Recovering microbial genomes from metagenomes in hypersaline environments: The Good,the Bad and the Ugly |
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| Affiliation: | 1. Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain;2. Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain;3. Multidisciplinary Institute of Environmental Studies Ramon Margalef, University of Alicante, Alicante, Spain;1. Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain;2. Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez–Center for Applied Ecology and Sustainability, Santiago de Chile, Chile;3. Department of Physiology, Genetics and Microbiology, and Multidisciplinary Institute for Environmental Studies Ramon Margalef, University of Alicante, Alicante, Spain;1. School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People’s Republic of China;2. School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, People’s Republic of China;1. National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India;2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India;3. Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, India;4. Chemical Engineering and Process Development (CEPD) Division, CSIR-National Chemical Laboratory (NCL), Pune, India;1. Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany;2. Deutsches Zentrum für Infektionsforschung (DZIF), Standort Braunschweig-Hannover, Braunschweig, Germany;3. German Center for Integrative Biodiversity Research (iDiv) Jena Halle Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany;1. Department of Microbiology, The Ohio State University, Columbus, OH 43210, United States;2. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Australia;3. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States;4. Ronin Institute, Montclair, NJ 07043, United States;5. Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL 32306, United States;6. Department of Soil, Water and Environmental Sciences, University of Arizona, Tucson, AZ 85716, United States;7. School of Biosciences, University of Exeter, Exeter, EX4 4QD, UK;8. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85716, United States;1. Marine Microbiology Group, Department of Animal and Bacterial Diversity, IMEDEA (CSIC-UIB), 07190 Esporles, Balearic Islands, Spain;2. School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA;3. Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK;4. Department of Microbiology, University of Georgia, Athens, GA, USA |
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| Abstract: | Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity. These extreme systems harbor relatively low species diversity but high intraspecific diversity, which can compromise metagenome assembly and therefore the whole binning process. The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches. Several scenarios have been analyzed in detail: (i) a good quality bin from a species highly abundant in the environment; (ii) an intermediate quality bin with incongruences that can be solved by further analyses and manual curation, and (iii) a low-quality bin to investigate the failure to recover a very abundant microbial genome as well as some possible solutions. The latter can be considered the “great metagenomics anomaly” and is mainly due to assembly problems derived from the microdiversity of naturally co-existing populations in nature. |
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| Keywords: | Microdiversity Binning Hypersaline |
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