Microbiome Management

Management of microbiome is crucially important due to their ability of performing fundamental functions in waste treatment processes. Since microorganisms are paramount for waste treatment installations, comprehending functions of microbiome is of great significance to develop suitable environment for efficient product recovery (Foo, Ling, Lee, & Chang, 2017; Oleskowicz-Popiel, 2018). In line with this objective, the waste treatment technologies need to be investigated by means of microbial community interactions.

To date many of existing and newfound techniques have been used to elucidate interactions in microbial communities (De los Reyes, Weaver, & Wang, 2015, Rivera-Pinto et al., 2018). Herein / In this section, we`ll review the technologies that are used for community structure analysis and microbial activity. Thereafter we`ll deal with the analyzes for detection and monitoring of microbiomes.Conventional analysis of microbiome begins with isolations of molecules such as DNA or RNA (Koch, Müller, Harms, & Harnisch, 2014).

Afterwards the fingerprinting techniques, DGGE (Denaturating Gradient Gel Electrophoresis), TGGE (Temperature Gradient Gel Electrophoresis), SSCP (Single Strand Conformation Polymorphism), T-RFLP (Terminal Restriction Fragment Length Polymorphism) practiced based on research of interest (Koch et al., 2014; Vanwonterghem, Jensen, Ho, Batstone, & Tyson, 2014). DGGE technique is used for detecting community shifts. Recently, DGGE fingerprinting method has been used to analyze microbial consortium in anaerobic digestion of glycerol and to characterize dynamics of microbial community involved in biogas production (Lim, Ge, & Tong, 2018; Vásquez & Nakasaki, 2018). SSCP technique detects subtle mutations and is broadly used to distinguish different genomic variants in microbial communities. Fingerprinting techniques provides understanding of metabolic capacity of microbiome however do not allow us to find out main activities of microorganisms. They need to be combined with additional analyses.

The one approach for further confirmations of fingerprinting, benefits from marker gene analyzes. To identify phylogeny of microbial community, two well-known marker genes, 16s rRNA (prokaryotes) and 18s rRNA (eukaryotes) have been capitalized for microbiome analyzes in waste treatment technologies (de Jonge, Moset, M�ller, & Nielsen, 2017; Guermazi- Toumi, Chouari, & Sghir, 2018, Zhao et al., 2018). Besides 16s rRNA and 18s rRNA, recent studies have shown that new marker genes can be developed to identify particular microorganism.

In a study, hgcA and 16s rRNA genes were exploited as a marker to detect Geobacterracca sp. that plays a role in Hg methylation pathway in waste treatment plant discharges (Bravo et al., 2018). Another study carried out by Ahmed et al., has indicated that a novel marker gene, crAssphage, can be utilized for management of sewage pollution (Ahmed, Payyappat, Cassidy, Besley, & Power, 2018). As in the case with mentioned studies, current technologies could be also deepened developing marker genes to put them into use of microbiomes in waste treatment processes.