Browsing by Subject "fungi"

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Aquatic Plants from Minnesota Part 3 - Antimicrobial Effects
(Water Resources Research Center, University of Minnesota, 1972-02) Abul-Hajj, Yusuf J.; Staba, E. John; Su, K. Lee
In this study the antimicrobial activity of the following 22 Minnesotan aquatic plants was investigated: Anacharis Canadensis, Calla Polustris, Carex lacstris, Ceratophyllum demersum, Chara vulgaris, Elecharis smallii, Lemna minor, Myriophyllum exalbescens, Nuphar variegatum, Nymphaea turberosa, Potamogeton amplifolius, P. natans, P. pectinatus, P. richardsonu, P. zosteriformis, Sagittaria cuneata, S. latifolia, Sparganium eurycarpum, S. fluctuans, Typha angustifolia, Vallisneria amiercana, and Zizania aquetica, Furthermore, the chemical constituents responsible for the significant antimicrobial effect were isolated and identified. The skellysolve F. chloroform, 80% ethanol and fresh water extracts of plant species were treated for antimicrobial activity employing the qualitative filter paper disc diffusion method and reference antibiotic discs. Ethanol (80%) extracts of Myriophyllum exalbescens (activity ratio of .34 as compared to the 30 mcg chloramphenicol discs) Nymphaea tuberose (leaf: .40, stem: .45) were moderately active against S. aureus. Ethanol (80%) extracts of Carex lacustris (activity ratio of .34 as compared to the 10 mcg streptomycin discs), Nymphaea tuberose (leaf: 1.01, stem: 1.10) and Nuphar variegatum collected in Lake Minnetonka (leaf: .73, stem: .58) were active against M. smegmatis. All extracts were relatively inactive against E. coli except the water extract of Potamogeton natans where a low activity ration of .10 as compare to the 30 mcg chloramphenicol discs was indicated. Skellysolve F stem extracts of Nuphar variegatum collected in the Pine Lake and Sparganium fluctuans showed a rather distinct action against C. albicans, the activity ratio as compared to the 100 units mycostatin discs were 2.06 and 1.08, respectively. Regarding antifungal activity, ethanol (80%) extracts of Carex lacustris (activity ratio of 1.08 as compared to 5% aq. Phenol standard), Nymphaea tuberosa (stem: .72) and skellysolve F extract of Potamogeton zosteriformis (.60) were active against Alternaria sp., 80% ethanol stem extracts of Nymphaea tuberosa and Nuphar variegatum were active against F. roseum with the activity ratios of .41 and .48 respectively, as compared to the 5% aqueous phenol standard. In general, the plant pathogenic fungi are more resistant than animal pathogenic organisms toward the actions of aquatic plant extract.
Biogas Production and Nutrient Recovery from Waste Streams
(2013-07) Ye, Yulin
Abstract Waste streams such as municipal wastewater and animal manure contain organic materials and nutrients that can be converted and recovered for bioenergy and renewable fertilizer production. In the first part of this thesis, the anaerobic co-digestion of dairy manure with kitchen waste and chicken fat was studied for the purpose of increasing biogas production. The methane yields of co-digestion substrates mixed at different ratios were determined by bio-methane potential tests. The highest methane yield, which was 114% higher than the baseline, was observed when dairy manure was mixed with kitchen waste and chicken fat at the ratio of 1:2:2 (volatile solids based). The mixed substrates were then fed to a lab-scale continuous stirred-tank reactor. The co-digestion was stable and biogas production was 1559�195 mL biogas/L·day at organic loading rate as high as 6.8g COD/L*day. In the second part, a new approach was proposed for phosphorus removal and recovery from wastewater. Nine strains were identified to have the capability of high phosphorus removal and storage comparable to Polyphosphate Accumulating Organisms (PAOs) in the Enhanced Biological Phosphorus Removal (EBPR) process. Batch experiment using synthetic wastewater showed that Mucor circinelloides can remove ~ 72-82% phosphorus when P to COD ratio was roughly 1:100. The phosphorus recovered from wastewater in the form of polyphosphate-containing fungal biomass could be used as fertilizer, providing a potential alternative to biological nutrient removal and a solution to sustainable agriculture.
Chemical Characterization of the Degradation of Necromass from Four Ascomycete Fungi: Implications for Soil Organic Carbon Turnover and Storage
(2020-12) Bruner, Valerie
Terrestrial soils store approximately twice as much carbon as is currently in the atmospheric CO2 pool. Despite its importance in the global carbon cycle, much is still unknown about the source, turnover, and stability of the soil organic matter (SOM) pool. For example, fungi are known to play an important role in shaping the chemistry of SOM by degrading common biopolymers, and fungal biomass has been found to be a significant portion of living microbial SOM, dominating over bacteria in some soils by as much as 90%. And yet, despite growing evidence that microbial necromass, or dead microbial tissue, may be a larger contributor to SOM than previously thought, very little is known about the specific degradation patterns of fungal necromass, and subsequently its potential chemical contributions to long-lived SOM pools. This study addresses these knowledge gaps through a time-series analysis of the degradation patterns of fungal tissue from four different saprotrophic Ascomyota species in temperate restored prairie soils. Fungal tissue was buried in a temperate soil and harvested at intervals from 1 day to one month. After harvest, chemical analysis of the dried tissue by thermochemolysis pyrolysis-GCMS was used for relative quantitation of compounds derived from lipids, aromatics, carbohydrates, nitrogen-containing, and unspecified residues. The degradation of these specific molecules, bulk fungal tissue, and bulk C and N within the tissue, is modeled to (1) show that a small portion of fungal necromass persists in the environment even after the period of the experiment and could serve as a contributor to long-lived SOM, and (2) provide quantitative information on the contribution of fungal tissue to global SOM pools.
Data from: Carbon cycling through plant and fungal herbarium specimens tracks the Suess effect over more than a century of environmental change
(2024-02-19) Michaud, Talia J; Hobbie, Erik A; Kennedy, Peter G; micha938@umn.edu; Michaud, Talia J; University of Minnesota Kennedy Lab
Although the anthropogenic decline in atmospheric carbon stable isotope ratios (d13C) over the last 150 years (termed the Suess effect) is well-studied, how different terrestrial trophic levels and modes reflect this decline remains unresolved. To evaluate the Suess effect as an opportunistic tracer of terrestrial forest carbon cycling, this study analyzed the d13C in herbarium specimens collected in Minnesota, USA from 1877-2019. Our results suggest that both broadleaf trees and ectomycorrhizal fungi relied on recent photosynthate to produce leaves and sporocarps, while saprotrophic fungi used carbon fixed from the atmosphere 32-55 years ago for sporocarp construction. The d13C values of saprotrophic fungal collections were also sensitive to the age of their plant C substrate, with sporocarps of twig specialists tracking changes in atmospheric d13C more closely than saprotrophs growing on wood. Collectively, this study indicated that natural history collections can quantitatively track carbon cycling among plants and fungi over time.
Early Decay Mechanisms of Brown Rot Wood-Degrading Fungi: Transcriptome Patterns, Cation Dynamics, and Substrate Chemistry Effects
(2024-05) Anderson, Claire
Fungi gained the capacity to degrade lignocellulose approximately 295 million years ago when they adapted oxidative enzymes to metabolize lignin – a mechanism still used by white rot fungi. Since then, brown rot fungi have evolved a carbohydrate-selective mechanism that uses reactive oxygen species (ROS) to cause extensive, nonspecific depolymerization in plant cell walls, thus solubilizing the carbohydrates and avoiding lignin removal. Brown rot fungi differentially express genes to create a sequence of decay starting with lignocellulose oxidation via ROS, followed by hemicellulose side chain cleavage and main chain degradation, then cellulose degradation via endoglucanases. It is still unclear how brown rot fungi regulate this elaborate mechanism and avoid subjecting their own enzymes and hyphae to ROS damage. Specifically, the process that turns ROS pathways on at the beginning of brown rot decay has not yet been identified, despite assumptions of an inducible mechanism. Many studies have suggested that the presence of either lignin or hemicellulose may initiate brown rot decay, but this has not been clearly shown experimentally.To address this knowledge gap, I captured the earliest stages of brown rot decay by Rhodonia placenta and analyzed the whole transcriptome at the incipient stage of decay to confirm delayed upregulation of the lignocellulose oxidation genes involved in ROS generation. I also examined the interactions between R. placenta and its lignocellulose substrate in two ways. First, I created a fine-resolution map of the cation translocation dynamics in R. placenta and white rot fungus Pleurotus ostreatus for comparison. Second, to examine the effects of lignin and hemicellulose on brown rot gene expression, I used mutant strains of model plant Arabidopsis thaliana with changes in cell wall chemistry as a substrate for R. placenta and examined the whole transcriptome response of the fungus to these modified lignocellulose substrates. This dissertation contributes more clarity to the transcriptomic details of early brown rot as well as the effects of substrate chemistry on brown rot decay. Understanding brown rot decay mechanisms offers potential to harness these pathways for biotechnology applications as well as to make better predictions about the fate of carbon stored in wood.
Effort Versus Reward: Preparing samples for fungal community characterization in high-throughput sequencing surveys of soils
(2015-03-25) Song, Zewei; Schlatter, Dan; Kennedy, Peter; Kinkel, Linda; Kistler, H.Corby; Nguyen, Nhu; Bates, Scott; songx208@umn.edu; Song, Zewei
Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in polymerase chain reaction (PCR), and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal operational taxonomic unit (OTU) richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.
Historical plant and fungal nitrogen isotopes and concentrations from Minnesota, USA, 1871–2016
(2023-11-06) Michaud, Talia J; micha938@umn.edu; Michaud, Talia J; University of Minnesota Kennedy Lab
Historical declines in plant tissue nitrogen concentrations and d15N have been interpreted as evidence of declining terrestrial ecosystem nitrogen status. To test whether plant mycorrhizal type influences trajectories of plant nitrogen status, and whether fungi also exhibit declining nitrogen status, we analyzed herbarium collections made in MN, USA, from 1871–2016.
Mechanisms of Invasion and the Microbiome of Introduced Species
(2016-05) David, Aaron
Invasive species represent a critical threat to ecosystems and ecological communities. Understanding the mechanisms behind their invasion is important for understanding why they invade and the consequences of their invasions. Furthermore, invasive species, like all macroscopic organisms, harbor symbiotic microbes that constitute their microbiomes. Symbionts have been implicated in invasion success of several species, and they also represent an opportunity to learn about community assembly. In this dissertation, I explore the causes and consequences of plant invasion, and the microbiomes that invasive species harbor. In Chapter 1, I explore how two invasive, congeneric beachgrasses (Ammophila arenaria and A. breviligulata) differently alter plant succession in Pacific Northwest, USA dunes. The newer invader, Ammophila breviligulata, occupied a wider distribution across dunes than the established invader, A. arenaria, allowing A. breviligulata to persist longer through successional time. In Chapter 2, I characterize the above- and belowground symbionts of these two Ammophila species and the native Elymus mollis. I found that symbiont communities aboveground are most influenced by host species and geographic distance from one another, while those belowground are most influenced by environmental filtering. In Chapter 3, I conducted two experiments to test the mechanisms by which A. breviligulata invades dunes dominated by A. arenaria. I found that A. breviligulata dominates by tolerating competition from A. arenaria, and that there is some evidence that A. arenaria might limit itself via negative plant-soil feedbacks. Finally, in Chapter 4, I explore the relationship between herbivory and symbiont communities using the invasive wetland forb Lythrum salicaria. I found positive associations between herbivory and symbiont communities indicative of facilitation.
Signature Wood Modifications that Reveal Decomposer Community History
(2015-02-13) Schilling, Jonathan; schillin@umn.edu; Schilling, Jonathan
Correlating plant litter decay rates with initial tissue traits (e.g. C, N contents) is common practice, but in woody litter, predictive relationships are often weak. Variability in predicting wood decomposition is partially due to territorial competition among fungal decomposers that, in turn, have a range of nutritional strategies (rot types) and consequences on residues. Given this biotic influence, researchers are increasingly using culture-independent tools in an attempt to link variability more directly to decomposer groups. Our goal was to complement these tools by using certain wood modifications as 'signatures' that provide more functional information about decomposer dominance than density loss. Specifically, we used dilute alkali solubility (DAS; higher for brown rot) and lignin:density loss (L:D; higher for white rot) to infer rot type (binary) and fungal nutritional mode (gradient), respectively. We first determined strength of pattern among 29 fungi of known rot type by correlating DAS and L:D with mass loss in birch and pine. Having shown robust relationships for both techniques above a density loss threshold, we then demonstrated and resolved two issues relevant to species consortia and field trials, 1) spatial patchiness creating gravimetric bias (density bias), and 2) brown rot imprints prior or subsequent to white rot replacement (legacy effects). Finally, we field-tested our methods in a New Zealand Pinus radiata plantation in a paired-plot comparison. Overall, results validate these lowcost techniques that measure the collective histories of decomposer dominance in wood. The L:D measure also showed clear potential in classifying 'rot type' along a spectrum rather than as a traditional binary type (brown versus white rot), as it places the nutritional strategies of wood-degrading fungi on a scale (L:D=0-5, in this case). These information-rich measures of consequence can provide insight into their biological causes, strengthening the links between traits, structure, and function during wood decomposition.
Special crop research grand (SCRG) - MnDRIVE potato biocontrol 2014 experiment
(2017-10-05) Song, Zewei; Hanson, Lindsey; Kinkel, Linda; songzewei@outlook.com; Song, Zewei
This is the sequencing data for characterizing the soil microbiomes (fungal and bacterial communties) following the application of bacterial inoculations as biocontrols of potato tuber disease. The archived files are raw sequencing data. The detailed processing pipeline will be included in the incoming peer reviewed paper.
What we learn from mushrooms: natural history data as a resource in fungal ecology
(2024-05) Michaud, Talia
Through their diverse ecological roles as mutualists, saprotrophs, and pathogens, fungi play a fundamental role in mediating forest carbon capture. Understanding fungal responses to global environmental change is therefore central to predicting forest feedbacks to accumulating atmospheric carbon dioxide. Short term research that isolates drivers of environmental change are common, despite knowledge that drivers of environmental change interact, producing emergent effects at multidecadal timescales. Similarly, existing research typically isolates fungal responses, though fungal activity is contingent on the activity of other organisms, particularly plants. In this context, I sought to produce research in my doctoral thesis that integrated plant and fungal responses to environmental change using natural history data. The use of herbarium collections and field surveys of fungal sporocarps (mushrooms) enables analysis spanning multiple decades, which can capture the cumulative effects of multiple drivers of environmental change. Together, my thesis hinges on documentation of fungi and plants in their natural environment, often called natural history data, and highlights the promising potential for using this approach in global change research.

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