Disentangling the mechanisms shaping the surface ocean microbiota

Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions

(2020) Máté Vass et al.   Scientific Reports

Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean

(2019) Clara Ruiz-González et al.   MOLECULAR ECOLOGY

Forfeiting the priority effect: turnover defines biofilm community succession

(2019) Colin J. Brislawn et al.   ISME Journal

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations

(2019) Philip Arevalo et al.   CELL

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

(2019) Guillem Salazar et al.   CELL

Global Trends in Marine Plankton Diversity across Kingdoms of Life

(2019) Federico M. Ibarbalz et al.   CELL

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes

(2018) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

β-Diversity, Community Assembly, and Ecosystem Functioning

(2018) Akira S. Mori et al.   TRENDS IN ECOLOGY & EVOLUTION

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current

(2018) Flavia Flaviani et al.   Frontiers in Microbiology

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

FastSpar: rapid and scalable correlation estimation for compositional data

(2018) Stephen C Watts et al.   BIOINFORMATICS

Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations

(2018) Stefan Lambert et al.   ISME Journal

Quantifying long-term recurrence in planktonic microbial eukaryotes

(2018) Caterina R. Giner et al.   MOLECULAR ECOLOGY

Are We Overestimating Protistan Diversity in Nature?

(2018) David A. Caron et al.   TRENDS IN MICROBIOLOGY

Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities

(2017) Wenxue Wu et al.   ISME Journal

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

(2017) Kerry A. Whittaker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marine Bacterioplankton Seasonal Succession Dynamics

(2017) Carina Bunse et al.   TRENDS IN MICROBIOLOGY

Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships

(2017) Justin R. Seymour et al.   Nature Microbiology

A family of interaction-adjusted indices of community similarity

(2016) Thomas Sebastian Benedikt Schmidt et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

Phytoplankton across Tropical and Subtropical Regions of the Atlantic, Indian and Pacific Oceans

(2016) Marta Estrada et al.   PLoS One

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Global diversity and biogeography of deep-sea pelagic prokaryotes

(2015) Guillem Salazar et al.   ISME Journal

Macroecological patterns of archaeal ammonia oxidizers in the Atlantic Ocean

(2015) Eva Sintes et al.   MOLECULAR ECOLOGY

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes

(2015) A. Z. Worden et al.   SCIENCE

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Metacommunity organisation, spatial extent and dispersal in aquatic systems: patterns, processes and prospects

(2014) Jani Heino et al.   FRESHWATER BIOLOGY

The transition between the niche and neutral regimes in ecology

(2014) C. K. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model

(2014) F. L. Hellweger et al.   SCIENCE

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

Beta diversity as the variance of community data: dissimilarity coefficients and partitioning

(2013) Pierre Legendre et al.   ECOLOGY LETTERS

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Biogeography of the uncultured marine picoeukaryote MAST-4: temperature-driven distribution patterns

(2013) Raquel Rodríguez-Martínez et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Bacterial taxa-area and distance-decay relationships in marine environments

(2013) L. Zinger et al.   MOLECULAR ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

General Patterns of Diversity in Major Marine Microeukaryote Lineages

(2013) Massimo C. Pernice et al.   PLoS One

Marine bacteria exhibit a bipolar distribution

(2013) W. J. Sul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for a persistent microbial seed bank throughout the global ocean

(2013) S. M. Gibbons et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

Body size and dispersal mode as key traits determining metacommunity structure of aquatic organisms

(2012) T. Bie et al.   ECOLOGY LETTERS

Eukaryotic versus prokaryotic marine picoplankton ecology

(2012) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

Ocean Science: The power of plankton

(2012) Paul Falkowski   NATURE

Beyond biogeographic patterns: processes shaping the microbial landscape

(2012) China A. Hanson et al.   NATURE REVIEWS MICROBIOLOGY

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

Disentangling the Drivers of   Diversity Along Latitudinal and Elevational Gradients

(2011) N. J. B. Kraft et al.   SCIENCE

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Local and regional factors influencing bacterial community assembly

(2011) Eva S. Lindström et al.   Environmental Microbiology Reports

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Using null models to disentangle variation in community dissimilarity from variation in α-diversity

(2011) Jonathan M. Chase et al.   Ecosphere

Eukaryotic Picoplankton in Surface Oceans

(2010) Ramon Massana   Annual Review of Microbiology

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

(2010) Ludwig Jardillier et al.   ISME Journal

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Limits to gene flow in a cosmopolitan marine planktonic diatom

(2010) G. Casteleyn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dormancy contributes to the maintenance of microbial diversity

(2010) S. E. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The merging of community ecology and phylogenetic biology

(2009) Jeannine Cavender-Bares et al.   ECOLOGY LETTERS

Regional invariance among microbial communities

(2009) Örjan Östman et al.   ECOLOGY LETTERS

Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities

(2009) Anders F Andersson et al.   ISME Journal

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Controls on Diatom Biogeography in the Ocean

(2009) P. Cermeno et al.   SCIENCE

Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species

(2008) Jonathan B. Losos   ECOLOGY LETTERS

A latitudinal diversity gradient in planktonic marine bacteria

(2008) J. A. Fuhrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE