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The 2025 Applied and Environmental Microbiology Gordon Research Conference took place July 13-18, 2025 at Mount Holyoke College in South Hadley, Massachusetts. The associated Gordon Research Seminar took place at the same location from July 12-13, 2025.
Environmental microbiology applied to planetary quarantine
The annual report presents the fiscal year (FY) 1990 research activities and accomplishments for the Catalysis and Biocatalysis Program of the Advanced Industrial Concepts Division (AICD), Office of Industrial Technologies of the Department of Energy (DOE). The mission of the AICD is to create a balanced program of high risk, long term, directed interdisciplinary research and development that will improve energy efficiency and enhance fuel flexibility in the industrial sector. The Catalysis and Biocatalysis Program's technical activities were organized into five work elements: the Molecular Modeling and Catalysis by Design element; the Applied Microbiology and Genetics element; the Bioprocess Engineering element; the Separations and Novel Chemical Processes element; and the Process Design and Analysis element.
Final Conference Program & Registration List
Soil microbes strongly influence the soil organic carbon (SOC) pool, which globally stores ~2,000 PgC. Specifically, the balance between microbial heterotrophic respiration (R H ), which degrades SOC, and plant–microbe interactions that stabilize SOC determines whether terrestrial ecosystems are a net source or sink of CO 2 to the atmosphere. Here, in this Review, we evaluate how climate change alters these competing processes. R H is approximately half of total soil respiration, at ~50 PgC yr −1 , with 70% occurring in topsoils. Warming accelerates microbial metabolism, with a 10 °C temperature increase estimated to raise R H by ~50%, an effect that is particularly strong in Arctic soils. Warming also reduces soil moisture, further modulating R H , which responds nonlinearly to soil moisture, being limited by saturation and desiccation and meeting a maximum at intermediate levels. Consequently, R H is highly sensitive to future precipitation changes and drought. However, soil management strategies could enhance SOC stocks and persistence under climate change. Bacterial and fungal inoculants can promote SOC production and stabilization, while deep-rooting plants increase SOC inputs to deeper layers that experience lower R H . Agricultural practices and biochar amendments can also enhance SOC and reduce R H . Expanding field trials across regions, climates and soil types would improve empirical understanding of these responses and support better representation of R H in predictive models, enabling more accurate assessments of climate impacts on SOC storage.
Engineering subcellular organization in microbes shows great promise in addressing bottlenecks in metabolic engineering efforts; however, rules guiding selection of an organization strategy or platform are lacking. Here, we study compartment morphology as a factor in mediating encapsulated pathway performance. Using the 1,2-propanediol utilization microcompartment (Pdu MCP) system from Salmonella enterica serovar Typhimurium LT2, we find that we can shift the morphology of this protein nanoreactor from polyhedral to tubular by removing vertex protein PduN. Analysis of the metabolic function between these Pdu microtubes (MTs) shows that they provide a diffusional barrier capable of shielding the cytosol from a toxic pathway intermediate, similar to native MCPs. However, kinetic modeling suggests that the different surface area to volume ratios of MCP and MT structures alters encapsulated pathway performance. Finally, we report a microscopy-based assay that permits rapid assessment of Pdu MT formation to enable future engineering efforts on these structures.
The microbiological aspects of clean room technology as applied to surgery were reviewed. The following pertinent subject areas were examined: (1) clean room technology per se and its utilization for surgery, (2) microbiological monitoring of the clean room surgical environment, (3) clean rooms and their impact on operating room environmental microbiology, and (4) the effect of the technology on surgical wound infection rates. Conclusions were drawn for each topic investigated.
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 A resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. Here, we propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
Abstract Efforts to drive catalytic reactions with light, inspired by natural processes like photosynthesis, have a long history and have seen significant recent growth. Successfully engineering systems using biomolecular and bioinspired catalysts to carry out light‐driven chemical reactions capitalizes on advantages offered from the fields of biocatalysis and photocatalysis. In particular, driving reactions under mild conditions and in water, in which enzymes are operative, using sunlight as a renewable energy source yield environmentally friendly systems. Furthermore, using enzymes and bioinspired systems can take advantage of the high efficiency and specificity of biocatalysts. There are many challenges to overcome to fully capitalize on the potential of light‐driven biocatalysis. In this mini‐review, we discuss examples of enzymes and engineered biomolecular catalysts that are activated via electron transfer from a photosensitizer in a photocatalytic system. We place an emphasis on selected forefront chemical reactions of high interest, including CH oxidation, proton reduction, water oxidation, CO 2 reduction, and N 2 reduction.
Nitrogen is the most limiting plant nutrient. Inexpensive natural gas has substantially reduced costs of ammonia fertilizer for intensive agriculture in the developed world, but its excessive use negatively impacts downstream ecosystems. By contrast, the availability of ammonia fertilizer is a major economic bottleneck for agriculture in developing countries. A dedicated lignocellulosic biomass crop could supply sufficient substrate to generate optimal nitrogen fertilizer on less than 5% of a grower’s food crop acreage. However, reimagining ammonia generation using biomass could significantly enhance sustainable agricultural productivity in developing countries when combined with emerging catalytic technologies.
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Major progress in the bioprocessing of lignocellulose to fuels and value-added chemicals has created the possibility of a low carbon-footprint economy. However, the current complexity and associated costs of lignocellulose conversion result in a higher price for ethanol than for fossil fuels. The cost of cellulosic ethanol production will be lowered by further progress in development of biorefinery technology that produces both ethanol and high-value chemicals with bio-based products that are beginning to penetrate consumer markets in the USA, Brazil, and worldwide. The cost-effectiveness of low carbon-footprint bioproducts will benefit from advances in supplying large amounts of biomass solids to the biorefinery. We describe here outcomes from a successful long-term international cooperation between the Laboratory of Renewable Resources Engineering (LORRE) at Purdue University in the United States and Brazil's Agricultural Research Corporation (EMBRAPA) and Federal University of Sâo Carlos (UFSCar), which has contributed practical pathways to enhance the biorefinery concept. Furthermore, this paper gives an overview of developments that address fundamental knowledge of lignocellulosic biomass pretreatment hydrolysis under optimized operational conditions and bioreactor configurations, and the science and engineering that contributes to the effective production of fuel and ethanol and value-added products from biomass.
Wood pallets are ubiquitous products that can be recovered and reused to enhance their service life and environmental performance. Repair/remanufacturing has an important role in extending the service life of the wood pallet. To quantify environmental performances of wood pallet reuse, this study developed representative life cycle inventory data for pallet repair/remanufacturing in the United States based on comprehensive industry-wide production data for 2018. A gate-to-gate life cycle assessment covering raw material supply, raw material transportation and pallet repair/remanufacturing showed that repair/remanufacturing often had the highest impacts, including primary energy consumption at 5.09 MJ and global warming impact at 0.355 kg CO 2 eq per repaired/remanufactured pallet. Electricity consumed onsite followed by nail input and the fuel used by forklifts during the manufacturing drove much of the impacts on the environment. Finally, the results of this study provide valuable information on the repair/remanufacturing impacts, allowing quantification and evaluation of the recovery stage on the overall environmental performance of wood pallets.
Triacetic acid lactone (TAL), an emerging bioprivileged molecule, can be produced microbially and further chemically upgraded to several high-value chemicals. In this work, several acidic and basic ion-exchange resins and activated charcoal were evaluated for their ability to adsorb microbially produced TAL. Activated charcoal and a weak base resin, Dowex 66, showed similar TAL adsorption capacity of 0.18 ± 0.002 g/g. At 15% w/v activated charcoal, about 98% of TAL present in fermentation broth could be adsorbed. Further, ethanol washing allowed recovery of 72% of adsorbed TAL. A biorefinery producing TAL from sucrose was designed, simulated, and evaluated (through technoeconomic analysis) under uncertainty, for an estimated TAL minimum product selling price (MPSP) of $\$4.27$/kg ($\$3.71$–4.94/kg; 5th–95th percentiles) given the current state of technology and $\$2.83$/kg ($\$2.46$–3.29/kg) following potential near-term improvements to fermentation. This work provides an adsorptive process for the recovery of microbially produced TAL that can be upgraded chemically to a range of industrial products.
Here, high-moisture pelleting of corn stover was tested in pilot- and commercial-scale systems. For the pilot-scale study, a 6.35 mm screen size hammer mill ground corn stover was reconditioned to moisture between 14 and 29.6% (w.b.), and 5, 7 and 9 L/D ratio pellet die were used. At 29% corn stover moisture content and L/D ratios of 5 and 9, the bulk density and durability of the pellets were ≤450 kg/m 3 and <90% and >540 kg/m 3 and >90%, respectively. Increasing the feedstock moisture and L/D ratio increased the pelleting energy. Increasing the hammer mill screen size to 11.11 mm reduced the bulk density but not the durability. The response surface models adequately described the pelleting process (R 2 ≥ 0.88), and analysis of variance showed a strong interaction between the process variables and pellet properties. Commercial-scale testing of high-moisture pelleting using 6.35 mm ground corn stover bales in the moisture range 24–26% (w.b.) produced pellets with a density of >675 kg/m 3 and durability of >98%, whereas increasing the hammer mill screen size to 11.11 mm reduced the bulk density by about 100 kg/m 3 but not the durability. The energy consumption of the commercial-scale unit operations for the high-moisture pelleting process was in the range 98–124 kW h/ton, which is 64–72% less energy than conventional pelleting that requires energy about 350 kW h/ton for biomass drying from 30% (w.b.) to 10% (w.b.) moisture content before pelleting. Pellets produced using high-moisture pelleting met International Organization for Standardization and Pellets Fuel Institute international standards. Published 2023. This article is a U.S. Government work and is in the public domain in the USA.
The feedstock supply chain of a biorefinery is critical in determining the economic and environmental performance of biofuels. This study investigated various feedstock supply chains for a centralized biorefinery based on different objective functions and how the biorefinery responds to supply chain volatility. For the analysis, a hypothetical centralized biorefinery was supplied by switchgrass grown on marginal lands in Michigan. From an economic standpoint, the minimum biofuel selling price is an important metric of the objective function, and the greenhouse gas mitigation potential is a similarly important metric for global warming impact. A trade-off therefore exists between the economic and environmental performance of biofuels under this system configuration. However, when a carbon tax credit is applied to soil organic carbon sequestration in switchgrass production, the metric of the objective function may not be the key factor in establishing a supply chain as long as it is associated with biorefinery capacity as well as economic or environmental values. Year-to-year fluctuations in cellulosic biomass yield (supply chain volatility) might also prevent the biorefinery from operating at full capacity. Cellulosic biomass pellets can serve as an auxiliary feedstock for the centralized cellulosic biorefinery system to minimize the impacts of supply chain volatility.
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