![Marine animal host-microbiome relationships](https://upload.wikimedia.org/wikipedia/commons/b/be/Marine_animal_host-microbiome_relationships.jpg)
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
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 (or microbe) is any microscopic livin ...
associating with diverse
marine animal
Marine life, sea life, or ocean life is the plants, animals and other organisms that live in the salt water of seas or oceans, or the brackish water of coastal estuaries. At a fundamental level, marine life affects the nature of the planet. M ...
hosts is moving the field into studies that address interactions between the animal host and a more multi-member
microbiome
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 wel ...
. 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.
In the oceans, it is challenging to find
eukaryotic organism
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bact ...
s that do not live in close relationship with a microbial partner. Host-associated microbiomes also influence
biogeochemical cycling
A biogeochemical cycle (or more generally a cycle of matter) is the pathway by which a chemical substance cycles (is turned over or moves through) the biotic and the abiotic compartments of Earth. The biotic compartment is the biosphere and the ...
within ecosystems with
cascading effects on biodiversity and ecosystem processes. The microbiomes of diverse marine animals are currently under study, from simplistic organisms including
sponge
Sponges, the members of the phylum Porifera (; meaning 'pore bearer'), are a basal animal clade as a sister of the diploblasts. They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through t ...
s and
ctenophores to more complex organisms such as
sea squirt
Ascidiacea, commonly known as the ascidians, tunicates (in part), and sea squirts (in part), is a polyphyletic class in the subphylum Tunicata of sac-like marine invertebrate filter feeders. Ascidians are characterized by a tough outer "tunic" m ...
s and
shark
Sharks are a group of elasmobranch fish characterized by a cartilaginous skeleton, five to seven gill slits on the sides of the head, and pectoral fins that are not fused to the head. Modern sharks are classified within the clade Selachimo ...
s.
Background
Within the vast
biological diversity
Biodiversity or biological diversity is the variety and variability of life on Earth. Biodiversity is a measure of variation at the genetic (''genetic variability''), species (''species diversity''), and ecosystem (''ecosystem diversity'') lev ...
that inhabits the world’s oceans, it would be challenging to find a
eukaryotic organism
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bact ...
that does not live in close relationship with a
microbial partner.
Such
symbioses, i.e., persistent interactions between host and microbe in which none of the partners gets harmed and at least one of them benefits, are ubiquitous from shallow reefs to
deep-sea hydrothermal vent
A hydrothermal vent is a fissure on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and hotspot ...
s. Studies on
coral
Corals are marine invertebrates within the class Anthozoa of the phylum Cnidaria. They typically form compact colonies of many identical individual polyps. Coral species include the important reef builders that inhabit tropical oceans and sec ...
s,
sponge
Sponges, the members of the phylum Porifera (; meaning 'pore bearer'), are a basal animal clade as a sister of the diploblasts. They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through t ...
s,
and
mollusk
Mollusca is the second-largest phylum of invertebrate animals after the Arthropoda, the members of which are known as molluscs or mollusks (). Around 85,000 extant species of molluscs are recognized. The number of fossil species is e ...
s
have revealed some of the profoundly important symbiotic roles microbes play in the lives of their hosts. These studies, however, have tended to focus on a small number of specific microbial taxa. In contrast, most hosts retain groups of many hundreds of different microbes (i.e., a
microbiome
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 wel ...
, which themselves can vary throughout the ontogeny of the host and as a result of environmental perturbations.
Rather than host-associated microbes functioning independently, complex multi-assemblage microbiomes have major impact on the fitness and function of their hosts. Studying these complex interactions and biological outcomes is difficult, but to understand the origin and evolution of organisms and populations and the structure and function of communities and ecosystems, the understanding of symbioses in host–microbiome systems needs advancing.
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There are many outstanding questions in ecology and evolution that could be addressed by expanding the phylogenetic and ecological breadth of host-associated microbiome studies, including all possible interactions throughout the microbiome. There is strong empirical evidence and new consensus that biodiversity (i.e., the richness of species and their interactions) pervasively influences the functioning of Earth’s ecosystems, including ecosystem productivity. However, this research has focused almost exclusively on macroorganisms. Because microbial symbionts are integral parts of most living organisms,
the understanding of how microbial symbionts contribute to host performance and adaptability needs broadening.
Foundations of productive ecosystems
Ecosystem engineers, such as many types of corals, deep-sea
mussel
Mussel () is the common name used for members of several families of bivalve molluscs, from saltwater and Freshwater bivalve, freshwater habitats. These groups have in common a shell whose outline is elongated and asymmetrical compared with other ...
s, and hydrothermal vent
tubeworm
A tubeworm is any worm-like sessile invertebrate that anchors its tail to an underwater surface and secretes around its body a mineral tube, into which it can withdraw its entire body.
Tubeworms are found among the following taxa:
* Annelida, the ...
s, contribute to
primary productivity
In ecology, primary production is the synthesis of organic compounds from atmospheric or aqueous carbon dioxide. It principally occurs through the process of photosynthesis, which uses light as its source of energy, but it also occurs through c ...
and create the structural habitats and nutrient resources that are the foundation of their respective ecosystems. All of these taxa engage in
mutualistic nutritional symbioses with microbes. There are many examples of marine nutritional mutualisms in which microbes enable hosts to utilize resources or substrates otherwise unavailable to the host alone. Such symbioses have been described in detail in reduced and anoxic sediments (e.g.,
lucinid clams,
stilbonematid nematodes, and gutless
oligochaetes
Oligochaeta () is a subclass of animals in the phylum Annelida, which is made up of many types of aquatic and terrestrial worms, including all of the various earthworms. Specifically, oligochaetes comprise the terrestrial megadrile earthworms ...
) and hydrothermal vents (e.g., the
giant tube worm
''Riftia pachyptila'', commonly known as the giant tube worm and less commonly known as the Giant beardworm, is a marine invertebrate in the phylum Annelida (formerly grouped in phylum Pogonophora and Vestimentifera) related to tube worm ...
or
deep-sea mussels). Moreover, many
foundational species of marine
macroalgae
Seaweed, or macroalgae, refers to thousands of species of macroscopic, multicellular, marine algae. The term includes some types of '' Rhodophyta'' (red), ''Phaeophyta'' (brown) and ''Chlorophyta'' (green) macroalgae. Seaweed species such as ...
are vitamin
auxotroph
Auxotrophy ( grc, αὐξάνω "to increase"; ''τροφή'' "nourishment") is the inability of an organism to synthesize a particular organic compound required for its growth (as defined by IUPAC). An auxotroph is an organism that displays this ...
s (for example, half of more than 300 surveyed species were unable to synthesize
cobalamin
Vitamin B12, also known as cobalamin, is a water-soluble vitamin involved in metabolism. It is one of eight B vitamins. It is required by animals, which use it as a cofactor in DNA synthesis, in both fatty acid and amino acid metabolism. ...
), and their productivity depends on provisioning from their
epiphytic
An epiphyte is an organism that grows on the surface of a plant and derives its moisture and nutrients from the air, rain, water (in marine environments) or from debris accumulating around it. The plants on which epiphytes grow are called phoroph ...
bacteria. Reefs often consist of
stony corals, one of the most well-known examples of a mutualistic symbiosis, in which the
dinoflagellate alga Symbiodiniaceae supplies the coral with
glucose
Glucose is a simple sugar with the molecular formula . Glucose is overall the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, using ...
,
glycerol
Glycerol (), also called glycerine in British English and glycerin in American English, is a simple triol compound. It is a colorless, odorless, viscous liquid that is sweet-tasting and non-toxic. The glycerol backbone is found in lipids known ...
, and
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
s, while the coral provides the algae with a protected environment and limiting compounds (e.g., nitrogen species) needed for photosynthesis. However, this is a classic example of a mutualistic symbiosis that is sensitive to environmental disturbances, which can disrupt the fragile interactions between host and microbe. When reefs become warm and eutrophic, mutualistic Symbiodiniaceae may induce cellular damage to the host and/or sequester more resources for their own growth, thereby injuring and parasitizing their hosts.
Reef fishes, which seek homes on
coral reef
A coral reef is an underwater ecosystem characterized by reef-building corals. Reefs are formed of colonies of coral polyps held together by calcium carbonate. Most coral reefs are built from stony corals, whose polyps cluster in groups.
Co ...
s, are important in fostering coral recovery in the wake of disturbance. Epulopiscium bacteria in the guts of surgeonfishes produce enzymes that allow their hosts to digest complex
polysaccharides, enabling the host fish to feed on tough, leathery red and brown macroalgae. This trophic innovation has facilitated
niche diversification among coral reef
herbivore
A herbivore is an animal anatomically and physiologically adapted to eating plant material, for example foliage or marine algae, for the main component of its diet. As a result of their plant diet, herbivorous animals typically have mouthpart ...
s.
Surgeonfishes are critical to the functioning of Indo-Pacific coral reefs, as they are among the only fishes capable of consuming large macroalgae that bloom in the wake of
ecosystem disturbance and suppress coral recovery.
![Olavius algarvensis from Elba, Italy](https://upload.wikimedia.org/wikipedia/commons/5/5f/Olavius_algarvensis_from_Elba%2C_Italy.jpg)
Along with more standard examples of nutritional symbioses in animals, recent advances in
genome sequencing
Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a ...
technology have led to the discovery of many endosymbiotic associations in
marine protists
Marine protists are defined by their habitat as protists that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Life originated as marine single-celled prokaryotes (bacteria an ...
(a protist is a general term to refer to a non-
monophyletic
In cladistics for a group of organisms, monophyly is the condition of being a clade—that is, a group of taxa composed only of a common ancestor (or more precisely an ancestral population) and all of its lineal descendants. Monophyletic gro ...
collection of
unicellular
A unicellular organism, also known as a single-celled organism, is an organism that consists of a single cell, unlike a multicellular organism that consists of multiple cells. Organisms fall into two general categories: prokaryotic organisms and ...
eukaryote
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
s that are not
fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
or in the
Plantae
Plants are predominantly Photosynthesis, photosynthetic eukaryotes of the Kingdom (biology), kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all curr ...
group) These illustrate the incorporation of various new biochemical functions, such as photosynthesis, nitrogen fixation and recycling, and methanogenesis, into protist hosts by endosymbionts. Endosymbiosis in protists is widespread and represents an important source of innovation. Previously unrecognized metabolic innovations of marine microbial symbioses that are ecologically important are discovered regularly. For example, ''
Candidatus
In prokaryote nomenclature, ''Candidatus'' (Latin for candidate of Roman office) is used to name prokaryotic phyla that are well characterized but yet-uncultured. Contemporary sequencing approaches, such as 16S sequencing or metagenomics, provide m ...
'' Kentron (a clade of
Gammaproteobacteria found in association with
ciliate
The ciliates are a group of alveolates characterized by the presence of hair-like organelles called cilia, which are identical in structure to flagellum, eukaryotic flagella, but are in general shorter and present in much larger numbers, with a ...
s) nourish their ciliate hosts in the genus ''
Kentrophoros'' and recycle
acetate and
propionate
Propionic acid (, from the Greek words πρῶτος : ''prōtos'', meaning "first", and πίων : ''píōn'', meaning "fat"; also known as propanoic acid) is a naturally occurring carboxylic acid with chemical formula CH3CH2CO2H. It is a liqu ...
, which are low-value cellular waste products from their hosts, into
biomass
Biomass is plant-based material used as a fuel for heat or electricity production. It can be in the form of wood, wood residues, energy crops, agricultural residues, and waste from industry, farms, and households. Some people use the terms bi ...
. Another example is the anaerobic marine
ciliate
The ciliates are a group of alveolates characterized by the presence of hair-like organelles called cilia, which are identical in structure to flagellum, eukaryotic flagella, but are in general shorter and present in much larger numbers, with a ...
''
Strombidium purpureum''. The ciliate lives under anaerobic conditions and harbors endosymbiotic
purple nonsulfur bacteria that contain both
bacteriochlorophyll a and spirilloxanthin. The endosymbionts are photosynthetically active; hence, this symbiosis represents an evolutionary transition of an aerobic organism to an anaerobic one while incorporating
organelle
In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' the ...
s.
Reproduction and host development
Extending beyond nutritional symbioses, microbial symbionts can alter the reproduction, development, and growth of their hosts. Specific bacterial strains in marine biofilms often directly control the recruitment of planktonic larvae and propagules, either by inhibiting settlement or by serving as a settlement cue. For example, the settlement of zoospores from the green alga Ulva intestinalis onto the biofilms of specific bacteria is mediated by their attraction to the quorum-sensing molecule, acyl-homoserine lactone, secreted by the bacteria. Classic examples of marine host–microbe developmental dependence include the observation that algal cultures grown in isolation exhibited abnormal morphologies and the subsequent discovery of morphogenesis-inducing compounds, such as thallusin, secreted by epiphytic bacterial symbionts. Bacteria are also known to influence the growth of marine plants, macroalgae, and phytoplankton by secreting phytohormones such as indole acetic acid and cytokinin-type hormones.
In the marine choanoflagellate Salpingoeca rosetta, both multicellularity and reproduction are triggered by specific bacterial cues, offering a view into the origins of bacterial control over animal development (reviewed by Woznica and King. The benefit to the bacteria, in return, is that they receive physical space to colonize at particular points in the water column typically accessible only to planktonic microbes. Perhaps the best-studied example of intimate host–microbe interactions controlling animal development is the Hawaiian bobtail squid Euprymna scolopes. It lives in a mutualistic symbiosis with the bioluminescent bacteria Aliivibrio fischeri. The bacteria are fed a solution of sugars and amino acids by the host and, in return, provide bioluminescence for countershading and predator avoidance.
This mutualism with microbes provides a selective advantage for the squid in predator–prey interactions. Another invertebrate example can be found in tubeworms, in which Hydroides elegans metamorphosis is mediated by a bacterial inducer and mitogen-activated protein kinase (MAPK) signaling in biofilms.
Biofouling and microbial community assembly
![Marine animals and their associated microbiomes](https://upload.wikimedia.org/wikipedia/commons/d/d1/Marine_animals_and_their_associated_microbiomes.jpg)
Some host-associated microbes produce compounds that prevent
biofouling
Biofouling or biological fouling is the accumulation of microorganisms, plants, algae, or small animals where it is not wanted on surfaces such as ship and submarine hulls, devices such as water inlets, pipework, grates, ponds, and rivers that ...
and regulate microbiome assembly and maintenance in many marine organisms, including sponges, macroalgae, and corals.
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For example, tropical corals harbor diverse bacteria in their surface mucus layer that produce quorum-sensing inhibitors and other antibacterial compounds as a defense against colonization and infection by potential microbial pathogens.
Epiphytic bacteria Epiphytic bacteria are bacteria which live non-parasitically on the surface of a plant on various organs such as the leaves, roots, flowers, buds, seeds and fruit. In current studies it has been determined that epiphytic bacteria generally don't har ...
of marine macroalgae excrete a diverse chemical arsenal capable of selectively shaping further bacterial colonization and deterring the settlement of biofouling marine invertebrates such as bryozoans.
As in corals, these diverse, microbially secreted compounds include not only bactericidal and bacteriostatic antibiotics but also compounds like halogenated furanones, cyclic dipeptides, and acyl-homoserine lactone mimics that disrupt bacterial quorum sensing and inhibit biofilm formation. The bacteria likely are able to utilize the carbon-rich exudates from their hosts.
For example, in the case of giant kelp, the alga emits approximately 20% of primary production as dissolved organic carbon.
Whereas these prior examples illustrate how the microbiomes can protect hosts from surface colonization, a similar phenomenon has also been observed internally in the shipworm Bankia setacea, in which symbionts produce a boronated tartrolon antibiotic thought to keep the wood-digesting cecum clear of bacterial foulants. By producing antimicrobial compounds, these microbes are able to defend their niche space to prevent other organisms from crowding them out.
Biogeochemical cycling
Host-associated microbiomes also influence biogeochemical cycling within ecosystems with cascading effects on biodiversity and ecosystem processes. For example, microbial symbionts comprise up to 40% of the biomass of their sponge hosts. Through a process termed the “sponge-loop,” they convert dissolved organic carbon released by reef organisms into
particulate organic carbon
Particulate organic matter (POM) is a fraction of total organic matter operationally defined as that which does not pass through a filter pore size that typically ranges in size from 0.053 to 2 millimeters.
Particulate organic carbon (POC) is ...
that can be consumed by
heterotrophic
A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...
organisms.
Along with the coral–Symbiodiniaceae mutualism, this sponge-bacterial symbiosis helps explain Darwin’s paradox, i.e., how highly productive coral reef ecosystems exist within otherwise oligotrophic tropical seas. Some sponge symbionts play a significant role in the marine phosphorus cycle by sequestering nutrients in the form of polyphosphate granules in the tissue of their host and nitrogen cycling, e.g., through nitrification, denitrification, and ammonia oxidation.
]. Many macroalgal-associated bacteria are specifically adapted to degrade complex algal polysaccharides (e.g., fucoidan, porphyran, and laminarin) and modify both the quality and quantity of organic carbon supplied to the ecosystem.
The sulfur-oxidizing gill endosymbionts of lucinid clams contribute to primary productivity through chemosynthesis and facilitate the growth of seagrasses (important foundation species) by lowering sulfide concentrations in tropical sediments. Gammaproteobacterial symbionts of lucinid clams and stilbonematid nematodes were also recently shown to be capable of nitrogen fixation (bacterial symbiont genomes encode and express nitrogenase genes, highlighting the role of symbiotic microbes in nutrient cycling in shallow marine systems.
These examples demonstrate the importance of microbial symbioses for the functioning of ocean ecosystems. Understanding symbioses with this same level of detail in the context of complex communities (i.e., whole microbiomes) remains ripe for exploration and, indeed, requires a more integrated framework from the fields of microbiology, evolutionary biology, community ecology, and oceanography. Individual taxa within the microbiome may help hosts withstand a wide range of environmental conditions, including those predicted under scenarios of climate change. Next, we explore two different avenues of how interdisciplinary collaborations could advance this line of research.
Examples
![Relationships between corals and their microbial symbionts](https://upload.wikimedia.org/wikipedia/commons/3/33/Relationships_between_corals_and_their_microbial_symbionts.jpg)
The microbiomes of diverse marine animals are currently under study, from simplistic organisms including sponges and ctenophores to more complex organisms such as sea squirts and sharks.
The relationship between the
Hawaiian bobtail squid and the bioluminescent bacterium ''
Aliivibrio fischeri
''Aliivibrio fischeri'' (also called ''Vibrio fischeri'') is a Gram-negative, rod-shaped bacterium found globally in marine environments. This species has bioluminescent properties, and is found predominantly in symbiosis with various marine anim ...
'' is one of the best studied symbiotic relationships in the sea and is a choice system for general symbiosis research. This relationship has provided insight into fundamental processes in animal-microbial symbioses, and especially biochemical interactions and signaling between the host and bacterium.
The gutless marine
oligochaete
Oligochaeta () is a subclass of animals in the phylum Annelida, which is made up of many types of aquatic and terrestrial worms, including all of the various earthworms. Specifically, oligochaetes comprise the terrestrial megadrile earthworm ...
worm ''
Olavius algarvensis
''Olavius algarvensis'' is a species of gutless oligochaete worm in the family Tubificidae which depends on symbiotic bacteria for its nutrition.
Habitats and research
''Olavius algarvensis'' lives in coastal sediments in the Mediterranean. It ...
'' is another relatively well-studied marine host to microbes. These three centimetre long worms reside within shallow marine sediments of the Mediterranean Sea. The worms do not contain a mouth or a digestive or excretory system, but are instead nourished with the help of a suite of extracellular bacterial endosymbionts that reside upon coordinated use of sulfur present in the environment. This system has benefited from some of the most sophisticated 'omics and visualization tools.
[Woyke, T., Teeling, H., Ivanova, N.N., Huntemann, M., Richter, M., Gloeckner, F.O., Boffelli, D., Anderson, I.J., Barry, K.W., Shapiro, H.J. and Szeto, E. (2006) "Symbiosis insights through metagenomic analysis of a microbial consortium". ''Nature'', 443(7114): 950–955. .] For example, multi-labeled probing has improved visualization of the microbiome and transcriptomics and proteomics have been applied to examine host–microbiome interactions, including energy transfer between the host and microbes and recognition of the consortia by the worm's innate immune system. The major strength of this system is that it does offer the ability to study host–microbiome interactions with a low diversity microbial consortium, and it also offers a number of host and microbial genomic resources
Corals
Coral
Corals are marine invertebrates within the class Anthozoa of the phylum Cnidaria. They typically form compact colonies of many identical individual polyps. Coral species include the important reef builders that inhabit tropical oceans and sec ...
s are one of the more common examples of an animal host whose symbiosis with microalgae can turn to dysbiosis, and is visibly detected as bleaching. Coral microbiomes have been examined in a variety of studies, which demonstrate how variations in the ocean environment, most notably temperature, light, and inorganic nutrients, affect the abundance and performance of the microalgal symbionts, as well as
calcification
Calcification is the accumulation of calcium salts in a body tissue. It normally occurs in the formation of bone, but calcium can be deposited abnormally in soft tissue,Miller, J. D. Cardiovascular calcification: Orbicular origins. ''Nature Ma ...
and physiology of the host.
Studies have also suggested that resident bacteria, archaea, and fungi additionally contribute to nutrient and organic matter cycling within the coral, with viruses also possibly playing a role in structuring the composition of these members, thus providing one of the first glimpses at a multi-domain marine animal symbiosis. The
gammaproteobacterium
Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genera-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically im ...
''
Endozoicomonas
''Endozoicomonas'' is a genus of Gram-negative, aerobic or facultatively anaerobic, chemoorganotrophic, rod-shaped, marine bacteria from the family of Hahellaceae. ''Endozoicomonas'' are symbionts of marine animals.
Scientific History
The ge ...
'' is emerging as a central member of the coral's microbiome, with flexibility in its lifestyle.
[Neave, M.J., Apprill, A., Ferrier-Pagès, C. and Voolstra, C.R. (2016) "Diversity and function of prevalent symbiotic marine bacteria in the genus ''Endozoicomonas''". ''Applied Microbiology and Biotechnology'', 100(19): 8315–8324. .] Given the recent mass bleaching occurring on reefs, corals will likely continue to be a useful and popular system for symbiosis and dysbiosis research.
''
Astrangia poculata
''Astrangia poculata'', the northern star coral or northern cup coral, is a species of non-reefbuilding stony coral in the family Rhizangiidae. It is native to shallow water in the western Atlantic Ocean and the Caribbean Sea. It is also found o ...
'', the northern star coral, is a temperate
stony coral
Scleractinia, also called stony corals or hard corals, are marine animals in the phylum Cnidaria that build themselves a hard skeleton. The individual animals are known as polyps and have a cylindrical body crowned by an oral disc in which a ...
, widely documented along the eastern coast of the United States. The coral can live with and without
zooxanthellae
Zooxanthellae is a colloquial term for single-celled dinoflagellates that are able to live in symbiosis with diverse marine invertebrates including demosponges, corals, jellyfish, and nudibranchs. Most known zooxanthellae are in the genus ''S ...
(algal symbionts), making it an ideal
model organism to study microbial community interactions associated with symbiotic state. However, the ability to develop
primers and
probes to more specifically target key microbial groups has been hindered by the lack of full length
16S rRNA sequences, since sequences produced by the Illumina platform are of insufficient length (approximately 250 base pairs) for the design of primers and probes. In 2019, Goldsmith et al demonstrated
Sanger sequencing
Sanger sequencing is a method of DNA sequencing that involves electrophoresis and is based on the random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. After first being developed by Fred ...
was capable of reproducing the biologically-relevant diversity detected by deeper
next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation ...
, while also producing longer sequences useful to the research community for probe and primer design (see diagram on right).
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Sponges
Sponge
Sponges, the members of the phylum Porifera (; meaning 'pore bearer'), are a basal animal clade as a sister of the diploblasts. They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through t ...
s are common members of the ocean's diverse benthic habitats and their abundance and ability to filter large volumes of seawater have led to the awareness that these organisms play critical roles in influencing benthic and pelagic processes in the ocean. They are one of the oldest lineages of animals, and have a relatively simple body plan that commonly associates with bacteria, archaea, algal protists, fungi, and viruses.
Sponge microbiomes are composed of specialists and generalists, and complexity of their microbiome appears to be shaped by host phylogeny. Studies have shown that the sponge microbiome contributes to nitrogen cycling in the oceans, especially through the oxidation of ammonia by archaea and bacteria. Most recently, microbial symbionts of tropical sponges were shown to produce and store polyphosphate granules, perhaps enabling the host to survive periods of phosphate depletion in oligotrophic marine environments. The microbiomes of some sponge species do appear to change in community structure in response to changing environmental conditions, including temperature and ocean acidification, as well as synergistic impacts.
Cetaceans
![Cetacean_blow's_bacteria](https://upload.wikimedia.org/wikipedia/commons/b/b5/Cetacean_blow%27s_bacteria.png)
The access of microbial samples from the gut out of marine mammals is limited because most species are rare, endangered, and deep divers. There are different techniques for sampling the cetacean's gut microbiome. The most common is collecting fecal samples from the environment and taking a probe from the center that is non-contaminated.
Besides there are studies from rectal swabs and rare studies from stranded dead or living animals direct from the intestine.
The outermost epidermal layer, i.e. the skin, is the first barrier that protects the individual from the outside world and the epidermal microbiome on it is considered an indicator not only of the health of the animal but is also considered an ecological indicator that shows the state of the surrounding environment. Knowing the microbiome of the skin of marine mammals under
''normal'' conditions has allowed us to understand how these communities are different from the free microbial communities found in the sea and how they can change according to abiotic and biotic variations, and also
''''communities vary between healthy and sick individuals
''''.
Cetacea
Cetacea (; , ) is an infraorder of aquatic mammals that includes whales, dolphins, and porpoises. Key characteristics are their fully aquatic lifestyle, streamlined body shape, often large size and exclusively carnivorous diet. They propel them ...
ns are in danger because they are affected by multiple stress factors which make them more vulnerable to various diseases. These animals have been noted to show high susceptibility to airway infections, but very little is known about their respiratory microbiome. Therefore, the sampling of the exhaled breath or "blow" of the cetaceans can provide an assessment of the state of health. Blow is composed of a mixture of
microorganism
A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...
s and
organic material
Organic matter, organic material, or natural organic matter refers to the large source of carbon-based compounds found within natural and engineered, terrestrial, and aquatic environments. It is matter composed of organic compounds that have c ...
, including
lipid
Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...
s,
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
s , and cellular debris derived from the linings of the airways which, when released into the relatively cooler outdoor air, condense to form a visible mass of vapor, which can be collected. There are various methods for collecting exhaled breath samples, one of the most recent is through the use of aerial drones. This method provides a safer, quieter, and less invasive alternative and often a cost-effective option for monitoring fauna and flora. Once obtained, the blow samples are taken to the laboratory and we proceed with the amplification and sequencing of the respiratory tract microbiota. The use of aerial drones has been more successful with large cetaceans due to slow swim speeds and larger blow sizes.
Marine holobionts
Reef-building corals are holobionts that include the coral itself (a eukaryotic
invertebrate
Invertebrates are a paraphyletic group of animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spine''), derived from the notochord. This is a grouping including all animals apart from the chordate ...
within class
Anthozoa),
photosynthetic
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in c ...
dinoflagellates called
zooxanthellae
Zooxanthellae is a colloquial term for single-celled dinoflagellates that are able to live in symbiosis with diverse marine invertebrates including demosponges, corals, jellyfish, and nudibranchs. Most known zooxanthellae are in the genus ''S ...
(''
Symbiodinium
: ''This is about the genus sometimes called Zoox. For the company, see Zoox (company)''
''Symbiodinium'' is a genus of dinoflagellates that encompasses the largest and most prevalent group of endosymbiotic dinoflagellates known. These unicell ...
''), and associated bacteria and viruses.
Co-evolutionary patterns exist for coral microbial communities and coral phylogeny.
File:Trophic connections of the coral holobiont in the planktonic food web.jpg, Coral holobiont
File:Processes within the seagrass holobiont.webp, Seagrass holobiont[ ]
Modified text was copied from this source, which is available under
Creative Commons Attribution 4.0 International License
File:The sponge holobiont.webp, Sponge holobiont
File:Climate change stressors and rhodolith holobiont fitness.webp,
References
Further references
* Stal, L. J. and Cretoiu, M. S. (Eds.) (2016
''The marine microbiome: an untapped source of biodiversity and biotechnological potential''Springer. {{ISBN, 9783319330006.
Microbiomes