期刊
MOLECULAR ECOLOGY
卷 30, 期 13, 页码 2937-2958出版社
WILEY
DOI: 10.1111/mec.15472
关键词
biodiversity; biomonitoring; ecosystem management; environmental DNA; implementation strategy; metabarcoding
资金
- Swiss National Science Foundation [31003A_179125]
- European Cross-Border Cooperation Programme
- 'Ramon y Cajal' contract [RYC-2012-11404]
- Spanish Ministry of Economy and Competitiveness
- Saudi Aramco-KAUST Center for Marine Environmental Observations
- French Agence Nationale de la Recherche [ANR-17-CE32-011]
- ERA-NET C-IPM BioAWARE
- UK Natural Environment Research Council [NE/N003756/1, NE/N006216/1]
- German Science Foundation (DFG) [STO414/15-1]
- New Zealand Ministry for Business, Innovation and Employment [CAWX1904, C05X1707]
- DNAquaNet COST Action [CA15219]
- European Union
- IKERBASQUE (Basque Foundation for Science)
- Basque Government
- Office Francais de la Biodiversite (OFB)
- NERC [NE/N006216/1, NE/N003756/1] Funding Source: UKRI
- Natural Environment Research Council [NE/N002431/1, NE/N002105/1, NE/N001710/1, NE/N006216/1, NE/N005678/1, NE/N003756/1] Funding Source: researchfish
- New Zealand Ministry of Business, Innovation & Employment (MBIE) [CAWX1904] Funding Source: New Zealand Ministry of Business, Innovation & Employment (MBIE)
A decade after the integration of high-throughput sequencing technologies into environmental science, genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems still faces challenges in implementation by regulatory frameworks. Technical limitations, conceptual issues, and diverse implementation strategies may contribute to the perception that routine application of this methodology is premature. Reviewing recent implementations, the strengths and limitations of four general implementation strategies for environmental genomics monitoring are discussed, with emphasis on the potential of integrating meiofauna and microorganisms into biomonitoring.
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or in development, hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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