Mat-forming ectomycorrhizal (EcM) fungi represent a prevalent constituent of many temperate forest ecosystems and create dramatic changes in soil structure and chemistry. EcM mat soil have been shown to have increased microbial respiration rates and have been hypothesized to harbor unique assemblages of fungi and bacteria. The objectives of this dissertation were to characterize and examine the fungal and bacterial communities associated with EcM mats in old-growth forests of the H.J. Andrews Experimental Forest located in the Oregon Cascades. Additionally, this work assessed the application of traditional, emerging, and novel molecular sampling techniques for determining microbial communities of environmental samples. This research investigated the microbial communities associated with two common EcM mat genera found in old-growth Douglas fir stands in the Pacific Northwest; Piloderma (Atheliales, Basidiomycota) and Ramaria (Gomphales, Basidiomycota). Soil samples were collected from Piloderma and Ramaria mats and surrounding non- mat soil for molecular analysis of nucleic acids. First, a comparative study was conducted to determine the most appropriate rDNA molecular sampling technique for microbial community characterization. Two next-generation sequencing methods, Roche 454 pyrosequencing and Illumina-based environmental sequencing, the latter developed by the author, were compared to a more traditional sequencing approach, i.e., Sanger sequencing of clone libraries. These findings informed the subsequent sampling of the fungal ITS and bacterial 16S rDNA fragment with 454 pyrosequencing to determine the microbial communities within mat and non-mat soils. Second, this work utilized a pyrosequencing approach to explore fungal community structure in EcM mat and non-mat soils. This work concluded that differences in microbial communities do exist between Piloderma mat, Ramaria mat, and non-mat soils, but the differences are largely quantitative with relatively few distinct taxonomic shifts in microbial constituents. Piloderma, Ramaria and Russula, in addition to being the dominant taxa found on mycorrhizal root tips, were found to be the most abundant taxa in bulk soils within their respective mat types or non-mat sample. The background fungal communities within the EcM mats in this study exhibited considerable taxonomic overlap with the exception of Piloderma vs. non-mat comparisons; Russula species dominated nonmat soils but tended to be excluded or significantly underrepresented in Piloderma mats. Lastly, this study explored the bacterial communities associated with Piloderma and Ramaria mats using lower- coverage 454-Jr pyrosequencing. Bacterial communities exhibited significant structure as a function of mat-type, soil horizon and pH, but this finding should be interpreted with respect to the nonrandom distribution of Piloderma-mats in the O- horizon and the Ramaria-mats in the A-horizon, and the tendancy for EcM mats to be more acidic than surrounding soils. Nonetheless, the total microbial (bacterial and fungal) community was typically dominated by the mat-forming taxa, or Russula, in the case of non-mat soils. While the presence of Piloderma mats did enrich or restrict some bacterial groups, soil pH was also found to be a significant driver of bacterial richness and taxonomic diversity. Fungal and bacterial richness were also found to be positively related to one another, regardless of soil horizon or EcM mat type. This work, taken together, contributes to the understanding of hyperdiversity and heterogeneity of microbial communities of temperate forest soils and highlights the potential for fungal and bacterial communities to be influenced by the presence of EcM mats. / Graduation date: 2012

[Truncated abstract] Recovery of soil nutrients, microbial populations and carbon (C) and nitrogen (N) cycling processes are critical to the success of rehabilitation following major ecosystem disturbance. Bauxite mining represents a major ecosystem disturbance to the jarrah (Eucalyptus marginata) forest in the south-west of Western Australia. Mining has created a mosaic of mined areas in various stages of succession surrounded by non-mined forest areas. Initial site preparations within rehabilitation areas such as contour ripping alter soil structure (creation of mound and furrows) and over time also influence the distribution of vegetation and litter. Current performance criteria developed by industry, government and other stakeholders have determined that before post-bauxite mined areas of jarrah forest can be integrated back into normal forest management practises they should be functional and demonstrate resilience to normal forest disturbances such as fire. Furthermore, resilience should be of a manner comparable to non-mined analogue forest sites. Currently little is known of the resilience of microbial communities and C and N cycling in rehabilitation sites to normal forest disturbances such as prescription burning. As such, before rehabilitated jarrah forests can be successfully integrated into broad scale forest management regimes, a more thorough knowledge of the potential impacts of burning practises on the soil microbial community and C and N cycling processes in these systems is required. ... While there are similar rates of C and N cycling the underlying microbial community structure was distinctly different; implying a high degree of functional redundancy with respect to C and N cycling. Differences in the C and N cycling and structure of the microbial communities were likely to be due to differences in soil environmental conditions (i.e. soil alkalinity/acidity, soil moisture) and C substrate availability which influence the physiological status of the microbial community and in turn are related to successional age of the forests. Results also suggest that the measurement of CLPP can be a useful approach for assessment of changes in the functional ability of microbial communities. However, the interpretation of how well these rehabilitation forests have recovered heterotrophic abilities was greatly affected by the methodological approach used (e.g. MicroRespTM or Degens and Harris, 1997). Importantly, results from Chapter 4 and 5 suggested that the effects of a moderate prescription fire on C and N processes, CLPP and microbial community structure of 18 year old rehabilitation forests are likely to be short-lived (< 2 years). Furthermore, the effects of the moderate spring prescription fire were not large enough to decouple C and N cycling processes over the short-term (< 1 years) which suggests that by 18 years of age rehabilitation forests demonstrate comparable functional resilience to a moderate prescription burn.

MESHWR / Department of Hydrology and Water Resources / See the attached abstract below

Indiana University-Purdue University Indianapolis (IUPUI) / Organic-rich substrates such as soil provide an excellent carbon source for bacteria. However, hydrocarbons such as those found in various ignitable liquids can also serve as a source of carbon to support bacterial growth. This is problematic for fire debris analysis as samples may be stored at room temperature for extended periods before they are analyzed due to case backlog. As a result, selective loss of key components due to bacterial metabolism can make identifying and classifying ignitable liquid residues by their chemical composition and boiling point range very difficult. The ultimate goal of this project is to preserve ignitable liquid residues against microbial degradation as efficiently and quickly as possible. Field and laboratory studies were conducted to monitor microbial degradation of gasoline and other ignitable liquids in soil samples. In addition to monitoring degradation in potting soil, as a worst case scenario, the effect of soil type and season were also studied. The effect of microbial action was also compared to the effect of weathering by evaporation (under nitrogen in the laboratory and by the passive headspace analysis of the glass fragments from the incendiary devices in the field studies). All studies showed that microbial degradation resulted in the significant loss of n-alkanes and lesser substituted alkylbenzenes predominantly and quickly, while more highly substituted alkanes and aromatics were not significantly affected. Additionally, the residential soil during the fall season showed the most significant loss of these compounds over the course of 30 days. To combat this problem, a chemical solution is to be immediately applied to the samples as they are collected. Various household and commercial products were tested for their efficacy at low concentrations to eliminate all living bacteria in the soil. Triclosan (2% (w/v) in NaOH) proved to be the most effective at preserving ignitable liquid residues for at least 30 days.