Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci

<p>Abstract</p> <p>Background</p> <p>The soil fungus <it>Rhizoctonia solani </it>anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of <it>R. solani </it>AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of <it>R. solani </it>AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of <it>R. solani </it>AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of <it>R. solani </it>AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89).</p> <p>Results</p> <p>Populations of <it>R. solani </it>AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of <it>R. solani </it>AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of <it>R. solani </it>AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Φ_{<it>ST </it>}= 0.257, significant at P < 0.05) but not for locus pP42F (Φ_{<it>ST </it>}= 0.034, not significant). Results based on NCA of the pP89 locus suggest that historical restricted gene flow is a plausible explanation for the geographical association of clades. Coalescent-based simulations of genealogical relationships between populations of <it>R. solani </it>AG-3 from potato and tobacco were used to estimate the amount and directionality of historical migration patterns in time, and the ages of mutations of populations. Low rates of historical movement of genes were observed between the potato and tobacco populations of <it>R. solani </it>AG-3.</p> <p>Conclusion</p> <p>The two sisters populations of the basidiomycete fungus <it>R. solani </it>AG-3 from potato and tobacco represent two genetically distinct and historically divergent lineages that have probably evolved within the range of their particular related Solanaceae hosts as sympatric species.</p

Soil Microbial Responses to Elevated CO2 and O3 in a Nitrogen-Aggrading Agroecosystem

Climate change factors such as elevated atmospheric carbon dioxide (CO2) and ozone (O3) can exert significant impacts on soil microbes and the ecosystem level processes they mediate. However, the underlying mechanisms by which soil microbes respond to these environmental changes remain poorly understood. The prevailing hypothesis, which states that CO2- or O3-induced changes in carbon (C) availability dominate microbial responses, is primarily based on results from nitrogen (N)-limiting forests and grasslands. It remains largely unexplored how soil microbes respond to elevated CO2 and O3 in N-rich or N-aggrading systems, which severely hinders our ability to predict the long-term soil C dynamics in agroecosystems. Using a long-term field study conducted in a no-till wheat-soybean rotation system with open-top chambers, we showed that elevated CO2 but not O3 had a potent influence on soil microbes. Elevated CO2 (1.5×ambient) significantly increased, while O3 (1.4×ambient) reduced, aboveground (and presumably belowground) plant residue C and N inputs to soil. However, only elevated CO2 significantly affected soil microbial biomass, activities (namely heterotrophic respiration) and community composition. The enhancement of microbial biomass and activities by elevated CO2 largely occurred in the third and fourth years of the experiment and coincided with increased soil N availability, likely due to CO2-stimulation of symbiotic N2 fixation in soybean. Fungal biomass and the fungi∶bacteria ratio decreased under both ambient and elevated CO2 by the third year and also coincided with increased soil N availability; but they were significantly higher under elevated than ambient CO2. These results suggest that more attention should be directed towards assessing the impact of N availability on microbial activities and decomposition in projections of soil organic C balance in N-rich systems under future CO2 scenarios

Genetic structure of populations of Rhizoctonia solani AG-3 on potato in eastern North Carolina

A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to identify and differentiate genotypes of Rhizoctonia solani anastomosis group 3 subgroup PT (AG-3 PT), a fungal pathogen of potato. Polymorphic co-dominant single-locus PCR-RFLP markers were identified after sequencing of clones from a genomic library and digestion with restriction enzymes. Multilocus genotypes were determined by a combination of PCR product and digestion with a specific restriction enzyme for each of seven loci. A sample of 104 isolates from one commercial field in each of five counties in eastern North Carolina was analyzed, and evidence for high levels of gene flow between populations was revealed. When data were clone-corrected and samples pooled into one single North Carolina population, random associations of alleles were found for all loci or pairs of loci, indicating random mating. However, when all genotypes were analyzed, the observed genotypic diversity deviated from panmixia and alleles within and between loci were not randomly associated. These findings support a model of population structure for R. solani AG-3 PT on potato that includes both recombination and clonality

Data from: Arbuscular mycorrhizal fungi increase organic carbon decomposition under elevated CO2

The extent to which terrestrial ecosystems can sequester carbon to mitigate climate change is a matter of debate. The stimulation of arbuscular mycorrhizal fungi (AMF) by elevated atmospheric carbon dioxide (CO2) has been assumed to be a major mechanism facilitating soil carbon sequestration by increasing carbon inputs to soil and by protecting organic carbon from decomposition via aggregation. We present evidence from four independent microcosm and field experiments demonstrating that CO2 enhancement of AMF results in considerable soil carbon losses. Our findings challenge the assumption that AMF protect against degradation of organic carbon in soil and raise questions about the current prediction of terrestrial ecosystem carbon balance under future climate-change scenarios

Impact of Clinical Factors on the Intestinal Microbiome in Infants With Gastroschisis

BACKGROUND: Infants with gastroschisis require operations and lengthy hospitalizations due to intestinal dysmotility. Dysbiosis may contribute to these problems. Little is known on the microbiome of gastroschisis infants. METHODS: The purpose of this study was to investigate the fecal microbiome in gastroschisis infants. Microbiome profiling was performed by sequencing the V4 region of the 16S rRNA gene. The microbiome of gastroschisis infants was compared to the microbiome of healthy controls, and the effects of mode of birth delivery, gestational age, antibiotic duration, and nutrition type on microbial composition and diversity were investigated. RESULTS: The microbiome of gastroschisis infants (n=13) was less diverse (Chao1, p < 0.001), lacked Bifidobacterium (p = 0.001) and had increased Staphylococcus (p = 0.007) compared to controls (n=83). Mode of delivery (R(2) = 0.04, p = 0.001), antibiotics duration greater than or equal to seven days (R(2) = 0.03, p = 0.003), age at sample collection (R(2) = 0.03, p = 0.009), and gestational age (R(2) = 0.02, p = 0.035) explained a small portion of microbiome variation. In gastroschisis infants, Escherichia-Shigella was the predominate genus, and those delivered via cesarean section had different microbial communities, predominantly Staphylococcus and Streptococcus, from those delivered vaginally. While antibiotic duration contributed to the variation in microbiome composition, there were no significant differences in taxa distribution or alpha diversity by antibiotic duration or nutrition type. CONCLUSION: The microbiome of gastroschisis infants is dysbiotic, and mode of birth delivery, antibiotic duration, and gestational age appear to contribute to microbial variation

Phylogeography of the Solanaceae-infecting Basidiomycota fungus AG-3 based on sequence analysis of two nuclear DNA loci-4

<p><b>Copyright information:</b></p><p>Taken from "Phylogeography of the Solanaceae-infecting Basidiomycota fungus AG-3 based on sequence analysis of two nuclear DNA loci"</p><p>http://www.biomedcentral.com/1471-2148/7/163</p><p>BMC Evolutionary Biology 2007;7():163-163.</p><p>Published online 13 Sep 2007</p><p>PMCID:PMC2048936.</p><p></p>correspondent to respective site numbers described in the additional files and . The inferred gene genealogies are based on 100,000 simulations of the coalescent with Waterston's estimates of Θ (M) = 2.57 for pP42F and 2.27 for pP89. The time scale is expressed in coalescent units of 4N (where N is the populations size). The letters below the tree designate the distinct haplotypes, their total or geographically distinct observed frequencies. Based on estimates of gene flow between the Northern US and Eastern NC populations from AG-3 PT (Table 2), the coalescent was inferred pooling the two populations of the pathogen for the pP42F locus