Microbial Ecology Pushes Frontiers in Biotechnology

Due to their diverse metabolic potentials and established manipulation techniques, microbes are considered to be excellent materials for biotechnology. Pure cultures of microbes are exploited in industrial processes to produce alcohols, organic acids, and polymeric materials (2). Furthermore, human society has a long history of using mixed microbial cultures to produce fermented foods (8). Naturally occurring microbial communities are also used in various environmental biotechnologies (25), such as waste­ water treatment, methanogenic digestion, bioremediation, and microbial fuel cells. The microbial communities involved in these processes have been the targets of intensive inves­ tigations because not only scientists, but also engineers are interested in how microbes work in such communities and/or how the performances of ecosystems are supported and influenced by individual microbes. Recent advances in microbial ecology have contributed to a better understanding of microbes and their activities in these processes, and provided the fundamentals for their future development. We herein focused on the latest research highlights in micro­ bial ecology that are relevant to processes in environmental biotechnology. Large volumes of wastewater are discharged due to the activities of human society, and most are treated by biological processes, such as activated­sludge processes. These processes exploit naturally occurring microbial communities, in which community structures are modified according to changes in the chemical compositions of wastewater and environmental conditions. Therefore, under­ standing microbes and their activities is considered important for the successful operation of these processes. Marked advances have recently been made in nucleotide­sequencing technologies, resulting in a new era of molecular and genomic approaches in microbial ecology (18, 28), including the pyrosequencing technique used to determine the nucleotide sequences of taxonomic marker­gene (e.g., 16S rRNA genes) fragments PCR-amplified from community metagenomes (5). Sato et al. used pyrosequencing to monitor bacterial population dynamics in laboratory activated­sludge reactors (26), and acquired more than 80,000 sequences for analyzing bacterial populations. Sufficient phylogenetic knowledge could even be obtained for specific genus-level lineages, such as Accumulibacter phosphatis. This genus is known to include phosphate­accumulating organisms that play important roles in the removal of phosphorus in wastewater­ treatment plants (7). These organisms also have the ability to accumulate biopolymers, such as polyhydroxyalkanoate (24). Nitrogen removal is another important task in the process of wastewater treatment, and the microbes responsible have been the focus of recent studies. Aerobic tanks are used for nitrification, in which ammonia is oxidized to nitrite by ammonia­oxidizing microbes and is further oxidized …