Journal of Microbiology

Journal Article

Dynamics of Microbial Community Structure, Function and Assembly Mechanism with Increasing Stand Age of Slash Pine (Pinus elliottii) Plantations in Houtian Sandy Area, South China: Xiaoyang Zhang , Si-Yi Xiong , Xiukun Wu , Bei-Bei Zeng , Yang-Mei Mo , Zhi-Cheng Deng , Qi Wei , Yang Gao , Licao Cui , Jianping Liu , Haozhi Long; J. Microbiol. 2023;61(11):953-966. Published online November 29, 2023; DOI: https://doi.org/10.1007/s12275-023-00089-7

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Establishing slash pine plantations is the primary method for restoring sandification land in the Houtian area of South China. However, the microbial variation pattern with increasing stand age remains unclear. In this study, we investigated microbial community structure and function in bare sandy land and four stand age gradients, exploring ecological processes that determine their assembly. We did not observe a significant increase in the absolute abundance of bacteria or fungi with stand age. Bacterial communities were dominated by Chloroflexi, Actinobacteria, Proteobacteria, and Acidobacteria; the relative abundance of Chloroflexi significantly declined while Proteobacteria and Acidobacteria significantly increased with stand age. Fungal communities showed succession at the genus level, with Pisolithus most abundant in soils of younger stands (1- and 6-year-old). Turnover of fungal communities was primarily driven by stochastic processes; both deterministic and stochastic processes influenced the assembly of bacterial communities, with the relative importance of stochastic processes gradually increasing with stand age. Bacterial and fungal communities showed the strongest correlation with the diameter at breast height, followed by soil available phosphorus and water content. Notably, there was a significant increase in the relative abundance of functional groups involved in nitrogen fixation and uptake as stand age increased. Overall, this study highlights the important effects of slash pine stand age on microbial communities in sandy lands and suggests attention to the nitrogen and phosphorus requirements of slash pine plantations in the later stages of sandy management.

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Wanxia Peng, Min Song, Hu Du, Shanghua Jiang, Fuping Zeng, Huijun Chen, Tongqing Song
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Assembly and co-occurrence pattern of microbial communities in bulk and rhizosphere soils of Pinus elliottii plantations on sandy lands in China
Haozhi Long, Si-Yi Xiong, Yang-Mei Mo, Bei-Bei Zeng, Bin-Xuan Shan, Ting Xiao, Yang Gao, Chaoyu Cui
Plant and Soil.2024;[Epub] CrossRef

Review

Temperature Matters: Bacterial Response to Temperature Change: Seongjoon Moon , Soojeong Ham , Juwon Jeong , Heechan Ku , Hyunhee Kim , Changhan Lee; J. Microbiol. 2023;61(3):343-357. Published online April 3, 2023; DOI: https://doi.org/10.1007/s12275-023-00031-x

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Abstract

Temperature is one of the most important factors in all living organisms for survival. Being a unicellular organism, bacterium requires sensitive sensing and defense mechanisms to tolerate changes in temperature. During a temperature shift, the structure and composition of various cellular molecules including nucleic acids, proteins, and membranes are affected. In addition, numerous genes are induced during heat or cold shocks to overcome the cellular stresses, which are known as heat- and cold-shock proteins. In this review, we describe the cellular phenomena that occur with temperature change and bacterial responses from a molecular perspective, mainly in Escherichia coli.

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Journal Article

Autoinducer-2 detection among commensal oral streptococci is dependent on pH and boric acid: Giancarlo A. Cuadra , Ashley J. Frantellizzi , Kimberly M. Gaesser , Steven P. Tammariello , Anika Ahmed; J. Microbiol. 2016;54(7):492-502. Published online June 28, 2016; DOI: https://doi.org/10.1007/s12275-016-5507-z

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Abstract

Autoinducer-2, considered a universal signaling molecule, is produced by many species of bacteria; including oral strains. Structurally, autoinducer-2 can exist bound to boron (borated autoinducer-2). Functionally, autoinducer-2 has been linked to important bacterial processes such as virulence and biofilm formation. In order to test production of autoinducer-2 by a given bacterial strain, a bioassay using marine bioluminescent bacteria Vibrio harveyi as a reporter for autoinducer-2 has been designed. We hypothesize that pH adjustment and addition of boron are required for optimal bioluminescence and accurate autoinducer-2 detection. Using this reporter strain we tested autoinducer-2 activity from two oral commensal species, Streptococcus gordonii DL1 and Streptococcus oralis 34. Spent broth was collected and adjusted to pH 7.5 and supplemented with boric acid prior to measuring autoinducer- 2 activity. Results show that low pH inhibits bioluminescence of the reporter strain, but pH 7.5 allows for bioluminescence induction and proper readings of autoinducer-2 activity. Addition of boric acid also has a positive effect on bioluminescence allowing for a more sensitive detection of autoinducer-2 activity. Our data suggests that although autoinducer- 2 is present in spent broth, low pH and/or low levels of boric acid become an obstacle for proper autoinducer-2 detection. For proper autoinducer-2 detection, we propose a protocol using this bioassay to include pH adjustment and boric acid addition to spent broth. Studies on autoinducer-2 activity in several bacteria species represent an important area of study as this universal signaling molecule is involved in critical bacterial phenotypes such as virulence and biofilm formation.

Citations

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Inhibitory effect of Lonicera japonica flos on Streptococcus mutans biofilm and mechanism exploration through metabolomic and transcriptomic analyses
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New Insights into Boron Essentiality in Humans and Animals
Andrei Biţă, Ion Romulus Scorei, Tudor Adrian Bălşeanu, Maria Viorica Ciocîlteu, Cornelia Bejenaru, Antonia Radu, Ludovic Everard Bejenaru, Gabriela Rău, George Dan Mogoşanu, Johny Neamţu, Steven A. Benner
International Journal of Molecular Sciences.2022; 23(16): 9147. CrossRef
Exogenous autoinducer-2 inhibits biofilm development of Desulfovibrio sp. Huiquan2017
Ee Li, Jiajia Wu, Dun Zhang
World Journal of Microbiology and Biotechnology.2021;[Epub] CrossRef
Efficacy of Preprocedural Boric Acid Mouthrinse in Reducing Viable Bacteria in Dental Aerosols Produced during Ultrasonic Scaling
Swet Nisha, Avinash Bettahalli Shivamallu, Sheela Kumar Gujjari, Pratibha Shashikumar, Nada Musharraf Ali, Madhuri Kulkarni
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Research Support, Non-U.S. Gov'ts

Isolation and Characterization of a Mycovirus in Lentinula edodes: Hyo-Kyoung Won , So-Jung Park , Dong-Kyu Kim , Myeung Ju Shin , Nari Kim , Song-Hee Lee , Young-Chul Kwon , Han Kyu Ko , Hyeon-Su Ro , Hyun-Sook Lee; J. Microbiol. 2013;51(1):118-122. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2351-2

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Abstract: A mycovirus was isolated from an edible mushroom, Lentinula edodes, that was suffering from a severe epidemic. Fractionation of the diseased cell extract by isopycnic centrifugation with 50% CsCl revealed that the diseased mushroom was infected by Lentinula edodes spherical virus (LeSV), a new spherical virus with a diameter of 55 nm. The particle of LeSV encapsidated the 12 kb RNA genome by a 120 kDa coat protein. BLAST analysis of the partially sequenced LeSV genome showed 95% sequence identity with a putative RNAdependent RNA polymerase (RdRp) gene of the mycovirus HKB, which was previously reported as being a doublestranded RNA (dsRNA) element. In contrast to HKB, the RNA genome in LeSV is encapsidated by the 120 kDa coat protein. To confirm that the LeSV coat protein is encoded by the viral genome, the N-terminal amino acid sequence of the coat protein was determined. The resulting N-terminal amino acid sequence, N-SALDVAPVVPELYFXXLEV-C, was found to be located in the middle of the HKB ORF1, suggesting that the LeSV coat protein was indeed encoded by the virus. To detect LeSV in L. edodes, a primer set targeting the RdRp gene was designed based on the partial sequence of the LeSV genome. RT-PCR analysis showed that 56 of the 84 commercially available dikaryotic cultivars carry LeSV. The transmission pattern of the virus was determined by analysing basidiospores from LeSV-infected and LeSVfree fruiting bodies. Nine out of 10 basidiospores from the LeSV-infected cultivars contained the virus while the spores from the LeSV-free parent were free of LeSV, suggesting that vertical transmission is the primary mode of LeSV propagation.

Development of SCAR Primers Based on a Repetitive DNA Fingerprint for Escherichia coli Detection: Aphidech Sangdee , Sitakan Natphosuk , Adunwit Srisathan , Kusavadee Sangdee; J. Microbiol. 2013;51(1):31-35. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2244-4

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Abstract: The present study aimed to use enterobacterial repetitive intergenic consensus (ERIC) fingerprints to design SCAR primers for the detection of Escherichia coli. The E. coli strains were isolated from various water sources. The primary presumptive identification of E. coli was achieved using MacConkey agar. Nineteen isolates were selected and confirmed to be E. coli strains based on seven biochemical characteristics. ERIC-PCR with ERIC 1R and ERIC 2 primers were used to generate DNA fingerprints. ERIC-PCR DNA profiles showed variant DNA profiles among the tested E. coli strains and distinguished all E. coli strains from the other tested bacterial strains. A 350 bp band that predominated in five E. coli strains was used for the development of the species-specific SCAR primers EC-F1 and EC-R1. The primers showed good specificity for E. coli, with the exception of a single false positive reaction with Sh. flexneri DMST 4423. The primers were able to detect 50 pg and 100 CFU/ml of genomic DNA and cells of E. coli, respectively.

A Quantitative and Direct PCR Assay for the Subspecies-Specific Detection of Clavibacter michiganensis subsp. michiganensis Based on a Ferredoxin Reductase Gene: Min Seok Cho , Jang Ha Lee , Nam Han Her , ChangKug Kim , Young-Joo Seol , Jang Ho Hahn , Ji Hyoun Baeg , Hong Gi Kim , Dong Suk Park; J. Microbiol. 2012;50(3):496-501. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1611-x

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Abstract: The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis is the causal agent of canker disease in tomato. Because it is very important to control newly introduced inoculum sources from commercial materials, the specific detection of this pathogen in seeds and seedlings is essential for effective disease control. In this study, a novel and efficient assay for the detection and quantitation of C. michiganensis subsp. michiganensis in symptomless tomato and red pepper seeds was developed. A pair of polymerase chain reaction (PCR) primers (Cmm141F/R) was designed to amplify a specific 141 bp fragment on the basis of a ferredoxin reductase gene of C. michiganensis subsp. michiganensis NCPPB 382. The specificity of the primer set was evaluated using purified DNA from 16 isolates of five C. michiganensis subspecies, one other Clavibacter species, and 17 other reference bacteria. The primer set amplified a single band of expected size from the genomic DNA obtained from the C. michiganensis subsp. michiganensis strains but not from the other C. michiganensis subspecies or from other Clavibacter species. The detection limit was a single cloned copy of the ferredoxin reductase gene of C. michiganensis subsp. michiganensis. In conclusion, this quantitative direct PCR assay can be applied as a practical diagnostic method for epidemiological research and the sanitary management of seeds and seedlings with a low level or latent infection of C. michiganensis subsp. michiganensis.

NOTE] Diversity Analysis of Burkholderia cepacia Complex in the Water Bodies of West Lake, Hangzhou, China: Yuan Fang , Guan-lin Xie , Miao-miao Lou , Bin Li , Ibrahim Muhammad; J. Microbiol. 2011;49(2):309-314. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0267-2

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Abstract: A survey of Burkholderia cepacia complex (Bcc) species was conducted in water bodies of West Lake in China. A total of 670 bacterial isolates were recovered on selective media. Out of them, 39.6% (265 isolates) were assigned to the following species: Burkholderia multivorans, Burkholderia cenocepacia recA lineage IIIA,
IIIB, Burkholderia stabilis, Burkholderia vietnamiensis, and Burkholderia seminalis while B. cenocepacia is documented as a dominant Bcc species in water of West Lake. In addition, all Bcc isolates tested were PCR negative for the cblA and esmR transmissibility marker genes except B. cenocepacia IIIB A8 which was positive for esmR genelater. The present study raises great concerns on the role of West Lake as a “reservoir” for potential Bcc pathogenic strains.

Detection of Xanthomonas arboricola pv. pruni by PCR Using Primers Based on DNA Sequences Related to the hrp Genes: So Yeon Park , Young Sun Lee , Young Jin Koh , Jae-Sun Hur , Jae Sung Jung; J. Microbiol. 2010;48(5):554-558. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0072-3

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Abstract: Efficient control of Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot on stone fruit, requires a sensitive and reliable diagnostic tool. A PCR detection method that utilizes primers to target the hrp gene cluster region was developed in this study. The nucleotide sequence of the PCR product amplified with primers specific for the hrp region of the xanthomonads and genomic DNA of X. arboricola pv. pruni was determined, and the sequence was aligned with that of X. campestris pv. campestris, which was obtained from the GenBank database. On the basis of the sequence of the amplified hrp region, a PCR primer set of XapF/R specific to X. arboricola pv. pruni was designed. This primer set yielded a 243-bp product from the genomic DNA of X. aboricola pv. pruni strains, but no products from other 21 strains of Xanthomonas or from two epiphytic bacterial species. Southern blot hybridization with the probe derived from the PCR product with the primer set and X. aboricola pv. pruni DNA confirmed the PCR results. The Xap primer system was successfully applied to detect the pathogen from infected peach fruits. When it was applied in field samples, the primer set was proved as a reliable diagnostic tool for specific detection of X. aboricola pv. pruni from peach orchards.

Development of a Latex Agglutination Test for Norovirus Detection: Heetae Lee , YoungBin Park , Misoon Kim , Youngmee Jee , Doo-sung Cheon , Hae Sook Jeong , GwangPyo Ko; J. Microbiol. 2010;48(4):419-425. Published online August 20, 2010; DOI: https://doi.org/10.1007/s12275-010-0071-4

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Abstract: Norovirus (NoV) is the leading cause of acute gastroenteritis worldwide. Currently, reverse transcription polymerase chain reaction (RT-PCR) is used commonly to detect NoVs in both clinical and environmental samples. However, RT-PCR requires expensive equipment and cannot be performed on site. In this study, a latex agglutination test (LAT) using antibody-labeled latex beads for detecting NoVs was developed. Two kinds of polyclonal antibodies, one generated from synthetic peptides and the other from E. coli-expressed NoV capsid proteins, were used to develop the LAT. Each of these polyclonal antibodies was immobilized on the surface of latex beads and tested for the ability to detect NoVs. Under optimized conditions, our LAT detected GII.4 NoV at concentrations as low as 3.3×105 RT-PCR units/ml in stool samples. The detection limit for the LAT was approximately 1.7×103 RT-PCR units. Forty-eight stool samples were tested for NoVs using this LAT. In comparison with an RT-PCR assay, the sensitivity and specificity of the LAT were 35% and 100%, respectively. With further optimization, this LAT used with appropriate antibodies could be applied for convenient detection of NoVs in clinical diagnosis and food monitoring.

Validation Study

Rapid Detection of Noroviruses in Fecal Samples and Shellfish by Nucleic Acid Sequence-based Amplification: Xiaoxia Kou , Qingping Wu , Jumei Zhang , Hongying Fan; J. Microbiol. 2006;44(4):403-408.; DOI: https://doi.org/2413 [pii]

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Abstract: The purpose of this study was to determine the efficacy of a nucleic acid sequence-based amplification (NASBA) method of detecting noroviruses in artificially and naturally contaminated shellfish. We used 58 fecal samples that tested positive for noroviruses with electron microscopy (EM) to develop an NASBA assay for these viruses. Oligonucleotide primers targeting the polymerase coding region were used to amplify the viral RNA in an isothermal process that resulted in the accumulation of RNA amplicons. These amplicons were detected by hybridization with digoxigenin-labeled oligonucleotide probes that were highly specific for genogroup I (GI) and genogroup II (GII) of noroviruses. The expected band of 327 bp appeared in denaturing agarose gel without any nonspecific band. The specific signal for each amplicon was obtained through Northern blotting in many repeats. All fecal samples of which 46 (79.3%) belonged to GII and 12 (20.6%) belonged to GI were positive for noroviruses by EM and by NASBA. Target RNA concentrations as low as 5 pg/ml were detected in fecal specimens using NASBA. When the assay was applied to artificially contaminated shellfish, the sensitivity to nucleic acid was 100 pg/1.5 g shellfish tissue. The potential use of this assay was also confirmed in naturally contaminated shellfish collected from different ponds in Guangzhou city of China, of which 24 (18.76%) out of 128 samples were positive for noroviruses; of these, 19 (79.6%) belonged to GII and 5 (20.4%) belonged to GI. The NASBA assay provided a more rapid and efficient way of detecting noroviruses in fecal samples and demonstrated its potential for detecting noroviruses in food and environmental samples with high specificity and sensitivity.

Journal Article

Detection of Hepatitis B Virus and Mycobacterium tuberculosis in Korean Dental Patients: Sun-A Lee , So Young Yoo , Kee-Sung Kay , Joong-Ki Kook; J. Microbiol. 2004;42(3):239-242.; DOI: https://doi.org/2082 [pii]

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Abstract: This study examined the detection rate of the hepatitis B virus (HBV) and Mycobacterium tuberculosis (Mtb) in serum and saliva samples, respectively, from 120 dental patients who were unaware if they have or had either hepatitis or tuberculosis. The frequencies of HBsAg and anti-HBs were determined using an immunochromatic assay. Mtb positivity was determined by the PCR method. Of the 120 patients, 7 (5.8%) were HBV positive and 30 (25.0%) were Mtb positive. This highlights the fact that dental health care workers (DHCWs) can be exposed to the risk of infection from blood- or saliva-borne pathogens as a consequence of their work. Therefore, it is very important to prevent cross infection between patients and dental personnel. Accordingly, laboratory tests prior to surgical treatment are needed to determine the infectious state of dental patients in order to prevent the transmission of infectious diseases in dental clinics.

Development of an In Planta Molecular Marker for the Detection of Chinese Cabbage (Brassica campestris ssp. pekinensis) Club Root Pathogen Plasmodiophora brassicae: Hee Jong Kim , Youn Su Lee; J. Microbiol. 2001;39(1):56-61.

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Abstract: Plasmodiophora brassicae is an obligate parasite, a causal organism of clubroot disease in crucifers that can survive in the soil as resting spores for many years. P. brassicae causes great losses in susceptible varieties of crucifers throughout the world. In this present study, an in planta molecular marker for the detection of P. bassicae was developed using an oligonucleotide primer set from the small subunit gene (18S like) and internal transcribed spacer (ITS) region of rDNA. The specific primer sequences determined were TCAGCTTGAATGCTAATGTG (ITS5) and CTACCTCATTTGAGATCTTTGA (PB-2). This primer set was used to specifically detect P. bassicae in planta. The amplicon using the specific primer set was about 1,000 bp. However, the test plant and other soil-borne fungi including Fusarium spp. and Rhizoctonia spp., as well as bacteria such as Pseudomonas spp. and Erwinia spp. did not show any reaction with the primer set.

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