Biology subjects

Kopf, S. H.

Publications and source records attributed to Kopf, S. H..

4 recordsLinked to original sources

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↗

bioRxiv2020

Enzyme specific isotope effects of the Nap and Nar nitrate reductases

Dissimilatory nitrate reduction (DNR) to nitrite is the first step in denitrification, the main process through which bioavailable nitrogen is removed from ecosystems. DNR fractionates the stable isotopes of nitrogen (14N, 15N) and oxygen (16O, 18O) and thus imparts an isotopic signature on residual pools of nitrate in many environments. Data on the relationship between the resulting isotopic pattern in oxygen versus nitrogen isotopes (18{varepsilon} / 15{varepsilon}) suggests systematic differences exist between marine and terrestrial ecosystems that are not fully understood. DNR can be catalyzed by both cytosolic (Nar) and periplasmic (Nap) nitrate reductases, and previous work has revealed differences in their 18{varepsilon} / 15{varepsilon} isotopic signatures. In this study, we thus examine the 18{varepsilon} / 15{varepsilon} of six different nitrate-reducing microorganisms that encode Nar, Nap or both enzymes, as well gene deletion mutants of the enzymes catalytic subunits (NarG and NapA) to test the hypothesis that enzymatic differences alone could explain the environmental observations. We find that the distribution of the 18{varepsilon} / 15{varepsilon} fractionation ratios of all examined nitrate reductases form two distinct, non-overlapping peaks centered around a 18{varepsilon} / 15{varepsilon} proportionality of 0.55 and a 18{varepsilon} / 15{varepsilon} proportionality of 0.91, respectively. All Nap reductases studied to date cluster around the lower proportionality (0.55) and none exceed a 18{varepsilon} / 15{varepsilon} proportionality of 0.68. Almost all Nar reductases, on the contrary, cluster tightly around the higher proportionality (0.91) with no values below a 18{varepsilon} / 15{varepsilon} proportionality of 0.84 with the notable exception of the Nar reductases from the genus Bacillus which fall around 0.62 and thus closely resemble the isotopic fingerprints of the Nap reductases. Our findings confirm the existence of two remarkably distinct isotopic end-members in the dissimilatory nitrate reductases that could indeed explain differences in coupled N and O isotope fractionation between marine and terrestrial systems, and almost but not fully match reductase phylogeny.

microbiology↗

bioRxiv2019

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom

Phototrophic microbial mats commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. Here we show that similar coexistence patterns and ecological niches can occur in suspended phototrophic blooms of an organic-rich estuary. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts were dominated by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We found multiple uncultured phototrophic lineages and present metagenome-assembled genomes of two uncultured organisms within the Chlorobiales. Apparently, those Chlorobiales populations were affected by Microviridae viruses. We suggest a sulfur cycle within the bloom in which elemental sulfur produced by phototrophs is reduced to sulfide by Desulfuromonas sp. These findings improve our understanding of the ecology and ecophysiology of phototrophic blooms and their impact on biogeochemical cycles.

microbiology↗

bioRxiv2018

Towards measuring growth rates of pathogens during infections by D2O-labeling lipidomics

RATIONALEMicrobial growth rate is an important physiological parameter that is challenging to measure in situ, partly because microbes grow slowly in many environments. Recently, it has been demonstrated that generation times of S. aureus in cystic fibrosis (CF) infections can be determined by D2O-labeling of actively synthesized fatty acids. To improve species specificity and allow growth rate monitoring for a greater range of pathogens during the treatment of infections, it is desirable to accurately quantify trace incorporation of deuterium into phospholipids.\n\nMETHODSLipid extracts of D2O-treated E. coli cultures were measured on LC-ESI-MS instruments equipped with TOF and Orbitrap mass analyzers, and used for comparison with the analysis of fatty acids by isotope-ratio GC-MS. We then develop an approach to enable tracking of lipid labeling, by following the transition from stationary into exponential growth in pure cultures. Lastly, we apply D2O-labeling lipidomics to clinical samples from CF patients with chronic lung infections.\n\nRESULTSLipidomics facilitates deuterium quantification in lipids at levels that are useful for many labeling applications (>0.03 at% D). In the E. coli cultures, labeling dynamics of phospholipids depend largely on their acyl chains and between phospholipids we notice differences that are not obvious from absolute concentrations alone. For example, cyclopropyl-containing lipids reflect the regulation of cyclopropane fatty acid synthase, which is predominantly expressed at the beginning of stationary phase. The deuterium incorporation into a lipid that is specific for S. aureus in CF sputum, indicates an average generation time of the pathogen on the order of one cell doubling per day.\n\nCONCLUSIONSThis study demonstrates how trace level measurement of stable isotopes in intact lipids can be used to quantify lipid metabolism in pure cultures and provides guidelines that enable growth rate measurements in microbiome samples after incubation with a low percentage of D2O.

biochemistry↗