http://microbecol.khu.ac.kr/PDF_paper/TiB2015.pdf

Proteobacteria: Microbial signature of dysbiosis in gut microbiota

The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within ...

The Microbiota-Gut-Brain Axis

Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.

The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms

We present here the hologenome theory of evolution, which considers the holobiont (the animal or plant with all of its associated microorganisms) as a unit of selection in evolution. The hologenome is defined as the sum of the genetic information of the host and its microbiota. The theory is based on four generalizations: (1) All animals and plants establish symbiotic relationships with microorganisms. (2) Symbiotic microorganisms are transmitted between generations. (3) The association between host and symbionts affects the fitness of the holobiont within its environment. (4) Variation in the hologenome can be brought about by changes in either the host or the microbiota genomes; under environmental stress, the symbiotic microbial community can change rapidly. These points taken together suggest that the genetic wealth of diverse microbial symbionts can play an important role both in adaptation and in evolution of higher organisms. During periods of rapid changes in the environment, the diverse microbial symbiont community can aid the holobiont in surviving, multiplying and buying the time necessary for the host genome to evolve. The distinguishing feature of the hologenome theory is that it considers all of the diverse microbiota associated with the animal or the plant as part of the evolving holobiont. Thus, the hologenome theory fits within the framework of the 'superorganism' proposed by Wilson and Sober.

Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution.

Coral microbiology is an emerging field, driven largely by a desire to understand, and ultimately prevent, the worldwide destruction of coral reefs. The mucus layer, skeleton and tissues of healthy corals all contain large populations of eukaryotic algae, bacteria and archaea. These microorganisms confer benefits to their host by various mechanisms, including photosynthesis, nitrogen fixation, the provision of nutrients and infection prevention. Conversely, in conditions of environmental stress, certain microorganisms cause coral bleaching and other diseases. Recent research indicates that corals can develop resistance to specific pathogens and adapt to higher environmental temperatures. To explain these findings the coral probiotic hypothesis proposes the occurrence of a dynamic relationship between symbiotic microorganisms and corals that selects for the coral holobiont that is best suited for the prevailing environmental conditions. Generalization of the coral probiotic hypothesis has led us to propose the hologenome theory of evolution.

The role of microorganisms in coral health, disease and evolution.

Summary Emerging diseases have been responsible for the death of about 30% of corals worldwide during the last 30 years. Coral biologists have predicted that by 2050 most of the world's coral reefs will be destroyed. This prediction is based on the assumption that corals can not adapt rapidly enough to environmental stress-related conditions and emerging diseases. Our recent studies of the Vibrio shiloi/Oculina patagonica model system of the coral bleaching disease indicate that corals can indeed adapt rapidly to changing envi- ronmental conditions by altering their population of symbiotic bacteria. These studies have led us to propose the Coral Probiotic Hypothesis. This hypoth- esis posits that a dynamic relationship exists between symbiotic microorganisms and environmen- tal conditions which brings about the selection of the most advantageous coral holobiont. Changing their microbial partners would allow the corals to adapt to changing environmental conditions more rapidly (days to weeks) than via mutation and selection (many years). An important outcome of the Probiotic Hypothesis would be development of resistance of the coral holobiont to diseases. The following evi- dence supports this hypothesis: (i) Corals contain a large and diverse bacterial population associated with their mucus and tissues; (ii) the coral-associated bacterial population undergoes a rapid change when environmental conditions are altered; and (iii) although lacking an adaptive immune system (no antibodies), corals can develop resistance to pathogens. The Coral Probiotic Hypothesis may help explain the evolutionary success of corals and mod- erate the predictions of their demise.

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The Coral Probiotic Hypothesis

ion from another concept, used to complete or add to the latter, such as in metaphysics, whereas the prefix holo(from Greek: holos = whole) is more appropriate because it is used in English to denote whole, entire, and entirety. Third, the term hologenome parallels the accepted term holobiont. What is the relationship between the hologenome concept and the classical phenomenon of symbiosis? The term symbiosis was first coined by Anton de Bary (1879) in the nineteenth century as ‘‘the living together of different species.’’ His broad definition is still generally accepted. The symbiotic system is usually constructed from a large partner termed the host and smaller partners called symbionts. This arbitrary division by dimension between host and symbiont may not fit all systems because size can be measured by cell number or by genome size, and in the case of many symbioses the microorganisms both outnumber their host and contain more genetic information. In spite of these limitations, the definition of host and symbiont based on size continues to be widely used, although it would be more appropriate to consider both the host and symbionts as constituents of the holobiont. Among the symbionts one finds endosymbionts and exosymbionts, referring to microrganisms living inside or outside host cells, respectively. Symbioses can also take many forms; most of them are defined as different levels of mutualism, when both the host and the symbiont benefit from the interaction. When the symbiont benefits and the host suffers damage, symbiosis is termed parasitism (or pathogenesis). Commensalism is accepted to be a close association of two or more dissimilar organisms where the association is advantageous to one and does not affect the other(s). These types of symbioses may change under different circumstances, for example, parasitic microorganisms can become beneficial under different circumstances (Taylor et al. 2005). The hologenome concept presents a novel way of looking at symbiosis. Until recently most of the important research on symbiosis has been carried out with a small number of model systems involving a host and a single primary symbiont, e.g., aphids and their endosymbiotic bacterium Buchnera sp (Wilson et al. 2010), the squid light organ and Vibrio fischeri (Nyholm and McFall-Ngai 2004), hard corals and their photosynthetic microalga of the genus Symbiodinium (Buddemeier et al. 2004), and legumes (Fabaceae) and nitrogen-fixing rhizobia (Ott et al. 2009). 4

The Hologenome Concept Human Animal and Plant Microbiota 2013th Edition

/pdf/the-holobiont-with-its-hologenome-is-a-level-of-selection-in-3ls9nm23j1.pdf

Ilana Zilber-Rosenberg

Papers

Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution.

The role of microorganisms in coral health, disease and evolution.

The Coral Probiotic Hypothesis

The Hologenome Concept Human Animal and Plant Microbiota 2013th Edition

The Holobiont With Its Hologenome Is A Level Of Selection In Evolution