Biology subjects

Calabrese, F.

Publications and source records attributed to Calabrese, F..

6 recordsLinked to original sources

bioRxiv2026

Compositional Heterogeneity Structures Microbial Microhabitats across Distinct Mineral Substrates

Microbial communities living on and in rocks operate at the microscale, where interactions with minerals fundamentally shape community structure and function. Yet the relationship between micron scale mineralogical configurations and microbial distributions remains poorly understood. We tested the hypothesis that microbial biomass spatially correlates with areas of heightened mineralogical heterogeneity by applying Raman microspectroscopy to rock samples from three geologically distinct substrates: authigenic carbonates from a marine methane seep, volcanic basalt from Iceland, and polymetallic nodules from the abyssal seafloor. Using spectral decomposition and multiple complementary metrics of compositional heterogeneity, we evaluated intra-pixel and inter-pixel heterogeneity patterns in relation to biomass distribution. Our analyses reveal three patterns across all sample types. 1) When spectra are deconstructed into their constituent components, biomass zones are disproportionately dominated by the biomass spectral component compared with primary mineral components in zones of different minerals. 2) Biomass spectra have more homogeneous compositional profiles than mineral spectra. 3) Biomass is surrounded by more heterogeneous microhabitats than mineral pixels. These findings demonstrate that biomass exerts a distinctive and consistent influence on Raman spectral signatures, both within and between pixels, in ways that mineral components do not. Our results establish generalizable principles linking microscale mineralogical properties to microbial biogeography; these properties could be used as a potential biosignature and may provide a standardized workflow applicable to diverse rock systems and astrobiological exploration strategies.

microbiology↗

bioRxiv2024

Dual-BONCAT Reveals Distinct Day- and Night-Active Microbial Populations in Salt Marsh Sediments

Bio-Orthogonal Non-Canonical Amino Acid Tagging (BONCAT) has emerged as a prominent molecular technique that enables microbial ecologists to visualize and identify metabolically active cells in cultures and complex microbial communities. To date, researchers have used just one non-canonical amino acid (ncAA) in a given experiment; here, we validate a novel approach using two different ncAAs in a single experiment. This advancement facilitates the detection of differentially active subpopulations within the same experimental context, thereby reducing the uncertainty and variability associated with parallel treatments, and providing precise spatial information about organisms that are active under distinct conditions or at different times. We show that both ncAAs can be taken up by E. coli cultures and by constituents of the Little Sippewissett Salt Marsh microbiome, resulting in fluorescence signals that are significantly higher than background and ncAA-free control experiments, as well as differential labeling patterns reflective of distinct subpopulations. As a proof of concept, we implemented this "dual-BONCAT" approach in salt marsh sediments, adding one ncAA during daytime hours and the other at night. Subpopulations of cells that were anabolically active during the day and/or night were distinguishable by both fluorescence microscopy, and by fluorescence-activated cell sorting. Subsequent high-throughput 16S rRNA gene amplicon sequencing of active subpopulations revealed that Methylobacterium, potentially feeding on plant exudate carbon, was preferentially active during the day, while sulfur-cycling taxa dominated the night-active population. Dual-BONCAT offers an important advancement in multiplexing substrate-analog probing techniques, providing a more realistic understanding of metabolic activity under distinct environmental conditions. ImportanceMicrobial communities are complex and dynamic, with different groups of microbes active under distinct conditions. Bio-Orthogonal Non-Canonical Amino Acid Tagging (BONCAT) uses synthetic amino acids to tag newly made proteins, allowing researchers to see and identify the active subset of a community. While BONCAT studies to date have used a single synthetic amino acid to evaluate cell activity in a single experimental context, here we introduce a new approach, "dual-BONCAT," using two synthetic amino acids to track differential responses to changing conditions. After validating the approach with E. coli, we deployed it in a salt marsh sediment community, finding that organisms potentially feeding on plant root sugars were more active during the day, and microbes likely metabolizing sulfur were more active at night. We believe dual-BONCAT will prove useful in many studies, as it illuminates microbial community responses to changing conditions, which has important implications for ecosystem dynamics.

microbiology↗

bioRxiv2022

TPH2 knockout male rats are aggressive, show less anxiety, and exhibit an altered oxytocin system

The central serotoninergic system is critical for stress responsivity and social behavior, and its dysregulations has been centrally implicated in virtually all neuropsychiatric disorders. Genetic serotonin depletion animal models could provide a tool to elucidate the causes and mechanisms of diseases and to develop new treatment approaches. Previously mice lacking tryptophan hydroxylase 2 (Tph2) have been developed, showing altered behaviors and neurotransmission. However, the effect of congenital serotonin deficiency on emotional and social behavior in rats is still largely unknown, as are the underlying mechanisms. In this study, we used Tph2 knockout (Tph2-/-) male rat model to study how the lack of serotonin in the rat brain affects anxiety-like and social behaviors. Since oxytocin is centrally implicated in these behaviors, we furthermore explored whether effects of Tph2 knockout on behavior would relate to changes in the oxytocin system. We show that Tph2-/- rats display reduced anxiety-like behavior and a high level of aggression in social interactions. In addition, oxytocin receptor expression was increased in the infralimbic and prelimbic cortex, paraventricular nucleus, dorsal raphe nucleus and some subregions of hippocampus, which was paralleled by increased levels of oxytocin in the medial frontal cortex, paraventricular nucleus, but not the dorsal raphe nucleus, central amygdala and hippocampus. In conclusion, our study demonstrated reduced anxiety but exaggerated aggression in Tph2-/- male rats and reveals for the first time a potential involvement of altered oxytocin system function. SIGNIFICANCE STATEMENTWe explored the changes in behavior and oxytocin system functioning in the tryptophan hydroxylase 2 (Tph2) knockout rat model, lacking serotonin in the brain. This rat model contributes to our understanding of the role of serotonin in psychiatric transdiagnostic features and underlying mechanisms. We found that Tph2 knockout male rats are aggressive, less anxious, and exhibit an altered oxytocin system. The observed changes in oxytocin signaling may lead to a new target for the treatment of diseases caused by genetic serotonin deficiency.

neuroscience↗

bioRxiv2020

BDNF Overexpression in the Prelimbic Cortex Does Not Reduce Anxiety- and Depression-like Behavior in Serotonin Knockout Rats

Depressive disorders are one of the leading causes of non-fatal health loss in the last decade. Adding to the burden, the available treatments not always properly work for some individuals. There is, therefore, a constant effort from clinical and preclinical studies to bring forward a better understanding of the disease and look for novel alternative therapies. Two target systems very well explored are the serotonin and the brain-derived neurotrophic factor (BDNF) systems. Selective serotonin reuptake inhibitors (SSRIs), a commonly used class of antidepressants, target the serotonin transporter (SERT) and increase serotonin levels, which in turn also leads to an increase in BDNF. A rat model lacking SERT (SERT knockout) has been a useful tool to study the interplay between serotonin and BDNF. SERT-/- rats present increased extracellular levels of serotonin, yet BDNF levels are decreased, especially in the prefrontal cortex (PFC) and hippocampus. The animals further display anxiety- and depression-like behavior. Therefore, BDNF might mediate the phenotype expressed by the SERT-/- rats. In this study, we sought to investigate whether overexpression of BDNF in the brain of SERT-/- rats would rescue its anxious and depressive-like behavior. Through stereotaxic surgery, SERT-/- and wild-type (WT) rats received BDNF or GFP lentivirus microinfusions into the prelimbic cortex subregion of the mPFC and were submitted to the sucrose consumption, open field test, and forced swim tests. Additionally, we measured hypothalamus-pituitary-adrenal (HPA)-axis reactivity. The results revealed that SERT-/- rats presented decreased sucrose intake, decreased locomotor activity, and increased escape-oriented behavior in the forced swim test compared to WT rats. BDNF upregulation in WT rats caused alterations in the HPA-axis function, resulting in elevated basal plasma corticosterone levels and decreased plasma corticosterone upon stress. In conclusion, BDNF overexpression in the PrL, in general, did not rescue SERT-/- rats from its depression- and anxiety-like behavior, and in WT animals, it caused a malfunction in the HPA-axis.

animal behavior and cognition↗

bioRxiv2020

BDNF overexpression in the ventral hippocampus promotes antidepressant- and anxiolytic-like activity in serotonin transporter knockout rats

Brain-derived neurotrophic factor is one of the most studied proteins playing a pivotal role in neuroplasticity events and vulnerability and resilience to stress-related disorders. Most importantly, BDNF is decreased in depressive patients, and increased after antidepressant treatment. Additionally, BDNF was found to be reduced in a genetic subset of depression susceptible patients carrying the human polymorphism in the serotonin transporter promoter region (5-HTTLPR). The serotonin knockout rat (SERT-/-) is one of the animal models used to investigate the underlying molecular mechanisms behind the genetic susceptibility to depression in humans. SERT-/- rats present decreased BDNF levels, especially BDNF exon IV, in the prefrontal cortex (PFC) and ventral hippocampus (vHIP), and display anxiety- and depression-like behavior. To investigate whether upregulating BDNF in the vHIP would meliorate the phenotype of SERT-/- rats, we overexpressed BDNF locally into the rat brain by means of stereotaxic surgery and submitted the animals to behavioral challenges, including the sucrose consumption, the open field, and forced swim tests. Additionally, we measured hypothalamus-pituitary-adrenal (HPA)-axis reactivity. The results showed that lentivirus-induced BDNF IV overexpression in the vHIP of SERT-/- rats promoted higher sucrose preference and sucrose intake, on the first day of the sucrose consumption test, indicative for decreased anhedonia-like behavior. Moreover, it decreased immobility time in the forced swim test, suggesting adaptive passive coping. Additionally, BDNF upregulation increased the time spent in the center of a novel environment, implying decreased novel-induced anxiety-like behavior. Finally, it promoted a stronger decrease in plasma corticosterone levels 60 minutes after restraint stress. In conclusion, modulation of BDNF IV levels in the vHIP of SERT-/- rats led to a positive behavioral outcome placing BDNF upregulation in the vHIP as a potential candidate for the development new therapeutic approaches targeting the improvement of depressive symptoms.

animal behavior and cognition↗

bioRxiv2017

Conductive particles enable syntrophic acetate oxidation between Geobacter and Methanosarcina from coastal sediments

Coastal sediments are rich in conductive minerals, which could impact microbial processes for which acetate is a central intermediate. In the methanogenic zone, acetate is consumed by methanogens and/or syntrophic acetate oxidizing (SAO) consortia. SAO consortia live under extreme thermodynamic pressure and their survival depends on successful partnership. Here we demonstrate that conductive minerals facilitate a SAO partnership between Geobacter and Methanosarcina from the coastal sediments of the Bothnian Bay, Baltic Sea. Bothnian methanogenic sediments showed a high apparent isotopic fractionation (c 1.07) characteristic of CO2-reductive methanogenesis. The native community was represented by electrogens such as Geobacter and methanogens like Methanosarcina. Upon the addition of conductive particles (activated carbon and magnetite) methanogenesis from acetate increased four fold. Geobacter (96% related to G. psychrophilus) and Methanosarcina (99% related to M. subterranea) dominated the conductive particle-spiked SAO communities. Using NanoSIMS we demonstrated that during SAO, Geobacter incorporated 82% of the labeled acetate as compared to only 18% by Methanosarcina. At the same time Geobacter converted 27% of the 13C-acetate to 13CO2 as detected by IRMS. Indigenous soluble shuttles were not involved in SAO, since spiking fresh cultures with spent-media filtrate had no effect on methanogenic rates. Our results demonstrate that Geobacter oxidizes acetate to CO2 while transferring electrons extracellularly via conductive particles to Methanosarcina, which utilizes them for CO2 reduction to methane. In natural environments, mediation of SAO by conductive particles between electrogens and methanogens could impact the iron and methane cycles.\n\nSignificanceAcetate oxidizing bacteria are known to thrive in mutualistic consortia in which H2 or formate is shuttled to a methane-producing Archaea partner. Here we discovered that they could instead transfer electrons via conductive minerals. Mineral-SAO (syntrophic acetate oxidation) could be a vital pathway for CO2-reductive methanogenesis in the environment, especially in sediments rich in conductive minerals. Mineral-SAO is therefore of potential importance for both iron and methane cycles in sediments and soils. Additionally, our observations imply that agricultural runoff or amendments with conductive chars could trigger a significant increase in methane emissions.

microbiology↗