Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.
The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2-13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics.
Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, United States of America.|Stanford University, Department of Biology, Stanford, CA, 94305, United States of America.
Michelle
http://orcid.org/0000-0002-0748-949X
M
Davison
Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, College Park, MD, 20742, United States of America.
Todd J
TJ
Treangen
Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, College Park, MD, 20742, United States of America.
Sergey
S
Koren
Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, College Park, MD, 20742, United States of America.|Department of Computer Science, University of Maryland, College Park, MD, 20742, United States of America.
Mihai
M
Pop
Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, United States of America.|Stanford University, Department of Biology, Stanford, CA, 94305, United States of America.
Devaki
D
Bhaya
D001435:Bacteriophages / Q000145:classification / Q000235:genetics; D018441:Biofilms; D020134:Catalytic Domain / Q000235:genetics; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D019295:Computational Biology / Q000379:methods; D010450:Endopeptidases / Q000235:genetics*; D004783:Environmental Microbiology; D018390:Gene Targeting; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D064307:Microbiota; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA
D010450:Endopeptidases; C001143:endolysin