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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.
The ENIGMA science focus area (SFA) is a multi-disciplinary, multi-institutional research effort focused on addressing foundational knowledge gaps in environmental microbial communities by studying groundwater and sediment microbiomes in the shallow subsurface at the contaminated Oak Ridge Reservation (ORR). We seek to discover and characterize the reciprocal interactions between the microbial communities and the geochemical and geophysical parameters of the shallow subsurface within the contamination plume. The primary goal of this subcontract was to develop experimental and computational tools to advance our understanding of microbial adaptation and community assembly in contaminated environments, with specific efforts in high-throughput genomic methods, microbial ecology tools, and studies of heavy metal contamination impacts.
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The Bakken Shale and underlying Three Forks Formation is an important oil and gas reservoir in the United States. The hydrocarbon resources in this region are accessible using unconventional oil and gas extraction methods, including horizontal drilling and hydraulic fracturing. However, the geochemistry and microbiology of this region are not well understood, although they are known to have major implications for productivity and water management. In this study, we analyzed the produced water from 14 unconventional wells in the Bakken Shale using geochemical measurements, quantitative PCR (qPCR), and 16S rRNA gene sequencing with the overall goal of understanding the complex dynamics present in hydraulically fractured wells. Bakken Shale produced waters from this study exhibit high measurements of total dissolved solids (TDS). These conditions inhibit microbial growth, such that all samples had low microbial loads except for one sample (well 11), which had higher 16S rRNA gene copies. Our produced water samples had elevated chloride concentrations typical of other Bakken waters. However, they also contained a sulfate concentration trend that suggested higher occurrence of sulfate reduction, especially in wells 11 and 18. The unique geochemistry and microbial loads recorded for wells 11 and 18 suggest that the heterogeneous nature of the producing formation can provide environmental niches with conditions conducive for microbial growth. This was supported by strong correlations between the produced water microbial community and the associated geochemical parameters including sodium, chloride, and sulfate concentrations. The produced water microbial community was dominated by 19 bacterial families, all of which have previously been associated with hydrocarbon-reservoirs. These families include Halanaerobiaceae, Pseudomonadaceae, and Desulfohalobiaceae which are often associated with thiosulfate reduction, biofilm production, and sulfate reduction, respectively. Notably, well 11 was dominated by sulfate reducers. Our findings expand the current understanding of microbial life in oil and gas related environments, provide new insights into how the unique produced water conditions shape microbial communities, and demonstrate thatproduced water chemistry is tightly linked with microbiota in the Bakken Shale. Finally, our study shows that additional research efforts are necessary to understand this ecosystem and highlights the need for work in other unconventional reservoirs.
ABSTRACT Purple sulfur bacteria (PSB) are capable of anoxygenic photosynthesis via oxidizing reduced sulfur compounds and are considered key drivers of the sulfur cycle in a range of anoxic environments. In this study, we show that Allochromatium vinosum (a PSB species) is capable of autotrophic growth using pyrite as the electron and sulfur source. Comparative growth profile, substrate characterization, and transcriptomic sequencing data provided valuable insight into the molecular mechanisms underlying the bacterial utilization of pyrite and autotrophic growth. Specifically, the pyrite-supported cell cultures (“py”’) demonstrated robust but much slower growth rates and distinct patterns from their sodium sulfide-amended positive controls. Up to ~200-fold upregulation of genes encoding various c - and b -type cytochromes was observed in “py,” pointing to the high relevance of these molecules in scavenging and relaying electrons from pyrite to cytoplasmic metabolisms. Conversely, extensive downregulation of genes related to LH and RC complex components indicates that the electron source may have direct control over the bacterial cells’ photosynthetic activity. In terms of sulfur metabolism, genes encoding periplasmic or membrane-bound proteins (e.g., FccAB and SoxYZ) were largely upregulated, whereas those encoding cytoplasmic proteins (e.g., Dsr and Apr groups) are extensively suppressed. Other notable differentially expressed genes are related to flagella/fimbriae/pilin(+), metal efflux(+), ferrienterochelin(−), and [NiFe] hydrogenases(+). Characterization of the biologically reacted pyrite indicates the presence of polymeric sulfur. These results have, for the first time, put the interplay of PSB and transition metal sulfide chemistry under the spotlight, with the potential to advance multiple fields, including metal and sulfur biogeochemistry, bacterial extracellular electron transfer, and artificial photosynthesis. IMPORTANCE Microbial utilization of solid-phase substrates constitutes a critical area of focus in environmental microbiology, offering valuable insights into microbial metabolic processes and adaptability. Recent advancements in this field have profoundly deepened our knowledge of microbial physiology pertinent to these scenarios and spurred innovations in biosynthesis and energy production. Furthermore, research into interactions between microbes and solid-phase substrates has directly linked microbial activities to the surrounding mineralogical environments, thereby enhancing our understanding of the relevant biogeochemical cycles. Our study represents a significant step forward in this field by demonstrating, for the first time, the autotrophic growth of purple sulfur bacteria using insoluble pyrite (FeS2) as both the electron and sulfur source. The presented comparative growth profiles, substrate characterizations, and transcriptomic sequencing data shed light on the relationships between electron donor types, photosynthetic reaction center activities, and potential extracellular electron transfer in these organisms capable of anoxygenic photosynthesis. Furthermore, the findings of our study may provide new insights into early-Earth biogeochemical evolutions, offering valuable constraints for understanding the environmental conditions and microbial processes that shaped our planet’s history.
The dataset is comprised of grain size, bulk density, carbon and nitrogen content, stable carbon isotopes, and radiocarbon content of soils sampled on the floodplain of the Koyukuk River near Huslia, AK. This dataset was collected to characterize sediment properties and floodplain organic carbon stocks in the discontinuous permafrost floodplain of the Koyukuk River. The data help quantify the flux and storage of sediment and carbon between the Koyukuk River and the surrounding floodplain as the river migrates laterally. The samples were collected in June 27 - July 9, 2018. The soil samples come from a total of 24 locations and were sampled in the upper 490 cm of the river cutbanks, point bars, and floodplain. Samples were analyzed for bulk density, full particle size distribution, nitrogen content and carbon content and isotopes, though not all samples were included in each analysis. An additional 10 samples of floodplain woody debris were measured for radiocarbon content. Data, detailed methods, analyses, and interpretations were previously published at: Douglas, M. M., Lingappa, U. F., Lamb, M. P., Rowland, J. C., West, A. J., Li, G., et al. (2021). Impact of river channel lateral migration on microbial communities across a discontinuous permafrost floodplain. Applied and Environmental Microbiology, 87(20), AEM.01339-21. https://doi.org/10.1128/AEM.01339-21 Douglas, M. M., Li, G. K., Fischer, W. W., Rowland, J. C., Kemeny, P. C., West, A. J., et al. (2022). Organic carbon burial by river meandering partially offsets bank erosion carbon fluxes in a discontinuous permafrost floodplain. Earth Surface Dynamics, 10(3), 421–435. https://doi.org/10.5194/esurf-10-421-2022 The dataset is comprised of a total of three separate data files based on the sample type and analysis, including a file that lists the sample locations, permafrost presence, and geomorphic landform.
The functional roles of bacterial symbionts associated with microalgae remain understudied despite the importance of microalgae in biotechnology and environmental microbiology. 16S rRNA gene sequencing was conducted to analyze bacterial communities associated with two microalgae optimized for growth with flue gas containing 5%–10% CO 2 . Two dominant bacteria with no taxonomic classification beyond the class level (Paceibacteria) were discovered repeatedly in the most productive algal cultures. Long-read metagenomic sequencing was conducted to yield high-quality metagenomes, from which two novel species were discovered under the Seqcode (seqco.de/r:ywe1blo2), Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov. The genus Phycocordibacter gen. nov. was proposed as the nomenclatural type of the family Phycocordibacteraceae fam. nov. and the order Phycocordibacterales ord. nov. Both bacteria possessed features typical of Patescibacteria such as reduced genomes (<800 kbp), lack of complete glycolysis and tricarboxylic acid (TCA) cycle pathways, and inability to synthesize amino acids. Instead, they rely on the reductive pentose phosphate pathway (Calvin cycle) for essential biosynthesis and redox balance. P. aenigmaticus may also rely on elemental sulfur oxidation (sdo), partial nitrite reduction (nirK), and sulfur-related amino acid metabolism (SAMe → SAH). Both bacteria were found in high relative abundance in cultures of Tetradesmus obliquus HTB1 (freshwater) and Nannochloropsis oceanica IMET1 (marine), suggesting a tight association with microalgae in various environments. The absence of full metabolic pathways for energy production suggests extreme metabolic limitations and obligate symbiosis, most likely with other bacteria associated with the microalgae.
Sulfate minerals are abundant on the Martian surface, and many of these evaporite deposits are thought to have precipitated from acidic fluids. On Earth, gypsum (CaSO 4 •2H 2 O) and other sulfates sometimes form under acidic conditions, so exploring the extremophilic life that occurs in these mineral environments can help evaluate the astrobiological potential of acid sulfate depositional settings. Here, we characterized the microbial communities associated with acidic gypsum deposits in a sulfuric acid cave, where sulfate precipitation is driven by sulfide-oxidizing bacteria and archaea. We used 16S rRNA gene sequencing and cell counts to characterize gypsum-associated microorganisms in freshly formed and relict deposits throughout the cave, to test how microbial community composition and abundance would vary with distance from the sulfidic water table and with the concentration of H 2 S(g) and other gases in the cave atmosphere. We found that actively forming gypsum in the lower cave levels was colonized by low-diversity communities that have few cells compared to other environments in the cave. The most abundant taxa were Acidithiobacillus, Metallibacterium, Mycobacteria, and three different Thermoplasmatales-group archaea, which occupied distinct niches based on proximity to sulfidic streams and the concentration of gases in the cave air. By contrast, deposits in older cave levels had more diverse communities that were distinct from those associated with freshly formed gypsum and likely represent a community reliant on different energy resources. These findings show that acidic sulfate deposits serve as habitats for extremophilic microorganisms and broaden our knowledge of the life associated with terrestrial sulfates.
In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.
The Lake Arrowhead Microbial Genomics Conference (formerly the E. coli and Small Genomes Conference, and the Microbial Genomes Conference) was held September 11-15, 2022, at the UCLA Conference Center at Lake Arrowhead, California. This conference is part of a yearly meeting initiated in 1991 to bring together genome sequencers, bioinformatics specialists, biologists, and geneticists, to forge interactions that would result in meaningful functional genomics. The goal of the meeting was to translate the influx of new genome sequencing information into useful biological studies. The Lake Arrowhead 2022 meeting had a major focus on microbial communities, the human microbiome, pathogens, phage therapy, bioinformatic methods of analysis, bioenergenics, and environmental microbiology. The field of genomics has reached the point where deriving the sequence of an organism’s entire genome is now seen as a beginning rather than an endpoint. Moreover, understanding the sequences of whole communities, and particularly those that make up different microbiomes, is now a central point of the field. The 2022 meeting covered microorganisms for which extensive analyses exist, and those for which new biological and technical strategies are being developed. The focus on biodiversity, the human microbiome, pathogenic organisms and methods of countering them, and bioenergetics added special significance to this meeting. This meeting was designed to have a mix of 36 invited presentations and poster sessions with more than 80 posters, and had 147 participants. This meeting has become established as a major annual microbial genomics conference during the last 29 years and has assured status and quality. It offers a major opportunity for young investigators and students to attend, present posters, and give talks. In fact, 50% of the invited speakers were early career stage scientists. An important impact of the conference was the forging of new collaborations between scientists and particularly young scientists with the array of multidisciplinary researchers at the meeting.
For presentation at the Gordon Conference in Applied and Environmental Microbiology, Mt. Holyoke, MA, July 16-21, 2023.
Poster for the Gordon Research Conference Applied and Environmental Microbiology, July 16-21 2023, South Hadley, MA.
Abstract Waste plastic presently accumulates in landfills or the environment. While natural microbial metabolisms can degrade plastic polymers, biodegradation of plastic is very slow. This study demonstrates that chemical deconstruction of polyethylene terephthalate (PET) with ammonium hydroxide can replace the rate limiting step (depolymerization) and by producing plastic-derived terephthalic acid and terephthalic acid monoamide. The deconstructed PET (DCPET) is neutralized with phosphoric acid prior to bioprocessing, resulting in a product containing biologically accessible nitrogen and phosphorus from the process reactants. Three microbial consortia obtained from compost and sediment degraded DCPET in ultrapure water and scavenged river water without addition of nutrients. No statistically significant difference was observed in growth rate compared to communities grown on DCPET in minimal culture medium. The consortia were dominated by Rhodococcus spp., Hydrogenophaga spp., and many lower abundance genera. All taxa were related to species known to degrade aromatic compounds. Microbial consortia are known to confer flexibility in processing diverse substrates. To highlight this, we also demonstrate that two microbial consortia can grow on similarly deconstructed polyesters, polyamides, and polyurethanes in water instead of medium. Our findings suggest that microbial communities may enable flexible bioprocessing of mixed plastic wastes when coupled with chemical deconstruction.
In the version of this article initially published, four people were missing from the alphabetical list of IMG/M Data Consortium members: Lauren V. Alteio of the Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria; Jeffrey L. Blanchard of the Biology Department, University of Massachusetts Amherst, Amherst, MA, USA; Kristen M. DeAngelis of the Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA; and William Rodriguez-Reillo of the Research Computing Division, Harvard Medical School, Boston, MA, USA. The error has been corrected in the PDF and HTML versions of the article.
Climate change amplifies many threats to human health. Despite advances in understanding climate change dynamics and impacts, there remains a critical gap in translating scientific knowledge into equitable, and community-driven health interventions. The inaugural One Earth, One Health workshop sought to explore this gap through human-centered design exercises involving interdisciplinary researchers from climate and Earth sciences, engineering, epidemiology, microbiology, and environmental health. Although participants did not co-develop solutions with affected communities, they used stakeholder role-playing to guide ideation and lay groundwork for actionable plans. Through these methods, participants identified community needs and proposed prototype solutions to alleviate health threats exacerbated by global environmental change. Prototypes were organized around infectious diseases, extreme weather, and air quality, as illustrative themes rather than an exhaustive set of risks. Key solutions included strategies for anticipatory systems and early warning (e.g., integrating environmental signals with health data), inclusive communication and infrastructure needs for responding to extreme weather events, and integrated platforms visualizing air quality trends to support tailored, context-aware guidance beyond one-size-fits-all alerts. The workshop highlighted opportunities such as leveraging machine learning, Earth observation, and real-time surveillance to protect communities, but also noted barriers including data quality, technological redundancy, privacy, and governance challenges. Additionally, participants emphasized the need for interdisciplinary teams capable of collaborating across sectors, breaking down silos and addressing gaps in training and education. Overall, the workshop illustrates how process-driven, human-centered approaches can help surface user needs and generate testable prototype concepts, while underscoring the importance of direct community partnership for implementation.
Hydrogen has been identified as a flexible energy carrier with zero or negative emission across multiple energy systems, and existing natural gas infrastructure could be leveraged if hydrogen gas (H2) was blended with methane (CH4). For example, subsurface methane storage reservoirs could be slightly modified to also store hydrogen if a methane/hydrogen blend were injected. However, the compatibility of methane storage reservoirs to include H2 injection has not been fully demonstrated, and this could lead to geochemical and microbiological reactions that alter the reservoir and stored gas content. It is essential that we understand the impact of H2 gas on the biogeochemistry of subsurface storage reservoirs before deploying large-scale H2-CH4 storage, We collected produced fluid from two separate methane storage reservoirs in the Southwestern US. First, we completed a baseline analysis of the biogeochemistry through qPCR, 16S rRNA sequencing, metagenomic sequencing, and geochemical analysis. Each reservoir was found to have unique geochemical conditions and a unique microbial community structure, with Site 1 having a higher TDS and an abundance of Shewanella and Site 2 having a lower TDS and high abundance of Eubacterium and Acetobacterium. Next, we ran a series of high pressure, high temperature reactors under hydrogen storage conditions with the biological sample from one of the storage reservoirs and a 20% H2-80% CH4 gas blend for up to 7 days. Our results show a decrease of hydrogen by 5% in reactors as early as 1-3 days. Previous hydrogen storage work has linked subsurface microorganisms with methanogenesis hydrogen sulfide production, acid production, and microbial corrosion. Our results show minimal change in the fluid chemistry, with the exception of a decrease in dissolved sulfate concentrations. Taxonomic sequencing demonstrated the presence of microorganisms capable of iron redox, acid generation, and hydrogen sulfide production throughout the reactors, suggesting microbial hydrogen consumption may occur through various metabolic pathways. This work demonstrates that site-specific geochemistry and microbiology may impact the efficiency of hydrogen storage in methane storage reservoirs.
Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.
The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry.