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Report from Microbial Resource Center for Fermentation and Brewing symposium “New Developments in Environmental Microbiology”


New Developments in Environmental Microbiology

On March 10 (Fri.), 2023, the 2022 Ryukoku University Microbial Resource Center for Fermentation and Brewing symposium “New Developments in Environmental Microbiology” was held via Zoom.

First, Center Director Tanabe offered his opening remarks and explained that this year’s symposium would include examples of research to date in the field of environmental microbiology, that new developments were needed from future research, and examples of studies undertaken using molecular biological techniques.

“Dominant species in funazushi lactic acid fermentation”

Presenter: Koichi Tanabe, Director of Resource Center for Fermentation and Brewing

Funazushi, a traditional fermented food of Shiga Prefecture, is prepared by pickling salted crucian carp and rice and allowing fermentation to take place during this pickling process. This study isolated and characterized lactic acid bacteria involved in lactic acid fermentation from multiple different funazushi in Shiga Prefecture. The lactic acid bacteria species Lentilactobacillus buchneri was isolated from all the funazushi, and analyzing the bacteria for genotype sequences in specific regions suggested the presence of multiple lineages of L. buchneri in the funazushi.

L. buchneri was also first detected in the funazushi during fermentation from the third week of the pickling process and became the dominant species by the second month of the pickling process. To determine how L. buchneri becomes the dominant species during the funazushi fermentation process, we analyzed L. buchneri for stress tolerance to the lactic acid, acetic acid, and NaCl present in funazushi and found L. buchneri exhibited tolerance to lactic acid. We also confirmed that L. buchneri itself does not produce any substances that suppress the growth of other bacteria, suggesting that L. buchneri may become the dominant species by the end of the funazushi fermentation process due to its tolerance for lactic acid produced by other lactic acid bacteria.

“Attempting to understand the behavior of nematode clusters in green manure plots”

Presenter: Erika Asamizu, Professor, Department of Life Sciences, Faculty of Agriculture, Ryukoku University

Green manure is fresh plant matter that is plowed into the soil to encourage decomposition by microorganisms for use as fertilizer. Metabolites from these plants may also be used as biological fumigants. Nematodes, meanwhile, are microscopic worms found everywhere on earth and plant parasitic species of nematode, such as root-knot nematodes, cause tremendous damage to crops. Recent research has shown that organic replenishment of the soil with green manure reduces harmful nematodes and pathogens and promotes a healthier soil environment.

We wanted to know how the soil food web is altered by adding green manure and why adding green manure results in fewer harmful nematodes. We are currently adding green manure and growing eggplants in the Ryukoku University fields and looking for changes in the chemical composition of the soil, bacterial flora, and nematode flora. Our investigations into the amounts of bacterial fauna and nematode flora in the soil and the species makeup of the bacterial fauna in the soil using genetic analysis, performed in the course of these field trials, suggest these investigations could be used as indicators of soil health.

“Fungal diversity based on environmental DNA”

Presenter: Shunsuke Matsuoka, Assistant Professor, Field Science Education and Research Center, Kyoto University

Few details are known about the extent of fungal diversity in nature or the spatial patterns of their habitats. This is because fungi are not easily recognized by the naked eye in the field and have a very diverse range of habitats. But since the turn of the century, DNA analysis and DNA metabarcoding by massively parallel sequencing especially have come into widespread use for the analysis of fungal diversity. We used this method to investigate ectomycorrhizal fungi, a type of fungi that live symbiotically with trees, to reveal patterns of fungal diversity and factors associated with these patterns.

However, sampling strategies that collect specimens from individual substrates such as tree mycorrhizae are extremely cost and time prohibitive. This issue has been addressed by a newly favored sampling strategy that relies on environmental DNA in water. We studied the environmental DNA in a stream running through the “Inochi no Mori” biotope within urban parkland in Umekoji, Kyoto City, and discovered that waterways may function as a “trap” that collects DNA from fungi living in the surrounding forest. Similar studies of environmental DNA based on DNA metabarcoding promise to facilitate more revealing investigations of fungal diversity and fungal ecosystems.