Journal of Microbiology

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: 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.

Journal Article

Autotrophy to Heterotrophy: Shift in Bacterial Functions During the Melt Season in Antarctic Cryoconite Holes.: Aritri Sanyal, Runa Antony, Gautami Samui, Meloth Thamban; J. Microbiol. 2024;62(8):591-609. Published online May 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00140-1

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Abstract: Microbes residing in cryoconite holes (debris, water, and nutrient-rich ecosystems) on the glacier surface actively participate in carbon and nutrient cycling. Not much is known about how these communities and their functions change during the summer melt-season when intense ablation and runoff alter the influx and outflux of nutrients and microbes. Here, we use high-throughput-amplicon sequencing, predictive metabolic tools and Phenotype MicroArray techniques to track changes in bacterial communities and functions in cryoconite holes in a coastal Antarctic site and the surrounding fjord, during the summer season. The bacterial diversity in cryoconite hole meltwater was predominantly composed of heterotrophs (Proteobacteria) throughout the season. The associated functional potentials were related to heterotrophic-assimilatory and -dissimilatory pathways. Autotrophic Cyanobacterial lineages dominated the debris community at the beginning and end of summer, while heterotrophic Bacteroidota- and Proteobacteria-related phyla increased during the peak melt period. Predictive functional analyses based on taxonomy show a shift from predominantly phototrophy-related functions to heterotrophic assimilatory pathways as the melt-season progressed. This shift from autotrophic to heterotrophic communities within cryoconite holes can affect carbon drawdown and nutrient liberation from the glacier surface during the summer. In addition, the flushing out and export of cryoconite hole communities to the fjord could influence the biogeochemical dynamics of the fjord ecosystem.

Reviews

Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms: Wonjae Kim, Yerim Park, Jaejoon Jung, Che Ok Jeon, Masanori Toyofuku, Jiyoung Lee, Woojun Park; J. Microbiol. 2024;62(3):249-260. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00115-2

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4 Citations

Abstract: The proliferation of harmful cyanobacterial blooms dominated by Microcystis aeruginosa has become an increasingly serious problem in freshwater ecosystems due to climate change and eutrophication. Microcystis-blooms in freshwater generate compounds with unpleasant odors, reduce the levels of dissolved O₂, and excrete microcystins into aquatic ecosystems, potentially harming various organisms, including humans. Various chemical and biological approaches have thus been developed to mitigate the impact of the blooms, though issues such as secondary pollution and high economic costs have not been adequately addressed. Red clays and H₂O₂ are conventional treatment methods that have been employed worldwide for the mitigation of the blooms, while novel approaches, such as the use of plant or microbial metabolites and antagonistic bacteria, have also recently been proposed. Many of these methods rely on the generation of reactive oxygen species, the inhibition of photosynthesis, and/or the disruption of cellular membranes as their mechanisms of action, which may also negatively impact other freshwater microbiota. Nevertheless, the underlying molecular mechanisms of anticyanobacterial chemicals and antagonistic bacteria remain unclear. This review thus discusses both conventional and innovative approaches for the management of M. aeruginosa in freshwater bodies.

Coordinated regulation of interferon and inflammasome signaling pathways by SARS-CoV-2 proteins: Na-Eun Kim , Yoon-Jae Song; J. Microbiol. 2022;60(3):300-307. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1502-8

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5 Citations

Abstract: Type I and III interferons (IFNs) and the nucleotide-binding domain (NBD) leucine-rich repeat (LRR)-containing receptor (NLR) family pyrin domain containing 3 (NLRP3) inflammasome play pivotal roles in the pathogenesis of SARS-CoV-2. While optimal IFN and inflammasome responses are essential for limiting SARS-CoV-2 infection, aberrant activation of these innate immune responses is associated with COVID-19 pathogenesis. In this review, we focus our discussion on recent findings on SARS-CoV-2-induced type I and III IFNs and NLRP3 inflammasome responses and the viral proteins regulating these mechanisms.

Journal Articles

Light affects picocyanobacterial grazing and growth response of the mixotrophic flagellate Poterioochromonas malhamensis: Thomas Weisse , Michael Moser; J. Microbiol. 2020;58(4):268-278. Published online January 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9567-8

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Abstract: We measured the grazing and growth response of the mixotrophic chrysomonad flagellate Poterioochromonas malhamensis on four closely related picocyanobacterial strains isolated from subalpine lakes in central Europe. The picocyanobacteria represented different pigment types (phycoerythrin- rich, PE, and phycocyanin-rich, PC) and phylogenetic clusters. The grazing experiments were conducted with laboratory cultures acclimated to 10 μmol photon/m2/sec (low light, LL) and 100 μmol photon/m2/sec (moderate light, ML), either in the dark or at four different irradiances ranging from low (6 μmol photon/m2/sec) to high (1,500 μmol photon/m2/ sec) light intensity. Poterioochromonas malhamensis preferred the larger, green PC-rich picocyanobacteria to the smaller, red PE-rich picocyanobacterial, and heterotrophic bacteria. The feeding and growth rates of P. malhamensis were sensitive to the actual light conditions during the experiments; the flagellate performed relatively better in the dark and at LL conditions than at high light intensity. In summary, our
results
found strain-specific ingestion and growth rates of the flagellate; an effect of the preculturing conditions, and, unexpectedly, a direct adverse effect of high light levels. We conclude that this flagellate may avoid exposure to high surface light intensities commonly encountered in temperate lakes during the summer.

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm: Ying Zheng , Tzen-Yuh Chiang , Chao-Li Huang , Xun Gong; J. Microbiol. 2018;56(5):337-345. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7438-3

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40 Citations

Abstract: As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.

Dominant genera of cyanobacteria in Lake Taihu and their relationships with environmental factors: Lijun Feng , Shiyou Liu , Wenxian Wu , Jiawen Ma , Pei Li , Hailing Xu , Na Li , Yaoyu Feng; J. Microbiol. 2016;54(7):468-476. Published online June 28, 2016; DOI: https://doi.org/10.1007/s12275-016-6037-4

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18 Citations

Abstract: Cyanobacterial blooms in freshwaters have become one of the most widespread of environmental problems and threaten water resources worldwide. Previous studies on cyanobacteria in Lake Taihu often collected samples from one site (like Meiliang Bay or Zhushan Bay) and focused on the variation in patterns or abundance of Microcystis during the blooming season. However, the distribution of cyanobacteria in Lake Taihu shows differing pattern in various seasons. In this study, water samples were collected monthly for one year at five sites in Lake Taihu with different trophic status and a physicochemical analysis and denaturing gradient gel electrophoresis (DGGE) were conducted. DGGE fingerprint analysis showed that Microcystis (7/35 bands) and Synechococcus (12/35 bands) were the two most dominant genera present during the study period at all five sites. Cyanobium (3/35 bands) was the third most common genus which has seldom been previously reported in Lake Taihu. Redundancy analysis (RDA) indicated that the cyanobacterial community structure was significantly correlated with NO3 --N, CODMn, and NH4 +-N in the winter and spring, whereas it was correlated with water temperature in the summer and autumn. Limiting the nutrient input (especially of N and C loading) in Lake Taihu would be a key factor in controlling the growth of different genera of cyanobacteria.

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

Directed analysis of cyanobacterial membrane phosphoproteome using stained phosphoproteins and titanium-enriched phosphopeptides§: Dong-Gi Lee , Joseph Kwon , Chi-Yong Eom , Young-Moon Kang , Seong Woon Roh , Kyung-Bok Lee , Jong-Soon Choi; J. Microbiol. 2015;53(4):279-287. Published online April 8, 2015; DOI: https://doi.org/10.1007/s12275-015-5021-8

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13 Citations

Abstract: Gel-free shotgun phosphoproteomics of unicellular cyanobacterium Synechocystis sp. PCC 6803 has not been reported up to now. The purpose of this study is to develop directed membrane phosphoproteomic method in Synechocystis sp. Total Synechocystis membrane proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and phosphoprotein-stained gel bands were selectively subjected to in-gel trypsin digestion. The phosphorylation sites of the resulting peptides were determined by assigning the neutral loss of [M-H3PO4] to Ser, Thr, and Tyr residues using nano-liquid chromatography 7 Tesla Fourier transform mass spectrometry. As an initial application, 111 proteins and 33 phosphoproteins were identified containing 11 integral membrane proteins. Identified four unknown phosphoproteins with transmembrane helices were suggested to be involved in membrane migration or transporters based on BLASTP search annotations. The overall distribution of hydrophobic amino acids in pTyr was lower in frequency than that of pSer or pThr. Positively charged amino acids were abundantly revealed in the surrounding amino acids centered on pTyr. A directed shotgun membrane phosphoproteomic strategy provided insight into understanding the fundamental regulatory processes underlying Ser, Thr, and Tyr phosphorylation in multi-layered membranous cyanobacteria.

NOTE] Effects of Light Intensity on Components and Topographical Structures of Extracellular Polysaccharides from the Cyanobacteria Nostoc sp.: Hongmei Ge , Ling Xia , Xuping Zhou , Delu Zhang , Chunxiang Hu; J. Microbiol. 2014;52(2):179-183. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-2720-5

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52 Citations

Abstract: A study on the effects of light intensity (40 and 80 μE/m2/sec) on the components and topographical structures of extracellular polysaccharides (EPS) was carried out in cyanobacteria Nostoc sp.. EPS yield increased with light intensity. However, light intensity did not significantly affect the EPS fractions and monosaccharide composition. Higher light intensity generally resulted in higher protein content of EPS in similar fractions. The topographical structure of EPS, investigated by atomic force microscopy, appeared as spherical lumps, chains and networks. The long chains were observed at higher light intensity. Thus, light intensity affected the yield and nature of EPS.

Diversity of Cyanobacterial Species and Phylotypes in Biofilms from the Littoral Zone of Lake Baikal: Ekaterina G. Sorokovikova , Olga I. Belykh , Anna S. Gladkikh , Oleg V. Kotsar , Irina V. Tikhonova , Oleg A. Timoshkin , Valentina V. Parfenova; J. Microbiol. 2013;51(6):757-765. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3240-4

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Abstract: The majority of naturally occurring biofilms contain numerous microorganisms that have not yet been cultured. Additionally, there is little information available regarding the genetic structure and species diversity of these communities. Therefore, we characterised the species diversity, structure and metagenome of biofilms grown on stones and steel plates in the littoral zone of Lake Baikal (East Siberia, Russia) by applying three different approaches. First, light microscopy enabled identification of the species diversity of biofilm-forming cyanobacteria on different substrates with the dominance of Rivularia rufescens, Tolypothrix limbata, Chamaesiphon fuscus, Сh. subglobosus, and Heteroleibleinia pusilla. Additionally, scanning electron microscopy was used to show the spatial structure of biofilms. Finally, sequence analysis of 30,660 16S rRNA clones indicated a high diversity within the biofilm communities, with the majority of the microbes being closely related to Cyanobacteria (8–46% sequences), Proteobacteria (14–43%), and Bacteroidetes (10– 41%). Rivularia sp., Pseudanabaena sp., and Chamaesiphon spp. were the dominant cyanobacterial phylotypes.

Review

MINIREVIEW] Toxin-producing Cyanobacteria in Freshwater: A Review of the Problems, Impact on Drinking Water Safety, and Efforts for Protecting Public Health: Melissa Y. Cheung , Song Liang , Jiyoung Lee; J. Microbiol. 2013;51(1):1-10. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2549-3

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181 Citations

Abstract: Cyanobacteria have adapted to survive in a variety of environments and have been found globally. Toxin-producing cyanobacterial harmful algal blooms (CHABs) have been increasing in frequency worldwide and pose a threat to drinking and recreational water. In this study, the prevalence, impact of CHABs and mitigation efforts were reviewed, focusing on the Lake Erie region and Ohio’s inland lakes that have been impacted heavily as an example so that the findings can be transferrable to other parts of the world that face the similar problems due to the CHABs in their freshwater environments. This paper provides a basic introduction to CHABs and their toxins as well as an overview of public health implications including exposure routes, health effects, and drinking water issues, algal bloom advisory practices in Ohio, toxin measurements results in Ohio public water supplies, and mitigation efforts.

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

Translocation of Green Fluorescent Protein to Cyanobacterial Periplasm Using Ice Nucleation Protein: Wipa Chungjatupornchai , Sirirat Fa-aroonsawat; J. Microbiol. 2009;47(2):187-192. Published online May 2, 2009; DOI: https://doi.org/10.1007/s12275-008-0188-x

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Abstract: The translocation of proteins to cyanobacterial cell envelope is made complex by the presence of a highly differentiated membrane system. To investigate the protein translocation in cyanobacterium Synechococcus PCC 7942 using the truncated ice nucleation protein (InpNC) from Pseudomonas syringae KCTC 1832, the green fluorescent protein (GFP) was fused in frame to the carboxyl-terminus of InpNC. The fluorescence of GFP was found almost entirely as a halo in the outer regions of cells which appeared to correspond to the periplasm as demonstrated by confocal laser scanning microscopy, however, GFP was not displayed on the outermost cell surface. Western blotting analysis revealed that InpNC-GFP fusion protein was partially degraded. The N-terminal domain of InpNC may be susceptible to protease attack; the remaining C-terminal domain conjugated with GFP lost the ability to direct translocation across outer membrane and to act as a surface display motif. The fluorescence intensity of cells with periplasmic GFP was approximately 6-fold lower than that of cells with cytoplasmic GFP. The successful translocation of the active GFP to the periplasm may provide a potential means to study the property of cyanobacterial periplasmic substances in response to environmental changes in a non-invasive manner.

Cyanobacterial Hybrid Kinase Sll0043 Regulates Phototaxis by Suppressing Pilin and Twitching Motility Protein: Bong-Jeong Shin , Jeehyun Oh , Sungsoo Kang , Young-Ho Chung , Young Mok Park , Young Hwan Kim , Seungil Kim , Jong Bhak , Jong-Soon Choi; J. Microbiol. 2008;46(3):300-308. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-007-0212-6

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8 Citations

Abstract: The unicellular cyanobacterium Synechocystis sp. PCC 6803 glides toward a light source through the interplay of positive phototaxis genes and proteins. In genetic analysis, the complete disruption of the hybrid sensory kinase sll0043 produced negative phototaxis. Furthermore, Sll0043 was found to be a hub protein by in silico prediction of protein-protein interaction, in which Sll0043 was predominantly linked to seven two-component proteins with high confidence. To understand the regulation and networking of positive phototaxis proteins, the proteomic profile of the sll0043 mutant was compared to that of wild-type. In the sll0043 mutant, 18 spots corresponding to 15 unique proteins were altered by 1.3 to 59 fold; the spots were identified by 2-DE/MALDI-MS analysis. Down-regulated proteins in the sll0043 null-mutant included chaperonins, superoxide dismutase, and phycocyanin β-subunit. In contrast, nine proteins involved in photosynthesis, translation, regulatory function, and other functions were up-regulated. In particular, a twitching motility protein (PilT1) was induced over 2-fold in sll0043 mutant. Moreover, semiquantitative and quantitative RT-PCR analysis revealed that pilin (pilA1), pili motor (pilT1), and pili switch gene (pilT2) were significantly increased in sll0043 mutant. These results suggest that the hybrid kinase Sll0043 regulates positive phototaxis by suppressing the expression of pili biosynthesis and regulatory genes and through the interplay with positive phototaxis/motility two-component proteins.

Alternative Alert System for Cyanobacterial Bloom, Using Phycocyanin as a Level Determinant: Chi-Yong Ahn , Seung-Hyun Joung , Sook-Kyoung Yoon , Hee-Mock Oh; J. Microbiol. 2007;45(2):98-104.; DOI: https://doi.org/2527 [pii]

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Abstract: Chlorophyll a concentration and cyanobacterial cell density are regularly employed as dual criteria for determinations of the alert level for cyanobacterial bloom. However, chlorophyll a is not confined only to the cyanobacteria, but is found universally in eukaryotic algae. Furthermore, the determination of cyanobacterial cell counts is notoriously difficult, and is unduly dependent on individual variation and trained skill. A cyanobacteria-specific parameter other than the cell count or chlorophyll a concentration is, accordingly, required in order to improve the present cyanobacterial bloom alert system. Phycocyanin has been shown to exhibit a strong correlation with a variety of bloom-related factors. This may allow for the current alert system criteria to be replaced by a three-stage alert system based on phycocyanin concentrations of 0.1, 30, and 700 μg/L. This would also be advantageous in that it would become far more simple to conduct measurements without the need for expensive equipment, thereby enabling the monitoring of entire lakes more precisely and frequently. Thus, an alert system with superior predictive ability based on highthroughput phycocyanin measurements appears feasible.

Factors Indicating Culture Status During Cultivation of Spirulina (Arthrospira) platensis: Choong-Jae Kim , Yun-Ho Jung , Hee-Mock Oh; J. Microbiol. 2007;45(2):122-127.; DOI: https://doi.org/2524 [pii]

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Abstract: Factors indicating culture status of two Spirulina platensis strains were monitored in a batch mode cultivation for 36 days. Changing mode in all factors showed a common turning point, indicating shift of cell or culture status. Mean biomass productivity was highly sustained until day 22, chlorophyll a concentration peaked on day 22, pH value was >12 on day 22, coil number was abruptly shortened on day 22, and floating activity was sustained at greater than 79% after day 22, indicating that day 22 is a criterion reflecting phase-transfer in cell physiology in a batch culture system. Many of these changes may have been caused by increased pH, suggesting that pH control is essential for mass production of S. platensis. Fluctuations in floating activity were likely induced by the number of cellular gas vacuoles. Consequently, coil number per trichome and floating activity of S. platensis could readily act as simple indicators for determination of culture status or harvesting time of cells.

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