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10 pages, 6 figures, 1 table. ; The planktonic archaeal assemblages of several anaerobic, sulfide-rich, aquatic environments were analyzed in space and time by PCR-denaturing gradient gel electrophoresis and sequencing of 16S rRNA gene fragments. The systems were sampled in different years between 1992 and 1998. PCR products were obtained directly from the original DNA without previous nested amplification and yielded successful fingerprints with mostly sharp bands in the gel. Nineteen samples from the anaerobic hypolimnia of 8 lakes and 1 coastal lagoon in NE Spain, Mallorca and Switzerland were compared and a temporal survey was carried out in one of the lakes (Lake Vilar). Between 4 and 14 well-defined bands appeared. All the sequenced bands belonged to Archaea. Although most of the water bodies shared the same climatic conditions and presence of sulfide, the limnological parameters were different among them and different fingerprints were observed in different lakes. Euryarchaeota, i.e., methanogen- and thermoplasma-related sequences, appeared in all the samples but crenarchaeota were recovered only from Lake Vilar. A temporal shift in the predominant members of the archaeal assemblage from crenarchaeota to members of the cluster of thermoplasmales and relatives took place in Lake Vilar between February and June. Sequences related to thermoplasmales and crenarchaeota were distantly related to cultured strains (81% similarity in 16S rDNA) and clustered with branches represented only by environmental clones, whereas sequences related to methanogens grouped with a sequence from an endosymbiont of 1 anaerobic ciliate. A new branch of freshwater euryarchaeota appeared within the cluster of thermoplasmales and relatives. Our study indicates the presence of dynamic archaeal populations in the water column of nonthermophilic, sulfide-rich environments, further extending the diversity and distribution of Archaea in nature. The temporal shift in community composition in Lake Vilar suggests that Archaea grow under in situ conditions. If this is the case, Archaea would be active players in the anaerobic biogeochemical cycles of these environments ; This work was financed by the Max Planck Society in Germany, by DGICyT grant number PB95-0222 from the Spanish Ministerio de Educación y Cultura and by project MIDAS (Microbial Diversity in Aquatic Systems, MAS3-CT97-0154) from the European Union. ; Peer reviewed

13 pages, 8 figures, 3 tables ; The microbial assemblages of Petit Saut reservoir and Sinnamary river (French Guiana, South America) were analyzed by biochemical analyses (pigments and specific fatty acids), and by polymerase chain reaction (PCR) denaturing gradient gel electrophoresis (DGGE) and sequence analysis of 16S rRNA gene fragments. Samples from a vertical profile in the reservoir and from a longitudinal profile downstream of the dam were analyzed and compared to a reference sample taken in the river, upstream of the reservoir. The distribution of bacterial populations could be explained by the physico-chemical conditions of the water and the hydrodynamics induced by the hydroelectric plant. Two bacterial Œbio-filters¹ were detected by biochemical analyses: methanotrophs at the oxycline level and phototrophic green sulfur bacteria below the oxycline. A statistical analysis of the DGGE fingerprints obtained for each sample showed that the different stations could be related in a dendrogram in good agreement with their geographic location. We detected 53 bands in the bacterial DGGE fingerprints and 3 bands in the archaeal DGGE. The phylogenetic affiliation of the predominant DGGE bands was inferred by a comparative 16S rDNA partial sequence analysis (450 to 500 base pairs). Sequences obtained from the reservoir and the river were related to Proteobacteria (α, β, and γ), Cyanobacteria, green sulfur bacteria, Cytophaga, Methanomicrobiaceae and Thermoplasmales. Thus, methanotrophs and green sulfur bacteria were detected, and bacteria involved in the iron biogeochemical cycle were also shown to be dominant. The 16S rDNA-based analysis indicated that new bacterial and archaeal lineages, not detected upstream of the dam, were present in the reservoir and that the microbial diversity of these assemblages was greater than previously described by biochemical analyses. Our data provide evidence that the former bacterial assemblage was completely modified by the impounding of the reservoir, in agreement with the different biogeochemical cycles established. Minor groups of bacteria became dominant in the reservoir while others disappeared, in adaptation to the new conditions induced by flooding of rain forest ; We thank sincerely all the staff of Petit Saut Laboratory for help, and technical and human support. We are also grateful to EDF/CNEH for financial support, and particularly to Chantal Sissakian. Parts of this work were also funded by project MIDAS (Microbial Diversity in Aquatic Systems, MAS3-CT97-0154) from the European Union. We also thank Professor Louis Labroue for starting this project and Mrs Yvette Durand for managing the administrative part of the project with virtuosity ; Peer reviewed

8 pages, 2 figures, 4 tables ; The present study assesses the contribution of dark carbon fixation to the primary production in the oxic/anoxic interface of a shallow estuarine environment that develops a salt-water wedge with the presence of sulfide. Primary production was partitioned into oxygenic photosynthesis, anoxygenic photosynthesis and dark fixation. The results show the importance of dark fixation in the oxic/anoxic interface with values higher than 5 mg carbon fixed per cubic meter and per hour in some cases. The average rate of primary production in the dark during the anoxic season for the Ebro River salt wedge resulted in 42 mg C m-2 d-1 in the interface. This represents at least twice the contribution of oxygenic photosynthesis to the primary production in such interface. Because this process is probably important in other salt-wedge or highly stratified estuaries with oxic/anoxic interfaces containing sulfide, the estimates of carbon fixation made so far for these systems may have been underestimated, and should therefore be revised taking into account the contribution of dark processes ; This work was financed by DGICyT grant PB87-0183 from the Spanish Ministerio de Educación y Ciencia. J.G.-C. was supported by a FPI scholarship from the Spanish Ministerio de Educación y Ciencia. During the writing of this work, E.O.C. was supported by MIDAS (MIcrobial Diversity in Aquatic Systems, MAS3-CT97-0154) from the European Union ; Peer reviewed

16 pages, 5 figures, 3 tables, supplementary information https://doi.org/10.1186/s12866-020-01884-7 ; Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths ; Projects Arctic Tipping Points (ATP, contract #226248), in the FP7 program of the European Union, and DOREMI (CTM2012–34294), from the Spanish Ministry of Economy and Competitiveness, allowed the collection of samples from the Arctic and NW Mediterranean Sea, respectively. Research, including laboratory experiments and analyses, was mainly funded by grant BIOSENSOMICS "Convocatoria 2015 de ayudas Fundación BBVA a investigadores y creadores culturales" and, MAGGY, Plan Nacional I + D + I 2017 (CTM2017–87736-R), awarded to S.G.A. Analyses were also possible thank to the King Abdullah University of Science and Technology (KAUST) through baseline funding to C.M.D. and a subaward agreement OSR-2014-CC-1973-02 between KAUST and Universitat Autònoma de Barcelona (UAB). Additional funding for analyses and interpretation of the data was provided by projects REMEI (ref. CTM2015–70340-R) and MIAU-S3 (ref. RTI2018-101025-B-I00) from the Spanish Ministry of Economy and Competitiveness

6 pages, 4 figures, 1 table.-- PMID: 18552178 [PubMed].-- Supporting information available at: http://www.pnas.org/content/105/25/8724/suppl/DCSupplemental ; Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO2 fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling. Copyright © 2008 National Academy of Sciences ; This work was supported by the European Union (contract EU-FP6-505403NoE Marine Genomics Europe), the Spanish Ministry of Education and Science (Grant CTM2004-02586/MAR), and the Swedish Research Council (Grant 621-2003-2692) ; Peer reviewed

14 pages, 6 figures, additional information https://doi.org/10.1038/s41564-021-00979-9.-- Data availability: Accession numbers for the data used and generated in this study can be found in Supplementary Table 12, which includes the Arctic MAGs Catalogue and their functional annotation (European Bioinformatics Institute BioStudies ID: S-BSST451) and the co-assembly of metagenomic samples used to generate the metagenomic bins (European Nucleotide Archive PRJEB41575). Accession numbers for the metagenomic and metatranscriptomic samples used in the fragment recruitment analyses can be found in Supplementary Table 13. Publicly available datasets used in this study include the following: CheckM v.1.0.11 (https://github.com/Ecogenomics/CheckM/releases/tag/v1.1.0), GTDB release 89 (https://data.gtdb.ecogenomic.org/releases/release89/), SILVA 132 (https://www.arb-silva.de/documentation/release-132/), KEGG release 89.1 (https://www.genome.jp/kegg/docs/relnote.html) and Pfam database release 31.0 (http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/). Source data are provided with this paper ; The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles ; This work acknowledges the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S). We thank the commitment of the following sponsors and research funding agencies: the Spanish Ministry of Economy and Competitiveness (project MAGGY, grant no. CTM2017-87736-R and Polar EcoGen PID2020-116489RB-I00), Horizon 2020-Research and Innovation Framework Programme (Atlantic ECOsystems assessment, forecasting & sustainability, grant no. H2020-BG-2019-2), Centre National de la Recherche Scientifique (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory, Genoscope/Commissariat à l'Énergie Atomique et aux Énergies Alternatives, the French Ministry of Research and the French Government's 'Investissements d'Avenir' programmes OCEANOMICS (project no. ANR-11-BTBR-0008), FRANCE GENOMIQUE (project no. ANR-10-INBS-09-08), MEMO LIFE (project no. ANR-10-LABX-54), Paris Sciences et Lettres University (project no. ANR-11-IDEX-0001-02), Eidgenössische Technische Hochschule Zürich and Helmut Horten Foundation, the Swiss National Foundation (project no. 205321_184955), MEXT/JSPS/KAKENHI (project nos. 16H06429, 16K21723, 16H06437 and 18H02279) ; Peer reviewed

AbstractThe deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem. ; We thank the R/V Hespérides captain and crew, the chief scientists in Malaspina expedition legs, and all project participants for their help in making this project possible. This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio program (Malaspina 2010 Expedition, ref. CSD2008-00077). The sequencing of 58 bathypelagic metagenomes was done by the U.S. Department of Energy Joint Genome Institute, supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02 05CH11231 to SGA (CSP 612 "Microbial metagenomics and transcriptomics from a global deep-ocean expedition"). Additional funding was provided by the project MAGGY (CTM2017-87736-R) to S.G.A. from the Spanish Ministry of Economy and Competitiveness, Grup de Recerca 2017SGR/1568 from Generalitat de Catalunya, and King Abdullah University of Science and Technology (KAUST) under contract OSR #3362 and by funding of the EMFF Program of the European Union (MERCLUB project, Grant Agreement 863584). The ICM researchers have had the institutional support of the "Severo Ochoa Centre of Excellence" accreditation (CEX2019-000928-S). High-Performance computing analyses were run at the Marine Bioinformatics Service (MARBITS, https://marbits.icm.csic.es) of the Institut de Ciències del Mar (ICM-CSIC), Barcelona, Supercomputing Center (Grant BCV-2013-2-0001) and KAUST's Ibex HPC. We thank Shook Studio for assistance with figure design and implementation and the anonymous reviewers for their comments to improve this manuscript. This paper is dedicated to the memory of Professor Vladimir B. Bajic, 2019.

15 pages, 7 figures, supplementary information https://doi.org/10.1038/s42003-021-02112-2.-- All data generated or analyzed during this study are included in this published article (and its supplementary information files). All raw sequences are publicly available at both DOE's JGI Integrated Microbial Genomes and Microbiomes (IMG/MER) and the European Nucleotide Archive (ENA). Individual metagenome assemblies, annotation files, and alignment files can be accessed at IMG/MER. All accession numbers are listed in Supplementary Data 1. The co-assembly for the MAG dataset construction can be found through ENA at https://www.ebi.ac.uk/ena with accession number PRJEB40454, the nucleotide sequence for each MAG and their annotation files can be found through BioStudies at https://www.ebi.ac.uk/biostudies with accession S-BSST457 and also in the companion website to this manuscript at https://malaspina-public.gitlab.io/malaspina-deep-ocean-microbiome/.-- All software used in this work is publicly available distributed by their respective developers, and it is described in "Methods", including the versions and options used. Additional custom scripts to assign taxonomy to the M-geneDB genes and to filter and format FRA results are available through BioStudies at https://www.ebi.ac.uk/biostudies with accession S-BSST457 ; The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem ; This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio program (Malaspina 2010 Expedition, ref. CSD2008-00077). The sequencing of 58 bathypelagic metagenomes was done by the U.S. Department of Energy Joint Genome Institute, supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02 05CH11231 to SGA (CSP 612 "Microbial metagenomics and transcriptomics from a global deep-ocean expedition"). Additional funding was provided by the project MAGGY (CTM2017-87736-R) to S.G.A. from the Spanish Ministry of Economy and Competitiveness, Grup de Recerca 2017SGR/1568 from Generalitat de Catalunya, and King Abdullah University of Science and Technology (KAUST) under contract OSR #3362 and by funding of the EMFF Program of the European Union (MERCLUB project, Grant Agreement 863584). The ICM researchers have had the institutional support of the "Severo Ochoa Centre of Excellence" accreditation (CEX2019-000928-S). High-Performance computing analyses were run at the Marine Bioinformatics Service (MARBITS, https://marbits.icm.csic.es) of the Institut de Ciències del Mar (ICM-CSIC), Barcelona, Supercomputing Center (Grant BCV-2013-2-0001) and KAUST's Ibex HPC ; Peer reviewed