Invited Speaker Australian Microbial Ecology 2022

Probing for Vampirovibrionia with a microbial toolbox (#61)

Emily White 1 , Laura Rix 1 , Paul N Evans 1 , Richard I Webb 2 , Philip Hugenholtz 1 , Mircea Podar 3 4 , Rochelle Soo 1
  1. School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, AUSTRALIA, Australia
  2. Centre for Microscopy and Microanalysis, The University of Queensland, St Lucia, QLD, Australia
  3. Oak Ridge National Laboratory, Oak Ridge, TN, USA
  4. Department of Microbiology, University of Tennessee, Knoxville, TN, USA

Until recently, Cyanobacteria were considered strictly photosynthetic organisms. However, this dogma was challenged when environmental 16S rRNA gene surveys revealed two basal cyanobacterial classes, 4C0d-2 (Vampiriovibrionia) and ML635J-21 (Sericyotochromatia) in a range of aphotic habitats. Our ability to extract genomes of individual microbial populations from metagenomic datasets has provided us with an opportunity to examine the metabolic potential of as-yet uncultured organisms, including these basal lineages. The draft genomes of Vampirovibrionia and Sericytochromatia from diverse environments have been characterised by metagenomic analyses and have confirmed our predictions that these organisms contain no genes associated with photosynthesis or CO2 fixation1,2.

 

Identifying potential genes in the genomes can provide us with insights into what the organism is capable of but culturing and experimental testing remains essential to confirm these inferences. The first cultured representative of the Vampirovibrionia, the predatory bacterium Vampirovibrio chlorellavorus, was co-cultured with its microalgae prey, Chlorella vulgaris, from a Ukranian freshwater reservoir and deposited in a culture collection in 1978. The lyophilised material was sequenced 36 years later, confirming its identity as a non-photosynthetic Cyanobacteria. However, attempts to resuscitate it have so far been unsuccessful3.

 

Earlier attempts to visualise the Vampirovibrionia have been unsuccessful due to the difficulty of identifying regions in the 16S rRNA gene specific to these organisms. We now take a different approach and aim to use a newly described technique, reverse-genomics isolation, which uses antibodies against predicted cell surface proteins to target specific bacteria. We aimed to enrich for Vampirovibironia from koala faecal samples where it has been shown to make up to 6.7% of the microbial population2,4. Based on the draft genomes of Vampirovibrionia recovered from the koala, we identified three proteins found on the outside of the cell as potential targets, an S-layer homology domain containing protein, penicillin binding protein and beta lactamase.

  1. Di Rienzi, S. C., Sharon, I., Wrighton, K. C. et al. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife 2:e01102 (2013)
  2. Soo, R. M., Skennerton, C. T., Sekiguchi, Y. et al. An expanded genomic representation of the phylum cyanobacteria. Genome Biol Evol 6(5) 1031-1045 (2014)
  3. Soo, R. M., Woodcroft, B. J., Parks, D. H. et al. Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus. PeerJ 3: e968 (2015)
  4. Cross, K. L., Campbell, J. H., Balachandran, M. et al. Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. Nat Biotechnol 37, 1314-1321 (2019).