PeerJ Expert Curations: Molecular Ecology (Prof. Ana I. F. Ribeiro-Barros)

Ana I. F. Ribeiro-Barros, is a research professor at the School of Agriculture, University of Lisbon, and visiting professor at Madeira University (Portugal), Eduardo Mondlane University and Gorongosa National Park (Mozambique). Her scientific activity is focused on the characterization, conservation, monitoring and management of agro-forestry resources: molecular ecology; landscape genomics; biodiversity; environmental stress; plant microbiome; root symbiosis. Identifiers: Ciência Vitae – 081F-E3CE-9D52; ORCID – 0000-0002-6071-6460; Scopus – 35557486600; Google Scholar.

Molecular ecology offers an exclusive opportunity to zoom in and out the intricate dynamics of (interconnected) ecosystems, biomes, and ultimately, the evolutionary and adaptation processes underlying life on Earth. Through the integration of ecology, environmental and molecular sciences (lato sensu), scientific knowledge can unravel the mysteries of ecological (inter)relationships at several levels – from gene to landscape. Under the current scenario of climate crisis and anthropogenic pressure, molecular ecology constitutes one of the main pillars of Planetary Health. Indeed, species adaptation to permanently changing environments depends primarily on genetic variation and associated environmental fitness traits. This selection of papers, published in PeerJ Life and Environment, is a showcase of the contribution of molecular ecology for fundamental and applied research. The following categories are emphasized: biodiversity and biogeography, evolutionary biology, environmental DNA and metabarcoding, functional genomics and metagenomics, all with impact on conservation biology. To illustrate these categories, I have selected the following papers:

See the Expert Curation collection page here: https://peerj.com/collections/140-molecular-ecology

Molecular Ecology in PeerJ Life & Environment

Credit: Mathew Schwartz

Negro and colleagues (2020) combined molecular tools, trophic niche variables, and migration distances, to investigate the diversity of diurnal birds of prey (raptor species), associated with interspecific competition, migration, and speciation in Europe. The results revealed a unique hotspot of raptors, many of which are migratory. However, the authors highlight that the impact of climate change on bird ecology is already visible in some trans-Saharan species, which are becoming non-migratory in southern Europe, and in some African species, that are entering Europe. Such changes, will impose species competition and new conservation challenges.

Credit: Roy Buri

Hervé et al. (2020) unravel the genomes of major microbial taxa from the termite gut, producing the largest genomic resource for arthropod-associated microorganisms, and providing a milestone contribution to the tree of life. Their work constitutes a solid baseline towards the understanding of the metabolic potential of termite gut microbiota in biogeochemical cycles in tropical and sub-tropical regions where such studies are incipient.

Credit: Loren Cassin-Sackett (10.1002_ece3.7401)

Näpflin et al. (2019) performed a comprehensive study on evolutionary genomics to investigate links, patterns and potential trade-offs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. The authors concluded that, despite the success of genome-wide analysis, the co-evolutionary dynamics of single host-pathogen interactions is rare, and that the integration of geographical and evolutionary time scales as well as environmental complexities, are practically non-existent. This calls up for the need of a more uniform research strategy towards the understanding of the causes and consequences of host-pathogen interactions and the creation of a roadmap to mitigate the continuous threat of pathogens in a changing world.

Credit: Institute of Marine Research

Antarctic benthic ecosystems hold a rich, yet understudied, biological diversity, owing to their harsh environmental conditions and remoteness. In their work, Clarke and co-authors (2021), compared environmental DNA (eDNA) from water and sediment samples, through metabarcoding, to characterise metazoan communities, creating the foundations for future DNA-based biodiversity assessments for Antarctic nearshore environments.

Credit: Timothy K

Sui et al. (2023) comprehensively investigated the bacterial root microbiome of mangrove species, providing the first insights on the microbial composition, diversity, and associated functions, and contributing to the understanding of the complex biochemical and molecular crosstalk between plants, soil, and microbes in this important ecosystem.

Credit: Peter Prokosch (grida.no/resources/4619)

Corals are the foundation of reef ecosystems, which are seriously threaten due to raising sea temperatures. In the work from Williams et al. (2021) the authors used a multiomic approach, combining transcriptomics and metabolomics, to understand coral response to thermal stress and the impact of heat on their reproductive health. The study revealed a set of key molecules and pathways associated with early and late stages of stress, suggesting that ocean warming may negatively impact the reproductive behavior in this species and that gene editing may the key to boost resilience to thermal stress in the long term.

Literature Cited

Negro JJ, Rodríguez-Rodríguez EJ, Rodríguez A, Bildstein K. 2022. Generation of raptor diversity in Europe: linking speciation with climate changes and the ability to migrate. PeerJ 10:e14505 https://doi.org/10.7717/peerj.14505

Hervé V, Liu P, Dietrich C, Sillam-Dussès D, Stiblik P, Šobotník J, Brune A. 2020. Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites. PeerJ 8:e8614 https://doi.org/10.7717/peerj.8614

Näpflin K, O’Connor EA, Becks L, Bensch S, Ellis VA, Hafer-Hahmann N, Harding KC, Lindén SK, Olsen MT, Roved J, Sackton TB, Shultz AJ, Venkatakrishnan V, Videvall E, Westerdahl H, Winternitz JC, Edwards SV. 2019. Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales. PeerJ 7:e8013 https://doi.org/10.7717/peerj.8013

Clarke LJ, Suter L, Deagle BE, Polanowski AM, Terauds A, Johnstone GJ, Stark JS. 2021. Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ 9:e12458 https://doi.org/10.7717/peerj.12458

Sui J, He X, Yi G, Zhou L, Liu S, Chen Q, Xiao X, Wu J. 2023. Diversity and structure of the root-associated bacterial microbiomes of four mangrove tree species, revealed by high-throughput sequencing. PeerJ 11:e16156 https://doi.org/10.7717/peerj.16156

Williams A, Pathmanathan JS, Stephens TG, Su X, Chiles EN, Conetta D, Putnam HM, Bhattacharya D. 2021. Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata.PeerJ 9:e12335 https://doi.org/10.7717/peerj.12335