Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap.
Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap.
复制标题
DOI：
10.1111/mec.15472
复制
发表时间：
2021-07
影响因子：
4.9
通讯作者：
Lanzén A
中科院分区：
文献类型：
--
作者：
Cordier T;Alonso-Sáez L;Apothéloz-Perret-Gentil L;Aylagas E;Bohan DA;Bouchez A;Chariton A;Creer S;Frühe L;Keck F;Keeley N;Laroche O;Leese F;Pochon X;Stoeck T;Pawlowski J;Lanzén A
在环境科学家将高通量测序技术整合到他们的工具箱中十年后，以基因组学为基础的对生物多样性和生态系统功能的人为影响的监测尚未通过监管框架实施。尽管环境基因组学在这方面的潜力得到了广泛承认，但技术限制和概念问题仍然阻碍着最终用户广泛应用环境基因组学。此外，可能实施的战略多种多样，可能会造成这样一种看法，即常规应用这一方法为时过早或处于“发展阶段”，从而限制监管机构将这些工具纳入法律框架。在这里，我们回顾了基于环境基因组学方法的最新实现，应用于生态系统的生物监测。在不将视角缩小到特定生境或生物群的情况下，本文旨在比较、审查和讨论环境基因组学用于监测的四种一般实施战略的优点和局限性：(A)基于分类的分析，侧重于确定已知的生物指标或所描述的类群；(B)从头开始的生物指标分析；(C)结构群落计量，包括推断的生态网络；和(D)功能群落计量(元基因组学或元转录基因组学)。我们强调后三种策略的效用，以整合小型动物和微生物，因为分类鉴定困难，这些微生物在生物监测中传统上不被利用。最后，我们提出了将环境基因组学落实到常规监测方案中的路线图，这些方案利用了最近的分析进展，同时指出了当前的局限性和未来的研究需要。
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.
登录
查看更多内容
影响因子：
4.4
作者：
Ashelford, KE;Chuzhanova, NA;Weightman, AJ
通讯作者：
Weightman, AJ
影响因子：
--
作者：
Blackman, Rosetta C.;Maechler, Elvira;Deiner, Kristy
通讯作者：
Deiner, Kristy
DOI：
10.1016/j.jembe.2008.07.006
发表时间：
2008-11-15
影响因子：
2
作者：
Anderson, Marti J.
通讯作者：
Anderson, Marti J.
影响因子：
6.9
作者：
Bagley, Mark;Pilgrim, Erik;Banerji, Aabir
通讯作者：
Banerji, Aabir
对真核生物的分类，命名法和多样性进行修订。
DOI：
10.1111/jeu.12691
发表时间：
2019-01
期刊：
The Journal of eukaryotic microbiology
影响因子：
--
作者：
Adl SM;Bass D;Lane CE;Lukeš J;Schoch CL;Smirnov A;Agatha S;Berney C;Brown MW;Burki F;Cárdenas P;Čepička I;Chistyakova L;Del Campo J;Dunthorn M;Edvardsen B;Eglit Y;Guillou L;Hampl V;Heiss AA;Hoppenrath M;James TY;Karnkowska A;Karpov S;Kim E;Kolisko M;Kudryavtsev A;Lahr DJG;Lara E;Le Gall L;Lynn DH;Mann DG;Massana R;Mitchell EAD;Morrow C;Park JS;Pawlowski JW;Powell MJ;Richter DJ;Rueckert S;Shadwick L;Shimano S;Spiegel FW;Torruella G;Youssef N;Zlatogursky V;Zhang Q
通讯作者：
Zhang Q