• Journal of Microbiology and Biotechnology
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• v.34 no.3
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• pp.580-588
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• 2024

Microbial communities in mangrove forests have recently been intensively investigated to explain the ecosystem function of mangroves. In this study, the soil microbial communities under young (<11 years-old) and old (>17 years-old) mangroves have been studied during dry and wet seasons. In addition, biogeochemical properties of sediments and methane emission from the two different mangrove ages were measured. The results showed that young and old mangrove soil microbial communities were significantly different on both seasons. Seasons seem to affect microbial communities more than the mangrove age does. Proteobacteria and Chloroflexi were two top abundant phyla showing >15%. Physio-chemical properties of sediment samples showed no significant difference between mangrove ages, seasons, nor depth levels, except for TOC showing significant difference between the two seasons. The methane emission rates from the mangroves varied depending on seasons and ages of the mangrove. However, this did not show significant correlation with the microbial community shifts, suggesting that abundance of methanogens was not the driving factor for mangrove soil microbial communities.

• The Plant Pathology Journal
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• v.40 no.5
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• pp.498-511
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• 2024

Bacterial wilt caused by Ralstonia solanacearum is a destructive disease that affects potato production, leading to severe yield losses. Currently, little is known about the changes in the assembly and functional adaptation of potato rhizosphere microbial communities during different stages of R. solanacearum infection. In this study, using amplicon and metagenomic sequencing approaches, we analyzed the changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere across four stages of R. solanacearum infection. The results showed that R. solanacearum infection led to significant changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere, with various microbial properties (including α,β-diversity, species composition, and community ecological functions) all being driven by R. solanacearum infection. The relative abundance of some beneficial microorganisms in the potato rhizosphere, including Firmicutes, Bacillus, Pseudomonas, and Mortierella, decreased as the duration of infection increased. Moreover, the related microbial communities played a significant role in basic metabolism and signal transduction; however, the functions involved in soil C, N, and P transformation weakened. This study provides new insights into the dynamic changes in the composition and functions of potato rhizosphere microbial communities at different stages of R. solanacearum infection to adapt to the growth promotion or disease suppression strategies of host plants, which may provide guidance for formulating future strategies to regulate microbial communities for the integrated control of soil-borne plant diseases.

• Journal of Environmental Science International
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• v.31 no.12
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• pp.1051-1059
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• 2022

This study investigated microbial communities and their diversity in a full-scale mesophilic anaerobic digester treating sewage sludge. Influent sewage sludge and anaerobic digester samples collected from a wastewater treatment plant in Busan were analyzed using high-throughput sequencing. It was found that the microbial community structure and diversity in the anaerobic digester could be affected by inoculation effect with influent sewage sludge. Nevertheless, distinct microbial communities were identified as the dominant microbial communities in the anaerobic digester. Twelve genera were identified as abundant bacterial communities, which included several groups of syntrophic bacteria communities, such as Candidatus Cloacimonas, Cloacimonadaceae W5, Smithella, which are (potential) syntrophic-propionate-oxidizing bacteria and Mesotoga and Thermovigra, which are (potential) syntrophic-acetate-oxidizing bacteria. Lentimicrobium, the most abundant genus in the anaerobic digester, may contribute to the decomposition of carbohydrates and the production of volatile fatty acids during the anaerobic digestion of sewage sludge. Of the methanogens identified, Methanollinea, Candidatus Methanofastidiosum, Methanospirillum, and Methanoculleus were the dominant hydrogenotrophic methanogens, and Methanosaeta was the dominant aceticlastic methanogens. The findings may be used as a reference for developing microbial indicators to evaluate the process stability and process efficiency of the anaerobic digestion of sewage sludge.

• Journal of Hydrogen and New Energy
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• v.30 no.3
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• pp.269-275
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• 2019

This study was conducted to evaluate the microbial communities in coupled system of a microbial electrolysis cell and an anaerobic digestion. Glucose, butyric acid, propionic acid and acetic acid were used as substrates. The maximum methane production and methane production rate of propionic acid respectively were $327.9{\pm}6.7mL\;CH_4/g\;COD$ and $28.3{\pm}3.1mL\;CH_4/g\;COD{\cdot}d$, which were higher than others. Microbial communities' analyses indicated that acetoclastic methangens were predominant in all systems. But the proportion of hydrogenotrophic methanogens was higher in the system using propionic acid as a substrate when compared to others. In coupled system of a microbial electrolysis cell and anaerobic digestion, the methane production was higher as the distribution of hydrogen, which was generated by substrate degradation, and proportion of hydrogenotrophic methanogens was higher.

• Microbiology and Biotechnology Letters
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• v.50 no.3
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• pp.404-413
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• 2022

The process of manufacturing craft beer involves a wide variety of spontaneous microorganisms, acting in different stages of the brewing process, that contribute to the distinctive characteristics of each style. The objective of this work was to compare the structure of microbial communities associated with two different craft beer styles (Doppelbock and Märzen lagers), at a late maturation stage, and to identify discriminative, or style-specific taxa. Bacterial and fungal microbial communities were analyzed by Illumina sequencing of 16S rRNA gene of prokaryotes and the ITS 2 spacer of fungi (eukaryotes). Fungal communities in maturating beer were dominated by the yeast Dekkera, and by lactic acid (Lactobacillus and Pediococcus) and acetic acid (Acetobacter) bacteria. The Doppelbock barrels presented more rich and diverse fungal communities. The Märzen barrels were more variable in terms of structure and composition of fungal and bacterial communities, with occurrence of exclusive taxa of fungi (Aspergillus sp.) and bacteria (L. kimchicus). Minority bacterial taxa, differently represented in the microbiome of each barrel, may underlie the variability between barrels and ultimately, the distinctive traits of each style. The composition of the microbial communities indicates that in addition to differences related to upstream stages of the brewing process, the contact with the wood barrels may contribute to the definition of style-specific microbiological traits.

• Korean Journal of Organic Agriculture
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• v.28 no.2
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• pp.235-250
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• 2020

Agricultural practices are known to have a crucial influence not only on soil physico-chemical properties but also on microbial communities. To investigate the effect of farming practices on soil microbial communities, a total of 10 soil samples were collected, including five conventional and five organic farming soils cultivated with peppers in plastic greenhouse. We conducted barcorded-pyrosequencing of V1-V3 regions of 16S rRNA genes to examine soil microbial communities of two different farming practices. Taxonomic classification of the microbial communities at the phylum level indicated that a total of 22 bacterial phyla were present across all samples. Among them, seven abundant phyla (>3%) including Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Bacteroidetes, Chloroflexi, and Gemmatimonadetes were found, and Proteobacteria (33.0 ± 5.7%), Actinobacteria (19.9 ± 9.7%), and Firmicutes (13.6 ± 5.0%) comprised more than 66% of the relative abundance of the microbial communities. Organic farming soils showed higher relative abundances of Proteobacteria and Firmicutes, while Actinobacteria and Chloroflexi were more abundant in conventional farming soils. Notably, the genera Bacillus (higher in organic farming soils) and Streptomyces (higher in conventional farming soils) exhibited significant variation in relative abundance between organic and conventional farming soils. Finally, correlation analysis identified significant relationships (p<0.05) between soil chemical properties, in particular, pH and organic matter content and microbial communities. Taken together, this study demonstrated that the changes of soil physico-chemical properties by agricultural farming practices effected significantly (p<0.05) on soil microbial communities.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.6
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• pp.1073-1085
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• 2012

Soil microbial communities are immensely diverse and complex with respect to species richness and community size. These communities play essential roles in agricultural soil because they are responsible for most of the nutrient cycles in the soil and influence the plant diversity and productivity. However, the majority of these microbes remain uncharacterized because of poor culturability. Next-generation sequencing techniques have revolutionized many areas of biology by providing cheaper and faster alternatives to Sanger sequencing. Among them, amplicon pyrosequencing is a powerful tool developed by 454 Life Sciences for assessing the diversity of complex microbial communities by sequencing PCR products or amplicons. This review summarizes the current opinions in amplicon sequencing of soil microbial communities, and provides practical guidance and advice on sequence quality control, aligning, clustering, OTU- and taxon-based analysis. The last section of this article includes a few representative studies conducted using amplicon pyrosequencing.

• Journal of Life Science
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• v.34 no.7
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• pp.453-464
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• 2024

The fermentation of ganjang is known to be greatly influenced by the microbial communities derived from its primary ingredients, meju and sea salt. This study investigated the effects of changes in meju size on the distribution and correlation of microbial communities in ganjang fermentation, to enhance its fermentation process. Ganjang was prepared using whole meju and meju divided into thirds, and samples were collected at 7-day intervals over a period of 28 days for microbial community analysis based on 16S rRNA gene sequencing. At the genus level, during fermentation, ganjang made with whole meju exhibited a dominance of Chromohalobacter (day 7), Pediococcus (day 14), Bacillus (day 21), and Pediococcus (day 28), whereas ganjang made with meju divided into thirds consistently showed a Pediococcus predominance over the 28 days. Beta-diversity analysis of microbial communities in ganjang with different meju sizes revealed significant separation of microbial communities at fermentation days 7 and 14 but not at days 21 and 28 across all experimental groups. The linear discriminant analysis effect size (LEfSe) was determined to identify biomarkers contributing to microbial community differences at days 7 and 14, showing that on day 7, potentially halophilic microbes such as Gammaproteobacteria, Firmicutes, Oceanospirillales, Halomonadaceae, Bacilli, and Chromohalobacter were prominent, whereas on day 14, lactic acid bacteria such as Pediococcus acidilactici, Lactobacillaceae, Pediococcus, Bacilli, Leuconostocaceae, and Weissella were predominant. Furthermore, correlation analysis of microbial communities at the genus and species levels revealed differences in correlation patterns between meju sizes, suggesting that meju size may influence microbial interactions within ganjang.

• Journal of Environmental Science International
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• v.30 no.12
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• pp.1093-1100
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• 2021

The present study investigated the effect of ammonia load on microbial communities in mesophilic anaerobic digestion of propionic acid. A laboratory-scale continuous anaerobic digester treating propionic acid as a sole organic substrate was operated under non-inhibitory condition and inhibitory conditions with ammonia (1.5 g and 3.5 g ammonia-N/L, respectively), and bacterial and archaeal communities in the steady states of each ammonia condition were analyzed using high-throughput sequencing. Thirteen bacterial families were detected as abundant bacterial groups in mesophilic anaerobic digestion of propionic acid. Increase in ammonia concentration resulted in significant shifts in microbial community structures. Syntorophobacter, Pelotomaculum, and Thermovigra were determined as the dominant groups of (potential) propionate oxidizing bacteria in the non-inhibitory condition, whereas Cryptanaerobacter and Aminobacterium were the dominant groups of (potential) propionate oxidizing bacteria in the ammonia-inhibitory condition. Methanoculleus and Methanosaeta were the dominant methanogens. Acetate-oxidation coupled with hydrogenotrophic methanogenesis might be enhanced with increases in the relative abundances of Methanoculleus and Tepidanaerobacter acetatoxydans under the ammonia-inhibitory condition. The results of the present study could be a valuable reference for microbial management of anaerobic digestion systems that are exposed to ammonia inhibition and propionic acid accumulation.

• Journal of Microbiology and Biotechnology
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• v.27 no.1
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• pp.130-140
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• 2017

It is vital to understand the changing characteristics of interphase microbial communities and interspecies synergism during the fermentation of Chinese liquors. In this study, microbial communities in the three indispensable phases (pit mud, zaopei, and huangshui) of Luzhou-flavored liquor manufacturing pits and their shifts during cellars use were first investigated by polyphasic culture-independent approaches. The archaeal and eubacterial communities in the three phases were quantitatively assessed by combined phospholipid ether lipids/phospholipid fatty acid analysis and fluorescence in situ hybridization. In addition, qualitative information regarding the microbial community was analyzed by PCR-denaturing gradient gel electrophoresis. Results suggested that the interphase microbial community profiles were quite different, and the proportions of specific microbial groups evolved gradually. Anaerobic bacteria and gram-positive bacteria were dominant and their numbers were higher in pit mud ($10^9$ cells/g) than in huangshui ($10^7$ cells/ml) and zaopei ($10^7$ cells/g). Hydrogenotrophic methanogenic archaea were the dominant archaea, and their proportions were virtually unchanged in pit mud (around 65%), whereas they first increased and then decreased in zaopei (59%-82%-47%) and increased with pit age in huangshui (82%-92%). Interactions between microbial communities, especially between eubacteria and methanogens, played a key role in the formation of favorable niches for liquor fermentation. Furthermore, daqu (an essential saccharifying and fermentative agent) and metabolic regulation parameters greatly affected the microbial community.