Microbial ecology of anaerobic digesters: the key players of anaerobiosis

Abstract

Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO2. The conversions of complex organic compounds to CH4 and CO2 are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.

Figure 1

Many different groups of bacteria within the anaerobic digester often compete for the same substrate and electron acceptor. Methane is produced by methane-forming bacteria and a variety of acids and alcohols are produced by sulfate reducing bacteria. Hydrogen is used with sulfate (SO₄ ⁻²) by sulfate-reducing bacteria and hydrogen sulfide (H₂S) is produced. [41].

Figure 2

Methanogenesis in anaerobic digestion as documented for normal waste treatment reactor systems [42]. The SAB consist mostly of Clostridium sp. at both mesophilic and thermophilic conditions [43]. The hydrogenotrophic methanogens in both mesophilic and thermophilic anaerobic digesters belong to the two orders of Methanobacteriales and Methanomicrobiales [44].

Figure 3

General scheme of biopolymer fermentation in the rumen. Products in boxes with darker borders are final products of the ruminal fermentation, while compounds in light-bordered boxes are intermediates [45].

Figure 4

The in situ hybridization process can be divided into four stages: (A) sampling and immediate fixation in formaldehyde to preserve the integrity of the cells, especially the ribosomes; (B) hybridization with a specific probe, labelled with a fluorescent dye at its 50-end and matched with a sequence of the 16S rRNA; (C) counterstaining with a universal marker (DAPI, which attaches nonspecifically to DNA molecules) or another more general probe labelled with a different fluorescent dye; (D) visualization via fluorescence microscopy. Direct quantification is possible by manual counting of hybridized cells (epifluorescence and laser confocal microscope) or by image analysis of digital photos (both microscopes) or automated counting with a flow cytometer.

Figure 5

Conceptualization of the role of currently available molecular biology and postgenomic techniques for analysis of microbial community structure, function, and metabolic transformation [46].