Susan Grayston


Relevant Degree Programs


Great Supervisor Week Mentions

Each year graduate students are encouraged to give kudos to their supervisors through social media and our website as part of #GreatSupervisorWeek. Below are students who mentioned this supervisor since the initiative was started in 2017.


I am very grateful for having Dr Sue Grayston from @ubcforestry and Dr Louise Nelson as supervisors. They are suportive, encouraging and inspiring. Thank you so much. #GreatSupervisor #UBC #UBCO @ubcokanagan @ubcLFS @UBC @UBCGradSchool


I am very grateful for having Dr. Sue Grayston and Dr. Louise Nelson as supervisors. They are suportive, encouraging and inspiring. Thank you so much. #GreatSupervisor #UBC #UBCO @ubcforestry @ubcokanagan


Graduate Student Supervision

Doctoral Student Supervision (Jan 2008 - Mar 2019)
The effects of variable-retention harvesting and stand age on fine-root decomposition and fungal communities in coastal temperate rainforests (2018)

Fine-root litter is the principal source of carbon (C) stored in forest soils and a dominant source of C for fungal decomposers. Differences in decomposer capacity among fungi may be an important determinant of fine-root decomposition. Variable-retention harvesting (VRH) provides refuge for ectomycorrhizal fungi, but its influence on fine-root decomposers is unknown, as are the effects of functional shifts in fungal communities on C cycling. I compared fungal communities decomposing fine-roots (in litterbags) under VRH (aggregate and dispersed retention), clearcut, and uncut stands at two sites (6- and 13-years post-harvest), and two decay stages (43-days and 1 year after burial), in Douglas-fir forests in coastal British Columbia. Fungal species and guilds were identified from fine-roots using high-throughput sequencing. Aggregate-retention maintained fungal communities similar to those found in uncut stands, but only at the 6-year post-harvest site. Ericoid and ectomycorrhizal guilds were not more abundant under VRH, but stand-age treatments (6-, 13-, and 70-years post-harvest) significantly structured species composition. Ectomycorrhizal abundance on decomposing fine roots may partially explain why fine roots typically decompose slower than surface litter. Stand age was a good predictor of vegetation and soil chemistry; grass and forb abundance, and nitrogen availability, were highest in young stands, whereas soil C and N increased in older stands. Despite differences among stand-age treatments, environmental factors were poor predictors of fungal community composition. However, in a 2-year decomposition study, environmental differences among treatments at the 6-year post-harvest site resulted in faster fine-root decomposition rates under clearcut harvesting, whereas 15-19% more C was retained under VRH and in uncut stands. As nitrate availability correlated with decomposition rate, management practices that reduce post-harvest nitrate availability are likely to result in lower C losses from fine-root decomposition. The effect of harvesting was not persistent as fine roots decomposed at similar rates in forests and openings at the 13-year post-harvest site. Altogether, aggregate-retention harvesting preserved fungal communities more commonly found in uncut stands, and slowed fine-root decomposition relative to clearcut harvesting. As such, this is a recommended harvesting practice in coastal British Columbia if fungal conservation and reduced harvesting-related C losses are management objectives.

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Incorporating stand-health metrics into monitoring the effects of soil disturbance during logging on long-term forest productivity (2016)

Stand volumes at rotation are usually predicted from models based on tree growth, assuming that fast-growing trees are, and will remain, healthy. However, greater-than-expected disease occurrence on dominant trees has been reported in regenerating forests in British Columbia (BC), suggesting that forest-productivity monitoring should include health measurements. In this thesis, I assess growth and health of lodgepole pine at six installations of the Long-Term Soil Productivity (LTSP) project 15 to 20 years after soil-disturbance treatments (organic-matter removal and soil compaction). To determine treatment effects on forest health, 5400 lodgepole pine seedlings at six sites were examined for vigour and pest occurrence. Treatment effects differed among sites, suggesting that the effects of the soil-disturbance treatments on forest health are context-dependent. Larger trees generally had higher frequency of disease, contradicting the assumption that fast-growing trees are healthy. Spectral-reflectance indices of greenness calculated from aerial images correlated with ground-based measures of tree vigour and foliar disease, indicating a role for remote-sensing techniques in forest health monitoring. Topsoil-nutrient content was reduced in the forest-floor removal treatment plots, with foliar phosphorus and potassium concentrations (%) being reduced in the three older sites in the sub-boreal spruce zone. The forest-floor removal treatment was also associated with lower abundance of ectomycorrhizae, but greater abundance Suillus sp., a fungus that is associated with nitrogen-fixing diazatrophic bacteria. The main predictive growth-and-yield model used in BC (called TASS with the interface TIPSY), underestimated tree height (m) but overestimated stand density (stems/ha) at the six sites, suggesting greater-than-predicted tree mortality. Monitoring forest health in conjunction with tree growth after free-to-grow standards are met is recommended for more accurate management of long-term forest productivity.

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Nitrogen cycling processes and microbial communities in reconstructed oil-sands soils (2016)

Covering 140,200 square km, the Athabasca Oil Sands deposit in Alberta is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The overall objective of this thesis was to measure, compare and understand processes underlying nitrogen cycling rates and microbial communities in 20- to 30- year-old reconstructed oil-sands soils and in natural boreal-forest soils. The use of ¹⁵N tracer methods in combination with massively parallel sequencing techniques of the 16S and ITS genes identified key dissimilarities between reconstructed and natural boreal-forest soils. In reconstructed soils, NH₄⁺ was mainly cycled through the recalcitrant organic-N pool. In natural soils, NH₄⁺ was produced from the recalcitrant organic-N pool, but predominantly consumed in the labile organic-N pool, suggesting greater prominence of microbial N-cycling activity in the natural soils compared to the reconstructed soils. Reconstructed soils also produced more NO₃- than they immobilized it resulting in net nitrification rates. Prokaryotic and fungal β-diversity, but not α-diversity, differed between reconstructed and natural forest soils. Microorganisms associated with a copiotrophic lifestyle were more abundant in reconstructed soils, whereas microorganisms associated with an oligotrophic lifestyle were more abundant in natural forest soils. Vegetation cover was the main factor influencing prokaryotic and fungal α-diversity in reconstructed and natural forest soils. Nitrogen deposition, pH, soil nutrient content and plant cover influenced prokaryotic and fungal β-diversity. The results of this thesis deepen our understanding of the distinct pedological environments of oil-sands reconstructed soils and highlighted the importance of above- and below-ground interactions in reconstructed and natural ecosystems.

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Microbial functional groups involved in greenhouse gas fluxes following site preparation and fertilization of wet low-productivity forest ecosystems (2015)

Forest site preparation and fertilization can improve stand productivity, but can alter the efflux rates of greenhouse gases (GHGs), CO2, CH4 and N2O, from wet soils. This study investigated the effects of these management practices on GHG fluxes (using static closed chambers), soil physico-chemical parameters, microbial community structure (using terminal-restriction fragment length polymorphism (TRFLP) of bacterial 16S and fungal ITS targets) and microbial functional group abundance (methanogens, methanotrophs, nitrifiers, denitrifiers, sulphate-reducing bacteria, using quantitative PCR) in both forest floor and mineral soils. The research took place in British Columbia (BC), Canada, at the Aleza Lake Research Forest (ALRF), near Prince George, in a hybrid spruce stand subject to mounding and at the Suquash Drainage Trial (SDT) site near Port McNeill, Vancouver Island, in a western redcedar‒western hemlock‒yellow cedar stand subject to drainage. Mounding reduced CO2 fluxes and carbon (C) concentrations, but created anaerobic hot-spots of CH4 and N2O fluxes. Ditch drainage increased soil C about 20% after 15 years and did not affect respiration rates, though CH4 fluxes were reduced. Fertilization transiently increased N2O fluxes up to a maximum of 209 µg m-2 h-1, two months following fertilization. Bacterial and fungal T-RFLP profiles showed distinct patterns based on soil layer, and were altered by mounding, drainage and fertilization. Up to 84.4% of variation in CO2 emissions could be explained, with almost 50% of explained variation allocated to soil temperature. CH4 flux variation was explained by soil water content, soil temperature, methanogen (mcrA) and methanotroph (pmoA) functional gene abundance. Variation in N2O fluxes were significantly explained by soil water content, soil pH, NH4-N concentration, AOB amoA, nitrate reductase (narG) gene and nirSK gene abundance. In addition to denitrification genes, these data highlight AOB as important determinants of denitrification either by mediating nitrification or by direct nitrifier denitrification. This study elucidates the influence of different microbial functional groups on GHG flux rates in forest ecosystems.

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Green-tree-retention harvesting as a tool to maintain soil microbial diversity and function in harvested sites (2013)

Green-tree or variable-retention harvesting is increasingly being used in the Pacific Northwest due to the perceived benefits to aboveground biodiversity. Little research has been conducted on the value of this harvesting practice for soil organisms, though retained live trees on harvested sites are thought to benefit belowground biodiversity by acting as “hubs” of both species-specific and symbiotic microbial communities. Access to these communities may be necessary for seedling growth and forest regeneration after harvest. Live trees support microbial communities by maintaining a constant source of labile carbon through litter and root exudates. The aim of this thesis dissertation project was to trace the flow of carbon from live trees retained on clear-cut sites in different variable-retention harvesting regimes into the soil microbial community to determine which variable-harvesting regime best maintained pre-harvest soil microbial communities and soil microbial function. Two variable-retention strategies were compared: aggregate-retention, where intact forest patches are retained, and dispersed-retention, where individual trees are retained across the site. Both harvesting strategies decreased the fungal to bacterial ratio although the dispersed-retention harvesting treatment mitigated the effects of harvesting on soil nutrient availability. Aggregate-retention harvesting, even within 9 meters of the retention patch, did not appear to influence nutrient availability, but evidence suggested the microbial community within this area was supported by recent plant-carbon. Through analysis of stable-isotope natural abundance and application of a novel stable-isotope labeling stem-injection technique, I was able to discern that individual trees support the fungal community up to 20 meters into a clear-cut. However, the lack of recently-derived labile plant carbon in clear-cuts resulted in changes to soil carbon-cycling. The microbial community in clear-cut sites appeared to rely on tightly recycled labile microbial-derived carbon that was probably released during microbial turnover, rather than dissolved organic carbon. In the highly disturbed clear-cut areas, the microbial communities may have lost some of their ability to break down recalcitrant soil organic matter. Both variable-retention strategies investigated affected soil microbial community composition; though it appeared that dispersed-retention best maintained microbial community function on harvested sites.

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Endophytic colonization and nitrogen fixation by Paenibacillus polymyxa in association with lodgepole pine and western redcedar (2011)

In this study I provide evidence of biological nitrogen fixation by endophytic, diazotrophic bacteria as a possible source of nitrogen for lodgepole pine (Pinus contorta var. latifolia (Dougl. Engelm.) and western redcedar (Thuja plicata Donn.); conifers that are known for their ability to grow in nitrogen-poor forests of western North America. Diazotrophic bacteria were isolated from root, stem and needle tissues of both tree species, growing on forested sites with contrasting N availability in the interior of British Columbia, Canada. Members of the genera Bacillus and Paenibacillus dominated the culturable, endophytic bacterial community in tissues of both tree species. A Paenibacillus polymyxa isolate strain P2b-2R from lodgepole pine at the nitrogen deficient site near Williams Lake, B.C., demonstrated high (5.1705 μmols C₂H₄/ml), replicable, nitrogenase activity, under laboratory conditions.P. polymyxa strain P2b-2R inoculated and control lodgepole pine and cedar seedlings were grown in a sand – turface mixture enriched with a 5 atom % excess ¹⁵N [Ca(¹⁵NO₃)₂] solution. Root, shoot and seedling length, fresh weight and dry weight demonstrated that both tree species accumulated significantly higher biomass when inoculated with strain P2b-2R. ¹⁵N atom % excess indicated that P2b-2R inoculated lodgepole pine and western redcedar derived 67.53 and 21.94% of their total foliar nitrogen from the atmosphere, respectively. Using in situ confocal laser scanning microscopy, cells of strain P2b-2R tagged with green fluorescent protein were found to colonize the root and stem cortical cells of lodgepole pine, both inter- and intracellularly. Sequences of nif B, H and D genes of strain P2b-2R were obtained using PCR. Phylogenies based on nifH and nifD genes of strain P2b-2R place these genes in monophyletic groups with those of free-living cyanobacteria and root nodule-forming Frankia, respectively. Within the genus Paenibacillus, based on nifH and nifD phylogenies, P. polymyxa was most closely related to P. massiliensis T7, a bacterium isolated from the rhizosphere of willow trees (Salix spp.) in Beijing. These results provide the first evidence of significant endophytic nitrogen fixation in conifer species growing under nitrogen-limited conditions and support the possibility of a novel, ecologically significant interaction between coniferous trees and diazotrophic bacteria.

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Fungal and bacterial contributions to hyphosphere enzyme activity (2010)

In temperate forests, trees form symbiotic associations with fungi on their roots; the majority being an ectomycorrhizal alliance. Ectomycorrhizal fungi (EMF) secrete phosphatase enzymes which mobilize phosphorus from soil organic matter to their host. Soil bacteria also contribute to phosphorus mobilization through phosphatase release. I characterized bacterial and EMF contributions to phosphatase activity in forest soils regenerating after stand-replacing wildfire or from clearcut logging followed by broadcast burning. Fire can cause ecosystem phosphorus loss and can change microbial community structure, but it is unclear what effects these changes have on phosphorus availability.To link EMF hyphae with phosphorus mobilization in forest soil, I developed a novel method for visualizing fine-scale soil enzyme activity in-situ. Visualization of phosphatase activity across a chronosequence forest stands demonstrated a change in the pattern of in-situ soil phosphatase activity; areas of phosphatase activity were smaller in stands less than 61 years-old (stand initiation to canopy closure) and became larger in stands 61 to 103 years-old (stem exclusion to post stem exclusion). To link EMF with areas of high and low phosphatase activity I also developed a new soil sampling method where enzyme activity was first visualized and then used to guide small, targeted, soil samples from the soil profile for molecular (T-RFLP) analysis. The number of EMF molecular signatures was not different between the high and low-phosphatase soil microsites in stands less than 61 years-old, but in older stands, there were typically more EMF signatures in areas of low phosphatase activity. Bacteria also contribute to soil phosphatase activity; therefore, I investigated the effect of EMF hyphae on the enzyme activities of nearby soil bacteria by trapping bacteria and EMF hyphae in-situ using sand-filled mesh bags. Bacteria from the bags with hyphal ingrowth had lower phosphatase activities than bacteria from bags without hyphae. Given the higher number of EMF signatures present in low compared to high phosphatase microsites and the lower phosphatase activities of bacteria near hyphae, it is possible that EMF species may be excluded from organic phosphorus or may compete for phosphorus by excluding other EMF and selecting for less competitive soil bacteria.

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Functional and compositional responses of microorganisms to reclamation of surface-mined boreal forest soils (2009)

Over the last four decades, surface mining of oil sands in the boreal forest of western Canada has created large areas of disturbed land. The current regulatory framework requires that derelict land be reclaimed to pre-disturbance conditions. This has prompted the need to assess the effectiveness of reclamation, which relies on the use of salvaged materials (e.g., tailings sand and overburden), on key ecosystem components such as soil microorganisms. In this thesis, I examined landscape-scale changes in soil microbial community composition and function in response to different reclamation amendments and in natural sites comprising a regional environmental gradient. Using molecular fingerprinting (phospholipid fatty acids and denaturing gradient gel electrophoresis) and phylogenetic analyses of 16S rRNA genes, I found that microbial communities in natural soils differed from those of reclaimed soils. This dissimilarity was driven by increasing abundances of fungal and actinomycetal biomarkers in natural soils. After 30 years, however, reclamation did not place soil microbial communities on a predictable recovery path. The composition of microorganisms was particularly affected by tailings sand-based amendments. Functional potential, determined with assays targeting the activities of enzymes responsible for macromolecule degradation, was mainly impacted by prescriptions containing overburden. Variance partitioning analyses indicated that microbial responses to reclamation were partially determined by vegetation cover development, soil pH, and the fungal-to-bacterial biomass ratio. pH effects on bacterial composition were partly driven by the abundance of Acidobacteria. The relative abundances of several bacterial biomarkers covaried with individual enzyme activities, suggesting certain sub-sets of the microbial communities were functionally relevant. I tested this idea experimentally by assembling a laboratory-scale reciprocal transplant of microorganisms sourced from two distinct peat types. My main finding was that differences in initial microbial community composition were functionally significant for lignin depolymerization, while the activities of nutrient-acquiring enzymes (a more ubiquitous function) were mostly influenced by peat type. Overall, my results indicate that the responses of abundant microbial populations to reclamation were largely accounted for by abiotic properties of reclamation materials and, indirectly, by the effects of reclamation on plant growth.

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Master's Student Supervision (2010-2017)
Translocation and accumulation of organic and inorganic nitrogen in wood resources colonized by the mycelial cord systems of the decay fungus Hypholoma fasciculare (2012)

Translocation of nitrogen (N) through mycelial cords of wood decay fungi is thought to be the mechanism responsible for the observed increase in absolute N content in woody debris over time. This research evaluates the ability of the mycelial cords of the wood ¹⁵decay fungus Hypholoma fasciculare to translocate and accumulate labeled organic (¹⁵N-glycine, N Douglas-fir litter) and inorganic N (¹⁵NH₄⁺, ¹⁵NO₃⁻) in its wood substrate. Each N form was supplied separately to the growing fronts of mycelial cords established over 67 days from wood blocks (Douglas-fir) in soil microcosms. Three sampling occasions (days 6, 18 and 30 after N addition) were used to identify trends in ¹⁵N transfer and total N accumulation. Wood blocks inoculated with Hypholoma fasciculare assimilated significantly more ¹⁵N than uninoculated blocks for all ¹⁵N treatments on at least one sampling occasion. After 73 days of incubation (day 6 sampling occasion), inoculated wood blocks increased in absolute N content by 211% relative to uninoculated control blocks, but 80% of this accumulated N was lost after 97 days of incubation (day 30 sampling occasion). The small amount of ¹⁵N that was transferred contrasted with the large increase in total N, suggesting that the site of N transfer was largely from the soil underneath wood blocks rather than at the site of ¹⁵N injection. The precipitous decline in absolute N content was attributed to visible indications of mycelial senescence. This research demonstrates that the mycelial cords of Hypoloma fasciculare are capable of translocating ¹⁵N into a wood substrate and can also greatly increase the absolute N content of wood blocks. The results are discussed in the context of fungal ecology as well as woody debris management.

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Enzyme activities and nitrogen transformations following fertilization of a Douglas-fir forest in coastal British Columbia (2010)

Forest fertilization has long been used to enhance tree growth and timber yield. More recently, fertilization has become the focus of increased interest as a potential method for increasing soil C uptake, vis-à-vis suppression of microbial enzymes that decompose recalcitrant soil organic matter (SOM). However, fertilization is also associated with increased emission of the potent greenhouse gas N₂O. In this study I evaluate the effect of N amendment on activities of soil enzymes and on N ammonification and nitrification rates in a chronosequence of Douglas-fir stands on Vancouver Island, British Columbia. Ammonification and nitrification rates were also compared between two different fertilizers, urea and slow-release urea, which is urea with a polymer coating to decrease the rate of N release. Fertilization significantly decreased the activity of the ligninases, phenol oxidase and peroxidase in the mineral soil layer of all stand ages. However, the effect appeared to be temporary, as there was no difference between treatment and control 63 days after fertilization. Activity rates of three enzymes that degrade labile SOM - cellobiohydrolase, betaglucosidase and NAGase - were also measured, and there was a small decrease in activity rates of these enzymes in the forest floor.Urea amendment increased net rates of ammonification and nitrification. Addition of slow-release urea resulted in lower rates of ammonification and nitrification compared to urea, but the rates remained elevated longer. Nitrification rates were increased the most in the clearcut stand (7 years old), and less so in the two older stands (18 and 57 years old). Ammonification and nitrification rates were approximately an order of magnitude higher in the forest floor than in the mineral soil, and the response to fertilization was also greatest in the forest floor. Nitrification was increased by fertilization, but this effect was only significant in the clearcut stand. Nitrification at all sites increased more with urea addition than with slow-release urea.Further research is recommended to determine if there is a minimum threshold of available N necessary to cause the suppression of microbial enzyme activities, and if it could be reached through operational applications of slow-release urea fertilizer.

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Microbial communities and enzyme activities related to C and N cycling in fertilized and unfertilized forests (2010)

The study was conducted at the fertilization demonstration plots of the Salal Cedar Hemlock Integrated Research Program. PH, moisture, N availability (NO₃⁻ and NH₄⁺), microbial biomass C,N and P, phospholipid fatty acids (PLFA), and enzyme activities were measured in the forest floor and mineral soil of western red cedar stands and western hemlock stands ten years following fertilization with N or P, or both.Results showed that forest floor had the largest effect on microbial and soil chemical variables, followed by forest type, and fertilization. N fertilization significantly increased overall bacterial PLFA abundance and reduced fungal PLFA abundance, while P fertilization significantly reduced AM fungal abundance in the organic layer of the hemlock stands. In addition, the stimulatory effect of N fertilization and inhibitory effect of P fertilization on phosphatase activity was still apparent 10 years after fertilization. Moreover, the effect of fertilization on microbial communities was more pronounced in the forest floor than at depth in the soil. Correlations between microbial community structure and function were weak.After 10 years, fertilization had not inhibited enzyme activities related to lignin decomposition, but had a significant effect on microbial community composition. Future effort should be directed to long-term and in situ research to understand microbial processes at a fundamental level, as well as linking this research with external factors, such as C costs related to fertilization treatment and shorted rotation length, to understand how microbial processes contribute to the bigger picture of C cycle related with forestry.

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Recent Tri-Agency Grants

The following is a selection of grants for which the faculty member was principal investigator or co-investigator. Currently, the list only covers Canadian Tri-Agency grants from years 2013/14-2016/17 and excludes grants from any other agencies.

  • Assessing arbuscular mycorrhizal inoculum and deer repellent as tools to increase western redcedar (Thuja plicata) regeneration in the presence of invasive deer - Natural Sciences and Engineering Research Council of Canada (NSERC) - Engage Grants Program (2016/2017)
  • Assessing the greenhouse gas emission mitigation potential of using wood waste in waste-to-energy generation through structural equation modeling - Natural Sciences and Engineering Research Council of Canada (NSERC) - Engage Grants Program (2014/2015)
  • Specificity of plant-microbe interactions in forest soils - Natural Sciences and Engineering Research Council of Canada (NSERC) - Discovery Grants Program - Individual (2014/2015)
  • The potential of retention trees to mitigate post-harvest soil carbon loss through reduction of root and soil organic matter decomposition mediated by the fungal community - Natural Sciences and Engineering Research Council of Canada (NSERC) - Strategic Projects (2013/2014)
  • Carbon and nitrogen fluxes in reconstructed oil sands soils - Natural Sciences and Engineering Research Council of Canada (NSERC) - Collaborative Research Opportunities Grants (2013/2014)
  • Microbial diversity and function in forest soils and the influence of rhizosphere carbon flow - Natural Sciences and Engineering Research Council of Canada (NSERC) - Discovery Grants Program - Individual (2013/2014)
  • Canada Research Chair in Soil microbial ecology for Dr. Susan Grayston - Canada Research Chairs - Canada Research Chair Tier II (NSERC) (2013/2014)

Current Students & Alumni

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