OOS 3-9 - Genome reconstruction from metagenomes to investigate microbial traits and strategies over secondary succession

Monday, August 7, 2017: 4:20 PM
Portland Blrm 256, Oregon Convention Center
Patrick J. Kearns, Plant Resilience Institute, Michigan State University, MI, Jackson W. Sorensen, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI and Ashley Shade, Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI

The succession and recovery of microbial communities after environmental disturbance has important implications for ecosystem function. Assembly and succession in microbial communities is driven in part by deterministic processes, such as local abiotic conditions and biotic interactions among microbial taxa. The biotic interactions underpinning succession likely depend on the ecological and metabolic strategies of community members, which can be considered as functional traits. One potential microbial trait is number of ribosomal operons each taxon has, which has been used as a proxy for changes in community-level heterotrophic strategy over succession. This assumes that copiotrophs have relatively more ribosomal operons, allowing them to rapidly respond to newly available resources, while oligotrophs have less. However, we have limited information about the metabolic capabilities and strategies of many environmental taxa, and how these capabilities correlate to ribosomal operon number. As an alternative approach to investigate the relationship between metabolic capability, ribosomal operon number, and succession, we use whole genome reconstruction from shotgun metagenome sequencing to examine both ribosomal operon number and corresponding functional potential of microbial taxa. This method avoids assumptions about ribosomal operon numbers among divergent environmental taxa and allows us directly to examine microbial ecological and metabolic strategies during succession.


To examine the interplay of ribosomal operon number, microbial metabolic strategies, and succession we used shotgun metagenome sequencing of surface soil samples from a chronosequence of fire impact overlaying the ongoing coal fire in Centralia, PA. The fire has been burning since 1962 and advances 3-7 m yr-1 along the coal seams. As the fire spreads into unafflicted areas, it allows previously affected sites to recover to ambient temperatures and affords an opportunity to examine secondary succession of microbial communities after a press disturbance. From the metagenomes, we reconstructed 256 genomes (completeness>50%, contamination <10%). A substantial proportion of genomes (~50%) were only identifiable as Bacteria or Archaea, allowing us to fortuitously examine the successional responses of divergent taxa. We mapped 16S rRNA gene amplicon sequences to the genome reconstructions to determine the number of ribosomal operons per taxon, over the chronosequence. Our results demonstrate an alternative approach to examine the community succession using metagenomes, and suggest that patterns in ribosomal operon number provides only partial insights into the  numerous strategies microbes employ over succession.