• Title/Summary/Keyword: Bacterial community structure

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Analysis of Bacterial Diversity and Community Structure in Forest Soils Contaminated with Fuel Hydrocarbon

  • Ahn Jae-Hyung;Kim Mi-Soon;Kim Min-Cheol;Lim Jong-Sung;Lee Goon-Taek;Yun Jun-Ki;Kim Tae-Sung;Kim Tae-San;Ka Jong-Ok
    • Journal of Microbiology and Biotechnology
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    • v.16 no.5
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    • pp.704-715
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    • 2006
  • Oil spill was found in 1999 from a diesel storage facility located near the top of Baekun Mountain in Uiwang City. Application of bioremediation techniques was very relevant in removing oil spills in this site, because the geological condition was not amenable for other onsite remediation techniques. For efficient bioremediation, bacterial communities of the contaminated site and the uncontaminated control site were compared using both molecular and cultivation techniques. Soil bacterial populations were observed to be stimulated to grow in the soils contaminated with diesel hydrocarbon, whereas fungal and actinomycetes populations were decreased by diesel contamination. Most of the dieseldegrading bacteria isolated from contaminated forest soils were strains of Pseudomonas, Ralstonia, and Rhodococcus species. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the profiles were different among the three contaminated sites, whereas those of the control sites were identical to each other. Analysis of 16S rDNA sequences of dominant isolates and clones showed that the bacterial community was less diverse in the oil-contaminated site than at the control site. Sequence analysis of the alkane hydroxylase genes cloned from soil microbial DNAs indicated that their diversity and distribution were different between the contaminated site and the control site. The results indicated that diesel contamination exerted a strong selection on the indigenous microbial community in the contaminated site, leading to predominance of well-adapted microorganisms in concurrence with decrease of microbial diversity.

Analysis of Plasmid pJP4 Horizontal Transfer and Its Impact on Bacterial Community Structure in Natural Soil

  • KIM TAE SUNG;KIM MI SOON;JUNG MEE KUM;JOE MIN JEONG;AHN JAE HYUNG;OH KYOUNG HEE;LEE MIN HYO;KIM MIN KYUN;KA JONG OK
    • Journal of Microbiology and Biotechnology
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    • v.15 no.2
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    • pp.376-383
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    • 2005
  • Alcaligenes sp. JMP228 carrying 2,4­dichlorophenoxyacetic acid (2,4-D) degradative plasmid pJP4 was inoculated into natural soil, and transfer of the plasmid pJP4 to indigenous soil bacteria was investigated with and without 2,4-D amendment. Plasmid pJP4 transfer was enhanced in the soils treated with 2,4-D, compared to the soils not amended with 2,4-D. Several different transconjugants were isolated from the soils treated with 2,4-D, while no indigenous transconjugants were obtained from the unamended soils. Inoculation of the soils with both the donor Alcaligenes sp. JMP228/pJP4 and a recipient Burkholderia cepacia DBO 1 produced less diverse transconjugants than the soils inoculated with the donor alone. Repetitive extragenic palindromic-polymerase chain reaction (REP-PCR) analysis of the transconjugants exhibited seven distinct genomic DNA fingerprints. Analysis of 16S rDNA sequences indicated that the transconjugants were related to members of the genera Burkholderia and Pandoraea. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes revealed that inoculation of the donor caused clear changes in the bacterial community structure of the 2,4-D­amended soils. The new 16S rRNA gene bands in the DGGE profile corresponded with the 16S rRNA genes of 2,4-D­degrading transconjugants isolated from the soil. The results indicate that introduction of the 2,4-D degradative plasmid as Alcaligenes sp. JMP228/pJP4 has a substantial impact on the bacterial community structure in the 2,4-D-amended soil.

Gut Microbiota of Tenebrio molitor and Their Response to Environmental Change

  • Jung, Jaejoon;Heo, Aram;Park, Yong Woo;Kim, Ye Ji;Koh, Hyelim;Park, Woojun
    • Journal of Microbiology and Biotechnology
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    • v.24 no.7
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    • pp.888-897
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    • 2014
  • A bacterial community analysis of the gut of Tenebrio molitor larvae was performed using pyrosequencing of the 16S rRNA gene. A predominance of genus Spiroplasma species in phylum Tenericutes was observed in the gut samples, but there was variation found in the community composition between T. molitor individuals. The gut bacteria community structure was not significantly affected by the presence of antibiotics or by the exposure of T. molitor larvae to a highly diverse soil bacteria community. A negative relationship was identified between bacterial diversity and ampicillin concentration; however, no negative relationship was identified with the addition of kanamycin. Ampicillin treatment resulted in a reduction in the bacterial community size, estimated using the 16S rRNA gene copy number. A detailed phylogenetic analysis indicated that the Spiroplasma-associated sequences originating from the T. molitor larvae were distinct from previously identified Spiroplasma type species, implying the presence of novel Spiroplasma species. Some Spiroplasma species are known to be insect pathogens; however, the T. molitor larvae did not experience any harmful effects arising from the presence of Spiroplasma species, indicating that Spiroplasma in the gut of T. molitor larvae do not act as a pathogen to the host. A comparison with the bacterial communities found in other insects (Apis and Solenopsis) showed that the Spiroplasma species found in this study were specific to T. molitor.

The Bacterial Community Structure in Biofilms of the RABC Process for Swine Butchery Wastewater Treatment (돼지 도축폐수 처리를 위한 RABC 공정의 생물막 세균군집 구조)

  • Sung, Gi-Moon;Lee, Dong-Geun;Park, Seong-Joo
    • Korean Journal of Microbiology
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    • v.47 no.1
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    • pp.56-65
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    • 2011
  • Culture-independent microscopic observations and 16S rDNA analyses were applied to describe the bacterial community inherent to the biofilm structure of the RABC (Rotating Activated Bacillus Contactors) process for swine butchery wastewater treatment. The ratios of Gram-positive bacterial counts to total bacterial counts of the RABC process were significantly increased in the last aeration tank as well as returned sludge, while those of the existing A2O (Anaerobic-Anoxic-Oxic) process maintained constant from aeration tanks to returned sludge. Totally nine phyla were recovered by 16S rDNA analysis, two of which were major groups: the Proteobacteria (64.1%) and the Actinobacteria (18.4%). The third major group was the endospore-forming Firmicutes (5.4%). The remaining six minor groups are the Bacteroidetes (3.3%), the Chlorobi (2.2%), the Nitrospirae (1.1%), the Chlorofleix (1.1%), the Acidobacteria (1.1%), and the Fusobacteria (1.1%). The ratio of endospore-forming bacteria was 19.4%, which was composed of the members of the Firmicutes phylum (5.4%) and the Intrasporangiaceae family (14.0%) of the Actinobacteria phylum. Nitrifying and denitrifying related- and phosphorus accumulating related-sequences were composed of 6.5% and 5.4% of total community, respectively, these could mean the high capacity of the RABC process to remove odor compounds and reduce eutrophication by efficient removing inorganic nutrients.

Phylogenetic Diversity of Bacteria Associated with the Marine Sponges, Spirastrella abata and Cinachyrella sp. (해면 Spirastrella abata와 Cinachyrella sp.의 공생 세균의 계통학적 다양성)

  • Cho, Hyun-Hee;Shim, Eun-Jung;Park, Jin-Sook
    • Korean Journal of Microbiology
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    • v.46 no.2
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    • pp.177-182
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    • 2010
  • The bacterial community structure of two marine sponges, Spirastrella abata and Cinachyrella sp. collected from Jeju Island, in April 2009, was analyzed by 16S rDNA-denaturing gradient gel electrophoresis (DGGE). DGGE banding patterns indicated 8 and 7 bands for Spirastrella abata and Cinachyrella sp., respectively. Comparative sequence analysis of variable DGGE bands revealed from 92% to 100% similarity to the known published sequences. The bacterial groups associated with Spirastrella abata were Alphaproteobacteria and Deltaproteobacteria. The bacterial community of Cinachyrella sp. consisted of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria. Alphaproteobacteria was common and predominant in both the sponge species. Deltaproteobacteria was found only in Spirastrella abata while Actinobacteria and Gammaproteobacteria were found only in Cinachyrella sp. The results revealed that though the common bacterial group was found in both the sponges, the bacterial community profiles differed between the two sponge species obtained from the same geographical location.

Characterization of microbiota diversity of engorged ticks collected from dogs in China

  • Wang, Seongjin;Hua, Xiuguo;Cui, Li
    • Journal of Veterinary Science
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    • v.22 no.3
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    • pp.37.1-37.14
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    • 2021
  • Background: Ticks are one of the most common external parasites in dogs, and are associated with the transmission of a number of major zoonoses, which result in serious harm to human health and even death. Also, the increasing number of pet dogs and pet owners in China has caused concern regarding human tick-borne illnesses. Accordingly, studies are needed to gain a complete understanding of the bacterial composition and diversity of the ticks that parasitize dogs. Objectives: To date, there have been relatively few reports on the analysis of the bacterial community structure and diversity in ticks that parasitize dogs. The objective of this study was to investigate the microbial composition and diversity of parasitic ticks of dogs, and assessed the effect of tick sex and geographical region on the bacterial composition in two tick genera collected from dogs in China. Methods: A total of 178 whole ticks were subjected to a 16S ribosomal RNA (rRNA) next generation sequencing analysis. The Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene was used to characterize the bacterial communities of the collected ticks. Sequence analysis and taxonomic assignment were performed using QIIME 2 and the GreenGene database, respectively. After clustering the sequences into taxonomic units, the sequences were quality-filtered and rarefied. Results: After pooling 24 tick samples, we identified a total of 2,081 operational taxonomic units, which were assigned to 23 phyla and 328 genera, revealing a diverse bacterial community profile. The high, moderate and low prevalent taxa include 46, 101, and 182 genera, respectively. Among them, dominant taxa include environmental bacterial genera, such as Psychrobacter and Burkholderia. Additionally, some known tick-associated endosymbionts were also detected, including Coxiella, Rickettsia, and Ricketssiella. Also, the potentially pathogenic genera Staphylococcus and Pseudomonas were detected in the tick pools. Moreover, our preliminary study found that the differences in microbial communities are more dependent on the sampling location than tick sex in the tick specimens collected from dogs. Conclusions: The findings of this study support the need for future research on the microbial population present in ticks collected from dogs in China.

Molecular and Cultivation-Based Characterization of Bacterial Community Structure in Rice Field Soil

  • KIM MI-SOON;AHN JAE-HYUNG;JUNG MEE-KUM;YU JI-HYEON;JOO DONGHUN;KIM MIN-CHEOL;SHIN HYE-CHUL;KIM TAESUNG;RYU TAE-HUN;KWEON SOON-JONG;KIM TAESAN;KIM DONG-HERN;KA JONG-OK
    • Journal of Microbiology and Biotechnology
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    • v.15 no.5
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    • pp.1087-1093
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    • 2005
  • The population diversity and seasonal changes of bacterial communities in rice soils were monitored using both culture-dependent approaches and molecular methods. The rice field plot consisted of twelve subplots planted with two genetically-modified (GM) rice and two non-GM rice plants in three replicates. The DGGE analysis revealed that the bacterial community structures of the twelve subplot soils were quite similar to each other in a given month, indicating that there were no significant differences in the structure of the soil microbial populations between GM rice and non-GM rice during the experiment. However, the DGGE profiles of June soil after a sudden flooding were quite different from those of the other months. The June profiles exhibited a few intense DNA bands, compared with the others, indicating that flooding of rice field stimulated selective growth of some indigenous microorganisms. Phylogenetic analysis of l6S rDNA sequences from cultivated isolates showed that, while the isolates obtained from April soil before flooding were relatively evenly distributed among diverse genera such as Arthrobacter, Streptomyces, Terrabacter, and Bacillus/Paenibacillus, those from June soil after flooding mostly belonged to the Arthrobacter species. Phylogenetic analysis of 16S rDNA sequences obtained from the soil by cloning showed that April, August, and October had more diverse microorganisms than June. The results of this study indicated that flooding of rice fields gave a significant impact on the indigenous microbial community structure; however, the initial structure was gradually recovered over time after a sudden flooding.

Analysis of Microbial Community Structure in Biological Wastewater Treatment Process of Mixed Wastewater Treatment Facility using Environmental·Ecological Technique (환경·생태학적 기법을 이용한 혼합폐수 처리장의 생물학적 처리공정 내의 미생물 군집 특성 분석)

  • Son, Hyeng-Sik;Lee, Sang-Joon;Son, Hee-Jong
    • KSBB Journal
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    • v.28 no.2
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    • pp.80-85
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    • 2013
  • The bacterial community structure in a biological reactor fed influent from a wastewater treatment system was investigated by denaturing gradient gel electrophoresis (DGGE) and in situ hybridization. Sludges were collected from three biological reactors (aerobic, oxic, and anoxic tanks) at the M wastewater treatment facility (WTF). The influent of the MWTF consisted of mixed tannery wastewater (40~65%) and seafood wastewater (35~60%). The treatment processes resulted in a removal efficiency for BOD (biochemical oxygen demand) and COD (chemical oxygen demand) of 83.6~98.2% and 72.8~84.6%, respectively for tannery wastewater than for seafood wastewater resulted in greater survival of biomass in the biological reactors and a higher removal of BOD, COD, and T-N of about 8~18%. In contrast, addition of greater amounts of seafood wastewater decreased the amount of biomass in the bioreactors due to the increasing concentration of chromium from that wastewater and it also. The dominant bacterial species during the high seafood wastewater input period were Burkholderia cepacia (JX901049) and an uncultured bacterium (JF247555), while Pseudomonas geniculata (HQ256559) was dominant during the high tannery wastewater input period. Flavobacteriumsp. BF.107 (FM173271) and Hyphomicrobium zavarzinii (Y14306) were dominant under anoxic conditions.

Evaluation of Field Application for the Developed Retrofitting Process and Analysis of Bacterial Community Structure in Pilot Plant (하수처리장 Retrofit 공정의 현장적용성 평가 및 세균 군집 분포 연구)

  • Kim, Mee-Kyung;Hong, Jun-Hyeok;Kim, Youn-Kwon;Ahn, Tae-Seok;Shin, Eung-Bai
    • Journal of Korean Society of Environmental Engineers
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    • v.28 no.3
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    • pp.240-248
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    • 2006
  • In this study, a retrofitting BNR process that was modified for the economical applicability was proposed and evaluated in the pilot plant($50m^3/d$). At the same time the bacterial community structure was investigated in the pilot plant by using FISH(fluorescent in situ hybridization) method. Economically 16% of the initial construction cost for the proposed process(introduction of a biological nutrient removal process of $60,000m^3/d$ scale basis) was reduced due to the absence of a bioreactor. Water treatment efficiencies and maintenance facilities of the modified process were satisfied with the strengthened discharge permits in Korea throughout a long term pilot plant operating including a winter season. Bacterial populations in the pilot plant and in the control plant(A2/O process, B SIP(Sewage Treatment Plant)) were remained uniformly during the test period, but bacterial structure in the bioreactor was changed drastically. Proportions of ${\beta}$-proteobacteria group including soil bacteria which play a important role in wastewater treatment increased $25{\sim}607%$ in population.

Bacterial Community Structure and Diversity Using 16S rDNA Analysis in the Intertidal Sediment of Ganghwa Island (16S rDNA 분석을 이용한 강화도 장화리 갯벌 퇴적물 내 미생물 군집구조 및 다양성)

  • Cho Hye Youn;Lee Jung-Hyun;Hyun Jung-Ho
    • Korean Journal of Microbiology
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    • v.40 no.3
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    • pp.189-198
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    • 2004
  • T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in two layers (0-1cm, 6-7cm depth) of the sediment from Janghwari intertidal flat in Ganghwa Island. The results of T-RFLP (terminal-restriction fragment length polymorphism) analysis using restriction enzyme HhaI showed that the T-RFs of various size ($60{\pm}2$) bp-($667{\pm}2$) bp) appeared evenly at the surface sediments but two T-RFs with 60(${\pm}2$)bp and 93 (${\pm}2$)bp predominated at 6-7cm depth. Analysis of partial sequences for 172 clones revealed that 98% of the clones were not matched with the sequences of cultured bacteria strains in the GenBank (${\geq}similarity$ 98%), and approximately 86% of them were classified as different phylotypes. Most clones belonged to $\alpha$-, $\gamma$-, and $\delta$-Proteobacteria, Acidobacteria/Holophaga and green nonsulfur bacteria group. Proteobacteria group occupied the highest proportion in both layers (69% at 0-1cm depth and 46% at 6-7cm depth). $\gamma$-Proteobacteria and $\delta$-Proteobacteria that are associated with oxidation and reduction of sulfur compounds were appeared to be dominant, and comprised 21.5% and 15.7% of total clones, respectively. Overall results indicated that extremely diverse bacterial groups were inhabiting in the sediment of Ganghwa intertidal flat, and bacterial communities associated with the behaviour of sulfur seemed to playa significant role in the biogeochemical environment in this anoxic sediment.