Characterization of the first cultured free-living representative of Candidatus Izimaplasma uncovers its unique biology

Abstract

Candidatus Izimaplasma, an intermediate in the reductive evolution from Firmicutes to Mollicutes, was proposed to represent a novel class of free-living wall-less bacteria within the phylum Tenericutes found in deep-sea methane seeps. Unfortunately, the paucity of marine isolates currently available has limited further insights into their physiological and metabolic features as well as ecological roles. Here, we present a detailed description of the phenotypic traits, genomic data and central metabolisms tested in both laboratorial and deep-sea environments of the novel strain zrk13, which allows for the first time the reconstruction of the metabolic potential and lifestyle of a member of the tentatively defined Candidatus Izimaplasma. On the basis of the description of strain zrk13, the novel species and genus Xianfuyuplasma coldseepsis is proposed. Notably, DNA degradation driven by X. coldseepsis zrk13 was detected in both laboratorial and in situ conditions, strongly indicating it is indeed a key DNA degrader. Moreover, the putative genes determining degradation broadly distribute in the genomes of other Izimaplasma members. Given extracellular DNA is a particularly crucial phosphorus as well as nitrogen and carbon source for microorganisms in the seafloor, Izimaplasma bacteria are thought to be important contributors to the biogeochemical cycling in the deep ocean.

Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling

“…Therefore, it is crucial to increase our capability for bringing microorganisms from the environment into culture [60], which will advance our understanding of their global biogeochemical cycles [48]. Among the uncultured majorities, the phylum Chloroflexi is ubiquitous and often abundant in sediments, soils and wastewater treatment systems, as well as in deep-sea extreme environments [64].…”

“…Therefore, it is crucial to increase our capability for bringing microorganisms from the environment into culture [60], which will advance our understanding of their global biogeochemical cycles [48]. Among the uncultured majorities, the phylum…”

“…The copyright holder for this preprint this version posted January 5, 2021. ; https://doi.org/10.1101/2021.01.05.425403 doi: bioRxiv preprint performed as described previously [46][47][48]. The sample was firstly preserved in 2.5% (v/v) glutaraldehyde for 8 h at 4 °C, washed three times with phosphate buffer saline (PBS) and then dehydrated in ethanol solutions of 30%, 50%, 70%, 90% and 100% for 10 min each time.…”

“…Thereafter, the copper grids were washed for 10 min in Milli-Q water and dried for 20 min at room temperature [45]. Ultrathin-section electron microscopic observation was performed as described previously [46][47][48]. The sample was firstly preserved in 2.5%…”

“…In combination with the reports that the other two Chloroflexi lineages (SAR202 group and Dehalococcoidia class) possessing potentials to drive sulfur metabolizations, it is reasonable to affirm the phylum Chloroflexi greatly contributes to the ocean sulfur cycling. Actually, we tried to check the metabolisms of strain ZRK33 that cultured in the deep-sea cold seep as performed previously [48], unfortunately, the cells of strain ZRK33 were invaded by some unknown microbes that leading the failure of in situ test toward its involvement of sulfur cycling. We are improving the experimental apparatus and procedure, which will greatly benefit us to check the central metabolisms of strain ZRK33 in situ in the near future.…”