Journal of Microbiology

Volume 46(2); April 2008

Review

REVIEW] The Microbiology of Phosphorus Removal in Activated Sludge Processes-the Current State of Play: Robert J. Seviour , Simon McIlroy; J. Microbiol. 2008;46(2):115-124. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-008-0051-0

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Abstract: This review discusses critically what we know and would like to know about the microbiology of phosphorus (P) removal in activated sludge systems. In particular, the description of the genome sequences of two strains of the polyphosphate accumulating organism found in these processes, Candidatus ‘Accumulibacter phosphatis’, allows us to address many of the previously unanswered questions relating to how these processes behave, and to raise new questions about the microbiology of P removal. This article attempts to be deliberately speculative, and inevitably subjective, but hopefully at the same time useful to those who have an active interest in these environmentally very important processes.

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

Characterization of the Depth-Related Changes in the Microbial Communities in Lake Hovsgol Sediment by 16S rRNA Gene-Based Approaches: Young-Do Nam , Youlboong Sung , Ho-Won Chang , Seong Woon Roh , Kyoung-Ho Kim , Sung-Keun Rhee , Jung-Chan Kim , Joo-Yong Kim , Jung-Hoon Yoon , Jin-Woo Bae; J. Microbiol. 2008;46(2):125-136. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0189-1

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Abstract: The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39~42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta- and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria (some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly deteced by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.

The GntR-Type Regulators GtrA and GtrB Affect Cell Growth and Nodulation of Sinorhizobium meliloti: Yi Wang , Ai-Min Chen , Ai-Yuan Yu , Li Luo , Guan-Qiao Yu , Jia-Bi Zhu , Yan-Zhang Wang; J. Microbiol. 2008;46(2):137-145. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0145-0

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Abstract: GntR-type transcriptional regulators are involved in the regulation of various biological processes in bacteria, but little is known about their functions in Sinorhizobium meliloti. Here, we identified two GntR-type transcriptional regulator genes, gtrA and gtrB, from S. meliloti strain 1021. Both the gtrA1 mutant and the gtrB1 mutant had lower growth rates and maximal cell yields on rich and minimal media, as well as lower cell motility on swimming plates, than did the wild-type strain. Both mutants were also symbiotically deficient. Alfalfa plants inoculated with wild-type strain 1021 formed pink elongated nodules on primary roots. In contrast, the plants inoculated with the gtrA1 and gtrB1 mutants formed relatively smaller, round, light pink nodules mainly on lateral roots. During the first 3~4 weeks post-inoculation, the plants inoculated with the gtrA1 and gtrB1 mutants were apparently stunted, with lower levels of nitrogenase activity, but there was a remarkable increase in the number of nodules compared to those inoculated with the wild-type strain. Moreover, the gtrA1 and gtrB1 mutants not only showed delayed nodulation, but also showed markedly reduced nodulation competition. These results demonstrated that both GtrA and GtrB affect cell growth and effective symbiosis of S. meliloti. Our work provides new insight into the functions of GntR-like transcriptional regulators.

The Ecology of Vibrio vulnificus, Vibrio cholerae, and Vibrio parahaemolyticus in North Carolina Estuaries: Karen Dyer Blackwell , James D. Oliver; J. Microbiol. 2008;46(2):146-153. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0216-2

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Abstract

While numerous studies have characterized the distribution and/or ecology of various pathogenic Vibrio spp., here we have simultaneously examined several estuarine sites for Vibrio vulnificus, V. cholerae, and V. parahaemolyticus. For a one year period, waters and sediment were monitored for the presence of these three pathogens at six different sites on the east coast of North Carolina in the United States. All three pathogens, identified using colony hybridization and PCR methods, occurred in these estuarine environments, although V. cholerae occurred only infrequently and at very low levels. Seventeen chemical, physical, and biological parameters were investigated, including salinity, water temperature, turbidity, dissolved oxygen, levels of various inorganic nutrients and dissolved organic carbon, as well as total vibrios, total coliforms, and E. coli. We found each of the Vibrio spp. in water and sediment to correlate to several of these environmental measurements, with water temperature and total Vibrio levels correlating highly (P<0.0001) with occurrence of the three pathogens. Thus, these two parameters may represent simple assays for characterizing the potential public health hazard of estuarine waters.

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Different Planctomycetes Diversity Patterns in Latitudinal Surface Seawater of the Open Sea and in Sediment: Qinglong Shu , Nianzhi Jiao; J. Microbiol. 2008;46(2):154-159. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-008-0002-9

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Abstract: The 16S rRNA gene approach was applied to investigate the diversity of Planctomycetes in latitudinal surface seawater of the Western Pacific Ocean. The results revealed that the Pirellula-Rhodopirellula-Blastopirellula clade dominated the Planctomycetes community at all surface seawater sites while the minority genera Gemmata and Planctomyces were only found at sites H5 and H2 respectively. Although the clone frequency of the PRB clade seemed stable (between 83.3% and 94.1%) for all surface seawater sites, the retrieved Pirellula-Rhodopirellula-Blastopirellula clade presented unexpected diversity. Interestingly, low latitude seawater appeared to have higher diversity than mid-latitudes. ∫-LIBSHUFF software analysis revealed significantly different diversity patterns between in latitudinal surface seawater and in the sediment of South China Sea station M2896. Our data suggested that different hydrological and geographic features contributed to the shift of Planctomycetes diversity in marine environments. This is, to our knowledge, the first systematic assessment of Planctomycetes in latitudinal surface seawater of the open sea and the first comparison of diversity pattern between surface seawater and sediments and has broadened our understanding of Planctomycetes diversity in marine environments.

Journal Article

Prevalence of Antibodies in Response to Legionella Species, Analysis of a Healthy Population from Jeollanam-do Province, Korea: Hae Kyung Lee , Mi Kyeong Woo , Yong In Ju , Soo Jin Baek , Hyeon Je Song , Jin Su Choi , Sun Seog Kweon , Doo Young Jeon , Yeon Ho Kang; J. Microbiol. 2008;46(2):160-164. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0181-9

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Abstract

Seroepidemological investigation of antibodies to Legionella species in 500 healthy individuals from a single geographical location in Korea was conducted by indirect fluorescent antibody assay (IFA). Considering an antibody titer of ≥1:128 as positive reaction, 15.2% of total sera were positive. In males and females older than 40 years old, levels of IgM and IgG were 1.2% and 14%, respectively. The sera with antibody titers of ≥1:128 to Legionella species accounted for 85 sera, and 9 sera of these were reacted to more than one Legionella species. Reactivity to L. bozemanii, L. micdadei, L. longbeachae, L. pneumophila sg 6, and L. gormanii were 32.9%, 20%, 15%, 10.6%, and 8%, respectively. However, L. pneumophila sg 1, sg 2, and sg 3 did not react to any sera. Serological analysis revealed that the level of antibody in response to L. bozemanii was more prevalent than L. pneumophila. Our results suggest that the antibodies of non-L. pneumophila species, such as L. bozemanii, may be highly prevalent in healthy population within Korea. Although conclusions based on the findings of this study must be cautiously considered given that the population sampled were sourced from a single province, we have added to the knowledge base of serodiagnosis of infections due to non-L. pneumophila species in Korea.

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Legionnaires’ Disease Surveillance and Public Health Policies in Italy: A Mathematical Model for Assessing Prevention Strategies
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Research Support, Non-U.S. Gov'ts

Molecular Characterization of Polychlorinated Biphenyl-Dechlorinating Populations in Contaminated Sediments: Kyoung-Hee Oh , Ellen B. Ostrofsky , Young-Cheol Cho; J. Microbiol. 2008;46(2):165-173. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0214-4

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Abstract: Polychlorinated biphenyl (PCB)-dechlorinating microorganisms were characterized in PCB-contaminated sediments using amplified ribosomal DNA restriction analysis (ARDRA). The sediments were prepared by spiking Aroclor 1248 into PCB-free sediments, and were inoculated with microorganisms eluted from St. Lawrence River sediments. PCB-free sediments inoculated with the same inoculum served as the control. Four restriction fragment length polymorphism (RFLP) groups in the eubacterial and two in the archaeal domain were found exclusively in PCB-spiked sediment clone libraries. Sequence analysis of the four eubacterial clones showed homology to Escherichia coli, Lactosphaera pasteurii, Clostridium thermocellum, and Dehalobacter restrictus. The predominant archaeal sequence in the PCB-spiked sediment clone library was closely related to Methanosarcina barkeri, which appear to support earlier findings that methanogens are involved in PCB dechlorination. When the dot-blot hybridization was performed between the sediment DNA extract and the probes designed with eubacterial RFLP groups, the intensity of two of eubacterial RFLP groups, which showed high sequence homology to C. pascui and D. restrictus, was highly correlated with the number of dechlorinating microorganisms suggesting these two members intend to contribute to PCB dechlorination.

Bacterial Communities in the Initial Stage of Marine Biofilm Formation on Artificial Surfaces: Jin-Woo Lee , Ji-Hyun Nam , Yang-Hoon Kim , Kyu-Ho Lee , Dong-Hun Lee; J. Microbiol. 2008;46(2):174-182. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-008-0032-3

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Abstract

Succession of bacterial communities during the first 36 h of biofilm formation in coastal water was investigated at 3~15 h intervals. Three kinds of surfaces (i.e., acryl, glass, and steel substratum) were submerged in situ at Sacheon harbor, Korea. Biofilms were harvested by scraping the surfaces, and the compositions of bacterial communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of 16S rRNA genes. While community structure based on T-RFLP analysis showed slight differences by substratum, dramatic changes were commonly observed for all substrata between 9 and 24 h. Identification of major populations by 16S rRNA gene sequences indicated that γ-Proteobacteria (Pseudomonas, Acinetobacter, Alteromonas, and uncultured γ-Proteobacteria) were predominant in the community during 0~9 h, while the ratio of α-Proteobacteria (Loktanella, Methylobacterium, Pelagibacter, and uncultured α-Proteobacteria) increased 2.6~4.8 folds during 24~36 h of the biofilm formation, emerging as the most predominant group. Previously, α-Proteobacteria were recognized as the pioneering organisms in marine biofilm formation. However, results of this study, which revealed the bacterial succession with finer temporal resolution, indicated some species of γ-Proteobacteria were more important as the pioneering population. Measures to control pioneering activities of these species can be useful in prevention of marine biofilm formation.

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Mutant Selection of Hahella chejuensis KCTC 2396 and Statistical Optimization of Medium Components for Prodigiosin Yield-Up: Sung Jin Kim , Hong Kum Lee , Yoo Kyung Lee , Joung Han Yim; J. Microbiol. 2008;46(2):183-188. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-008-0037-y

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Abstract: Prodigiosin is a natural red pigment with algicidal activity against Cochlodinium polykrikoides, a major harmful red-tide microalga. To increase the yield of prodigiosin, a mutant of Hahella chejuenesis KCTC 2396, assigned M3349, was developed by an antibiotic mutagenesis using chloramphenicol. When cultured in Sucrose-based Marine Broth medium (SMB), M3349 could produce prodigiosin at 1.628±0.06 g/L, while wild type producing at 0.658±0.12 g/L under the same conditions. To increase the yield of prodigiosin production by M3349, significant medium components were determined using a two-level Plackett-Burman statistical design technique. Among fourteen components included in SMB medium, NaCl, Na2SiO3, MgCl2, H3BO3, Na2HPO4, Na2SO4, and CaCl2 were determined to be important for prodigiosin production. The medium formulation was finally optimized using a Box-Behnken design as follows: sucrose 10.0, peptone 8.0, yeast extract 2.0, NaCl 10.0, Na2SO4 12.0, CaCl2 1.8, MgCl2 0.7 g/L; and H3BO3 22.0, Na2HPO4 20.0, Na2SiO3 8.0 mg/L. The predicted maximum yield of prodigiosin in the optimized medium was 2.43 g/L by the Box-Behnken design, while the practical production was 2.60±0.176 g/L, which was 3.9 times higher than wild type with SMB Medium (0.658 g/L).

Fatty Acid Biosynthesis in Eukaryotic Photosynthetic Microalgae: Identification of a Microsomal Delta 12 Desaturase in Chlamydomonas reinhardtii: Xiaoyuan Chi , Xiaowen Zhang , Xiangyu Guan , Ling Ding , Youxun Li , Mingqing Wang , Hanzhi Lin , Song Qin; J. Microbiol. 2008;46(2):189-201. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0223-3

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Abstract

Polyunsaturated fatty acids (PUFAs) are important components of infant and adult nutrition because they serve as structural elements of cell membranes. Fatty acid desaturases are responsible for the insertion of double bonds into pre-formed fatty acid chains in reactions that require oxygen and reducing equivalents. In this study, the genome-wide characterization of the fatty acid desaturases from seven eukaryotic photosynthetic microalgae was undertaken according to the conserved histidine-rich motifs and phylogenetic profiles. Analysis of these genomes provided insight into the origin and evolution of the pathway of fatty acid biosynthesis in eukaryotic plants. In addition, the candidate enzyme from Chlamydomonas reinhardtii with the highest similarity to the microsomal Δ12 desaturase of Chlorella vulgaris was isolated, and its function was verified by heterologous expression in yeast (Saccharomyces cerevisiae).

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Sequence and Phylogenetic Analyses of Novel Glucosyltransferase Genes of Mutans Streptococci Isolated from Pig Oral Cavity: Noriko Shinozaki-Kuwahara , Kazuko Takada , Masatomo Hirasawa; J. Microbiol. 2008;46(2):202-208. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0199-z

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Abstract: Nucleotide sequences of water-insoluble glucan-producing glucosyltransferase (gtf) genes of new mutans streptococci isolated from pig oral cavity, Streptococcus orisuis JCM14035, and of Streptococcus criceti HS-6 were determined. The gtf gene of S. orisuis JCM14035 consisted of a 4,401 bp ORF encoding for a 1,466 amino acids, and was revealed to belong to the gtfI group. The percent homology of amino acid sequence of the GTF-I from S. orisuis and S. criceti are 95.0%, however, this score ranges from 77.0% to 78.0% when compared to Streptococcus sobrinus 6715. The deduced N-terminal amino acid sequence was considered responsible for the secretion of GTF-I in S. orisuis JCM14035 and S. criceti HS-6 with high similarity to known GTF proteins from other streptococci. In addition, two other conserved regions, i.e., N-terminal putative catalytic-site and C-terminal glucan binding domain, were also found in GTF-Is of S. orisuis JCM14035 and S. criceti HS-6. Phylogenetic analysis suggested that S. orisuis JCM14035 and S. criceti HS-6, closely related to each other, resemble S. sobrinus and S. downei based on the amino acid sequences of the GTFs.

Journal Article

Phage Types and Pulsed-Field Gel Electrophoresis Patterns of Salmonella enterica serovar Enteritidis Isolated from Humans and Chickens: Sung Hun Kim , Shukho Kim , Sung Guen Chun , Mi-Sun Park , Jeong Hyun Park , Bok-Kwon Lee; J. Microbiol. 2008;46(2):209-213. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0197-1

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Abstract: We analyzed 66 Salmonella Enteritidis isolates in 2002. Thirty isolates were obtained from human patients with diarrhea, and 36 were obtained from chickens. A total of ten phage types (PT) were identified in the human and chicken isolates. PT1 and PT21 were the predominant PTs in both the human (20% and 13%) and chicken (17% and 47%) isolates. Twelve pulsotypes were generated by PFGE and divided into two major groups. Most of the PFGE types were categorized into cluster group 1. Eighteen chicken isolates in cluster group 1 showed high-level genetic association (>95%) with 22 other human isolates. Additionally, six chicken isolates from cluster group 2 showed fairly high-level genetic association (>95%) with the other seven human isolates. The highest levels of genetic association in humans and chickens were seen with A5-PT21 (11 isolates), A2-PT1 (7 isolates), and B1-PT4 (6 isolates). The Pulsed-Field Gel Electrophoresis (PFGE) and phage typing provided conclusive evidence that human Salmonella infections are attributable to the consumption of contaminated chicken.

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

Functional Analysis of pilQ Gene in Xanthomanas oryzae pv. oryzae, Bacterial Blight Pathogen of Rice: Seon-Hwa Lim , Byoung-Ho So , Ji-Chun Wang , Eun-Seong Song , Young-Jin Park , Byoung-Moo Lee , Hee-Wan Kang; J. Microbiol. 2008;46(2):214-220. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0173-9

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Abstract: Bacterial blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most devastating bacterial disease in rice. A virulence-attenuated mutant strain HNU89K9 of X. oryzae pv. oryzae (KACC10331), with a transposon insertion in the pilQ gene was used for this study. The pilQ was involved in the gene cluster pilMNOPQ of the Xoo genome. Growth rate of the pilQ mutant was similar to that of wild-type. At level of amino acids, PilQ of Xoo showed that a high sequence identities more than 94% and 70% to Xanthomonas species and to Xyllela fastidiosa, respectively but a low sequence homology less than 30% to other bacterial species. The twitching motility forming a marginal fringe on PSA media was observed on colony of the wild-type strain KACC10331, but not in mutant HNU89K9. Wild-type Xoo cells formed a biofilm on the surface of the PVC plastic test tube, while the mutant strain HNU89K9 did not form a biofilm. The results suggest that the pilQ gene of X. oryzae pv. oryzae plays a critical role in pathogenicity, twitching motility, and biofilm formation.

Anti-Tumor Activity of Acinetobacter baumannii Outer Membrane Protein A on Dendritic Cell-Based Immunotherapy against Murine Melanoma: Jun Sik Lee , Jung Wook Kim , Chul Hee Choi , Won Kee Lee , Hae Young Chung , Je Chul Lee; J. Microbiol. 2008;46(2):221-227. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-008-0052-z

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Abstract: Acinetobacter baumannii outer membrane protein A (AbOmpA) is a major surface protein that is an important pathogen-associated molecular pattern. Based on our previous findings that AbOmpA induced the phenotypic maturation of dendritic cells (DCs) and drove the Th1 immune response in vitro, we investigated the therapeutic efficacy of AbOmpA-pulsed DC vaccines in a murine melanoma model. The surface expression of co-stimulatory molecules (CD80 and CD86) and major histocompatibility complex class I and II molecules was higher in DCs pulsed with AbOmpA alone or with a combination of B16F10 cell lysates than that of DCs pulsed with B16F10 cell lysates. AbOmpA stimulated the maturation of murine splenic DCs in vivo. In a therapeutic model of murine melanoma, AbOmpA-pulsed DCs significantly retarded tumor growth and improved the survival of tumor-bearing mice. AbOmpA-pulsed DCs significantly enhanced CD8+, interleukin-2+ T cells and CD4+, interferon-γ+ T cells in tumor-bearing mice. These results provide evidence that AbOmpA may be therapeutically useful in adjuvant DC immunotherapy against poorly immunogenic melanoma without tumor-specific antigens.

Antibacterial Characteristics of Curcuma xanthorrhiza Extract on Streptococcus mutans Biofilm: Jung-Eun Kim , Hee-Eun Kim , Jae-Kwan Hwang , Ho-Jeong Lee , Ho-Keun Kwon , Baek-Il Kim; J. Microbiol. 2008;46(2):228-232. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0167-7

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Abstract

This study evaluated the antibacterial effects of a natural Curcuma xanthorrhiza extract (Xan) on a Streptococcus mutans biofilm by examining the bactericidal activity, inhibition of acidogenesis and morphological alteration. Xan was obtained from the roots of a medicinal plant in Indonesia, which has shown selective antibacterial effects on planktonic S. mutans. S. mutans biofilms were formed on slide glass over a 72 h period and treated with the following compounds for 5, 30, and 60 min: saline, 1% DMSO, 2 mg/ml chlorhexidine (CHX), and 0.1 mg/ml Xan. The Xan group exposed for 5 and 30 min showed significantly fewer colony forming units (CFU, 57.6 and 97.3%, respectively) than those exposed to 1% DMSO, the negative control group (P<0.05). These CFU were similar in number to those slides exposed to CHX, the positive control group. Xan showed similar bactericidal effect to that of CHX but the dose of Xan was one twentieth that of CHX. In addition, the biofilms treated with Xan and CHX maintained a neutral pH for 4 h, which indicates that Xan and CHX inhibit acid production. Scanning electron microscopy showed morphological changes in the cell wall and membrane of the Xan-treated biofilms; an uneven surface and a deformation in contour. Overall, natural Xan has strong bactericidal activity, inhibitory effects on acidogenesis, and alters the microstructure of S. mutans biofilm. In conclusion, Xan has potential in anti-S. mutans therapy for the prevention of dental caries.

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