• 한국지하수토양환경학회지:지하수토양환경
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• 제21권4호
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• pp.50-59
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• 2016

Spatial and temporal changes in nitrification activities and distribution of microbial population of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in paddy soils were investigated. Soil samples were collected in March and October 2015 from rice paddy with and without the presence of confined animal feeding operations. Incubation experiments and quantitative polymerase chain reaction showed that AOA's contribution to nitrification kinetics was much higher in locations where organic nitrogen in animal waste is expected to significantly contribute to overall nitrogen budget, and temporal variations in nitrification kinetics were much smaller for AOA than AOB. These differences were interpreted to indicate that different microbial responses of two microbial populations to the types and concentrations of nitrogen substrates were the main determining factors of nitrification processes in the paddy soils. The copy numbers of ammonium monooxygenase gene showed that AOA colonized the paddy soils in higher numbers than AOB with stable distribution while AOB showed variation especially in March. Although small in numbers, AOB population turned out to exert more influence on nitrification potential than AOA, which was attributed to higher fluctuation in AOB cell numbers and nitrification reaction rate per cells.

• Journal of Microbiology and Biotechnology
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• 제23권9호
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• pp.1187-1196
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• 2013

Global warming will have far-reaching effects on our ecosystem. However, its effects on Antarctic soils have been poorly explored. To assess the effects of warming on microbial abundance and community composition, we sampled Antarctic soils from the King George Island in the Antarctic Peninsula and incubated these soils at elevated temperatures of $5^{\circ}C$ and $8^{\circ}C$ for 14 days. The reduction in total organic carbon and increase in soil respiration were attributed to the increased proliferation of Bacteria, Fungi, and Archaea. Interestingly, bacterial ammonia monooxygenase (amoA) genes were predominant over archaeal amoA, unlike in many other environments reported previously. Phylogenetic analyses of bacterial and archaeal amoA communities via clone libraries revealed that the diversity of amoA genes in Antarctic ammonia-oxidizing prokaryotic communities were temperature-insensitive. Interestingly, our data also showed that the amoA of Antarctic ammonia-oxidizing bacteria (AOB) communities differed from previously described amoA sequences of cultured isolates and clone library sequences, suggesting the presence of novel Antarctic-specific AOB communities. Denitrification-related genes were significantly reduced under warming conditions, whereas the abundance of amoA and nifH increased. Barcoded pyrosequencing of the bacterial 16S rRNA gene revealed that Proteobacteria, Acidobacteria, and Actinobacteria were the major phyla in Antarctic soils and the effect of short-term warming on the bacterial community was not apparent.

• 상하수도학회지
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• 제26권3호
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• pp.399-408
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• 2012

The overall goal of this study was to characterize and quantify ammonia-oxidizing bacteria (AOB) in four different full-scale sequence batch reactor (SBR) wastewater treatment plants. Also, this study focused on assessing the occurrence of the alternative ammonia-oxidizing microbes such as anammox (anaerobic ammonia oxidation) bacteria (AMX) and ammonia-oxidizing archaea (AOA) in these systems. Based on total AOB numbers and the estimated cell density in the mixed liquor samples, AOB constituted 0.3 - 1.8% of the total bacterial population in the four WWTPs. Based on clone library, Nitrosomonas ureae-like AOB were dominant in plant A and B, while plant C and D had Nitrosomonas nitrosa-like AOB as major AOB group. The four different AMX primer sets targeting AMX 16S rRNA gene produced PCR amplicons distantly related to Chlamydia and Planctomycetales group bacteria. However, it was not clear these groups of bacteria perform anammox reaction in the SBR plants. Also, molecular evidence of AOA was found in one of the SBR plants, with a sequence located in the deep branch of the sediment creanarchaeota group.

• 미생물학회지
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• 제43권3호
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• pp.232-235
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• 2007

해양 및 토양에서의 암모니아 산화는 세균에 비해 Crenarchaeota 그룹의 archaea에 의해 우세하게 일어나고 있음이 알려졌다. 서해 갯벌에서, 배양에 의존하지 알고, 특정 암모니아 산화유전자(amoA)를 가진 archaea을 동정하고자 디지털 PCR법을 응용한 nested PCR법을 개발하였다. amoA와 16S rRNA유전자가 동시에 증폭된 샘플의 분석결과, 16S rRNA유전자에 비해 amoA 유전자의 다양성 이 높았으며, I.1a 그룹의 crenarchaea가 I.1b 그룹의 crenarchaea보다 갯벌지역에서 암모니아 산화에 우점적으로 기여하고 있음을 알 수 있었다. 본 연구에서 시도된, 디지털 PCR과 multiplex-nested PCR을 접목한 접근법을 이용하면 특정 기능유전자를 가진 미생물을 환경에서 검증하는데 응용할 수 있을 것이다.

• KSBB Journal
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• 제26권3호
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• pp.237-242
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• 2011

As a number of archaea are ubiquitously found in non-extreme habitats, elucidation of their functional roles becomes currently an emerging issue. However, most of them are unable to grow in pure culture and so it remains to be established. In order to find genes lacking in the genome of an ammonia-oxidizing archaeon (AOA), we here report on the comparative analyses of an AOA genome with those of experimentally or theoretically established minimal genomes for independent growth. We assessed the genes lacking in AOA using logic of clusters of orthologous groups (COG), remote homology, consensus sequence weight matrix, function-based motif or domain, and then further excluded genes encoding hypothetical orarchaea-specific proteins. The results of these combination analyses revealed 19 candidate genes lacking in the genome of an AOA. Thus, our results provide a possibility of inducing independent growth of AOA when supplemented with product (s) of the lacking gene (s), and also give a chance for finding new proteins with novel sequence or structure space even if the predicted lacking-genes will be found using another algorithms or biochemical studies.

• 미생물학회지
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• 제48권2호
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• pp.125-133
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• 2012

혐기성 소화는 음식물 쓰레기와 같은 폐기물로부터 재생 가능한 에너지원으로 메탄을 생성하는 공정이다. 본 연구에서는 음식물 쓰레기와 폐수를 동시에 처리하는 3단계 메탄생산 공정을 이용한 혐기성 소화공정의 bacteria와 archaea 군집 변화를 조사하였다. 3단계 메탄생산 공정은 음식물 쓰레기 및 폐수를 메탄과 이산화탄소로 전환하는 반혐기성 가수분해/산생성, 혐기성 산생성과 혐기성 메탄생성조로 구성되어있으며, 16 rRNA 유전자 라이브러리의 염기서열 분석과 정량 PCR 등의 분자생물학적 방법으로 주요 미생물 군집을 조사하였다. 메탄생산 공정의 주요 미생물 군집은 VFA-산화 박테리아와 Methanoculleus 속에 속하는 hydrogenotrophic methanogen의 두 종(species)이었다. 또한, 소수의 Picrophilaceae 과(Thermoplasmatales 목)의 archaea도 확인하였다. 음식물을 이용한 3단계 메탄생산 공정은 acetogenesis를 기반으로 하는 고전적 메탄생성 공정과 달리 주로 hydrogenotrophic methanogen의 분해 경로에 의해 이루어 짐을 알 수 있다. 이들 균주의 우점은 중온 소화공정, 중성 pH, 높은 암모니아 농도, 짧은 HRT, Tepidanaerobacter 속 등과 같은 VFA 산화세균과의 상호작용 등에서 기인한 것으로 생각된다.

• 미생물학회지
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• 제50권2호
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• pp.164-168
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• 2014

북극지역은 지구온난화로 인하여 생태계에 큰 영향을 받고 있다. 본 연구는 북극 Svalbard 지역에서 육지 빙하의 해빙(ice melt)의 영향을 받는 해양퇴적층에서 질산화 과정에 핵심역할을 하는 고세균의 질산화유전자(ammonia monooxygenase, AMO)의 공간적 분포의 변화를 조사하였다. 해빙으로 인한 퇴적물 퇴적속도와 고세균 AMO의 alpha subunit를 코딩하는 amoA 유전자와의 관계를 클론라이브러리 분석을 통하여 분석하였다. 육지와 근접하여 퇴적속도가 가장 빠른 정점(188)에서 고세균 amoA 유전자의 다양성이 육지에서 비교적 먼 지역의 정점(176과 184)에 비해 현저히 낮음을 알 수 있었다. 3 정점의 고세균 amoA 유전자 클론들의 평균 아미노산 서열의 상동성은 94%(염기서열 91%)로 나타났다. 176과 184 정점에서 분석된 고세균 amoA 유전자 클론들 중 약 45%가 Nitosopumilus clade와 근연관계에 있는 반면, 188 지역의 경우 낮은 염농도에서 발견되는 Nitrosoarchaeaum clade와 근연관계에 있는 클론들이 발견되었다. 토양 고세균유래 amoA 유전자는 육지에 근접하여 해빙에 의한 영향을 가장 많이 받는 188정점에서만 발견이 되었다. 본 연구를 통하여, 해빙으로 인하여 육지로부터 운반되는 퇴적물의 량이 증가함에 따라, 해양퇴적층의 질소순환관련 미생물 군집에 변화가 유발되는 것으로 추정되며, 고세균의 amoA 유전자가 해양퇴적층 질소순환생태계 변화의 지표로 이용될 수 있음을 알 수 있었다.

• Journal of Microbiology and Biotechnology
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• 제25권5호
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• pp.569-578
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• 2015

Cold water paddy field soils are relatively unproductive, but can be ameliorated by supplementing with inorganic fertilizer from animal waste-based composts. The yield of two rice cultivars was significantly raised by providing either chicken manure or cow dung-based compost. The application of these composts raised the soil pH as well as both the total nitrogen and ammonium nitrogen content, which improved the soil's fertility and raised its nitrification potential. The composts had a measurable effect on the abundance of nitrogencycling-related soil microbes, as measured by estimating the copy number of various bacterial and archaeal genes using quantitative real-time PCR. The abundance of ammonia oxidizing archaea and bacteria was markedly encouraged by the application of chicken manure-based compost. Supplementation with the composts helped promote the availability of soil nitrogen in the cold water paddy field, thereby improving the soil's productivity and increasing the yield of the rice crop.