scholarly journals Patterns of Community Change among Ammonia Oxidizers in Meadow Soils upon Long-Term Incubation at Different Temperatures

2003 ◽  
Vol 69 (10) ◽  
pp. 6152-6164 ◽  
Author(s):  
Sharon Avrahami ◽  
Ralf Conrad
Keyword(s):  
Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Change ◽  
Effect Of Temperature ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Moist Soil ◽  
Α Subunit ◽  
Mean Temperature

ABSTRACT The effect of temperature on the community structure of ammonia-oxidizing bacteria was investigated in three different meadow soils. Two of the soils (OMS and GMS) were acidic (pH 5.0 to 5.8) and from sites in Germany with low annual mean temperature (about 10°C), while KMS soil was slightly alkaline (pH 7.9) and from a site in Israel with a high annual mean temperature (about 22°C). The soils were fertilized and incubated for up to 20 weeks in a moist state and as a buffered (pH 7) slurry amended with urea at different incubation temperatures (4 to 37°C). OMS soil was also incubated with less fertilizer than the other soils. The community structure of ammonia oxidizers was analyzed before and after incubation by denaturing gradient gel electrophoresis (DGGE) of the amoA gene, which codes for the α subunit of ammonia monooxygenase. All amoA gene sequences found belonged to the genus Nitrosospira. The analysis showed community change due to temperature both in moist soil and in the soil slurry. Two patterns of community change were observed. One pattern was a change between the different Nitrosospira clusters, which was observed in moist soil and slurry incubations of GMS and OMS. Nitrosospira AmoA cluster 1 was mainly detected below 30°C, while Nitrosospira cluster 4 was predominant at 25°C. Nitrosospira clusters 3a, 3b, and 9 dominated at 30°C. The second pattern, observed in KMS, showed a community shift predominantly within a single Nitrosospira cluster. The sequences of the individual DGGE bands that exhibited different trends with temperature belonged almost exclusively to Nitrosospira cluster 3a. We conclude that ammonia oxidizer populations are influenced by temperature. In addition, we confirmed previous observations that N fertilizer also influences the community structure of ammonia oxidizers. Thus, Nitrosospira cluster 1 was absent in OMS soil treated with less fertilizer, while Nitrosospira cluster 9 was only found in the sample given less fertilizer.

scholarly journals Effect of Toxic Metals on Indigenous Soil β-Subgroup Proteobacterium Ammonia Oxidizer Community Structure and Protection against Toxicity by Inoculated Metal-Resistant Bacteria

1999 ◽  
Vol 65 (1) ◽  
pp. 95-101 ◽  
Author(s):  
John R. Stephen ◽  
Yun-Juan Chang ◽  
Sarah J. Macnaughton ◽  
George A. Kowalchuk ◽  
Kam T. Leung ◽  
...  
Keyword(s):  
Community Structure ◽  
Toxic Metals ◽  
Heterotrophic Bacteria ◽  
Ammonia Oxidizer ◽  
Resistant Bacteria ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Gene Encoding ◽  
Α Subunit ◽  
Mining Sites

ABSTRACT Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. Of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, we focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the ammonia oxidizers that are members of the beta subgroup of the Proteobacteria (β-subgroup ammonia oxidizers). In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH3 and NH4 + levels in soil samples. The gene encoding the α-subunit of ammonia monooxygenase (amoA) was selected as a functional molecular marker for the β-subgroup ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of ammonia oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from culturedNitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of β-subgroup ammonia oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of β-subgroup ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, ammonia began to accumulate in metal-treated soils toward the end of the experiment.

scholarly journals Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
A. E. Bernhard ◽  
J. Beltz ◽  
A. E. Giblin ◽  
B. J. Roberts
Keyword(s):  
Gulf Of Mexico ◽  
New England ◽  
Salt Marshes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Biogeographic Patterns ◽  
Potential Nitrification

AbstractFew studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.

scholarly journals Molecular Analysis of Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in Compost and Composted Materials

1999 ◽  
Vol 65 (2) ◽  
pp. 396-403 ◽  
Author(s):  
George A. Kowalchuk ◽  
Zinaida S. Naoumenko ◽  
Piet J. L. Derikx ◽  
Andreas Felske ◽  
John R. Stephen ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Transformations ◽  
Rt Pcr ◽  
Gene Encoding ◽  
Specific Pcr ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
Almost All

ABSTRACT Although the practice of composting animal wastes for use as biofertilizers has increased in recent years, little is known about the microorganisms responsible for the nitrogen transformations which occur in compost and during the composting process. Ammonia is the principle available nitrogenous compound in composting material, and the conversion of this compound to nitrite in the environment by chemolithotrophic ammonia-oxidizing bacteria is an essential step in nitrogen cycling. Therefore, the distribution of ammonia-oxidizing members of the β subdivision of the class Proteobacteriain a variety of composting materials was assessed by amplifying 16S ribosomal DNA (rDNA) and 16S rRNA by PCR and reverse transcriptase PCR (RT-PCR), respectively. The PCR and RT-PCR products were separated by denaturing gradient gel electrophoresis (DGGE) and were identified by hybridization with a hierarchical set of oligonucleotide probes designed to detect ammonia oxidizer-like sequence clusters in the genera Nitrosospira and Nitrosomonas. Ammonia oxidizer-like 16S rDNA was detected in almost all of the materials tested, including industrial and experimental composts, manure, and commercial biofertilizers. A comparison of the DGGE and hybridization results after specific PCR and RT-PCR suggested that not all of the different ammonia oxidizer groups detected in compost are equally active. amoA, the gene encoding the active-site-containing subunit of ammonia monooxygenase, was also targeted by PCR, and template concentrations were estimated by competitive PCR. Detection of ammonia-oxidizing bacteria in the composts tested suggested that such materials may not be biologically inert with respect to nitrification and that the fate of nitrogen during composting and compost storage may be affected by the presence of these organisms.

scholarly journals Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment

2010 ◽  
Vol 76 (22) ◽  
pp. 7626-7634 ◽  
Author(s):  
Nejc Stopnišek ◽  
Cécile Gubry-Rangin ◽  
Špela Höfferle ◽  
Graeme W. Nicol ◽  
Ines Mandič-Mulec ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Inorganic Nitrogen ◽  
Peat Soil ◽  
Selective Advantage ◽  
Ammonia Oxidizer ◽  
Ammonium Concentration ◽  
Rrna Gene ◽  
Ammonia Oxidizers ◽  
Ammonia Release

ABSTRACT Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and “deep peat” lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.

scholarly journals Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean

2000 ◽  
Vol 66 (5) ◽  
pp. 1960-1969 ◽  
Author(s):  
Nasreen Bano ◽  
James T. Hollibaugh
Keyword(s):  
Arctic Ocean ◽  
16S Rrna Genes ◽  
The Arctic ◽  
Rrna Genes ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Major Band ◽  
Pcr Product ◽  
The Arctic Ocean

ABSTRACT The spatial distribution and diversity of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria(hereinafter referred to as ammonia oxidizers) in the Arctic Ocean were determined. The presence of ammonia oxidizers was detected by PCR amplification of 16S rRNA genes using a primer set specific for this group of organisms (nitA and nitB, which amplifies a 1.1-kb fragment between positions 137 and 1234, corresponding to Escherichia coli 16S rDNA numbering). We analyzed 246 samples collected from the upper water column (5 to 235 m) during March and April 1995, September and October 1996, and September 1997. Ammonia oxidizers were detected in 25% of the samples from 5 m, 80% of the samples from 55 m, 88% of the samples from 133 m, and 50% of the samples from 235 m. Analysis of nitA-nitB PCR product by nested PCR-denaturing gradient gel electrophoresis (DGGE) showed that all positive samples contained the same major band (band A), indicating the presence of a dominant, ubiquitous ammonia oxidizer in the Arctic Ocean basin. Twenty-two percent of the samples contained additional major bands. These samples were restricted to the Chukchi Sea shelf break, the Chukchi cap, and the Canada basin; areas likely influenced by Pacific inflow. The nucleotide sequence of the 1.1-kb nitA-nitB PCR product from a sample that contained only band A grouped with sequences designated group 1 marine Nitrosospira-like sequences. PCR-DGGE analysis of 122 clones from four libraries revealed that 67 to 71% of the inserts contained sequences with the same mobility as band A. Nucleotide sequences (1.1 kb) of another distinct group of clones, found only in 1995 samples (25%), fell into the group 5 marineNitrosomonas-like sequences. Our results suggest that the Arctic Ocean β-proteobacterial ammonia oxidizers have low diversity and are dominated by marine Nitrosospira-like organisms. Diversity appears to be higher in Western Arctic Ocean regions influenced by inflow from the Pacific Ocean through the Bering and Chukchi seas.

scholarly journals Community Structure of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria in Soil Treated with the Insecticide Imidacloprid

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Mariusz Cycoń ◽  
Zofia Piotrowska-Seget
Keyword(s):  
Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Wiener Index ◽  
Nitrification Rate ◽  
Ammonia Oxidizing Bacteria ◽  
Community Members ◽  
Insecticide Treatment ◽  
Soil Nitrification ◽  
Ammonia Oxidizing Archaea ◽  
Gradient Gel Electrophoresis

The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the10*FRdosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of theSandHvalues in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of theSandHvalues was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4+, known as the most important factor which determines the contribution of these microorganisms to soil nitrification.

Numbers, activities, and diversity of autotrophic ammonia-oxidizing bacteria in a freshwater, eutrophic lake sediment

1991 ◽  
Vol 37 (11) ◽  
pp. 828-833 ◽  
Author(s):  
W. T. Smorczewski ◽  
E. L. Schmidt
Keyword(s):  
Lake Sediment ◽  
Environmental Changes ◽  
Ammonia Oxidation ◽  
Eutrophic Lake ◽  
Ammonia Oxidizer ◽  
Most Probable Number ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Probable Number ◽  
Nitrite Oxidizers

The microbiological and chemical potential for ammonia oxidation in a freshwater, eutrophic lake sediment was examined in relation to environmental changes caused by seasonal, dimictic circulation. Poulations of both ammonia and nitrite oxidizers as estimated by most probable number (MPN) were sustained throughout extended anaerobic summer intervals, with nitrite oxidizers outnumbering ammonia oxidizers by a factor ranging from 3.0 to 8.1. Ammonia oxidation potential on a per cell basis was affected by seasonal changes and was seen to decrease as oxygen was removed from the sediments. Pure-culture isolations from a positive MPN tube inoculated with oxygenated sediment and representing a single point in a seasonal cycle produced ammonia-oxidizing strains belonging to the genus Nitrosospira. These strains did not react with known ammonia-oxidizer serotypes and, therefore, extend the serological diversity of this group of bacteria. An immunofluorescence analysis of MPN tubes from sediment collected during a period of lake stratification revealed progressive changes in the diversity of the ammonia-oxidizer population. The genera Nitrosomonas, Nitrosolobus, and Nitrosospira, including the novel serotype of Nitrosospira isolated from the sediment a year earlier, were found to coexist in well-oxygenated sediment. This diversity was seen to disappear, with Nistrosomonas surviving, as anaerobic conditions persisted. Key words: ammonia oxidizers, lake sediments, nitrifiers, nitrification.

scholarly journals amoAGene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom

2014 ◽  
Vol 81 (1) ◽  
pp. 159-165 ◽  
Author(s):  
Jialin Li ◽  
David B. Nedwell ◽  
Jessica Beddow ◽  
Alex J. Dumbrell ◽  
Boyd A. McKew ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Dry Weight ◽  
Estuarine Sediments ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type ◽  
Gene Abundance ◽  
Nitrification Potential ◽  
Gradient Gel Electrophoresis ◽  
Colne Estuary

ABSTRACTNitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw]−1day−1in June, increasing to 37.4 μmol N gdw−1day−1in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw−1day−1in June, increasing to 11.7 μmol N gdw−1day−1in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOBamoAgene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally.Nitrosomonasspp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOAamoAgene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possiblyNitrosomonasspp.) were of major significance in nitrification.

scholarly journals Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

2021 ◽  
Author(s):  
Man-Young Jung ◽  
Christopher J. Sedlacek ◽  
K. Dimitri Kits ◽  
Anna J. Mueller ◽  
Sung-Keun Rhee ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Oxidation Kinetic ◽  
Ammonia Oxidizer ◽  
Substrate Affinity ◽  
Kinetic Properties ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Kinetic Measurements ◽  
Ammonia Oxidizing Archaea ◽  
Wide Range

AbstractNitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co- occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest substrate affinity of any characterized AOA, which are similar to previously determined affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values strongly supports the hypothesis that – like for AOB – ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

scholarly journals Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria

2021 ◽  
Author(s):  
Michelle M McKnight ◽  
Josh D Neufeld
Keyword(s):  
Microbial Communities ◽  
Ammonia Oxidation ◽  
16S Rrna Gene Sequencing ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ammonia Oxidizer ◽  
Future Research ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers

Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.

Sign in / Sign up

Export Citation Format

Share Document