Key Questions for Next-Generation Biomonitoring

Makiola, Andreas; Compson, Zacchaeus G.; Baird, Donald J.; Barnes, Matthew A.; Boerlijst, Sam P.; Bouchez, Agnès; Brennan, Georgina; Буш, А. А.; Canard, Elsa; Cordier, Tristan; Creer, Simon; Curry, R. Allen; David, Patrice; Dumbrell, Alex J.; Gravel, Dominique; Hajibabaei, Mehrdad; Hayden, Brian; Hoorn, Berry van der; Jarne, Philippe; Jones, J. Iwan; Karimi, Battle; Keck, François; Kelly, Martyn; Knot, Ineke E.; Krol, Louie; Massol, François; Monk, Wendy; Murphy, John M.; Pawłowski, Jan; Poisot, Timothée; Porter, Teresita M.; Randall, Kate C.; Ransome, Emma; Ravigné, Virginie; Raybould, Alan; Robin, Stéphane; Schrama, Maarten; Schatz, Bertrand; Tamaddoni‐Nezhad, Alireza; Trimbos, Krijn B.; Vacher, Corinne; Vasselon, Valentin; Wood, Susie; Woodward, Guy; Bohan, David

doi:10.3389/fenvs.2019.00197

Cited by 85 publications

(60 citation statements)

References 114 publications

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“…Here a word of caution is needed as scientists from around the world need to publish their findings to progress their careers and/or to obtain research funding. Managing large data sets and having access to global databases on climatic and soil information, is often a privilege for well-resourced research teams (in terms of bibliographic subscriptions, computing power and technical knowledge, and software 107,108 ). Given the diversity of global conditions (both scientific and environmental), data mobilization alone is not the solution and needs to be paired with the priority to have more national (and local) surveys across a large number of sites and with a deeper taxonomic level.…”

Section: Resultsmentioning

confidence: 99%

Blind spots in global soil biodiversity and ecosystem function research

et al. 2020

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Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.

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Section: Resultsmentioning

confidence: 99%

Blind spots in global soil biodiversity and ecosystem function research

et al. 2020

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“…Co-occurrence networks can be refined through filtering based on mathematical rules [e.g., probability of interaction (Morales-Castilla et al, 2015)], known phylogenetic relationships (Morales-Castilla et al, 2015), or trait matching (Compson et al, 2018(Compson et al, , 2019. By automating construction of networks and food webs, they can be linked to large biomonitoring datasets, providing new opportunities for complex, diagnostic development that will hopefully be more targeted and predictive than traditional bioindicators (Makiola et al, 2020) and, because networks provide taxa-free biodiversity estimates, will provide the potential for global indicator development [e.g., Essential Biodiversity Variables (Kissling et al, 2018)]. Furthermore, synergistic advancements will arise from merging occupancy modeling and machine learning approaches to create more robust ecological networks.…”

Section: Food Webs and Functional Genes: Connecting Biostructure To Ementioning

confidence: 99%

“…Collectively, these advancements will equip resource managers with powerful bioassessment tools for rapid, whole ecosystem assessments, as functional profiles can have much greater discriminatory power compared to taxonomic profiles, especially in cases where taxonomic profiles are highly variable (Turnbaugh et al, 2009;Huttenhower et al, 2012;Xu et al, 2014). Further, these advances will facilitate bioindicator development (Makiola et al, 2020), as tools capitalizing on the biostructure in a system-such ecological networks and heuristic food webs-can potentially provide higher resolution information that is more sensitive to environmental change and has a much wider breadth of application [e.g., estimating trophic position of heuristic food web members: (Compson et al, 2019)]. Finally, by linking DNA-based food webs to functional gene assessments, it will be possible to relate community and food web structure to ecosystem function at unprecedented spatial and temporal scales, enabling scientists to test global hypotheses arising from metacommunity theory (Leibold and Chase, 2017).…”

Section: Food Webs and Functional Genes: Connecting Biostructure To Ementioning

confidence: 99%

Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale

Compson¹,

McClenaghan²,

Singer³

et al. 2020

Front. Ecol. Evol.

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Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.

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“…Innovations in HTS, and, more specifically, DNA metabarcoding, enable accurate and cost-effective biodiversity assessments at a level of taxonomic coverage and precision previously unavailable (Ji et al, 2013;Clare, 2014;Deiner et al, 2017;Pawlowski et al, 2018;Bush et al, 2019;Makiola et al, 2020). Recent studies have used metabarcoding techniques to investigate the feeding ecology of carnivores (Shehzad et al, 2012;Torre et al, 2013;Walsh, 2015;Xiong et al, 2017), herbivores (Soininen et al, 2009;Czernik et al, 2013;Kartzinel et al, 2015;Coverdale et al, 2016;Iwanowicz et al, 2016;Erickson et al, 2017;Pansu et al, 2019), and omnivores (De Barba et al, 2014;Robeson et al, 2018; for a review see Sousa et al, 2019).…”

Section: Introductionmentioning

confidence: 99%