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      Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia ( Oreochromis shiranus) and North African catfish ( Clarias gariepinus)

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          Abstract

          The majority of seafood is farmed, with most finfish coming from freshwater ponds. Ponds are often fertilized to promote microbial productivity as a natural feed source to fish. To understand if pond fertilization with livestock manure induces a probiotic or prebiotic effect, we communally reared tilapia ( Oreochromis shiranus), and North African catfish ( Clarias gariepinus), for 4 weeks under seven manure treatments including layer chicken, broiler chicken, guinea fowl, quail, pig, cow, vs. commercial feed to evaluate microbial community dynamics of the manure, pond water, and fish feces using 16S and 18S rRNA marker genes along with metagenome sequencing. Catfish growth, but not tilapia, was positively associated with plankton abundance ( p = 0.0006, R 2 = 0.4887) and greatest in ponds fertilized with quail manure (ANOVA, p < 0.05). Manure was unique and influenced the 16S microbiome in pond water, tilapia gut, and catfish gut and 18S community in pond water and catfish guts (PERMANOVA, p = 0.001). On average, 18.5%, 18.6%, and 45.3% of manure bacteria sOTUs, (sub‐operational taxonomic units), were present in the water column, catfish feces, and tilapia feces which comprised 3.7%, 12.8%, and 10.9% of the total microbial richness of the communities, respectively. Antibiotic resistance genes were highest in the manure and water samples followed by tilapia feces and lowest in catfish feces ( p < 0.0001). In this study, we demonstrate how the bacterial and eukaryotic microbial composition of fish ponds are influenced by specific livestock manure inputs and that the gut microbiome of tilapi a is more sensitive and responsive than catfish to these changes. We conclude that animal manure used as fertilizer induces a primarily prebiotic effect on the pond ecosystem rather than a direct probiotic effect on fish.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

            The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
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              EMPeror: a tool for visualizing high-throughput microbial community data

              Background As microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers of samples, new analysis tools are required to relate the distribution of microbes among larger numbers of communities, and to use increasingly rich and standards-compliant metadata to understand the biological factors driving these relationships. In particular, the Earth Microbiome Project drives these needs by profiling the genomic content of tens of thousands of samples across multiple environment types. Findings Features of EMPeror include: ability to visualize gradients and categorical data, visualize different principal coordinates axes, present the data in the form of parallel coordinates, show taxa as well as environmental samples, dynamically adjust the size and transparency of the spheres representing the communities on a per-category basis, dynamically scale the axes according to the fraction of variance each explains, show, hide or recolor points according to arbitrary metadata including that compliant with the MIxS family of standards developed by the Genomic Standards Consortium, display jackknifed-resampled data to assess statistical confidence in clustering, perform coordinate comparisons (useful for procrustes analysis plots), and greatly reduce loading times and overall memory footprint compared with existing approaches. Additionally, ease of sharing, given EMPeror’s small output file size, enables agile collaboration by allowing users to embed these visualizations via emails or web pages without the need for extra plugins. Conclusions Here we present EMPeror, an open source and web browser enabled tool with a versatile command line interface that allows researchers to perform rapid exploratory investigations of 3D visualizations of microbial community data, such as the widely used principal coordinates plots. EMPeror includes a rich set of controllers to modify features as a function of the metadata. By being specifically tailored to the requirements of microbial ecologists, EMPeror thus increases the speed with which insight can be gained from large microbiome datasets.
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                Author and article information

                Contributors
                hastingszidana@yahoo.co.uk
                robknight@ucsd.edu
                Journal
                Microbiologyopen
                Microbiologyopen
                10.1002/(ISSN)2045-8827
                MBO3
                MicrobiologyOpen
                John Wiley and Sons Inc. (Hoboken )
                2045-8827
                31 August 2018
                December 2018
                : 7
                : 6 ( doiID: 10.1002/mbo3.2018.7.issue-6 )
                : e00716
                Affiliations
                [ 1 ] Marine Biology Research Division Scripps Institution of Oceanography University of California San Diego La Jolla California
                [ 2 ] Department of Pediatrics University of California San Diego La Jolla California
                [ 3 ] Department of Fisheries Fisheries Research Unit Monkey Bay Malawi
                [ 4 ] Center for Microbiome Innovation Jacobs School of Engineering University of California San Diego La Jolla California
                [ 5 ] National Aquaculture Center Domasi Malawi
                [ 6 ] Department of Computer Science and Engineering University of California San Diego La Jolla California
                Author notes
                [*] [* ] Correspondence

                Rob Knight, Professor, Director of Center for Microbiome Innovation, University of California San Diego, La Jolla, CA.

                Email: robknight@ 123456ucsd.edu

                and

                Hastings Zidana, Director, National Aquaculture Centre, Domasi, Zomba, Malawi.

                Email: hastingszidana@ 123456yahoo.co.uk

                Author information
                http://orcid.org/0000-0002-7202-965X
                Article
                MBO3716
                10.1002/mbo3.716
                6291788
                30168288
                cc74274f-31f8-4d42-b289-7f72c0d895c0
                © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 20 April 2018
                : 15 July 2018
                : 01 August 2018
                Page count
                Figures: 5, Tables: 0, Pages: 15, Words: 11271
                Funding
                Funded by: Fulbright Program research
                Categories
                Original Article
                Original Articles
                Custom metadata
                2.0
                mbo3716
                December 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.5.4 mode:remove_FC converted:13.12.2018

                Microbiology & Virology
                16s rrna,18s rrna,african catfish,antibiotic resistance genes,aquaculture,fish microbiome,freshwater ecology,metagenomics,microbiome,tilapia

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