Special Issue in the journal PeerJ Advancing the Environmental DNA and RNA Toolkit for Aquatic Ecosystem Monitoring and Management. Applications of nucleic acids-based methods for biodiversity monitoring have flourished in the past decade. Technological advances in DNA and RNA analyses have driven the development of increasingly rapid and cost-effective approaches to describing biological communities across biomes. The unprecedented detection of environmental DNA and RNA (eDNA/eRNA) in water, sediment, biofilm, or many other sample types can reveal critical information on the past and current status of aquatic communities. The recent wave of dedicated case-studies has shown applicability of eDNA/eRNA methods and their potential for mitigating anthropogenic pressure on our rapidly changing aquatic ecosystems. However, the immediate implementation of eDNA/eRNA tools is currently limited by the lack of best practice methods that enable adoption across governments, private and community sectors. This special issue will highlight exciting innovations in molecular approaches and recent practical solutions using fit-for-purpose eDNA/eRNA-based tools for monitoring and managing aquatic ecosystems, including applications in biosecurity, aquaculture, offshore exploration, monitoring and conservation of aquatic ecosystems. We welcome papers that focus on methodological developments: practical solutions around sampling, sample processing and analytical workflow as well as fit-for-purpose eDNA/eRNA-based monitoring tools, including field-deployable technologies that support point-of-need research or citizen science applications. Full submissions of accepted abstracts should be completed by September 30th, 2022. Authors that require more time should contact communities@peerj.com to request an extension.

Special Issue in the journal Freshwater Biology Interpreting environmental and evolutionary change in freshwater systems using DNA preserved in sediments. The recovery of the molecular information from aquatic sedimentary archives has shown its potential to reconstruct past changes in aquatic biodiversity caused by natural or human-induced environmental changes. In this special issue in the journal Freshwater Biology, we welcome papers using freshwater sedimentary DNA to answer ecological questions related to (i) the past diversity of lake biota - including micro- and macro- fauna and hydrophytes (ii) the effects of natural and anthropogenic-induced environmental changes (e.g., eutrophication, climate change, fire regime, invasive species) on biological communities and their evolution (iii) long-term biotic interactions within aquatic food webs (iv) long-term changes in the functions and metabolism of lake ecosystems. In addition, we welcome methodological papers still needed to ensure reliability of the sedimentary DNA to analyze past biological diversity. If you wish to submit your manuscript to this special issue, you need first to send an email to eric.capo@hotmail.fr and frpick@uOttawa.ca with an abstract and the list of authors. Submission deadline for manuscripts is 30 June 2022.

Special Issue in the journal Diversity Revealing the Puzzle of the Past through Ancient Biomolecules: From Wild to Tame Faunal Diversity. Starting four decades ago, the study of ancient biomolecules gave us the opportunity to disentangle the complexity of processes that shaped the ancient faunal diversity across millennia at an unprecedented molecular level. Studies addressing demographic dynamics, divergence and admixture among populations, determining probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species first used short mitochondrial DNA fragments, then eventually whole genomes, epigenomes, proteomes, and even lipids. However, even now, few studies explore the possibility of interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropic impact. In this Special Issue of Diversity we aim to bring the story of extinct and extant faunal diversity to life, from wild to domesticated populations, retrieved from subsurface and surface archaeological and palaeontological deposits, by analysing ancient biomolecules (DNA, proteins, lipids, and stable isotopes). The manuscripts should provide insight and present new challenges and perspectives on the spatio-temporal ancient faunal diversity within palaeoecological contexts. Deadline for manuscript submissions 30 April 2022.

Special Issue in the journal AIMS Microbiology Progress in paleomicrobial ecology research. Whereas several thousands of years ago humans already started to change the coastal landscape in many regions of the world, long-term records of microbial ecosystem changes caused by anthropogenic activities are limited and/or are restricted to documenting the minority of taxa that left behind diagnostic microscopic features and/or chemical fossils (lipid biomarkers) in sedimentary records. In addition, extracting and sequencing genetic signatures of past plankton preserved in aquatic sedimentary archives (i.e., sediment ancient DNA; sed aDNA) is rapidly gaining popularity. Paired with paleoenvironmental proxy data, analysis of ancient plankton DNA using molecular tools has shown to be an extremely promising approach in elucidating whole ecosystem responses (including members of the microbial loop that lack a fossil record) to natural Quaternary climate variability vs. more recent anthropogenic perturbations plus the role microbial communities have played in past biogeochemical cycling processes. Marine coastal sed aDNA records are still severely understudied especially from the tropics and there are several challenges to overcome before it is possible to take full advantage of the rapidly evolving field of sedimentary paleogenomics. For this special issue we welcome all contributions that involve the study of paleomicrobiomes preserved in sedimentary records from coastal marine environments as well as from marine influenced basins and terrestrial saline lakes. All manuscripts will be peer-reviewed before their acceptance for publication. The deadline for manuscript submission is 15 August 2022.