Sponges,the members of the phylum Porifera,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 them,consisting of jelly-like mesohyl sandwiched between two thin layers of cells.
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics,ecogenomics,community genomics or microbiomics.
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.
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,which is invisibly small to 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.
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.
Poribacteria are a candidate phylum of bacteria originally discovered in the microbiome of marine sponges (Porifera). Poribacteria are Gram-negative primarily aerobic mixotrophs with the ability for oxidative phosphorylation,glycolysis,and autotrophic carbon fixation via the Wood –Ljungdahl pathway. Poribacterial heterotrophy is characterised by an enriched set of glycoside hydrolases,uronic acid degradation,as well as several specific sulfatases. This heterotrophic repertoire of poribacteria was suggested to be involved in the degradation of the extracellular sponge host matrix.
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.
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.
Halomonas meridiana is a bacterial species discovered in 1990 in the hypersaline lakes of Vestfold Hills,Antarctica.
The Earth BioGenome Project (EBP) is an initiative that aims to sequence and catalog the genomes of all of Earth's currently described eukaryotic species over a period of ten years. The initiative would produce an open DNA database of biological information that provides a platform for scientific research and supports environmental and conservation initiatives. A scientific paper presenting the vision for the project was published in PNAS in April 2018,and the project officially launched November 1,2018.
Endozoicomonas is a genus of Gram-negative,aerobic or facultatively anaerobic,chemoorganotrophic,rod-shaped,marine bacteria from the family of Endozoicomonadaceae. Endozoicomonas are symbionts of marine animals.
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.
Gert Wörheide is a German marine biologist who works mainly on marine invertebrates. He earned his doctorate in geobiology from Georg-August-Universität,following this with a post-doctorate at Queensland Museum (1998-2002),where he worked with John Hooper on sponges,a collaboration which continues.
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.
Pseudoceratina is a genus of sponge within the family Pseudoceratinidae. They are characterized by possession of a dendritic fiber skeleton lacking laminar bark but containing pith. They have been found in a variety of habitats including the Great Barrier reef,the Red Sea,and Jamaica. Sponges of this genus have a microbiome known to produce a variety of chemicals that are used in pharmaceutical and anti-fouling activities. Notably,a species in this genus produces a chemical that is effective in inhibiting the migration of metastatic breast cancer cells.
Mónica Medina is a professor of organismal biology at the Pennsylvania State University. She is known for environmental activism,such as fighting to protect Varadero Reef,and her research on the ecology and evolution of symbiosis by studying the relationships between cnidarian,endosymbiotic dinoflagellates,and other microbes.
Sponge microbiomes are diverse communities of microorganisms in symbiotic association with marine sponges as their hosts. These microorganisms include bacteria,archaea,fungi,viruses,among others. The sponges have the ability to filter seawater and recycle nutrients while providing a safe habitat to many microorganisms,which provide the sponge host with fixed nitrogen and carbon,and stimulates the immune system. Together,a sponge and its microbiome form a holobiont,with a single sponge often containing more than 40 bacterial phyla,making sponge microbial environments a diverse and dense community. Furthermore,individual holobionts work hand in hand with other near holobionts becoming a nested ecosystem,affecting the environment at multiple scales.
