Intensive research on molecular microbiological methods has accelerated the development of cutting-edge technologies, e.g., a high-throughput sequencer, microscopy, and mass spectrometry, at a surprisingly fast pace. The development of these technologies has allowed researchers, whose expertise does not lie in environmental microbiology and microbial ecology, to elucidate the functions and activities of microbial communities in engineered systems. Expanding knowledge on microbial communities has paved the way for discovering novel microorganisms and their unique metabolic traits that can potentially be harnessed in engineered systems. The present literature review introduces state-of-the-art high-resolution microbiological methods to observe genes, cells, microbial activities, and metabolites applicable to natural and engineered ecosystems. In addition, the latest findings on microbial ecophysiologies, guided by the application of these methods, and future perspectives toward innovations for water and wastewater treatment bioreactors are summarized.

We have tried to investigate the applicability of nitric oxide (NO) , which has been drawing attention as an information transmitter substance for most organisms, as a new operational factor for nitrous oxide (N₂O) production by ammonia-oxidizing bacteria (AOB) . Nitrifying sludge was cultivated in a lab-scale sequencing batch reactor fed with an inorganic substrate. NO was blown into the reactor in the aeration or mixing phase during cycle operations. The N₂O production and nitrifying performance in the aeration phase were monitored. The obtained results showed that NO enhanced both nitrification performance and N₂O production in most cases. However, the direct effect of NO on N₂O production was not clear, because both dissolved oxygen (DO) and nitrite concentrations, which are well-known factors strongly affecting N₂O production, also varied. Accordingly, the mathematical model, named the Conversion Model, was developed to eliminate the effects of DO and nitrite. The model analysis revealed that the NO supply in the aeration phase has the direct decreasing effect on N₂O production by AOB, whereas the NO supply in the mixing phase has the direct increasing effect on that. These findings suggest that proper control of the NO concentration could lead to the reduction of N₂O production by AOB.

In this study, we developed a method of determining tetramethylammonium hydroxide and tetramethylammonium salts, present in industrial wastewater as tetramethylammonium ions (TMA) , by liquid chromatography-tandem mass spectrometry (LC-MS/MS) . Tetramethylammonium hydroxide was used as a standard solution. The lower limit of quantification for TMA analysis by solid-phase extraction (SPE) using a weak cation exchange resin (Oasis WCX) was 0.00034 mg L^-1, and the recovery of surrogate standards ranged from 50 to 120%. We investigated 30 industrial wastewater samples from Fukuoka Prefecture by the developed TMA analysis method. TMA was detected in two samples, H and X, with concentrations of 0.0014 and 2.5 mg L^-1, respectively. In sample X, the immobilization of Daphnia magna was observed even at 50% dilution, and the 48 h-EC₅₀ was 62%. The toxicity removal test indicated reduced toxicity for sample X after SPE-WCX.

As a basic study of the application of dye microcapsules (DMC) to Lagrangian actinometry, collimated beam tests were conducted using a DMC-Lagrangian actinometer (DMC-LA) , and a new method of calculating the UV dose distributions was developed. It was statistically confirmed that the distributions of the fluorescence intensity of DMC-LA well fitted lognormal distributions. By applying the lognormal distributions, the UV dose distributions could be calculated directly from the flow cytometer measurement results of each DMC particle without the complicated deconvolution operation required in previous studies using dyed microspheres. The obtained UV dose distributions showed that the variances were kept sufficiently narrow that the log survival rates did not deviate from the initial slope line, at least when the average UV dose was less than 150 mJ cm^-2. This result strongly suggested that the tailing phenomenon of log survival rates in biodosimetry is due to causes other than the UV dose distributions.

The formation and disappearance of thermal stratification and hypoxic water were investigated by vertical and continuous observations of the water temperature, dissolved oxygen concentration, and oxidation–reduction potential from an automatic profiler sensor in Lake Kitaura in summer. Furthermore, the benthic flux of the dissolved inorganic phosphorus (PO₄-P) from sediment in Lake Kitaura was estimated from the results of water quality observations at short intervals using an automatic water sampler. The observed results showed that the conditions for forming thermal stratification were a temperature of 25 ℃ or higher and a wind velocity of less than 6.0 m s^-1. Thermal stratification disappeared when the wind velocity exceeded 6.0 m s^-1 for 2 h or more, internal Froude number (Fr_i) increased from 0.3 to 1.0, and Wedderburn number (We) decreased from 0.5 to less than 0.1. Hypoxic water was formed 1–2 days after the formation of thermal stratification. The estimated benthic flux of PO₄-P from sediment in the field in summer may be 99.1 mg m^-2 d^-1 or higher.

In Osaka Bay, where total nitrogen (TN) and dissolved inorganic nitrogen (DIN) have decreased significantly, we investigated changes in biomass and seasonal fluctuation patterns at each trophic level of the ecosystem. The water temperature, which can affect the structure of an ecosystem, did not increase during the survey period of 1990 to 2019. The decrease in DIN caused the decrease in phytoplankton abundance represented by chlorophyll-a and the primary production. This resulted in a decline in the population of zooplanktons, such as ciliates and copepods, and a decrease in larval fish abundance. The ecosystem in the bay was a bottom-up system in which the biomass of each trophic level responded almost linearly to the amount of primary production. The decrease in TN caused the expansion of the DIN depletion period from only summer in the 1990s to spring–summer in the 2010s. The biomass of fish larvae, especially that of inner-bay species, greatly decreased, whereas anchovy, a wide-area migratory fish, did not decrease, resulting in the dominance of anchovy over other fish species.