Microbes in the Water Infrastructure: Underpinning Our Society

How do you feel when you hear the words " wastewater, " " sludge, " " sewer, " and " sewage " ? These words may make you feel uncomfortable. However, as Victor Hugo wrote in " Les Misérables, " these words are inevitably related to human society (16): " ... The history of men is reflected in the history of sewers. The Germoniae narrated Rome. The sewer of Paris has been an ancient and formidable thing. It has been a sepulchre, it has served as an asylum. Crime, intelligence, social protest, liberty of conscience, thought, theft, all that human laws persecute or have persecuted, is hidden in that hole ... " Since ancient Roman times, sewer pipe/tunnel networks have been built beneath urban areas to gather sewage/wastewater discharged from human activity (9). Biological treatment technologies such as activated sludge (3–5) and anaerobic digestion (AD) (6, 41) have been developed since the early 1900s to remediate sewage/wastewater constituents. Nowadays, these biological treatment processes are used as the core technology of modern municipal wastewater treatment processes (WWTP) and have become the underlying infrastructure for society. Within these processes, diverse microorganisms (eukaryotes [15, 33] and prokaryotes [35, 56]) form " sludge " and play a critical role in sewage/wastewater remediation. Thus, the characterization of sludge microbial assemblages and identification of their in situ functions have been conducted using cultivation, microscopic, and molecular techniques. Nitrification, the stepwise biological conversion of ammonia to nitrate, is an important step in municipal WWTP. The long-term (i.e., between 5 and 6 years) microbial community monitoring of activated sludge systems by employing the modern massive parallel sequencing of 16S rRNA gene amplicons revealed the temporal dynamics of core community members including nitrifying bacteria (i.e., Nitrosomonas, Nitrospira, and " Ca. Nitrotoga ") (20, 51). Microradiography combined with fluorescent in situ hybridization (MAR-FISH) showed that " Ca. Nitrotoga "-type nitrite-oxidizing bacteria (NOB) may play a role in nitrite-dependent autotrophic carbon fixation (30). Using the β-subunit of the nitrite oxidore-ductase (nxrB) gene, amplicon pyrosequencing uncovered the high diversity of Nitrospira spp., expanding to lineages I, II, and the novel 'WWTP Ingolstadt 454 lineage', in activated sludge systems (13). Fujitani and colleagues (12) enriched Nitrospira-type NOB from nitrifying sludge by using a laboratory-scale continuous feeding reactor with porous polyester non-woven fabric materials as biomass carriers. They then successfully isolated the novel bacterial species " Nitrospira japonica, " associated with Nitrospira lineage II …