Department of Ecology and Evolutionary Biology

Plants make up 80 percent of our food, but up to 40 percent of global food crops are lost to plant pests and diseases each year (FAO, 2019). Scientists try to mitigate disease impacts by identifying microscopic pathogens such as fungi and running experiments to study their traits and how they affect plants. In this module, students build on previous knowledge of ecosystem interactions and energy flow by learning about pathogenic fungi that consume plants. Students may be familiar with edible mushrooms and the role of fungi in decomposition, but this module highlights another ecosystem function of fungi — agents of plant disease. This module synthesizes broad concepts in biology and ecology with an emphasis on agricultural implications. Students collect diseased leaf samples from around their neighborhood, culture their own fungal species, and explore the diversity of fungi that infect local plants. Students learn sterile technique, microscopy, and other lab skills central to microbiology, as well as practice writing predictions, collecting data, and analyzing trends to grow their skills as scientists. This hands-on exploration of the world of fungi gives students an exciting and concrete first experience in microbiology research. This document package includes a lesson plan, procedures, and a slide deck. The slide deck is to be used by instructors teaching the Fungal Fighters lab module. 

Due to global loss and degradation of salt marshes, restoration and conservation havebecome necessary to protect and preserve salt marsh systems. Restoration can exacerbate the common environmental stressors – salinity and drought – present in Mediterranean salt marsh ecosystems. Grading and clearing of land to restore tidal influence and remove non-native weeds creates large expanses of bare soil, increasing evaporation rates. As moisture is lost, salts are concentrated in the soil, making growing conditions more difficult for transplants. Multiple species are usually planted during revegetation efforts, but different species are likely to vary in tolerance to moisture and salinity stress; yet, the relative effect of these stressors on manyCalifornia salt marsh natives are unknown. To address this knowledge gap, we appliedgreenhouse watering treatments to five perennials common in central California coast salt marshes. We evaluated response to water volume and salinity by measuring survival, growth, and tissue water potential. As predicted, drought significantly reduced tissue water potential for all five species; however, only three species showed a significant decline in water potential with increasing of salinity treatments. Contrary to expectations, growth was unaffected by drought or salinity treatments. Our results suggest these species have broad tolerance to drought and salinitystress they may encounter in the salt marsh ecotone.

One mechanism of invasive species success is the production of allelopathic chemicals that negatively affect native competitors. A highly invasive shrub, Cytisus scoparius, impedes Douglas-fir tree establishment in clearcuts, even years after its removal. This impediment may be from the allelopathic alkaloids of C. scoparius that could indirectly hinder Douglas-fir by inhibiting their mutualistic ectomycorrhizal fungi (EMF). I extracted and quantified alkaloids from C. scoparius tissue for use in a laboratory bioassay. I then tested if and how these alkaloids affected EMF growth. In a second assay, I tested the effects of three concentrations of pure sparteine, the primary alkaloid in C. scoparius , on fungal growth. Sparteine was the only alkaloid recovered from the extraction which yielded 0.32 mg sparteine/g fresh weight, a lower concentration than previously reported values. Both the crude extract and pure sparteine significantly affected fungal growth, but only sparteine produced a species-specific response. Growth was inhibited by increasing sparteine concentrations, and most species were inhibited at 1.4 mM, the concentration found in C. scoparius. One common EMF, Wilcoxina mikolae, was unaffected by sparteine while others, like Suillus caerulescens and Cenococcum geophilum, were more sensitive and stopped growing entirely at 5 to 10 mM. These results suggest that the alkaloids of C. scoparius may seriously hinder EMF, and indirectly Douglas-fir, contributing to the competitive dominance of the invasive shrub.

At Joint Base Lewis-McChord, tree plantations have failed repeatedly in areas that had once supported Douglas fir forest, with Scotch broom invasion replacing forest. Maximizing the effectiveness of Scotch broom control is a top management priority. The studies presented here have two main foci: timing of control relative to the Scotch broom life cycle, and chemical vs. manual control. We also explore the effects of forest edges on Douglas fir seedling survival and mycorrhizal colonization. 

We set up a large-scale experiment (6.3ha total treatment area) at 5 heavily invaded sites in which all broom was mechanically removed in 2007. Each site contained 4 blocks of 12 treatments. We measured density of newly germinated seedlings using 24m-long, 10cm-wide belt transects, and percent cover of Scotch broom using line-intercept method on 24m transects.

Seedling density (representing germination from the seedbank) peaked in year 2 and varied dramatically among sites, with one site showing an averageof nearly 350 seedlings/m².

Scotch broom percent cover in control plots increased most rapidly between years 2 and 3, by the fourth year reaching over 150% cover in one site and around 100% cover in two other sites. In contrast, the slowest growing site had only about 20% cover after four years. Plant size also varied across sites. By the fourth year, average plant height was around 2.5m in two of the sites, but only around 1m in the slowest growing site.

Chemical vs. mechanical control of seedlings.

We compared different approaches to removing broom seedlings at a large scale. Mechanical control comprised “scarifying” the soil to scrape off all seedlings with a mulcher, while chemical control was a broadcast spray of triclopyr herbicide.  We also compared a single scarify treatment to multiple years of treatment (to stimulate and then exhaust the seedbank). With percent cover three years later as the response variable, we found few generalizable differences among treatments. In two sites, herbicide strongly reduced (by over 75%) Scotch broom cover. In one site, multiple years of scarification reduced (by about 50%) cover.

Chemical control across seasons.

We incorporated the question of seasonality into the herbicide component of our experiment because of a lack of consensus among practitioners about the best time of year to spray Scotch broom. We sprayed whole plots (56’ x 56’) with Garlon 4 Ultra (triclopyr) in March, May, or September of 2009, and quantified percent cover of Scotch broom in 2012. All the spray treatments had strongly reduced broom cover relative to controls, with the exception of one site that had very low cover altogether. The effect of the treatment did not vary with season in four of the five sites. In the fifth site, March spray was less effective.

Chemical vs. mechanical control of older plants.

We compared brushcutting to triclopyr spray on 2.5-year old plants in September 2010,.  Herbicide led to a significantly higher kill rate per plant, consistently 80-95% across all sites, compared to variable rates (25-95%) for brush cutting. However, two years later percent cover of Scotch broom was showing only a non-significant trend toward better results with herbicide. Both brushcutting and triclopyr spray strongly reduced percent cover of Scotch broom compared to the untreated control in all but one site. 

Edge effects, soil inoculum, and mycorrhizae.

Our early studies suggested that Douglas-fir seedlings planted near adult trees or forest edges established with much higher success than more isolated seedlings. We did a large-scale, well-replicated experiment to test whether tree establishment was consistently higher near forest edges, and also whether mycorrhizal fungi play a role in this edge effect. At the same five sites, we established transects along forest edges and paired transects 15-25m out into the clearcut. We planted 958 Douglas fir seedlings, and we transplanted soil with each seedling: half received forest soil and the other half received soil from the invaded clearcut. Survival was much higher on the forest edge, and mycorrhizal colonization was also higher on the edge.  However, the effect of transplanting soil inoculum was not significant, and even the non-significant trend disappeared completely by the second year. Our results suggest that sites that are otherwise inhospitable for young trees and in which plantations have failed may still show potential to regenerate slowly, starting at the edges. These results also have implications for how the geometry of forest harvest methods influences reforestation success.

Sustainable forestry has been practiced for over a hundred years on the 16,000 ha of commercial forest lands on Joint Base Lewis-McChord. In the latter half of the 20^thcentury, the invasive shrub Scotch broom spread across the base, creating new challenges for reforestation efforts. Large areas of forest were essentially taken over by Scotch broom after trees were harvested.  Plantations have shown repeated failures, resulting in serious financial losses as well as a negative effect on military training. The primary objective of our project was to examine the impact of Scotch broom on establishment and growth of Douglas fir seedlings, and the effectiveness of different approaches to Scotch broom control in the forestry context. Here we report results from a number of related studies on [1] Douglas fir survival in previously invaded clearcuts, [2] Edge effects on Douglas fir survival, [3] Stimulating germination with disturbance, [4] Increase in Scotch broom cover after initial removal, [5]Variation across seasons in the effectiveness of Garlon 4 (triclopyr) herbicide, and [6]Legacy effects: Scotch broom effects on soil.

1. Douglas fir survival in previously invaded clearcuts. We set up a large-scale experiment (6.3ha total treatment area) with 12 treatments at 5 sites. We planted 7,448 two-year-old Douglas fir seedlings in March 2008 and censused 3,800 focal trees. In response to very high mortality, we replanted all focal trees in November 2008 or in March 2009. By September 2009, over 90% of these tree seedlings had died. This was the first documented evidence that direct competition from Scotch broom was not involved in Douglas fir plantation failure. Rather, soil or other abiotic conditions in the invaded clearcuts made these sites inhospitable to Douglas fir regeneration. We found no significant difference in survival between trees planted in November and trees planted in March.

2. Edge effects on Douglas fir survival. In a smaller study of 424 tree seedlings planted at different distances from two forest edges, we found a significant effect of distance from the nearest adult tree, and no difference between a north-facing and a south-facing edge, on survival through the first year. In another related study in March 2009, we planted Douglas fir seedlings along the edges of the same clearcuts described above, and we found higher survival along those edges than in the center of the clearcuts.

3. Stimulating germination with disturbance. Soil scarification is thought to stimulate germination of Scotch broom seeds out of the seedbank, relative to germination from seeds below established vegetation.We tested whether this effect of scarification is due to the physical disturbance of the soil or simply due to the removal of shade and competing vegetation. We compared Scotch broom germination from (1) control plots that had two-year-old undisturbed vegetation including Scotch broom, (2) plots scarified the previous year, and (3) plots treated with triclopyr the previous year. We found that both treatments had significantly more germination relative to the control, showing that part of the response to scarification is simply the removal of competition from established vegetation. In addition, scarified plots had significantly higher germination than herbicide plots, confirming that soil disruption had an additional stimulating effect on Scotch broom germination.

4. Increase in Scotch broom cover after initial removal.We tracked the rate of increase in percent cover of the invader Scotch broom over time in five sites. Patterns of Scotch broom cover after two years closely tracked patterns of seedling density in the first year rather than patterns of stump resprouting. However, after three years, the rank order of Scotch broom cover began to diverge from the initial germination data.

5. Variation across seasons in the effectiveness of Garlon 4 (triclopyr) herbicide. Restoration experts differ in their opinions about when is the best time to treat Scotch broom, often advocating for the importance of targeting the peak flowering season, or the dry season when the plant is most stressed. We quantified the effectiveness of chemical control in different seasons, spraying whole plots (56’ x 56’) with Garlon 4 Ultra (triclopyr) in March, May, or September of 2009, and measuring percent cover of Scotch broom in 2010. For this short-term response, all the spray treatments had strong effects relative to controls, and the effect of treatment seasonality was very small by comparison.

6. Legacy effects: Scotch broom effects on soil. Scotch broom is a nitrogen-fixing plant and therefore may ‘fertilize’ soils with increased N. At the same time, however, the plant produces N-rich defense compounds (alkaloids) that have been shown elsewhere to inhibit the growth and activity of some plants and microbes. Both of these effects may affect Douglas fir growth not only directly, but also indirectly via mycorrhizal associations, which may themselves be altered by changes in soil chemistry. We did a 19-month greenhouse experiment comparing invaded and uninvaded soils, with amendments of Scotch broom “mulch” (plant material added) and activated carbon (to bind allelochemicals). Both Douglas fir growth and mycorrhizal colonization were suppressed in invaded soils. Adding Scotch broom mulch to uninvaded soils increased Douglas fir growth, suggesting a nitrogen fertilization effect, but only in the presence of activated carbon.

The pest plant Scotch broom (Cytisus scoparius) is hindering effective reforestation at Fort Lewis, resulting in both a loss of land available for military training as well as a loss of native forest habitat for native plants and animals. Our primary objective was to examine the relative effectiveness of different broom control strategies that are appropriate for the forestry context, where the use of fire is not permitted. This document reports on the first year’s activities of a large research collaboration between personnel at the University of California Santa Cruz and at Fort Lewis. Key research questions include: What are the costs and benefits of an extended preliminary treatment phase, including two or even three years of soil scarification and control of small broom plants before planting? What is the relative effectiveness of chemical and mechanical treatment?

We set up a large-scale experiment (6.3ha total treatment area) at 5 sites, with a blocked design of 4 blocks per site with 6 plots per block. The plots were 56’x56’, designed to accommodate 49 tree seedlings (7x7) at 8’ spacing.  Scotch broom plants were removed from the entire site in fall of 2007 before the start of the experiment. We quantified Scotch broom stump density, mean diameter and height in each plot, as well as stump resprout rate and number of seedlings in spring of 2008. Initial stump density and size varied across sites. The resprout rate was low in four of the five sites, averaging 4 - 13% of stumps, but one site showed a very high resprout rate of 36%. Average seedling density, representing germination from the seedbank, varied across sites from <5 seedlings/m²to >100 seedlings/m². Most of the variation in seedling number was among sites (56%), followed by small-scale variation from quadrat to quadrat (30%), and plot to plot (12%). Almost no variation was seen across blocks within sites. We planted 7,448 two-year-old Douglas fir seedlings in March 2008. Over half of all Douglas fir seedlings died between March and September in almost all blocks, with close to 100% of the trees dying in one site, and over 80% of trees dying in some of the blocks of all sites. This was an unexpectedly high mortality rate, substantially higher mortality in these invaded clearcuts than mortality seen in other reforestation projects in smaller forest clearings on Fort Lewis.