Apart from the basic input, the right course of fermentation process is determined by the appropriate microorganism populations and the parameters such as: pH, particle size, ionic strength (salinity) and concentration of nutrients and toxic compounds. Three microorganism groups are involved in the process of anaerobic transformation of organic substances in fermentation gas: acid forming bacteria, acetate bacteria and methanogenic bacteria. The first two phases are dominated by the bacteria which are both obligate, facultative and absolute anaerobes (Clostridium spp., Bifidobacterium spp., Streptococcus spp., Enterobacter spp., Bacillus spp., Pseudomonas spp., Aerobacter spp., Alcaligenes spp, Escherichia spp, Lactobacillus spp, Micrococcus spp. czy Flavobacterium spp.) [Nimmrichter, Kuebler, 1999]. Their number during the mesophile fermentation is estimated for between 108-109 per 1ml [Hartman, 1999]. The rate of bacteria growth at both phases fluctuates from 5 hrs, in the presence of carbohydrates to 72 hrs during fat decomposition [Heidrich, Nieścier, 1999]. Presented research aimed at determining the quantity and quality of biogas depending on the microbiological environment in fractions originating from agriculture and agro-food industry. To achieve the objective of research, was evaluated the number and biodiversity of microorganisms that inhabit selected agricultural raw materials used in the production of biogas. A very important aspect of the study was to investigate the species composition of the bacteria and fungi population at different stages of fermentation process. Isolation of microorganisms from selected agricultural raw materials that stimulate the production of biogas could contribute in the future to optimize the process of its obtaining. The following substrates were used in the investigations: distillery’s grain, ensilaged beet pulp, rapeseed cake from biofuel manufacturing, apple pulp, fresh brewer’s grains (wet), corn silage harvested by silage harvester without grain squeezer, corn silage harvested by silage harvester combined with grain squeezer, cellulose from paper industry. Results of analysis of biogass yield in relation to dry mass revealed the highest productivity of the input from waste cellulose from paper industry at low productivity of biomass from agri-food industry. A delay in biogas volume increment visible in the course of fermentation of inputs from agri-food industry biomass is caused by the pasteurization of the mass which lacks microbiological environment, where microorganisms of methane fermentation multiply very slowly. The strongest inhibition of growth and delay in biogass formation was observed in the inputs made on the basis of distillery’s grains and fresh brewers’ grains. A normal productivity of biogass generation was obtained for the inputs prepared from cellulose and corn silage harvested by silage harvester equipped with grain squeezer.
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