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 Article

Effects of mycosubtilin homolog algicides from a marine bacterium, Bacillus sp. SY-1, against the harmful algal bloom species Cochlodinium polykrikoides: Seong-Yun Jeong , Hong-Joo Son; J. Microbiol. 2021;59(4):389-400. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1086-8

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The marine bacterium, Bacillus sp. SY-1, produced algicidal compounds that are notably active against the bloom-forming alga Cochlodinium polykrikoides. We isolated three algicidal compounds and identified these as mycosubtilins with molecular weights of 1056, 1070, and 1084 (designated MS 1056, 1070, and 1084, respectively), based on amino acid analyses and 1H, 13C, and two-dimensional nuclear magnetic resonance spectroscopy, including 1H-15N heteronuclear multiple bond correlation analysis. MS 1056 contains a β- amino acid residue with an alkyl side chain of C15, which has not previously been seen in known mycosubtilin families. MS 1056, 1070, and 1084 showed algicidal activities against C. polykrikoides with 6-h LC50 values of 2.3 ± 0.4, 0.8 ± 0.2, and 0.6 ± 0.1 μg/ml, respectively. These compounds also showed significant algicidal activities against other harmful algal bloom species. In contrast, MS 1084 showed no significant growth inhibitory effects against other organisms, including bacteria and microalgae, although does inhibit the growth of some fungi and yeasts. These observations imply that the algicidal bacterium Bacillus sp. SY-1 and its algicidal compounds could play an important role in regulating the onset and development of harmful algal blooms in natural environments.

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Review

The functional study of human proteins using humanized yeast: Seho Kim , Juhee Park , Taekyung Kim , Jung-Shin Lee; J. Microbiol. 2020;58(5):343-349. Published online April 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0136-y

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Abstract

The functional and optimal expression of genes is crucial for survival of all living organisms. Numerous experiments and efforts have been performed to reveal the mechanisms required for the functional and optimal expression of human genes. The yeast Saccharomyces cerevisiae has evolved independently of humans for billions of years. Nevertheless, S. cerevisiae has many conserved genes and expression mechanisms that are similar to those in humans. Yeast is the most commonly used model organism for studying the function and expression mechanisms of human genes because it has a relatively simple genome structure, which is easy to manipulate. Many previous studies have focused on understanding the functions and mechanisms of human proteins using orthologous genes and biological systems of yeast. In this review, we mainly introduce two recent studies that replaced human genes and nucleosomes with those of yeast. Here, we suggest that, although yeast is a relatively small eukaryotic cell, its humanization is useful for the direct study of human proteins. In addition, yeast can be used as a model organism in a broader range of studies, including drug screening.

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Research Support, Non-U.S. Gov't

Seasonal Changes in Nitrogen-Cycle Gene Abundances and in Bacterial Communities in Acidic Forest Soils: Jaejoon Jung , Jinki Yeom , Jiwon Han , Jisun Kim , Woojun Park; J. Microbiol. 2012;50(3):365-373. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1465-2

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Abstract

The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change.

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