Complete Genome Sequence of the Ammonia-Oxidizing Bacterium Nitrosospira sp. Strain NRS527, Isolated from the Rhizoplane of Paddy Rice

This work reports the complete genome sequence of the chemoautotrophic ammonia-oxidizing bacterium Nitrosospira sp. strain NRS527. The assembled genome is composed of a circular chromosome and two plasmids (80,750 bp and 41,389 bp, respectively).

Microbiomes inhabiting rice roots and rhizosphere

Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.

Cobalt-dependent inhibition of nitrite oxidation in Nitrobacter winogradskyi

Nitrobacter winogradskyi is an abundant, intensively studied autotrophic nitrite-oxidizing bacterium, which is frequently used as a model strain in the two-step nitrification of ammonia (NH₃) to nitrate (NO₃^-) via nitrite (NO₂^-), either in activated sludge, agricultural field studies or more recently in artificial microbial consortia for organic hydroponics. We observed a hitherto unknown cobalt ion-dependent inhibition of cell growth and NO₂^- oxidation activity of N. winogradskyi in a mineral medium, which strongly depended on accompanying Ca²⁺ and Mg²⁺ concentrations. This inhibition was bacteriostatic, but susceptible to natural chelators. l-Histidine effectively restored cell growth and NO₂^- oxidation activity of N. winogradskyi in mineral media containing Co²⁺ with >90% recovery. Our results suggest that Co²⁺ competed with alkaline earth metals during uptake and that its toxicity was significantly reduced by complexation.

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

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.

Characteristics of an ammonia-oxidizing bacterium with a plasmid isolated from alkaline soils and its phylogenetic relationship

An ammonia-oxidizing bacterium, strain TCH716, was isolated from alkaline soil at Harbin city, China. The cells of strain TCH716 are lobate (0.8-1.5 x 1.0-2.0 microm), gram-negative, obligately aerobic, and nonmotile. Colonies (1-2 mm in diameter) on gellan gum plate culture are reddish, circular, and smooth. The G + C content of DNA is 54.78 mol%. Its percentage of 16S rRNA gene sequence similarity (%) to Nitrosolobus multiformis ATCC 25196T (type strain) is 98.56%. This bacterium has an optimal growth temperature and pH at 30 degrees C and 8.0-8.5, respectively. The concentration of ammonium sulfate in the HEPES medium for optimum growth of this bacterium is 38 mM. Strain TCH716 was found to have a plasmid (approximately 6.5 kbp) that possessed a plasmid-linked gene for sulfonamide resistance. Phosphoglycerate kinase, RubisCO and PEPC were found to possess high specific activities compared to the activities of these enzymes in strain ATCC 25978T. In identification of strain TCH716, both morphological characteristics (compartmentalized cells) and the phylogenetic relationship based on 16S rRNA gene sequence are important. Based on results obtained, strain TCH716 belongs to the genus Nitrosolobus, and designated as Nitrosolobus sp. TCH716.

Nitrosomonas communis strain YNSRA, an ammonia-oxidizing bacterium, isolated from the reed rhizoplane in an aquaponics plant

An ammonia-oxidizing bacterium (strain YNSRA) was isolated from the rhizoplane of the reed (Phragmites communis) used in an aquaponics plant which is a wastewater treatment plant. Strain YNSRA was identified as Nitrosomonas communis by taxonomic studies. The hydroxylamine-cytochrome c reductase (HCR) of strain YNSRA was found to have a higher activity (25.60 u/mg) than that of Nitrosomonas europaea ATCC25978T (8.94 u/mg). Ribulose-1,5-bisphosphate carboxylase (RubisCO) activity was detected at very low levels in strain YNSRA, whereas strain ATCC25978T had definite activity.

Phylogenetic relationships among ammonia-oxidizing bacteria as revealed by gene sequences of glyceraldehyde 3-phosphate dehydrogenase and phosphoglycerate kinase

The three previously recognized genera of 'Nitrosolobus', Nitrosospira and 'Nitrosovibrio' were combined into one genus, Nitrosospira, on the basis of 16S rDNA sequence similarities. However, this classification has been controversial for some time, since the marked differences in their shapes suggest that they are not closely related. In this study, the phylogenetic analyses of the three groups using two genotypical markers, glyceraldehyde-3-phosphate dehydrogenase (GAP, gap), and 3-phosphoglycerate kinase (PGK, pgk), were performed. In the phylogenetic tree inferred from gap and pgk, the three genera appeared as clearly separated clusters. This is the first study of markers that are able to reveal the precise phylogenetic relationship among 'Nitrosolobus', Nitrosospira and 'Nitrosovibrio'.

Identification of genus Nitrosovibrio, ammonia-oxidizing bacteria, by comparison of N-terminal amino acid sequences of phosphoglycerate kinase

Nitrosospira, Nitrosolobus, and Nitrosovibrio, three genera of ammonia-oxidizing bacteria (AOB), are morphologically distinct from each other (Nitrosospira: spiral, Nitrosolobus: lobate, Nitrosovibrio: slender curved rods). However, these three genera cannot be classified using the phylogenetic tree based on 16S rDNA sequences. Phosphoglycerate kinase (PGK) was purified from 10 AOB strains as an index for identification, and its enzymatic properties were investigated. No distinction could be made between these three genera of AOB, because there was no notable difference in the molecular weight, K(m), or other properties of their PGKs. However, the N-terminal amino acid residues of PGK of Pro(P)-1, Ile(I)-6 and Asp(D)-12 have sequences characteristic of genus Nitrosovibrio (three strains) in four AOB genera. Therefore, it is proved possible to use the differences in the sequence to identify individual strains of the genus Nitrosovibrio.