Biology subjects

Sessions, A. L.

Publications and source records attributed to Sessions, A. L..

4 recordsLinked to original sources

bioRxiv2025

Symbiotic entrenchment through ecological Catch-22

Symbiotic organisms frequently evolve obligate dependencies on hosts, but the evolutionary changes that entrench such lifestyles are poorly understood. Ant societies are vulnerable to parasitic "myrmecophiles": impostor species that infiltrate colonies and are often unable to survive outside of them. Here we show that obligate dependence of a myrmecophile on its host arises from irreversibility of the fundamental steps that achieve social acceptance inside the nest. We report a convergent system in which parallel rove beetle lineages (Staphylinidae) evolved from free-living ancestors to parasitize the same host ant. Exploiting this system, we uncover cellular mechanisms by which these beetles mimic host ant cuticular hydrocarbons (CHCs): nestmate recognition pheromones, which function pleiotropically to prevent desiccation. We present evidence of a biological stealth mechanism in a rove beetle in which the CHC biosynthetic machinery becomes transcriptionally silenced on entering the nest. Silencing transforms the beetle into a chemical blank slate onto which ant CHCs are horizontally transferred via interspecies grooming behavior. This strategy leads to identical chemical resemblance and seamless social integration within the colony. CHC pathway silencing is irreversible, however, forcing the beetle into a chronic, physically close dependence on ants to both maintain nestmate status and prevent desiccation. Loss of CHC silencing renders the beetle detectable to ants; conversely, loss of behavioral attraction to ants renders the beetle desiccation prone. Our findings show how symbiotic entrenchment can arise from a Catch-22-like ratchet operating at the organismal level.

evolutionary biology↗

bioRxiv2025

Metabolic controls on the carbon isotope fractionations of bacterial fermentation

Microbial fermentation facilitates the initial breakdown of organic matter into small molecules, and is thought to be the rate-limiting step for mineralization under anoxic conditions. Fermentation is understudied in modern and ancient biogeochemistry due to a lack of environmental biomarkers that would constrain its activity. It has long been assumed that fermentation, like respiration, does not express significant carbon isotope fractionations, precluding isotopic signals as a means of studying it in nature. Here, we tested this idea by growing pure cultures of four fermenting bacteria on glucose and measuring the carbon isotope compositions of the organic acids and alcohols produced. We found that fermentation exhibits a strong carbon isotope fractionation, ranging from -6{per thousand} to +16{per thousand}, depending on the fermentation product. This range can even be observed within a single organism. Using bioisotopic models that track site-specific isotope enrichments through metabolic networks, we constrained the enzymes responsible for these fractionations. Our models reproduced in vivo organic acid{delta} 13C values in all four organisms. These findings demonstrate that acetate 13C-enrichment is likely a consistent signature of fermentation. Furthermore, our study suggests that fermentation imposes an anaerobic trophic carbon isotope fractionation as organic carbon is passed from fermenters to secondary degraders like sulfate reducers. Looking to the geologic past, this trophic fractionation could have imprinted isotopic signals on the three billion year record of sedimentary organic carbon, specifically the inverse{delta} 13C pattern of Precambrian acyclic isoprenoid and n-alkane biomarkers. Pervasive evidence of fermentation in the rock record suggests its under-appreciated role in biogeochemical cycles throughout Earth history. Significance StatementMicroorganisms drive the global cycling of elements like carbon and regulate the Earths climate on both human and geologic timescales. Of particular importance is the microbial breakdown of organic matter, which generates greenhouse gases like methane. Fermenting bacteria play a crucial role in anaerobic carbon degradation. However, they remain largely invisible to our analyses. We explored the natural abundance of carbon stable isotopes in the molecular products of fermentation as a tool to study this metabolism in modern ecosystems and the ancient biosphere. We identified significant isotopic signals in molecules produced by fermenting bacteria and compared them to previously observed isotopic signals in molecular fossils in sedimentary rocks, which may provide evidence of microbial fermentation on the Precambrian Earth.

microbiology↗

bioRxiv2018

Refining the application of microbial lipids as tracers of Staphylococcus aureus growth rates in cystic fibrosis sputum

Chronic lung infections in cystic fibrosis (CF) could be treated more effectively if the effect of antimicrobials on pathogens in situ were known. Here, we compared changes in the microbial community composition and pathogen growth rates in longitudinal studies of CF patients undergoing intravenous antibiotic administration during pulmonary exacerbations. Microbial community composition was measured by NanoString DNA analysis and growth rates were obtained by incubating CF sputum with heavy water and tracing incorporation of deuterium into two different anteiso fatty acids (a-C15:0 and a-C17:0) using gas chromatography-mass spectrometry (GC/MS). Prior to this study, both lipids were thought to be specific for Staphylococcaceae and hence their isotopic enrichment was interpreted as a growth proxy for S. aureus. Our experiments revealed, however, that Prevotella is also a relevant microbial producer of a-C17:0 fatty acid in some CF patients, thus deuterium incorporation into these lipids is better interpreted as a more general pathogen growth rate proxy. Even accounting for a small non-microbial background source detected in some patient samples, a-C15:0 fatty acid still appear to be a relatively robust proxy for CF pathogens, revealing a median generation time of ~1.5 days, similar to prior observations. Contrary to our expectations, pathogen growth rates remained relatively stable throughout exacerbation treatment. We suggest two best practices for application of stable isotope probing in CF sputum: (1) parallel determination of microbial community composition in CF sputum using culture-independent tools, and (2) analysis of samples with a minimum a-C15:0 concentration of 0.1 weight percent of saturated fatty acids.\n\nIMPORTANCEIn chronic lung infections, populations of microbial pathogens change and mature in ways that are often unknown, which makes it challenging to identify appropriate treatment options. A promising tool to better understand the physiology of microorganisms in a patient is stable-isotope probing, which we previously developed to estimate the growth rates of S. aureus in cystic fibrosis (CF) sputum. Here, we tracked microbial communities in a cohort of CF patients and found that anteiso fatty acids can also originate from other sources in CF sputum. This awareness led us to develop an new workflow for the application of stable isotope probing in this context, improving our ability to estimate pathogen generation times in clinical samples.

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↗