Marine holobiont

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The holobiont concept is a renewed paradigm in biology that can help to describe and understand complex systems, like the host-microbe interactions that play crucial roles in marine ecosystems. However, there is still little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them and their ecological consequences. The holobiont concept posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. [1]

Contents

History

Partners forming marine holobionts Partners forming marine holobionts.jpg
Partners forming marine holobionts 

The idea of holism started to regain popularity in biology when the endosymbiosis theory was first proposed by Konstantin Mereschkowski in 1905 and further developed by Ivan Wallin in 1925. Still accepted today, this theory posits a single origin for eukaryotic cells through the symbiotic assimilation of prokaryotes to form first mitochondria and later plastids (the latter through several independent symbiotic events) via phagocytosis (reviewed in Archibald, 2015). [2] These ancestral and founding symbiotic events, which prompted the metabolic and cellular complexity of eukaryotic life, most likely occurred in the ocean. [3] [1]

Despite the general acceptance of the endosymbiosis theory, the term holobiosis or holobiont did not immediately enter the scientific vernacular. It was coined independently by the German Adolf Meyer-Abich in 1943, [4] [5] and by Lynn Margulis in 1990, who proposed that evolution has worked mainly through symbiosis-driven leaps that merged organisms into new forms, referred to as “holobionts”, and only secondarily through gradual mutational changes. [6] [7] However, the concept was not widely used until it was co-opted by coral biologists over a decade later. Corals and the dinoflagellate algae called Zooxanthellae are one of the most iconic examples of symbioses found in nature; most corals are incapable of long-term survival without the products of photosynthesis provided by their endosymbiotic algae. Rohwer et al. (2002) [8] were the first to use the word holobiont to describe a unit of selection sensu Margulis  [9] for corals, where the holobiont comprised the cnidarian polyp (host), Zooxanthellae algae, various ectosymbionts (endolithic algae, prokaryotes, fungi, other unicellular eukaryotes), and viruses. [1]

Although initially driven by studies of marine organisms, much of the research on the emerging properties and significance of holobionts has since been carried out in other fields of research: the microbiota of the rhizosphere of plants or the animal gut became predominant models and have led to an ongoing paradigm shift in agronomy and medical sciences. [10] [11] [12] Holobionts occur in terrestrial and aquatic habitats alike, and several analogies between these ecosystems can be made. For example, in all of these habitats, interactions within and across holobionts such as induction of chemical defenses, nutrient acquisition, or biofilm formation are mediated by chemical cues and signals in the environment, dubbed infochemicals. [13] [14] [15] [16] Nevertheless, we can identify two major differences between terrestrial and aquatic systems. First, the physicochemical properties of water result in higher chemical connectivity and signaling between macro- and micro-organisms in aquatic or moist environments. In marine ecosystems, carbon fluxes also appear to be swifter and trophic modes more flexible, leading to higher plasticity of functional interactions across holobionts. [17] Moreover, dispersal barriers are usually lower, allowing for faster microbial community shifts in marine holobionts. [18] [19] Secondly, phylogenetic diversity at broad taxonomic scales (i.e., supra-kingdom, kingdom and phylum levels), is higher in aquatic realms compared to land, with much of the aquatic diversity yet to be uncovered, [20] [21] especially marine viruses. [22] [23] [24] [1]

Russian Doll complexity

Schematic view of the "Russian Doll" complexity and dynamics of holobionts, according to diverse spatiotemporal scales (see text on left for explanation) Russian Doll complexity and dynamics of holobionts.jpg
Schematic view of the “Russian Doll” complexity and dynamics of holobionts, according to diverse spatiotemporal scales 
(see text on left for explanation)

The boundaries of holobionts are usually delimited by a physical gradient, which corresponds to the area of local influence of the host, e.g., in unicellular algae the so-called phycosphere. [25] However, they may also be defined in a context-dependent way as a Russian matryoshka doll, setting the boundaries of the holobiont depending on the interactions and biological functions that are being considered. Thus holobionts may encompass all levels of host-symbiont associations from intimate endosymbiosis with a high degree of co-evolution up to the community and ecosystem level; a concept referred to as "nested ecosystems" (see diagram). [26] [27] [1]

In the diagram on the right, the host (blue circles), and associated microbes (all other shapes) including bacteria and eukaryotes that may be inside (i.e., endosymbiotic) or outside the host (i.e., ectosymbiotic) are connected by either beneficial (solid orange lines), neutral (solid blue lines) or pathogenic (dashed black lines) interactions, respectively. Changes from beneficial or neutral to pathogenic interactions are typical cases of dysbiosis. The different clusters are illustrated by the following examples: 1, a model holobiont in a stable physiological condition (e.g., in controlled laboratory condition); 2 and 3, holobionts changing during their life cycle or subjected to stress conditions—examples of vertically transmitted microbes are indicated by light blue arrows; 4 and 5, marine holobionts in the context of global sampling campaigns or long-term time series—examples of horizontal transmission of microbes and holobionts are illustrated by pink arrows. [1]

Such a conceptual perspective raises fundamental questions not only regarding the interaction between the different components of holobionts and processes governing their dynamics, but also of the relevant units of selection and the role of coevolution. For instance, plant and animal evolution involves new functions co-constructed by members of the holobiont or elimination of functions redundant among them, [28] and it is likely that these processes are also relevant in marine holobionts. Eugene Rosenberg et al. have argued that all animals and plants can be considered holobionts, and thus advocate the hologenome theory of evolution, suggesting that natural selection acts at the level of the holobiont and its hologenome. [29] [30] This interpretation of Margulis' definition of a holobiont considerably broadened fundamental concepts in evolution and speciation and has not been free of criticism, [31] especially when applied at the community or ecosystem level. [32] More recently, it has been shown that species that interact indirectly with the host can also be important in shaping coevolution within mutualistic multi-partner assemblages. [33] Thus, the holobiont concept and the underlying complexity of holobiont systems should be better defined and further considered when addressing evolutionary and ecological questions. [1]

Marine holobiont models

Example holobionts

Influence on ecological processes

Climate change and the rhodolith holobiont Climate change stressors and rhodolith holobiont fitness.webp

Work on model systems has demonstrated that motile and macroscopic marine holobionts can act as dissemination vectors for geographically restricted microbial taxa. Pelagic mollusks or vertebrates are textbook examples of high dispersal capacity organisms (e.g., against currents and through stratified water layers). It has been estimated that fish and marine mammals may enhance the original dispersion rate of their microbiota by a factor of 200 to 200,000  [57] and marine birds may even act as bio-vectors across ecosystem boundaries. [58] This host-driven dispersal of microbes can include non-native or invasive species as well as pathogens. [57] [1]

A related ecological function of holobionts is their potential to sustain rare species. Hosts provide an environment that favors the growth of specific microbial communities distinct from the surrounding environment (including rare microbes). They may, for instance, provide a nutrient-rich niche in the otherwise nutrient-poor surroundings. [59] [60] [61] [62] [63] [1]

Lastly, biological processes regulated by microbes are important drivers of global biogeochemical cycles. [64] [65] [66] In the open ocean, it is estimated that symbioses with the cyanobacterium UCYN-A contribute about 20% to total N2 fixation. [67] [68] In benthic systems, sponges and corals may support entire ecosystems via their involvement in nutrient cycling thanks to their microbial partners, [69] [70] [71] [27] functioning as sinks and sources of nutrients. In particular the “sponge loop” recycles dissolved organic matter and makes it available to higher trophic levels in the form of detritus. [72] [70] [73] In coastal sediments, bivalves hosting methanogenic archaea have been shown to increase the benthic methane efflux by a factor of up to eight, potentially accounting for 9.5% of total methane emissions from the Baltic Sea. [74] This metabolic versatility is accomplished because of the simultaneous occurrence of disparate biochemical machineries (e.g., aerobic and anaerobic pathways) in individual symbionts, providing new metabolic abilities to the holobiont, such as the synthesis of specific essential amino acids, photosynthesis, or chemosynthesis. [34] [75] Furthermore, the interaction between host and microbiota can potentially extend the metabolic capabilities of a holobiont in a way that augments its resilience to environmental changes, [76] [77] [78] [79] [80] or allow it to cross biotope boundaries (e.g., Woyke et al., 2006) and colonize extreme environments (Bang et al., 2018). Holobionts thus contribute to marine microbial diversity and possibly resilience in the context of global environmental changes  [57] and it is paramount to include the holobiont concept in predictive models that investigate the consequences of human impacts on the marine realm and its biogeochemical cycles. [1]

Holobiont assembly and regulation

Mind map of concepts related to marine holobionts Mind map of concepts related to marine holobionts.jpg
Mind map of concepts related to marine holobionts 

Two critical challenges partially addressed by using model systems are (1) to decipher the factors determining holobiont composition and (2) to elucidate the impacts and roles of the different partners in these complex systems over time. Some marine organisms such as bivalves transmit part of the microbiota maternally. [81] [82] In other marine holobionts, vertical transmission may be weak and inconsistent, whereas mixed modes of transmission (vertical and horizontal) or intermediate modes (pseudo-vertical, where horizontal acquisition frequently involves symbionts of parental origin) are more common. [83] Identifying the factors shaping holobiont composition and understanding their evolution is highly relevant for marine organisms given that most marine hosts display a high specificity for their microbiota and even patterns of phylosymbiosis, [84] [85] [86] despite a highly connected and microbe-rich environment. [1]

During microbiota transmission (whether vertical or horizontal), selection by the host and/or by other components of the microbiome, is a key process in establishing or maintaining a holobiont microbial community that is distinct from the environment. The immune system of the host, e.g., via the secretion of specific antimicrobial peptides, [87] [88] is one way of performing this selection in both marine and terrestrial holobionts. [1]

Another way of selecting a holobiont microbial community is by chemically mediated microbial gardening. This concept has been demonstrated for land plants, where root exudates manipulate microbiome composition. [89] In marine environments, the phylogenetic diversity of hosts and symbionts suggests both conserved and marine-specific chemical interactions, but studies are still in their infancy. For instance, seaweeds can chemically garden beneficial microbes, facilitating normal morphogenesis and increasing disease resistance, [52] [90] and seaweeds and corals structure their surface-associated microbiome by producing chemoattractants and antibacterial compounds. [14] [91] There are fewer examples of chemical gardening in unicellular hosts, but it seems highly likely that similar processes are in place. [92] [93] [1]

In addition to selection, ecological drift, dispersal and evolutionary diversification have been proposed as key processes in community assembly, but are difficult to estimate in microbial communities. [94] The only data currently at our disposal to quantify these processes are the diversity and distribution of microbes. Considering the high connectivity of aquatic environments, differences in marine microbial communities are frequently attributed to a combination of selection and drift, rather than limited dispersal, [61] a conclusion which in the future could be refined by conceptual models developed for instance for soil microbial communities. [93] [95] ) Diversification is mainly considered in the sense of coevolution or adaptation to host selection, which may also be driven by the horizontal acquisition of genes. However, cospeciation is challenging to prove  [96] [32] and only few studies have examined this process in marine holobionts to date, each focused on a restricted number of actors. [97] [98] [1]

Perturbations in the transmission or the recruitment of the microbiota can lead to dysbiosis, and eventually microbial infections. [28] [93] Dysbiotic microbial communities are frequently determined by stochastic processes and thus display higher variability in their composition than those of healthy individuals. This observation in line with the "Anna Karenina principle", [99] although there are exceptions to this rule. [93] A specific case of dysbiosis is the so-called "Rasputin effect" where benign endosymbionts opportunistically become detrimental to the host due to processes such as reduction in immune response under food deprivation, coinfections, or environmental pressure. [100] Many diseases are now interpreted as the result of a microbial imbalance and the rise of opportunistic or polymicrobial infections upon host stress. [101] For instance in reef-building corals, warming destabilizes cnidarian-dinoflagellate associations, and some beneficial Symbiodiniacea strains switch their physiology and sequester more resources for their own growth at the expense of the coral host, leading to coral bleaching and even death. [102] [1]

Increasing our knowledge on the contribution of these processes to holobiont community assembly in marine systems is a key challenge, which is of particular urgency today in the context of ongoing global change. Moreover, understanding how the community and functional structure of resident microbes are resilient to perturbations remains critical to predict and promote the health of their host and the ecosystem. Yet, the contribution of the microbiome is still missing in most quantitative models predicting the distribution of marine macro-organisms, or additional information on biological interactions would be required to make the former more accurate. [103] [1]

Related Research Articles

<span class="mw-page-title-main">Endosymbiont</span> Organism that lives within the body or cells of another organism

An endosymbiont or endobiont is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον endon "within", σύν syn "together" and βίωσις biosis "living".) Examples are nitrogen-fixing bacteria, which live in the root nodules of legumes, single-cell algae inside reef-building corals and bacterial endosymbionts that provide essential nutrients to insects.

Joan Roughgarden is an American ecologist and evolutionary biologist. She has engaged in theory and observation of coevolution and competition in Anolis lizards of the Caribbean, and recruitment limitation in the rocky intertidal zones of California and Oregon. She has more recently become known for her rejection of sexual selection, her theistic evolutionism, and her work on holobiont evolution.

Symbiotic bacteria are bacteria living in symbiosis with another organism or each other. For example, rhizobia living in root nodules of legumes provide nitrogen fixing activity for these plants.

<span class="mw-page-title-main">Microbiota</span> Community of microorganisms

Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.

For the American folk-rock singer-songwriter, see Nancy Moran.

<span class="mw-page-title-main">Marine microorganisms</span> Any life form too small for the naked human eye to see that lives in a marine environment

Marine microorganisms are defined by their habitat as microorganisms living in a marine environment, that is, in the saltwater of a sea or ocean or the brackish water of a coastal estuary. A microorganism is any microscopic living organism or virus, that is too small to see with the unaided human eye without magnification. Microorganisms are very diverse. They can be single-celled or multicellular and include bacteria, archaea, viruses and most protozoa, as well as some fungi, algae, and animals, such as rotifers and copepods. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify viruses as microorganisms, but others consider these as non-living.

The hologenome theory of evolution recasts the individual animal or plant as a community or a "holobiont" – the host plus all of its symbiotic microbes. Consequently, the collective genomes of the holobiont form a "hologenome". Holobionts and hologenomes are structural entities that replace misnomers in the context of host-microbiota symbioses such as superorganism, organ, and metagenome. Variation in the hologenome may encode phenotypic plasticity of the holobiont and can be subject to evolutionary changes caused by selection and drift, if portions of the hologenome are transmitted between generations with reasonable fidelity. One of the important outcomes of recasting the individual as a holobiont subject to evolutionary forces is that genetic variation in the hologenome can be brought about by changes in the host genome and also by changes in the microbiome, including new acquisitions of microbes, horizontal gene transfers, and changes in microbial abundance within hosts. Although there is a rich literature on binary host–microbe symbioses, the hologenome concept distinguishes itself by including the vast symbiotic complexity inherent in many multicellular hosts. For recent literature on holobionts and hologenomes published in an open access platform, see the following reference.

<span class="mw-page-title-main">Root microbiome</span> Microbe community of plant roots

The root microbiome is the dynamic community of microorganisms associated with plant roots. Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi, and archaea. The microbial communities inside the root and in the rhizosphere are distinct from each other, and from the microbial communities of bulk soil, although there is some overlap in species composition.

<span class="mw-page-title-main">Phycosphere</span> Microscale mucus region that is rich in organic matter surrounding a phytoplankton cel

The phycosphere is a microscale mucus region that is rich in organic matter surrounding a phytoplankton cell. This area is high in nutrients due to extracellular waste from the phytoplankton cell and it has been suggested that bacteria inhabit this area to feed on these nutrients. This high nutrient environment creates a microbiome and a diverse food web for microbes such as bacteria and protists. It has also been suggested that the bacterial assemblages within the phycosphere are species-specific and can vary depending on different environmental factors.

<span class="mw-page-title-main">Microbiome</span> Microbial community assemblage and activity

A microbiome is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al., but supplemented with two explanatory paragraphs. The first explanatory paragraph pronounces the dynamic character of the microbiome, and the second explanatory paragraph clearly separates the term microbiota from the term microbiome.

The initial acquisition of microbiota is the formation of an organism's microbiota immediately before and after birth. The microbiota are all the microorganisms including bacteria, archaea and fungi that colonize the organism. The microbiome is another term for microbiota or can refer to the collected genomes.

<span class="mw-page-title-main">Marine microbial symbiosis</span>

Microbial symbiosis in marine animals was not discovered until 1981. In the time following, symbiotic relationships between marine invertebrates and chemoautotrophic bacteria have been found in a variety of ecosystems, ranging from shallow coastal waters to deep-sea hydrothermal vents. Symbiosis is a way for marine organisms to find creative ways to survive in a very dynamic environment. They are different in relation to how dependent the organisms are on each other or how they are associated. It is also considered a selective force behind evolution in some scientific aspects. The symbiotic relationships of organisms has the ability to change behavior, morphology and metabolic pathways. With increased recognition and research, new terminology also arises, such as holobiont, which the relationship between a host and its symbionts as one grouping. Many scientists will look at the hologenome, which is the combined genetic information of the host and its symbionts. These terms are more commonly used to describe microbial symbionts.

<span class="mw-page-title-main">Eugene Rosenberg</span>

Eugene Rosenberg is a microbiologist at the Faculty of Life Sciences at Tel Aviv University, an expert in the field of applied environmental microbiology, in particular his work on Myxobacteria, microorganisms to combat pollution (bioremediation), and the Hologenome theory of evolution.

<span class="mw-page-title-main">Holobiont</span> Host and associated species living as a discrete ecological unit

A holobiont is an assemblage of a host and the many other species living in or around it, which together form a discrete ecological unit through symbiosis, though there is controversy over this discreteness. The components of a holobiont are individual species or bionts, while the combined genome of all bionts is the hologenome. The holobiont concept was initially introduced by the German theoretical biologist Adolf Meyer-Abich in 1943, and then apparently independently by Dr. Lynn Margulis in her 1991 book Symbiosis as a Source of Evolutionary Innovation. The concept has evolved since the original formulations. Holobionts include the host, virome, microbiome, and any other organisms which contribute in some way to the functioning of the whole. Well-studied holobionts include reef-building corals and humans.

Hologenomics is the omics study of hologenomes. A hologenome is the whole set of genomes of a holobiont, an organism together with all co-habitating microbes, other life forms, and viruses. While the term hologenome originated from the hologenome theory of evolution, which postulates that natural selection occurs on the holobiont level, hologenomics uses an integrative framework to investigate interactions between the host and its associated species. Examples include gut microbe or viral genomes linked to human or animal genomes for host-microbe interaction research. Hologenomics approaches have also been used to explain genetic diversity in the microbial communities of marine sponges.

Endozoicomonas gorgoniicola is a Gram-negative and facultative anaerobic bacterium from the genus of Endozoicomonas. Individual cells are motile and rod-shaped. Bacteria in this genus are symbionts of coral. E. gorgoniicola live specifically with soft coral and were originally isolated from a species of Plexaura, an octocoral, off the coast of Bimini in the Bahamas. The presence of this bacterium in a coral microbiome is associated with coral health.

Vertical transmission of symbionts is the transfer of a microbial symbiont from the parent directly to the offspring. Many metazoan species carry symbiotic bacteria which play a mutualistic, commensal, or parasitic role. A symbiont is acquired by a host via horizontal, vertical, or mixed transmission.

<span class="mw-page-title-main">Marine microbiome</span>

All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. However, new explorations into the diversity of marine microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment.

<span class="mw-page-title-main">Plant microbiome</span>

The plant microbiome, also known as the phytomicrobiome, plays roles in plant health and productivity and has received significant attention in recent years. The microbiome has been defined as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity".

<span class="mw-page-title-main">Plant holobiont</span>

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a holobiont. Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments.

References

  1. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Dittami, Simon M.; et al. (2021). "A community perspective on the concept of marine holobionts: Current status, challenges, and future directions". PeerJ. 9: e10911. doi: 10.7717/peerj.10911 . PMC   7916533 . PMID   33665032. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  2. ↑ Archibald, John M. (2015). "Endosymbiosis and Eukaryotic Cell Evolution". Current Biology. 25 (19): R911–R921. doi: 10.1016/j.cub.2015.07.055 . PMID   26439354. S2CID   16089231.
  3. ↑ Martin, William; Baross, John; Kelley, Deborah; Russell, Michael J. (2008). "Hydrothermal vents and the origin of life". Nature Reviews Microbiology. 6 (11): 805–814. doi:10.1038/nrmicro1991. PMID   18820700. S2CID   1709272.
  4. ↑ Meyer-Abich A. (1943). "Beiträge zur Theorie der Evolution der Organismen. I. Das typologische Grundgesetz und seine Folgerungen für Phylogenie und Entwicklungsphysiologie" [Contributions to the evolutionary theory of organisms: I. The basic typological law and its implications] Acta Biotheoretica, 7: 1–80
  5. ↑ Baedke, Jan; Fábregas‐Tejeda, Alejandro; Nieves Delgado, Abigail (2020). "The holobiont concept before Margulis". Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 334 (3): 149–155. doi: 10.1002/jez.b.22931 . PMID   32039567. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  6. ↑ Margulis, Lynn; Fester, René (1991). Symbiosis as a Source of Evolutionary Innovation: Speciation and Morphogenesis. MIT Press. ISBN   9780262132695.
  7. ↑ o'Malley, Maureen A. (2017). "From endosymbiosis to holobionts: Evaluating a conceptual legacy". Journal of Theoretical Biology. 434: 34–41. Bibcode:2017JThBi.434...34O. doi:10.1016/j.jtbi.2017.03.008. PMID   28302492.
  8. ↑ Rohwer, F.; Seguritan, V.; Azam, F.; Knowlton, N. (2002). "Diversity and distribution of coral-associated bacteria". Marine Ecology Progress Series. 243: 1–10. Bibcode:2002MEPS..243....1R. doi: 10.3354/meps243001 .
  9. ↑ Rosenberg, Eugene; Koren, Omry; Reshef, Leah; Efrony, Rotem; Zilber-Rosenberg, Ilana (2007). "The hologenome theory disregards the coral holobiont: Reply from Rosenberg et al". Nature Reviews Microbiology. 5 (10): 826. doi: 10.1038/nrmicro1635-c2 . S2CID   8258214.
  10. ↑ Bulgarelli, Davide; Schlaeppi, Klaus; Spaepen, Stijn; Van Themaat, Emiel Ver Loren; Schulze-Lefert, Paul (2013). "Structure and Functions of the Bacterial Microbiota of Plants". Annual Review of Plant Biology. 64: 807–838. doi:10.1146/annurev-arplant-050312-120106. PMID   23373698.
  11. ↑ Shreiner, Andrew B.; Kao, John Y.; Young, Vincent B. (2015). "The gut microbiome in health and in disease". Current Opinion in Gastroenterology. 31 (1): 69–75. doi:10.1097/MOG.0000000000000139. PMC   4290017 . PMID   25394236.
  12. ↑ Faure, Denis; Simon, Jean-Christophe; Heulin, Thierry (2018). "Holobiont: A conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems". New Phytologist. 218 (4): 1321–1324. doi: 10.1111/nph.15199 . PMID   29738088.
  13. ↑ Loh, John; Pierson, Elizabeth A.; Pierson, Leland S.; Stacey, Gary; Chatterjee, Arun (2002). "Quorum sensing in plant-associated bacteria". Current Opinion in Plant Biology. 5 (4): 285–290. doi:10.1016/S1369-5266(02)00274-1. PMID   12179960.
  14. 1 2 Harder, Tilmann; Campbell, Alexandra H.; Egan, Suhelen; Steinberg, Peter D. (2012). "Chemical Mediation of Ternary Interactions Between Marine Holobionts and Their Environment as Exemplified by the Red Alga Delisea pulchra". Journal of Chemical Ecology. 38 (5): 442–450. doi:10.1007/s10886-012-0119-5. PMID   22527059. S2CID   14117311.
  15. ↑ Rolland, Jean luc; Stien, Didier; Sanchez-Ferandin, Sophie; Lami, Raphaël (2016). "Quorum Sensing and Quorum Quenching in the Phycosphere of Phytoplankton: A Case of Chemical Interactions in Ecology" (PDF). Journal of Chemical Ecology. 42 (12): 1201–1211. doi:10.1007/s10886-016-0791-y. PMID   27822708. S2CID   16684025.
  16. ↑ Saha, Mahasweta; Berdalet, Elisa; Carotenuto, Ylenia; Fink, Patrick; Harder, Tilmann; John, Uwe; Not, Fabrice; Pohnert, Georg; Potin, Philippe; Selander, Erik; Vyverman, Wim; Wichard, Thomas; Zupo, Valerio; Steinke, Michael (2019). "Using chemical language to shape future marine health". Frontiers in Ecology and the Environment. 17 (9): 530–537. doi:10.1002/fee.2113. hdl: 1854/LU-8640919 . S2CID   191151384.
  17. ↑ Mitra, A.; Flynn, K. J.; Burkholder, J. M.; Berge, T.; Calbet, A.; Raven, J. A.; Granéli, E.; Glibert, P. M.; Hansen, P. J.; Stoecker, D. K.; Thingstad, F.; Tillmann, U.; Våge, S.; Wilken, S.; Zubkov, M. V. (2014). "The role of mixotrophic protists in the biological carbon pump". Biogeosciences. 11 (4): 995–1005. Bibcode:2014BGeo...11..995M. doi: 10.5194/bg-11-995-2014 . hdl: 10453/117781 . CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  18. ↑ Kinlan, Brian P.; Gaines, Steven D. (2003). "Propagule Dispersal in Marine and Terrestrial Environments: A Community Perspective". Ecology. 84 (8): 2007–2020. doi:10.1890/01-0622.
  19. ↑ Burgess, Scott C.; Baskett, Marissa L.; Grosberg, Richard K.; Morgan, Steven G.; Strathmann, Richard R. (2016). "When is dispersal for dispersal? Unifying marine and terrestrial perspectives". Biological Reviews. 91 (3): 867–882. doi:10.1111/brv.12198. PMID   26118564. S2CID   9877585.
  20. ↑ De Vargas, C.; et al. (2015). "Eukaryotic plankton diversity in the sunlit ocean". Science. 348 (6237). doi:10.1126/science.1261605. hdl: 10261/117736 . PMID   25999516. S2CID   12853481.
  21. ↑ Thompson, Luke R.; et al. (2017). "A communal catalogue reveals Earth's multiscale microbial diversity". Nature. 551 (7681): 457–463. Bibcode:2017Natur.551..457T. doi:10.1038/nature24621. PMC   6192678 . PMID   29088705. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  22. ↑ Middelboe, Mathias; Brussaard, Corina (2017). "Marine Viruses: Key Players in Marine Ecosystems". Viruses. 9 (10): 302. doi: 10.3390/v9100302 . PMC   5691653 . PMID   29057790. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  23. ↑ Gregory, Ann C.; et al. (2019). "Marine DNA Viral Macro- and Microdiversity from Pole to Pole". Cell. 177 (5): 1109–1123.e14. doi:10.1016/j.cell.2019.03.040. PMC   6525058 . PMID   31031001.
  24. ↑ Dominguez-Huerta, Guillermo; Zayed, Ahmed A.; Wainaina, James M.; Guo, Jiarong; Tian, Funing; Pratama, Akbar Adjie; Bolduc, Benjamin; Mohssen, Mohamed; Zablocki, Olivier; Pelletier, Eric; Delage, Erwan (10 June 2022). "Diversity and ecological footprint of Global Ocean RNA viruses". Science. 376 (6598): 1202–1208. doi: 10.1126/science.abn6358 . ISSN   0036-8075. PMID   35679415.
  25. ↑ Seymour, Justin R.; Amin, Shady A.; Raina, Jean-Baptiste; Stocker, Roman (2017). "Zooming in on the phycosphere: The ecological interface for phytoplankton–bacteria relationships". Nature Microbiology. 2 (7): 17065. doi:10.1038/nmicrobiol.2017.65. hdl: 10453/102139 . PMID   28555622. S2CID   25219954.
  26. ↑ McFall-Ngai, Margaret; Hadfield, Michael G.; Bosch, Thomas C. G.; Carey, Hannah V.; Domazet-Lošo, Tomislav; Douglas, Angela E.; Dubilier, Nicole; Eberl, Gerard; Fukami, Tadashi; Gilbert, Scott F.; Hentschel, Ute; King, Nicole; Kjelleberg, Staffan; Knoll, Andrew H.; Kremer, Natacha; Mazmanian, Sarkis K.; Metcalf, Jessica L.; Nealson, Kenneth; Pierce, Naomi E.; Rawls, John F.; Reid, Ann; Ruby, Edward G.; Rumpho, Mary; Sanders, Jon G.; Tautz, Diethard; Wernegreen, Jennifer J. (2013). "Animals in a bacterial world, a new imperative for the life sciences". Proceedings of the National Academy of Sciences. 110 (9): 3229–3236. Bibcode:2013PNAS..110.3229M. doi: 10.1073/pnas.1218525110 . PMC   3587249 . PMID   23391737.
  27. 1 2 3 Pita, L.; Rix, L.; Slaby, B. M.; Franke, A.; Hentschel, U. (2018). "The sponge holobiont in a changing ocean: From microbes to ecosystems". Microbiome. 6 (1): 46. doi: 10.1186/s40168-018-0428-1 . PMC   5845141 . PMID   29523192. S2CID   3856584. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  28. 1 2 Selosse, Marc-André; Bessis, Alain; Pozo, María J. (2014). "Microbial priming of plant and animal immunity: Symbionts as developmental signals". Trends in Microbiology. 22 (11): 607–613. doi:10.1016/j.tim.2014.07.003. PMID   25124464.
  29. ↑ Rosenberg, Eugene; Sharon, Gil; Atad, Ilil; Zilber-Rosenberg, Ilana (2010). "The evolution of animals and plants via symbiosis with microorganisms". Environmental Microbiology Reports. 2 (4): 500–506. doi:10.1111/j.1758-2229.2010.00177.x. PMID   23766221.
  30. ↑ Rosenberg, Eugene; Zilber-Rosenberg, Ilana (2018). "The hologenome concept of evolution after 10 years". Microbiome. 6 (1): 78. doi: 10.1186/s40168-018-0457-9 . PMC   5922317 . PMID   29695294. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  31. ↑ Douglas, Angela E.; Werren, John H. (2016). "Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts". mBio. 7 (2): e02099. doi:10.1128/mBio.02099-15. PMC   4817262 . PMID   27034285.
  32. 1 2 Moran, Nancy A.; Sloan, Daniel B. (2015). "The Hologenome Concept: Helpful or Hollow?". PLOS Biology. 13 (12): e1002311. doi: 10.1371/journal.pbio.1002311 . PMC   4670207 . PMID   26636661. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  33. ↑ Guimarães, Paulo R.; Pires, Mathias M.; Jordano, Pedro; Bascompte, Jordi; Thompson, John N. (2017). "Indirect effects drive coevolution in mutualistic networks". Nature. 550 (7677): 511–514. Bibcode:2017Natur.550..511G. doi:10.1038/nature24273. PMID   29045396. S2CID   205261069.
  34. 1 2 Dubilier, Nicole; Bergin, Claudia; Lott, Christian (2008). "Symbiotic diversity in marine animals: The art of harnessing chemosynthesis". Nature Reviews Microbiology. 6 (10): 725–740. doi:10.1038/nrmicro1992. PMID   18794911. S2CID   3622420.
  35. ↑ Rubin-Blum, Maxim; Antony, Chakkiath Paul; Sayavedra, Lizbeth; Martínez-Pérez, Clara; Birgel, Daniel; Peckmann, Jörn; Wu, Yu-Chen; Cardenas, Paco; MacDonald, Ian; Marcon, Yann; Sahling, Heiko; Hentschel, Ute; Dubilier, Nicole (2019). "Fueled by methane: Deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts". The ISME Journal. 13 (5): 1209–1225. doi:10.1038/s41396-019-0346-7. PMC   6474228 . PMID   30647460. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  36. ↑ Duperron, Sébastien; Halary, Sébastien; Lorion, Julien; Sibuet, Myriam; Gaill, Françoise (2008). "Unexpected co-occurrence of six bacterial symbionts in the gills of the cold seep mussel Idas sp. (Bivalvia: Mytilidae)". Environmental Microbiology. 10 (2): 433–445. doi:10.1111/j.1462-2920.2007.01465.x. PMID   18093159.
  37. ↑ Petersen, Jillian M.; Kemper, Anna; Gruber-Vodicka, Harald; Cardini, Ulisse; Van Der Geest, Matthijs; Kleiner, Manuel; Bulgheresi, Silvia; Mußmann, Marc; Herbold, Craig; Seah, Brandon K.B.; Antony, Chakkiath Paul; Liu, Dan; Belitz, Alexandra; Weber, Miriam (2017). "Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation". Nature Microbiology. 2 (1): 16195. doi:10.1038/nmicrobiol.2016.195. PMC   6872982 . PMID   27775707.
  38. ↑ Ponnudurai, Ruby; Kleiner, Manuel; Sayavedra, Lizbeth; Petersen, Jillian M.; Moche, Martin; Otto, Andreas; Becher, Dörte; Takeuchi, Takeshi; Satoh, Noriyuki; Dubilier, Nicole; Schweder, Thomas; Markert, Stephanie (2017). "Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis". The ISME Journal. 11 (2): 463–477. doi:10.1038/ismej.2016.124. PMC   5270565 . PMID   27801908.
  39. ↑ Decelle, Johan; Colin, Sébastien; Foster, Rachel A. (2015). "Photosymbiosis in Marine Planktonic Protists". Marine Protists. pp. 465–500. doi:10.1007/978-4-431-55130-0_19. ISBN   978-4-431-55129-4.
  40. ↑ Not, Fabrice; Probert, Ian; Gerikas Ribeiro, Catherine; Crenn, Klervi; Guillou, Laure; Jeanthon, Christian; Vaulot, Daniel (2016). "Photosymbiosis in Marine Pelagic Environments". The Marine Microbiome. pp. 305–332. doi:10.1007/978-3-319-33000-6_11. ISBN   978-3-319-32998-7.
  41. ↑ Seyedsayamdost, Mohammad R.; Case, Rebecca J.; Kolter, Roberto; Clardy, Jon (2011). "The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis". Nature Chemistry. 3 (4): 331–335. Bibcode:2011NatCh...3..331S. doi:10.1038/nchem.1002. PMC   3376411 . PMID   21430694.
  42. ↑ Segev, Einat; Wyche, Thomas P.; Kim, Ki Hyun; Petersen, Jörn; Ellebrandt, Claire; Vlamakis, Hera; Barteneva, Natasha; Paulson, Joseph N.; Chai, Liraz; Clardy, Jon; Kolter, Roberto (2016). "Dynamic metabolic exchange governs a marine algal-bacterial interaction". eLife. 5. doi: 10.7554/eLife.17473 . PMC   5148602 . PMID   27855786.
  43. ↑ Hollants, Joke; Leliaert, Frederik; Verbruggen, Heroen; De Clerck, Olivier; Willems, Anne (2013). "Host specificity and coevolution of Flavobacteriaceae endosymbionts within the siphonous green seaweed Bryopsis". Molecular Phylogenetics and Evolution. 67 (3): 608–614. doi:10.1016/j.ympev.2013.02.025. hdl: 1854/LU-3236190 . PMID   23499613.
  44. ↑ Arboleda, Enrique; Hartenstein, Volker; Martinez, Pedro; Reichert, Heinrich; Sen, Sonia; Sprecher, Simon; Bailly, Xavier (2018). "An Emerging System to Study Photosymbiosis, Brain Regeneration, Chronobiology, and Behavior: The Marine Acoel Symsagittifera roscoffensis" (PDF). BioEssays. 40 (10): e1800107. doi:10.1002/bies.201800107. PMID   30151860. S2CID   52095265.
  45. ↑ Baumgarten, Sebastian; Simakov, Oleg; Esherick, Lisl Y.; Liew, Yi Jin; Lehnert, Erik M.; Michell, Craig T.; Li, Yong; Hambleton, Elizabeth A.; Guse, Annika; Oates, Matt E.; Gough, Julian; Weis, Virginia M.; Aranda, Manuel; Pringle, John R.; Voolstra, Christian R. (2015). "The genome of Aiptasia, a sea anemone model for coral symbiosis". Proceedings of the National Academy of Sciences. 112 (38): 11893–11898. Bibcode:2015PNAS..11211893B. doi: 10.1073/pnas.1513318112 . PMC   4586855 . PMID   26324906.
  46. ↑ Wolfowicz, Iliona; Baumgarten, Sebastian; Voss, Philipp A.; Hambleton, Elizabeth A.; Voolstra, Christian R.; Hatta, Masayuki; Guse, Annika (2016). "Aiptasia sp. Larvae as a model to reveal mechanisms of symbiont selection in cnidarians". Scientific Reports. 6: 32366. Bibcode:2016NatSR...632366W. doi:10.1038/srep32366. PMC   5007887 . PMID   27582179.
  47. ↑ Ohdera, Aki H.; Abrams, Michael J.; Ames, Cheryl L.; Baker, David M.; Suescún-Bolívar, Luis P.; Collins, Allen G.; Freeman, Christopher J.; Gamero-Mora, Edgar; Goulet, Tamar L.; Hofmann, Dietrich K.; Jaimes-Becerra, Adrian; Long, Paul F.; Marques, Antonio C.; Miller, Laura A.; Mydlarz, Laura D.; Morandini, Andre C.; Newkirk, Casandra R.; Putri, Sastia P.; Samson, Julia E.; Stampar, Sérgio N.; Steinworth, Bailey; Templeman, Michelle; Thomé, Patricia E.; Vlok, Marli; Woodley, Cheryl M.; Wong, Jane C.Y.; Martindale, Mark Q.; Fitt, William K.; Medina, Mónica (2018). "Upside-Down but Headed in the Right Direction: Review of the Highly Versatile Cassiopea xamachana System". Frontiers in Ecology and Evolution. 6. doi: 10.3389/fevo.2018.00035 . hdl: 11449/176281 . CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  48. ↑ Lehnert, Erik M.; Burriesci, Matthew S.; Pringle, John R. (2012). "Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: The transcriptome of aposymbiotic A. Pallida". BMC Genomics. 13: 271. doi: 10.1186/1471-2164-13-271 . PMC   3427133 . PMID   22726260.
  49. ↑ McFall-Ngai, Margaret J. (2014). "The Importance of Microbes in Animal Development: Lessons from the Squid-Vibrio Symbiosis". Annual Review of Microbiology. 68: 177–194. doi:10.1146/annurev-micro-091313-103654. PMC   6281398 . PMID   24995875.
  50. ↑ Cooper, Matthew B.; Kazamia, Elena; Helliwell, Katherine E.; Kudahl, Ulrich Johan; Sayer, Andrew; Wheeler, Glen L.; Smith, Alison G. (2019). "Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae". The ISME Journal. 13 (2): 334–345. doi:10.1038/s41396-018-0274-y. PMC   6331578 . PMID   30228381.
  51. ↑ Wichard, Thomas (2015). "Exploring bacteria-induced growth and morphogenesis in the green macroalga order Ulvales (Chlorophyta)". Frontiers in Plant Science. 6: 86. doi: 10.3389/fpls.2015.00086 . PMC   4347444 . PMID   25784916.
  52. 1 2 Kessler, Ralf W.; Weiss, Anne; Kuegler, Stefan; Hermes, Cornelia; Wichard, Thomas (2018). "Macroalgal-bacterial interactions: Role of dimethylsulfoniopropionate in microbial gardening by Ulva(Chlorophyta)". Molecular Ecology. 27 (8): 1808–1819. doi:10.1111/mec.14472. PMID   29290092. S2CID   46763098.
  53. ↑ Thompson JR, Rivera HE, Closek CJ, Medina M (2014). "Microbes in the coral holobiont: partners through evolution, development, and ecological interactions". Frontiers in Cellular and Infection Microbiology. 4: 176. doi: 10.3389/fcimb.2014.00176 . PMC   4286716 . PMID   25621279.
  54. ↑ Zilius, Mindaugas; Bonaglia, Stefano; Broman, Elias; Chiozzini, Vitor Gonsalez; Samuiloviene, Aurelija; Nascimento, Francisco J. A.; Cardini, Ulisse; Bartoli, Marco (2020). "N2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont". Scientific Reports. 10 (1): 13966. doi:10.1038/s41598-020-70834-0. PMC   7435186 . PMID   32811860. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  55. ↑ Ugarelli K, Chakrabarti S, Laas P, Stingl U (December 2017). "The Seagrass Holobiont and Its Microbiome". Microorganisms. 5 (4): 81. doi: 10.3390/microorganisms5040081 . PMC   5748590 . PMID   29244764. CC-BY icon.svg Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License
  56. ↑ Cavalcanti GS, Shukla P, Morris M, Ribeiro B, Foley M, Doane MP, Thompson CC, Edwards MS, Dinsdale EA, Thompson FL (September 2018). "Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification". BMC Genomics. 19 (1): 701. doi: 10.1186/s12864-018-5064-4 . PMC   6154897 . PMID   30249182. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  57. 1 2 3 Troussellier, Marc; Escalas, Arthur; Bouvier, Thierry; Mouillot, David (2017). "Sustaining Rare Marine Microorganisms: Macroorganisms as Repositories and Dispersal Agents of Microbial Diversity". Frontiers in Microbiology. 8: 947. doi: 10.3389/fmicb.2017.00947 . PMC   5447324 . PMID   28611749.
  58. ↑ Bouchard Marmen, Mariève; Kenchington, Ellen; Ardyna, Mathieu; Archambault, Philippe (2017). "Influence of seabird colonies and other environmental variables on benthic community structure, Lancaster Sound Region, Canadian Arctic". Journal of Marine Systems. 167: 105–117. Bibcode:2017JMS...167..105B. doi: 10.1016/j.jmarsys.2016.11.021 .
  59. ↑ Smriga, Steven; Sandin, Stuart A.; Azam, Farooq (2010). "Abundance, diversity, and activity of microbial assemblages associated with coral reef fish guts and feces". FEMS Microbiology Ecology. 73 (1): 31–42. doi: 10.1111/j.1574-6941.2010.00879.x . PMID   20455942.
  60. ↑ Webster, Nicole S.; Taylor, Michael W.; Behnam, Faris; Lücker, Sebastian; Rattei, Thomas; Whalan, Stephen; Horn, Matthias; Wagner, Michael (2009). "Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts". Environmental Microbiology. 12 (8): 2070–2082. doi:10.1111/j.1462-2920.2009.02065.x. PMC   2936111 . PMID   21966903.
  61. 1 2 Burke, C.; Steinberg, P.; Rusch, D.; Kjelleberg, S.; Thomas, T. (2011). "Bacterial community assembly based on functional genes rather than species". Proceedings of the National Academy of Sciences. 108 (34): 14288–14293. Bibcode:2011PNAS..10814288B. doi: 10.1073/pnas.1101591108 . PMC   3161577 . PMID   21825123.
  62. ↑ Burke, Catherine; Thomas, Torsten; Lewis, Matt; Steinberg, Peter; Kjelleberg, Staffan (2011). "Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis". The ISME Journal. 5 (4): 590–600. doi:10.1038/ismej.2010.164. PMC   3105733 . PMID   21048801. S2CID   9982783.
  63. ↑ Chiarello, Marlène; Auguet, Jean-Christophe; Bettarel, Yvan; Bouvier, Corinne; Claverie, Thomas; Graham, Nicholas A. J.; Rieuvilleneuve, Fabien; Sucré, Elliot; Bouvier, Thierry; Villéger, Sébastien (2018). "Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet". Microbiome. 6 (1): 147. doi: 10.1186/s40168-018-0530-4 . PMC   6109317 . PMID   30143055.
  64. ↑ Falkowski, P. G.; Fenchel, T.; Delong, E. F. (2008). "The Microbial Engines That Drive Earth's Biogeochemical Cycles". Science. 320 (5879): 1034–1039. Bibcode:2008Sci...320.1034F. doi:10.1126/science.1153213. PMID   18497287. S2CID   2844984.
  65. ↑ Madsen, Eugene L. (2011). "Microorganisms and their roles in fundamental biogeochemical cycles". Current Opinion in Biotechnology. 22 (3): 456–464. doi:10.1016/j.copbio.2011.01.008. PMID   21333523.
  66. ↑ Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; Sharon, Itai; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Singh, Andrea; Wilkins, Michael J.; Karaoz, Ulas; Brodie, Eoin L.; Williams, Kenneth H.; Hubbard, Susan S.; Banfield, Jillian F. (2016). "Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system". Nature Communications. 7: 13219. Bibcode:2016NatCo...713219A. doi:10.1038/ncomms13219. PMC   5079060 . PMID   27774985.
  67. ↑ Thompson, A. W.; Foster, R. A.; Krupke, A.; Carter, B. J.; Musat, N.; Vaulot, D.; Kuypers, M. M. M.; Zehr, J. P. (2012). "Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga". Science. 337 (6101): 1546–1550. Bibcode:2012Sci...337.1546T. doi:10.1126/science.1222700. PMID   22997339. S2CID   7071725.
  68. ↑ Martínez-Pérez, Clara; Mohr, Wiebke; Löscher, Carolin R.; Dekaezemacker, Julien; Littmann, Sten; Yilmaz, Pelin; Lehnen, Nadine; Fuchs, Bernhard M.; Lavik, Gaute; Schmitz, Ruth A.; Laroche, Julie; Kuypers, Marcel M. M. (2016). "The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle". Nature Microbiology. 1 (11): 16163. doi:10.1038/nmicrobiol.2016.163. PMID   27617976. S2CID   7051606.
  69. ↑ Raina, Jean-Baptiste; Tapiolas, Dianne; Willis, Bette L.; Bourne, David G. (2009). "Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur". Applied and Environmental Microbiology. 75 (11): 3492–3501. Bibcode:2009ApEnM..75.3492R. doi:10.1128/AEM.02567-08. PMC   2687302 . PMID   19346350.
  70. 1 2 Fiore, Cara L.; Jarett, Jessica K.; Olson, Nathan D.; Lesser, Michael P. (2010). "Nitrogen fixation and nitrogen transformations in marine symbioses". Trends in Microbiology. 18 (10): 455–463. doi:10.1016/j.tim.2010.07.001. PMID   20674366.
  71. ↑ Cardini, Ulisse; Bednarz, Vanessa N.; Naumann, Malik S.; Van Hoytema, Nanne; Rix, Laura; Foster, Rachel A.; Al-Rshaidat, Mamoon M. D.; Wild, Christian (2015). "Functional significance of dinitrogen fixation in sustaining coral productivity under oligotrophic conditions". Proceedings of the Royal Society B: Biological Sciences. 282 (1818). doi:10.1098/rspb.2015.2257. PMC   4650168 . PMID   26511052.
  72. ↑ De Goeij, Jasper M.; Van Oevelen, Dick; Vermeij, Mark J. A.; Osinga, Ronald; Middelburg, Jack J.; De Goeij, Anton F. P. M.; Admiraal, Wim (2013). "Surviving in a Marine Desert: The Sponge Loop Retains Resources within Coral Reefs". Science. 342 (6154): 108–110. Bibcode:2013Sci...342..108D. doi:10.1126/science.1241981. PMID   24092742. S2CID   6720678.
  73. ↑ Rix, Laura; Goeij, Jasper M.; Oevelen, Dick; Struck, Ulrich; Al‐Horani, Fuad A.; Wild, Christian; Naumann, Malik S. (2017). "Differential recycling of coral and algal dissolved organic matter via the sponge loop". Functional Ecology. 31 (3): 778–789. doi: 10.1111/1365-2435.12758 .
  74. ↑ Bonaglia, Stefano; Brüchert, Volker; Callac, Nolwenn; Vicenzi, Alessandra; Chi Fru, Ernest; Nascimento, Francisco J. A. (2017). "Methane fluxes from coastal sediments are enhanced by macrofauna". Scientific Reports. 7 (1): 13145. Bibcode:2017NatSR...713145B. doi:10.1038/s41598-017-13263-w. PMC   5640653 . PMID   29030563.
  75. ↑ Venn, A.A.; Loram, J.E.; Douglas, A.E. (2008). "Photosynthetic symbioses in animals". Journal of Experimental Botany. 59 (5): 1069–1080. doi: 10.1093/jxb/erm328 . PMID   18267943.
  76. ↑ Berkelmans, Ray; Van Oppen, Madeleine J.H (2006). "The role of zooxanthellae in the thermal tolerance of corals: A 'nugget of hope' for coral reefs in an era of climate change". Proceedings of the Royal Society B: Biological Sciences. 273 (1599): 2305–2312. doi:10.1098/rspb.2006.3567. PMC   1636081 . PMID   16928632.
  77. ↑ Gilbert, Scott F.; McDonald, Emily; Boyle, Nicole; Buttino, Nicholas; Gyi, Lin; Mai, Mark; Prakash, Neelakantan; Robinson, James (2010). "Symbiosis as a source of selectable epigenetic variation: Taking the heat for the big guy". Philosophical Transactions of the Royal Society B: Biological Sciences. 365 (1540): 671–678. doi:10.1098/rstb.2009.0245. PMC   2817139 . PMID   20083641.
  78. ↑ Dittami, Simon M.; Duboscq-Bidot, Laëtitia; Perennou, Morgan; Gobet, Angélique; Corre, Erwan; Boyen, Catherine; Tonon, Thierry (2016). "Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures". The ISME Journal. 10 (1): 51–63. doi:10.1038/ismej.2015.104. PMC   4681850 . PMID   26114888.
  79. ↑ Shapira, Michael (2016). "Gut Microbiotas and Host Evolution: Scaling up Symbiosis". Trends in Ecology & Evolution. 31 (7): 539–549. doi:10.1016/j.tree.2016.03.006. PMID   27039196.
  80. ↑ Godoy, Oscar; Bartomeus, Ignasi; Rohr, Rudolf P.; Saavedra, Serguei (2018). "Towards the Integration of Niche and Network Theories". Trends in Ecology & Evolution. 33 (4): 287–300. doi:10.1016/j.tree.2018.01.007. hdl: 10261/164597 . PMID   29471971.
  81. ↑ Bright, Monika; Bulgheresi, Silvia (2010). "A complex journey: Transmission of microbial symbionts". Nature Reviews Microbiology. 8 (3): 218–230. doi:10.1038/nrmicro2262. PMC   2967712 . PMID   20157340.
  82. ↑ Funkhouser, Lisa J.; Bordenstein, Seth R. (2013). "Mom Knows Best: The Universality of Maternal Microbial Transmission". PLOS Biology. 11 (8): e1001631. doi: 10.1371/journal.pbio.1001631 . PMC   3747981 . PMID   23976878.
  83. ↑ Björk, Johannes R.; Díez-Vives, Cristina; Astudillo-García, Carmen; Archie, Elizabeth A.; Montoya, José M. (2019). "Vertical transmission of sponge microbiota is inconsistent and unfaithful". Nature Ecology & Evolution. 3 (8): 1172–1183. doi:10.1038/s41559-019-0935-x. PMC   6914380 . PMID   31285574.
  84. ↑ Brooks, Andrew W.; Kohl, Kevin D.; Brucker, Robert M.; Van Opstal, Edward J.; Bordenstein, Seth R. (2016). "Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History". PLOS Biology. 14 (11): e2000225. doi: 10.1371/journal.pbio.2000225 . PMC   5115861 . PMID   27861590.
  85. ↑ Kazamia, Elena; Helliwell, Katherine Emma; Purton, Saul; Smith, Alison Gail (2016). "How mutualisms arise in phytoplankton communities: Building eco‐evolutionary principles for aquatic microbes". Ecology Letters. 19 (7): 810–822. doi:10.1111/ele.12615. PMC   5103174 . PMID   27282316.
  86. ↑ Pollock, F. Joseph; McMinds, Ryan; Smith, Styles; Bourne, David G.; Willis, Bette L.; Medina, Mónica; Thurber, Rebecca Vega; Zaneveld, Jesse R. (2018). "Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny". Nature Communications. 9 (1): 4921. Bibcode:2018NatCo...9.4921P. doi:10.1038/s41467-018-07275-x. PMC   6250698 . PMID   30467310.
  87. ↑ Franzenburg, S.; Walter, J.; Kunzel, S.; Wang, J.; Baines, J. F.; Bosch, T. C. G.; Fraune, S. (2013). "Distinct antimicrobial peptide expression determines host species-specific bacterial associations". Proceedings of the National Academy of Sciences. 110 (39): E3730–E3738. Bibcode:2013PNAS..110E3730F. doi: 10.1073/pnas.1304960110 . PMC   3785777 . PMID   24003149.
  88. ↑ Zheng, Danping; Liwinski, Timur; Elinav, Eran (2020). "Interaction between microbiota and immunity in health and disease". Cell Research. 30 (6): 492–506. doi:10.1038/s41422-020-0332-7. PMC   7264227 . PMID   32433595.
  89. ↑ Lebeis, S. L.; Paredes, S. H.; Lundberg, D. S.; Breakfield, N.; Gehring, J.; McDonald, M.; Malfatti, S.; Glavina Del Rio, T.; Jones, C. D.; Tringe, S. G.; Dangl, J. L. (2015). "Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa". Science. 349 (6250): 860–864. Bibcode:2015Sci...349..860L. doi: 10.1126/science.aaa8764 . PMID   26184915. S2CID   2914865.
  90. ↑ Saha, Mahasweta; Weinberger, Florian (2019). "Microbial "gardening" by a seaweed holobiont: Surface metabolites attract protective and deter pathogenic epibacterial settlement" (PDF). Journal of Ecology. 107 (5): 2255–2265. doi:10.1111/1365-2745.13193. S2CID   165054090.
  91. ↑ Ochsenkühn, Michael A.; Schmitt-Kopplin, Philippe; Harir, Mourad; Amin, Shady A. (2018). "Coral metabolite gradients affect microbial community structures and act as a disease cue". Communications Biology. 1: 184. doi:10.1038/s42003-018-0189-1. PMC   6218554 . PMID   30417121.
  92. ↑ Gribben, Paul E.; Nielsen, Shaun; Seymour, Justin R.; Bradley, Daniel J.; West, Matthew N.; Thomas, Torsten (2017). "Microbial communities in marine sediments modify success of an invasive macrophyte". Scientific Reports. 7 (1): 9845. Bibcode:2017NatSR...7.9845G. doi:10.1038/s41598-017-10231-2. PMC   5575248 . PMID   28852143.
  93. 1 2 3 4 Cirri, Emilio; Pohnert, Georg (2019). "Algae−bacteria interactions that balance the planktonic microbiome". New Phytologist. 223 (1): 100–106. doi: 10.1111/nph.15765 . PMID   30825329.
  94. ↑ Nemergut, Diana R.; Schmidt, Steven K.; Fukami, Tadashi; O'Neill, Sean P.; Bilinski, Teresa M.; Stanish, Lee F.; Knelman, Joseph E.; Darcy, John L.; Lynch, Ryan C.; Wickey, Phillip; Ferrenberg, Scott (2013). "Patterns and Processes of Microbial Community Assembly". Microbiology and Molecular Biology Reviews. 77 (3): 342–356. doi:10.1128/MMBR.00051-12. PMC   3811611 . PMID   24006468.
  95. ↑ Dini-Andreote, Francisco; Stegen, James C.; Van Elsas, Jan Dirk; Salles, Joana Falcão (2015). "Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession". Proceedings of the National Academy of Sciences. 112 (11): E1326–E1332. Bibcode:2015PNAS..112E1326D. doi: 10.1073/pnas.1414261112 . PMC   4371938 . PMID   25733885.
  96. ↑ Vienne, D. M.; Refrégier, G.; López‐Villavicencio, M.; Tellier, A.; Hood, M. E.; Giraud, T. (2013). "Cospeciation vs host‐shift speciation: Methods for testing, evidence from natural associations and relation to coevolution". New Phytologist. 198 (2): 347–385. doi: 10.1111/nph.12150 . PMID   23437795.
  97. ↑ Peek, A. S.; Feldman, R. A.; Lutz, R. A.; Vrijenhoek, R. C. (1998). "Cospeciation of chemoautotrophic bacteria and deep sea clams". Proceedings of the National Academy of Sciences. 95 (17): 9962–9966. Bibcode:1998PNAS...95.9962P. doi: 10.1073/pnas.95.17.9962 . PMC   21444 . PMID   9707583.
  98. ↑ Lanterbecq, Déborah; Rouse, Grey W.; Eeckhaut, Igor (2010). "Evidence for cospeciation events in the host–symbiont system involving crinoids (Echinodermata) and their obligate associates, the myzostomids (Myzostomida, Annelida)". Molecular Phylogenetics and Evolution. 54 (2): 357–371. doi:10.1016/j.ympev.2009.08.011. PMID   19686859.
  99. ↑ Zaneveld, Jesse R.; McMinds, Ryan; Vega Thurber, Rebecca (2017). "Stress and stability: Applying the Anna Karenina principle to animal microbiomes". Nature Microbiology. 2 (9): 17121. doi:10.1038/nmicrobiol.2017.121. PMID   28836573. S2CID   37180263.
  100. ↑ The Rasputin Effect: When Commensals and Symbionts Become Parasitic. Advances in Environmental Microbiology. Vol. 3. 2016. doi:10.1007/978-3-319-28170-4. ISBN   978-3-319-28168-1. S2CID   7567999.
  101. ↑ Egan, Suhelen; Gardiner, Melissa (2016). "Microbial Dysbiosis: Rethinking Disease in Marine Ecosystems". Frontiers in Microbiology. 7: 991. doi: 10.3389/fmicb.2016.00991 . PMC   4914501 . PMID   27446031.
  102. ↑ Baker, David M.; Freeman, Christopher J.; Wong, Jane C.Y.; Fogel, Marilyn L.; Knowlton, Nancy (2018). "Climate change promotes parasitism in a coral symbiosis". The ISME Journal. 12 (3): 921–930. doi:10.1038/s41396-018-0046-8. PMC   5864192 . PMID   29379177.
  103. ↑ Bell, James J.; Rovellini, Alberto; Davy, Simon K.; Taylor, Michael W.; Fulton, Elizabeth A.; Dunn, Matthew R.; Bennett, Holly M.; Kandler, Nora M.; Luter, Heidi M.; Webster, Nicole S. (2018). "Climate change alterations to ecosystem dominance: How might sponge-dominated reefs function?" (PDF). Ecology. 99 (9): 1920–1931. doi:10.1002/ecy.2446. PMID   29989167. S2CID   51609262.

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