Journal of Microbiology

Research article

Temporal changes in culturable fungal community composition with their plastic degradation capacities in the marine plastisphere through mesocosm experiments: Sumin Jo, Ji Seon Kim, Wonjun Lee, Chang Wan Seo, Young Woon Lim; J. Microbiol. 2026;64(8):e2605011. Published online August 31, 2026; DOI: https://doi.org/10.71150/jm.2605011

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Abstract PDF Supplementary Material: Plastic waste in marine environments provides novel habitats for diverse organisms, forming distinct microbial ecosystems known as the ‘plastisphere’. Although bacteria of the plastisphere have been widely studied, the role of fungi in plastisphere formation and plastic degradation remains largely unexplored. Thus, we investigated temporal changes in culturable fungal community composition on three common plastic types—high-density polyethylene, low-density polyethylene, and polypropylene—across the early (seven days) and mature (30 days) plastisphere developmental stages through a marine mesocosm experiment. In total, 436 fungal strains were isolated and identified as belonging to 179 taxa, with Penicillium, Cladosporium, Trichoderma, Aspergillus, and Fusarium as the dominant genera. Temporal shifts in the species richness of the dominant genera were observed: Cladosporium showed higher species richness at the early stage, whereas that of Trichoderma increased at the mature stage. Plastic degradation assays revealed that 54.6% of the strains exhibited measurable degradation capacity, with patterns varying by plastic type rather than fungal developmental stage. Scanning electron microscope observations revealed surface damage patterns including cracks, pitting, and erosion on the plastic surfaces. These findings provide novel insights into the composition and functional heterogeneity of culturable fungal communities in the marine plastisphere and suggest that plastisphere fungi play diverse ecological roles beyond direct plastic degradation.

Review

Synthetic biology strategies for sustainable bioplastic production by yeasts: Huong-Giang Le, Yongjae Lee, Sun-Mi Lee; J. Microbiol. 2025;63(3):e2501022. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501022

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The increasing environmental concerns regarding conventional plastics have led to a growing demand for sustainable alternatives, such as biodegradable plastics. Yeast cell factories, specifically Saccharomyces cerevisiae and Yarrowia lipolytica, have emerged as promising platforms for bioplastic production due to their scalability, robustness, and ease of manipulation. This review highlights synthetic biology approaches aimed at developing yeast cell factories to produce key biodegradable plastics, including polylactic acid (PLA), polyhydroxyalkanoates (PHAs), and poly (butylene adipate-co-terephthalate) (PBAT). We explore recent advancements in engineered yeast strains that utilize various synthetic biology strategies, such as the incorporation of new genetic elements at the gene, pathway, and cellular system levels. The combined efforts of metabolic engineering, protein engineering, and adaptive evolution have enhanced strain efficiency and maximized product yields. Additionally, this review addresses the importance of integrating computational tools and machine learning into the Design-Build-Test-Learn cycle for strain development. This integration aims to facilitate strain development while minimizing effort and maximizing performance. However, challenges remain in improving strain robustness and scaling up industrial production processes. By combining advanced synthetic biology techniques with computational approaches, yeast cell factories hold significant potential for the sustainable and scalable production of bioplastics, thus contributing to a greener bioeconomy.

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International Journal of Biological Macromolecules.2026; 379: 153992. CrossRef
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npj Materials Sustainability.2025;[Epub] CrossRef

Review

Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems: Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park; J. Microbiol. 2024;62(11):933-950. Published online October 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00172-7

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Abstract PDF

Many of the world's freshwater ecosystems suffer from cyanobacteria-mediated blooms and their toxins. However, a mechanistic understanding of why and how Microcystis aeruginosa dominates over other freshwater cyanobacteria during warmer summers is lacking. This paper utilizes comparative genomics with other cyanobacteria and literature reviews to predict the gene functions and genomic architectures of M. aeruginosa based on complete genomes. The primary aim is to understand this species' survival and competitive strategies in warmer freshwater environments. M. aeruginosa strains exhibiting a high proportion of insertion sequences (~ 11%) possess genomic structures with low synteny across different strains. This indicates the occurrence of extensive genomic rearrangements and the presence of many possible diverse genotypes that result in greater population heterogeneities than those in other cyanobacteria in order to increase survivability during rapidly changing and threatening environmental challenges. Catalase-less M. aeruginosa strains are even vulnerable to low light intensity in freshwater environments with strong ultraviolet radiation. However, they can continuously grow with the help of various defense genes (e.g., egtBD, cruA, and mysABCD) and associated bacteria. The strong defense strategies against biological threats (e.g., antagonistic bacteria, protozoa, and cyanophages) are attributed to dense exopolysaccharide (EPS)-mediated aggregate formation with efficient buoyancy and the secondary metabolites of M. aeruginosa cells. Our review with extensive genome analysis suggests that the ecological vulnerability of M. aeruginosa cells can be overcome by diverse genotypes, secondary defense metabolites, reinforced EPS, and associated bacteria.

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Edi Sudianto, Denis Baurain, Luc Cornet, Jennifer Wisecaver
Genome Biology and Evolution.2026;[Epub] CrossRef
Cyanophage Infections in a Sponge Intracellular Cyanobacterial Symbiont
Tzipora Peretz, Esther Cattan‐Tsaushu, Chiara Conti, Benyamin Rosental, Laura Steindler, Sarit Avrani
Environmental Microbiology.2025;[Epub] CrossRef
Public goods-mediated bacterial interplay in aquatic ecosystems
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Water Research.2025; 287: 124310. CrossRef
Horizontal Gene Transfer and Recombination in Cyanobacteriota
Devaki Bhaya, Gabriel Birzu, Eduardo P.C. Rocha
Annual Review of Microbiology .2025; 79(1): 685. CrossRef

Review

The crosstalk between bacteria and host autophagy: host defense or bacteria offense: Lin Zheng , Fang Wei , Guolin Li; J. Microbiol. 2022;60(5):451-460. Published online April 29, 2022; DOI: https://doi.org/10.1007/s12275-022-2009-z

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Abstract PDF

Xenophagy is a specific selective autophagy for the elimination of intracellular bacteria. Current evidence suggests that the processes for host autophagy system to recognize and eliminate invading bacteria are complex, and vary according to different pathogens. Although both ubiquitin-dependent and ubiquitin-independent autophagy exist in host to defense invading bacteria, successful pathogens have evolved diverse strategies to escape from or paralyze host autophagy system. In this review, we discuss the mechanisms of host autophagy system to recognize and eliminate intracellular pathogens and the mechanisms of different pathogens to escape from or paralyze host autophagy system, with a particular focus on the most extensively studied bacteria.

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Article

Screening of small molecules attenuating biofilm formation of Acinetobacter baumannii by inhibition of ompA promoter activity: Seok Hyeon Na , Hyejin Jeon , Man Hwan Oh , Yoo Jeong Kim , Je Chul Lee; J. Microbiol. 2021;59(9):871-878. Published online August 27, 2021; DOI: https://doi.org/10.1007/s12275-021-1394-z

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Abstract PDF

Anti-virulence therapeutic strategies are promising alternatives against drug-resistant pathogens. Outer membrane protein A (OmpA) plays a versatile role in the pathogenesis and antimicrobial resistance of Acinetobacter baumannii. Therefore, OmpA is an innovative target for anti-virulence therapy against A. baumannii. This study aimed to develop a high-throughput screening (HTS) system to discover small molecules inhibiting the ompA promoter activity of A. baumannii and screen chemical compounds using the bacterial growth-based HTS system. The ompA promoter and open reading frame of nptI fusion plasmids that controlled the expression of nptI encoding resistance to kanamycin by the ompA promoter were constructed and then transformed into A. baumannii ATCC 17978. This reporter strain was applied to screen small molecules inhibiting the ompA promoter activity in a chemical library. Of the 7,520 chemical compounds, 15 exhibited ≥ 70% growth inhibition of the report strain cultured in media containing kanamycin. Three compounds inhibited the expression of ompA and OmpA in the outer membrane of A. baumannii ATCC 17978, which subsequently reduced biofilm formation. In conclusion, our reporter strain is useful for large-scale screening of small molecules inhibiting the ompA expression in A. baumannii. Hit compounds identified by the HTS system are promising scaffolds to develop novel therapeutics against A. baumannii.

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Aye Mya Sithu Shein, Parichart Hongsing, O’Rorke Kevin Smith, Phatthranit Phattharapornjaroen, Kazuhiko Miyanaga, Longzhu Cui, Hitoshi Ishikawa, Mohan Amarasiri, Peter N. Monk, Anthony Kicic, Tanittha Chatsuwan, Daniel Pletzer, Paul G. Higgins, Shuichi Ab
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Article

Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti: Olga Y. Burenina , Daria A. Elkina , Anzhela Y. Migur , Tatiana S. Oretskaya , Elena Evguenieva-Hackenberg , RolK. Hartmann , Elena A. Kubareva; J. Microbiol. 2020;58(11):945-956. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0283-1

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Abstract PDF

6S RNA, a conserved and abundant small non-coding RNA found in most bacteria, regulates gene expression by inhibiting RNA polymerase (RNAP) holoenzyme. 6S RNAs from α-proteobacteria have been studied poorly so far. Here, we present a first in-depth analysis of 6S RNAs from two α-proteobacteria species, Bradyrhizobium japonicum and Sinorhizobium meliloti. Although both belong to the order Rhizobiales and are typical nitrogen-fixing symbionts of legumes, their 6S RNA expression profiles were found to differ: B. japonicum 6S RNA accumulated in the stationary phase, thus being reminiscent of Escherichia coli 6S RNA, whereas S. meliloti 6S RNA level peaked at the transition to the stationary phase, similarly to Rhodobacter sphaeroides 6S RNA. We demonstrated in vitro that both RNAs have hallmarks of 6S RNAs: they bind to the σ70-type RNAP holoenzyme and serve as templates for de novo transcription of so-called product RNAs (pRNAs) ranging in length from ~13 to 24 nucleotides, with further evidence of the synthesis of even longer pRNAs. Likewise, stably bound pRNAs were found to rearrange the 6S RNA structure to induce its dissociation from RNAP. Compared with B. japonicum 6S RNA, considerable conformational heterogeneity was observed for S. meliloti 6S RNA and its complexes with pRNAs, even though the two 6S RNAs share ~75% sequence identity. Overall, our findings suggest that the two rhizobial 6S RNAs have diverged with respect to their regulatory impact on gene expression throughout the bacterial life cycle.

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Katrin Damm, Paul Klemm, Marcus Lechner, Dominik Helmecke, Roland K. Hartmann
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