Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment

• Published in: Trends in microbiology (Regular ed.) 2024-08
• Main Authors: Cook, Lauren S.J., Briscoe, Andrew G., Fonseca, Vera G., Boenigk, Jens, Woodward, Guy, Bass, David
• Format: Article
• Language: English
• Subjects: bioindicator; biomonitoring; ecosystem; holobiome; indicator; microbiome
• ISSN: 0966-842X; 1878-4380; 1878-4380
• DOI: 10.1016/j.tim.2024.07.003

Microbes (bacteria, Archaea, microeukaryotes, and viruses) are highly diverse taxonomically and functionally in most environments, and as symbionts of other organisms.Microbes are represented in eDNA/eRNA samples largely by viable cells, reflecting close association between function and taxonomy at high spatial and temporal resolution, and offering a wealth of information for inferring biotic indices and bioindicators that remains largely untapped.Microbial environmental DNA and RNA (eNA) from signals from across the Tree of Life are complementary, capturing responses to stressors and ecological change at different spatial and temporal scales, and integrating the effects of change across the whole food web.Holobionts and microbial consortia represent ecological units which may be more sensitive indicators of ecosystem function and health than eNA signals solely based on individual species or environmental biodiversity. Microbial environmental DNA and RNA (collectively ‘eNA’) originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production. Microbial environmental DNA and RNA (collectively ‘eNA’) originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life app