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      Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation

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          Abstract

          Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora damicornis and surrounding seawater) putatively beneficial microorganisms for corals (pBMCs), including five Pseudoalteromonas sp., a Halomonas taeanensis and a Cobetia marina-related species strains. The results from a controlled aquarium experiment in two temperature regimes (26 °C and 30 °C) and four treatments (pBMC; pBMC with pathogen challenge – Vibrio coralliilyticus, VC; pathogen challenge, VC; and control) revealed the ability of the pBMC consortium to partially mitigate coral bleaching. Significantly reduced coral-bleaching metrics were observed in pBMC-inoculated corals, in contrast to controls without pBMC addition, especially challenged corals, which displayed strong bleaching signs as indicated by significantly lower photopigment contents and F v / F m ratios. The structure of the coral microbiome community also differed between treatments and specific bioindicators were correlated with corals inoculated with pBMC (e.g., Cobetia sp.) or VC (e.g., Ruegeria sp.). Our results indicate that the microbiome in corals can be manipulated to lessen the effect of bleaching, thus helping to alleviate pathogen and temperature stresses, with the addition of BMCs representing a promising novel approach for minimizing coral mortality in the face of increasing environmental impacts.

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          Probiotic bacteria as biological control agents in aquaculture.

          There is an urgent need in aquaculture to develop microbial control strategies, since disease outbreaks are recognized as important constraints to aquaculture production and trade and since the development of antibiotic resistance has become a matter of growing concern. One of the alternatives to antimicrobials in disease control could be the use of probiotic bacteria as microbial control agents. This review describes the state of the art of probiotic research in the culture of fish, crustaceans, mollusks, and live food, with an evaluation of the results obtained so far. A new definition of probiotics, also applicable to aquatic environments, is proposed, and a detailed description is given of their possible modes of action, i.e., production of compounds that are inhibitory toward pathogens, competition with harmful microorganisms for nutrients and energy, competition with deleterious species for adhesion sites, enhancement of the immune response of the animal, improvement of water quality, and interaction with phytoplankton. A rationale is proposed for the multistep and multidisciplinary process required for the development of effective and safe probiotics for commercial application in aquaculture. Finally, directions for further research are discussed.
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            Functional metagenomic profiling of nine biomes.

            Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
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              Plant growth-promoting rhizobacteria (PGPR): Their potential as antagonists and biocontrol agents

              Bacteria that colonize plant roots and promote plant growth are referred to as plant growth-promoting rhizobacteria (PGPR). PGPR are highly diverse and in this review we focus on rhizobacteria as biocontrol agents. Their effects can occur via local antagonism to soil-borne pathogens or by induction of systemic resistance against pathogens throughout the entire plant. Several substances produced by antagonistic rhizobacteria have been related to pathogen control and indirect promotion of growth in many plants, such as siderophores and antibiotics. Induced systemic resistance (ISR) in plants resembles pathogen-induced systemic acquired resistance (SAR) under conditions where the inducing bacteria and the challenging pathogen remain spatially separated. Both types of induced resistance render uninfected plant parts more resistant to pathogens in several plant species. Rhizobacteria induce resistance through the salicylic acid-dependent SAR pathway, or require jasmonic acid and ethylene perception from the plant for ISR. Rhizobacteria belonging to the genera Pseudomonas and Bacillus are well known for their antagonistic effects and their ability to trigger ISR. Resistance-inducing and antagonistic rhizobacteria might be useful in formulating new inoculants with combinations of different mechanisms of action, leading to a more efficient use for biocontrol strategies to improve cropping systems.
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                Author and article information

                Contributors
                +55 21 2562-6740 , raquelpeixoto@micro.ufrj.br , rspeixoto@ucdavis.edu
                Journal
                ISME J
                ISME J
                The ISME Journal
                Nature Publishing Group UK (London )
                1751-7362
                1751-7370
                5 December 2018
                5 December 2018
                April 2019
                : 13
                : 4
                : 921-936
                Affiliations
                [1 ]ISNI 0000 0001 2294 473X, GRID grid.8536.8, Institute of Microbiology, , Federal University of Rio de Janeiro (UFRJ), ; Rio de Janeiro, Brazil
                [2 ]IMAM-AquaRio – Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil
                [3 ]ISNI 0000 0001 2294 473X, GRID grid.8536.8, Instituto de Química, , Universidade Federal do Rio de Janeiro (UFRJ), ; Rio de Janeiro, Brazil
                [4 ]ISNI 0000 0004 1936 9684, GRID grid.27860.3b, Genome Center, University of California, ; Davis, CA USA
                [5 ]ISNI 0000 0004 0492 3830, GRID grid.7492.8, Department of Environmental Microbiology, , Helmholtz Centre for Environmental Research – UFZ, ; Leipzig, Germany
                [6 ]ISNI 0000 0001 1013 0288, GRID grid.418375.c, Department of Microbial Ecology, , The Netherlands Institute of Ecology (NIOO-KNAW), ; Wageningen, The Netherlands
                [7 ]ISNI 0000 0004 1936 9684, GRID grid.27860.3b, Evolution and Ecology, , University of California, ; Davis, CA USA
                [8 ]ISNI 0000 0004 1936 9684, GRID grid.27860.3b, Medical Microbiology and Immunology, , University of California, ; Davis, CA USA
                [9 ]ISNI 0000 0004 0474 1797, GRID grid.1011.1, College of Science and Engineering, , James Cook University, ; Townsville, Australia
                [10 ]ISNI 0000 0001 0328 1619, GRID grid.1046.3, Australian Institute of Marine Science, ; Townsville, Australia
                Author information
                http://orcid.org/0000-0002-7950-3975
                http://orcid.org/0000-0002-9536-3132
                Article
                323
                10.1038/s41396-018-0323-6
                6461899
                30518818
                01d95b9d-0f8b-45ae-bf65-564d1c41f9be
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 18 April 2018
                : 3 November 2018
                : 17 November 2018
                Categories
                Article
                Custom metadata
                © International Society for Microbial Ecology 2019

                Microbiology & Virology
                microbial ecology,climate-change ecology
                Microbiology & Virology
                microbial ecology, climate-change ecology

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