title: Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools.
abstract: In this study, we report the distribution and abundance of cold-adaptation proteins in microbial mat communities in the perennially ice-covered Lake Joyce, located in the McMurdo Dry Valleys, Antarctica. We have used MG-RAST and R code bioinformatics tools on Illumina HiSeq2000 shotgun metagenomic data and compared the filtering efficacy of these two methods on cold-adaptation proteins. Overall, the abundance of cold-shock DEAD-box protein A (CSDA), antifreeze proteins (AFPs), fatty acid desaturase (FAD), trehalose synthase (TS), and cold-shock family of proteins (CSPs) were present in all mat samples at high, moderate, or low levels, whereas the ice nucleation protein (INP) was present only in the ice and bulbous mat samples at insignificant levels. Considering the near homogeneous temperature profile of Lake Joyce (0.08-0.29 °C), the distribution and abundance of these proteins across various mat samples predictively correlated with known functional attributes necessary for microbial communities to thrive in this ecosystem. The comparison of the MG-RAST and the R code methods showed dissimilar occurrences of the cold-adaptation protein sequences, though with insignificant ANOSIM (R = 0.357; p-value = 0.012), ADONIS (R(2) = 0.274; p-value = 0.03) and STAMP (p-values = 0.521-0.984) statistical analyses. Furthermore, filtering targeted sequences using the R code accounted for taxonomic groups by avoiding sequence redundancies, whereas the MG-RAST provided total counts resulting in a higher sequence output. The results from this study revealed for the first time the distribution of cold-adaptation proteins in six different types of microbial mats in Lake Joyce, while suggesting a simpler and more manageable user-defined method of R code, as compared to a web-based MG-RAST pipeline.
authors.affiliation: Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
authors.forename: Hyunmin
authors.initials: H
authors.lastname: Koo
authors.affiliation: Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Hakim
authors.affiliation: Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
authors.forename: Phillip R E
authors.initials: PR
authors.lastname: Fisher
authors.affiliation: Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Grueneberg
authors.affiliation: Carl Sagan Center for the Study of Life in the Universe, Mountain View, CA 94043, USA. Electronic address: dandersen@seti.org.
authors.forename: Dale T
authors.initials: DT
authors.lastname: Andersen
authors.affiliation: Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA. Electronic address: abej@uab.edu.
authors.forename: Asim K
authors.initials: AK
authors.lastname: Bej
mesh_terms: D000864:Antarctic Regions; D021301:Antifreeze Proteins / Q000032:analysis* / Q000235:genetics; D001425:Bacterial Outer Membrane Proteins / Q000032:analysis / Q000235:genetics; D001426:Bacterial Proteins / Q000032:analysis / Q000235:genetics; D001483:Base Sequence; D003080:Cold Temperature; D019295:Computational Biology / Q000379:methods; D017753:Ecosystem; D044943:Fatty Acid Desaturases / Q000032:analysis; D005964:Glucosyltransferases / Q000032:analysis; D007053:Ice / Q000032:analysis; D060106:Lakes / Q000382:microbiology*; D056186:Metagenomics / Q000379:methods*; D014871:Water Microbiology
chemical_list: D021301:Antifreeze Proteins; D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D007053:Ice; C062260:cold shock protein CS7.4, Bacteria; C063113:ice nucleation protein; D044943:Fatty Acid Desaturases; D005964:Glucosyltransferases; C099692:trehalose synthase
keywords: Antifreeze protein; CspA; Ice nucleation protein; MG-RAST; McMurdo Dry Valleys; Perennially ice-covered lakes; R code; Trehalose synthase