You are here

Harvard Forest >

Harvard Forest Symposium Abstract 2019

  • Title: Giant viruses, chlamydia, vampire bacteria and the diversity of soil microbial life at Harvard Forest
  • Primary Author: Jeffrey Blanchard (University of Massachusetts - Amherst )
  • Additional Authors: Lauren Alteio (University of Massachusetts - Amherst )
  • Abstract:

    1Truchon A, 2Alteio L, 3Schulz F, 4Koestlbacher S, 5Delafont V, 6Luong K, 2Barnett J, 6Lefoulon E, 3Goudeau D, 3Ryan EM, 6Slatko B, 4Horn M, 3Malmstrom RR, 3Woyke T, 2,7Blanchard JL

    1Microbiology Department, University of Massachusetts, Amherst, MA, USA
    2Graduate Program in Organismal and Evolutionary Biology, University of Massachusetts, Amherst, MA, USA
    3U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
    4Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
    5Université de Poitiers, Poitiers, France
    6Genome Biology Division, New England BioLabs, Ipswich, MA, USA
    7Biology Department, University of Massachusetts, Amherst, MA, USA

    The Harvard Forest Long Term Ecological Research site in Petersham, MA is home to long-term experimental soil warming sites heated continuously to 5° C above ambient temperature since 1991 (Prospect Hill), 2003 (Barre Woods) and 2006 (SWaN). The net short-term effect of warming on forest soil communities is increased microbial activity, which translates to increased CO2 flux to the atmosphere and lower soil organic carbon levels. Several challenges remain to directly link soil communities to changes in soil CO2 efflux. Consequently, it is essential that we develop alternative methods for analyzing community composition and function of active community members. Cells were suspended from the organic and mineral layers of a warmed and control soil core from the Barre Woods experimental site followed by centrifugation and filtration (5 µm) to remove soil particles and larger eukaryotic organisms. Cells were labeled using SYBR green and separated by fluorescence activated cell sorting. To improve cost efficiency and throughput over single cells genomic methods, 360 subpools of 100 cells each were sequenced. This approach, termed mini-metagenomics, resulted in ~2,000 distinct genome bins. Phylogenomic analysis revealed a surprising diversity of microbial life. Sixteen new lineages of giant viruses were discovered for the first time in a forest soil ecosystem. Intracellular and host-dependent bacteria (Chlamydiae, Legionellales, Bacteriodetes, Rickettsiales and TM6/Dependentiae) were enriched in the data set relative to abundances in our traditional metagenomics data set of DNA extracted directly from the soil and further over-represented among high quality genome bins. Among the bins were several relatives of unusual parasitic vampire bacteria. PacBio sequencing of full length 16S rRNA and Illumina sequencing of the 16S V4 region ruled out contamination as a source of these bacteria and extended the genetic diversity of the above clades. The mini-metagenome assembled genomes (mini-MAG) were used to map traditional metagenomic and metatranscriptomic reads lending support for the presence of these bacteria as active soil community members. This collection of mini-MAGs exposes a reservoir of genetic diversity in difficult to cultivate organisms, some of which are related to human pathogens. Taking the Chlamydiae as an example, we retrieve mini-MAGs representing 11 novel chlamydial families. Comparative genome analysis is ongoing to reveal evolutionary features related to bacterial invasion and persistence in eukaryotic cells.

  • Research Category: Biodiversity Studies