Journal of Microbiology

Journal Articles

Characterization and Comparative Genomic Analysis of vB_BceM_CEP1: A Novel Temperate Bacteriophage Infecting Burkholderia cepacia Complex: Momen Askoura, Eslam K Fahmy, Safya E Esmaeel, Wael A H Hegazy, Aliaa Abdelghafar; J. Microbiol. 2024;62(11):1035-1055. Published online November 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00185-2

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Abstract: The increasing prevalence of multidrug-resistant bacteria imminently threatens public health and jeopardizes nearly all aspects of modern medicine. The Burkholderia cepacia complex (Bcc) comprises Burkholderia cepacia and the related species of Gram-negative bacteria. Members of the Bcc group are opportunistic pathogens responsible for various chronic illnesses, including cystic fibrosis and chronic granulomatous disease. Phage therapy is emerging as a potential solution to combat the antimicrobial resistance crisis. In this study, a temperate phage vB_BceM_CEP1 was isolated from sewage and fully characterized. Transmission electron microscopy indicated that vB_BceM_CEP1 belongs to the family Peduoviridae. The isolated phage demonstrated enhanced environmental stability and antibiofilm potential. One-step growth analysis revealed a latent period of 30 min and an average burst size of 139 plaque-forming units per cell. The genome of vB_BceM_CEP1 consists of 32,486 bp with a GC content of 62.05%. A total of 40 open reading frames were annotated in the phage genome, and none of the predicted genes was annotated as tRNA. Notably, genes associated with antibiotic resistance, host virulence factors, and toxins were absent from the vB_BceM_CEP1 genome. Based on its unique phenotype and phylogeny, the isolated phage vB_BceM_CEP1 is classified as a new temperate phage with lytic activity. The findings of this study enhance our understanding of the diversity of Bcc phages.

The Gut Microbiota Mediates the Protective Effects of Spironolactone on Myocardial Infarction: Lu Li, Jian-Yong Sun, Yu-Lin Li, Shi-Wei Zhu, Sheng-Zhong Duan; J. Microbiol. 2024;62(10):883-895. Published online September 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00164-7

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Myocardial infarction (MI) is a type of cardiovascular disease that influences millions of human beings worldwide and has a great rate of mortality and morbidity. Spironolactone has been used as a critical drug for the treatment of cardiac failure and it ameliorates cardiac dysfunction post-MI. Despite these findings, whether there is a relationship between the therapeutic effects of spironolactone and the gut microorganism after MI has not been determined. In our research, we used male C57BL/6 J mice to explore whether the gut microbiota mediates the beneficial function of spironolactone after myocardial infarction. We demonstrated that deletion of the gut microbiota eliminated the beneficial function of spironolactone in MI mice, displaying exacerbated cardiac dysfunction, cardiac infarct size. In addition, the gut microbiota was altered by spironolactone after sham or MI operation in mice. We also used male C57BL/6 J mice to investigate the function of a probiotic in the myocardial infarction. In summary, our findings reveal a precious role of the gut flora in the therapeutic function of spironolactone on MI.

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The role of the gut microbiota in the onset and progression of heart failure: insights into epigenetic mechanisms and aging
Giulia Matacchione, Francesco Piacenza, Lorenzo Pimpini, Yuri Rosati, Serena Marcozzi
Clinical Epigenetics.2024;[Epub] CrossRef

Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil: Abhilash Bhattacharjee, Anil Kumar Singh; J. Microbiol. 2024;62(7):511-523. Published online June 21, 2024; DOI: https://doi.org/10.1007/s12275-024-00129-w

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Abstract: Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.

Review

Structural Insights into the Lipopolysaccharide Transport (Lpt) System as a Novel Antibiotic Target: Yurim Yoon, Saemee Song; J. Microbiol. 2024;62(4):261-275. Published online May 31, 2024; DOI: https://doi.org/10.1007/s12275-024-00137-w

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Abstract: Lipopolysaccharide (LPS) is a critical component of the extracellular leaflet within the bacterial outer membrane, forming an effective physical barrier against environmental threats in Gram-negative bacteria. After LPS is synthesized and matured in the bacterial cytoplasm and the inner membrane (IM), LPS is inserted into the outer membrane (OM) through the ATP-driven LPS transport (Lpt) pathway, which is an energy-intensive process. A trans-envelope complex that contains seven Lpt proteins (LptA-LptG) is crucial for extracting LPS from the IM and transporting it across the periplasm to the OM. The last step in LPS transport involves the mediation of the LptDE complex, facilitating the insertion of LPS into the outer leaflet of the OM. As the Lpt system plays an essential role in maintaining the impermeability of the OM via LPS decoration, the interactions between these interconnected subunits, which are meticulously regulated, may be potential targets for the development of new antibiotics to combat multidrug-resistant Gram-negative bacteria. In this review, we aimed to provide an overview of current research concerning the structural interactions within the Lpt system and their implications to clarify the function and regulation of LPS transport in the overall process of OM biogenesis. Additionally, we explored studies on the development of therapeutic inhibitors of LPS transport, the factors that limit success, and future prospects.

Journal Articles

Coumarin-based combined computational study to design novel drugs against Candida albicans: Akhilesh Kumar Maurya , Nidhi Mishra; J. Microbiol. 2022;60(12):1201-1207. Published online November 10, 2022; DOI: https://doi.org/10.1007/s12275-022-2279-5

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Abstract

Candida species cause the most prevalent fungal illness, candidiasis. Candida albicans is known to cause bloodstream infections. This species is a commensal bacterium, but it can cause hospital–acquired diseases, particularly in COVID-19 patients with impaired immune systems. Candida infections have increased in patients with acute respiratory distress syndrome. Coumarins are both naturally occurring and synthetically produced. In this study, the biological activity of 40 coumarin derivatives was used to create a three-dimensional quantitative structure activity relationship (3D-QSAR) model. The training and test minimum inhibitory concentration values of C. albicans active compounds were split, and a regression model based on statistical data was established. This model served as a foundation for the creation of coumarin derivative QSARs. This is a unique way to create new therapeutic compounds for various ailments. We constructed novel structural coumarin derivatives using the derived QSAR model, and the models were confirmed using molecular docking and molecular dynamics simulation.

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Coumarin derivatives ameliorate the intestinal inflammation and pathogenic gut microbiome changes in the model of infectious colitis through antibacterial activity
Hui-su Jung, Yei Ju Park, Bon-Hee Gu, Goeun Han, Woonhak Ji, Su mi Hwang, Myunghoo Kim
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Therapeutic Effects of Coumarins with Different Substitution Patterns
Virginia Flores-Morales, Ana P. Villasana-Ruíz, Idalia Garza-Veloz, Samantha González-Delgado, Margarita L. Martinez-Fierro
Molecules.2023; 28(5): 2413. CrossRef
Cyclometalated iridium(III) complexes combined with fluconazole: antifungal activity against resistant C. albicans
Jun-Jian Lu, Zhi-Chang Xu, Hou Zhu, Lin-Yuan Zhu, Xiu-Rong Ma, Rui-Rui Wang, Rong-Tao Li, Rui-Rong Ye
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef

Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead): Seomin Kang , Jae-Yun Lee , Jeong Eun Han , Yun-Seok Jeong , Do-Hun Gim , Jin-Woo Bae; J. Microbiol. 2022;60(9):890-898. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-2075-2

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Abstract

Two novel bacterial strains, KSM-R2A25T and KSM-R2A30T, were isolated from intestines of Cyclina sinensis (corb shell) and Channa argus (northern snakehead), respectively. Both specimens were collected in Korea. The strains were Gramstain- negative, non-motile, and strictly aerobic. According to phylogenetic analyses based on 16S rRNA gene sequences, strains belonged to the genus Flavobacterium within the family Flavobacteriaceae. 16S rRNA gene sequences of strains KSMR2A25T and KSM-R2A30T were closely related to Flavobacterium cucumis DSM 18830T and Flavobacterium aquaticum JC164T with sequence similarities of 97.77% and 98.54%, respectively. Further genomic analyses including reconstruction of the UBCG tree and overall genome-related indices suggested them as novel species of the genus Flavobacterium. Both strains contained menaquinone with six isoprene units (MK-6) as a major isoprenoid quinone and iso-C15:1 G, iso- C15:0, and iso-C16:0 as major cellular fatty acids. The major polar lipid in both strains was phosphatidylethanolamine. The genomic G + C contents of strains KSM-R2A25T and KSMR2A30T were 31.7 and 31.9%, respectively. Based on the polyphasic taxonomic study presented here, strains KSM-R2A25T and KSM-R2A30T represent novel species of the genus Flavobacterium, for which the names Flavobacterium cyclinae sp. nov and Flavobacterium channae sp. nov are proposed. The type strains of F. cyclinae sp. nov and F. channae sp. nov are KSM-R2A25T (= KCTC 82978T = JCM 34997T) and KSMR2A30T (= KCTC 82979T = JCM 34998T), respectively.

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Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef
Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nihed Ajmi, Enes Said Gunduz, Huban Gocmen, Muhammed Duman
Systematic and Applied Microbiology.2024; 47(4): 126518. CrossRef
The first report of submandibular lymph node infection with Flavobacterium ceti in a horse and its complete genome sequence
Seung-Ho Ryu, Beomsoon Jang, Byung-Sun Kim, Kun Taek Park
Microbial Pathogenesis.2024; 197: 107096. CrossRef
Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Transcriptomic insights into the immune response of the intestine to Aeromonas veronii infection in northern snakehead (Channa argus)
Peng Sun, Di Zhang, Na Li, Xiao-Fei Li, Yi-Han Ma, Hui Li, Ye Tian, Tao Wang, Shahrood Ahmed Siddiquid, Wu-wen Sun, Lei Zhang, Xiao-Feng Shan, Chun-Feng Wang, Ai-Dong Qian, Dong-Xing Zhang
Ecotoxicology and Environmental Safety.2023; 255: 114825. CrossRef
Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum s
Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. CrossRef
Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Eradication of drug-resistant Acinetobacter baumannii by cell-penetrating peptide fused endolysin: Jeonghyun Lim , Jaeyeon Jang , Heejoon Myung , Miryoung Song; J. Microbiol. 2022;60(8):859-866. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-2107-y

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Abstract

Antimicrobial agents targeting peptidoglycan have shown successful results in eliminating bacteria with high selective toxicity. Bacteriophage encoded endolysin as an alternative antibiotics is a peptidoglycan degrading enzyme with a low rate of resistance. Here, the engineered endolysin was developed to defeat multiple drug-resistant (MDR) Acinetobacter baumannii. First, putative endolysin PA90 was predicted by genome analysis of isolated Pseudomonas phage PBPA. The His-tagged PA90 was purified from BL21(DE3) pLysS and tested for the enzymatic activity using Gram-negative pathogens known for having a high antibiotic resistance rate including A. baumannii. Since the measured activity of PA90 was low, probably due to the outer membrane, cell-penetrating peptide (CPP) DS4.3 was introduced at the N-terminus of PA90 to aid access to its substrate. This engineered endolysin, DS-PA90, completely killed A. baumannii at 0.25 μM, at which concentration PA90 could only eliminate less than one log in CFU/ml. Additionally, DS-PA90 has tolerance to NaCl, where the ~50% of activity could be maintained in the presence of 150 mM NaCl, and stable activity was also observed with changes in pH or temperature. Even MDR A. baumannii strains were highly susceptible to DS-PA90 treatment: five out of nine strains were entirely killed and four strains were reduced by 3–4 log in CFU/ml. Consequently, DS-PA90 could protect waxworm from A. baumannii-induced death by ~70% for ATCC 17978 or ~44% for MDR strain 1656-2 infection. Collectively, our data suggest that CPP-fused endolysin can be an effective antibacterial agent against Gramnegative pathogens regardless of antibiotics resistance mechanisms.

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Antimicrobial peptide thanatin fused endolysin PA90 (Tha-PA90) for the control of Acinetobacter baumannii infection in mouse model
Jeonghyun Lim, Heejoon Myung, Daejin Lim, Miryoung Song
Journal of Biomedical Science.2024;[Epub] CrossRef
Tissue damage alleviation and mucin inhibition by P5 in a respiratory infection mouse model with multidrug-resistant Acinetobacter baumannii
Jun Hee Oh, Jonggwan Park, Hee Kyoung Kang, Hee Joo Park, Yoonkyung Park
Biomedicine & Pharmacotherapy.2024; 181: 117724. CrossRef
Potential of antimicrobial peptide-fused endolysin LysC02 as therapeutics for infections and disinfectants for food contact surfaces to control Cronobacter sakazakii
Doyeon Kim, Jinwoo Kim, Minsik Kim
Food Control.2024; 157: 110190. CrossRef
Gram-negative endolysins: overcoming the outer membrane obstacle
Hazel M Sisson, Simon A Jackson, Robert D Fagerlund, Suzanne L Warring, Peter C Fineran
Current Opinion in Microbiology.2024; 78: 102433. CrossRef
LysJEP8: A promising novel endolysin for combating multidrug‐resistant Gram‐negative bacteria
Jose Vicente Carratalá, Neus Ferrer‐Miralles, Elena Garcia‐Fruitós, Anna Arís
Microbial Biotechnology.2024;[Epub] CrossRef
You get what you test for: The killing effect of phage lysins is highly dependent on buffer tonicity and ionic strength
Roberto Vázquez, Diana Gutiérrez, Zoë Dezutter, Bjorn Criel, Philippe de Groote, Yves Briers
Microbial Biotechnology.2024;[Epub] CrossRef
Endolysins: a new antimicrobial agent against antimicrobial resistance. Strategies and opportunities in overcoming the challenges of endolysins against Gram-negative bacteria
Fazal Mehmood Khan, Fazal Rasheed, Yunlan Yang, Bin Liu, Rui Zhang
Frontiers in Pharmacology.2024;[Epub] CrossRef
Characterization of Three Different Endolysins Effective against Gram-Negative Bacteria
Tae-Hwan Jeong, Hye-Won Hong, Min Soo Kim, Miryoung Song, Heejoon Myung
Viruses.2023; 15(3): 679. CrossRef
Design strategies for positively charged endolysins: Insights into Artilysin development
Jose Vicente Carratalá, Anna Arís, Elena Garcia-Fruitós, Neus Ferrer-Miralles
Biotechnology Advances.2023; 69: 108250. CrossRef

Assessing the microcystins concentration through optimized protein phosphatase inhibition assay in environmental samples: Kyoung-Hee Oh , Kung-Min Beak , Yuna Shin , Young-Cheol Cho; J. Microbiol. 2022;60(6):602-609. Published online April 30, 2022; DOI: https://doi.org/10.1007/s12275-022-2020-4

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Abstract

Protein phosphatase (PPase) inhibition assay (PPIA) is widely used to analyze the concentration of microcystins (MCs) because it is comparatively less expensive and faster than other assays. This study aimed to optimize the PPIA by determining a suitable reaction terminator and an optimal methanol concentration in the sample. The most suitable reaction time was 90 min, with the corresponding methanol concentration in the sample being 15% or less. When p-nitrophenyl phosphate (pNPP) was used as a substrate, copper chloride solution was suitably used as a reaction terminator, and when 4- methylumbelliferyl phosphate (MUP) was used, a glycine buffer not only increased the measurement sensitivity of the reaction product but also terminated the enzymatic reaction. When PPase 1 and MUP were used as an enzyme and a substrate, respectively, the limit of quantitation for MC-leucine/ arginine (LR) was 0.02 μg/L, whereas it was 0.1 μg/L when pNPP was used as a substrate. The proposed method facilitated the measurement of MC-LR concentration without additional pretreatments, such as concentration or purification; therefore, this method was suitable and feasible for the continuous monitoring of MCs in drinking water.

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Analyzing MC-LR distribution characteristics in natural lakes by a novel fluorescence technology
Xiangyu Hu, Zhaomin Wang, Xiao Ye, Ping Xie, Yong Liu
Environmental Pollution.2024; 342: 123123. CrossRef
Magnetic solid phase extraction coupled with high-performance liquid chromatography-diode array detection based on assembled magnetic covalent organic frameworks for selective extraction and detection of microcystins in aquatic foods
Tianliang Wang, Hongzhen Xie, Yuting Cao, Qing Xu, Ning Gan
Journal of Chromatography A.2022; 1685: 463614. CrossRef

Characterization of components of a reducing system for SoxR in the cytoplasmic membrane of Escherichia coli: Kang-Lok Lee , Kyung-Chang Lee , Joon-Hee Lee , Jung-Hye Roe; J. Microbiol. 2022;60(4):387-394. Published online March 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1667-1

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Abstract

A reducing system of SoxR, a regulator of redox-active molecules, was identified as rsxABCDGE gene products and RseC in Escherichia coli through genetic studies. We found that ApbE was an additional component of the reducer system. Bacterial two hybrid analysis revealed that these proteins indeed had multiple interactions among themselves. RseC and RsxB formed the core of the complex, interacting with more than five other components. RsxC, the only cytoplasmic component of the system, interacted with SoxR. It might be linked with the rest of the complex via RsxB. Membrane fractions containing the wild type complex but not the mutant complex reduced purified SoxR using NADH as an electron source. These results suggest that Rsx genes, RseC, and ApbE can form a complex using NAD(P)H to reduce SoxR.

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AcrAB-TolC efflux pump overexpression and tet(A) gene mutation increase tigecycline resistance in Klebsiella pneumoniae
Zhaoxin Xia, Jing zhou, Nana Gao, Ge Li, Runde Liu, Guoping Lu, Jilu Shen
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
The Na+-translocating NADH:quinone oxidoreductase (Na+-NQR): Physiological role, structure and function of a redox-driven, molecular machine
Julia Steuber, Günter Fritz
Biochimica et Biophysica Acta (BBA) - Bioenergetics.2024; 1865(4): 149485. CrossRef
Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum
Ruba Abdulrahman Ashy
Saudi Journal of Biological Sciences.2023; 30(10): 103789. CrossRef

Review

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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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.

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The impact of polymorphic variants of interferon receptor genes on COVID-19 severity and antibiotic resistance
E. A. Krieger, O. V. Samodova, O. A. Svitich, R. V. Samoilikov, E. A. Meremianina, L. V. Ivanova, N. A. Bebyakova, E. N. Ilina, A. V. Pavlenko, Yu. I. Esin, A. L. Arkhipova, S. N. Kovalchuk, A. V. Kudryavtsev
Russian Journal of Infection and Immunity.2024; 13(6): 1027. CrossRef
SARS-CoV-2 ORF8 as a Modulator of Cytokine Induction: Evidence and Search for Molecular Mechanisms
Marília Inês Móvio, Giovana Waner Carneiro de Almeida, Isabella das Graças Lopes Martines, Gilmara Barros de Lima, Sergio Daishi Sasaki, Alexandre Hiroaki Kihara, Emma Poole, Michael Nevels, Maria Cristina Carlan da Silva
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Exploration of Immunology.2022; : 303. CrossRef
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Journal of Microbiology.2022; 60(3): 235. CrossRef
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Frontiers in Immunology.2022;[Epub] CrossRef

Journal Articles

The synergy effect of arbuscular mycorrhizal fungi symbiosis and exogenous calcium on bacterial community composition and growth performance of peanut (Arachis hypogaea L.) in saline alkali soil: Dunwei Ci , Zhaohui Tang , Hong Ding , Li Cui , Guanchu Zhang , Shangxia Li , Liangxiang Dai , Feifei Qin , Zhimeng Zhang , Jishun Yang , Yang Xu; J. Microbiol. 2021;59(1):51-63. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-021-0317-3

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Abstract

Peanut (Arachis hypogaea. L) is an important oil seed crop. Both arbuscular mycorrhizal fungi (AMF) symbiosis and calcium (Ca2+) application can ameliorate the impact of saline soil on peanut production, and the rhizosphere bacterial communities are also closely correlated with peanut salt tolerance; however, whether AMF and Ca2+ can withstand high-salinity through or partially through modulating rhizosphere bacterial communities is unclear. Here, we used the rhizosphere bacterial DNA from saline alkali soil treated with AMF and Ca2+ alone or together to perform high-throughput sequencing of 16S rRNA genes. Taxonomic analysis revealed that AMF and Ca2+ treatment increased the abundance of Proteobacteria and Firmicutes at the phylum level. The nitrogenfixing bacterium Sphingomonas was the dominant genus in these soils at the genus level, and the soil invertase and urease activities were also increased after AMF and Ca2+ treatment, implying that AMF and Ca2+ effectively improved the living environment of plants under salt stress. Moreover, AMF combined with Ca2+ was better than AMF or Ca2+ alone at altering the bacterial structure and improving peanut growth in saline alkali soil. Together, AMF and Ca2+ applications are conducive to peanut salt adaption by regulating the bacterial community in saline alkali soil.

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Arbuscular mycorrhizal fungi drive bacterial community assembly in halophyte Suaeda salsa
Fengwei Diao, Bingbing Jia, Junqing Luo, Shengli Ding, Tai Liu, Wei Guo
Microbiological Research.2024; 282: 127657. CrossRef
Functional Characterization of Core and Unique Calcite-Dissolving Bacteria Communities from Peanut Fields
Alan Peper, Carter J. Newton, Sheena Lim, Wendy Zheng, Timothy Brenneman, Li Yang
Phytopathology®.2024; 114(5): 1011. CrossRef
Bacterial community composition of Hungarian salt-affected soils under different land uses
Ravi Kumar Gangwar, András Táncsics, Marianna Makádi, Milán Farkas, Mátyás Cserháti, Erika Michéli, Márta Fuchs, Tamás Szegi
Biologia Futura.2024; 75(3): 339. CrossRef
Peanut production in saline-alkali land of Yellow River Delta: influence of spatiotemporal changes of meteorological conditions and soil properties
Feifei Qin, Zhihong Xin, Jianguo Wang, Jialei Zhang, Jishun Yang, Feng Guo, Zhaohui Tang, Dunwei Ci
BMC Plant Biology.2024;[Epub] CrossRef
Multi-year crop rotation and quicklime application promote stable peanut yield and high nutrient-use efficiency by regulating soil nutrient availability and bacterial/fungal community
Liyu Yang, Caibin Wang, Xinhua He, Haiyan Liang, Qi Wu, Xuewu Sun, Miao Liu, Pu Shen
Frontiers in Microbiology.2024;[Epub] CrossRef
Arbuscular Mycorrhizal Fungi Restored the Saline–Alkali Soil and Promoted the Growth of Peanut Roots
Dunwei Ci, Feifei Qin, Zhaohui Tang, Guanchu Zhang, Jialei Zhang, Tong Si, Jishun Yang, Yang Xu, Tianyi Yu, Manlin Xu, Kang He
Plants.2023; 12(19): 3426. CrossRef
Green manure increases peanut production by shaping the rhizosphere bacterial community and regulating soil metabolites under continuous peanut production systems
Yang Xu, Hong Ding, Guanchu Zhang, Zelun Li, Qing Guo, Hao Feng, Feifei Qin, Liangxiang Dai, Zhimeng Zhang
BMC Plant Biology.2023;[Epub] CrossRef
The multifaceted roles of Arbuscular Mycorrhizal Fungi in peanut responses to salt, drought, and cold stress
Yuexu Liu, Jinhao Lu, Li Cui, Zhaohui Tang, Dunwei Ci, Xiaoxia Zou, Xiaojun Zhang, Xiaona Yu, Yuefu Wang, Tong Si
BMC Plant Biology.2023;[Epub] CrossRef
Advances and future research in ecological stoichiometry under saline-alkali stress
Keyi Zhang, Lei Chang, Guanghui Li, Yuefen Li
Environmental Science and Pollution Research.2023; 30(3): 5475. CrossRef
Arbuscular mycorrhizal fungi increased peanut (Arachis hypogaea L.) yield by changing the rhizosphere microbial community structure in saline-alkali soil
Jia Kang, Wenlong Yang, Shangwu Liu, Ning Xuan, Yahui Shao, Yun Geng, Muhammad Afzal, Yingxin Zhang, Shousong Yue, Rubina Mushtaq, Gao Chen
Frontiers in Microbiology.2023;[Epub] CrossRef
Distribution of microbial communities in seasonally frozen soil layers on the Tibetan Plateau and the driving environmental factors
Xiaojie Wang, Zhiqiang Yu, Guofeng Shen, Hefa Cheng, Shu Tao
Environmental Science and Pollution Research.2023; 30(1): 1919. CrossRef
Effects of phosphogypsum on enzyme activity and microbial community in acid soil
Changan Li, Yonggang Dong, Yun Yi, Juan Tian, Chao Xuan, Yan Wang, Yuanbo Wen, Jianxin Cao
Scientific Reports.2023;[Epub] CrossRef
Microbial keystone taxa drive crop productivity through shifting aboveground-belowground mineral element flows
Jia Lin Wang, Kai Lou Liu, Xue Qiang Zhao, Gui-Feng Gao, Yong Hong Wu, Ren Fang Shen
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Peanut and cotton intercropping increases productivity and economic returns through regulating plant nutrient accumulation and soil microbial communities
Wei Xie, Kai Zhang, Xiaoying Wang, Xiaoxia Zou, Xiaojun Zhang, Xiaona Yu, Yuefu Wang, Tong Si
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Illumina MiSeq Sequencing Reveals Correlations among Fruit Ingredients, Environmental Factors, and AMF Communities in Three Lycium Barbarum Producing Regions of China
Kaili Chen, Gang Huang, Yuekun Li, Xinrui Zhang, Yonghui Lei, Yang Li, Jie Xiong, Yanfei Sun, Kristen M. DeAngelis
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Genome-Wide Identification of Auxin Response Factors in Peanut (Arachis hypogaea L.) and Functional Analysis in Root Morphology
Lu Luo, Qian Wan, Zipeng Yu, Kun Zhang, Xiurong Zhang, Suqing Zhu, Yongshan Wan, Zhaojun Ding, Fengzhen Liu
International Journal of Molecular Sciences.2022; 23(10): 5309. CrossRef
Impact of an arbuscular mycorrhizal fungal inoculum and exogenous methyl jasmonate on the performance of tall fescue under saline-alkali condition
Hui Liu, Huimin Tang, Xiaozhen Ni, Yajie Zhang, Yingchao Wang
Frontiers in Microbiology.2022;[Epub] CrossRef
The resistance of peanut to soil-borne pathogens improved by rhizosphere probiotics under calcium treatment
Wei Zhang, Bo-wen Zhang, Jie-fu Deng, Lin Li, Tu-yong Yi, Yan-yun Hong
BMC Microbiology.2021;[Epub] CrossRef
Arbuscular mycorrhizal fungi alleviate salinity stress in peanut: Evidence from pot‐grown and field experiments
Wenjie Qin, Hengyu Yan, Bingyin Zou, Runze Guo, Dunwei Ci, Zhaohui Tang, Xiaoxia Zou, Xiaojun Zhang, Xiaona Yu, Yuefu Wang, Tong Si
Food and Energy Security.2021;[Epub] CrossRef

Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina: Kah-Ooi Chua , Wah-Seng See-Too , Jia-Yi Tan , Sze-Looi Song , Hoi-Sen Yong , Wai-Fong Yin , Kok-Gan Chan; J. Microbiol. 2020;58(12):988-997. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0325-8

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Abstract

In this study, bacterial strains Ha5T, Ta1, and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were identified as bacterial symbionts of the ant belonging to family Acetobacteraceae and were distinguished as different strains based on distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15–37°C (optimum, 28–30°C) and in the presence of 0–1.5% (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1 ω7c, C16:0, C19:0 ω8c cyclo, C14:0, and C16:0 2-OH. Strains Ha5T, Ta1, and Jb2 shared highest 16S rRNA gene sequence similarity (94.56–94.63%) with Neokomagataea tanensis NBRC106556T of family Acetobacteraceae. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (< 71%), in silico DNA-DNA hybridization (< 38%) and average amino acid identity (< 67%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1, and Jb2 represent a novel species of a novel genus in family Acetobacteraceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5T as the type strain.

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Aristophania vespae gen. nov., sp. nov., isolated from wasps, is related to Bombella and Oecophyllibacter, isolated from bees and ants
Juan Guzman, Miyoung Won, Anja Poehlein, Atena Sadat Sombolestani, Daniela Mayorga-Ch, David Laureys, Jessika De Clippeleer, Peter Kämpfer, Rolf Daniel, Andreas Vilcinskas, Peter Vandamme, Soon-Wo Kwon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years
Mizue Anda, Shun Yamanouchi, Salvatore Cosentino, Mitsuo Sakamoto, Moriya Ohkuma, Masako Takashima, Atsushi Toyoda, Wataru Iwasaki
Nature Communications.2023;[Epub] CrossRef
Formicincola oecophyllae gen. nov. sp. nov., a novel member of the family Acetobacteraceae isolated from the weaver ant Oecophylla smaragdina
Kah-Ooi Chua, Yvonne Jing Mei Liew, Wah-Seng See-Too, Jia-Yi Tan, Hoi-Sen Yong, Wai-Fong Yin, Kok-Gan Chan
Antonie van Leeuwenhoek.2022; 115(8): 995. CrossRef
Pharmacological potential of ants and their symbionts – a review
Surbhi Agarwal, Garima Sharma, Kavita Verma, Narayanan Latha, Vartika Mathur
Entomologia Experimentalis et Applicata.2022; 170(12): 1032. CrossRef
Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
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In vitro disinfection efficacy and clinical protective effects of common disinfectants against acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio isolates in Pacific white shrimp Penaeus vannamei: Peizhuo Zou , Qian Yang , Hailiang Wang , Guosi Xie , Zhi Cao , Xing Chen , Wen Gao , Jie Huang; J. Microbiol. 2020;58(8):675-686. Published online July 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9537-1

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Abstract

Acute hepatopancreatic necrosis disease (AHPND) is one of the most significant bacterial diseases in global shrimp culture, causing severe economic losses. In the present study, we carried out in vitro antimicrobial tests to investigate the disinfection efficacy of 14 common disinfectants toward different AHPND-causing Vibrio spp., including eight isolates of V. parahaemolyticus, four isolates of V. campbellii, and one isolate of V. owensii. Polyhexamethylene biguanidine hydrochloride (PHMB) was revealed to possess the strongest inhibitory activity. Through analyzing and evaluating the results of antimicrobial tests and acute toxicity test, we selected PHMB and hydrogen peroxide (H2O2) for further clinical protection test. Clinical manifestations indicated that both PHMB (2 mg/L and 4 mg/L) and H2O2 (12 mg/L) could effectively protect juvenile Penaeus vannamei from the infection of V. parahaemolyticus isolate Vp362 at 106 CFU/ml, and the survival rate was over 80%. When the bacterial concentration was reduced to 105 CFU/ml, 104 CFU/ml, and 103 CFU/ml, the survival rate after treated by 1 mg/L PHMB was 64.44%, 93.33%, and 100%, respectively. According to the results, PHMB and H2O2 showed a lower toxicity while a better protection activity, particularly against a lower concentration of the pathogens. Therefore, these two disinfectants are proved to be promising disinfectants that can be applied to prevent and control AHPND in shrimp culture. Moreover, the methods of this study also provided valuable information for the prevention of other important bacterial diseases and suggested a reliable means for screening potential drugs in aquaculture.

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Basigin binds bacteria and activates Dorsal signaling to promote antibacterial defense in Penaeus vannamei
Linwei Yang, Zi-ang Wang, Yushi Gan, Hongliang Zuo, Hengwei Deng, Shaoping Weng, Jianguo He, Xiaopeng Xu
Fish & Shellfish Immunology.2023; 142: 109123. CrossRef
Clinical protective effects of polyhexamethylene biguanide hydrochloride (PHMB) against Vibrio parahaemolyticus causing translucent post-larvae disease (VTPD) in Penaeus vannamei
Tianchang Jia, Tingting Xu, Jitao Xia, Shuang Liu, Wenqiang Li, Ruidong Xu, Jie Kong, Qingli Zhang
Journal of Invertebrate Pathology.2023; 201: 108002. CrossRef

The relationship between bacterial diversity and organic carbon mineralization in soft rock and sand compound soil: Zhen Guo , Juan Li , Lei Ge , Chenxi Yang , Jichang Han; J. Microbiol. 2020;58(9):750-760. Published online July 24, 2020; DOI: https://doi.org/10.1007/s12275-020-0130-4

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Abstract

The soil organic carbon (SOC) mineralization rate in sandy soil plays an important role in improving soil quality, and a research is needed to determine management practices that optimize the mineralization rate. When sandy soil is improved by adding soft rock, the specific promotion process of bacterium to SOC mineralization remain unclear. To investigate these mechanisms, we selected four treatments with soft rock to sand volume ratios of 0:1 (CK), 1:5 (C1), 1:2 (C2) and 1:1 (C3) to study. The mineralization rate of organic carbon was measured using the lye absorption method. Highthroughput sequencing and scanning electron microscopy were used to determine the bacterial community structure and soil microstructure, respectively. The results showed that the organic carbon content of the sandy soil increased significantly (182.22–276.43%) after using the soft rock treatments. The SOC mineralization rate could be divided into two stages: a rapid decline during days 1–8 and a slow decline during days 8–60. With increased incubation time, the intensity of the cumulative release of organic carbon gradually weakened. Compared with the CK treatment, the SOC mineralization accumulation (Ct) and the potential mineralizable organic carbon content (C0) in the C1, C2, and C3 treatments increased significantly, by 106.98–225.94% and 112.22– 254.08%, respectively. The cumulative mineralization rate (Cr) was 18.11% and 21.38% smaller with treatments C2 and C3, respectively. The SOC mineralization rate constant (k) decreased significantly after the addition of soft rock, while the half-turnover period (Th) changed inversely with k. Compared with the CK treatment, the number of gene copies of the soil bacteria increased by 15.38–272.53% after adding soft rock, with the most significant increase in treatment C3. The bacterial diversity index also increased significantly under treatment C3. The three dominant bacteria were Proteobacteria, Actinobacteria, and Chloroflexi. The correlation between Cr and one of the non-dominant bacteria, Firmicutes, was large, and the bacteria had a significant positive correlation with k. At the same time, the abundance of Firmicutes under treatments C2 and C3 was small. As the proportion of soft rock increased, the soil particles changed from point contact to surface contact, and the adhesion on the surface of the particles gradually increased. Results from this study show that the retention time of SOC can be increased and the carbon sequestration effect is better when the ratio of soft rock to sand is set to 1:2.

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Siltation of check dams alters microbial communities and thus limits organic carbon mineralization
Xiaojun Liu, Yi Zhang, Peng Li, Lie Xiao
Soil and Tillage Research.2024; 236: 105949. CrossRef
Tree species mixing enhances rhizosphere soil organic carbon mineralization of conifers in subtropical plantations
Wen-Qing Li, Zi-Jun Wu, Ying-Ying Zong, G. Geoff Wang, Fu-Sheng Chen, Yuan-Qiu Liu, Jian-Jun Li, Xiang-Min Fang
Forest Ecology and Management.2022; 516: 120238. CrossRef
Response of soil structure and crop yield to soft rock in Mu Us sandy land, China
Jian Zhang, Zhen Guo
Scientific Reports.2022;[Epub] CrossRef

The effects of deletion of cellobiohydrolase genes on carbon source-dependent growth and enzymatic lignocellulose hydrolysis in Trichoderma reesei: Meibin Ren , Yifan Wang , Guoxin Liu , Bin Zuo , Yuancheng Zhang , Yunhe Wang , Weifeng Liu , Xiangmei Liu , Yaohua Zhong; J. Microbiol. 2020;58(8):687-695. Published online June 10, 2020; DOI: https://doi.org/10.1007/s12275-020-9630-5

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Abstract

The saprophytic fungus Trichoderma reesei has long been used as a model to study microbial degradation of lignocellulosic biomass. The major cellulolytic enzymes of T. reesei are the cellobiohydrolases CBH1 and CBH2, which constitute more than 70% of total proteins secreted by the fungus. However, their physiological functions and effects on enzymatic hydrolysis of cellulose substrates are not sufficiently elucidated. Here, the cellobiohydrolase-encoding genes cbh1 and cbh2 were deleted, individually or combinatively, by using an auxotrophic marker-recycling technique in T. reesei. When cultured on media with different soluble carbon sources, all three deletion strains (Δcbh1, Δcbh2, and Δcbh1Δcbh2) exhibited no dramatic variation in morphological phenotypes, but their growth rates increased apparently when cultured on soluble cellulase-inducing carbon sources. In addition, Δcbh1 showed dramatically reduced growth and Δcbh1Δcbh2 could hardly grew on microcrystalline cellulose (MCC), whereas all strains grew equally on sodium carboxymethyl cellulose (CMC-Na), suggesting that the influence of the CBHs on growth was carbon source-dependent. Moreover, five representative cellulose substrates were used to analyse the influence of the absence of CBHs on saccharification efficiency. CBH1 deficiency significantly affected the enzymatic hydrolysis rates of various cellulose substrates, where acid pre-treated corn stover (PCS) was influenced the least. CBH2 deficiency reduced the hydrolysis of MCC, PCS, and acid pre-treated and delignified corncob but improved the hydrolysis ability of filter paper. These results demonstrate the specific contributions of CBHs to the hydrolysis of different types of biomass, which could facilitate the development of tailor-made strains with highly efficient hydrolysis enzymes for certain biomass types in the biofuel industry.

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An efficient CRISPR/Cas9 genome editing system based on a multiple sgRNA processing platform in Trichoderma reesei for strain improvement and enzyme production
Jiaxin Zhang, Kehang Li, Yu Sun, Cheng Yao, Weifeng Liu, Hong Liu, Yaohua Zhong
Biotechnology for Biofuels and Bioproducts.2024;[Epub] CrossRef
Transcriptome-wide analysis of a superior xylan degrading isolate Penicillium oxalicum 5–18 revealed active lignocellulosic degrading genes
Shuang Hu, Pei Han, Bao-Teng Wang, Long Jin, Hong-Hua Ruan, Feng-Jie Jin
Archives of Microbiology.2024;[Epub] CrossRef
Engineering the secretome of Aspergillus niger for cellooligosaccharides production from plant biomass
Fernanda Lopes de Figueiredo, Fabiano Jares Contesini, César Rafael Fanchini Terrasan, Jaqueline Aline Gerhardt, Ana Beatriz Corrêa, Everton Paschoal Antoniel, Natália Sayuri Wassano, Lucas Levassor, Sarita Cândida Rabelo, Telma Teixeira Franco, Uffe Hasb
Microbial Cell Factories.2024;[Epub] CrossRef
Constitutive overexpression of cellobiohydrolase 2 in Trichoderma reesei reveals its ability to initiate cellulose degradation
Yubo Wang, Meibin Ren, Yifan Wang, Lu Wang, Hong Liu, Mei Shi, Yaohua Zhong
Engineering Microbiology.2023; 3(1): 100059. CrossRef
Inducer-free recombinant protein production in Trichoderma reesei: secretory production of endogenous enzymes and heterologous nanobodies using glucose as the sole carbon source
Toshiharu Arai, Mayumi Wada, Hiroki Nishiguchi, Yasushi Takimura, Jun Ishii
Microbial Cell Factories.2023;[Epub] CrossRef
The Influence of Trctf1 Gene Knockout by CRISPR–Cas9 on Cellulase Synthesis by Trichoderma reesei with Various Soluble Inducers
Yudian Chen, Yushan Gao, Zancheng Wang, Nian Peng, Xiaoqin Ran, Tingting Chen, Lulu Liu, Yonghao Li
Fermentation.2023; 9(8): 746. CrossRef
The effect of cellobiohydrolase 1 gene knockout for composition and hydrolytic activity of the enzyme complex secreted by filamentous fungus Penicillium verruculosum
Valeriy Yu. Kislitsin, Andrey M. Chulkin, Ivan N. Zorov, Yuri А. Denisenko, Arkadiy P. Sinitsyn, Alexandra M. Rozhkova
Bioresource Technology Reports.2022; 18: 101023. CrossRef
Deciphering the efficient cellulose degradation by the thermophilic fungus Myceliophthora thermophila focused on the synergistic action of glycoside hydrolases and lytic polysaccharide monooxygenases
Xing Qin, Jiahuan Zou, Kun Yang, Jinyang Li, Xiaolu Wang, Tao Tu, Yuan Wang, Bin Yao, Huoqing Huang, Huiying Luo
Bioresource Technology.2022; 364: 128027. CrossRef

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