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Grand challenges in marine biogeochemistry / Eric P. Achterberg -- A statistical gap-filling method to interpolate global monthly surface ocean carbon dioxide data / Steve D. Jones, Corinne Le Quere, Christian Rodenbeck, Andrew C. Manning, and Are Olsen -- The seasonal sea-ice zone in the glacial southern ocean as a carbon sink / Andrea Abelmann, Rainer Gersonde, Gregor Knorr, Xu Zhang, Bernhard Chapligin, Edith Maier, Oliver Esper, Hans Friedrichsen, Gerrit Lohmann, Hanno Meyer, and Ralf Tiedemann -- On the influence of interseasonal sea surface temperature on surface water pCO2 at 49.0'n/16.5'w and 56.5'n/52.6'w in the north atlantic ocean / Nsikak U. Benson, Oladele O. Osibanjo, Francis E. Asuquo, and Winifred U. Anake -- Carbon export by small particles in the norwegian sea / Giorgio Dall'Olmo and Kjell Arne Mork -- Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump / S. Agusti, J.I. Gonzalez-Gordillo, D. Vaque, M. Estrada, M.I. Cerezo, G. Salazar, J.M. Gasol, and C.M. Duarte -- Carbon export efficiency and phytoplankton community composition in the atlantic sector of the Arctic Ocean / Frederic A.C. Le Moigne, Alex J. Poulton, Stephanie A. Henson, Chris J. Daniels, Glaucia M. Fragoso, Elaine Mitchell, Sophie Richier, Benjamin C. Russell, Helen E.K. Smith, Geraint A. Tarling, Jeremy R. Young, and Mike Zubkov -- Ocean warming-acidification synergism undermines dissolved organic matter assembly / Chi-Shuo Chen, Jesse M. Anaya, Eric Y-T Chen, Erik Farr, and Wei-Chun Chin -- Ocean acidification with (de)eutrophication will alter future phytoplankton growth and succession / Kevin J. Flynn, Darren R. Clark, Aditee Mitra, Heiner Fabian, Per J. Hansen, Patricia M. Glibert, Glen L. Wheeler, Diane K. Stoecker, Jerry C. Blackford, and Colin Brownlee -- Coccolithophore calcification response to past ocean acidification and climate change / Sarah A. O'Dea, Samantha J. Gibbs, Paul R. Bown, Jeremy R. Young, Alex J. Poulton, Cherry Newsam, and Paul A. Wilson -- Near-shore antarctic ph variability has implications for the design of ocean acidification experiments / Lydia Kapsenberg, Amanda L. Kelley, Emily C. Shaw, Todd R. Martz, and Gretchen E. Hofmann

13 pages, 2 figures, 4 tables ; Biological wastewater treatment processes are based on the exploitation of the concerted activity of microorganisms. Knowledge on the microbial community structure and the links to the changing environmental conditions is therefore crucial for the development and optimization of biological systems by engineers. The advent of molecular techniques occurred in the last decades quickly showed the inadequacy of culture-dependent methodologies to unveil the great level of diversity present in sludge samples. Initially, culture-independent technologies and more recently the application of –omics in wastewater microbiology, have drawn a new view of microbial diversity and function of wastewater treatment systems. This article reviews the current knowledge on the topic placing emphasis on crucial microbial processes carried out in biological wastewater treatment systems driven by specific groups of microbes, such as nitrogen and phosphorus removal bacteria, filamentous and electrogenic microorganisms, as well as Archaea. Despite the recent –omics has offered substantial insights into the diversity and ecophysiology of these bacteria never envisioned before by providing millions of sequence reads at an unprecedented scale, studies based on high-throughput sequencing are still scarce. In order to obtain significant gains in the analysis of structure–function relationships, a greater sequencing investment is needed, particularly to uncover gene expression patterns of functionally relevant genes ; Authors thank their institutions and lab colleagues for support. IF was supported by grant 308392 from the European Union's Seventh Framework Programme ; Peer Reviewed

[Background] Microbial fuel cells (MFCs) operating with complex microbial communities have been extensively reported in the past, and are commonly used in applications such as wastewater treatment, bioremediation or in-situ powering of environmental sensors. However, our knowledge on how the composition of the microbial community and the different types of electron transfer to the anode affect the performance of these bioelectrochemical systems is far from complete. To fill this gap of knowledge, we designed a set of three MFCs with different constrains limiting direct and mediated electron transfer to the anode. ; [Results] The results obtained indicate that MFCs with a naked anode on which a biofilm was allowed unrestricted development (MFC-A) had the most diverse archaeal and bacterial community, and offered the best performance. In this MFC both, direct and mediated electron transfer, occurred simultaneously, but direct electron transfer was the predominant mechanism. Microbial fuel cells in which the anode was enclosed in a dialysis membrane and biofilm was not allowed to develop (MFC-D), had a much lower power output (about 60% lower), and a prevalence of dissolved redox species that acted as putative electron shuttles. In the anolyte of this MFC, Arcobacter and Methanosaeta were the prevalent bacteria and archaea respectively. In the third MFC, in which the anode had been covered by a cation selective nafion membrane (MFC-N), power output decreased a further 5% (95% less than MFC-A). In this MFC, conventional organic electron shuttles could not operate and the low power output obtained was presumably attributed to fermentation end-products produced by some of the organisms present in the anolyte, probably Pseudomonas or Methanosaeta. ; [Conclusion] Electron transfer mechanisms have an impact on the development of different microbial communities and in turn on MFC performance. Although a stable current was achieved in all cases, direct electron transfer MFC showed the best performance concluding that biofilms are the major contributors to current production in MFCs. Characterization of the complex microbial assemblages in these systems may help us to unveil new electrogenic microorganisms and improve our understanding on their role to the functioning of MFCs. ; This work was partially funded by projects RTC-2016-5766-2, CTQ2014–54553-C3–2-R and CTQ2014–61809-EXP to JM from the Spanish Government, with participation of the European Regional Development Fund. ; Peer reviewed

[Background] Microbial fuel cells (MFCs) operating with complex microbial communities have been extensively reported in the past, and are commonly used in applications such as wastewater treatment, bioremediation or in-situ powering of environmental sensors. However, our knowledge on how the composition of the microbial community and the different types of electron transfer to the anode affect the performance of these bioelectrochemical systems is far from complete. To fill this gap of knowledge, we designed a set of three MFCs with different constrains limiting direct and mediated electron transfer to the anode. ; [Results] The results obtained indicate that MFCs with a naked anode on which a biofilm was allowed unrestricted development (MFC-A) had the most diverse archaeal and bacterial community, and offered the best performance. In this MFC both, direct and mediated electron transfer, occurred simultaneously, but direct electron transfer was the predominant mechanism. Microbial fuel cells in which the anode was enclosed in a dialysis membrane and biofilm was not allowed to develop (MFC-D), had a much lower power output (about 60% lower), and a prevalence of dissolved redox species that acted as putative electron shuttles. In the anolyte of this MFC, Arcobacter and Methanosaeta were the prevalent bacteria and archaea respectively. In the third MFC, in which the anode had been covered by a cation selective nafion membrane (MFC-N), power output decreased a further 5% (95% less than MFC-A). In this MFC, conventional organic electron shuttles could not operate and the low power output obtained was presumably attributed to fermentation end-products produced by some of the organisms present in the anolyte, probably Pseudomonas or Methanosaeta. ; [Conclusion] Electron transfer mechanisms have an impact on the development of different microbial communities and in turn on MFC performance. Although a stable current was achieved in all cases, direct electron transfer MFC showed the best performance concluding that biofilms are the major contributors to current production in MFCs. Characterization of the complex microbial assemblages in these systems may help us to unveil new electrogenic microorganisms and improve our understanding on their role to the functioning of MFCs. ; This work was partially funded by projects RTC-2016-5766-2, CTQ2014–54553-C3–2-R and CTQ2014–61809-EXP to JM from the Spanish Government, with participation of the European Regional Development Fund. ; Peer reviewed

7 pages, 1 figure ; Prokaryotes are extremely abundant in the ocean where they drive biogeochemical cycles. The recent development and application of - omics techniques has provided an astonishing amount of information revealing the existence of a vast diversity of functional genes and a large heterogeneity within each gene. The big challenge for microbial ecologists is now to understand the ecological relevance of this variability for ecosystem functioning, a question that remains largely understudied. This brief review highlights some of the latest advances in the study of the diversity of biogeochemically relevant functional genes in the sunlit ocean. © 2015 Elsevier Ltd. ; The author's work is partially supported by grants DEVOTES (FP7-ENV-2012-308392) and MICRO-3B (FP7-OCEAN-2011-287589) funded by European Union, grants HOTMIX (CTM2011-30010/MAR), DOREMI (CTM2012-34294) and PANGENOMICS (CGL2011-26848) funded by the Spanish Government, and grant XTM (2014SGR/1179) funded by the Catalan Government ; Peer Reviewed

Danovaro, Roberto . et al.-- 25 pages, 9 figures, 2 tables ; Marine environmental monitoring has tended to focus on site-specific methods of investigation. These traditional methods have low spatial and temporal resolution and are relatively labor intensive per unit area/time that they cover. To implement the Marine Strategy Framework Directive (MSFD), European Member States are required to improve marine monitoring and design monitoring networks. This can be achieved by developing and testing innovative and cost-effective monitoring systems, as well as indicators of environmental status. Here, we present several recently developed methodologies and technologies to improve marine biodiversity indicators and monitoring methods. The innovative tools are discussed concerning the technologies presently utilized as well as the advantages and disadvantages of their use in routine monitoring. In particular, the present analysis focuses on: (i) molecular approaches, including microarray, Real Time quantitative PCR (qPCR), and metagenetic (metabarcoding) tools; (ii) optical (remote) sensing and acoustic methods; and (iii) in situ monitoring instruments. We also discuss their applications in marine monitoring within the MSFD through the analysis of case studies in order to evaluate their potential utilization in future routine marine monitoring. We show that these recently-developed technologies can present clear advantages in accuracy, efficiency and cost ; This manuscript is a result of DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status) project, funded by the European Union under the 7th Framework Programme, "The Ocean of Tomorrow" Theme (grant agreement no. 308392) (http://www.devotes-project.eu). Further financial assistance was provided to VS and ER by the European Union under the ENPI CBC Mediterranean Sea Basin Programme (Sustainability and Tourism in the Mediterranean—S&T Med Strategic Project) ; Peer Reviewed

12 pages, 5 figures, 1 table, supplementary information https://doi.org/10.1038/s41396-021-01053-2 ; Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality ; This research was funded by grants REMEI (CTM2015-70340-R), MIAU (RTI2018-101025-B-I00), and ECLIPSE (PID2019-110128RB-I00) from the Spanish Ministry of Science and Innovation, by the Grup de Recerca de la Generalitat de Catalunya (2017SGR/1568) and received support from the Spanish government through the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S). Adrià Auladell was supported by a Spanish FPI grant and IF received the support of the Fundación BBVA through the 'Becas Leonardo a Investigadores y Creadores Culturales' 2019 Program ; Peer reviewed

16 pages, 6 figures, 2 tables ; Sequencing of rRNA gene polymerase chain reaction amplicons (rRNA tags) is the most common approach for investigating microbial diversity. The recent development of high-throughput sequencing (HTS) technologies has enabled the exploration of microbial biodiversity at an unprecedented scale, greatly expanding our knowledge on the microbiomes of marine ecosystems. These approaches provide accurate, fast, and cost efficient observations of the marine communities, and thus, may be suitable tools in biodiversity monitoring programs. To reach this goal, consistent and comparable methodologies must be used over time and within sites. Here, we have performed a cross-platform study of the two most common HTS methodologies, i.e., 454-pyrosequencing and Illumina tags to evaluate their usefulness in biodiversity monitoring and assessment of environmental status. Picoplankton biodiversity has been compared through both methodologies by sequencing the 16 and 18 S rRNA genes of a set of samples collected in the coast of Barcelona (NW Mediterranean). The results show that, despite differences observed in the rare OTUs retrieved, both platforms provide a comparable view of the marine picoplankton communities. On a taxonomic level, there was an accurate overlap in the detected phyla between the two methods and the overall estimates of alpha- and betadiversity were comparable. In addition, we explored the concept of "indicator species" and found that certain taxa (i.e., members of the Gammaproteobacteria among others) as well as the ratio between some phylogenetic groups (i.e., the ratio of Alphaproteobacteria/Gammaproteobacteria, Alteromonas/SAR11, and Alteromonas + Oceanospirillales/SAR11) have potential for being useful indicators of environmental status. The data show that implementing new protocols and identifying indicators of environmental status based on rRNA amplicon sequencing is feasible, and that is worth exploring whether the identified indices are universally applicable ; This manuscript is a result of DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing GEnS) project, funded by the European Union (grant agreement no. 308392), and a MINECO Grant GRADIENTS Fine-scale structure of cross-shore GRADIENTS along the Mediterranean coast (CTM2012-39476-C02) ; Peer Reviewed

Alberti, Adriana . et al.-- 20 pages, 6 figures, 2 tables ; A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems ; We thank the commitment of the following people and sponsors: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Government 'Investissements d'Avenir' programmes OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08), Agence Nationale de la Recherche, European Union FP7 (MicroB3/No.287589) and the U.S. National Science Foundation awards DEB-1031049, OCE-0623288, OCE-821374 and OCE-1019242 (to M.E.S. and R.S.) and OCE-1335810 (to R.S.). Additional funding was provided by Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS and by Japan Society for the Promotion of Science (JSPS)/KAKENHI (grant numbers 26430184, 16H06429, 16K21723 and 16H06437). We also thank the support and commitment of agnès b. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the Eléctricité de France (EDF) Foundation, Fondation pour la recherche sur la biodiversité (FRB), the Foundation Prince Albert II de Monaco, the Tara Foundation, its schooner and teams ; Peer Reviewed