Journal of Microbiology

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Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter: Christiana Abiola, Joo-Han Gwak, Ui-Ju Lee, Aderonke Odunayo Adigun, Sung-Keun Rhee; J. Microbiol. 2025;63(4):e2502002. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2502002

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Abstract PDF Supplementary Material: Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera “Candidatus Nitrosocosmicus” and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.

Journal Articles

Enhancing Seed Germination of Cremastra appendiculata: Screening and Identification of Four New Symbiotic Fungi in the Psathyrellaceae Family: Zhangneng Pan, Jing Wang, Shanshan He, Haiyang Zhao, Xinyue Dong, Tao Feng, Yanyan Meng, Xiaojun Li; J. Microbiol. 2024;62(8):671-682. Published online June 28, 2024; DOI: https://doi.org/10.1007/s12275-024-00148-7

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Several coprinoid fungi have been identified as promotors of Cremastra appendiculata seed germination, while others appear ineffective. This study aimed to discern which genera within the Psathyrellaceae family exhibit this capability and to identify the most effective coprinoid fungi for the cultivation of C. appendiculata. We collected 21 coprinoid fungi from diverse sources and symbiotically cultured them with C. appendiculata seeds. 9 fungi were found to induce seed germination and support seed development, specifically within the genera Coprinellus, Tulosesus, and Candolleomyces. In contrast, fungi that failed to promote germination predominantly belonged to the genera Coprinopsis and Parasola. Notably, four fungi-Coprinellus xanthothrix, Coprinellus pseudodisseminatus, Psathyrella singeri, and Psathyrella candolleana-were documented for the first time as capable of enhancing C. appendiculata seed germination. Strain 218LXJ-10, identified as Coprinellus radians, demonstrated the most significant effect and has been implemented in large-scale production, underscoring its considerable practical value. These findings contribute vital scientific insights for the conservation and sustainable use of C. appendiculata resources.

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Culture conditions of symbiotic fungus Coprinellus radians and its effects on seedlings of Cremastra appendiculata (D.Don.) Makino (Orchidaceae)
Liqin Wang, Jingyi Zhang, Qiuyu Lv, Gonggu Lv, Guangquan Lv, Xin Xiao, Fulin Yan, Miao Liu, Mingsheng Zhang
Canadian Journal of Plant Science.2025; 105: 1. CrossRef
Solid vermicompost and its liquid derivative exhibit strong biocontrol properties against Myzus persicae aphids on sweet pepper
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Soil water content as a critical factor for stable bacterial community structure and degradative activity in maritime Antarctic soil: Dockyu Kim , Namyi Chae , Mincheol Kim , Sungjin Nam , Eungbin Kim , Hyoungseok Lee; J. Microbiol. 2020;58(12):1010-1017. Published online December 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0490-9

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Recent increases in air temperature across the Antarctic Peninsula may prolong the thawing period and directly affect the soil temperature (Ts) and volumetric soil water content (SWC) in maritime tundra. Under an 8°C soil warming scenario, two customized microcosm systems with maritime Antarctic soils were incubated to investigate the differential influence of SWC on the bacterial community and degradation activity of humic substances (HS), the largest constituent of soil organic carbon and a key component of the terrestrial ecosystem. When the microcosm soil (KS1-4Feb) was incubated for 90 days (T = 90) at a constant SWC of ~32%, the initial HS content (167.0 mg/g of dried soil) decreased to 156.0 mg (approximately 6.6% loss, p < 0.05). However, when another microcosm soil (KS1-4Apr) was incubated with SWCs that gradually decreased from 37% to 9% for T = 90, HS degradation was undetected. The low HS degradative activity persisted, even after the SWC was restored to 30% with water supply for an additional T = 30. Overall bacterial community structure remained relatively stable at a constant SWC setting (KS1-4Feb). In contrast, we saw marked shifts in the bacterial community structure with the changing SWC regimen (KS1-4Apr), suggesting that the soil bacterial communities are vulnerable to drying and re-wetting conditions. These microcosm experiments provide new information regarding the effects of constant SWC and higher Ts on bacterial communities for HS degradation in maritime Antarctic tundra soil.

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The effects of cigarettes and alcohol on intestinal microbiota in healthy men: Renbin Lin , Yawen Zhang , Luyi Chen , Yadong Qi , Jiamin He , Mengjia Hu , Ying Zhang , Lina Fan , Tao Yang , Lan Wang , Misi Si , Shujie Chen; J. Microbiol. 2020;58(11):926-937. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0006-7

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Abstract PDF

Human intestinal microbiota is affected by the exogenous microenvironment. This study aimed to determine the effects of cigarettes and alcohol on the gut microbiota of healthy men. In total, 116 healthy male subjects were enrolled and divided into four groups: non-smoking and non-drinking (Group A), smoking only (Group B), drinking only (Group C), and smoking and drinking combined (Group D). Fecal samples were collected and sequenced using 16S rRNA to analyze the microbial composition. Short-chain fatty acid (SCFAs) levels in feces were determined by gas chromatography. We found that cigarette and alcohol consumptions can alter overall composition of gut microbiota in healthy men. The relative abundances of phylum Bacteroidetes and Firmicutes and more than 40 genera were changed with cigarette and alcohol consumptions. SCFAs decreased with smoking and alcohol consumption. Multivariate analysis indicated that when compared with group A, group B/C/D had higher Bacteroides, and lower Phascolarctobacterium, Ruminococcaceae_ UCG-002, Ruminococcaceae_UCG-003, and Ruminiclostridium_ 9 regardless of BMI and age. Additionally, the abundance of Bacteroides was positively correlated with the smoking pack-year (r = 0.207, p < 0.05), the abundance of predicted pathway of bacterial toxins (r = 0.3672, p < 0.001) and the level of carcinoembryonic antigen in host (r = 0.318, p < 0.01). Group D shared similar microbial construction with group B, but exerted differences far from group C with lower abundance of Haemophilus. These results demonstrated that cigarette and alcohol consumption separately affected the intestinal microbiota and function in healthy men; furthermore, the co-occurrence of cigarette and alcohol didn’t exacerbate the dysbiosis and cigarette played the predominated role on the alteration.

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Host-specificity of symbiotic mycorrhizal fungi for enhancing seed germination, protocorm formation and seedling development of over-collected medicinal orchid, Dendrobium devonianum: Hui Huang , Xiao-Meng Zi , Hua Lin , Jiang-Yun Gao; J. Microbiol. 2018;56(1):42-48. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7225-1

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Abstract PDF

All orchids maintain an obligate relationship with mycorrhizal symbionts during seed germination. In most cases, germination-enhancing fungi have been isolated from roots of mature plants for conservation and cultivation purposes. To understand the germination biology of Dendrobium devonianum, an over-collected medicinal orchid, the seeds of D. devonianum were inoculated with a fungal strain (FDd1) isolated from naturally occurring protocorms of D. devonianum and two other germination-enhancing fungal strains (FDaI7 and FCb4) from D. aphyllum and Cymbidium mannii, respectively. The fungal strain was isolated from five protocorms of D. devonianum and identified as a species of the genus Epulorhiza. In germination trials, treatments with all of the three fungal strains showed a significant promoting effect on seed germination and protocorm formation, compared with the control treatment (no inoculation). However, FDd1 fungal strain showed the greatest effectiveness followed by FDaI7 and FCb4. For all inoculation and control treatments, seeds developed to protocorms regardless of the presence of illumination, whereas protocorms did not develop to seedlings unless illumination was provided. The results of our manipulative experiments confirmed the hypothesis that mycorrhizae associated with orchid seedlings are highly host-specific, and the degree of specificity may be life stagespecific under in vitro conditions. The specific mycorrhizal symbionts from protocorms can enhance restoration efforts and the conservation of orchids such as D. devonianum.

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Research Support, Non-U.S. Gov'ts

Analyses of Bacterial Communities in Meju, a Korean Traditional Fermented Soybean Bricks, by Cultivation-Based and Pyrosequencing Methods: Yi-Seul Kim , Min-Cheol Kim , Soon-Wo Kwon , Soo-Jin Kim , In-Cheol Park , Jong-Ok Ka , Hang-Yeon Weon; J. Microbiol. 2011;49(3):340-348. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0302-3

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Abstract PDF

Despite the importance of meju as a raw material used to make Korean soy sauce (ganjang) and soybean paste (doenjang), little is known about the bacterial diversity of Korean meju. In this study, the bacterial communities in meju were examined using both culture-dependent and independent methods in order to evaluate the diversity of the bacterial population. Analyses of the 16S rRNA gene sequences of the bacterial strains isolated from meju samples showed that the dominant species were related to members of the genera Bacillus, Enterococcus, and Pediococcus. The community DNAs extracted from nine different meju samples were analyzed by barcoded pyrosequencing method targeting of the V1 to V3 hypervariable regions of the 16S rRNA gene. In total, 132,374 sequences, with an average read length of 468 bp, were assigned to several phyla, with Firmicutes (93.6%) representing the predominant phylum, followed by Proteobacteria (4.5%) and Bacteroidetes (0.8%). Other phyla accounted for less than 1% of the total bacterial sequences. Most of the Firmicutes were Bacillus and lactic acid bacteria, mainly represented by members of the genera Enterococcus, Lactococcus, and Leuconostoc, whose ratio varied among different samples. In conclusion, this study indicated that the bacterial communities in meju were very diverse and a complex microbial consortium containing various microorganisms got involved in meju fermentation than we expected before.

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Application of Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis to Monitor Effect of Biocontrol Agents on Rhizosphere Microbial Community of Hot Pepper (Capsicum annuum L.): Young Tae Kim , Myoungho Cho , Je Yong Jeong , Hyang Burm Lee , Seung Bum Kim; J. Microbiol. 2010;48(5):566-572. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0126-6

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Abstract PDF: Microbial communities in hot pepper (Capsicum annuum L.) cultivation fields under different cultivation methods were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis. Rhizosphere soil and leaf samples were collected from control, conventional and nature-friendly cultivation fields between May and July, 2009. Two Bacillus subtilis strains were applied to nature-friendly cultivation fields as biocontrol agents during the sampling period. Relative abundances of bacteria and plant pathogenic fungi related T-RFs were also measured to monitor the effect of biocontrol agents on potential plant pathogenic fungi. In the principal component analysis (PCA) based on T-RFLP profiles, the microbial communities from rhizosphere soil samples in July, including bacteria and fungi, showed distinct difference between nature-friendly cultivation fields and other cultivation fields. However, there was no correlation between cultivation methods and leaf microbial communities at any sampling period. Changes in the abundance of bacteria related T-RF in the rhizosphere of nature-friendly cultivation fields were observed clearly two months after application of biocontrol agent, while the abundance of plant pathogenic fungi related T-RFs significantly decreased.

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