A community perspective on the concept of marine holobionts: current status, challenges, and future directions

The holobiont concept before Margulis

(2020) Jan Baedke et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Spatial metabolomics of in situ host–microbe interactions at the micrometre scale

(2020) Benedikt Geier et al.   Nature Microbiology

Interaction between microbiota and immunity in health and disease

(2020) Danping Zheng et al.   CELL RESEARCH

Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts

(2019) Maxim Rubin-Blum et al.   ISME Journal

Algae−bacteria interactions that balance the planktonic microbiome

(2019) Emilio Cirri et al.   NEW PHYTOLOGIST

Algal Remodeling in a Ubiquitous Planktonic Photosymbiosis

(2019) Johan Decelle et al.   CURRENT BIOLOGY

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Not all animals need a microbiome

(2019) Tobin J Hammer et al.   FEMS MICROBIOLOGY LETTERS

Microbial “gardening” by a seaweed holobiont: Surface metabolites attract protective and deter pathogenic epibacterial settlement

(2019) Mahasweta Saha et al.   JOURNAL OF ECOLOGY

Vertical transmission of sponge microbiota is inconsistent and unfaithful

(2019) Johannes R. Björk et al.   Nature Ecology & Evolution

Using chemical language to shape future marine health

(2019) Mahasweta Saha et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Climate change alterations to ecosystem dominance: how might sponge-dominated reefs function?

(2018) James J. Bell et al.   ECOLOGY

Climate change promotes parasitism in a coral symbiosis

(2018) David M. Baker et al.   ISME Journal

Macroalgal-bacterial interactions: Role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta)

(2018) Ralf W. Kessler et al.   MOLECULAR ECOLOGY

Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems

(2018) Denis Faure et al.   NEW PHYTOLOGIST

Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

(2018) Manuel Kleiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards the Integration of Niche and Network Theories

(2018) Oscar Godoy et al.   TRENDS IN ECOLOGY & EVOLUTION

Stable-Isotope Probing of Human and Animal Microbiome Function

(2018) David Berry et al.   TRENDS IN MICROBIOLOGY

Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?

(2018) Corinna Bang et al.   ZOOLOGY

High resolution time series reveals cohesive but short-lived communities in coastal plankton

(2018) Antonio M. Martin-Platero et al.   Nature Communications

The sponge holobiont in a changing ocean: from microbes to ecosystems

(2018) L. Pita et al.   Microbiome

A de novo approach to disentangle partner identity and function in holobiont systems

(2018) Arnaud Meng et al.   Microbiome

The hologenome concept of evolution after 10 years

(2018) Eugene Rosenberg et al.   Microbiome

Hologenomics: Systems-Level Host Biology

(2018) Kevin R. Theis   mSystems

Coastal urbanisation affects microbial communities on a dominant marine holobiont

(2018) Ezequiel M. Marzinelli et al.   npj Biofilms and Microbiomes

An Emerging System to Study Photosymbiosis, Brain Regeneration, Chronobiology, and Behavior: The Marine Acoel Symsagittifera roscoffensis

(2018) Enrique Arboleda et al.   BIOESSAYS

Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae

(2018) Matthew B. Cooper et al.   ISME Journal

Role of Chemical Mediators in Aquatic Interactions across the Prokaryote–Eukaryote Boundary

(2018) Thomas Wichard et al.   JOURNAL OF CHEMICAL ECOLOGY

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

(2018) Marlène Chiarello et al.   Microbiome

Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny

(2018) F. Joseph Pollock et al.   Nature Communications

Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters

(2018) Julien de Lorgeril et al.   Nature Communications

Chemically-Mediated Interactions Between Macroalgae, Their Fungal Endophytes, and Protistan Pathogens

(2018) Marine Vallet et al.   Frontiers in Microbiology

Shifting paradigms in restoration of the world's coral reefs

(2017) Madeleine J. H. van Oppen et al.   GLOBAL CHANGE BIOLOGY

Influence of seabird colonies and other environmental variables on benthic community structure, Lancaster Sound Region, Canadian Arctic

(2017) Mariève Bouchard Marmen et al.   JOURNAL OF MARINE SYSTEMS

From endosymbiosis to holobionts: Evaluating a conceptual legacy

(2017) Maureen A. O’Malley   JOURNAL OF THEORETICAL BIOLOGY

Phagocytosis of microbial symbionts balances the carbon and nitrogen budget for the deep-water boreal sponge Geodia barretti

(2017) S. P. Leys et al.   LIMNOLOGY AND OCEANOGRAPHY

Indirect effects drive coevolution in mutualistic networks

(2017) Paulo R. Guimarães et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

The emerging science of linked plant-fungal invasions

(2017) Ian A. Dickie et al.   NEW PHYTOLOGIST

Meta-mass shift chemical profiling of metabolomes from coral reefs

(2017) Aaron C. Hartmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

N2-fixing tropical legume evolution: a contributor to enhanced weathering through the Cenozoic?

(2017) Dimitar Z. Epihov et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ocean biogeochemistry modeled with emergent trait-based genomics

(2017) V. J. Coles et al.   SCIENCE

Marine Viruses: Key Players in Marine Ecosystems

(2017) Mathias Middelboe et al.   Viruses-Basel

Microbial communities in marine sediments modify success of an invasive macrophyte

(2017) Paul E. Gribben et al.   Scientific Reports

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes

(2017) Sebastien Colin et al.   eLife

Subcellular tracking reveals the location of dimethylsulfoniopropionate in microalgae and visualises its uptake by marine bacteria

(2017) Jean-Baptiste Raina et al.   eLife

Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

(2017) Marc Troussellier et al.   Frontiers in Microbiology

Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience

(2017) Raquel S. Peixoto et al.   Frontiers in Microbiology

Stress and stability: applying the Anna Karenina principle to animal microbiomes

(2017) Jesse R. Zaneveld et al.   Nature Microbiology

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

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

Methane fluxes from coastal sediments are enhanced by macrofauna

(2017) Stefano Bonaglia et al.   Scientific Reports

Holobionts and the ecology of organisms: Multi-species communities or integrated individuals?

(2016) Derek Skillings   BIOLOGY & PHILOSOPHY

Tracking microbial interactions with NanoSIMS

(2016) Niculina Musat et al.   CURRENT OPINION IN BIOTECHNOLOGY

How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes

(2016) Elena Kazamia et al.   ECOLOGY LETTERS

Differential recycling of coral and algal dissolved organic matter via the sponge loop

(2016) Laura Rix et al.   FUNCTIONAL ECOLOGY

Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis

(2016) Ruby Ponnudurai et al.   ISME Journal

Quorum Sensing and Quorum Quenching in the Phycosphere of Phytoplankton: a Case of Chemical Interactions in Ecology

(2016) Jean luc Rolland et al.   JOURNAL OF CHEMICAL ECOLOGY

Diving into marine genomics with CRISPR/Cas9 systems

(2016) Tsuyoshi Momose et al.   Marine Genomics

Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence

(2016) Robert A. Quinn et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gut Microbiotas and Host Evolution: Scaling Up Symbiosis

(2016) Michael Shapira   TRENDS IN ECOLOGY & EVOLUTION

Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts

(2016) Angela E. Douglas et al.   mBio

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

(2016) Andrew W. Brooks et al.   PLOS BIOLOGY

Dynamic metabolic exchange governs a marine algal-bacterial interaction

(2016) Einat Segev et al.   eLife

Microbial Dysbiosis: Rethinking Disease in Marine Ecosystems

(2016) Suhelen Egan et al.   Frontiers in Microbiology

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

(2016) Jillian M. Petersen et al.   Nature Microbiology

The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle

(2016) Clara Martínez-Pérez et al.   Nature Microbiology

Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians

(2016) Iliona Wolfowicz et al.   Scientific Reports

When is dispersal for dispersal? Unifying marine and terrestrial perspectives

(2015) Scott C. Burgess et al.   BIOLOGICAL REVIEWS

Enhancing microalgal biomass productivity by engineering a microalgal–bacterial community

(2015) Dae-Hyun Cho et al.   BIORESOURCE TECHNOLOGY

Endosymbiosis and Eukaryotic Cell Evolution

(2015) John M. Archibald   CURRENT BIOLOGY

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography

(2015) Ezequiel M. Marzinelli et al.   ENVIRONMENTAL MICROBIOLOGY

Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures

(2015) Simon M Dittami et al.   ISME Journal

Mycorrhizal ecology and evolution: the past, the present, and the future

(2015) Marcel G. A. van der Heijden et al.   NEW PHYTOLOGIST

Building coral reef resilience through assisted evolution

(2015) Madeleine J. H. van Oppen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

(2015) Francisco Dini-Andreote et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome ofAiptasia, a sea anemone model for coral symbiosis

(2015) Sebastian Baumgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional significance of dinitrogen fixation in sustaining coral productivity under oligotrophic conditions

(2015) Ulisse Cardini et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa

(2015) S. L. Lebeis et al.   SCIENCE

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Effect of molybdenum on nodulation, plant yield and nitrogen uptake in hairy vetch (Vicia villosaRoth)

(2015) Faridul Alam et al.   SOIL SCIENCE AND PLANT NUTRITION

The Hologenome Concept: Helpful or Hollow?

(2015) Nancy A. Moran et al.   PLOS BIOLOGY

Exploring bacteria-induced growth and morphogenesis in the green macroalga order Ulvales (Chlorophyta)

(2015) Thomas Wichard   Frontiers in Plant Science

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach

(2015) Philippe Bordron et al.   MicrobiologyOpen

The ocean sampling day consortium

(2015) Anna Kopf et al.   GigaScience

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

Open science resources for the discovery and analysis of Tara Oceans data

(2015) Stéphane Pesant et al.   Scientific Data

The Importance of Microbes in Animal Development: Lessons from the Squid-Vibrio Symbiosis

(2014) Margaret J. McFall-Ngai   Annual Review of Microbiology

Potential application of algicidal bacteria for improved lipid recovery with specific algae

(2014) Eric M. Lenneman et al.   FEMS MICROBIOLOGY LETTERS

Changes in the global value of ecosystem services

(2014) Robert Costanza et al.   GLOBAL ENVIRONMENTAL CHANGE-HUMAN AND POLICY DIMENSIONS

Ecological theory as a foundation to control pathogenic invasion in aquaculture

(2014) Peter De Schryver et al.   ISME Journal

A metabolic approach to study algal-bacterial interactions in changing environments

(2014) Simon M. Dittami et al.   MOLECULAR ECOLOGY

Gnotobiotics:

(2014) Sarah C. P. Williams   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

(2014) J. J. Faith et al.   Science Translational Medicine

Microbial priming of plant and animal immunity: symbionts as developmental signals

(2014) Marc-André Selosse et al.   TRENDS IN MICROBIOLOGY

Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries

(2014) Martin S. Llewellyn et al.   Frontiers in Microbiology

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Construction of bacteria–eukaryote synthetic mutualism

(2013) Isao Kubo et al.   BIOSYSTEMS

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

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

Host specificity and coevolution of Flavobacteriaceae endosymbionts within the siphonous green seaweed Bryopsis

(2013) Joke Hollants et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution

(2013) D. M. de Vienne et al.   NEW PHYTOLOGIST

Distinct antimicrobial peptide expression determines host species-specific bacterial associations

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

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Surviving in a Marine Desert: The Sponge Loop Retains Resources Within Coral Reefs

(2013) Jasper M. de Goeij et al.   SCIENCE

Emerging importance of holobionts in evolution and in probiotics

(2013) Yadvir Singh et al.   Gut Pathogens

Mom Knows Best: The Universality of Maternal Microbial Transmission

(2013) Lisa J. Funkhouser et al.   PLOS BIOLOGY

Screening and selection of growth-promoting bacteria for Dunaliella cultures

(2013) M. Le Chevanton et al.   Algal Research-Biomass Biofuels and Bioproducts

Searching for Solutions in Aquaculture: Charting a Sustainable Course

(2012) Dane Klinger et al.   Annual Review of Environment and Resources

Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida

(2012) Erik M Lehnert et al.   BMC GENOMICS

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier et al.   CLINICAL MICROBIOLOGY AND INFECTION

Synthetic ecology – A way forward for sustainable algal biofuel production?

(2012) Elena Kazamia et al.   JOURNAL OF BIOTECHNOLOGY

Chemical Mediation of Ternary Interactions Between Marine Holobionts and Their Environment as Exemplified by the Red Alga Delisea pulchra

(2012) Tilmann Harder et al.   JOURNAL OF CHEMICAL ECOLOGY

Growth and Thallus Morphogenesis ofUlva mutabilis(Chlorophyta) Depends on A Combination of Two Bacterial Species Excreting Regulatory Factors

(2012) Michael Spoerner et al.   JOURNAL OF PHYCOLOGY

Interactions between Diatoms and Bacteria

(2012) S. A. Amin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A road map for the development of community systems (CoSy) biology

(2012) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga

(2012) A. W. Thompson et al.   SCIENCE

Hidden Fungi, Emergent Properties: Endophytes and Microbiomes

(2011) Andrea Porras-Alfaro et al.   Annual Review of Phytopathology

Microorganisms and their roles in fundamental biogeochemical cycles

(2011) Eugene L Madsen   CURRENT OPINION IN BIOTECHNOLOGY

Quantitative tracking of the growth of individual algal cells in microdroplet compartments

(2011) Jie Pan et al.   Integrative Biology

The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis

(2011) Mohammad R. Seyedsayamdost et al.   Nature Chemistry

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species

(2010) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis

(2010) Catherine Burke et al.   ISME Journal

The L4 time-series: the first 20 years

(2010) R. Harris   JOURNAL OF PLANKTON RESEARCH

A complex journey: transmission of microbial symbionts

(2010) Monika Bright et al.   NATURE REVIEWS MICROBIOLOGY

Reduced anxiety-like behavior and central neurochemical change in germ-free mice

(2010) K. M. Neufeld et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Symbiosis as a source of selectable epigenetic variation: taking the heat for the big guy

(2010) S. F. Gilbert et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Nitrogen fixation and nitrogen transformations in marine symbioses

(2010) Cara L. Fiore et al.   TRENDS IN MICROBIOLOGY

The evolution of animals and plants via symbiosis with microorganisms

(2010) Eugene Rosenberg et al.   Environmental Microbiology Reports

Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur

(2009) J.-B. Raina et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Helgoland Roads, North Sea: 45 Years of Change

(2009) Karen Helen Wiltshire et al.   Estuaries and Coasts

Evidence for cospeciation events in the host–symbiont system involving crinoids (Echinodermata) and their obligate associates, the myzostomids (Myzostomida, Annelida)

(2009) Déborah Lanterbecq et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Photolysis of iron-siderophore chelates promotes bacterial-algal mutualism

(2009) S. A. Amin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological processes: A key element in strategies for nature conservation

(2009) Andrew F. Bennett et al.   ECOLOGICAL MANAGEMENT & RESTORATION

Unexpected co-occurrence of six bacterial symbionts in the gills of the cold seep mussel Idas sp. (Bivalvia: Mytilidae)

(2008) Sébastien Duperron et al.   ENVIRONMENTAL MICROBIOLOGY

Photosynthetic symbioses in animals

(2008) A.A. Venn et al.   JOURNAL OF EXPERIMENTAL BOTANY

Hydrothermal vents and the origin of life

(2008) William Martin et al.   NATURE REVIEWS MICROBIOLOGY

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

(2008) Nicole Dubilier et al.   NATURE REVIEWS MICROBIOLOGY

The Microbial Engines That Drive Earth's Biogeochemical Cycles

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