Environmental Microbiology and Ecotoxicology Lab
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Environmental Microbiology
One focus in our lab is to study the ecophysiological and genetic mechanisms of microbial mercury (Hg) methylation and methylmercury (MeHg) degradation (Fig. 1). For instance, one species of methanogens was first confirmed as a novel Hg methylator (Yu et al. 2013. AEM. 79(20): 6325-6330), suggesting methanogens acting as a new guild of Hg methylating microbes aside from the SRB and iron reducing bacteria.
Further study by Yu et al. (Fig. 2, Yu et al. 2018. ISME J 12: 1826–1835) clearly established that, syntrophy among methanogen, SRB and Syntrophobacter significantly stimulated Hg methylation over that from the monoculture alone. This novel study indicated that syntrophic associations between Syntrophobacter and Desulfovibrio in freshwater and coastal ecosystems significantly stimulated MeHg synthesis. The research could lead to the technology used for final remediation of almost ubiquious contamination of Hg and MeHg in natural aquatic ecosystems and wetlands.
Fig. 2. Microbial Hg methylation by syntrophic interactions and pathways in freshwater and marine ecosystems (revised from Yu et al. 2018. ISME J 12:1826–1835).
Fig. 1. Microbial Hg biotransformation mechanisms with functional genes (revised from Yu et al. 2012. ES&T 46 (5), 2684-2691).
Microbial Stilbene Degradation in Plant Allelopathy
Bacteria or archaea play a key role in the interactions with plants in carbon cycling, energy utilization, hormone synthesis, and pathogen infection. One interesting phenomenon is stilbene allelopathy, in which plants such as peanuts and grapes could synthesize and release varied stilbenoid chemicals such as resveratrol and pterostilbene to inhibit fungal infection (Fig. 3). Stilbenoids are also natural products with pharmaceutical functions for anticancer and antioxidation. The microbial metabolism pathway and the gene expression of carotenoid cleavage oxygenases which degrade stilbenes are intriguing (Fig. 4).
Fig. 3. Analogs of resveratrol synthesized by plants as antifungal allelochemicals (Yu et al. 2019. AEM 85, e02154-18. https://doi.org/10.1128/AE) .
Fig. 4. Proposed degradation pathways for pterostilbene and resveratrol in Sphingobium sp. JS1018, and phylogeny of cco genes in microbes (Yu et al. 2019. AEM 85, e02154-18).
Microbial Metagenomics and Bioinformatics
Microbial metagenomics are very important tools in characterizing functioning genes and microbial communities in bioremediation and microbial interactions with plants and animals. Our lab also employs a variety of bioinformatic programs to explore molecular evolution, in-situ microbial communities, and genome features of isolated functioning species in contaminated habitats (Fig. 5) and biofuel studies.
Figure 5. Microbial community abundance and potential mercury methylating microbes in the sediment samples of Caddo Lake, Texas.
Aquatic Ecotoxicology and Metal Bioavailability
Trophic transfer of toxic metals (e.g., Hg, Cd, Cr, Se) from bacteria or microbial eukaryote (algae) to microzooplankton is the key entry link for metal accumulation in fish or macroinvertebrates (e.g.,bivalves), and even mammals via biogeochemical cycling. Contamination of metals (Yu, Yu & Gui et al. 2018. Aquat Toxicol 203: 179-186), organic pollutants (Xie, Yu & Yu et al. 2021. Sci Total Environ 800: 149512), and microplastics (Zhang, Luo & Yu et al. 2021. Environ Pollut 270, 116057) in aquatic fish products or seafood will cause severe health issues of human and mammals. The bioavailability studies of metals and organic pollutants in the aquatic food webs provide fundamental perspectives for aquatic ecotoxicology.
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