Effects of swine manure fertilization on autotrophic ammonia oxidizing bacteria in soil

Ceccherini, Maria Teresa; Castaldini, M.; Piovanelli, C.; Hastings, Richard; McCarthy, Alan J.; Bazzicalupo, Marco; Miclaus, N.

doi:10.1016/s0929-1393(97)00034-6

Cited by 26 publications

(9 citation statements)

References 24 publications

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“…Data are, however, subject to biases associated with molecular techniques and the choice of appropriate primers. Nitrification potential decreased with depth at the unpolluted LA site, but not at the polluted HA site, suggesting an effect of ammonium concentration, as observed previously (Ceccherini et al, 1998;Mendum et al, 1999;Petersen et al, 2003;Chu et al, 2007), and a potential effect on total ammonia oxidizer abundance. Greater nitrification potential may also reflect greater specific activity, but other environmental factors important in nitrification (temperature, pH) were similar at both sites and the major difference was the ammonium supply rate.…”

Section: Ammonia Oxidizer Activity and Abundancesupporting

confidence: 73%

Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile

Höfferle

Nicol

Pal

et al. 2010

FEMS Microbiology Ecology

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Oxidation of ammonia, the first step in nitrification, is carried out in soil by bacterial and archaeal ammonia oxidizers and recent studies suggest possible selection for the latter in low-ammonium environments. In this study, we investigated the selection of ammonia-oxidizing archaea and bacteria in wetland soil vertical profiles at two sites differing in terms of the ammonium supply rate, but not significantly in terms of the groundwater level. One site received ammonium through decomposition of organic matter, while the second, polluted site received a greater supply, through constant leakage of an underground septic tank. Soil nitrification potential was significantly greater at the polluted site. Quantification of amoA genes demonstrated greater abundance of bacterial than archaeal amoA genes throughout the soil profile at the polluted site, whereas bacterial amoA genes at the unpolluted site were below the detection limit. At both sites, archaeal, but not the bacterial community structure was clearly stratified with depth, with regard to the soil redox potential imposed by groundwater level. However, depth-related changes in the archaeal community structure may also be associated with physiological functions other than ammonia oxidation.

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Section: Ammonia Oxidizer Activity and Abundancesupporting

confidence: 73%

Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile

Höfferle

Nicol

Pal

et al. 2010

FEMS Microbiology Ecology

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“…However, our results suggest that changes in nitrification enzyme activity could be partly due to changes in the composition of the ammonia-oxidizing community. Such concurrent changes in the activity and genetic structure of the ammonia-oxidizing community have been reported in response to application of swine manure to soils (Ceccherini et al 1998). In contrast, Avrahami et al (2002) observed increased nitrification activity after ammonium addition to soil without any changes in the community structure of ammonium oxidizers.…”

Section: Grazing Induces Changes In Microbial Community Composition Amentioning

confidence: 55%

Effects of Grazing on Microbial Functional Groups Involved in Soil N Dynamics

Patra

Abbadie

Clays-Josserand

et al. 2005

Ecological Monographs

224

144

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Enhancement of soil nitrogen (N) cycling by grazing has been observed in many grassland ecosystems. However, whether grazing affects the activity only of the key microbial functional groups driving soil N dynamics or also affects the size (cell number) and/or composition of these groups remains largely unknown. We studied the enzyme activity, size, and composition of five soil microbial communities (total microbial and total bacterial communities, and three functional groups driving N dynamics: nitrifiers, denitrifiers, and free N2 fixers) in grassland sites experiencing contrasting sheep grazing regimes (one light grazing [LG] site and one intensive grazing [IG] site) at two topographical locations. Enzyme activity was determined by potential carbon mineralization, nitrification, denitrification, and N2 fixation assays. The size of each community (except N2 fixers) was measured by the most‐probable‐number technique. The composition of the total soil microbial community was characterized by phospholipid fatty acid analysis (PLFA), and the genetic structure of the total bacterial community was assessed by ribosomal intergenic spacer analysis. The genetic structures of the ammonia‐oxidizing, nitrate‐reducing, and N2‐fixing communities were characterized by polymerase chain reaction and restriction fragment length polymorphism (PCR‐RFLP) or by polymerase chain reaction and denaturing gradient gel electrophoresis (PCR‐DGGE) targeting group‐specific genes. Greater enzyme activities, particularly for nitrification, were observed in IG than in LG sites at both topographical locations. The numbers of heterotrophs, nitrifiers, and denitrifiers were higher in IG than in LG sites at both topographical locations. The amplitude of changes in community size was higher than that of community enzyme activity. Phospholipid and nucleic acid analyses showed that the composition/structure of all the communities, except nitrate reducers, differed between IG and LG sites at both locations. For each community, changes in activity were correlated with changes in the occurrence of a few individual PLFAs or DNA fragments. Our results thus indicate that grazing enhances the activity of soil microbial communities but also concurrently induces changes in the size and composition/structure of these communities on the sites studied. Although the generality of our conclusions should be tested in other systems, these results are of major importance for predicting the effects of future disturbances or changed grazing regimes on the functioning of grazed ecosystems.

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“…In studies of Italian agricultural plots, Hastings et al (64) and Ceccherini et al (35) detected both Nitrosospira-and Nitrosomonas-like sequences in plots fertilized with swine manure yet only detected Nitrosospira-like sequences in nonfertilized plots. Although the nucleotide sequences of recovered DNA fragments were not determined, these results seem to support the more traditional idea that high-ammonia conditions stimulate nitrosomonad populations (18).…”

Section: The Characterization Of Ammonia-oxidizing Bacteria In the Enmentioning

confidence: 99%

“…Recovery of sequence information from such phylogenetic gaps can lead to probe refinement, as has been the case for probes targeting AOB (122). In cases where AOB do not represent a large proportion of the total microbial community, it has been necessary to introduce PCR amplification steps into hybridization strategies (35). Although addition of PCR step(s) prior to hybridization can increase the sensitivity of slot-blot hybridization assays, this also compromises the ability to obtain quantitative results.…”

Section: Development Of Phylogenetically Based Primers and Probesmentioning

confidence: 99%

Ammonia-Oxidizing Bacteria: A Model for Molecular Microbial Ecology

Kowalchuk

Stephen²

2001

Annu. Rev. Microbiol.

1,150

725

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The eutrophication of many ecosystems in recent decades has led to an increased interest in the ecology of nitrogen transformation. Chemolitho-autotrophic ammonia-oxidizing bacteria are responsible for the rate-limiting step of nitrification in a wide variety of environments, making them important in the global cycling of nitrogen. These organisms are unique in their ability to use the conversion of ammonia to nitrite as their sole energy source. Because of the importance of this functional group of bacteria, understanding of their ecology and physiology has become a subject of intense research over recent years. The monophyletic nature of these bacteria in terrestrial environments has facilitated molecular biological approaches in studying their ecology, and progress in this field has been rapid. The ammonia-oxidizing bacteria of the beta-subclass Proteobacteria have become somewhat of a model system within molecular microbial ecology, and this chapter reviews recent progress in our knowledge of their distribution, diversity, and ecology.

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Effects of swine manure fertilization on autotrophic ammonia oxidizing bacteria in soil

Cited by 26 publications

References 24 publications

Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile

Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile

Effects of Grazing on Microbial Functional Groups Involved in Soil N Dynamics

Ammonia-Oxidizing Bacteria: A Model for Molecular Microbial Ecology

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