We characterised the spatial structure of soil microbial communities in an unimproved grazed upland grassland in the Scottish Borders. A range of soil chemical parameters, cultivable microbes, protozoa, nematodes, phospholipid fatty acid (PLFA) profiles, community-level physiological profiles (CLPP), intra-radical arbuscular mycorrhizal community structure, and eubacterial, actinomycete, pseudomonad and ammonia-oxidiser 16S rRNA gene profiles, assessed by denaturing gradient gel electrophoresis (DGGE) were quantified. The botanical composition of the vegetation associated with each soil sample was also determined. Geostatistical analysis of the data revealed a gamut of spatial dependency with diverse semivariograms being apparent, ranging from pure nugget, linear and non-linear forms. Spatial autocorrelation generally accounted for 40-60% of the total variance of those properties where such autocorrelation was apparent, but accounted for 97% in the case of nitrate-N. Geostatistical ranges extending from approximately 0.6-6 m were detected, dispersed throughout both chemical and biological properties. CLPP data tended to be associated with ranges greater than 4.5 m. There was no relationship between physical distance in the field and genetic similarity based on DGGE profiles. However, analysis of samples taken as close as 1 cm apart within a subset of cores suggested some spatial dependency in community DNA-DGGE parameters below an 8 cm scale. Spatial correlation between the properties was generally weak, with some exceptions such as between microbial biomass C and total N and C. There was evidence for scale-dependence in the relationships between properties. PLFA and CLPP profiling showed some association with vegetation composition, but DGGE profiling did not. There was considerably stronger association between notional sheep urine patches, denoted by soil nutrient status, and many of the properties. These data demonstrate extreme spatial variation in community-level microbiological properties in upland grasslands, and that despite considerable numeric ranges in the majority of properties, overarching controlling factors were not apparent.
To assess links between the diversity of nitrite-oxidizing bacteria (NOB) in agricultural grassland soils and inorganic N fertilizer management, NOB communities in fertilized and unfertilized soils were characterized by analysis of clone libraries and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Previously uncharacterized Nitrospira-like sequences were isolated from both long-term-fertilized and unfertilized soils, but DGGE migration patterns indicated the presence of additional sequence types in the fertilized soils. Detailed phylogenetic analysis of Nitrospira-like sequences suggests the existence of one newly described evolutionary group and of subclusters within previously described sublineages, potentially representing different ecotypes; the new group may represent a lineage of noncharacterized Nitrospira species. Clone libraries of Nitrobacter-like sequences generated from soils under different long-term N management regimes were dominated by sequences with high similarity to the rhizoplane isolate Nitrobacter sp. strain PJN1. However, the diversity of Nitrobacter communities did not differ significantly between the two soil types. This is the first cultivation-independent study of nitrite-oxidizing bacteria in soil demonstrating that nitrogen management practices influence the diversity of this bacterial functional group.Nitrogen fertilization is the most important management strategy for the improvement of agricultural crops. However, up to 60% of N fertilizer applied can be lost through leaching of mobile N compounds (NO 3 Ϫ ) and transformation into N 2 O and N 2 (53), leading to water pollution and contributing to global warming. The key process during natural N cycling is microbial chemolithoautotrophic nitrification, the conversion of NH 4 ϩ to NO 3 Ϫ via NO 2 Ϫ . Autotrophic nitrification is carried out by two distinct groups, ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), and it is generally assumed that the first step is rate-limiting (50). This assumption is based mainly on observations that NO 2 Ϫ concentrations are low or negligible in most natural systems. Consequently, with the exception of high-N-load sewage-processing systems, where nitrite concentrations are high (NO 2 Ϫ -N up to 70 mg liter Ϫ1 ) (17, 22) and nitrite washout is of concern (41, 63), research into community composition, activity, and environmental responses of nitrifying bacteria has focused on AOB (37). These studies have demonstrated the influence of land use management regimes on the diversity and activity of AOB, as well as links to changes in ammonia oxidation rates (4, 9, 11, 49, 70), but a comprehensive understanding of soil nitrification also requires characterization of NOB.Analysis of NOB in natural environments has been limited by reliance on traditional, cultivation-based methods. In contrast to AOB, for which most 16S rRNA gene sequences of cultured organisms and related environmental clones fall within a monophyletic group (51, 66), NOB are classified into...
This study reports on the attachment preference of a faecally derived bacterium, Escherichia coli, to soil particles of defined size fractions. In a batch sorption experiment using a clay loam soil it was found that 35% of introduced E. coli cells were associated with soil particulates >2 μm diameter. Of this 35%, most of the E. coli (14%) were found to be associated with the size fraction 15-4 μm. This was attributed to the larger number of particles within this size range and its consequently greater surface area available for attachment. When results were normalised with respect to estimates of the surface area available for bacterial cell attachment to each size fraction, it was found that E. coli preferentially attached to those soil particles within the size range 30-16 μm. For soil particles >2 μm, E. coli showed at least 3.9 times more preference to associate with the 30-16 μm than any other fraction. We report that E.coli can associate with different soil particle size fractions in varying proportions and that this is likely to impact on the hydrological transfer of cells through soil and have clear implications for our wider understanding of the attachment dynamics of faecally derived bacteria in soils of different compositions.
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