Biology subjects

Douglas, T. A.

Publications and source records attributed to Douglas, T. A..

6 recordsLinked to original sources

bioRxiv2026

Biotic versus environmental controls on microbial degradation of permafrost organic matter

Permafrost thaw exposes ancient organic matter to microbial degradation, which is predicted to release globally significant quantities of greenhouse gases into the atmosphere. Though microorganisms drive these processes, the relative importance of biotic (taxonomic and functional community composition) versus environmental (e.g., soil physicochemistry) drivers and their interactions are unknown. Using a novel in situ thaw experiment conducted at the Cold Regions Research and Engineering Laboratorys Permafrost Tunnel near Fairbanks, Alaska, we experimentally separated the effects of soil physicochemistry and microbial communities under "real-world" thaw conditions. To simulate thaw, active layer soil, Holocene permafrost (2 kya), and Pleistocene permafrost (40 kya) were sterilized, inoculated with microbial communities from the different soils, enclosed in 0.22 {micro}m membrane bags to prevent immigration, and buried in the active layer. We retrieved the bags after two weeks and two months of thaw and characterized microbial community structure (16S rRNA and ITS2 amplicon sequencing), functional potential (metagenome sequencing), and soil organic matter (OM) composition at the molecular level (FT-ICR MS). Soil had a stronger effect on bacterial community and gene assemblages than inoculum, and the effects of inoculum were stronger and longer-lasting on community structure than functional potential. Pleistocene permafrost initially contained approximately eleven times more dissolved organic carbon than the other soils, and was enriched in OM derived from microbial necromass and low molecular weight organic acids. This carbon was rapidly depleted during thaw and OM compositional characteristics became increasingly similar to active layer and Holocene permafrost, paralleling shifts in Pleistocene permafrost functional gene profiles and bacterial community structure towards those of other soils. Overall, this work provides new insights into the susceptibility of OM to microbial degradation in compositionally distinct permafrost soils, and ways in which Pleistocene Yedoma permafrost carbon is likely to be particularly vulnerable to permafrost thaw.

microbiology↗

bioRxiv2025

Growth Optimization Predicts Microbial Success in a Permafrost Thaw Experiment

Ongoing climate warming is thawing global permafrost, making vast pools of organic carbon available as microbial growth substrates. Uncertainty surrounding microbial successional dynamics limits our ability to parameterize the global-scale biogeochemical consequences of this thawing permafrost. We developed a genomic index of growth optimization to predict whether individual taxa increase or decrease in abundance during early thaw and validate our approach using incubation experiments from permafrost collected in Interior Alaska.

microbiology↗

bioRxiv2025

Consistent microorganisms respond during aerobic thaw of Alaskan permafrost soils

Arctic systems are experiencing warming at four times the rate of the global average, causing permafrost--permanently frozen soil, ice, organic matter, and bedrock--to thaw. Permafrost thaw exposes previously unavailable soil carbon and nutrients to decomposition--a process mediated by microbes--which releases greenhouse gases such as carbon dioxide and methane into the atmosphere. While it is well-established that thaw alters the composition and function of the permafrost microbiome, patterns revealing common responses to thaw across different permafrost soil types have not yet emerged. Here, we address how permafrost thaw impacts microbiome diversity, alters species abundance, and contributes to carbon flux in the Arctic. We sampled peat-like, mineral, and organic-mineral permafrost from three locations in central and northern Alaska and assessed their abiotic soil properties and microbiome characteristics during a 3-month laboratory microcosm incubation. In all sites, prokaryotic biomass increased following thaw, measured as 16S rRNA gene copy number and absolute abundance. This change in biomass was positively correlated with cumulative respiration, indicating an increase in microbial activity post-thaw. We assessed the thaw response of microbial taxa across three sites, identifying taxa that significantly increased in abundance post-thaw. Common responders shared across all sites belonged to the families Beijerinckiaceae, Burkholderiaceae, Clostridiaceae, Oxalobacteraceae, Pseudomonadaceae, and Sporichthyaceae, indicating a common set of taxa that consistently respond to thaw regardless of site-specific conditions. Alpha diversity decreased with thaw across all sites, which likely reflects the increased dominance of specific thaw-responsive taxa, which may be driving post-thaw biogeochemistry and increased respiration. Taken together, we deepen the understanding of different permafrost microbiomes and their response to thaw, which has implications for the permafrost-climate feedback and allows for better predictions of how Arctic ecosystem structure and function respond to change.

microbiology↗

bioRxiv2025

Microbial Resuscitation and Growth Rates in Deep Permafrost: Lipid Stable Isotope Probing Results from the Permafrost Research Tunnel in Fox, Alaska

Permafrost is at increasing risk of thaw as cold regions in the Northern Hemisphere continue to warm. Of particular concern is ice-rich, organic-rich, syngenetic "yedoma" type permafrost. The lability of organic carbon in permafrost post-thaw largely depends on the rate at which microorganisms resuscitate and proliferate after thousands of years in below-freezing, dark, anaerobic conditions. However, the resuscitation and growth rates of microorganisms in deep permafrost are unknown. To quantify these rates, we conducted lipid stable isotope probing (lipid-SIP) on permafrost cores collected from four locations within the Permafrost Tunnel near Fairbanks, Alaska. We compare rates of microbial growth, marker gene sequences, and greenhouse gas (CO2, CH4) emissions across cores held anaerobically at ambient and elevated temperatures. In deep, ancient permafrost, microbial biomass turnover is exceedingly slow, often undetectable, within the first month following thaw. Our results indicate microbial growth in response to anaerobic thaw has a notable lag period, where only 0.001 - 0.01% of cells turn over per day. This suggests a slow reawakening that could provide some buffer between anomalous warmth and C degradation if permafrost refreezes seasonally. However, within six months, microbial communities undergo dramatic restructuring and succession, producing communities that are distinct from both the emplaced ancient and overlying surface communities. These results have critical implications for predictions of microbial biogeochemical contributions in a warming arctic, especially as thaw proceeds into deeper and more ancient permafrost horizons. Plain Language SummaryPermafrost, earth material like soil, rock, or ice continually frozen for more than two years, contains more organic carbon than is currently in the atmosphere as CO2. As the Arctic warms and permafrost thaws, ancient microbes can reactivate, allowing the degradation of organic carbon that has accumulated in permafrost over millenia, resulting in the release of greenhouse gases. In this work, we measured the rates at which permafrost microorganisms resuscitate during thaw and related these growth rates to changes in microbial community composition and greenhouse gas emissions. Key PointsO_LIMicrobial growth is extremely slow within the first 30 days of thaw. Temperature may drive which taxa are active, but not growth rates. C_LIO_LISubsurface microbes show a preference for glycolipids over phospholipids, suggesting a possible cryotolerance adaptation. C_LIO_LIAncient, entrapped gases may be the primary source of emissions in early thaw stages. C_LI

microbiology↗

bioRxiv2018

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods such as metagenomic and 16S rRNA gene sequencing. However, these methods do not distinguish between active, dead, and dormant cells. This is of particular concern in ancient permafrost where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this we applied: (i) live/dead differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19K, 27K, and 33K). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools and how they change over geologic time. We found clear evidence that cells capable of forming endospores are not necessarily dormant and that the propensity to form endospores differed among taxa. Specifically, Bacilli are more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of Clostridia, which are more likely to persist as vegetative cells over geologic timescales. We also found that exogenous DNA preserved within permafrost does not bias DNA sequencing results since its removal did not significantly alter the microbial community composition. These results extend the findings of a previous study that showed permafrost age and ice content largely control microbial community diversity and cell abundances.\n\nImportanceThe study of permafrost transcends the study of climate change and exobiology. Permafrost soils store more than half earths soil carbon despite covering {bsim}15% of the land area (Tarnocai et al 2009). This permafrost carbon is rapidly degraded following thaw (Tarnocai C et al 2009, Schuur et al 2015). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling post thaw. Permafrost is also an analog for frozen extraterrestrial environments and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive permafrost we can focus efforts searching for evidence of life on cryogenic cosmic bodies. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains across geologic timescales.

microbiology↗

bioRxiv2018

ImageJ Macro for Counting Stationary vs. Moving Items in Videos

In microfluidic devices, it is often necessary to determine whether cells or particles are stationary or moving. Here we outline the development of an ImageJ macro that can be used to analyze a video of moving, fluorescently labeled particles or cells, and determine which objects are stationary and which objects are moving at each point in time, providing information on the percentage of cells moving as well as their median radius.

cell biology↗