Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients’ specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
Highlights
The history of Planctomycetes dates back to 1924 with a study of the September plankton of Lake Langymanyos (Budapest, Hungary)
Testing co-culture of Gemmata spp. with E. coli filtrate, we showed that the number of both G. obscuriglobus and Gemmata massiliana colonies were significantly higher on basic medium supplemented with E. coli filtrate than on the standard medium (p < 0.0001) (Kaboré et al, 2019a)
Several factors have been implicated in the colonization of sponge surfaces by Planctomycetes, including the adhesion factors present on the surface of certain species of Planctomycetes (Stalks, holfasts, frimbriae) that favor their attachment to marine sponges. These associations could be explained by the fact that the sponges which secrete various unknown molecules, or sulphated polysaccharides (Wegner et al, 2013) via the algae hosted by the sponge, or molecules such as siderophores secreted by Proteobacteria associated with biofilms
Summary
The history of Planctomycetes dates back to 1924 with a study of the September plankton of Lake Langymanyos (Budapest, Hungary). Planctomycetes are widely distributed in terrestrial (Buckley et al, 2006; Ivanova et al, 2016; Stackebrandt et al, 1993; Wang et al, 2002; Slobodkina et al, 2015) and aquatic environments (Gimesi, 1924; Franzmann and Skerman, 1984; Schlesner, 1994; Glöckner et al, 2003; Pimentel-Elardo et al, 2003; Woebken et al, 2007; Sipkema et al, 2011; Webster and Taylor, 2012; Aghnatios and Drancourt, 2015) including, brackish and marine water (Wang et al, 2002; Woebken et al, 2007; Hempel et al, 2008), freshwater (Franzmann and Skerman, 1984; Wang et al, 2002; Bondoso et al, 2011; Andrei et al, 2019), and wastewater (Chouari et al, 2003; Lage et al, 2012) with diverse environmental and physicochemical conditions Both terrestrial and aquatic habitats differing in salinity (from hypersaline to freshwater), oxygen availability (from the oxic water-column to anoxic sediments), trophic level (from oligotrophic lakes to eutrophic wastewater), and temperature (from cold-water marine snow to hot springs) (Kahan, 1961; Giovannoni et al, 1987; Kerger et al, 1988; DeLong et al, 1993; Schlesner, 1994; Vergin et al, 1998; Miskin et al, 1999; Kirkpatrick et al, 2006; Slobodkina et al, 2015; Slobodkina et al, 2016). To circumvent these isolation bottlenecks, news culture media formulation, novel approaches and technical manipulations are needed to recovery news strains from various habitats, including human blood which are very important for us
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