Journal of Microbiology

Volume 52(1); January 2014

Review

MINIREVIEW] Microbial Leaching of Metals from Solid Industrial Wastes: Debaraj Mishra , Young Ha Rhee; J. Microbiol. 2014;52(1):1-7. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3532-3

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86 Citations

Abstract: Biotechnological applications for metal recovery have played a greater role in recovery of valuable metals from low grade sulfide minerals from the beginning of the middle era till the end of the twentieth century. With depletion of ore/minerals and implementation of stricter environmental rules, microbiological applications for metal recovery have been shifted towards solid industrial wastes. Due to certain restrictions in conventional processes, use of microbes has garnered increased attention. The process is environmentally-friendly, economical and cost-effective. The major microorganisms in recovery of heavy metals are acidophiles that thrive at acidic pH ranging from 2.0–4.0. These microbes aid in dissolving metals by secreting inorganic and organic acids into aqueous media. Some of the well-known acidophilic bacteria such as Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferrooxidans and Sulfolobus spp. are wellstudied for bioleaching activity, whereas, fungal species like Penicillium spp. and Aspergillus niger have been thoroughly studied for the same process. This mini-review focuses on the acidophilic microbial diversity and application of those microorganisms toward solid industrial wastes.

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

Pb Tolerance and Bioaccumulation by the Mycelia of Flammulina velutipes in Artificial Enrichment Medium: Changwei Zhu , Zhengpeng Li , Decai Li , Yan Xin; J. Microbiol. 2014;52(1):8-12. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-2560-3

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Abstract: Mushrooms have the ability to accumulate high concentrations of heavy metals, which gives them potential for use as bioremediators of environmental contamination. The Pb2+ tolerance and accumulation ability of living mycelia of Flammulina velutipes were studied in this work. Mycelial growth was inhibited when exposed to 1 mM Pb2+. The colony diameter on solid medium decreased almost 10% compared with the control. Growth decreased almost 50% when the Pb2+ concentration increased to 4 mM in the medium, with the colony diameter decreasing from 80 mm to 43.4 mm, and dry biomass production in liquid cultures decreasing from 9.23±0.55 to 4.27±0.28 g/L. Lead ions were efficiently accumulated in the mycelia. The amount of Pb2+ in the mycelia increased with increasing Pb2+ concentration in the medium, with the maximum concentration up to 707±91.4 mg/kg dry weight. We also show evidence that a large amount of the Pb2+ was adsorbed to the mycelial surface, which may indicate that an exclusion mechanism is involved in Pb tolerance. These results demonstrate that F. velutipes could be useful as a remediator of heavy metal contamination because of the characteristics of high tolerance to Pb2+ and efficient accumulation of Pb2+ ions by the mycelia.

Molecular Characterization of the Alpha Subunit of Multicomponent Phenol Hydroxylase from 4-Chlorophenol-Degrading Pseudomonas sp. Strain PT3: Wael S. El-Sayed , Mohamed K. Ibrahim , Salama A. Ouf; J. Microbiol. 2014;52(1):13-19. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3250-x

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Abstract: Multicomponent phenol hydroxylases (mPHs) are diiron enzymes that use molecular oxygen to hydroxylate a variety of phenolic compounds. The DNA sequence of the alpha subunit (large subunit) of mPH from 4-chlorophenol (4-CP)- degrading bacterial strain PT3 was determined. Strain PT3 was isolated from oil-contaminated soil samples adjacent to automobile workshops and oil stations after enrichment and establishment of a chlorophenol-degrading consortium. Strain PT3 was identified as a member of Pseudomonas sp. based on sequence analysis of the 16S rRNA gene fragment. The 4-CP catabolic pathway by strain PT3 was tentatively proposed to proceed via a meta-cleavage pathway after hydroxylation to the corresponding chlorocatechol. This hypothesis was supported by polymerase chain reaction (PCR) detection of the LmPH encoding sequence and UV/VIS spectrophotometric analysis of the culture filtrate showing accumulation of 5-chloro-2-hydroxymuconic semialdehyde (5-CHMS) with λmax 380. The detection of catabolic genes involved in 4-CP degradation by PCR showed the presence of both mPH and catechol 2,3-dioxygenase (C23DO). Nucleotide sequence analysis of the alpha subunit of mPH from strain PT3 revealed specific phylogenetic grouping to known mPH. The metal coordination encoding regions from strain PT3 were found to be conserved with those from the homologous dinuclear oxo-iron bacterial monooxygenases. Two DE(D)XRH motifs was detected in LmPH of strain PT3 within an approximate 100 amino acid interval, a typical arrangement characteristic of most known PHs.

Analysis of Bacterial Diversity in Sponges Collected from Chuuk and Kosrae Islands in Micronesia: In-Hye Jeong , Kyoung-Ho Kim , Hyi-Seung Lee , Jin-Sook Park; J. Microbiol. 2014;52(1):20-26. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3619-x

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Abstract: The bacteria resident in sponges collected from Chuuk Lagoon and Kosrae Island of Micronesia were investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. These sponges were clustered into 5 groups based on their bacterial composition. Diversity indexes and cumulative rank abundance curves showed the different compositions of bacterial communities in the various groups of sponges. Reads related to the phylum Chloroflexi were observed predominantly (9.7–68.2%) in 9 sponges of 3 groups and unobserved in the other 2 groups. The Chloroflexi-containing group had similar bacterial patterns at the phylum and lower taxonomic levels, for example, significant proportions of Acidobacteria, Gemmatimonadetes, SBR1093, and PAUC34f were observed in most members of this group. The three groups in the Chloroflexi- containing group, however, showed some minor differences in the composition and diversity. The other two groups contained high proportions of Proteobacteria (>87%) or Bacteroidetes (>61%) and different composition and diversity compared to the Chloroflexi-containing group and each other. Four pairs of specimens with the same species showed similar bacterial profiles, but, the bacteria in sponges were highly specific at the individual level.

Analysis of the Abilities of Endophytic Bacteria Associated with Banana Tree Roots to Promote Plant Growth: Leandro Fernandes Andrade , Gleika Larisse Oliveira Dorasio de Souza , Silvia Nietsche , Adelica Aparecida Xavier , Marcia Regina Costa , Acleide Maria Santos Cardoso , Marlon Cristian Toledo Pereira , Débora Francine Gomes Silva Pereira; J. Microbiol. 2014;52(1):27-34. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3019-2

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61 Citations

Abstract: A total of 40 endophytic bacterial isolates obtained from banana tree roots were characterized for their biotechnological potential for promoting banana tree growth. All isolates had at least one positive feature. Twenty isolates were likely diazotrophs and formed pellicles in nitrogen-free culture medium, and 67% of these isolates belonged to the genus Bacillus sp. The isolates EB-04, EB-169, EB-64, and EB-144 had N fixation abilities as measured by the Kjeldahl method and by an acetylene reduction activity assay. Among the 40 isolates, 37.5% were capable of solubilizing inorganic phosphate and the isolates EB-47 and EB-64 showed the highest solubilization capacity. The isolate EB-53 (Lysinibacillus sp.) had a high solubilization index, whereas 73% of the isolates had low solubilization indices. The synthesis of indole-3- acetic acid (IAA) in the presence of L-tryptophan was detected in 40% of the isolates. The isolate EB-40 (Bacillus sp.) produced the highest amount of IAA (47.88 μg/ml) in medium supplemented with L-tryptophan and was able to synthesize IAA in the absence of L-tryptophan. The isolates EB-126 (Bacillus subtilis) and EB-47 (Bacillus sp.) were able to simultaneously fix nitrogen, solubilize phosphate and produce IAA in vitro. The results of this study demonstrated that the isolates analyzed here had diverse abilities and all have the potential to be used as growth-promoting microbial inoculants for banana trees.

Cloning and Functional Analysis of the Gβ Gene Mgb1 and the Gγ Gene Mgg1 in Monascus ruber: Li Li , Lu He , Yong Lai , Yanchun Shao , Fusheng Chen; J. Microbiol. 2014;52(1):35-43. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3072-x

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30 Citations

Abstract: The ascomycetous fungus Monascus ruber is one of the most well-known species widely used to produce Monascus-fermentation products for natural food colorants and medicine. Our previous research on the Gα subunit Mga1 and the regulator of G protein signaling MrflbA indicated that heterotrimeric G protein signaling pathways were involved in aspects of growth, sporulation and secondary metabolite production in M. ruber. To better understand the G protein signaling pathways in this fungus, a Gβ subunit gene (Mgb1) and a Gγ subunit gene (Mgg1) were cloned and investigated in the current study. The predicted Mgb1 protein consisted of 353 amino acids and Mgg1 consisted of 94 amino acids, sharing marked similarity with Aspergillus Gβ and Gγ subunits, respectively. Targeted deletion (Δ) of Mgb1 or Mgg1
result
ed in phenotypic alterations similar to those resulting from ΔMga1, i.e., restricted vegetative growth, lowered asexual sporulation, impaired cleistothecial formation, and enhanced citrinin and pigment production. Moreover, deletion of Mgg1 suppressed the defects in asexual development and in biosynthesis of citrinin and pigment caused by the absence of MrflbA function. These results provide evidence that Mgb1 and Mgg1 form a functional Gβγ dimer and the dimer interacts with Mga1 to mediate signaling pathways, which are negatively controlled by MrflbA, for growth, reproduction and citrinin and pigment biosynthesis in M. ruber.

Journal Articles

Optimization of Water Absorbing Exopolysaccharide Production on Local Cheap Substrates by Bacillus Strain CMG1403 Using One Variable at a Time Approach: Muhammadi , Muhammad Afzal; J. Microbiol. 2014;52(1):44-52. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-2622-6

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Abstract: Optimum culture conditions, and carbon and nitrogen sources for production of water absorbing exopolysaccharide by Bacillus strain CMG1403 on local cheap substrates were determined using one variable at a time approach. Carbon source was found to be sole substrate for EPS biosynthesis in the presence of yeast extract that supported the growth only and hence, indirectly enhanced the EPS yield. Whereas, urea only coupled with carbon source could enhance the EPS production but no effect on growth. The maximum yield of EPS was obtained when Bacillus strain CMG1403 was grown statically in neutral minimal medium with 25% volumetric aeration at 30°C for 10 days. Under these optimum conditions, a maximum yield of 2.71±0.024, 3.82±0.005, 4.33±0.021, 4.73±0.021, 4.85±0.024, and 5.52±0.016 g/L culture medium was obtained with 20 g (sugar) of sweet whey, glucose, fructose, sucrose, cane molasses and sugar beet the most efficient one respectively as carbon sources. Thus, the present study showed that under optimum culture conditions, the local cheap substrates could be superior and efficient alternatives to synthetic carbon sources providing way for an economical production of water absorbing EPS by indigenous soil bacterium Bacillus strain CMG1403.

Application of Statistical Experimental Design for Optimization of Silver Nanoparticles Biosynthesis by a Nanofactory Streptomyces viridochromogenes: Noura El-Ahmady El-Naggar , Nayera A.M. Abdelwahed; J. Microbiol. 2014;52(1):53-63. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3410-z

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Abstract: Central composite design was chosen to determine the combined effects of four process variables (AgNO3 concentration, incubation period, pH level and inoculum size) on the extracellular biosynthesis of silver nanoparticles (AgNPs) by Streptomycesviridochromogenes. Statistical analysis of the results showed that incubation period, initial pH level and inoculum size had significant effects (P􌥑0.05) on the biosynthesis of silver nanoparticles at their individual level. The maximum biosynthesis of silver nanoparticles was achieved at a concentration of 0.5% (v/v) of 1 mM AgNO3, incubation period of 96 h, initial pH of 9 and inoculum size of 2% (v/v). After optimization, the biosynthesis of silver nanoparticles was improved by approximately 5-fold as compared to that of the unoptimized conditions. The synthetic process of silver nanoparticle generation using the reduction of aqueous Ag+ ion by the culture supernatants of S. viridochromogenes was quite fast, and silver nanoparticles were formed immediately by the addition of AgNO3 solution (1 mM) to the cell-free supernatant. Initial characterization of silver nanoparticles was performed by visual observation of color change from yellow to intense brown color. UV-visible spectrophotometry for measuring surface plasmon resonance showed a single absorption peak at 400 nm, which confirmed the presence of silver nanoparticles. Fourier Transform Infrared Spectroscopy analysis provided evidence for proteins as possible reducing and capping agents for stabilizing the nanoparticles. Transmission Electron Microscopy revealed the extracellular formation of spherical silver nanoparticles in the size range of 2.15–7.27 nm. Compared to the cell-free supernatant, the biosynthesized AgNPs revealed superior antimicrobial activity against Gram-negative, Gram-positive bacterial strains and Candida albicans.

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

Cyclic Dipeptides from Lactic Acid Bacteria Inhibit the Proliferation of Pathogenic Fungi: Min-Kyu Kwak , Rui Liu , Min-Kyu Kim , Dohyun Moon , Andrew HyoungJin Kim , Sung-Hyun Song , Sa-Ouk Kang; J. Microbiol. 2014;52(1):64-70. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3520-7

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55 Citations

Abstract: Lactobacillus plantarum LBP-K10 was identified to be the most potent antifungal strain from Korean traditional fermented vegetables. The culture filtrate of this strain showed remarkable antifungal activity against Ganoderma boninense. Five fractions from the culture filtrate were observed to have an inhibitory effect against G. boninense. Also, the electron ionization and chemical ionization indicated that these compounds might be cyclic dipeptides. Of the five active fractions, two fractions showed the most significant anti-Ganoderma activity, and one of these fractions inhibited the growth of Candida albicans. These compounds were identified to be cis-cyclo(L-Val-L-Pro) and cis-cyclo(L-Phe-L-Pro), as confirmed by X-ray crystallography.

Proteomic Comparison between Salmonella Typhimurium and Salmonella Typhi: Yue Wang , Kuan-Yeh Huang , Yanan Huo; J. Microbiol. 2014;52(1):71-76. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3204-3

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Abstract: The genus Salmonella contains more than 2500 serovars. While most cause the self-limiting gastroenteritis, a few serovars can elicit typhoid fever, a severe systemic infection. S. enterica subsp. enterica serovar Typhimurium and S. Typhi are the representatives of the gastroenteritis and typhoid fever types of Salmonella. In this study, we adopted Stable Isotope Labeling with Amino acids in Cell culture (SILAC) technology to quantitatively compare the proteomes of the two serovars. We found several proteins with serovar- specific expression, which could be developed as new biomarkers for clinical serotype diagnosis. We found that flagella and chemotaxis genes were down-regulated in S. Typhi in comparison with S. Typhimurium. We attributed this observation to the fact that the smooth cellular structure of S. Typhi may better fit its systemic lifestyle. Instead of known virulence factors that were located within Salmonella Pathogenecity Islands, a number of core genes, which were involved in metabolism and transport of carbohydrates and amino acids, showed differential expression between the two serovars. Further studies on the roles of these differentially- expressed genes in the pathogenesis should be undertaken.

Surface Display of the HPV L1 Capsid Protein by the Autotransporter Shigella IcsA: Dan Xu , Xiaofeng Yang , Depu Wang , Jun Yu , Yili Wang; J. Microbiol. 2014;52(1):77-82. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3235-9

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Abstract: Autotransporters have become attractive tools for surface expression of foreign proteins in Gram-negative bacteria. In this study, the Shigella autotransporter IcsA, has been exploited to express the human papillomavirus (HPV) type 16 L1 capsid protein in Shigella sonnei and Escherichia coli. The L1 gene was fused in-frame to replace the coding sequence of the IcsA passenger domain that is responsible for actin-based motility. The resultant hybrid protein could be detected by an anti-L1 antibody on the surface of S. sonnei and E. coli. In E. coli, the protein was expressed on the entire surface of the bacterium. In contrast, the protein was detected mainly at one pole of the Shigella bacterium. However, the protein became evenly distributed on the surface of the Shigella bacterium when the icsP gene was removed. Our study demonstrated the possibility of exploiting autotransporters for surface expression of large, heterologous viral proteins, which may be a useful strategy for vaccine development.

NOTE] Pedobacter soyangensis sp. nov., Isolated from Lake Soyang in Korea: Yochan Joung , Heeyoung Kang , Haneul Kim , Beom-Il Lee , O-Seob Kwon , Kiseong Joh; J. Microbiol. 2014;52(1):83-87. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3284-0

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Abstract: Strain HME6451T was isolated from Lake Soyang in Korea. Phylogenetic tree based on 16S rRNA gene sequence showed that strain HME6451T formed a lineage within the genus Pedobacter. The strain HME6451T was closely related to Pedobacter daechungensis (95.4% sequence similarity), Pedobacter lentus (94.4%), and Pedobacter glucosidilyticus (93.8%). And strain HME6451T was a Gram-staining-negative, short rodshaped, strictly aerobic bacterium. The major fatty acids were iso-C15:0 (41.2%), summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c; 23.1%), and iso-C17:0-3OH (10.1%). The polar lipids of HME6451T were consisted of one phosphatidylethanolamine, one unidentified aminolipid, one unidentified phospholipid and four unidentified polar lipids. The DNA G+C content was 36.0 mol%. On the basis of the evidence presented in this study, strain HME6451T represent a novel species of the genus Pedobacter, for which the name Pedobacter soyangensis sp. nov., is proposed the type strain HME6451T (=KCTC 23467T =CECT 7865T).

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