Coral reef ecosystems contribute ~$30 billion USD annually to the global economy and harbor 1/4 of all known marine species. However, human activities have driven the loss of 50% of the world’s reefs over the last 30 years, and 90% of remaining reefs are predicted to be threatened by 2030. Thus, there is an urgent need for human interventions to support reef resilience to warming seas, overharvesting and pollution. Various studies have documented the influence of microbial symbionts on host physiology, demonstrated that some hosts are relatively mutable in the symbionts they harbor, and shown that symbionts can shift under stress. The large population sizes and short generation times of microorganisms allow them to rapidly evolve traits such as heat tolerance. Furthermore, trophic interactions between corals and their predators may facilitate the dispersal of microbial symbionts to prospective hosts across reefs. Over the last five years, my research group has sought creative ways to leverage microbial symbionts (e.g., dinoflagellates in the family Symbiodiniaceae, bacteria, viruses) and trophic interactions to improve coral colony and reef health. This talk will describe these efforts and associated challenges, and identify areas where transdisciplinary collaborations may offer solutions.
Past PMB Seminars
For a schedule of all Plant & Microbial Biology events, seminars, and lectures visit our calendar.
Transcriptome homeostasis in Arabidopsis: nuclear-cytoplasmic cross-talk and RNA buffering
My lab investigates the roles of mRNA decay in shaping the Arabidopsis transcriptome. Measurements of mRNA decay rates has revealed both detailed information on the roles of some mRNA decay components and demonstrated wide-spread mRNA buffering (compensation for changes in mRNA half-life that maintains normal mRNA abundances). Roles of mRNA decay and buffering in a transcriptome response to stimulus will be discussed.
The mitochondrial central dogma in health and disease
Mitochondria are the nexus of eukaryotic cellular energy metabolism and major signaling hubs that integrate information from within and without the cell to implement cell function. The product of an ancient endosymbiotic event, over millennia mitochondria have co-opted host cell resident resources, and in the process, the host and endosymbiont metabolism have become inextricably linked. Like the prokaryotes from which they are derived, mitochondria have a highly organized ultrastructure and also propagate a small DNA genome, packaged into proteinaceous structures termed 'mitochondrial nucleoids' and distributed throughout dynamic networks. I will discuss how mitochondrial form and function are integrated, the implications for spatiotemporal regulation of mitochondrial genome maintenance, and how these pathways may be co opted by mitochondrial viruses for their own survival.
Metabolic adaptation to transition metal starvation from bacteria to man
My group has long-standing interests in transition metal homeostasis, particularly in bacterial pathogens, in processes that may well be important during infections. An important antimicrobial weapon employed by the infected host is nutritional immunity, where high affinity transition metal binding proteins are deployed to sites of infections in an effort to starve bacteria of transition metal nutrients, including iron, manganese and zinc. We are particularly interested in pathogen adaptation to zinc (and iron) restriction and have focused these studies on the Gram-negative ESKAPE pathogen, Acinetobacter baumannii. These studies have lead to the identification and characterization of GTP-hydrolysis powered zinc metallochaperones, which are proposed to deliver a specific metal to a specific or small subset of apo-enzyme “clients”, but only under conditions of nutritional zinc deficiency. Our progress toward understanding these specialized zinc metallochaperones, conserved from bacterial to man, as well as specific metabolic processes in A. baumannii that are negatively impacted by transition metal restriction will be discussed.
Unraveling the role of lanthanides in biology: Discoveries, applications, and open questions
Lanthanides metals, long appreciated for their essential roles in technology, have recently been identified as critical elements for biology. Like other life metals, they are found in poorly soluble sources in nature, yet are widely used as cofactors for alcohol dehydrogenases involved in methylotrophy and one-carbon metabolism. My laboratory is studying how methylotrophs can sense, transport, use, and store lanthanides. We have identified a novel lanthanide chelator that we named methylolanthanin that is secreted to sequester lanthanides by the methylotroph Methylobacterium extorquens AM1. In addition, we have identified a lanthanide transport system, novel trafficking enzymes and new classes of enzymes that use lanthanides. My laboratory has also expanded the role of lanthanides to multi-carbon metabolism with substrates such as sugars and aromatic acids in organisms other than M. extorquens AM1, and we are currently identifying the metabolic involvement of these metals in diverse pathways. In addition, we are identifying how lanthanide biochemistry affects microbe-microbe and microbe-plant interactions. Finally, we have developed bacterial chassis for efficient lanthanide biomining to further the energy and agricultural industries.
[POSTPONED] The Control of Transposable Elements in Plants
Transposable Elements are fragments of DNA that can move themselves from one place in a genome to another, creating mutations and potentially genome instability. To control transposable elements, eukaryotic cells target them with chromatin modifications and/or DNA methylation to repress their transcription, and this regulation can be heritable (epigenetic). The Slotkin lab's long-term goal has been understand how plant cells first recognize transposable elements and trigger the cycle of chromatin modification and epigenetic silencing. We have used the transfer of foreign transposable elements from other plant species and fungi into the reference plant Arabidopsis to study the de novo initiation of epigenetic silencing, and through this process uncovered how to keep a foreign transposable element active in a plant genome. This control over transposable element activity is useful for genome engineering, as we can now control the activity, insertion site, cargo and timing of transposable elements in Arabidopsis and the major crop Soybean. Using transposable elements and a programmable nuclease such as Cas9 has provided us newfound control over transposable elements and the evolutionary processes they drive.
The secret life of cheese: Complexity of species interactions in a simple-ish microbiome
Previous work from my lab leveraged the tractability of the cheese microbiome to dissect the mechanisms and impacts of microbial interactions. Using a combination of top-down and bottom-up approaches, we have revealed complex interactions even in a relatively simple microbiome. This work has highlighted the importance of fungi in shaping communities, and the potential roles of horizontal gene transfer in shaping interactions and microbial evolution. At Arcadia Science, we are exploring ways to identify evolutionary innovations across the tree of life, including signatures such as horizontal gene transfer.
[Tsujimoto Lecture] Phenomics of Stomata and Water Use Efficiency in C4 crops
The Leakey group takes an integrative approach to understanding and improving the water use efficiency of C4 grasses. The talk will highlight recent work in physiology, genomics, genetics, agronomy that exploits new AI-enabled phenotyping techniques.
Genomics for Immunity: from natural diversity to precise modifications
The innate immune system is ancient and shared across kingdoms. Most organisms utilize innate immunity in the absence of an adaptive immunity to recognize rapidly evolving pathogens and elicit disease resistance response. Our laboratory works with plant, bacterial and fungal host-pathogen systems to understand biodiversity of the innate immune receptors and responses as well as the biodiversity of pathogens. Our goal is to apply this knowledge towards rapid, precise and sustainable engineering of disease resistance.
Fungi and Friends: An Expanded View of Fungal-Bacterial Interactions and Their Effects on Soil Biogeochemistry
The hyphosphere—the region of soil that surrounds fungal hyphae—is a hotspot of interactions that shape terrestrial microbial community composition and function. For example, arbuscular mycorrhizal fungi (AMF) can consume more than 20% of plant photosynthetic carbon (C) and shape both the composition and functionality of surrounding hyphosphere microbial communities. In collaboration with surrounding biota, mycorrhizae also mobilize N and water and stimulate the formation of stable soil carbon. To evaluate the quantitative impact of such ‘cross-kingdom’ interactions—involving fungi, bacteria, archaea, protists, microfauna and viruses—our group uses stable isotope probing (SIP) and metagenomics/transcriptomics to assess taxon-specific growth and mortality. Taken together, our findings illustrate how plant-associated fungi support enhanced biotic activity, resilience to water limitation, and faster turnover of native soil organic matter and fresh plant photosynthates in the hyphosphere.