamen 361100, China
| | - Kar-Hoe Loh
- Institute of Ocean and Earth Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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26
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Zhang K, Ho KP, Chatterjee A, Park G, Li Z, Catalano JG, Parker KM. RNA Hydrolysis at Mineral-Water Interfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37216349 DOI: 10.1021/acs.est.3c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe2O3) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kun-Pu Ho
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Grace Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Zhiyao Li
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jeffrey G Catalano
- Department of Earth & Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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27
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Yang J, Zhang L, Mu Y, Wang J, Yu H, Zhang X. Unsupervised biological integrity assessment by eDNA biomonitoring of multi-trophic aquatic taxa. ENVIRONMENT INTERNATIONAL 2023; 175:107950. [PMID: 37182420 DOI: 10.1016/j.envint.2023.107950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/12/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Abstract
The biological integrity of global freshwater ecosystems is threatened by ever-increasing environmental stressors due to increased human activities, such as land-use change, eutrophication, toxic pollutants, overfishing, and exploitation. Traditional ecological assessments of lake or riverine ecosystems often require human supervision of a pre-selected reference area, using the current state of the reference area as the expected state. However, selecting an appropriate reference area has become increasingly difficult with the expansion of human activities. Here, an unsupervised biological integrity assessment framework based on environmental DNA metabarcoding without a prior reference area is proposed. Taxon richness, species dominance, co-occurrence network density, and phylogenetic distance were used to assess the aquatic communities in the Taihu Lake basin. Multi-gene metabarcoding revealed comprehensive biodiversity at multiple trophic levels including algae, protists, zooplankton, and fish. Fish sequences were mainly derived from 12S, zooplankton mainly from mitochondrial cytochrome C oxidase subunit I, and algae and protists mainly from 18S. There were significant differences in community composition among lakes, rivers, and reservoirs but no significant differences in the four fundamental biological indicators. The algal and zooplankton integrities were positively correlated with protist and fish integrities, respectively. Additionally, the algal integrity of lakes was found to be significantly lower than that of rivers. The unsupervised assessment framework proposed in this study allows different ecosystems, including the same ecosystem in different seasons, to adopt the same indicators and assessment methods, which is more convenient for environmental management and decision-making.
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Affiliation(s)
- Jianghua Yang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lijuan Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yawen Mu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China; Jiangsu Provincial Environmental Monitoring Center, Nanjing 210019, China
| | - Jiangye Wang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China.
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28
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Tessler M, Cunningham SW, Ingala MR, Warring SD, Brugler MR. An Environmental DNA Primer for Microbial and Restoration Ecology. MICROBIAL ECOLOGY 2023; 85:796-808. [PMID: 36735064 DOI: 10.1007/s00248-022-02168-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 12/28/2022] [Indexed: 05/04/2023]
Abstract
Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.
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Affiliation(s)
- Michael Tessler
- Department of Biology, St. Francis College, Brooklyn, NY, USA.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA.
| | - Seth W Cunningham
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | | | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC, 29902, USA
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29
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Bass D, Christison KW, Stentiford GD, Cook LSJ, Hartikainen H. Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology. Trends Parasitol 2023; 39:285-304. [PMID: 36759269 DOI: 10.1016/j.pt.2022.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 02/11/2023]
Abstract
Detection of pathogens, parasites, and other symbionts in environmental samples via eDNA/eRNA (collectively eNA) is an increasingly important source of information about their occurrence and activity. There is great potential for using such detections as a proxy for infection of host organisms in connected habitats, for pathogen monitoring and surveillance, and for early warning systems for disease. However, many factors require consideration, and appropriate methods developed and verified, in order that eNA detections can be reliably interpreted and adopted for surveillance and assessment of disease risk, and potentially inclusion in international standards, such as the World Organisation for Animal Health guidelines. Disease manifestation results from host-symbiont-environment interactions between hosts, demanding a multifactorial approach to interpretation of eNA signals.
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Affiliation(s)
- David Bass
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
| | - Kevin W Christison
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa; Department of Forestry, Fisheries and the Environment, Private Bag X2, Vlaeberg, 8012, South Africa
| | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
| | - Lauren S J Cook
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, UK
| | - Hanna Hartikainen
- University of Nottingham, School of Life Sciences, University Park, NG7 2RD, Nottingham, UK
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30
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Martinez ND. Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology. Ecol Evol 2023; 13:e9872. [PMID: 36911308 PMCID: PMC9994474 DOI: 10.1002/ece3.9872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/18/2023] [Accepted: 02/09/2023] [Indexed: 03/11/2023] Open
Abstract
Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.
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Affiliation(s)
- Neo D. Martinez
- Center for Complex Networks and Systems, School of Informatics, Computing, and EngineeringIndiana University, BloomingtonIndianaBloomingtonUSA
- Pacific Ecoinformatics and Computational Ecology LabCABerkeleyUSA
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31
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von Ammon U, Pochon X, Casanovas P, Trochel B, Zirngibl M, Thomas A, Witting J, Joyce P, Zaiko A. Net overboard: Comparing marine eDNA sampling methodologies at sea to unravel marine biodiversity. Mol Ecol Resour 2023; 23:440-452. [PMID: 36226834 DOI: 10.1111/1755-0998.13722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 08/09/2022] [Accepted: 09/29/2022] [Indexed: 01/04/2023]
Abstract
Environmental DNA (eDNA) analyses are powerful for describing marine biodiversity but must be optimized for their effective use in routine monitoring. To maximize eDNA detection probabilities of sparsely distributed populations, water samples are usually concentrated from larger volumes and filtered using fine-pore membranes, often a significant cost-time bottleneck in the workflow. This study aimed to streamline eDNA sampling by investigating plankton net versus bucket sampling, direct versus sequential filtration including self-preserving filters. Biodiversity was assessed using metabarcoding of the small ribosomal subunit (18S rRNA) and mitochondrial cytochrome c oxidase I (COI) genes. Multispecies detection probabilities were estimated for each workflow using a probabilistic occupancy modelling approach. Significant workflow-related differences in biodiversity metrics were reported. Highest amplicon sequence variant (ASV) richness was attained by the bucket sampling combined with self-preserving filters, comprising a large portion of microplankton. Less diversity but more metazoan taxa were captured in the net samples combined with 5 μm pore size filters. Prefiltered 1.2 μm samples yielded few or no unique ASVs. The highest average (~32%) metazoan detection probabilities in the 5 μm pore size net samples confirmed the effectiveness of preconcentration plankton for biodiversity screening. These results contribute to streamlining eDNA sampling protocols for uptake and implementation in marine biodiversity research and surveillance.
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Affiliation(s)
| | - Xavier Pochon
- Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | | | | | | | | | - Jan Witting
- SEA Education Association, Woods Hole, Massachusetts, USA
| | - Paul Joyce
- SEA Education Association, Woods Hole, Massachusetts, USA
| | - Anastasija Zaiko
- Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
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32
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Johnson MD, Freeland JR, Parducci L, Evans DM, Meyer RS, Molano-Flores B, Davis MA. Environmental DNA as an emerging tool in botanical research. AMERICAN JOURNAL OF BOTANY 2023; 110:e16120. [PMID: 36632660 DOI: 10.1002/ajb2.16120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
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Affiliation(s)
- Mark D Johnson
- Engineering Research and Development Center, Construction Engineering Research Laboratory (CERL), Champaign, IL, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joanna R Freeland
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Laura Parducci
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236, Uppsala, Sweden
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brenda Molano-Flores
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Mark A Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
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33
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Koerich G, Fraser CI, Lee CK, Morgan FJ, Tonkin JD. Forecasting the future of life in Antarctica. Trends Ecol Evol 2023; 38:24-34. [PMID: 35934551 DOI: 10.1016/j.tree.2022.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 12/24/2022]
Abstract
Antarctic ecosystems are under increasing anthropogenic pressure, but efforts to predict the responses of Antarctic biodiversity to environmental change are hindered by considerable data challenges. Here, we illustrate how novel data capture technologies provide exciting opportunities to sample Antarctic biodiversity at wider spatiotemporal scales. Data integration frameworks, such as point process and hierarchical models, can mitigate weaknesses in individual data sets, improving confidence in their predictions. Increasing process knowledge in models is imperative to achieving improved forecasts of Antarctic biodiversity, which can be attained for data-limited species using hybrid modelling frameworks. Leveraging these state-of-the-art tools will help to overcome many of the data scarcity challenges presented by the remoteness of Antarctica, enabling more robust forecasts both near- and long-term.
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Affiliation(s)
- Gabrielle Koerich
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Fraser J Morgan
- Manaaki Whenua - Landcare Research, Auckland 1072, New Zealand; Te Pūnaha Matatini, Centre of Research Excellence in Complex Systems, Auckland, New Zealand
| | - Jonathan D Tonkin
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Te Pūnaha Matatini, Centre of Research Excellence in Complex Systems, Auckland, New Zealand; Bioprotection Aotearoa, Centre of Research Excellence, Canterbury, New Zealand.
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34
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Sarshar M, Scribano D, Palamara AT, Ambrosi C, Masotti A. The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions. Front Mol Biosci 2022; 9:1088783. [PMID: 36619166 PMCID: PMC9810633 DOI: 10.3389/fmolb.2022.1088783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein-RNA and RNA-RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,Department of Infectious Diseases, National Institute of Health, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,IRCCS San Raffaele Roma, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
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35
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van der Heyde M, Bunce M, Nevill P. Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157617. [PMID: 35901901 DOI: 10.1016/j.scitotenv.2022.157617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Ecological restoration of terrestrial environments is a globally important process to combat the loss of biodiversity and ecosystem services. Holistic monitoring of restored biota and active management of restoration is necessary to improve restoration processes and outcomes, and provide evidence to stakeholders that targets are being achieved. Increasingly, environmental DNA (eDNA) metabarcoding is used as a restoration monitoring tool because it is able to generate biodiversity data rapidly, accurately, non-destructively, and reliably, on a wide breadth of organisms from soil microbes to mammals. The overall objective of this review is to discuss the key factors to consider in the use of environmental DNA for monitoring of restored terrestrial ecosystems, hopefully improving monitoring, and ultimately, restoration outcomes. We identified that the majority of eDNA based studies of ecosystem restoration are currently conducted in Europe, North America, and Australia, and that almost half of total studies were published in 2021-22. Soil was the most popular sample substrate, soil microbial communities the most targeted taxa, and forests the most studied ecosystem. We suggest there is no 'one size fits all' approach to restoration monitoring using eDNA, and discuss survey design. Factors to consider include substrate selection, sample collection and storage, assay selection, and data interpretation, all of which require careful planning to obtain reliable, and accurate information that can be used for restoration monitoring and decision making. We explore future directions for research and argue that eDNA metabarcoding can be a useful tool in the restoration monitoring 'toolkit', but requires informed application and greater accessibility to data by a wide spectrum of stakeholders.
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Affiliation(s)
- Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia.
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia; Institute of Environmental Science and Research (ESR), Kenepuru, Porirua 5022, New Zealand
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia
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36
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Comparative environmental RNA and DNA metabarcoding analysis of river algae and arthropods for ecological surveys and water quality assessment. Sci Rep 2022; 12:19828. [PMID: 36400924 PMCID: PMC9674700 DOI: 10.1038/s41598-022-23888-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is widely used for species analysis, while the use of environmental RNA (eRNA) metabarcoding is more limited. We conducted comparative eDNA/eRNA metabarcoding of the algae and arthropods (aquatic insects) in water samples from Naka River, Japan, to evaluate their potential for biological monitoring and water quality assessment. Both methods detected various algae and arthropod species; however, their compositions were remarkably different from those in traditional field surveys (TFSs), indicating low sensitivity. For algae, the species composition derived from eDNA and eRNA metabarcoding was equivalent. While TFSs focus on attached algae, metabarcoding analysis theoretically detects both planktonic and attached algae. A recently expanded genomic database for aquatic insects significantly contributed to the sensitivity and positive predictivity for arthropods. While the sensitivity of eRNA was lower than that of eDNA, the positive predictivity of eRNA was higher. The eRNA of terrestrial arthropods indicated extremely high or low read numbers when compared with eDNA, suggesting that eRNA could be an effective indicator of false positives. Arthropod and algae eDNA/eRNA metabarcoding analysis enabled water quality estimates from TFSs. The eRNA of algae and arthropods could thus be used to evaluate biodiversity and water quality and provide insights from ecological surveys.
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37
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Nagler M, Podmirseg SM, Ascher‐Jenull J, Sint D, Traugott M. Why eDNA fractions need consideration in biomonitoring. Mol Ecol Resour 2022; 22:2458-2470. [PMID: 35652762 PMCID: PMC9545497 DOI: 10.1111/1755-0998.13658] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/12/2022] [Accepted: 05/26/2022] [Indexed: 11/29/2022]
Abstract
The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. Here, we review the fractions of eDNA, describe how to obtain them from environmental samples and present a four-scenario concept that aims at enhancing spatial and temporal resolution of eDNA-based monitoring. Importantly, we highlight how the appropriate choice of eDNA fractions precludes misinterpretation of eDNA-based biodiversity data. Finally, future avenues of research towards eDNA fraction-specific analyses are outlined to unravel the full potential of eDNA-based studies targeting micro- and macro-organisms.
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Affiliation(s)
| | | | | | - Daniela Sint
- Department of ZoologyUniversität InnsbruckInnsbruckAustria
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38
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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39
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Lopez MLD, Lin YY, Schneider SQ, Hsieh CH, Shiah FK, Machida RJ. Allometric scaling of interspecific RNA transcript abundance to extend the use of metatranscriptomics in characterizing complex communities. Mol Ecol Resour 2022; 23:52-63. [PMID: 36062315 PMCID: PMC10087904 DOI: 10.1111/1755-0998.13711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022]
Abstract
Metatranscriptomics allows profiling of community messenger RNA (mRNA) and ribosomal RNA (rRNA) transcript abundance under certain environmental conditions. However, variations in the proportion of RNA transcripts across different community size structures remain less explained, thus limiting the possible applications of metatranscriptomics in community studies. Here, we extended the assumptions of the growth-rate hypothesis (GRH) and the metabolic theory of ecology (MTE) to validate the allometric scaling of interspecific RNA transcript (mRNA and rRNA) abundance through metatranscriptomic analysis of mock communities consisting of model organisms. Results suggest that body size imposes significant constraints on RNA transcript abundance. Interestingly, the relationship between the total mitochondrial transcript abundance (mRNA and rRNA slopes were -0.30 and -0.28, respectively) and body size aligned with the MTE assumptions with slopes close to -¼, while the nuclear transcripts displayed much steeper slopes (mRNA and rRNA slopes were -0.33 and -0.40, respectively). The assumed temperature dependence was not observed in this study. At the gene level, the allometric slopes range from 0 to -1. Overall, the above results showed that larger individuals have lesser RNA transcript abundance per tissue mass than smaller ones regardless of temperature. Analyses of field-collected microcrustacean zooplankton samples demonstrated that the correction of size effect, using the allometric exponents derived from the model organism mock community, explains better the patterns of interspecific RNA transcripts abundance within the metatranscriptome. Integrating allometry with metatranscriptomics can extend the use of RNA transcript reads in estimating ecological processes within complex communities.
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Affiliation(s)
- Mark Louie D Lopez
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ya-Ying Lin
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei, Taiwan
| | - Stephan Q Schneider
- Institute of Organismic and Cellular Biology, Academia Sinica, Nankang District, Taipei, Taiwan
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Da'an District, Taipei, Taiwan.,Environmental Change Research Center, Academia Sinica, Nankang District, Taipei, Taiwan
| | - Fuh-Kwo Shiah
- Environmental Change Research Center, Academia Sinica, Nankang District, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei, Taiwan
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40
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Hempel CA, Wright N, Harvie J, Hleap JS, Adamowicz S, Steinke D. Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments. Nucleic Acids Res 2022; 50:9279-9293. [PMID: 35979944 PMCID: PMC9458450 DOI: 10.1093/nar/gkac689] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/05/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022] Open
Abstract
Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.
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Affiliation(s)
- Christopher A Hempel
- To whom correspondence should be addressed. Tel: +1 519 824 4120; Fax: +1 519 824 5703;
| | - Natalie Wright
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Julia Harvie
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jose S Hleap
- SHARCNET, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
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41
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Banerjee P, Stewart KA, Dey G, Antognazza CM, Sharma RK, Maity JP, Saha S, Doi H, de Vere N, Chan MWY, Lin PY, Chao HC, Chen CY. Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AOB PLANTS 2022; 14:plac031. [PMID: 35990516 PMCID: PMC9389569 DOI: 10.1093/aobpla/plac031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Kathryn A Stewart
- Institute of Environmental Science, Leiden University, 2333 CC Leiden, The Netherlands
| | - Gobinda Dey
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Caterina M Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Jyoti Prakash Maity
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Santanu Saha
- Post Graduate Department of Botany, Bidhannagar College, Salt Lake City, Kolkata 700064, India
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K
| | - Michael W Y Chan
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Pin-Yun Lin
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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42
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Hanson MC, Petch GM, Ottosen TB, Skjøth CA. Climate change impact on fungi in the atmospheric microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154491. [PMID: 35283127 DOI: 10.1016/j.scitotenv.2022.154491] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/13/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The atmospheric microbiome is one of the least studied microbiomes of our planet. One of the most abundant, diverse and impactful parts of this microbiome is arguably fungal spores. They can be very potent outdoor aeroallergens and pathogens, causing an enormous socio-economic burden on health services and annual damages to crops costing billions of Euros. We find through hypothesis testing that an expected warmer and drier climate has a dramatic impact on the atmospheric microbiome, conceivably through alteration of the hydrological cycle impacting agricultural systems, with significant differences in leaf wetness between years (p-value <0.05). The data were measured via high-throughput sequencing analysis using the DNA barcode marker, ITS2. This was complemented by remote sensing analysis of land cover and dry matter productivity based on the Sentinel satellites, on-site detection of atmospheric and vegetation variables, GIS analysis, harvesting analysis and footprint modelling on trajectory clusters using the atmospheric transport model HYSPLIT. We find the seasonal spore composition varies between rural and urban zones reflecting both human activities (e.g. harvest), type and status of the vegetation and the prevailing climate rather than mesoscale atmospheric transport. We find that crop harvesting governs the composition of the atmospheric microbiome through a clear distinction between harvest and post-harvest beta-diversity by PERMANOVA on Bray-Curtis dissimilarity (p-value <0.05). Land cover impacted significantly by two-way ANOVA (p-value <0.05), while there was minimal impact from air mass transport over the 3 years. The hypothesis suggests that the fungal spore composition will change dramatically due to climate change, an until now unforeseen effect affecting both food security, human health and the atmospheric hydrological cycle. Consequently the management of crop diseases and impact on human health through aeroallergen exposure need to consider the timing of crop treatments and land management, including post harvest, to minimize exposure of aeroallergens and pathogens.
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Affiliation(s)
- M C Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK.
| | - G M Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
| | - T-B Ottosen
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK; Department of Air and Sensor Technology, Danish Technological Institute, Kongsvang Allé 29, DK-8000 Aarhus C, Denmark
| | - C A Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK.
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43
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An Integrative Analysis Revealing ZFHX4-AS1 as a Novel Prognostic Biomarker Correlated with Immune Infiltrates in Ovarian Cancer. J Immunol Res 2022; 2022:9912732. [PMID: 35795530 PMCID: PMC9251081 DOI: 10.1155/2022/9912732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
Ovarian cancer (OC) is the main cause of deaths worldwide in female reproductive system malignancies. Growing studies have indicated that eRNAs could regulate cellular activities in various tumors. Yet the potential roles of eRNAs in OC progression have not been elucidated. Thus, comprehensive assays were needed to screen the critical eRNAs and to explore their possible function in OC. We used Kaplan–Meier methods to identify survival-associated eRNAs in OC based on TCGA datasets. The levels of ZFHX4-AS1 were examined using TCGA datasets. Further exploration was carried out based on the following assays: clinical and survival assays, GO terms, and KEGG assays. TIMER was applied to delve into the relationships between ZFHX4-AS1 and tumor immune infiltration. In this research, we observed 71 survival-related eRNAs in OC patients. ZFHX4-AS1 was highly expressed in OC specimens and predicted a poor prognosis of OC patients. In addition, high ZFHX4-AS1 expression was positively related to the advanced stages of OC specimens. Multivariate assays revealed that ZFHX4-AS1 was an independent prognostic factor for overall survival of OC patients. KEGG analysis indicated that ZFHX4-AS1 may play a regulatory effect on TGF-beta signaling, PI3K-Akt signaling, and proteoglycans in cancer. The pan-cancer validation indicated that ZFHX4-AS1 was related to survival in eight tumors, namely, UCEC, STAD, SARC, OV, ACC, KICH, KIRC, and BLCA. The expression of ZFHX4-AS1 was correlated with the levels of B cells, T cell CD8+, neutrophil, macrophage, and myeloid dendritic cells. Simultaneously, ZFHX4-AS1 may be a prognostic biomarker and a distinctly immunotherapy-related eRNA in OC.
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44
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Jeffery NW, Lehnert SJ, Kess T, Layton KKS, Wringe BF, Stanley RR. Application of Omics Tools in Designing and Monitoring Marine Protected Areas For a Sustainable Blue Economy. Front Genet 2022; 13:886494. [PMID: 35812740 PMCID: PMC9257101 DOI: 10.3389/fgene.2022.886494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/16/2022] [Indexed: 11/15/2022] Open
Abstract
A key component of the global blue economy strategy is the sustainable extraction of marine resources and conservation of marine environments through networks of marine protected areas (MPAs). Connectivity and representativity are essential factors that underlie successful implementation of MPA networks, which can safeguard biological diversity and ecosystem function, and ultimately support the blue economy strategy by balancing ocean use with conservation. New “big data” omics approaches, including genomics and transcriptomics, are becoming essential tools for the development and maintenance of MPA networks. Current molecular omics techniques, including population-scale genome sequencing, have direct applications for assessing population connectivity and for evaluating how genetic variation is represented within and among MPAs. Effective baseline characterization and long-term, scalable, and comprehensive monitoring are essential for successful MPA management, and omics approaches hold great promise to characterize the full range of marine life, spanning the microbiome to megafauna across a range of environmental conditions (shallow sea to the deep ocean). Omics tools, such as eDNA metabarcoding can provide a cost-effective basis for biodiversity monitoring in large and remote conservation areas. Here we provide an overview of current omics applications for conservation planning and monitoring, with a focus on metabarcoding, metagenomics, and population genomics. Emerging approaches, including whole-genome sequencing, characterization of genomic architecture, epigenomics, and genomic vulnerability to climate change are also reviewed. We demonstrate that the operationalization of omics tools can enhance the design, monitoring, and management of MPAs and thus will play an important role in a modern and comprehensive blue economy strategy.
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Affiliation(s)
- Nicholas W. Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
- *Correspondence: Nicholas W. Jeffery,
| | - Sarah J. Lehnert
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, NL, Canada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, NL, Canada
| | - Kara K. S. Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Brendan F. Wringe
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
| | - Ryan R.E. Stanley
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
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45
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Kagzi K, Hechler RM, Fussmann GF, Cristescu ME. Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions. Mol Ecol Resour 2022; 22:2640-2650. [DOI: 10.1111/1755-0998.13655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/16/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Kaushar Kagzi
- Department of Biology McGill University Montréal QC Canada
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL)
| | - Robert M. Hechler
- Department of Biology McGill University Montréal QC Canada
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL)
| | - Gregor F. Fussmann
- Department of Biology McGill University Montréal QC Canada
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL)
| | - Melania E. Cristescu
- Department of Biology McGill University Montréal QC Canada
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL)
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46
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Giraud C, Callac N, Boulo V, Lam JS, Pham D, Selmaoui-Folcher N, Wabete N. The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission. Front Microbiol 2022; 13:886752. [PMID: 35633721 PMCID: PMC9133551 DOI: 10.3389/fmicb.2022.886752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
The many ecological niches present in an organism harbor distinct microorganisms called microbiota. Different factors can influence the establishment of these commensal microbial communities. In a previous article, we have concluded that some bacterial lineages associated with the early larval stages of the Pacific blue shrimp Litopenaeus stylirostris could be acquired from the breeders via a potential vertical transmission. The present study was conducted in order to investigate this hypothesis. Using HiSeq sequencing of the V4 region of 16S rRNA gene, we analyzed the active microbiota associated with the eggs and the nauplii of L. stylirsotris as well as with the reproductive organs of their breeders. Microbial communities associated with the rearing water were also considered to discriminate environmental microbial lineages. Using these analyses, we highlight a set of core bacterial families present in all samples and composed of members of Colwelliaceae, Alteromonadaceae, Pseudoalteromonadaceae, Saccharospirillaceae, Oceanospirillaceae, Vibrionaceae, Burkholderiaceae, Rhodobacteraceae, Flavobacteraceae, and Corynebacteriaceae; showing the importance of the environment in the establishment of the larval microbiota. We also present specific bacteria affiliated to the Arcobacteraceae, Rhodobacteraceae, Comamonadaceae, and Colwelliaceae families, which were only found in the breeders and their offspring strengthening the hypothesis of a potential vertical transmission shaping the active microbiota of the eggs and the nauplii of L. stylirostris.
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Affiliation(s)
- Carolane Giraud
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
- Institut des Sciences Exactes et Appliquées (ISEA), University of New Caledonia, Noumea, New Caledonia
- *Correspondence: Carolane Giraud,
| | - Nolwenn Callac
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
- Nolwenn Callac,
| | - Viviane Boulo
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
| | | | - Dominique Pham
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
| | - Nazha Selmaoui-Folcher
- Institut des Sciences Exactes et Appliquées (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Nelly Wabete
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
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47
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van Rees CB, Hand BK, Carter SC, Bargeron C, Cline TJ, Daniel W, Ferrante JA, Gaddis K, Hunter ME, Jarnevich CS, McGeoch MA, Morisette JT, Neilson ME, Roy HE, Rozance MA, Sepulveda A, Wallace RD, Whited D, Wilcox T, Kimball JS, Luikart G. A framework to integrate innovations in invasion science for proactive management. Biol Rev Camb Philos Soc 2022; 97:1712-1735. [PMID: 35451197 DOI: 10.1111/brv.12859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches has produced tools with the potential to greatly accelerate invasion research and management, innovation has far outpaced implementation and coordination. Technological and methodological syntheses are urgently needed to close the growing implementation gap and facilitate interdisciplinary collaboration and synergy among evolving disciplines. A broad review is necessary to demonstrate the utility and relevance of work in diverse fields to generate actionable science for the ongoing invasion crisis. Here, we review such advances in relevant fields including remote sensing, epidemiology, big data analytics, environmental DNA (eDNA) sampling, genomics, and others, and present a generalized framework for distilling existing and emerging data into products for proactive IAS research and management. This integrated workflow provides a pathway for scientists and practitioners in diverse disciplines to contribute to applied invasion biology in a coordinated, synergistic, and scalable manner.
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Affiliation(s)
- Charles B van Rees
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Sean C Carter
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Chuck Bargeron
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Timothy J Cline
- U.S. Geological Survey, Northern Rocky Mountain Science Center, 2327 University Way STE 2, Bozeman MT 59717 & 320 Grinnel Drive, West Glacier, MT, 59936, U.S.A
| | - Wesley Daniel
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Jason A Ferrante
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Keith Gaddis
- NASA Biological Diversity and Ecological Forecasting Programs, 300 E St. SW, Washington, DC, 20546, U.S.A
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Catherine S Jarnevich
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue Bldg C, Fort Collins, CO, 80526, U.S.A
| | - Melodie A McGeoch
- Department of Environment and Genetics, La Trobe University, Plenty Road & Kingsbury Drive, Bundoora, Victoria, 3086, Australia
| | - Jeffrey T Morisette
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Matthew E Neilson
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Helen E Roy
- UK Centre for Ecology & Hydrology, MacLean Building, Benson Lane, Crowmarsh Gifford, OX10 8BB, U.K
| | - Mary Ann Rozance
- Northwest Climate Adaptation Science Center, University of Washington, Box 355674, Seattle, WA, 98195, U.S.A
| | - Adam Sepulveda
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Rebekah D Wallace
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Diane Whited
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Taylor Wilcox
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - John S Kimball
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Gordon Luikart
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
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48
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Boileau J, Calvet C, Pioch S, Moulherat S. Ecological equivalence assessment: The potential of genetic tools, remote sensing and metapopulation models to better apply the mitigation hierarchy. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114415. [PMID: 34995946 DOI: 10.1016/j.jenvman.2021.114415] [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: 08/30/2021] [Revised: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Within the framework of the mitigation hierarchy, biodiversity offsetting is the main tool promoted to reach No Net Loss. One of the determining factors of offsetting success is the evaluation of ecological equivalence. Various equivalence assessment methods (EAMs) have been developed to provide a framework to evaluate the balance between expected biodiversity losses and gains. In the context of achieving No Net Loss, EAMs must address challenges of Operationality, Currency, Uncertainty, Spatial scale and Time frame. In this study, we investigated the way the most widely used EAMs address these challenges, positing that certain tools from ecological science could limit the trade-offs between these challenges and improve the ecological assessment process. To this end, we analysed the risks and benefits associated with the inclusion of genetic tools (landscape genetics and eDNA), remote sensing and metapopulation models in selected EAMs. Our results revealed trade-offs between these five challenges, in particular between Operationality and Currency. The EAMs varied strongly in these two aspects, depending on the general assessment approach and the biodiversity component they focus on. To a lesser degree, Time frame and Spatial scale also differed between the methods. We identified that the integration of the different tools differs among them, being easier for remote sensing and metapopulation models than for the genetic tools. Nevertheless, the integration resulted in benefits compared to the current use of the methods - benefits that included improving the objectivation of the assessment and the automatization potential. The tools also show potential for automatization, which could have major benefits for operationality. In terms of risks, the integration of these tools increases the technical complexity of the methods, requiring new skills, and would change the overall approach of the ecological assessment.
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Affiliation(s)
- Jules Boileau
- TerrOïko - Oïkolab, 2 Place Dom Devic, BP26, 81540, Sorèze, France; CEFE, Univ. Montpellier, CNRS, EPHE, CIRAD, Institut Agro, Montpellier, France; Laboratoire de Géographie et d'Aménagement de Montpellier, Université Paul Valéry, site de Saint Charles, Route de Mende, 34199, Montpellier, France.
| | - Coralie Calvet
- CEFE, Univ. Montpellier, CNRS, EPHE, CIRAD, Institut Agro, Montpellier, France; CEEM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Sylvain Pioch
- Laboratoire de Géographie et d'Aménagement de Montpellier, Université Paul Valéry, site de Saint Charles, Route de Mende, 34199, Montpellier, France
| | - Sylvain Moulherat
- TerrOïko - Oïkolab, 2 Place Dom Devic, BP26, 81540, Sorèze, France; Station d'Ecologie Théorique et Expérimentale (UMR 5321), 2 Route du CNRS, 09200, Moulis, France
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49
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Bizic M, Ionescu D, Karnatak R, Musseau CL, Onandia G, Berger SA, Nejstgaard JC, Lischeid G, Gessner MO, Wollrab S, Grossart HP. Land-use type temporarily affects active pond community structure but not gene expression patterns. Mol Ecol 2022; 31:1716-1734. [PMID: 35028982 DOI: 10.1111/mec.16348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/30/2021] [Accepted: 01/04/2022] [Indexed: 11/30/2022]
Abstract
Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics, to understand the responses of active bacterial, archaeal, and eukaryotic communities, to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel eDNA study which revealed the homogenization of biodiversity across KH conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced in eukaryotes than in bacteria. In contrast, gene expression patterns did not differ between months or across land-use type, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results show that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.
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Affiliation(s)
- M Bizic
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - D Ionescu
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - R Karnatak
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - C L Musseau
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Institute of Biology, Free University of Berlin, Berlin, Germany
| | - G Onandia
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Research Platform Data Analysis and Simulation, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - S A Berger
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - J C Nejstgaard
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - G Lischeid
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Research Platform Data Analysis and Simulation, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Institute for Environmental Sciences and Geography, Potsdam University, Potsdam, Germany
| | - M O Gessner
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Department of Ecology, Berlin Institute of Technology (TU Berlin), Berlin, Germany
| | - S Wollrab
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - H-P Grossart
- Departments of Experimental Limnology and Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin and Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
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50
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Yates MC, Cristescu ME, Derry AM. Integrating physiology and environmental dynamics to operationalize environmental DNA (eDNA) as a means to monitor freshwater macro-organism abundance. Mol Ecol 2021; 30:6531-6550. [PMID: 34592014 DOI: 10.1111/mec.16202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/03/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022]
Abstract
Research has demonstrated consistent positive correlations between organism abundance and absolute environmental DNA (eDNA) concentrations. Robust correlations in laboratory experiments indicate strong functional links, suggesting the potential for eDNA to monitor organism abundance in nature. However, correlations between absolute eDNA concentrations and organism abundance in nature tend to be weaker because myriad biotic and abiotic factors influence steady-state eDNA concentrations, decoupling its direct functional link with abundance. Additional technical challenges can also weaken correlations between relative organism abundance and relative eDNA data derived from metabarcoding. Future research must account for these factors to improve the inference of organism abundance from eDNA, including integrating the effects of organism physiology on eDNA production, eDNA dynamics in lentic/lotic systems, and key environmental parameters that impact estimated steady-state concentrations. Additionally, it is critical to manage expectations surrounding the accuracy and precision that eDNA can provide - eDNA, for example, cannot provide abundance estimates comparable to intensively managed freshwater fisheries that enumerate every individual fish. Recent developments, however, are encouraging. Current methods could provide meaningful information regarding qualitative conservation thresholds and emergent research has demonstrated that eDNA concentrations in natural ecosystems can provide rough quantitative estimates of abundance, particularly when models integrate physiology and/or eDNA dynamics. Operationalizing eDNA to infer abundance will probably require more than simple correlations with organism biomass/density. Nevertheless, the future is promising - models that integrate eDNA dynamics in nature could represent an effective means to infer abundance, particularly when traditional methods are considered too "costly" or difficult to obtain.
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Affiliation(s)
| | | | - Alison M Derry
- Université du Québec à Montréal, Montréal, Québec, Canada
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