With recent methodological advances, molecular markers are increasingly used for semi‐quantitative analyses of fungal communities. The aim to preserve quantitative relationships between genotypes through PCR places new demands on primers to accurately match target sites and provide short amplicons. The internal transcribed spacer (ITS) region of the ribosome encoding genes is a commonly used marker for many fungal groups. Here, we describe three new primers – fITS7, gITS7 and fITS9, which may be used to amplify the fungal ITS2 region by targeting sites in the 5.8S encoding gene. We evaluated the primers and compared their performance with the commonly used ITS1f primer by 454‐sequencing of both artificially assembled templates and field samples. When the entire ITS region was amplified using the ITS1f/ITS4 primer combination, we found strong bias against species with longer amplicons. This problem could be overcome by using the new primers, which produce shorter amplicons and better preserve the quantitative composition of the template. In addition, the new primers yielded more diverse amplicon communities than the ITS1f primer.

Estimates suggest that only one-tenth of the true fungal diversity has been described. Among numerous fungal lineages known only from environmental DNA sequences, Soil Clone Group 1 is the most ubiquitous. These globally distributed fungi may dominate below-ground fungal communities, but their placement in the fungal tree of life has been uncertain. Here, we report cultures of this group and describe the class, Archaeorhizomycetes, phylogenetically placed within subphylum Taphrinomycotina in the Ascomycota. Archaeorhizomycetes comprises hundreds of cryptically reproducing filamentous species that do not form recognizable mycorrhizal structures and have saprotrophic potential, yet are omnipresent in roots and rhizosphere soil and show ecosystem and host root habitat specificity.

Climate change impacts on soil microbial communities could alter the structure of terrestrial ecosystems and biogeochemical cycles of the Earth. We used 16S rRNA gene microarrays to evaluate changes in the composition of grassland soil microbial communities under rainfall amendments simulating alternative climate change scenarios, and to compare these to responses of overlying plants and invertebrates. Following 5 years of rainfall manipulation, soil bacteria and archaea in plots where natural rain was supplemented differed little from ambient controls, despite profound treatment-related changes in the overlying grassland. During the sixth and seventh year, seasonal differences in bacterial and archaeal assemblages emerged among treatments, but only when watering exacerbated or alleviated periods of particularly aberrant conditions in the ambient climate. In contrast to effects on plants and invertebrates, effects on bacteria and archaea did not compound across seasons or years, indicating that soil microbial communities may be more robust than associated aboveground macroorganisms to certain alterations in climate.

gIn Mediterranean-type grassland ecosystems, the timing of rainfall events controls biogeochemical cycles, as well as the phenology and productivity of plants and animals. Here, we investigate the effect of short-term (days) soil environmental conditions on microbial community structure and composition during a natural wetting and drying cycle. Soil samples were collected from a meadow in Northern California at four time points after the first two rainfall events of the rainy season. We used 16S rRNA microarrays (PhyloChip) to track changes in bacterial and archaeal community composition. Microbial communities at time points 1 and 3 were significantly different than communities at time points 2 and 4. Based on ordination analysis, the available carbon, soil moisture, and temperature explained most of the variation in community structure. For the first time, a complementary and more comprehensive approach using linear regression and generalized logical networks were used to identify linear and nonlinear associations among environmental variables and with the relative abundance of subfamilies. Changes in soil moisture and available carbon were correlated with the relative abundance of many phyla. Only the phylum Actinobacteria showed a lineage-specific relationship to soil moisture but not to carbon or nitrogen. The results indicate that the use of a high taxonomic rank in correlations with nutritional indicators might obscure divergent subfamily-level responses to environmental parameters. An important implication of this research is that there is short-term variation in microbial community composition driven in part by rainfall fluctuation that may not be evident in long-term studies with coarser time resolution.