A loamy sand soil sampled from a species-rich permanent grassland at a long-term experimental site (Wildekamp, Bennekom, The Netherlands) was used to construct soil microcosms in which the microbial community compositions had been modified by fumigation at different intensities (depths). As expected, increasing depth of fumigation was shown to result in progressively increasing effects on the microbiological soil parameters, as determined by cultivation-based as well as cultivation-independent (PCR-DGGE, PLFA) methods. Both at 7 and at 60 days after fumigation, shifts in the bacterial, fungal and protozoan communities were noted, indicating that altered community compositions had emerged following a transition phase. At the level of bacteria culturable on plates, an increase of the prevalence of bacterial r-strategists was noted at 7 days followed by a decline at 60 days, which also hinted at the effectiveness of the fumigation treatments. The survival of a non-toxigenic Escherichia coli O157:H7 derivative, strain T, was then assessed over 60 days in these microcosms, using detection via colony forming units counts as well as via PCR-DGGE. Both data sets were consistent with each other. Thus, a clear effect of fumigation depth on the survival of the invading strain T was noted, as a progressive increase of depth coincided with a progressively enhanced inoculant survival rate. As fumigation depth was presumably inversely related to community complexity, this was consistent with the hypothesis that soil systems with reduced biological complexity offer enhanced opportunities for invading microbial species to establish and persist. The significance of this finding is discussed in the light of the ongoing discussion about the complexity-invasiveness relationship within microbial communities, in particular regarding the opportunities of pathogens to persist.

Four extraction methods, including a novel one, were compared for their efficiencies in producing DNA from three contrasting agricultural soils. Molecular analyses (PCR-denaturing gradient gel electrophoresis [DGGE] and clone libraries) focusing on different microbial groups were used as assessment criteria. Per soil, the DNA yields differed between extraction methods. Clear effects of method on apparent richness and community structure were found. Actinobacterial diversity based on soil DNA produced by two divergent methods revealed that a hitherto-undescribed group was obtained by the novel method.

Actinobacteria are major producers of secondary metabolites; however, it is unclear how they are distributed in the environment. DNA was extracted from forest, pasture and cultivated soils, street sediments (dust and material in place), and sediments affected by animal activity (e.g. guano, vermicompost) and characterised with two actinobacterial and a bacterial-specific 16S rDNA primer set. Amplicons (140/156) generated with the two actinobacterial-specific and amplicons (471) generated with bacterial-specific primers were analysed. Amplicons from actinobacterial-specific primer were disproportionately actinomycetal from animal-affected (soil) samples and street sediments and either verrucomicrobial (i.e. non-actinobacterial) and from a novel non-actinomycetal actinobacterial group for soils. Actinobacterial amplified ribosomal DNA restriction analysis and terminal restriction fragment length polymorphism fingerprints clustered by land use, with cultivated soils clustering apart from uncultivated soils. Actinobacterial amplicons generated with eubacterial primers were overwhelmingly from (116/126) street sediments; acidobacterial amplicons from soils (74/75). In two street samples, >90% of clones were actinomycetal. Actinomycetes are selected in terrestrial soils and sediments by cultivation, urbanisation and animal activity.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-010-9752-0) contains supplementary material, which is available to authorized users.

Actinomycetes produce many pharmaceutically useful compounds through type I polyketide biosynthetic pathways. Soil has traditionally been an important source for these actinomycete-derived pharmaceuticals. As the rate of antibiotic discovery has decreased and the incidence of antibiotic resistance has increased, researchers have looked for alternatives to soil for bioprospecting. Street sediment, where actinomycetes make up a larger fraction of the bacterial population than in soil, is one such alternative environment. To determine if these differences in actinomycetal community structure are reflected in type I polyketide synthases (PKSI) distribution, environmental DNA from soils and street sediments was characterized by sequencing amplicons of PKSI-specific PCR primers. Amplicons covered two domains: the last 80 amino acids of the ketosynthase (KS) domain and the first 240 amino acids of the acyltransferase (AT) domain. One hundred and ninety clones from ten contrasting soils from six regions and nine street sediments from six cities were sequenced. Twenty-five clones from two earthworm-affected samples were also sequenced. UniFrac lineage-specific analysis identified two clades that clustered with actinomycetal GenBank matches that were street sediment-specific, one similar to the PKSI segment of the mycobactin siderophore involved in mycobacterial virulence. A clade of soil-specific sequences clustered with GenBank matches from the ambruticin and jerangolid pathways of Sorangium cellulosum. All three of these clades were found in sites >700 km apart. Street sediments are enriched in actinomycetal PKSIs. Non-actinomycetal PKSI pathways may be more chemically diverse than actinomycetal PKSIs. Common soil and street sediment PKIs are globally distributed.