The microbial ocean from genomes to biomes

Genome sequencing in microfabricated high-density picolitre reactors

Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693

The human microbiome project

Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091

Environmental genome shotgun sequencing of the sargasso sea

Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376

Real-Time DNA Sequencing from Single Polymerase Molecules

Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., et al. (2009) · Science · doi:10.1126/science.1162986 · Cited by 3,732

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R. L., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565

Isolation of an autotrophic ammonia-oxidizing marine archaeon

Könneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., & Stahl, D. A. (2005) · Nature · doi:10.1038/nature03911 · Cited by 2,864

A Molecular View of Microbial Diversity and the Biosphere

Pace, N. R. (1997) · Science · doi:10.1126/science.276.5313.734 · Cited by 2,797

Community structure and metabolism through reconstruction of microbial genomes from the environment

Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

Rusch, D. B., Halpern, A. L., Sutton, G. G., Heidelberg, K. B., Williamson, S. J., Yooseph, S., Wu, D., Eisen, J. A., Hoffman, J., Remington, K., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050077 · Cited by 2,044

The Uncultured Microbial Majority

Rappé, M. S., & Giovannoni, S. J. (2003) · Annual Review of Microbiology · doi:10.1146/annurev.micro.57.030502.090759 · Cited by 2,017

Exploring the biodiversity of anammox in Atlantis II and Kebrit brine pools' interfaces

Farag, I. (2012)

Fine-Grained Bacterial Compositional Analsysis of the Port Everglades Inlet (Broward County, FL) Microbiome using High Throughput DNA Sequencing

O’Connell, L. M. (2015) · NSUWorks (Nova Southeastern University)

Bioinformatic approaches for new insights into old marine metagenomic data sets

Magasin, J. D. (2016) · eScholarship (California Digital Library)

RNA based research – development, application and analysis within the MIMAS project

Klindworth, A. (2012) · Max Planck Digital Library

Microbial community dynamics of a coastal Alabama salt marsh impacted by the deepwater horizon oil spill

Rajan, S. (2015)

Linking photochemical carbon transformations and microbial responses in the Amazon River plume

Green, J. L. (2013)

Peer Review #1 of "Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China (v0.2)"

(2018) · PeerJ · doi:10.7287/peerj.6042v0.2/reviews/1

Bottom-up Drivers of Bacterial Community Composition and Metabolism of Dissolved Organic Carbon in the Santa Barbara Channel, CA

Wear, E. K. (2017) · eScholarship (California Digital Library)

Machine learning prediction in genomic sequences of prokaryotic viruses from metagenomic datasets

Amgarten, D. (2022) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.95.2022.tde-17022022-091454

Peer Review #2 of "Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China (v0.1)"

(2018) · PeerJ · doi:10.7287/peerj.6042v0.1/reviews/2

Astrobiology

McSWEEN, H. Y., Jr., Moersch, J. E., Burr, D. M., Dunne, W. M., Emery, J. P., Kah, L. C., & McCanta, M. C. (2019) · Cambridge University Press eBooks · doi:10.1017/9781316535769.017

CLASSIFICATION OF EPIPHYTE BACTERIA FOUND IN COTTON PLANT IN UZBEKISTAN

O'.Xayitova, A. E. (2022) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.7410737

Co-culture 13C-metabolic flux analysis: a novel approach to elucidate the metabolism of multi-microorganism systems

Gebreselassie, N. A. (2024) · Library, Museums and Press - UDSpace (University of Delaware) · doi:10.58088/zka9-qv33

Deep CCZ Biodiversity Synthesis Workshop Friday Harbor, Washington, USA, 1-4 October 2019.

(ISA), I. S. A. (2019) · Institutional Archive of Ifremer (French Research Institute for Exploitation of the Sea)

Evolutionary Ecology Of Ribosomal Rna Copy Number: Studies In Soil Prokaryote And Nematode Communities

Williamson, M. R. (2019) · UND Scholarly Commons (University of North Dakota)

Bioinformatic investigations in marine microbial ecology

Heller, P. (2014) · eScholarship (California Digital Library)

Biodiversity and Seasonality of Endophytic Fungi Associated with Six Aquatic Macrophytes Collected from the Nile River System (Assiut, Upper Egypt)

Gaber, F. E.-Z., Khallil, A.-R. M., Hassan, E. A., & Mahmoud, G. A. (2025) · Assiut University Journal of Multidisciplinary Scientific Research · doi:10.21608/aunj.2025.417337.1140

Geographical distribution and driving force of microbial communities in different trenches

Zhang, Y., Wang, P., & Jing, H. (2026) · Ecological Indicators · doi:10.1016/j.ecolind.2026.114667

Understanding environmental and anthropogenic factors affecting dinoflagellate communities in the Black and Caspian seas

Perez, M. S. (2021) · Bristol Research (University of Bristol)

Approches multifactorielles pour l’étude d’interactions entre l’huître creuse Crassostrea gigas et deux Vibrio pathogènes, V. splendidus et V. aestuarianus : épidémiologie, variabilité de la sensibilité de l’hôte et pathogenèse

Decker, S. D. (2010) · theses.fr (ABES) · doi:10.70675/64d01b64z53acz44e5z9655zb70c01b648b6

Étude des communautés microbiennes (bactéries, archaea et eucaryotes) et de leurs variations spatiotemporelles dans la mine de Carnoulès fortement contaminée en arsenic

Volant, A. (2012) · theses.fr (ABES) · doi:10.70675/b823dcb0z92dfz413fza2cfz8c4d84949fb4

Dynamique de la structure des génomes et de leur biogéographie dans l’océan : analyses comparatives des données métagénomiques du projet Tara Oceans pour l’étude de la microalgue Bathycoccus et des communautés planctoniques globales

Vannier, T. (2017) · theses.fr (ABES) · doi:10.70675/619eba22z5d39z440az9d76z2c404589ecf8

Influence des oscillations anoxie/oxie sur des communautés microbiennes hydrocarbonoclastes de sédiments intertidaux

Terrisse, F. (2014) · theses.fr (ABES) · doi:10.70675/bb188aeez1349z4ca6zaad5z79a64ce590f5

Structure de l'écosystème planctonique : apport des données à haut débit de séquençage et d'imagerie

Silva, O. D. (2021) · theses.fr (ABES) · doi:10.70675/1bea65e9z90a1z442eza616z8deebff8eabb

Structure et dynamique de la communauté bactérienne libre et attachée dans les écosystèmes lacustres

Parveen, B. (2012) · theses.fr (ABES) · doi:10.70675/99c5b642z889bz4467z9bcbzd1cc7ace079d

Impact of microbial ecology on the microalgal-bacterial nexus for the production of microalgal biomass

Saleha, Z., Siddiqui, S. Z., & Nayak, A. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-29262-0.00010-1

Forces Shaping Diversity of Hydrogen Peroxide Detoxification Potential in Ocean Microbial Ecosystems

Goldberg, H., Dyhrman, S. T., DeMers, M. A., Braakman, R., & Hennon, G. M. M. (2026) · Environmental Microbiology · doi:10.1111/1462-2920.70315

Microbial Communities in Natural Mineral Waters of Bulgaria: Diversity and Biotechnological Potential

Slavov, A. K., Tamburadzhiev, I., & Goranov, B. G. (2026) · Limnological Review · doi:10.3390/limnolrev26020026

Thermophilic spore-forming bacteria biofilms in foods and beverages: Current knowledge, industrial risks, and emerging control strategies

Moshood, M. A., Sitoe, E. D. P. E., & Sant’Ana, A. S. (2026) · Food Microbiology · doi:10.1016/j.fm.2026.105207

Deep-sea mining disturbing the differentiation of structures and functions of benthic microbial communities in the South China Sea

Liu, H., Wang, P., Luo, J., Chen, S., & Jing, H. (2026) · Total Environment Microbiology · doi:10.1016/j.temicr.2026.100099

The interactive microbial ocean

Brussaard, C. P. D., Bidle, K. D., Pedrós‐Alió, C., & Legrand, C. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.255 · Cited by 18

Modeling and Prediction of Marine Microbial Populations in the Genomic Era

Hood, R. R., Laws, E. A., Follows, M. J., & Siegel, D. A. (2007) · Oceanography · doi:10.5670/oceanog.2007.61 · Cited by 16

Genomic perspectives in microbial oceanography

DeLong, E. F., & Karl, D. M. (2005) · Nature · doi:10.1038/nature04157 · Cited by 269

Deciphering Metabolic Currencies That Support Marine Microbial Networks

Durham, B. P. (2021) · mSystems · doi:10.1128/msystems.00763-21 · Cited by 16

Swimming with microbes: an individual-based modelling approach to ocean microbial ecology across scales

Christensen, A. K. (2021) · doi:10.25560/96428