Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

Thorsten Stoeck, Larissa Frühe, Dominik Forster, Tristan Cordier, Catarina I.M. Martins, Jan Pawlowski, Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture. Marine Pollution Bulletin. ,vol. 127, pp. 139- 149 ,(2018) , 10.1016/J.MARPOLBUL.2017.11.065

Nigel Keeley, Susanna A. Wood, Xavier Pochon, Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment Ecological Indicators. ,vol. 85, pp. 1044- 1057 ,(2018) , 10.1016/J.ECOLIND.2017.11.014

Valentin Vasselon, Agnès Bouchez, Frédéric Rimet, Stéphan Jacquet, Rosa Trobajo, Méline Corniquel, Kálmán Tapolczai, Isabelle Domaizon, Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring Methods in Ecology and Evolution. ,vol. 9, pp. 1060- 1069 ,(2017) , 10.1111/2041-210X.12960

Jolinda Pollock, Laura Glendinning, Trong Wisedchanwet, Mick Watson, The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies Applied and Environmental Microbiology. ,vol. 84, pp. 2- ,(2018) , 10.1128/AEM.02627-17

Zhili He, Ping Zhang, Linwei Wu, Andrea M Rocha, Qichao Tu, Zhou Shi, Bo Wu, Yujia Qin, Jianjun Wang, Qingyun Yan, Daniel Curtis, Daliang Ning, Joy D Van Nostrand, Liyou Wu, Yunfeng Yang, Dwayne A Elias, David B Watson, Michael WW Adams, Matthew W Fields, Eric J Alm, Terry C Hazen, Paul D Adams, Adam P Arkin, Jizhong Zhou, None, Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning Mbio. ,vol. 9, ,(2018) , 10.1128/MBIO.02435-17

Peter Manning, Fons van der Plas, Santiago Soliveres, Eric Allan, Fernando T. Maestre, Georgina Mace, Mark J. Whittingham, Markus Fischer, Redefining ecosystem multifunctionality. Nature Ecology and Evolution. ,vol. 2, pp. 427- 436 ,(2018) , 10.1038/S41559-017-0461-7

Daniel Hering, Angel Borja, J Iwan Jones, Didier Pont, Pieter Boets, Agnes Bouchez, Kat Bruce, Stina Drakare, Bernd Hänfling, Maria Kahlert, Florian Leese, Kristian Meissner, Patricia Mergen, Yorick Reyjol, Pedro Segurado, Alfried Vogler, Martyn Kelly, None, Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Water Research. ,vol. 138, pp. 192- 205 ,(2018) , 10.1016/J.WATRES.2018.03.003

Florian Leese, Agnès Bouchez, Kessy Abarenkov, Florian Altermatt, Ángel Borja, Kat Bruce, Torbjørn Ekrem, Fedor Čiampor, Zuzana Čiamporová-Zaťovičová, Filipe O. Costa, Sofia Duarte, Vasco Elbrecht, Diego Fontaneto, Alain Franc, Matthias F. Geiger, Daniel Hering, Maria Kahlert, Belma Kalamujić Stroil, Martyn Kelly, Emre Keskin, Igor Liska, Patricia Mergen, Kristian Meissner, Jan Pawlowski, Lyubomir Penev, Yorick Reyjol, Ana Rotter, Dirk Steinke, Bas van der Wal, Simon Vitecek, Jonas Zimmermann, Alexander M. Weigand, Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action Advances in Ecological Research. ,vol. 58, pp. 63- 99 ,(2018) , 10.1016/BS.AECR.2018.01.001

Miren Martínez-Santos, Anders Lanzén, Jessica Unda-Calvo, Iker Martín, Carlos Garbisu, Estilita Ruiz-Romera, Treated and untreated wastewater effluents alter river sediment bacterial communities involved in nitrogen and sulphur cycling. Science of The Total Environment. ,vol. 633, pp. 1051- 1061 ,(2018) , 10.1016/J.SCITOTENV.2018.03.229

Louise K J Nilsson, Anil Sharma, Raj K Bhatnagar, Stefan Bertilsson, Olle Terenius, Presence of Aedes and Anopheles mosquito larvae is correlated to bacteria found in domestic water-storage containers. FEMS Microbiology Ecology. ,vol. 94, ,(2018) , 10.1093/FEMSEC/FIY058