Abstract Ammonia-oxidizing Bacteria Research Articles

Diversity of amoA and pmoA Genes in Extremely Saline Alkaline Soils of the Former Lake Texcoco

Ammonia-oxidizing bacteria (AOB) and aerobic methane oxidizing-bacteria (MOB) were studied in three extreme soils of the former Lake Texcoco, Mexico, with pH ranging from 8.5 to 10.5 and electrolytic conductivity (EC) from 0.67 to 84.76 dS m−1, and in two arable soils. Soil DNA was extracted with three different methods and total DNA was used as a template to amplify the pmoA and amoA functional genes and subsequently sequenced by pyrosequencing. The amoA gene sequences clustered as uncultured AOB dominated in the Texcoco soils, while Nitrosospira was dominant in the arable soils. Sequences of MOB associated with Nitrosococcus-rel (Type I) dominated (>85%) in the Texcoco soils, but they were more diverse in the arable soils, for example, JR2, JR3, Methylocaldum USC-g (Type I), USC-a (Type II) and gp23 (pxmA). Aerobic methane oxidizing-bacteria and AOB microbial diversity were significantly related to EC and pH (p < 0.05). As such, the lower MOB and AOB microbial diversity in the Texcoco soil compared to the arable soil was determined by its higher EC and pH.

Ammonia- and Methane-Oxidizing Bacteria: The Abundance, Niches and Compositional Differences for Diverse Soil Layers in Three Flooded Paddy Fields

Ammonia oxidizing bacteria (AOB), Ammonia oxidizing archaea (AOA) and methane oxidizing bacteria (MOB) play cogent roles in oxidation and nitrification processes, and hence have important ecological functions in several ecosystems. However, their distribution and compositional differences in different long-term flooded paddy fields (FPFs) management at different soil depths remains under-investigated. Using qPCR and phylogenetic analysis, this study investigated the abundance, niches, and compositional differences of AOA, AOB, and MOB along with their potential nitrification and oxidation rate in three soil layers from three FPFs (ShaPingBa (SPB), HeChuan (HC), and JiDi (JD)) in Chongqing, China. In all the FPFs, CH4 oxidation occurred mainly in the surface (0–3 cm) and subsurface layers (3–5 cm). A significant difference in potential methane oxidation and nitrification rates was observed among the three FPFs, in which SPB had the highest. The higher amoA genes are the marker for abundance of AOA compared to AOB while pmoA genes, which is the marker for MOB abundance and diversity, indicated their significant role in the nitrification process across the three FPFs. The phylogenetic analysis revealed that AOA were mainly composed of Nitrososphaera, Nitrosospumilus, and Nitrosotalea, while the genus Nitrosomonas accounted for the greatest proportion of AOB in the three soil layers. MOB were mainly composed of Methylocaldum and Methylocystis genera. Overall, this finding pointed to niche differences as well as suitability of the surface and subsurface soil environments for the co-occurrence of ammonia oxidation and methane oxidation in FPFs.

Seasonal population changes in the ammonia-oxidizing bacteria community structure of Songhua Lake, China

Abstract Ammonia-oxidizing bacteria (AOB) and the effects of environmental characteristics on the AOB community distribution were investigated in the Songhua Lake in May, August, October and December of 2011. Profiles of the AOB communities were generated using denaturing gradient gel electrophoresis (DGGE) to assess the expression of 16S rRNA genes followed by DNA sequence analysis. The dominant AOB groups were affiliated with Nitrosomonas and Nitrosospira spp. The effects of environmental characteristics on the AOB community distribution were analyzed by the ordination technique of redundancy analysis. The environmental characteristics significantly influencing the AOB community structure were different in the four seasons. The suspended solids (SS), ammonia nitrogen (NH 4 + -N) and nitrate nitrogen (NO 3 − -N) differed in May, the pH, NH 4 + -N, NO 3 − -N and total nitrogen (TN) differed in August, and the NH 4 + -N, DO and TN differed in December. None of the assessed environmental variables displayed heterogeneity in October. This study suggested that seasonal variation and nutrient differences might be responsible for the differences in the key environmental characteristics used to determine the distribution of the AOB communities in all seasons.

Diversity of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during composting of municipal sludge

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play an important role in the oxidation of ammonia. The diversity and relative abundance of AOA and AOB in compost samples from four composting stages [initial (day 0), heating (day 3), thermophilic (day 12), and cooling (day 28) stage ] were analyzed using the amoA gene as a functional marker. The number of operational taxonomic units (OTUs) found in each stage during sewage sludge composting was 33.3 % to 66.6 % of the total OTUs for AOB and 43.8 % to 62.5 % for AOA, with OTUs defined on the basis of a 5 % difference in nucleotides. Phylogenetic analysis showed that the AOB amoA sequences related to the Nitrosomonas lineage were dominant throughout the entire composting process. Most of the AOA amoA sequences fell into a soil/sediment cluster containing “Candidatus Nitrososphaera gargensis”. These results indicate that different ammonia oxidizers were present in different stages during composting, but that the dominant phylogenetic types were stable.

Research on Immobilized Ammonia-Oxidizing Bacteria by Sodium Alginate

Ammonia-oxidizing bacteria were immobilized by sodium alginate. Immobilized conditions and ammonium removal ability of immobilized cells were researched. The results showed that the optimal immobilized conditions were: 4.5% sodium alginate with 2.0% calcium chloride, 2000 immobilized balls, 1000mL immobilized medium, pH 8, 30°C, 110r/min. Immobilized ammonia-oxidizing bacteria were recycled six times under the optimal immobilized conditions. Immobilized ammonia-oxidizing bacteria at the optimal conditions had better ammonium removal ability than non-immobilized ammonia-oxidizing and were good for preservation. Removal rate of ammonia nitrogen of immobilized ammonia-oxidizing bacteria reached 89.51%.

Emergent Macrophytes Act Selectively on Ammonia-Oxidizing Bacteria and Archaea

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were quantified in the sediments and roots of dominant macrophytes in eight neutral to alkaline coastal wetlands. The AOA dominated in most samples, but the bacterial-to-archaeal amoA gene ratios increased with increasing ammonium levels and pH in the sediments. For all plant species, the ratios increased on the root surface relative to the adjacent bulk sediment. This suggests that root surfaces in these environments provide conditions favoring enrichment of AOB.

Dynamics of specific ammonia-oxidizing bacterial populations and nitrification in response to controlled shifts of ammonium concentrations in wastewater

Ammonia-oxidizing bacteria (AOB) are essential for the nitrification process in wastewater treatment. To retain these slow-growing bacteria in wastewater treatment plants (WWTPs), they are often grown as biofilms, e.g., on nitrifying trickling filters (NTFs) or on carriers in moving bed biofilm reactors (MBBRs). On NTFs, a decreasing ammonium gradient is formed because of the AOB activity, resulting in low ammonium concentrations at the bottom and reduced biomass with depth. To optimize the NTF process, different ammonium feed strategies may be designed. This, however, requires knowledge about AOB population dynamics. Using fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy, we followed biomass changes during 6 months, of three AOB populations on biofilm carriers. These were immersed in aerated MBBR tanks in a pilot plant receiving full-scale wastewater. Tanks were arranged in series, forming a wastewater ammonium gradient mimicking an NTF ammonium gradient. The biomass of one of the dominating Nitrosomonas oligotropha-like populations increased after an ammonium upshift, reaching levels comparable to the high ammonium control in 28 days, whereas a Nitrosomonas europaea-like population increased relatively slowly. The MBBR results, together with competition studies in NTF systems fed with wastewater under controlled ammonium regimes, suggest a differentiation between the two N. oligotropha populations, which may be important for WWTP nitrification.

Ammonia-Oxidizing Bacteria in Biofilters Removing Trihalomethanes Are Related to Nitrosomonas oligotropha

Ammonia-oxidizing bacteria (AOB) in nitrifying biofilters degrading four regulated trihalomethanes-trichloromethane, bromodichloromethane, dibromochloromethane, and tribromomethane-were related to Nitrosomonas oligotropha. N. oligotropha is associated with chloraminated drinking water systems, and its presence in the biofilters might indicate that trihalomethane tolerance is another reason that this bacterium is dominant in chloraminated systems.

Characterization of ammonia oxidizing bacteria associated with weeds in a Japanese paddy field using amoA gene fragments

Ammonia oxidizing bacteria (AOB) are important microorganisms in rice paddy field ecosystems because they play a key role in the nitrogen (N) cycle by converting ammonia (NH3) to nitrite (NO− 2). In this study, we investigated AOB associated with three types of weeds in a Japanese paddy field (semi-aquatic Echinochloa oryzicola Vasing, floating Lemna paucicostata Hegelm and submerged Najas graminea Delile) using molecular techniques polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and DNA sequencing targeting ammonia monooxygenase (amoA) gene. This work confirmed that rice paddy weeds harbor AOB and that the community composition is different for each type of weed. However, all AOB sequences associated with the tested weeds were closely related to known species of Nitrosospira-like AOB isolated from soil, suggesting that AOB associated with weeds were not specific to weeds and can also be found in the soil. Nitosomanas-like AOB were not detected on any of the weeds tested. In addition, the most dominant AOB strains present in the tested weeds were closely related to Nitrosospira sp. Ka3 and Nitrosospira sp. CT2F. The phylogenetic tree revealed that most of the AOB detected in the present study belonged to amoA cluster 1.

Analysis of communities of ammonia oxidizers, methanotrophs, and methanogens associated with microcrustaceans in the floodwater of a rice field microcosm

Ammonia-oxidizing bacteria (AOB), methanotrophs (MOB), and methanogens that were associated with Moina sp., Mesocyclops sp., Heterocypris sp. in the floodwater of a rice field microcosm were studied by using DGGE and sequence analysis with amoA / pmoA and methanogen-specific primer sets. Only one AOB and two MOB DGGE bands with the same mobility were detected, irrespective of the microcrustaceans. Effect of the incubation period was observed only in the AOB community associated with Moina sp., and an additional AOB clone appeared in the late period of incubation. Sequence analysis of the bands revealed that both of the closest relatives of the AOB clones belonged to uncultured ammonium monooxygenase genes of α-Proteobacteria, while those of the MOB clones to Methylomicrobium buryatense, an uncultured methanotroph bacterium, and Methylococcus capsulatus within type I methanotrophs belonging to γ-Proteobacteria. In contrast, no amplification products of 16S rDNA of the methanogenic archaea were obtained from any of the microcrustacean samples, indicating the absence or very small populations of methanogens.

Analysis of ammonia-oxidizing bacteria from hypersaline Mono Lake, California, on the basis of 16S rRNA sequences.

Ammonia-oxidizing bacteria were detected by PCR amplification of DNA extracted from filtered water samples throughout the water column of Mono Lake, California. Ammonia-oxidizing members of the beta subdivision of the division Proteobacteria (beta-subdivision Proteobacteria) were detected using previously characterized PCR primers; target sequences were detected by direct amplification in both surface water and below the chemocline. Denaturing gradient gel electrophoresis analysis indicated the presence of at least four different beta-subdivision ammonia oxidizers in some samples. Subsequent sequencing of amplified 16S rDNA fragments verified the presence of sequences very similar to those of cultured Nitrosomonas strains. Two separate analyses, carried out under different conditions (different reagents, locations, PCR machines, sequencers, etc.), 2 years apart, detected similar ranges of sequence diversity in these samples. It seems likely that the physiological diversity of nitrifiers exceeds the diversity of their ribosomal sequences and that these sequences represent members of the Nitrosomonas europaea group that are acclimated to alkaline, high-salinity environments. Primers specific for Nitrosococcus oceanus, a marine ammonia-oxidizing bacterium in the gamma subdivision of the Proteobacteria, did not amplify target from any samples.

Nitrous oxide production and methane oxidation by different ammonia-oxidizing bacteria.

Ammonia-oxidizing bacteria (AOB) are thought to contribute significantly to N2O production and methane oxidation in soils. Most of our knowledge derives from experiments with Nitrosomonas europaea, which appears to be of minor importance in most soils compared to Nitrosospira spp. We have conducted a comparative study of levels of aerobic N2O production in six phylogenetically different Nitrosospira strains newly isolated from soils and in two N. europaea and Nitrosospira multiformis type strains. The fraction of oxidized ammonium released as N2O during aerobic growth was remarkably constant (0.07 to 0.1%) for all the Nitrosospira strains, irrespective of the substrate supply (urea versus ammonium), the pH, or substrate limitation. N. europaea and Nitrosospira multiformis released similar fractions of N2O when they were supplied with ample amounts of substrates, but the fractions rose sharply (to 1 to 5%) when they were restricted by a low pH or substrate limitation. Phosphate buffer (versus HEPES) doubled the N2O release for all types of AOB. No detectable oxidation of atmospheric methane was detected. Calculations based on detection limits as well as data in the literature on CH4 oxidation by AOB bacteria prove that none of the tested strains contribute significantly to the oxidation of atmospheric CH4 in soils.

Fluidized-bed enrichment of marine ammonia-to-nitrite oxidizers and their ability to degrade chloroaliphatics

Ammonia-oxidizing bacteria from marine sediment (Puget Sound, WA) were selectively enriched in a fluidized-bed system (FBS). The enrichment culture converted ammonia stoichiometrically to nitrite. During continuous feed, steady-state ammonia removal was 0.20 mmol/l/h. In a batch fed FBS, at an initial 3.4 mM ammonia concentration, ammonia removal rate was 12 mmol/h/g protein. The enrichment culture degraded cis-1,2-dichloroethene, trichloroethene, methylene chloride and chloroform. Allylthiourea, a specific ammonia monooxygenase inhibitor, prevented degradation suggesting catalysis by nitrifiers. Other compounds, including 1,1,1-trichloroethane, 4-mono-, 2,4,6-trichloro-, 2,3,4,6-tetrachloro-, and pentachlorophenol were not removed. Immunofluorescence assay and polymerase chain reaction (PCR) methods showed that the enrichment culture contained a marine Nitrosomonas species. Extracted DNA from the culture was amplified using 16s rRNA PCR primers designed for the autotrophic ammonium oxidizers of the β-subgroup including marine Nitrosomonas spp., but not with primers designed for Nitrosococcus oceanus. Transmission electron micrographs of the enrichment culture showed bacteria with internal membranes that were similar to those of Nitrosomonas.

Microbiological aspects of ammonia oxidation of swine waste

Ammonia-oxidizing bacteria were present at 102 MPN/mL (most probable number per millilitre) in swine waste, and they were outnumbered by a factor of 105 by the heterotrophs of the indigenous flora. To study these ammonia-oxidizing bacteria we attempted to isolate them in pure culture. We succeeded in increasing the concentration of these bacteria by successive transfers to an inorganic medium, but the heterotrophs were always dominant. To overcome this problem Nitrosomonas europaea ATCC 19718 was adapted to grow in stabilized swine waste. With this adapted strain it was shown that the number of cells inoculated into swine waste rapidly decreased both under the aerobic conditions used to oxidize the organic matter of swine waste and under the anaerobic conditions found in stored swine waste. Ammonia oxidation was delayed when adapted N. europaea was inoculated into a partially stabilized swine waste as compared with results in a completely stabilized waste. A biofilm of 107 MPN/cm2 of N. europaea was developed after 114 days of incubation at 29 °C on polyvinyl chloride discs covered with geotextile in a rotating biological contactor using an inorganic medium. This biofilm was gradually adapted to stabilized swine waste and the rate of disappearance of ammonia reached 270 mg∙L−1∙day−1 in the compartment of the reactor containing 2.5 L of waste. Key words: amonia-oxidizing bacteria, swine waste, ammonia oxidation, biofilm, most probable number.

The numbers and distribution of ammonia-oxidizing bacteria in some Northern Territory and South Australian soils

Ammonia-oxidizing bacteria were detected in 75 soil samples from the Northern Territory and South Australia. Silica gel plates gave soil counts comparable with those obtained in liquid media. The counts varied from 20 to 8000 cells per gram of soil. Nitrosogloea merismoides was detected in 53 of the soils, Nitrosornonas europaea in 39 soils, and Nitrosococcus nitrosus in 14 soils. There was little difference between the numbers and types of nitrifying bacteria present in the desert soils compared with those from the more temperate areas, nor did the average annual rainfall have any appreciable effect.