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      Diversities and potential biogeochemical impacts of mangrove soil viruses

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          Abstract

          Background

          Mangroves are ecologically and economically important forests of the tropics. As one of the most carbon-rich biomes, mangroves account for 11% of the total input of terrestrial carbon into oceans. Although viruses are considered to significantly influence local and global biogeochemical cycles, little information is available regarding the community structure, genetic diversity and ecological roles of viruses in mangrove ecosystems.

          Methods

          Here, we utilised viral metagenomics sequencing and virome-specific bioinformatics tools to study viral communities in six mangrove soil samples collected from different mangrove habitats in Southern China.

          Results

          Mangrove soil viruses were found to be largely uncharacterised. Phylogenetic analyses of the major viral groups demonstrated extensive diversity and previously unknown viral clades and suggested that global mangrove viral communities possibly comprise evolutionarily close genotypes. Comparative analysis of viral genotypes revealed that mangrove soil viromes are mainly affected by marine waters, with less influence coming from freshwaters. Notably, we identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from mangrove viruses, most of which participate in biolysis of complex polysaccharides, which are abundant in mangrove soils and organism debris. Host prediction results showed that viral CAZyme genes are diverse and probably widespread in mangrove soil phages infecting diverse bacteria of different phyla.

          Conclusions

          Our results showed that mangrove viruses are diverse and probably directly manipulate carbon cycling by participating in biomass recycling of complex polysaccharides, providing the knowledge essential in revealing the ecological roles of viruses in mangrove ecosystems.

          Electronic supplementary material

          The online version of this article (10.1186/s40168-019-0675-9) contains supplementary material, which is available to authorized users.

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          Most cited references49

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          Virioplankton: Viruses in Aquatic Ecosystems

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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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              Microbial hotspots and hot moments in soil: Concept & review

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                Author and article information

                Contributors
                jinmin@tio.org.cn
                596317752@qq.com
                ruizhang@xmu.edu.cn
                quwu2339525@126.com
                871163954@qq.com
                +86-592-2195323 , zeng@tio.org.cn
                Journal
                Microbiome
                Microbiome
                Microbiome
                BioMed Central (London )
                2049-2618
                11 April 2019
                11 April 2019
                2019
                : 7
                : 58
                Affiliations
                [1 ]GRID grid.420213.6, State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, ; Xiamen, China
                [2 ]ISNI 0000 0001 2264 7233, GRID grid.12955.3a, State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, , Xiamen University, ; Xiamen, China
                [3 ]Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
                Article
                675
                10.1186/s40168-019-0675-9
                6460857
                30975205
                df1ea588-5ce6-4934-9a2a-13d13f545790
                © The Author(s). 2019

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 24 October 2018
                : 28 March 2019
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100010823, China Ocean Mineral Resources Research and Development Association;
                Award ID: DY135-B-04
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 41606144
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100003392, Natural Science Foundation of Fujian Province;
                Award ID: 2016J05098
                Award Recipient :
                Funded by: Scientific Research Foundation of Third Institute of Oceanography, SOA
                Award ID: 2015019
                Award Recipient :
                Funded by: Public Science and Technology Research Funds Projects of Ocean
                Award ID: 201505026-2
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2019

                mangrove soil,viruses,viromes,carbon cycling,auxiliary metabolic genes

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