Oral Presentation Australian Microbial Ecology 2022

Candidatus Mycosynbacter amalyticus and the CPR insight into the world of the “microbial dark matter” and their role in the wastewater microbial community (#53)

Jayson JA Rose 1 , Steven Batinovic 1 , Robert J Seviour 1 , Steve Petrovski 1
  1. La Trobe University, Brunswick, VIC, Australia

Wastewater treatment plants frequently suffer from foaming events worldwide. Wastewater foaming is a major operational disruption that costs the industry millions of dollars every year. Gordonia amarae is the most common organism implicated in the stabilisation of wastewater treatment foams, with no effective treatment for these events. Recently, a novel parasitic bacterium from the phylum Candidatus Saccharibacteria was isolated from wastewater filtrate, capable of lysing G. amarae (Batinovic et al., 2021). This bacterium, Ca. Mycosynbacter amalyticus, is the first reported biological entity that lyses G. amarae and represents the first environmental member of Saccharibacteria – outside of the human oral biome (He et al., 2015) – to be isolated as a co-culture in the laboratory. The phylum Saccharibacteria belongs to a subset of organisms named the candidate phyla radiation (CPR), commonly referred to as the “microbial dark matter”, as these organisms are readily detected, however, elude traditional methods of cultivation. The recent co-isolation of these organisms helps explain the continued inability to culture them independently. Using transmission electron microscopy and next generation sequencing (NGS) we show that this bacterium has an ultra-small cell size of ~450nm and contains a highly reduced 1.08Mbp genome. By performing optical density assays (OD600nm), we were also able to demonstrate the lytic capability of M. amalyticus when cocultured with G. amarae, observing a 38% reduction in OD600nm of G. amarae at stationary phase (Batinovic et al., 2021). Since then, further screening of wastewater filtrate has led to the isolation of three additional uncharacterised members of the Saccharibacteria. Through NGS and genomic characterisation, it was revealed that these taxa all possess highly reduced genomes and have been identified as close relatives of M. amalyticus, two belonging to the genus Mycosynbacter, and one delineating into its own separate genus. All three new isolates are obligate parasites capable of inducing G. amarae lysis, providing further evidence that members of the CPR tend to be ultra-small and parasitic in nature.  Further characterisation of these organisms can help explain the role they play in wastewater treatment plants, and how they influence the bacterial community.

  1. Batinovic S, Rose JJ, Ratcliffe J, Seviour RJ, Petrovski S. Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. Nature Microbiology. 2021 Jun;6(6):703-11.
  2. He X, McLean JS, Edlund A, Yooseph S, Hall AP, Liu SY, Dorrestein PC, Esquenazi E, Hunter RC, Cheng G, Nelson KE. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proceedings of the National Academy of Sciences. 2015 Jan 6;112(1):244-9.