Rapid and specific method for evaluating Streptomyces competitive dynamics in complex soil communities

The Termite Fecal Nest: A Framework for the Opportunistic Acquisition of Beneficial Soil Streptomyces (Actinomycetales: Streptomycetaceae)

Mutualistic associations between insects and microorganisms must imply gains for both partners, and the emphasis has mostly focused on coevolved host-symbiont systems. However, some insect hosts may have evolved traits that allow for various means of association with opportunistic microbial communities, especially when the microbes are omnipresent in their environment. It was previously shown that colonies of the subterranean termite Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) build nests out of fecal material that host a community of Streptomyces Waksman and Henrici (Actinomycetales: Streptomycetaceae). These Actinobacteria produce an array of bioactive metabolites that provides a level of protection for termites against certain entomopathogenic fungi. How C. formosanus acquires and maintains this association remains unknown. This study shows that the majority of Streptomyces isolates found in field termite fecal nest materials are identical to Streptomyces isolates from soils surrounding the nests and are not vertically inherited. A survey of Streptomyces communities from C. formosanus fecal nest materials sampled at 20 locations around the world revealed that all nests are reliably associated with a diverse Streptomyces community. The C. formosanus fecal nest material therefore provides a nutritional framework that can recruit beneficial Streptomyces from the soil environment, in the absence of long-term coevolutionary processes. A diverse Streptomyces community is reliably present in soils, and subterranean termite colonies can acquire such facultative symbionts each social cycle into their fecal nest. This association probably emerged as an exaptation from the existing termite nest structure and benefits both the termite and the opportunistic colonizing bacteria.

Distribution, abundance and activity of geosmin and 2-methylisoborneol-producing Streptomyces in drinking water reservoirs

While cyanobacteria have been widely recognised as the most common cause of geosmin and 2-methylisoborneol related taste and odour (T&O) episodes in drinking water supplies, many reported occurrences could not be attributed to these organisms. The Streptomyces genus of soil bacteria also includes producers of these compounds, however their potential role in such occurrences is poorly understood and often disregarded on the basis that they are terrestrial rather than aquatic organisms, with their detection in water samples assumed to reflect the presence of dormant spores rather than metabolically active vegetative cells. Using qPCR and a differential cell lysis technique for DNA extraction, allowing distinction of spores from vegetative cells, the aim of this study was to determine the distribution, abundance and potential activity of Streptomyces species across a range of aquatic and marginal habitat zones in two drinking water reservoirs, including: exposed soil, submerged sediments, plant debris and emergent macrophytes at the margins; marginal and offshore surface waters; deep offshore waters; and offshore benthic sediments. Marginal substrates including soil, sediment and plant debris were identified as the dominant habitat zones for Streptomyces, (concentrations up to 1.1 × 10⁷ cells g^-1) supporting the concept of 'wash-in' from the margins due to run-off or water level rise following rainfall, as the likely pathway for Streptomyces induced T&O in reservoirs. However, vegetative cells were also found to comprise a substantial proportion of Streptomyces populations in the reservoir water mass itself (>90% in some surface and bottom water samples), suggesting the potential for these bacteria to be metabolically active in the water and therefore contribute to in situ production of T&O metabolites.

Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity

BACKGROUND

Host plant roots, mycorrhizal mycelium and microbes are important and potentially interacting factors shaping the performance of mycorrhization helper bacteria (MHB). We investigated the impact of a soil microbial community on the interaction between the extraradical mycelium of the ectomycorrhizal fungus Piloderma croceum and the MHB Streptomyces sp. AcH 505 in both the presence and the absence of pedunculate oak microcuttings.

RESULTS

Specific primers were designed to target the internal transcribed spacer of the rDNA and an intergenic region between two protein encoding genes of P. croceum and the intergenic region between the gyrA and gyrB genes of AcH 505. These primers were used to perform real-time PCR with DNA extracted from soil samples. With a sensitivity of 10 genome copies and a linear range of 6 orders of magnitude, these real-time PCR assays enabled the quantification of purified DNA from P. croceum and AcH 505, respectively. In soil microcosms, the fungal PCR signal was not affected by AcH 505 in the absence of the host plant. However, the fungal signal became weaker in the presence of the plant. This decrease was only observed in microbial filtrate amended microcosms. In contrast, the PCR signal of AcH 505 increased in the presence of P. croceum. The increase was not significant in sterile microcosms that contained plant roots.

CONCLUSIONS

Real-time quantitative PCR assays provide a method for directly detecting and quantifying MHB and mycorrhizal fungi in plant microcosms. Our study indicates that the presence of microorganisms and plant roots can both affect the nature of MHB-fungus interactions, and that mycorrhizal fungi may enhance MHB growth.

Pathogen variation and urea influence selection and success of Streptomyces mixtures in biological control

Success in biological control of plant diseases remains inconsistent in the field. A collection of well-characterized Streptomyces antagonists (n = 19 isolates) was tested for their capacities to inhibit pathogenic Streptomyces scabies (n = 15 isolates). There was significant variation among antagonists in ability to inhibit pathogen isolates and among pathogens in their susceptibility to inhibition. Only one antagonist could inhibit all pathogens, and antagonist-pathogen interactions were highly specific, highlighting the limitations of single-strain inoculum in biological control. However, the collection of pathogens could be inhibited by several combinations of antagonists, suggesting the potential for successful antagonist mixtures. Urea generally increased effectiveness of antagonists at inhibiting pathogens in vitro (increased mean inhibition zones) but its specific effects varied among antagonist-pathogen combinations. In greenhouse trials, urea enhanced the effectiveness of antagonist mixtures relative to individual antagonists in controlling potato scab. Although antagonist mixtures were frequently antagonistic in the absence of urea, all n= 2 and n = 3 antagonist-isolate combinations were synergistic in the presence of urea. This work provides insights into the efficacy of single- versus multiple-strain inocula in biological control and on the potential for nutrients to influence mixture success.

Effects of plant host species and plant community richness on streptomycete community structure

We investigated soil streptomycete communities associated with four host plant species (two warm season C4 grasses: Andropogon gerardii, Schizachyrium scoparium and two legumes: Lespedeza capitata, Lupinus perennis), grown in plant communities varying in species richness. We used actinobacteria-selective PCR coupled with pyrosequencing to characterize streptomycete community composition and structure. The greatest pairwise distances between communities were observed in contrasts between monocultures of different plant species, indicating that plant species exert distinct selective effects on soil streptomycete populations. Increasing plant richness altered the composition and structure of streptomycete communities associated with each host plant species. Significant relationships between plant community characteristics, soil edaphic characteristics, and streptomycete community structure suggest that host plant effects on soil microbial communities may be mediated through changes to the soil environment. Co-occurring streptomycete taxa also shared consistent relationships with soil edaphic properties, providing further indication of the importance of habitat preference for taxon occurrence. Physical distance between sampling points had a significant influence on streptomycete community similarity. This work provides a detailed characterization of soil streptomycete populations across a field scale and in relation to plant host identity and plant community richness.

Implications of pyrosequencing error correction for biological data interpretation

There has been a rapid proliferation of approaches for processing and manipulating second generation DNA sequence data. However, users are often left with uncertainties about how the choice of processing methods may impact biological interpretation of data. In this report, we probe differences in output between two different processing pipelines: a de-noising approach using the AmpliconNoise algorithm for error correction, and a standard approach using quality filtering and preclustering to reduce error. There was a large overlap in reads culled by each method, although AmpliconNoise removed a greater net number of reads. Most OTUs produced by one method had a clearly corresponding partner in the other. Although each method resulted in OTUs consisting entirely of reads that were culled by the other method, there were many more such OTUs formed in the standard pipeline. Total OTU richness was reduced by AmpliconNoise processing, but per-sample OTU richness, diversity and evenness were increased. Increases in per-sample richness and diversity may be a result of AmpliconNoise processing producing a more even OTU rank-abundance distribution. Because communities were randomly subsampled to equalize sample size across communities, and because rare sequence variants are less likely to be selected during subsampling, fewer OTUs were lost from individual communities when subsampling AmpliconNoise-processed data. In contrast to taxon-based diversity estimates, phylogenetic diversity was reduced even on a per-sample basis by de-noising, and samples switched widely in diversity rankings. This work illustrates the significant impacts of processing pipelines on the biological interpretations that can be made from pyrosequencing surveys. This study provides important cautions for analyses of contemporary data, for requisite data archiving (processed vs. non-processed data), and for drawing comparisons among studies performed using distinct data processing pipelines.

Diversity analysis of streptomycetes and associated phosphotranspherase genes in soil

An attempt was made to verify the observation that Streptomyces griseus was prevalent in soil based on isolation work. A genus-specific PCR was developed for Streptomyces based on the housekeeping gene atpD and used to investigate species diversity within selected soils. The presence of S. griseus was investigated to determine coexistence of resistance-only streptomycin phosphotransferase (strA) in the same soil as streptomycin producers. Two additional PCR-based assays were developed; one specific for strA in association with production, the other for more diverse strA and other related phosphotranferases. Both the S. griseus atpD and strA genes were below the PCR detection limit in all soils examined. A number of more diverse phosphotransferase genes were amplified, a minority of which may be associated with streptomycin production. We conclude that neither streptomycin producers nor S. griseus are prevalent in the fresh or chitin and starch-amended soils examined (less than 0.1% of soil actinobacteria). One of the soil sites had received plantomycin (active ingredient: streptomycin) and diversity studies suggested that this altered the streptomycete populations present in the soil.

Quantification of Frankia in soils using SYBR Green based qPCR

A SYBR Green based qPCR method was developed for the quantification of clusters 1 and 3 of the actinomycete Frankia in soils. Primer nifHr158 was designed to be used as reverse primer in combination with forward primer nifHf1 specifically amplifying a 191-bp fragment of the nifH gene of these Frankia. The primer combination was tested for specificity on selected pure cultures, and by comparative sequence analyses of randomly selected clones of a clone library generated with these primers from soil DNA extracts. After adjustments of DNA extraction conditions, and the determination of extraction efficiencies used for sample normalization, copy numbers of nifH genes representing Frankia of clusters 1 and 3 were quantified in different mineral soils, resulting in cell density estimates for these Frankia of up to 10(6) cells [g soil {dry weight}](-1) depending on the soil. Despite indications that the nifH gene is not a perfect target for the quantification of Frankia, the qPCR method described here provides a new tool for the quantification and thus a more complete examination of the ecology of Frankia in soils.

Rapid discrimination of potato scab-causing Streptomyces species based on the RNase P RNA gene sequences

Scab disease significantly damages potatoes and other root crops. Some Streptomyces species have been reported as potato-scab pathogens. Identification of the phytopathogenic Streptomyces is mainly done on the basis of the 16S rRNA gene, but use of this gene has some limitations for discriminating these strains because they share high similarities of 16S rRNA gene sequences. We tested the RNase P RNA (rnpB) gene as a taxonomic marker to clarify the relationship among closely related scab-causing Streptomyces strains. The rnpB genes were analyzed for 41 strains including 9 isolates from Jeju, Korea. There were 4 highly variable regions including nucleotide gaps in the rnpB genes. Interspecies similarity of the rnpB gene in tested Streptomyces strains was lower than about 97%, while the intraspecies similarity was higher than about 98%. Phylogenetic analysis demonstrated that the rnpB tree has similar topology to the 16S rRNA gene tree, but produces a more divergent phyletic lineage. These results revealed that the rnpB gene could be used as a powerful taxonomic tool for rapid differentiation of closely related Streptomyces species. In addition, it was also suggested that the variable regions marked as α, β, γ, and δ in the rnpB gene could be useful markers for the detection of specific Streptomyces species.