Degradation of Atrazine by White Rot and Soil Fungi

The widespread use of atrazine in agriculture has lead to an abundance of this toxic chemical in the environment. Fungi that have the ability to degrade atrazine into less toxic products have been identified and used in the remediation of atrazine. In this study atrazine degradation in a defined liquid media was characterized in a diverse group of white rot basidiomycete and deuteromycete soil fungi. Atrazine did not have an effect on fungal growth although each species produced a different amount of biomass in culture. Statistical analysis showed that biomass production was an important factor in determining the amount of atrazine removed. Two of the twelve fungal species tested, Armillaria gallica and Aspergillus niger, removed amounts of atrazine from culture. Analysis of high pressure liquid chromatography chromatograms did not show the production of atrazine degradation products in fungal cultures that could be differentiated from control chromatograms. Gas chromatography-mass spectrometry analysis of organic extracts of fungal cultures also indicated that no chlorinated atrazine metabolites were produced in any of the cultures although unidentified compounds were detected in Mycena leaiana, Aspergillus flavus, and Aspergillus niger cultures that may be hydroxylated atrazine metabolites. These data indi cate that atrazine degradation did not occur in most of the fungal cultures and although it may have occurred in Mycena leaiana, Aspergillus flavus, and/or Aspergillus niger, albeit at appreciable levels only in Aspergillus niger and Armillaria gallica. Removal of atrazine from Aspergillus niger and Armillaria gallica cultures might have been due to atrazine sequestration in fungal biomass although the culture conditions might not have been conducive to atrazine degradation

Mechanisms of decay and interspecific interactions of white and brown rot fungi

University of Minnesota Ph.D. dissertation.April 2018. Major: Bioproducts/Biosystems Science Engineering and Management. Advisor: Jonathan Schilling. 1 computer file (PDF); xiii, 195 pages.Wood is the largest source of biotic carbon on earth and the principle drivers of its decay are basidiomycete fungi. The biochemical mechanisms of wood decay by basidiomycete fungi are fundamental processes in forest ecosystems that dictate carbon evolution rates, soil organic matter deposition, and overall ecosystem function. These decay mechanisms are also unique in their ability to efficiently convert recalcitrant woody biomass to fermentable sugars and can serve as a biological template for industrial lignocellulose conversion to make renewable biofuels more economical. However, basidiomycete wood decay mechanisms are not fully understood and therefore not replicable in vitro, due in part to a lack of understanding of how decay mechanisms change throughout the progression of decay. In addition, gene transcripts and proteins used to facilitate decay are produced in concert with other biomolecules with non-degradative functions which makes resolution of degradative genes difficult. This dissertation contributes to resolving these problems by describing the temporal progression of decay among several species of wood-degrading basidiomycetes and functionally categorizing genes and secreted proteins involved in mediating interspecific interactions. This was done by first spatially resolving decay into a temporal sequence by growing model brown-rot fungi directionally on thin wood wafers. This system was used to co-localize changes in fungal physiology with chemical changes in wood substrates and the production of fungal metabolites to identify the functional significance of those physiological changes. The same wafer culture design was then used to resolve changes in fungal secretomes between two phylogenetically disparate brown-rot species over the course of decay using proteomics co-localized with lignocellulose-degrading enzyme assays. Interspecific differences were further investigated by comparing decay performance of the same two fungi on a Poales substrate, sorghum bagasse. Sorghum decay rates along with component removal and enzyme assays were monitored during decay to determine the genetic and biochemical basis of substrate preferences of the two species. Temporal alterations to fungal secretomes were compared among several model white and brown-rot fungi as well. Comparative proteomics concurrent with lignocellulose-degrading enzyme assays were used to identify common patterns among both rot types, as well as interspecific variability of decay mechanisms within species. Finally, changes in gene expression, protein secretion, and enzyme activity profiles in response to fungal competitors were described by modifying the thin wood wafer microcosms to incorporate two brown-rot species grown in opposition to one another. Resolution of decay into a sequence revealed a biphasic decay mechanism in brown-rot fungi delineated by early stage, non-hydrolytic pretreatment followed by later stage glycoside hydrolase-mediated saccharification. Proteomic investigation confirmed this pattern by showing later stage secretomes contain a greater proportion of glycoside hydrolases and their activities than earlier stages of decay. Brown-rot secretomes varied considerably by species as did their ability to degrade sorghum bagasse, likely due to a difference in the ability to hydrolyze ferulic acid esters present in sorghum biomass. Comparison of white and brown-rot secretomes identified a common segregation of decay into a biphasic decay mechanism characterized by high lignolysis, in white-rot fungi, upon wood colonization followed by later stage glycoside hydrolase secretion in both decay types. Considerable interspecific variability in decay mechanism within decay types was also detected, with the white-rot species producing different suites of ligninolytic enzymes and brown-rot species diverging in the types of glycoside hydrolases produced. Investigation of interspecific interactions identified several proteins exclusively produced during the interaction of two brown-rot species as well as identifying the general downregulation of lignocellulose-degrading genes during the interaction. In addition, comparative transcriptomics identified two different interaction strategies employed by species and implicates several secondary metabolite-synthesizing genes in facilitating interspecific interactions. Overall, this work contributes toward functional categorization of a wide range of basidiomycete proteins and provides a better understanding of decay mechanisms and interspecific interactions in these understudied organisms

Brown rot-type fungal decomposition of sorghum bagasse: variable success and mechanistic implications

Sweet sorghum is a promising crop for a warming, drying African climate, and basic information is lacking on conversion pathways for its lignocellulosic residues (bagasse). Brown rot wood-decomposer fungi use carbohydrate-selective pathways that, when assessed on sorghum, a grass substrate, can yield information relevant to both plant biomass conversion and fungal biology. In testing sorghum decomposition by brown rot fungi (Gloeophyllum trabeum, Serpula lacrymans), we found that G. trabeum readily degraded sorghum, removing xylan prior to removing glucan. Serpula lacrymans, conversely, caused little decomposition. Ergosterol (fungal biomarker) and protein levels were similar for both fungi, but S. lacrymans produced nearly 4x lower polysaccharide-degrading enzyme specific activity on sorghum than G. trabeum, perhaps a symptom of starvation. Linking this information to genome comparisons including other brown rot fungi known to have a similar issue regarding decomposing grasses (Postia placenta, Fomitopsis pinicola) suggested that a lack of CE 1 feruloyl esterases as well as low xylanase activity in S. lacrymans (3x lower than in G. trabeum) may hinder S. lacrymans, P. placenta, and F. pinicola when degrading grass substrates. These results indicate variability in brown rot mechanisms, which may stem from a differing ability to degrade certain lignincarbohydrate complexes

Modelling the Material Resistance of Wood—Part 3: Relative Resistance in above- and in-Ground Situations—Results of a Global Survey

Durability-based designs with timber require reliable information about the wood properties and how they affect its performance under variable exposure conditions. This study aimed at utilizing a material resistance model (Part 2 of this publication) based on a dose–response approach for predicting the relative decay rates in above-ground situations. Laboratory and field test data were, for the first time, surveyed globally and used to determine material-specific resistance dose values, which were correlated to decay rates. In addition, laboratory indicators were used to adapt the material resistance model to in-ground exposure. The relationship between decay rates in- and above-ground, the predictive power of laboratory indicators to predict such decay rates, and a method for implementing both in a service life prediction tool, were established based on 195 hardwoods, 29 softwoods, 19 modified timbers, and 41 preservative-treated timbers

Modeling the material resistance of wood—part 2:Validation and optimization of the meyer-veltrup model

Service life planning with timber requires reliable models for quantifying the effects of exposure-related parameters and the material-inherent resistance of wood against biotic agents. The Meyer-Veltrup model was the first attempt to account for inherent protective properties and the wetting ability of wood to quantify resistance of wood in a quantitative manner. Based on test data on brown, white, and soft rot as well as moisture dynamics, the decay rates of different untreated wood species were predicted relative to the reference species of Norway spruce (Picea abies). The present study aimed to validate and optimize the resistance model for a wider range of wood species including very durable species, thermally and chemically modified wood, and preservative treated wood. The general model structure was shown to also be suitable for highly durable materials, but previously defined maximum thresholds had to be adjusted (i.e., maximum values of factors accounting for wetting ability and inherent protective properties) to 18 instead of 5 compared to Norway spruce. As expected, both the enlarged span in durability and the use of numerous and partly very divergent data sources (i.e., test methods, test locations, and types of data presentation) led to a decrease in the predictive power of the model compared to the original. In addition to the need to enlarge the database quantity and improve its quality, in particular for treated wood, it might be advantageous to use separate models for untreated and treated wood as long as the effect of additional impact variables (e.g., treatment quality) can be accounted for. Nevertheless, the adapted Meyer-Veltrup model will serve as an instrument to quantify material resistance for a wide range of wood-based materials as an input for comprehensive service life prediction software