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Title: Diversity of Active Viral Infections within the Sphagnum Microbiome

Abstract

ABSTRACT Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnumpeat bog. The vegetative portions of six Sphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. Wemore » developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of theSphagnummicrobiome. IMPORTANCE Sphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. Furthermore, this study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.« less

Authors:
 [1];  [2];  [2]; ORCiD logo [3]; ORCiD logo [3]; ORCiD logo [1];  [4]
  1. Univ. of Tennessee, Knoxville, TN (United States)
  2. Georgia Inst. of Technology, Atlanta, GA (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1482449
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Applied and Environmental Microbiology; Journal Volume: 84; Journal Issue: 23
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; viruses; RNA-Seq; Sphagnum; peat bogs; microbial ecology

Citation Formats

Stough, Joshua M. A., Kolton, Max, Kostka, Joel E., Weston, David J., Pelletier, Dale A., Wilhelm, Steven W., and Cann, Isaac. Diversity of Active Viral Infections within the Sphagnum Microbiome. United States: N. p., 2018. Web. doi:10.1128/AEM.01124-18.
Stough, Joshua M. A., Kolton, Max, Kostka, Joel E., Weston, David J., Pelletier, Dale A., Wilhelm, Steven W., & Cann, Isaac. Diversity of Active Viral Infections within the Sphagnum Microbiome. United States. doi:10.1128/AEM.01124-18.
Stough, Joshua M. A., Kolton, Max, Kostka, Joel E., Weston, David J., Pelletier, Dale A., Wilhelm, Steven W., and Cann, Isaac. Thu . "Diversity of Active Viral Infections within the Sphagnum Microbiome". United States. doi:10.1128/AEM.01124-18.
@article{osti_1482449,
title = {Diversity of Active Viral Infections within the Sphagnum Microbiome},
author = {Stough, Joshua M. A. and Kolton, Max and Kostka, Joel E. and Weston, David J. and Pelletier, Dale A. and Wilhelm, Steven W. and Cann, Isaac},
abstractNote = {ABSTRACT Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of theSphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnumpeat bog. The vegetative portions of sixSphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of theSphagnummicrobiome. IMPORTANCE Sphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. Furthermore, this study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.},
doi = {10.1128/AEM.01124-18},
journal = {Applied and Environmental Microbiology},
number = 23,
volume = 84,
place = {United States},
year = {Thu Nov 15 00:00:00 EST 2018},
month = {Thu Nov 15 00:00:00 EST 2018}
}