Journal of Microbiology

Research Article

Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition: Seohyun Ahn, Min Cho, Michael J. Sadowsky, Jeonghwan Jang; J. Microbiol. 2025;63(2):e2411019. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411019

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Abstract PDF Supplementary Material: Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were thought to be carried-out by anaerobic bacteria constrained to anoxic conditions as they use nitrate (NO₃^-) as a terminal electron acceptor instead of molecular O₂. Three soil bacilli, Neobacillus spp. strains PS2-9 and PS3-12 and Bacillus salipaludis PS3-36, were isolated from rice paddy field soil in Korea. The bacterial strains were selected as possible candidates performing aerobic denitrification and DNRA as they were observed to reduce NO₃^- and produce extracellular NH₄⁺ regardless of oxygen presence at the initial screening. Whole genome sequencing revealed that these strains possessed all the denitrification and DNRA functional genes in their genomes, including the nirK, nosZ, nirB, and nrfA genes, which were simultaneously cotranscribed under aerobic condition. The ratio between the assimilatory and dissimilatory NO₃^- reduction pathways depended on the availability of a nitrogen source for cell growth, other than NO₃^-. Based on the phenotypic and transcriptional analyses of the NO₃^- reductions, all three of the facultative anaerobic strains reduced NO₃^- likely in both assimilatory and dissimilatory pathways under both aerobic and anoxic conditions. To our knowledge, this is the first report that describes coexistence of NO₃^- assimilation, denitrification, and DNRA in a Bacillus or Neobacillus strain under aerobic condition. These strains may play a pivotal role in the soil nitrogen cycle.

Review

[Minireview]Potential roles of condensin in genome organization and beyond in fission yeast: Kyoung-Dong Kim; J. Microbiol. 2021;59(5):449-459. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1039-2

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The genome is highly organized hierarchically by the function of structural maintenance of chromosomes (SMC) complex proteins such as condensin and cohesin from bacteria to humans. Although the roles of SMC complex proteins have been well characterized, their specialized roles in nuclear processes remain unclear. Condensin and cohesin have distinct binding sites and mediate long-range and short-range genomic associations, respectively, to form cell cycle-specific genome organization. Condensin can be recruited to highly expressed genes as well as dispersed repeat genetic elements, such as Pol III-transcribed genes, LTR retrotransposon, and rDNA repeat. In particular, mitotic transcription factors Ace2 and Ams2 recruit condensin to their target genes, forming centromeric clustering during mitosis. Condensin is potentially involved in various chromosomal processes such as the mobility of chromosomes, chromosome territories, DNA reannealing, and transcription factories. The current knowledge of condensin in fission yeast summarized in this review can help us understand how condensin mediates genome organization and participates in chromosomal processes in other organisms.

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Journal Articles

Thermococcus indicus sp. nov., a Fe(III)-reducing hyperthermophilic archaeon isolated from the Onnuri Vent Field of the Central Indian Ocean ridge: Jae Kyu Lim , Yun Jae Kim , Jhung-Ahn Yang , Teddy Namirimu , Sung-Hyun Yang , Mi-Jeong Park , Yong Min Kwon , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee , Kae Kyoung Kwon; J. Microbiol. 2020;58(4):260-267. Published online April 1, 2020; DOI: https://doi.org/10.1007/s12275-020-9424-9

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Abstract

A strictly anaerobic, dissimilatory Fe(III)-reducing hyperthermophilic archaeon, designated as strain IOH1T, was isolated from a new deep-sea hydrothermal vent (Onnuri Vent Field) area in the Central Indian Ocean ridge. Strain IOH1T showed > 99% 16S rRNA gene sequence similarity with Thermococcus celericrescens TS2T (99.4%) and T. siculi DSM 12349T (99.2%). Additional three species T. barossii SHCK-94T (99.0%), T. celer Vu13T (98.8%), and T. piezophilus (98.6%) showed > 98.6% of 16S rRNA gene sequence similarity, however, the maximum OrthoANI value is 89.8% for the genome of T. celericrescens TS2T. Strain IOH1T cells are coccoid, 1.2–1.8 μm in diameter, and motile by flagella. Growth was at 70–82°C (optimum 80°C), pH 5.4–8.0 (optimum pH 6.0) with 2–4% (optimum 3%) NaCl. Growth of strain IOH1T was enhanced by starch, pyruvate, D(+)-maltose and maltodextrin as a carbon sources, and elemental sulfur as an electron acceptor; clearly different from those of related species T. celecrescens DSM 17994T and T. siculi DSM 12349T. Strain IOH1T, T. celercrescence DSM 17994T, and T. siculi DSM 12349T reduced soluble Fe(III)-citrate present in the medium, whereas the amount of total cellular proteins increased with the concomitant accumulation of Fe(II). We determined a circular chromosome of 2,234 kb with an extra-chromosomal archaeal plasmid, pTI1, of 7.7 kb and predicted 2,425 genes. The DNA G + C content was 54.9 mol%. Based on physiological properties, phylogenetic, and genome analysis, we proposed that strain IOH1T (= KCTC 15844T = JCM 39077T) is assigned to a new species in the genus Thermococcus and named Thermococcus indicus sp. nov.

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Macrobenthic communities in the polymetallic nodule field, Indian Ocean, based on multicore and box core analysis
Santosh Gaikwad, Sabyasachi Sautya, Samir Damare, Maria Brenda Luzia Mascarenhas-Pereira, Vijayshree Gawas, Jayesh Patil, Mandar Nanajkar, Sadiq Bukhari
Frontiers in Marine Science.2024;[Epub] CrossRef
Thermococcus argininiproducens sp. nov., an arginine biosynthesis archaeal species isolated from the Central Indian Ocean ridge
Yeong-Jun Park, Jae Kyu Lim, Yun Jae Kim, Sung-Hyun Yang, Hyun Sook Lee, Sung Gyun Kang, Jung-Hyun Lee, Youngik Yang, Kae Kyoung Kwon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Spatial comparison and temporal evolution of two marine iron-rich microbial mats from the Lucky Strike Hydrothermal Field, related to environmental variations
Aina Astorch-Cardona, Mathilde Guerre, Alain Dolla, Valérie Chavagnac, Céline Rommevaux
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James F. Holden, Harita Sistu
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WeiShu ZHAO, Xiang XIAO
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Sophie L Nixon, Emily Bonsall, Charles S Cockell
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Aharon Oren, George M. Garrity
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Thermococcus aciditolerans sp. nov., a piezotolerant, hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent chimney in the Southwest Indian Ridge
Xue-Gong Li, Hong-Zhi Tang, Wei-Jia Zhang, Xiao-Qing Qi, Zhi-Guo Qu, Jun Xu, Long-Fei Wu
International Journal of Systematic and Evolutionary Microbiology.2021;[Epub] CrossRef
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Xiang Zeng, Karine Alain, Zongze Shao
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Microbial transformation of Se oxyanions in cultures of Delftia lacustris grown under aerobic conditions: Shrutika L. Wadgaonkar , Yarlagadda V. Nancharaiah , Claus Jacob , Giovanni Esposito , Piet N. L. Lens; J. Microbiol. 2019;57(5):362-371. Published online March 21, 2019; DOI: https://doi.org/10.1007/s12275-019-8427-x

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Abstract

Delftia lacustris is reported for the first time as a selenate and selenite reducing bacterium, capable of tolerating and growing in the presence of ≥ 100 mM selenate and 25 mM selenite. The selenate reduction profiles of D. lacustris were investigated by varying selenate concentration, inoculum size, concentration and source of organic electron donor in minimal salt medium. Interestingly, the bacterium was able to reduce both selenate and selenite under aerobic conditions. Although considerable removal of selenate was observed at all concentrations investigated, D. lacustris was able to completely reduce 0.1 mM selenate within 96 h using lactate as the carbon source. Around 62.2% unaccounted selenium (unidentified organo-selenium compounds), 10.9% elemental selenium and 26.9% selenite were determined in the medium after complete reduction of selenate. Studies of the enzymatic activity of the cell fractions show that the selenite/selenate reducing enzymes were intracellular and independent of NADPH availability. D. lacustris shows an unique metabolism of selenium oxyanions to form elemental selenium and possibly also selenium ester compounds, thus a potential candidate for the remediation of selenium-contaminated wastewaters in aerobic environments. This novel finding will advance the field of bioremediation of selenium-contaminated sites and selenium bio-recovery and the production of potentially beneficial organic and inorganic reactive selenium species.

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Ramona Riedel, Karsten Meißner, Arne Kaschubowski, Dirk Benndorf, Marion Martienssen, Burga Braun
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Foliar application of microbial nano-selenium enhances selenium uptake and alleviates oxidative stress
Fang Ma, Lichen Yang, Tiantian Zhao, Yongqiang Yuan, Shixue Zheng
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Micaela Pescuma, Francisca Aparicio, Roberto D. Zysler, Enio Lima, Claudia Zapata, Jorge A. Marfetán, M.Laura Vélez, Omar F. Ordoñez
Biotechnology Reports.2023; 37: e00787. CrossRef
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Elham Lashani, Hamid Moghimi, Raymond J Turner, Mohammad Ali Amoozegar
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Dong-Wook Hyun, Hojun Sung, Pil Soo Kim, Ji-Hyun Yun, Jin-Woo Bae
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Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings: Ui-Gi Min , So-Jeong Kim , Heeji Hong , Song-Gun Kim , Joo-Han Gwak , Man-Young Jung , Jong-Geol Kim , Jeong-Geol Na , Sung-Keun Rhee; J. Microbiol. 2016;54(6):413-419. Published online May 27, 2016; DOI: https://doi.org/10.1007/s12275-016-6086-8

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Abstract

A strictly anaerobic bacterium, strain B5T, was isolated from sediment of an abandoned coal mine in Taebaek, Republic of Korea. Cells of strain B5T were non-spore-forming, straight, Gram-positive rods. The optimum pH and temperature for growth were pH 7.0 and 30°C, respectively, while the strain was able to grow within pH and temperature ranges of 5.5– 7.5 and 25–45°C, respectively. Growth of strain B5T was observed at NaCl concentrations of 0 to 6.0% (w/v) with an optimum at 3.0–4.0% (w/v). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and three unknown polar lipids. Strain B5T grew anaerobically by reducing nitrate, nitrite, ferric-citrate, ferric-nitrilotriacetate, elemental sulfur, thiosulfate, and anthraquinone- 2-sulfonate in the presence of proteinaceous compounds, organic acids, and carbohydrates as electron donors. The isolate was not able to grow by fermentation. Strain B5T did not grow under aerobic or microaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B5T is most closely related to the genus Tepidibacillus (T. fermentans STGHT; 96.3%) and Vulcanibacillus (V. modesticaldus BRT; 94.6%). The genomic DNA G+C content (36.9 mol%) of strain B5T was higher than those of T. fermentans STGHT (34.8 mol%) and V. modesticaldus BRT (34.5 mol%). Based on its phenotypic, chemotaxonomic, and phylogenetic properties, we describe a new species of a novel genus Calculibacillus, represented by strain B5T (=KCTC 15397T =JCM 19989T), for which we propose the name Calculibacillus koreensis gen. nov., sp. nov.

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Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives
Sharareh Harirchi, Taner Sar, Mohaddaseh Ramezani, Habibu Aliyu, Zahra Etemadifar, Seyed Ali Nojoumi, Fatemeh Yazdian, Mukesh Kumar Awasthi, Mohammad J. Taherzadeh
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Research Support, Non-U.S. Gov'ts

Molecular Analysis of Spatial Variation of Iron-Reducing Bacteria in Riverine Alluvial Aquifers of the Mankyeong River: So-Jeong Kim , Dong-Chan Koh , Soo-Je Park , In-Tae Cha , Joong-Wook Park , Jong-Hwa Na , Yul Roh , Kyung-Seok Ko , Kangjoo Kim , Sung-Keun Rhee; J. Microbiol. 2012;50(2):207-217. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1342-z

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Abstract: Alluvial aquifers are one of the mainwater resources in many countries. Iron reduction in alluvial aquifers is often a major anaerobic process involved in bioremediation or causing problems, including the release of As trapped in Fe(III) oxide. We investigated the distribution of potential iron-reducing bacteria (IRB) in riverine alluvial aquifers (B1, B3, and B6 sites) at the Mankyeong River, Republic of Korea. Inactive iron reduction zones, the diversity and abundance of IRB can be examined using a clone library and quantitative PCR analysis of 16S rRNA genes. Geobacter spp. are potential IRB in the iron-reducing zone at the B6 (9 m) site, where high Fe(II) and arsenic (As) concentrations were observed. At the B3 (16 m) site, where low iron reduction activity was predicted, a dominant clone (10.6%) was 99% identical in 16S rRNA gene sequence with Rhodoferax ferrireducens. Although a major clone belonging to Clostridium spp. was found, possible IRB candidates could not be unambiguously determined at the B1 (18 m) site. Acanonical correspondence analysis demonstrated that, among potential IRB, only the Geobacteraceae were well correlated with Fe(II) and As concentrations. Our results indicate high environmental heterogeneity, and thus high spatial variability, in thedistribution of potential IRB in the riverine alluvial aquifersnear the Mankyeong River.

Characterization of Plant-Growth Promoting Diazotrophic Bacteria Isolated from Field Grown Chinese Cabbage under Different Fertilization Conditions: Woo-Jong Yim , Selvaraj Poonguzhali , Munusamy Madhaiyan , Pitchai Palaniappan , M. A. Siddikee , Tongmin Sa; J. Microbiol. 2009;47(2):147-155. Published online May 2, 2009; DOI: https://doi.org/10.1007/s12275-008-0201-4

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Abstract: Diazotrophic bacteria isolated from the rhizosphere of Chinese cabbage were assessed for other plant growth promoting characteristics viz., production of IAA, ethylene, ACC deaminase, phosphate solubilization, and gnotobiotic root elongation. Their effect on inoculation to Chinese cabbage was also observed under growth chamber conditions. A total of 19 strains that showed higher nitrogenase activity identified by 16S rRNA gene sequence analysis were found to be the members of the genera Pseudomonas and Agrobacterium belonging to α- and γ-Proteobacteria groups. These strains were also efficient in producing IAA and ACC deaminase though they produced low levels of ethylene and no phosphate solubilization. In addition, inoculation of selected diazotrophic bacterial strains significantly increased seedling length, dry weight, and total nitrogen when compared to uninoculated control. The colonization of crop plants by diazotrophic bacteria can be affected by many biotic and abiotic factors, and further studies are oriented towards investigating the factors that could influence the establishment of a selected bacterial community.

Electrochemical Reduction of Xylose to Xylitol by Whole Cells or Crude Enzyme of Candida peltata: Sun Mi Park , Byung In Sang , Dae Won Park , Doo Hyun Park; J. Microbiol. 2005;43(5):451-455.; DOI: https://doi.org/2276 [pii]

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Abstract: In this study, whole cells and a crude enzyme of Candida peltata were applied to an electrochemical bioreactor, in order to induce an increment of the reduction of xylose to xylitol. Neutral red was utilized as an electron mediator in the whole cell reactor, and a graphite-Mn(IV) electrode was used as a catalyst in the enzyme reactor in order to induce the electrochemical reduction of NAD+ to NADH. The efficiency with which xylose was converted to xylitol in the electrochemical bioreactor was five times higher than that in the conventional bioreactor, when whole cells were employed as a biocatalyst. Meanwhile, the xylose to xylitol reduction efficiency in the enzyme reactor using the graphite-Mn (IV) electrode and NAD+ was twice as high as that observed in the conventional bioreactor which utilized NADH as a reducing power. In order to use the graphite-Mn(IV) electrode as a catalyst for the reduction of NAD+ to NADH, a bioelectrocatalyst was engineered, namely, oxidoreductase (e.g. xylose reductase). NAD+ can function in this biotransformation procedure without any electron mediator or a second oxidoreductase for NAD+/NADH recycling

Reduction of hexavalent chromium by pseudomonas aeruginosa HP014: Oh, Young Sook , choi, Sung Chan; J. Microbiol. 1997;35(1):25-29.

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Abstract: Microbial reduction of hexavalent (VI) to trivalent (III) chromium decreases its toxicity by two orders of magnitude. In order to investigate the nature of Cr-reduction, Cr-resistant Pseudomonas aeruginosa HP014 was isolated and tested for its reduction capability. At the concentration of 0.5 mM Cr(VI), cell growth was not inhibited by the presence of Cr(VI) in a liquid medium, and Cr(VI) reduction was accompanied by ell growth. When cell-free extract was tested, the reduction of Cr(VI) showed a saturation kinetics with the maximum specific activity of 0.33 umol min^-1 mg^-1 cell protein, and an apparent K. of 1.73 mM Cr(VI). The activity required either NADH or NADPH as an electron donor. However, NADPH gave 50% as much activity as NADH. To locate the reductase activity, cell free extract was centrifuged at 150,000×g, and subsequently the supernatant and pelleted membrane fractions were tested for Cr(VI) reduction activity. The supernatant of the centrifugation showed almost the same Cr(VI) reduction activity as compared with that of the cell-free extract, indicating that the Cr(VI)-reducing activity of P. aeruginosa HP-14 is due to soluble enzyme. Moreover, the activity appeared to be the highest among the known activities, suggesting that the strain might be useful for remediation of Cr(VI)-contaminated sites.

Isolation and Identification of an Anaerobic Dissimilatory Fe(III)-Reducing Bacterium, Shewanella putrefaciens IR-1: Moon-Sik Hyun , Byung-Hong Kim , In-Seop Chang , Hyung-Soo Park , Hyung-Joo Kim , Gwang-Tae Kim , Mi-a Kim , Doo-Hyun Park; J. Microbiol. 1999;37(4):206-212.

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Abstract: In order to isolate a Fe(III)-reducer from the natural environment, soil samples were collected from various patty fields and enriched with ferric citrate as a source of Fe(III) under anaerobic condition. Since the enrichment culture was serially performed, the Fe(III)-reduction activity was serially diluted and cultivated on an agar plate containing lactate and ferric citrate in an anaerobic glove box. A Gram negative, motile, rod-shpaped and facultative anaerobic Fe(III)-reducer was isolated based on its highest Fe(III)-reduction activity, Bacterial growth was coupled with oxidation of lactate to Fe(III)-reduction, but the isolate fermented pyruvate without Fe(III), The isolate reduced an insoluble ferric iron (FeOOH) as well as a soluble ferric iron (ferric citrate). Using the BBL crystal enteric/non-fermentor identification kit and 16S rDNA sequence analysis, the isolate was identifice as Shewanella putrefaciens IR-1.

Reduction of Hexavalent Chromium by Escherichia coli ATCC 33456 in Batch and Continuous Cultures: Woo Chul Bae , Tae Gu Kang , In Kyong Kang , You Jung Won , Byeong Chul Jeong; J. Microbiol. 2000;38(1):36-39.

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Abstract: Toxic hexavalent chromium, Cr(VI), was reduced to a less toxic trivalent chromium form by E. coli ATCC 33456. The suitable electron donor for Cr(VI) reduction was glucose. E. coli ATCC 33456 was more resistant to metal cations than other reported Cr(VI) reducing microorganisms. Cell growth was inhibited by the presence of Cr(VI) in a liquid medium and Cr(VI) reduction accompanied cell growth. With a hydraulic retention time of 20 h, Cr(VI) reducing efficiency was 100% to 84% when Cr(VI) concentration in the influent was in the range of 10 to 40 mg L^-1. Specific rate of Cr(VI) concentration in the influent was 2.41 mg Cr(VI) g DCW^-1 h^-1 when 40 mg :^-1 of Cr(VI) influent was used. This result suggested the potential application of E. coli ATCC 33456 for the detoxification of Cr(VI) in Cr(VI) contaminated wastewater.

Inhibitory Effect of Nitrate on Fe(III) and Humic Acid Reduction in Shewanella putrefaciens DK-1: Il-Gyu Lee , Sang-Jin Kim , Tae-Young Ahn; J. Microbiol. 2000;38(3):180-182.

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Abstract: The inhibitory effects of nitrate on Fe(III) and humic acid reduction were examined in Shewanella putrefaciens DK-1. There is no difference in Fe(III) reduction until 25 hours between cultures using Fe(III) alone as an electron acceptor and using Fe(III) and nitrate as electron acceptors, but after 25 hours Fe(II) production was decreased drastically when Fe(II) and nitrate were used as electron acceptors. The production of AHQDS (2,6-anthrahydroquinon disulfonate) showed similar patterns when AQDS alone and both AQDS and Fe(III) were used as electron acceptors. When AQDS (2,6-anthraquinon disulfonate) and nitrate were used as electron accepors, the production of AHQDS was completely inhibited.

Removal and Inactivation of Hepatitis A Virus during Manufacture of a High Purity Antihemophilic Factor VIII Concentrate from Human Plasma: In Seop Kim , Yong Woon Choi , Sung Rae Lee , Mahl Soon Lee , Ki Ho Huh , Soungmin Lee; J. Microbiol. 2001;39(1):67-73.

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Abstract: A validation study was conducted to evaluate the efficacy and mechanism of the cryo-precipitation, monoclonal anti-FVIIIc antibody (mAb) chromatography, Q-Sepharose chromatography, and lyophilization steps involved in the manufacture of high purity factor VIII (GreenMono) from human plasma, in the removal and/or inactivation of hepatitis A virus (HAV). Samples from the relevant stages of the production process were spiked with HAV and subjected to scale-down processes mimicking the manufacture of the high purity factor VIII concentrate. Samples were collected at each step and immediately titrated using a 50% tissue culture infectious dose (TCID50) and then the virus reduction factors were evaluated. HAV was effectively partitioned from factor VIII during cryo-precipitation with the log reduction factor of 3.2. The mAb chromatography was the most effective step for removal of HAV with the log reduction factor of ³4.3. HAV infectivity was not detected in the fraction of factor VIII, while most of HAV infectivity was recovered in the fractions of flow through and wash during mAb chromatography. Q-Sepharose chromatography showed the lowest efficacy for partitioning HAV with the log reduction factor of 0.7. Lyophilization was an effective step in inactivating HAV with the log reduction factor of 2.3. The cumulative log reduction factor, ³10.5, achieved for the entire manufacturing process was several magnitudes greater than the potential HAV load of current plasma pools.

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