• Journal of Soil and Groundwater Environment
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• v.21 no.4
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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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• v.23 no.9
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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.

• Journal of Korean Society of Water and Wastewater
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• v.26 no.3
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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.

• Korean Journal of Microbiology
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• v.43 no.3
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• pp.232-235
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• 2007

Mesophilic Crenarchaeota have been known to be predominant among ammonia-oxidizing microorganisms in terrestrial and marine environments. In this study, we determined the archaeal phylotypes carrying specific amoA by combining digital PCR and multiplex-nested PCR. Analysis of samples in which amoA and 16S rRNA gene were amplified showed that amoA gene diversity was relatively higher than that of 16S rRNA gene. Nitrifying archaeal group I.1a was dominant over I.1b group of crenarchaota and euryarchaeota. This approach could be applied for interrelating a functional gene to a specific phylotype in natural environments.

• KSBB Journal
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• v.26 no.3
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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.

• Korean Journal of Microbiology
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• v.48 no.2
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• pp.125-133
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• 2012

Anaerobic digestion is an alternative method to digest food wastes and to produce methane that can be used as a renewable energy source. We investigated bacterial and archaeal community structures in a three-stage methane production process using food wastes with concomitant wastewater treatment. The three-stage methane process is composed of semianaerobic hydrolysis/acidogenic, anaerobic acidogenic, and strictly anaerobic methane production steps in which food wastes are converted methane and carbon dioxide. The microbial diversity was determined by the nucleotide sequences of 16S rRNA gene library and quantitative real-time PCR. The major eubacterial population of the three-stage methane process was belonging to VFA-oxidizing bacteria. The archaeal community consisted mainly of two species of hydrogenotrophic methanogen (Methanoculleus). Family Picrophilaceae (Order Thermoplasmatales) was also observed as a minor population. The predominance of hydrogenotrophic methanogen suggests that the main degradation pathway of this process is different from the classical methane production systems that have the pathway based on acetogenesis. The domination of hydrogenotrophic methanogen (Methanoculleus) may be caused by mesophilic digestion, neutral pH, high concentration of ammonia, short HRT, and interaction with VFA-oxidizing bacteria (Tepidanaerobacter etc.).

• Korean Journal of Microbiology
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• v.50 no.2
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• pp.164-168
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• 2014

The ecosystem of the Arctic region has been increasingly affected by global warming. Archaeal ammonia monooxygenase alpha subunit coding gene (amoA) which is a key enzyme for nitrification was used to investigate the effect of runoff water of ice melt on microbial community of nitrogen cycle. The archaeal amoA genes at coastal area of Svalbard, Arctic region were PCR-amplified and sequenced after clone library construction. Analysis of archaeal amoA gene clone libraries suggested that the station 188 which is in the vicinity to the area of runoff water harbor lower ammonia-oxidizing archaeal diversity than the station 176 and 184. The average amino acid sequence identity within all archaeal amoA gene clones was 94% (with 91% nucleotide sequence identity). While all the clones of the station 188 were affiliated with Nitrosoarchaeaum clade containing strains isolated from low-salinity and terrestrial environments, about 45% of total clones of the station 176 and 184 were related to marine Nitosopumilus clade. Interestingly, other typical archaeal amoA gene clones of thaumarchaeal I.1b clade frequently retrieved from terrestrial environments was identified at station 188. Microbial community of nitrogen cycle in marine sediment might be affected by input of sediments caused by runoff glacier melt waters.

• Journal of Microbiology and Biotechnology
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• v.25 no.5
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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.