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Microbiomes of open water and coastal pelagic environments

Guest Editors:
Professor Connie Lovejoy, BSc, PhD, Université Laval, Québec,
Professor Joy Watts, PhD, University of Portsmouth, UK

Submission Status: Closed |   Submission Deadline: Closed

This collection is no longer accepting submissions

Microbiome and Environmental Microbiome are calling for submissions to our Collection on Microbiomes of open water and coastal pelagic environments. 

The aim of the collection is bringing together research on open water and coastal pelagic environments.  Given the technological and bioinformatics advancements, combined with recent and ongoing global sampling efforts across oceans and coastal aquatic systems, a focused collection on marine pelagic microbiomes is needed.

Meet the Guest Editors

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Connie Lovejoy: Université Laval, Canada

Dr Connie Lovejoy research is mainly focused on integrative biology using genomics, transcriptomics and bioinformatics, applied to environmental microbiology. The goal is to understand where and how the microbial communities of oceans and smaller bodies of water interact with global energy and nutrient cycles. She has specific oceanic projects in the Arctic Ocean and the North Atlantic, her freshwater research has been focused on ponds and lakes of Northern Québec and Ellesmere Island. This research is possible because of affiliations with ArcticNet, Québec Ocean, Centre d’Études Nordiques and the CNRS Unité Mixte Internationale- Takuvik. Other international projects led by her team include genomic and transcriptomics of five chromist algae from the Arctic Ocean.

Joy Watts: University of Portsmouth, UK

Dr Joy Watts is Associate Dean for Research and Innovation and a Professor of Environmental Microbiology with her research focusing upon the application of molecular tools to understand the microbial diversity and important interactions that can degrade recalcitrant organic compounds, such as lignin. This includes diversity and function of microbes associated with the GI tracts of wood eating organisms, detection of antimicrobial resistance in aquaculture and marine systems. She has active expert panel roles for the European Commission Horizon 2020 programme, is an editorial board member for journals, including Nature Scientific Reports, is Editor-in-Chief for Environmental Microbiome, and is an advisor for the Marine Microbiome Policy Report. With a funding track record from the European Commission, NERC and Innovate UK.


About the collection

Microbiome and Environmental Microbiome are calling for submissions to our Collection on Microbiomes of open water and coastal pelagic environments.

The aim of the collection is bringing together research on open water and coastal pelagic environments. Given the technological and bioinformatics advancements, combined with recent and ongoing global sampling efforts across oceans and coastal aquatic systems, a focused collection on marine pelagic microbiomes is needed.    

Oceans cover 70% of the planet and the microbial communities have a dominant role in global carbon, nitrogen, phosphorus and sulfur cycles.  Microbes associated with sinking organic matter also ensure a more rapid remineralisation of silica and other elements. While phytoplankton are the main agents for fixing inorganic carbon and support higher trophic levels in the marine ecosystem, they also have effectively drawn down anthropogenic CO2 from the atmosphere, which can eventually sink to deeper waters. This fixed carbon has been a carbon sink since the beginning of the Anthropocene. The net effect of oceanic carbon sequestration is dependent on the structure and complexity of planktonic marine microbiomes. Global marine waters are a myriad of niches that are evident from the surface to the deep sea, and across latitudes and longitudes. In addition, complex atmospheric and terrestrial teleconnections influence, nutrients, temperature, light and oxygen, all of which select for microbial consortia. 

The collection will consider new research and invited reviews investigating microbiomes of, for example, regional seas, depth strata in the ocean, and coastal interfaces. The central focus of the microbiomes could also include, phytoplankton, heterotrophic protists, bacteria, archaea and viruses.

This Collection supports and amplifies research related to SDG14.

Image credit: © katatonia82 / Getty

  1. Plastic pollution is a severe threat to marine ecosystems. While some microbial enzymes can degrade certain plastics, the ability of the global ocean microbiome to break down diverse environmental plastics rem...

    Authors: Victor Gambarini, Cornelis J. Drost, Joanne M. Kingsbury, Louise Weaver, Olga Pantos, Kim M. Handley and Gavin Lear
    Citation: Environmental Microbiome 2024 19:34
  2. Aerobic anoxygenic phototrophs are metabolically highly active, diverse and widespread polyphyletic members of bacterioplankton whose photoheterotrophic capabilities shifted the paradigm about simplicity of th...

    Authors: Iva Stojan, Danijela Šantić, Cristian Villena-Alemany, Željka Trumbić, Frano Matić, Ana Vrdoljak Tomaš, Ivana Lepen Pleić, Kasia Piwosz, Grozdan Kušpilić, Živana Ninčević Gladan, Stefanija Šestanović and Mladen Šolić
    Citation: Environmental Microbiome 2024 19:28
  3. Understanding the characteristics and structure of populations is fundamental to comprehending ecosystem processes and evolutionary adaptations. While the study of animal and plant populations has spanned a fe...

    Authors: Ramiro Logares
    Citation: Microbiome 2024 12:67
  4. Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytopl...

    Authors: Feng-Qing Wang, Daniel Bartosik, Chandni Sidhu, Robin Siebers, De-Chen Lu, Anke Trautwein-Schult, Dörte Becher, Bruno Huettel, Johannes Rick, Inga V. Kirstein, Karen H. Wiltshire, Thomas Schweder, Bernhard M. Fuchs, Mia M. Bengtsson, Hanno Teeling and Rudolf I. Amann
    Citation: Microbiome 2024 12:32
  5. Coastal ecosystem variability at tropical latitudes is dependent on climatic conditions. During the wet, rainy season, extreme climatic events such as cyclones, precipitation, and winds can be intense over a s...

    Authors: M. Meyneng, H. Lemonnier, R. Le Gendre, G. Plougoulen, F. Antypas, D. Ansquer, J. Serghine, S. Schmitt and R. Siano
    Citation: Environmental Microbiome 2024 19:10
  6. Marine bacterioplankton underpin the health and function of coral reefs and respond in a rapid and sensitive manner to environmental changes that affect reef ecosystem stability. Numerous meta-omics surveys ov...

    Authors: Marko Terzin, Patrick W. Laffy, Steven Robbins, Yun Kit Yeoh, Pedro R. Frade, Bettina Glasl, Nicole S. Webster and David G. Bourne
    Citation: Environmental Microbiome 2024 19:5
  7. Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecos...

    Authors: Wenchao Deng, Zihao Zhao, Yufang Li, Rongguang Cao, Mingming Chen, Kai Tang, Deli Wang, Wei Fan, Anyi Hu, Guangcheng Chen, Chen-Tung Arthur Chen and Yao Zhang
    Citation: Microbiome 2023 11:270
  8. The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genom...

    Authors: Yanting Liu, Thorsten Brinkhoff, Martine Berger, Anja Poehlein, Sonja Voget, Lucas Paoli, Shinichi Sunagawa, Rudolf Amann and Meinhard Simon
    Citation: Microbiome 2023 11:265
  9. Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for ene...

    Authors: Abhishek Srivastava, Daniele De Corte, Juan A. L. Garcia, Brandon K. Swan, Ramunas Stepanauskas, Gerhard J. Herndl and Eva Sintes
    Citation: Microbiome 2023 11:239
  10. Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processe...

    Authors: Pavla Debeljak, Barbara Bayer, Ying Sun, Gerhard J. Herndl and Ingrid Obernosterer
    Citation: Microbiome 2023 11:187
  11. Hadal trenches (>6000 m) are the deepest oceanic regions on Earth and depocenters for organic materials. However, how these enigmatic microbial ecosystems are fueled is largely unknown, particularly the propor...

    Authors: Xiao-Yu Zhu, Yang Li, Chun-Xu Xue, Ian D. E. A. Lidbury, Jonathan D. Todd, David J. Lea-Smith, Jiwei Tian, Xiao-Hua Zhang and Jiwen Liu
    Citation: Microbiome 2023 11:175
  12. Marine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutr...

    Authors: Aleix Obiol, David López-Escardó, Eric D. Salomaki, Monika M. Wiśniewska, Irene Forn, Elisabet Sà, Dolors Vaqué, Martin Kolísko and Ramon Massana
    Citation: Microbiome 2023 11:134
  13. Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, the...

    Authors: Adrien Vigneron, Perrine Cruaud, Connie Lovejoy and Warwick F. Vincent
    Citation: Microbiome 2023 11:104

Submission Guidelines

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This Collection welcomes submission of Research Articles. Before submitting your manuscript, please ensure you have read the submission guidelines of the journal you are submitting to Microbiome and Environmental Microbiome. Articles for this Collection should be submitted via our submission system, Snapp Microbiome and Environmental Microbiome. During the submission process you will be asked whether you are submitting to a Collection, please select Microbiomes of open water and coastal pelagic environments from the dropdown menu.

Articles will undergo the standard peer-review process of the journal they are considered in Microbiome, Environmental Microbiome and are subject to all of the journal’s standard policies. Articles will be added to the Collection as they are published. The Guest Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Guest Editors have competing interests is handled by another Editorial Board Member who has no competing interests.