Characteristics of Newly Isolated Nitrifying Bacteria from Rhizoplane of Paddy Rice.

Tomiyama, Hirofumi; Ohshima, Mifuyu; Ishii, Satoko; Satoh, Keisuke; Takahashi, Reiji; Isobe, Katsunori; Iwano, Hidetoshi; Tokuyama, Tatsuaki

doi:10.1264/jsme2.2001.101

Cited by 23 publications

(14 citation statements)

References 22 publications

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“…Rice field soil does also contain substantial populations of AOA, but the relative role AOA versus AOB for ammonia oxidation remained unclear (Prosser and Nicol, 2008). To our knowledge NOB have so far not been studied in paddy soil, except that a strain was isolated from the rhizoplane of rice (Tomiyama et al, 2001). In the rhizosphere of another Chinese paddy soil, the abundance of amoA genes and transcripts of AOA was found to be higher than of AOB (Chen et al, 2011).…”

Section: Introductionmentioning

confidence: 94%

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil

Xia

Angel

et al. 2013

Environmental Microbiology

130

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The dynamics of populations and activities of ammonia-oxidizing and nitrite-oxidizing microorganisms were investigated in rice microcosms treated with two levels of nitrogen. Different soil compartments (surface, bulk, rhizospheric soil) and roots (young and old roots) were collected at three time points (the panicle initiation, heading and maturity periods) of the season. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of their amoA genes (coding for a subunit of ammonia monooxygenase), that of nitrite oxidizers (NOB) by quantifying the nxrA gene (coding for a subunit of nitrite oxidase of Nitrobacter spp.) and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by measuring the rates of potential ammonia oxidation and nitrite oxidation and by quantifying the copy numbers of amoA and nxrA transcripts. Potential nitrite oxidation activity was much higher than potential ammonia oxidation activity and was not directly affected by nitrogen amendment demonstrating the importance of ammonia oxidizers as pace makers for nitrite oxidizer populations. Marked differences in the distribution of bacterial and archaeal ammonia oxidizers, and of Nitrobacter-like and Nitrospira-like nitrite oxidizers were found in the different compartments of planted paddy soil indicating niche differentiation. In bulk soil, ammonia-oxidizing bacteria (Nitrosospira and Nitrosomonas) were at low abundance and displayed no activity, but in surface soil their activity and abundance was high. Nitrite oxidation in surface soil was dominated by Nitrospira spp. By contrast, ammonia-oxidizing Thaumarchaeota and Nitrobacter spp. seemed to dominate nitrification in rhizospheric soil and on rice roots. In contrast to soil compartment, the level of N fertilization and the time point of sampling had only little effect on the abundance, composition and activity of the nitrifying communities. The results of our study show that in rice fields population dynamics and activity of nitrifiers is mainly differentiated by the soil compartments rather than by nitrogen amendment or season.

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Section: Introductionmentioning

confidence: 94%

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil

Xia

Angel

et al. 2013

Environmental Microbiology

130

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“…Accordingly, media containing organic matter have come to be used in autotrophic and heterotrophic AOB research (Joo et al . 2005; Laanbroek and Bär‐Gilissen 2002; Tomiyama et al . 2001).…”

Section: Introductionmentioning

confidence: 99%

“…Of these autotrophic AOB, N. europaea was found to grow on organic matter (Hommes et al 2003), and some heterotrophic bacteria have been shown to have nitrification activity (Papen et al 1989;Verstraete and Alexander 1972). Accordingly, media containing organic matter have come to be used in autotrophic and heterotrophic AOB research (Joo et al 2005;Laanbroek and Bär-Gilissen 2002;Tomiyama et al 2001).…”

Section: Introductionmentioning

confidence: 99%

Improvement of media for thermophilic ammonia-oxidizing bacteria in compost

Shimaya

Hashimoto

2008

Soil Science and Plant Nutrition

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Thermophilic ammonia‐oxidizing bacteria (AOB) have the potential to reduce ammonium emissions from commercial‐scale animal waste composting operations. Two new media have been designed to culture and enumerate thermophilic AOB species. C‐1 medium was designed to reflect compost composition. C‐2 medium and CQ‐2 medium were modified synthetic organic wastewater for the cultivation and enumeration of AOB, respectively. These new media have several advantages over the conventional medium. C‐2 medium is effective for nitrification at 50°C, and C‐1 and C‐2 media support reasonable growth of thermophilic AOB. Furthermore, C‐1 and CQ‐2 media allow enumeration of thermophilic AOB during the composting process. This is the first report of the successful cultivation and enumeration of thermophilic AOB in compost. These results suggest the possibility of isolation and manipulation of novel thermophilic AOB species for environmental bioremediation.

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“…Simultaneously, we supplied evidence that supported our previous results related to the use of housekeeping genes. Table 1 lists the 16 AOB used in the present study, their abbreviations and the origins of their pure cultures (Ida et al 2004(Ida et al , 2005Potter and Fothergill-Gilmore 1991;Satoh et al 2003;Takahashi et al 2001;Tomiyama et al 2001). The AOB were cultured using HEPES medium under conditions previously described (Satoh et al 2003).…”

Section: Introductionmentioning

confidence: 99%

Classification of chemoautotrophic ammonia-oxidizing bacteria using pyruvate kinase genes as high resolution phylogenetic markers

Ida

Takahashi

Satoh

et al. 2006

Soil Science and Plant Nutrition

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The phylogenetic relationship of β-proteobacterial ammonia-oxidizing bacteria (AOB) is mainly based on comparative sequence analyses of the genes encoding the 16S rRNA (16S rDNA) and the active site polypeptide of the ammonia monooxygenase (AmoA). However, classification of AOB with different morphotypes is not possible based solely on these markers. Pyruvate kinase (PYK), which is a key enzyme in the glycolytic pathway, functions at a primary metabolic intersection. The gene sequence of PYK is known to be a phylogenetic marker for bacteria and has been used for this purpose. The phylogenetic relationships of closely related AOB, 'Nitrosolobus', 'Nitrosovibrio' and Nitrosospira, were estimated based on pyk (PYK), a housekeeping and protein-coding gene. As a result, the pyk phylogenetic tree of the AOB showed a high resolution compared with the tree based on 16S rDNA sequences. Therefore, we conclude that analysis of the PYK gene sequences could play an important role in the in-depth classification and identification of AOB at a rank below the genus level.

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Characteristics of Newly Isolated Nitrifying Bacteria from Rhizoplane of Paddy Rice.

Cited by 23 publications

References 22 publications

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil

Improvement of media for thermophilic ammonia-oxidizing bacteria in compost

Classification of chemoautotrophic ammonia-oxidizing bacteria using pyruvate kinase genes as high resolution phylogenetic markers

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