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      • KCI등재

        Use of Terminal Restriction Length Polymorphism (T-RFLP) Analysis to Evaluate Uncultivable Microbial Community Structure of Soil

        Puneet Singh Chauhan,Charlotte C. Shagol,Woojong Yim,Sherlyn C. Tipayno,Chang-Gi Kim,Tongmin Sa 한국토양비료학회 2011 한국토양비료학회지 Vol.44 No.1

        Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.

      • KCI등재

        Use of Terminal Restriction Length Polymorphism (T-RFLP) Analysis to Evaluate Uncultivable Microbial Community Structure of Soil

        Chauhan, Puneet Singh,Shagol, Charlotte C.,Yim, Woo-Jong,Tipayno, Sherlyn C.,Kim, Chang-Gi,Sa, Tong-Min Korean Society of Soil Science and Fertilizer 2011 한국토양비료학회지 Vol.44 No.1

        Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.

      • Assessment of paddy soil bacterial diversity under long term fertilizer management practices employing high throughput 454 GS-FLX titanium pyrosequencing

        Puneet Singh Chauhan,Woojong Yim,Tongmin Sa 한국토양비료학회 2011 한국토양비료학회 학술발표회 초록집 Vol.2011 No.5

        Bar-coded 454 GS-FLX titanium pyrosequencing of the 16S rRNA gene was used to evaluate the bacterial diversity of paddy soil samples managed under long term fertilizer practices. Since 1954, chemical fertilizers have been applied in the fields as N?P2O5?K2O and compost have been added as fermented rice straw at 0, 7.5, 7.5, 15.0, 22.5 and 30.0 Mg ㏊?¹ in APK, CAPK, UPKC750, UPKC1500, UPKC2250 and UPKC3000 treatments, respectively, while control did not receive any chemical fertilizer or compost. A total of 22646, individual sequences comprising 9842 operational taxonomic units (OTU) at 97% similarities with 75∼77% library coverage were obtained from the 7 soil samples. The 10 most abundant bacterial groups were the Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, Nitrospirae, Chlorobi, Actinobacteria, Planctomycetes, Firmicutes and Gemmatimonadetes. Significant changes in the diversity and evenness measures recorded and Venn diagram showed sharing of various species among the 7 soil samples. pair wise ∫-Libshuff analysis indicated significant differences (P < 0.001) among the community structure of the samples. These results suggested that the changes in bacterial diversity and community structure of the paddy soil are influenced by long term fertilizer management practices.

      • KCI등재

        Effect of Methylobacterium oryzae CBMB20 Inoculation and Methanol Spray on Growth of Red Pepper (Capsicum annuum L.) at Different Fertilizer levels

        Puneet Singh Chauhan,Gil-Seung Lee(이길승),Min-Kyoung Lee(이민경),Woo-Jong Yim(임우종),Gyeong-Ja Lee(이경자),Young-Sang Kim(김영상),Jong-Bae Chung(정종배),Tong-Min Sa(사동민) 한국토양비료학회 2010 한국토양비료학회지 Vol.43 No.4

        지속가능한 친환경농업을 위해서는 비료와 함께 식물생장촉진 미생물 또는 생장조절물질을 적절히 혼합 사용하는 것이 바람직하다. 본 연구에서는 Methylobacterium oryzae CBMB20의 근권토양접종과 메탄올 엽면살포에 따른 고추의 생육촉진 효과를 유기질 비료의 시용 수준별로 조사하였다. M. oryzae CBMB20의 근권토양접종과 메탄올 엽면살포는 각기 고추생육을 증대시켰다. 또한 이들을 동시에 혼합 처리하였을 경우에는 고추의 생장촉진 효과가 더욱 현저하게 나타났다. M. oryzae CBMB20의 근권토양접종과 메탄올 엽면살포에 따른 고추 생장촉진 효과는 유기질 비료의 시용수준이 낮은 경우에 더욱 현저하게 나타났다. M. oryzae CBMB20와 메탄올을 혼합 처리한 경우 권장시비수준 100%와 300% 처리 사이에 고추생육과 수량에서 유의성 있는 차이가 없었다. 시비량이 지나치게 많을 경우 생장촉진제의 처리효과를 거둘 수 없으며, 적정한 시비수준에서 M. oryzae CBMB20와 메탄올을 혼합 처리함으로써 고추를 비롯한 작물의 생장과 수량을 유지하면서도 시비량을 크게 줄일 수 있을 것으로 판단된다. Fertilizers, plant growth promoting microbes and plant growth regulators should be combined together and used in order to achieve a maximal plant growth and yield in modern sustainable and ecological agricultural systems. In this study rhizosphere inoculation of Methylobacterium oryzae CBMB20 and foliar application of methanol were tested for their ability to promote the growth of red pepper plant at different levels of organic fertilizer. Rhizosphere inoculation of M. oryzae CBMB20 and foliar spray of methanol could promote red pepper plant growth and yield, and the growth promoting effect induced by the combined treatment of M. oryzae CBMB20 inoculation and foliar spray of methanol was more distinctive. This result suggests that a synergistic growth promoting effect of methanol spray and M. oryzae CBMB20 inoculation can be obtained in the combined treatment of the two growth promoting factors. The growth promoting effect was more significant in the lower fertilization rate, and the plant growth was not significantly different between 100 and 300% fertilizer treatments where both M. oryzae CBMB20 inoculation and foliar spray of methanol were included. This result indicates that, with the plant growth promoting effect of M. oryzae CBMB20 and methanol, fertilizer application rate can be profoundly reduced without any significant decreases in biomass accumulation and yield of crops.

      • KCI등재

        Effect of Inoculation of Methylobacterium oryzae on the Growth of Red Pepper at Different Organic Fertilizer Levels

        Puneet Singh Chauhan,Gil-Seung Lee(이길승),Min-Kyoung Lee(이민경),Woo-Jong Yim(임우종),Gyeong-Ja Lee(이경자),Young-Sang Kim(김영상),Jong-Bae Chung(정종배),Tong-Min Sa(사동민) 한국토양비료학회 2010 한국토양비료학회지 Vol.43 No.4

        다양한 유기질비료 수준에서 Methylobacterium oryzae CBMB20의 처리가 고추의 생육촉진에 미치는 영향을 조사하였다. 유기질비료 권장시비수준의 70, 85, 100, 120% 시용구에서 시비량이 증가함에 따라 고추의 신장, 건물중 및 수량에서 유의성 있는 증가를 확인하였다. M. oryzae CBMB20의 접종 처리에서 고추의 생장이 증가하였으며, 고추의 수량 또한 각 유기질 비료 수준별로 10~35% 증가하였다. 수확기에 조사한 근권토양의 메탄올자화세균의 밀도는 M. oryzae CBMB20 처리구에서 2.51~2.63 log CFU g<SUP>-1</SUP> soil 이었으며, 미처리구에서는 1.0 log CFU g<SUP>-1</SUP> soil 이하로 나타났다. 따라서 접종한 M. oryzae CBMB20은 고추 작물 근권토양에 효과적으로 군집하였으며, 식물생장촉진 호르몬의 분비 등의 작용을 통한 작물생장촉진효과를 발휘한 것으로 판단된다. M. oryzae CBMB20을 접종하지 않은 경우에는 고추의 최대 생장과 수량이 유기질 비료 권장시비 수준 120%에서 나타났으나, M. oryzae CBMB20을 접종한 경우에는 최대 생장과 수량이 권장시비 수준에서 나타났다. 이러한 결과는 식물생장촉진미생물의 접종을 통하여 비료 사용량의 절감 가능성을 제시하는 것이며, 식물생장 촉진 미생물 제제로서 M. oryzae CBMB20의 활용이 가능하리라 사료된다. Plant growth promoting ability of Methylobacterium oryzae CBMB20 was evaluated under different levels of organic fertilizer application on red pepper plants in a pot experiment. Oil cake as an organic N fertilizer was applied at the rates of 70, 85, 100 and 120% of the conventional recommended level. Each treatment was further treated with or without M. oryzae CBMB20 inoculation. The recommended amount of compost for red pepper was added in all the treatments. Results revealed that plant height, dry biomass and fruit yield were enhanced in increasing order as the rate of fertilization increased. Overall plant growth was improved due to the inoculation of M. oryzae CBMB20 and red pepper fruit yield was also increased by 10-35% in the plants inoculated with M. oryzae CBMB20 at different rates of organic fert1izer application. Total methylotrophic bacterial population in rhizosphere soil measured at the time of harvest was significantly higher in M. oryzae CBMB20 inoculated treatments. The growth promoting effect of M. oryzae CBMB20 found in red pepper could be due to the effective colonization of the bacteria in the rhizosphere and its ability of enhancing nutrient availability and producing plant growth hormones. With the plant growth promoting effect of M. oryzae CBMB20, the rate of organic fertilizer application can be reduced without any significant decreases in biomass production and yield of red pepper.

      • KCI등재후보

        Metagenomics Analysis of Thrombus Samples Retrieved from Mechanical Thrombectomy

        Vajpeyee Atulabh,Chauhan Puneet Singh,Pandey Swapnil,Tiwari Shivam,Yadav Lokendra Bahadur,Shroti Akhilesh Kumar,Vajpeyee Manisha 대한신경중재치료의학회 2021 Neurointervention Vol.16 No.1

        Purpose: The purpose of this study was to assess the microbiota in middle cerebral artery thrombi retrieved in mechanical thrombectomy arising out of symptomatic carotid plaque within 6 hours of acute ischemic stroke. Thrombi were subjected to next-generation sequencing for a bacterial signature to determine their role in atherosclerosis.Materials and Methods: We included 4 human middle cerebral artery thrombus samples (all patients were male). The median age for the patients was 51±13.6 years. Patients enrolled in the study from Pacific Medical University and Hospital underwent mechanical thrombectomy in the stroke window period. All patients underwent brain magnetic resonance angiography (MRA) and circle of Willis and neck vessel MRA along with the standard stroke workup to establish stroke etiology. Only patients with symptomatic carotid stenosis and tandem lesions with ipsilateral middle cerebral artery occlusion were included in the study. Thrombus samples were collected, stored at –80 degrees, and subjected to metagenomics analysis.Results: Of the 4 patients undergoing thrombectomy for diagnosis with ischemic stroke, all thrombi recovered for bacterial DNA in qPCR were positive. More than 27 bacteria were present in the 4 thrombus samples. The majority of bacteria were <i>Lactobacillus, Stenotrophomonas, Pseudomonas, Staphylococcus</i>, and <i>Finegoldia</i>.Conclusion: Genesis of symptomatic atherosclerotic carotid plaque leading to thromboembolism could be either due to direct mechanisms like acidification and local inflammation of plaque milieu with lactobacillus, biofilm dispersion leading to inflammation like with pseudomonas fluorescence, or enterococci or indirect mechanisms like Toll 2 like signaling by gut microbiota.

      • KCI등재

        Research Trends on Plant Associated Beneficial Bacteria as Biofertilizers for Sustainable Agriculture

        Tongmin Sa(사동민),Puneet Singh Chauhan 한국토양비료학회 2009 한국토양비료학회지 Vol.42 No.S2

        생물비료는 아직도 한국에서는 생소한 용어다. 한국에서 생물비료라 함은 식물추출액, 퇴비류- 다양한 형태의 미생물 혼합제 등으로 인식되고 있다. 그러나 최근에는 식물영양요소의 흡수나 이용도를 증진시키는 토양미생물 사용으로 언급하기도 한다. 본 개관은 식물성장을 증진시키는 것으로 알려진 PGPR 서로 다른 기작과 실질적 역할에 대하여 검토하였다. The sustainability of conventional agriculture which is characterized by input dependent an ecologically simplified food production system is vague. Chemicals and present practices used in agriculture are not only costly but also have widespread implications on human and animal health, food quality and safety and environmental quality. Thus there is a need for alternative farming practices to sustain food production for the escalating population and conserve environment for future generations. The present research scenario in the area of plant microbe interactions for maintainingsustainable agriculture suggests that thelevel of internal regulation in agro-ecosystems is largely dependent on the level of plant and microbial diversity present in the soil. In agro-ecosystems, biodiversity performs a variety of ecological services beyond the production of food, including recycling of nutrients, regulation of microclimate and local hydrological processes, suppression of undesirable organisms and detoxification of noxious chemicals. Controlling the soil microflora to enhance the predominance of beneficial and effective microorganisms can help improve and maintain soil chemical and physical properties. The role of beneficial soil microorganisms in sustainable productivity has been well construed. Some plant bacteria referred to as plant growthpromoting rhizobacteria (PGPR) can contribute to improve plant growth, nutrient uptake and microbial diversity when inoculated to plants. Term PGPR was initially used to describe strains of naturally occurring non-symbiotic soil bacteria have the ability to colonize plant roots and stimulateplant growth. PGPR activity has been reported in strains belonging to several other genera, such as Azotobacter, Azospirillum, Arthrobacter, Bacillus, Burkhokderia, Methylobacterium, and Pseudomonas etc. PGPR stimulate plant growth directly either by synthesizing hormones such as indole acetic acid or by promoting nutrition, for example, by phosphate solubilization or more generally by accelerating mineralization processes. They can also stimulate growth indirectly, acting as biocontrol agents by protecting the plant against soil borne fungal pathogens or deleterious bacteria. Present review focuses on some recent developments to evolve strategies for better biotechnological exploitation of PGPR’s.

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