Allison R. Wong

Bio: Allison R. Wong is an academic researcher from Pacific Northwest National Laboratory. The author has contributed to research in topics: Metagenomics & Ecology. The author has an hindex of 3, co-authored 5 publications receiving 41 citations. Previous affiliations of Allison R. Wong include Environmental Molecular Sciences Laboratory.

Intracellular pathways for lignin catabolism in white-rot fungi.

Abstract: Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in nature. While lignin depolymerization by WRF has been extensively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here, we employ 13C-isotope labeling, systems biology approaches, and in vitro enzyme assays to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel carbon from lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems and furthermore establish a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts-a key step toward enabling a sustainable bioeconomy.

Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils.

Abstract: Wetland soils are one of the largest natural contributors to the emission of methane, a potent greenhouse gas. Currently, microbial contributions to methane emissions from these systems emphasize the roles of acetoclastic and hydrogenotrophic methanogens, while less frequently considering methyl-group substrates (e.g., methanol and methylamines). Here, we integrated laboratory and field experiments to explore the potential for methylotrophic methanogenesis in Old Woman Creek (OWC), a temperate freshwater wetland located in Ohio, USA. We first demonstrated the capacity for methylotrophic methanogenesis in these soils using laboratory soil microcosms amended with trimethylamine. However, subsequent field porewater nuclear magnetic resonance (NMR) analyses to identify methanogenic substrates failed to detect evidence for methylamine compounds in soil porewaters, instead noting the presence of the methylotrophic substrate methanol. Accordingly, our wetland soil-derived metatranscriptomic data indicated that methanol utilization by the Methanomassiliicoccaceae was the likely source of methylotrophic methanogenesis. Methanomassiliicoccaceae relative contributions to mcrA transcripts nearly doubled with depth, accounting for up to 8% of the mcrA transcripts in 25-cm-deep soils. Longitudinal 16S rRNA amplicon and mcrA gene surveys demonstrated that Methanomassiliicoccaceae were stably present over 2 years across lateral and depth gradients in this wetland. Meta-analysis of 16S rRNA sequences similar (>99%) to OWC Methanomassiliicoccaceae in public databases revealed a global distribution, with a high representation in terrestrial soils and sediments. Together, our results demonstrate that methylotrophic methanogenesis likely contributes to methane flux from climatically relevant wetland soils.IMPORTANCE Understanding the sources and controls on microbial methane production from wetland soils is critical to global methane emission predictions, particularly in light of changing climatic conditions. Current biogeochemical models of methanogenesis consider only acetoclastic and hydrogenotrophic sources and exclude methylotrophic methanogenesis, potentially underestimating microbial contributions to methane flux. Our multi-omic results demonstrated that methylotrophic methanogens of the family Methanomassiliicoccaceae were present and active in a freshwater wetland, with metatranscripts indicating that methanol, not methylamines, was the likely substrate under the conditions measured here. However, laboratory experiments indicated the potential for other methanogens to become enriched in response to trimethylamine, revealing the reservoir of methylotrophic methanogenesis potential residing in these soils. Collectively, our approach used coupled field and laboratory investigations to illuminate metabolisms influencing the terrestrial microbial methane cycle, thereby offering direction for increased realism in predictive process-oriented models of methane flux in wetland soils.

Decrypting bacterial polyphenol metabolism in an anoxic wetland soil.

Abstract: Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially unavailable under anoxia, a supposition that has not been thoroughly investigated in any soil type. Here, we use anoxic soil reactors amended with and without a chemically defined polyphenol to test this hypothesis, employing metabolomics and genome-resolved metaproteomics to interrogate soil microbial polyphenol metabolism. Challenging the idea that polyphenols are not bioavailable under anoxia, we provide metabolite evidence that polyphenols are depolymerized, resulting in monomer accumulation, followed by the generation of small phenolic degradation products. Further, we show that soil microbiome function is maintained, and possibly enhanced, with polyphenol addition. In summary, this study provides chemical and enzymatic evidence that some soil microbiota can degrade polyphenols under anoxia and subvert the assumed polyphenol lock on soil microbial metabolism.

Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation

Abstract: Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation.We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems.These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. Video Abstract.

Biodegradable Antimicrobial Food Packaging: Trends and Perspectives

Abstract: This review presents a perspective on the research trends and solutions from recent years in the domain of antimicrobial packaging materials. The antibacterial, antifungal, and antioxidant activities can be induced by the main polymer used for packaging or by addition of various components from natural agents (bacteriocins, essential oils, natural extracts, etc.) to synthetic agents, both organic and inorganic (Ag, ZnO, TiO2 nanoparticles, synthetic antibiotics etc.). The general trend for the packaging evolution is from the inert and polluting plastic waste to the antimicrobial active, biodegradable or edible, biopolymer film packaging. Like in many domains this transition is an evolution rather than a revolution, and changes are coming in small steps. Changing the public perception and industry focus on the antimicrobial packaging solutions will enhance the shelf life and provide healthier food, thus diminishing the waste of agricultural resources, but will also reduce the plastic pollution generated by humankind as most new polymers used for packaging are from renewable sources and are biodegradable. Polysaccharides (like chitosan, cellulose and derivatives, starch etc.), lipids and proteins (from vegetal or animal origin), and some other specific biopolymers (like polylactic acid or polyvinyl alcohol) have been used as single component or in blends to obtain antimicrobial packaging materials. Where the package’s antimicrobial and antioxidant activities need a larger spectrum or a boost, certain active substances are embedded, encapsulated, coated, grafted into or onto the polymeric film. This review tries to cover the latest updates on the antimicrobial packaging, edible or not, using as support traditional and new polymers, with emphasis on natural compounds.

Effect of Long-Term Intake of Dietary Titanium Dioxide Nanoparticles on Intestine Inflammation in Mice

Abstract: Early stage exposure of foodborne substances, such as brightening agent titanium dioxide nanoparticles (TiO2 NPs), can cause long-term effects in adulthood. We aimed to explore the potential adverse effect of long-term dietary intake of TiO2 NPs. After feeding for 2-3 months from weaning, TiO2 NPs-exposed mice showed lower body weight and induced intestinal inflammation. However, this phenomenon was not observed in gut microbiota-removed mice. TiO2 NPs exposure rarely affected the diversity of microbial communities, but significantly decreased the abundance of several probiotic taxa including Bifidobacterium and Lactobacillus. Additionally, TiO2 NPs aggravated DSS-induced chronic colitis and immune response in vivo, and reduced the population of CD4+T cells, regulatory T cells, and macrophages in mesenteric lymph nodes. Therefore, dietary TiO2 NPs could interfere with the balance of immune system and dynamic of gut microbiome, which may result in low-grade intestinal inflammation and aggravated immunological response to external stimulus, thus introducing potential health risk.

Microbiological insights into anaerobic digestion for biogas, hydrogen or volatile fatty acids (VFAs): a review

Abstract: ABSTRACT In the past decades, considerable attention has been directed toward anaerobic digestion (AD), which is an effective biological process for converting diverse organic wastes into biogas, volatile fatty acids (VFAs), biohydrogen, etc. The microbial bioprocessing takes part during AD is of substantial significance, and one of the crucial approaches for the deep and adequate understanding and manipulating it toward different products is process microbiology. Due to highly complexity of AD microbiome, it is critically important to study the involved microorganisms in AD. In recent years, in addition to traditional methods, novel molecular techniques and meta-omics approaches have been developed which provide accurate details about microbial communities involved AD. Better understanding of process microbiomes could guide us in identifying and controlling various factors in both improving the AD process and diverting metabolic pathway toward production of selective bio-products. This review covers various platforms of AD process that results in different final products from microbiological point of view. The review also highlights distinctive interactions occurring among microbial communities. Furthermore, assessment of these communities existing in the anaerobic digesters is discussed to provide more insights into their structure, dynamics, and metabolic pathways. Moreover, the important factors affecting microbial communities in each platform of AD are highlighted. Finally, the review provides some recent applications of AD for the production of novel bio-products and deals with challenges and future perspectives of AD.

Recent Innovations in Emulsion Science and Technology for Food Applications.

Abstract: Emulsion technology has been used for decades in the food industry to create a diverse range of products, including homogenized milk, creams, dips, dressings, sauces, desserts, and toppings. Recently, however, there have been important advances in emulsion science that are leading to new approaches to improving food quality and functionality. This article provides an overview of a number of these advanced emulsion technologies, including Pickering emulsions, high internal phase emulsions (HIPEs), nanoemulsions, and multiple emulsions. Pickering emulsions are stabilized by particle-based emulsifiers, which may be synthetic or natural, rather than conventional molecular emulsifiers. HIPEs are emulsions where the concentration of the disperse phase exceeds the close packing limit (usually >74%), which leads to novel textural properties and high resistance to gravitational separation. Nanoemulsions contain very small droplets (typically d < 200 nm), which leads to useful functional attributes, such as high optical clarity, resistance to gravitational separation and aggregation, rapid digestion, and high bioavailability. Multiple emulsions contain droplets that have smaller immiscible droplets inside them, which can be used for reduced-calorie, encapsulation, and delivery purposes. This new generation of advanced emulsions may lead to food and beverage products with improved quality, health, and sustainability.

Nanocellulose-based composites for packaging applications

Abstract: Cellulose is one of the most interesting bioresources owing to its abundance, renewability, and biodegradability. Nanocellulose (NC), which can be isolated from natural cellulosic sources or synthesized by bacteria, has gained much research focus in recent years thanks to its non toxicity, recyclability, biodegradability, and reinforcing capability. The outstanding physical and mechanical properties of NC including high elastic modulus, high surface area, high strength, and high gas barrier properties have prompted its use in biomedical, cosmetic, electronics, and food packaging industries. In this review, we focus on NC sources, extraction methods, and use for the development of sustainable packaging materials. The processing methods of NC-based composites films, the effect of NC incorporation on the properties of packaging films, and health-related issues are discussed.