The Peruvian upwelling system is one of the most productive ecosystems in the ocean. Continuous upwelling of nutrient-rich water generates high primary production, supporting an efficient food web and leading to high fishery yields. An extensive oxygen minimum zone underlying the productive surface waters gives rise to high losses of fixed nitrogen via denitrification and anaerobic ammonium oxidation. This results in nutrient ratios of upwelled waters deviating strongly from Redfield stoichiometry, with a high N deficit and excess P. How this unusual nutrient stoichiometry affects plankton community production and succession and how this feeds back on biogeochemical cycling are still not well understood. To address these questions, an in situ mesocosm experiment was conducted in the coastal upwelling system off Peru in the framework of the Collaborative Research Center 754 "Climate-Biogeochemistry Interactions in the Tropical Ocean". The field experiment took place from January to April 2017 during a coastal El Niño, a rare event of El Niño conditions confined to Peruvian coastal waters. Key objectives of this mesocosm study, which involved 57 researchers from 10 nations, were to unravel the interplay of pelagic ecology and biogeochemistry under the unique environmental conditions of the Peruvian upwelling system. This special issue in Biogeosciences is intended as a collective outlet for publications resulting from this study, covering the broad range of research topics from seawater chemistry to plankton ecology and pelagic biogeochemistry.

The last 50 years have enabled significant progress in our ability to describe and model both the oceanic and atmospheric environments of the Indian Ocean and their interactions with the sea floor and coastal regimes. However, our understanding of the major processes of the Indian Ocean is still far from complete and is rudimentary in many respects. This SI compiles various synthesis articles about the recent results of the 2nd International Indian Ocean Expedition Program (IIOE-2: https://iioe-2.incois.gov.in/). The synthesis articles will review and highlight results of physical, biogeochemical, ecological, geological, coastal and atmospheric studies from all parts of the Indian Ocean. Moreover, the SI will serve to illustrate some of the key questions that are relevant for future research on the grand challenges in the Indian Ocean system.

In the vast low-nutrient—low-chlorophyll (LNLC) ocean, the vertical nutrient supply from the subsurface to the sunlit surface waters is low, and atmospheric contribution of nutrients may be 1 order of magnitude greater over short timescales. Recently, significant experimental, field and modeling work allowed us to better link atmospheric deposition with nutrient availability, ocean productivity, carbon cycling and marine emissions. By improving our understanding on how atmospheric inputs are impacting biological activity and the carbon balance in oligotrophic environments, their representation in biogeochemical models at different timescales and space scales will be better assessed. In particular, processes may be affected by ongoing environmental changes in the ocean such as a decrease in pH and an increase in temperature.

This special issue aims at gathering contributions from both experimental and modeling approaches showing how natural or anthropogenic inputs from the atmosphere can impact biogeochemical and ecological processes in the present and future oligotrophic ocean. It will present the results obtained during the PEACETIME (ProcEss studies at the Air-sEa Interface after dust deposition in the MEditerranean sea) cruise conducted in 2017 in the Mediterranean Sea, but the special issue is open to any submissions provided that the subject is consistent with the objectives defined above.

The distribution of oxygen in the ocean is controlled by physical, biogeochemical and biological processes. Both the supply and consumption of oxygen are sensitive to climate change in ways that are not fully understood. Recent observations suggest that the oxygen content of the ocean is declining (ocean deoxygenation) and the oxygen minimum zones and costal hypoxia sites are expanding with tremendous effects on the ocean’s ecosystems and living organisms. Following the EUR-OCEANS conference on “Ocean Deoxygenation” in Toulouse, France, in 2011, the 46th International Liège Colloquium on “Low Oxygen Environments in Marine, Fresh and Estuarine Waters” in 2014 and the discussion meeting of the Royal Society London on “Ocean Ventilation and Deoxygenation in a Warming World” in 2016, the purpose of the international conference on “Ocean Deoxygenation: Drivers & Consequences – Past|Present|Future” that took place in Kiel, 3–7 Sept 2018 organised by the Collaborative Research Centre 754 “Climate-Biogeochemical Interactions in the Tropical Ocean” was to − focus on the past, present and future state of oxygen in the ocean on global, regional and local scales − analyse mechanisms and feedbacks critical to identify natural and anthropogenic causes of oxygen variability − determine impacts on biogeochemical cycles and ecosystems.

This special issue is open to all submissions on ocean deoxygenation and is not limited to conference participants.

Purpose of special issue: The Collaborative Research Centre 754 “Climate-Biogeochemical Interactions in the Tropical Ocean” has been investigating the newly recognised threat of ocean deoxygenation since 2008. Before the project's end in 2019, the International Conference on Ocean Deoxygenation was organised in Kiel, Germany in September 2018 with over 300 participants (https://conference.sfb754.de/event/1/). Following the conference the proposed inter-journal special issue aims at presenting the recent research advances and highlights in the field of ocean deoxygenation. The special issue shall not be limited to conference participants but be open to all submissions.