title: Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes.
abstract: The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This "microbial dark matter" represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum "Calescamantes" (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O2, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs.
authors.affiliation: Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA.|Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA.
authors.forename: Eric D
authors.initials: ED
authors.lastname: Becraft
authors.affiliation: School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA.|Department of Biology, California State University, San Bernardino, California, USA.
authors.forename: Jeremy A
authors.initials: JA
authors.lastname: Dodsworth
authors.affiliation: School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA.
authors.forename: Senthil K
authors.initials: SK
authors.lastname: Murugapiran
authors.affiliation: Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA.
authors.forename: J Ingemar
authors.initials: JI
authors.lastname: Ohlsson
authors.affiliation: Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, USA.
authors.forename: Brandon R
authors.initials: BR
authors.lastname: Briggs
authors.affiliation: Departments of Bioengineering and Applied Physics, Stanford University and the Howard Hughes Medical Institute, Stanford, California, USA.
authors.forename: Jad
authors.initials: J
authors.lastname: Kanbar
authors.affiliation: Departments of Bioengineering and Applied Physics, Stanford University and the Howard Hughes Medical Institute, Stanford, California, USA.
authors.forename: Iwijn
authors.initials: I
authors.lastname: De Vlaminck
authors.affiliation: Departments of Bioengineering and Applied Physics, Stanford University and the Howard Hughes Medical Institute, Stanford, California, USA.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
authors.affiliation: Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, USA.|State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China.
authors.forename: Hailiang
authors.initials: H
authors.lastname: Dong
authors.affiliation: School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA.|Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Nevada, USA.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Hedlund
authors.affiliation: Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA wswingley@niu.edu.
authors.forename: Wesley D
authors.initials: WD
authors.lastname: Swingley
mesh_terms: D002681:China; D019295:Computational Biology / Q000379:methods*; D064349:Genome, Microbial; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D045482:Hot Springs / Q000382:microbiology*; D000069550:Machine Learning; D056186:Metagenomics / Q000379:methods*; D014481:United States