Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories

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.

Structure and Long-Term Stability of the Microbiome in Diverse Diatom Cultures

“…Three OTUs related to the Planctomycetes were also abundant, representing 2.5% of total sequences and 8 to 15% of their culture. Planctomycetes in particular is a group that is poorly represented in cultures, despite its importance in many ecosystems and its dominance in the important biogeochemical process of anaerobic ammonia oxidation ( 68 ). Like Hyphomonas , planctomycete bacteria produce a specialized holdfast and alternate between swimming and sessile life stages, making them ideal symbionts for larger microalgae.…”

Phytate and Microbial Suspension Amendments Increased Soybean Growth and Shifted Microbial Community Structure

“…We found two bacteria, Tepidisphaera mucosa and Gemmata sp., as hub taxa in the root biotope and three bacteria, Thermostilla marina , Gemmata sp., and Zavarzinella formosa , as hub taxa in the rhizosphere, all of which are Planctobacteria. Their wide distribution [ 69 ] and ability to degrade plant-derived polymers and exopolysaccharides formed by other bacteria has recently been documented [ 70 ]. Six Planctobacteria and a Chloroflexi were identified as global hub taxa in the co-occurrence network ( Figure 5 C), but no fungal taxon was included in the hub microbiota list.…”

Phytate and Microbial Suspension Amendments Increased Soybean Growth and Shifted Microbial Community Structure

“…We found two bacteria, Tepidisphaera mucosa and Gemmata sp., as hub taxa in the root biotope and three bacteria, Thermostilla marina, Gemmata sp., and Zavarzinella formosa, as hub taxa in the rhizosphere, all of which are Planctobacteria. Their wide distribution [42] and ability to degrade plant-derived polymers and exopolysaccharides formed by other bacteria has recently been documented [43]. Six Planctobacteria and a Chloro exi were identi ed as global hub taxa in the co-occurrence network (Fig.…”