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Tn5 Transposon-based Mutagenesis for Engineering Phage-resistant Strains of Escherichia coli BL21 (DE3)
Yinfeng Wang , Guanhua Xuan , Houqi Ning , Jiuna Kong , Hong Lin , Jingxue Wang
J. Microbiol. 2023;61(5):559-569.   Published online May 22, 2023
DOI: https://doi.org/10.1007/s12275-023-00048-2
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AbstractAbstract PDF
Escherichia coli is a preferred strain for recombinant protein production, however, it is often plagued by phage infection during experimental studies and industrial fermentation. While the existing methods of obtaining phage-resistant strains by natural mutation are not efficient enough and time-consuming. Herein, a high-throughput method by combining Tn5 transposon mutation and phage screening was used to produce Escherichia coli BL21 (DE3) phage-resistant strains. Mutant strains PR281-7, PR338-8, PR339-3, PR340-8, and PR347-9 were obtained, and they could effectively resist phage infection. Meanwhile, they had good growth ability, did not contain pseudolysogenic strains, and were controllable. The resultant phage-resistant strains maintained the capabilities of producing recombinant proteins since no difference in mCherry red fluorescent protein expression was found in phage-resistant strains. Comparative genomics showed that PR281-7, PR338-8, PR339-3, and PR340-8 mutated in ecpE, nohD, nrdR, and livM genes, respectively. In this work, a strategy was successfully developed to obtain phage-resistant strains with excellent protein expression characteristics by Tn5 transposon mutation. This study provides a new reference to solve the phage contamination problem.

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  • Establishment and improvement of genetic manipulation tools for Fusobacterium nucleatum
    Zhiwei Guan, Hailong Wang, Qiang Feng
    Engineering Microbiology.2025; 5(1): 100192.     CrossRef
  • Antiviral effects of heme oxygenase-1 against canine coronavirus and canine influenza virus in vitro
    Jae-Hyeong Kim, Dong-Hwi Kim, Kyu-Beom Lim, Joong-Bok Lee, Seung-Yong Park, Chang-Seon Song, Sang-Won Lee, Dong-Hun Lee, Do-Geun Kim, Hun-Young Yoon, In-Soo Choi
    Journal of Microbiology.2025; 63(5): e2501029.     CrossRef
Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants
Geeta Chhetri , Inhyup Kim , Minchung Kang , Jiyoun Kim , Yoonseop So , Taegun Seo
J. Microbiol. 2022;60(1):1-10.   Published online November 26, 2021
DOI: https://doi.org/10.1007/s12275-022-1474-8
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  • 43 Web of Science
  • 46 Crossref
AbstractAbstract PDF
Two novel Gram-negative, aerobic, asporogenous, motile, rodshaped, orange and white pigmented, designated as LEGU1T and G19T, were isolated from the roots of rice plants, collected from Goyang, South Korea. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that they belonged to the genus Devosia and formed a different lineage and clusters with different members of the genus Devosia. These strains shared common chemotaxonomic features. In particular, they had Q-10 as the sole quinone, phosphatidylglycerol, diphosphatidylglycerol as the principal polar lipids and C16:0, C18:1 ω7c 11-methyl and summed feature 8 (comprising C18:1 ω7c/ C18:1 ω6c) as the main fatty acids. The draft genome sequences of strains LEGU1T and G19T were 3,524,978 and 3,495,520 bp in size, respectively. Their average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 72.8–81.9% and 18.7–25.1%, respectively, with each other and type strains of related species belonging to the genus Devosia, suggesting that these two strains represent novel species. The G + C content of strains LEGU1T and G19T were 62.1 and 63.8%, respectively. Of the two strains, only LEGU1T produced carotenoid and flexirubin-type pigment. Both strains produced siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Siderophore biosynthesis genes, auxin responsive genes and tryptophan biosynthesis genes were present in their genomes. The present study aimed to determine the detailed taxonomic positions of the strains using the modern polyphasic approach. Based on the results of polyphasic analysis, these strains are suggested to be two novel bacterial species within the genus Devosia. The proposed names are D. rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., respectively. The plant growth promoting effects of these strains suggest that they can be exploited to improve rice crop productivity. The type strain of D. rhizoryzae is LEGU1T (KCTC 82712T = NBRC 114485T) and D. oryziradicis is G19T (KCTC 82688T = NBRC 114842T).

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  • Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter
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  • Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato)
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    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
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  • Chryseobacterium tagetis sp. nov., a plant growth promoting bacterium with an antimicrobial activity isolated from the roots of medicinal plant (Tagetes patula)
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    The Journal of Antibiotics.2022; 75(6): 312.     CrossRef
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    International Journal of Systematic and Evolutionary Microbiology.2022;[Epub]     CrossRef
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Review
Against friend and foe: Type 6 effectors in plant-associated bacteria
Choong-Min Ryu
J. Microbiol. 2015;53(3):201-208.   Published online March 3, 2015
DOI: https://doi.org/10.1007/s12275-015-5055-y
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  • 32 Crossref
AbstractAbstract PDF
Bacterial secretion systems play critical roles in communication with neighboring bacteria and in the modulation of host immune responses via the secretion of small proteins called effectors. Several secretion systems have been identified and these are denoted types I-II. Of these, the type VI secretion system (T6SS) and its effectors were only recently elucidated. Most studies on the role and significance of the T6SS and its effectors have focused on human pathogens. In this review, type 6 effectors from plant-associated beneficial and pathogenic bacteria are discussed, including effectors from Agrobacterium tumefaciens, Dickeya dadanti, Rhizobium leguminosarum, Pectobacterium atroseptium, Ralstonia solanacearum, Pseudomonas syringae, Pseudomonas fluorescens, and Pseudomonas protegens. Type 6 effectors act in symbiosis, biofilm formation, virulence, and interbacterial competition. Understanding the impact of type 6 effectors on pathogenesis will contribute to the management of bacterial pathogens in crop plants by allowing the manipulation of intra and inter-specific interactions.

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Research Support, Non-U.S. Gov'ts
Two Rhizobacterial Strains, Individually and in Interactions with Rhizobium sp., Enhance Fusarial Wilt Control, Growth, and Yield in Pigeon Pea
Swarnalee Dutta , Pranjal Morang , Nishanth Kumar S , B.S. Dileep Kumar
J. Microbiol. 2014;52(9):778-784.   Published online September 2, 2014
DOI: https://doi.org/10.1007/s12275-014-3496-3
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AbstractAbstract PDF
A Pseudomonas aeruginosa strain, RRLJ 04, and a Bacillus cereus strain, BS 03, were tested both individually and in combination with a Rhizobium strain, RH 2, for their ability to enhance plant growth and nodulation in pigeon pea (Cajanus cajan L.) under gnotobiotic, greenhouse and field conditions. Both of the rhizobacterial strains exhibited a positive effect on growth in terms of shoot height, root length, fresh and dry weight, nodulation and yield over the non-treated control. Co-inoculation of seeds with these strains and Rhizobium RH 2 also reduced the number of wilted plants, when grown in soil infested with Fusarium udum. Gnotobiotic studies confirmed that the suppression of wilt disease was due to the presence of the respective PGPR strains. Seed bacterization with drug-marked mutants of RRLJ 04 and BS 03 confirmed their ability to colonize and multiply along the roots. The results suggest that co-inoculation of these strains with Rhizobium strain RH 2 can be further exploited for enhanced growth, nodulation and yield in addition to control of fusarial wilt in pigeon pea.

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Biological Control and Plant Growth Promoting Capacity of Rhizobacteria on Pepper under Greenhouse and Field Conditions
Mi-Seon Hahm , Marilyn Sumayo , Ye-Ji Hwang , Seon-Ae Jeon , Sung-Jin Park , Jai Youl Lee , Joon-Hyung Ahn , Byung-Soo Kim , Choong-Min Ryu , Sa-Youl Ghim
J. Microbiol. 2012;50(3):380-385.   Published online June 30, 2012
DOI: https://doi.org/10.1007/s12275-012-1477-y
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AbstractAbstract PDF
Plant growth promoting rhizobacteria Ochrobactrum lupini KUDC1013 and Novosphingobium pentaromativorans KUDC1065 isolated from Dokdo Island, S. Korea are capable of eliciting induced systemic resistance (ISR) in pepper against bacterial spot disease. The present study aimed to determine whether plant growth-promoting rhizobacteria (PGPR) strains including strain KUDC1013, strain KUDC1065, and Paenibacillus polymyxa E681 either singly or in combinations were evaluated to have the capacity for potential biological control and plant growth promotion effect in the field trials. Under greenhouse conditions, the induced systemic resistance (ISR) effect of treatment with strains KUDC1013 and KUDC1065 differed according to pepper growth stages. Drenching of 3-week-old pepper seedlings with the KUDC-1013 strain significantly reduced the disease symptoms. In contrast, treatment with the KUDC1065 strain significantly protected 5-week-old pepper seedlings. Under field conditions, peppers treated with PGPR mixtures containing E681 and KUDC1013, either in a two-way combination, were showed greater effect on plant growth than those treated with an individual treatment. Collectively, the application of mixtures of PGPR strains on pepper might be considered as a potential biological control under greenhouse and field conditions.

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Isolation and Characterization of Plant Growth-Promoting Rhizobacteria from Wheat Roots by Wheat Germ Agglutinin Labeled with Fluorescein Isothiocyanate
Jian Zhang , Jingyang Liu , Liyuan Meng , Zhongyou Ma , Xinyun Tang , Yuanyuan Cao , Leni Sun
J. Microbiol. 2012;50(2):191-198.   Published online April 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1472-3
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AbstractAbstract PDF
Thirty-two isolates were obtained from wheat rhizosphere by wheat germ agglutinin (WGA) labeled with fluorescein isothiocyanate (FITC). Most isolates were able to produce indole acetic acid (65.6%) and siderophores (59.3%), as well as exhibited phosphate solubilization (96.8%). Fourteen isolates displayed three plant growth-promoting traits. Among these strains, two phosphate-dissolving ones, WS29 and WS31, were evaluated for their beneficial effects on the early growth of wheat (Triticum aestivum Wan33). Strain WS29 and WS31 significantly promoted the development of lateral roots by 34.9% and 27.6%, as well as increased the root dry weight by 25.0% and 25.6%, respectively, compared to those of the control. Based on 16S rRNA gene sequence comparisons and phylogenetic positions, both isolates were determined to belong to the genus Bacillus. The proportion of isolates showing the properties of plant growth-promoting rhizobacteria (PGPR) was higher than in previous reports. The efficiency of the isolation of PGPR strains was also greatly increased by WGA labeled with FITC. The present study indicated that WGA could be used as an effective tool for isolating PGPR strains with high affinity to host plants from wheat roots. The proposed approach could facilitate research on biofertilizers or biocontrol agents.

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Gram-positive Rhizobacterium Bacillus amyloliquefaciens FZB42 Colonizes Three Types of Plants in Different Patterns
Ben Fan , Rainer Borriss , Wilfrid Bleiss , Xiaoqin Wu
J. Microbiol. 2012;50(1):38-44.   Published online February 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1439-4
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AbstractAbstract PDF
The colonization of three types of different plants, Zea mays, Arabidopsis thaliana, and Lemna minor, by GFP-labeled Gram-positive rhizobacterium Bacillus amyloliquefaciens FZB42 was studied in gnotobiotic systems using confocal laser scanning microscopy and electron microscopy. It was demonstrated that FZB42 was able to colonize all the plants. On one hand, similar to some Gram-negative rhizobacteria like Pseudomonas, FZB42 favored the areas such as the concavities in root surfaces and the junctions where lateral roots occurred from the primary roots; on the other hand, we clearly demonstrated that root hairs were a popular habitat to the Gram-positive rhizobacterium. FZB42 exhibited a specific colonization pattern on each of the three types of plants. On Arabidopsis, tips of primary roots were favored by FZB42 but not so on maize. On Lemna, FZB42 accumulated preferably along the grooves between epidermal cells of roots and in the concave spaces on ventral sides of fronds. The results suggested L. minor to be a promising tool for investigations on plant-microbial interaction due to a series of advantages it has. Colonization of maize and Arabidopsis roots by FZB42 was also studied in the soil system. Comparatively, higher amount of FZB42 inoculum (~108 CFU/ml) was required for detectable root colonization in the soil system, where the preference of FZB42 cells to root hairs were also observed.

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Bacterial Structure and Characterization of Plant Growth Promoting and Oil Degrading Bacteria from the Rhizospheres of Mangrove Plants
Flávia Lima do Carmo , Henrique Fragoso dos Santos , Edir Ferreira Martins , Jan Dirk van Elsas , Alexandre Soares Rosado , Raquel Silva Peixoto
J. Microbiol. 2011;49(4):535-543.   Published online September 2, 2011
DOI: https://doi.org/10.1007/s12275-011-0528-0
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AbstractAbstract PDF
Most oil from oceanic spills converges on coastal ecosystems, such as mangrove forests, which are threatened with worldwide disappearance. Particular bacteria that inhabit the rhizosphere of local plant species can stimulate plant development through various mechanisms; it would be advantageous if these would also be capable of degrading oil. Such bacteria may be important in the preservation or recuperation of mangrove forests impacted by oil spills. This study aimed to compare the bacterial structure, isolate and evaluate bacteria able to degrade oil and stimulate plant growth, from the rhizospheres of three mangrove plant species. These features are particularly important taking into account recent policies for mangrove bioremediation, implying that oil degradation as well as plant maintenance and health are key targets. Fifty-seven morphotypes were isolated from the mangrove rhizospheres on Bushnell-Haas (BH) medium supplemented with oil as the sole carbon source and tested for plant growth promotion. Of this strains, 60% potentially fixed nitrogen, 16% showed antimicrobial activity, 84% produced siderophores, 51% had the capacity to solubilize phosphate, and 33% produced the indole acetic acid hormone. Using gas chromatography, we evaluated the oil-degrading potential of ten selected strains that had different morphologies and showed Plant Growth Promoting Rhizobacteria (PGPR) features. The ten tested strains showed a promising degradation profile for at least one compound present in the oil. Among degrader strains, 46% had promising PGPR potential, having at least three of the above capacities. These strains might be used as a consortium, allowing the concomitant degradation of oil and stimulation of mangrove plant survival and maintenance.

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Bacillus megaterium Strain XTBG34 Promotes Plant Growth by Producing 2-Pentylfuran
Changsong Zou , Zhifang Li , Diqiu Yu
J. Microbiol. 2010;48(4):460-466.   Published online August 20, 2010
DOI: https://doi.org/10.1007/s12275-010-0068-z
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AbstractAbstract PDF
Several chemical changes in soil are associated with plant growth-promoting rhizobacteria. An endosporeforming bacterium, strain XTBG34, was isolated from a Xishuangbanna Tropical Botanical Garden soil sample and identified as Bacillus megaterium. The strain’s volatiles had remarkable plant growth promotion activity in Arabidopsis thaliana plants; after 15 days treatment, the fresh weight of plants inoculated with XTBG34 was almost 2-fold compared with those inoculated with DH5α. Head space volatile compounds produced by XTBG34, trapped with headspace solid phase microextraction and identified by gas chromatography–mass spectrometry, included aldehydes, alkanes, ketones and aroma components. Of the 11 compounds assayed for plant growth promotion activity in divided Petri plates, only 2-pentylfuran increased plant growth. We have therefore identified a new plant growth promotion volatile of B. megaterium XTBG34, which deserves further study in the mechanisms of interaction between plant growth-promoting rhizobacteria and plants.

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