Biology subjects

Caro, T. A.

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

5 recordsLinked to original sources

bioRxiv2026

SIP-enabled multi-omics reveals soil microbiome responses to drought and rehydration

The activity of the soil microbiome, and its balance of anabolic (organic C consuming) and catabolic (CO2-releasing) reactions, determines the magnitude and direction of soil carbon fluxes. Over half a century of research has revealed that soil water dynamics are key controllers of microbial activity. With increasing hydroclimate volatility expected across many regions of the Earth, there is a greater need to describe and quantify microbial responses to drought and rehydration cycles. In this study, we conducted rainfall exclusion experiments at two archetypical Mediterranean-type field sites. After rainfall exclusion and subsequent soil rehydration, we applied a SIP-enabled, multi-omics methodology to generate a multi-faceted case study of microbial growth, greenhouse gas fluxes, and the forms of carbon that drive both. Our results indicate that rehydration increases microbial anabolic processes by orders of magnitude, shifting cell generation times from years to days within just minutes. High-intensity drought increases the lag period before microbial growth resumes, but both stable-isotope probing and metagenomic inference agree that microbial communities exhibit greater capacity for rapid growth following drought stress. Furthermore, significant shifts in the soil metabolome are observed following drought and rehydration, implicating specific osmolytes as key to the microbial response and indicating metabolite diversity as a key modulator of microbiome functioning. Together, our results provide constraints on microbial activity rates in soil and mechanisms underpinning microbial responses to drought and rewetting. These findings motivate further research into microbial responses under increasingly volatile hydroclimate regimes and downstream contributions to the global carbon cycle. Significance StatementSoil is a major global store and source of carbon. The microbiome determine the fate of soil organic carbon, and the microbiome is ultimately controlled by soil water dynamics. Early, innovative experiments by H.F. Birch defined "The Birch Effect" - the observation that soils emit CO2 following drying and subsequent rehydration. However, it remains unclear when, and to what magnitude, soil microorganisms are actively growing following this rehydration, and what biological mechanisms explain the observed CO2 pulse. In this work, we apply an array of methodologies to address this question, describing rates of microbial growth during drought and rewetting. Our results provide crucial insights into how soil microbiomes will respond to increasing hydroclimate volatility across the globe.

microbiology↗

bioRxiv2025

Dissolved inorganic carbon supports robust anabolism and methanogenesis in actively serpentinizing rocks

Serpentinites, hydrated ultramafic rocks that produce [hyper]alkaline, reducing, H2-rich groundwaters, host subsurface microbial ecosystems. Though in the presence of enormous reducing power, life in serpentinizing systems is limited by oxidant and carbon availability. The forms of carbon that support the serpentinite-hosted microbiome, and their rates of biological assimilation, remain poorly understood. In this work, we quantify the habitability of subsurface environments shaped by serpentinization and examine the forms of carbon that support their microbial constituents, focusing specifically on dissolved inorganic carbon, acetate, and formate. We access reacted groundwater from Earths largest terrestrial serpentinizing body and measure carbon assimilation at the single-cell level. Across all conditions, we consistently observe robust assimilation of dissolved inorganic carbon into microbial biomass. Notably, we find that dissolved inorganic carbon supports the majority of methanogenic activity in the system, even at hyperalkaline conditions (pH > 11). Inferred bioenergetic fluxes suggest that rates of biological hydrogen-consumption and methanogenesis are relevant at the landscape scale. We identify a strong potential for the microbiome to be stimulated by increases in H2 and CO2, a finding with implications for the search for life on other planetary bodies and for the growing deployment of fluid injection technologies in ultramafic rocks, such as geological hydrogen production or carbon mineralization. Significance StatementWhen iron-rich rocks interact with water, they undergo a "serpentinization" reaction that results in the production of H2 and [hyper]alkaline fluids. This abiotic process does not operate alone but rather supports and interacts with microbial life. However, it remains unknown to what extent the stressors of subsurface life under [hyper]alkaline conditions may limit microbial activity. In this work, we quantify the rates at which microorganisms transform different carbon sources across a range of serpentinizing conditions. We find that serpentinizing rocks host a remarkably robust microbiome, a finding that motivates the targeting of serpentinizing systems for life detection efforts in our solar system, as well as further analysis of efforts to leverage serpentinites for industrial-scale geological H2 and carbon drawdown projects.

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↗

bioRxiv2023

Quantitative measurement of microbial growth rate with Raman microspectroscopy

Rates of microbial activity and growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable Isotope Probing (SIP) is a standard method for assessing microbial activity and involves measuring the incorporation of an isotopically labeled compound into microbial biomass. Here, we assess the utility of Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We generate calibrations of microbial biomass 2H values and find that Raman microspectroscopy reliably quantifies 2H incorporation ranging between 0 and 40 at. %. Applying the results of this calibration to a SIP model, we explicitly parameterize the factors controlling microbial growth quantification, demonstrating how Raman-SIP can measure the growth of microorganisms with doubling times ranging from hours to years. Furthermore, we correlatively compare our Raman-derived measurements with those of nanoscale secondary ion mass spectrometry (nanoSIMS) to compare the relative strengths of nanoSIMS- and Raman-based SIP approaches. We find that Raman microspectroscopy is a robust, accessible methodology that can readily differentiate and quantify the growth of individual microbial cells in complex samples. ImportanceGrowth rate, the rate at which organisms grow and reproduce, is a key metric with which to evaluate microbial physiology and contributions to system-level processes. The heterogeneity of microbial growth across space, time, and populations is often difficult to capture with bulk-scale techniques. Single-cell methods hold promise for measuring the heterogeneity of microbial growth rates and responses to changing conditions in situ, without the need for cultivation of microbial isolates. In this study, we evaluated the ability of Raman microspectroscopy, a non-destructive and rapid technique, to measure the assimilation of isotopically labeled water into individual microbial cells and thereby calculate their rates of growth. We explicitly parameterize the factors controlling the quantification of microbial growth rate and compare this technique to standard methods. The framework we report allows researchers to couple single-cell and aggregate rate measurements to functional or system-level properties, a forefront challenge in microbiology.

microbiology↗

bioRxiv2022

Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil

The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that average apparent generation times in soil are quite slow (20 to 64 days) but also highly variable at the compound-specific level (6 to 1137 days), suggesting differential growth rates between community subsets. We observe that low-biomass communities can exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities. SignificanceGeneration times, how quickly organisms grow and reproduce, are a key feature of biology. However, there are few measurements of microbial generation times in soil, despite the crucial importance of soil microbes to terrestrial ecosystems. By measuring the rate at which isotopically labeled water is incorporated into microbial membranes, we find that the generation times of soil microorganisms are far longer than those typically observed in culture. Surprisingly, we observe that lower-biomass soils exhibited faster growth rates than high-biomass soils. More abundant microorganisms are not necessarily the fastest growing and most soil microorganisms are slow growers. Our results underscore the importance of considering slow and variable growth rates when studying microbial communities and their contributions to ecosystem processes.

microbiology↗