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Open Access Publications from the University of California

Scholarly Works (4 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2019)

The plant microbiome has proven to be an essential and often overlooked aspect of plant physiological ecology. Plant interactions with microbes are thought to have enabled the transition of plants from aquatic to terrestrial systems, thus co-evolving for millions of years. Consequently, microbes have important consequences for plant performance, nutrient cycling, and potentially even plant species ranges. However, our knowledge of these processes derives from only a few model systems. My dissertation explores these relationships in coast redwood forests where, despite their notoriety, plant-microbial relationships remain unexplored. Redwoods are the largest and some of the oldest plants on Earth, yet their geographical ranges are very constrained. As such, redwood forests serve as an excellent system to explore plant-microbial interactions and how they might expand or limit species ranges.

In Chapter 1, I demonstrate two unexpected and important findings related to the redwood root mycobiome. First, I show for the first time that, in addition to its expected association with arbuscular-mycorrhizal fungi (AMF), redwood roots are also associated with with ecto- and ericoid mycorrhizal fungi. To our knowledge, this is the first evidence that this predominantly AMF-associated tree is also colonized by the other two primary types of mycorrhizal fungi. These findings challenge the common practice of AMF-specific sequencing methods and the paradigm that plant species are assumed to associate with only one type of mycorrhizal fungi. This is important because it may link this tree species to the surrounding trees and shrubs that co-occur in these habitats. Secondly, I describe unique structures, which I call “rhizonodes”, that show many parallels in microbial community assembly to well-described nodules in N-fixing plants where rhizonodes act as reservoirs of AMF in the redwood roots. The presence of rhizonodes similarly are a unique finding that seem to occur in other predominantly AMF-associated tree species, but have been widely overlooked. We posit that these structures may be important domiciles for AMF in many of the upwards of 80% of plant species predicted to form relationships with this group. These findings also suggest that arbuscular mycorrhizal fungi (AMF) may play key roles in redwood physiology.

In Chapter 2, I focus on redwood association with AMF and the functional consequences of these interactions for plant hosts. I found that mycorrhization of coast redwood proceeds a number of downstream consequences for redwood hosts including in morphology, growth, allocation, hormonal physiology, drought-response, and leaf-level physiology. In addition, I found that mycorrhizal seedlings demonstrate progressively higher rates of photosynthesis compared to non-mycorrhizal seedlings in response to rising CO2. Together, these findings indicate that mycorrhizal fungi are likely to become increasingly important more broadly for plant response to climate change.

In Chapter 3, I demonstrate the importance of site-specific water-availability on the root-associated bacterial community in redwood. Previous work on crop plants has shown that artificial drought selects for monoderm bacteria, or bacterial taxa with a single, thick cell-wall layer. I present evidence of similar trends for a long-lived tree species in response to local water-availability. While the consequences of interactions with these types of bacteria remain unknown, as increased intensity and severity of drought are predicted as a result of climate change, I highlight the importance of testing the downstream consequences of monoderm versus diderm dominated bacterial communities on plant physiology, nutrient cycling, and ecosystem function.

Taken together, these studies suggest that the root microbiome is an important axis in understanding the response of redwood forest to climatic and environmental change predicted in the Anthropocene. Further, our study of a basal gymnosperm highlights important gaps in our understanding and categorization of plant-microbe interactions and emphasizes the importance of future investigations on non-model plant organisms.

    Cover page: The Redwood Microbiome: Microbial community composition and functional consequences of plant-microbe interactions for the tallest species on Earth
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2021)
    Range shifts of infectious plant disease are expected under climate change. As plant diseases move, emergent abiotic-biotic interactions are predicted to modify their distributions, leading to unexpected changes in disease risk. Evidence of these complex range shifts due to climate change, however, remains largely speculative. Here, we combine a long-term study of the infectious tree disease, white pine blister rust, with a six-year field assessment of drought-disease interactions in the southern Sierra Nevada. We find that climate change between 1996 and 2016 moved the climate optimum of the disease into higher elevations. The nonlinear climate change-disease relationship contributed to an estimated 5.5 (4.4-6.6) percentage points (p.p.) decline in disease prevalence in arid regions and an estimated 6.8 (5.8-7.9) p.p. increase in colder regions. Though climate change likely expanded the suitable area for blister rust by 777.9 (1.0-1392.9) km2 into previously inhospitable regions, the combination of host-pathogen and drought-disease interactions contributed to a substantial decrease (32.79%) in mean disease prevalence between surveys. Specifically, declining alternate host abundance suppressed infection probabilities at high elevations, even as climatic conditions became more suitable. Further, drought-disease interactions varied in strength and direction across an aridity gradient-likely decreasing infection risk at low elevations while simultaneously increasing infection risk at high elevations. These results highlight the critical role of aridity in modifying host-pathogen-drought interactions. Variation in aridity across topographic gradients can strongly mediate plant disease range shifts in response to climate change.
      Cover page: Nonlinear shifts in infectious rust disease due to climate change
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2022)
      Elucidating the temporal dynamics of arbuscular mycorrhizal (AM) fungi is critical for understanding their functions. Furthermore, research investigating the temporal dynamics of AM fungi in response to agricultural practices remains in its infancy. We investigated the effect of nitrogen fertilisation and watering reduction on the temporal dynamics of AM fungi, across the lifespan of wheat. Nitrogen fertilisation decreased AM fungal spore density (SD), extraradical hyphal density (ERHD), and intraradical colonisation rate (IRCR) in both watering conditions. Nitrogen fertilisation affected AM fungal community composition in soil but not in roots, regardless of watering conditions. The temporal analysis revealed that AM fungal ERHD and IRCR were higher under conventional watering and lower under reduced watering in March than in other growth stages at low (≤ 70 kg N ha-1  yr-1 ) but not at high (≥ 140) nitrogen fertilisation levels. AM fungal SD was lower in June than in other growth stages and community composition varied with plant development at all nitrogen fertilisation levels, regardless of watering conditions. This study demonstrates that high nitrogen fertilisation levels disrupt the temporal dynamics of AM fungal hyphal growth but not sporulation and community composition.
        Cover page: Nitrogen fertilisation disrupts the temporal dynamics of arbuscular mycorrhizal fungal hyphae but not spore density and community composition in a wheat field
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2024)
        Most of Earths trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earths land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.
          Cover page: Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities.
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