Biology subjects

Masiello, C. A.

Publications and source records attributed to Masiello, C. A..

7 recordsLinked to original sources

bioRxiv2025

Mechanisms of soil carbon preservation illuminated by model mineral-associated organic matter

A central control on atmospheric CO2 is the stabilization of organic carbon in soils. While there are well-described properties associated with stable soil carbon, such as interactions with minerals and conserved chemical features, determining the mechanisms underlying these properties is challenged by soil complexity and heterogeneity. Here we synthesize a naturally complex, tunable model form of mineral-associated organic matter (LabMAOM) to explore mechanisms of stable soil carbon formation and persistence. We show that mineral association and ambient organic matter synergistically stabilize LabMAOM against microbial decomposition. Moreover, different starting compositions of organic matter yield a conserved final LabMAOM chemical composition consistent with natural soils. Our findings open new mechanistic understanding of stable soil carbon and will be of utility to climate modeling and soil health management.

synthetic biology↗

bioRxiv2025

Effects of matric versus osmotic potential changes on Variovorax beijingensis transcription

Soil microbes must continuously adapt to changes in water availability, which dynamically fluctuates with weather and irrigation, and these adaptations are closely linked to soil CO2 emissions. Soil water potential, which regulates microbe-available water, is controlled by both osmotic and matric potential, which both increase as soils dry. While both parameters can independently increase water potential, the genetic mechanisms underlying microbial responses to both are unknown, with potentially different mechanisms available for soil microbes to respond to these hydrologic parameters. To explore microbial responses to matric versus osmotic potential shifts, we evaluated the growth and transcription of Variovorax beijingensis in soils and liquid cultures of varying water potential. We find this microbe respires in dilute minimal medium (-240 {+/-}104 kPa), in liquid medium supplemented with sucrose (-1323 {+/-}20.8 kPa), and in a pair of matrices that span a similar range of pressures (-183 {+/-}55 and -1393 kPa {+/-}200 kPa). We show that the global gene expression patterns vary significantly across all four conditions, even when the matric potential and osmotic pressure are set to similar values. However, the direction of gene expression changes correlated for 68% of the transcripts arising from an increase in osmotic pressure within liquid medium and an increase in matric potential within the different soils. While a large overlap was observed in the Variovorax transcriptional response to shifts in both osmotic and matric potential, the responses were not identical, with matric potential shifts leading to 2.55-fold more genes exhibiting differential expression. IMPORTANCEIt remains hard to establish how changes in soil water properties affect microbial behaviors that regulate soil health, and the energy with which soil water is held is likely a holistic control on at least some of those microbial behaviors. This energy is controlled by parameters associated with soil saltiness (osmotic potential) and texture (matric potential), which both alter bioavailable water by contributing to total soil water potential. To investigate how the global transcriptional profile of a soil microbe changes when the microbe-available water is altered either by changing soil texture or by changing osmolyte concentrations, we varied osmotic and matric potential individually and performed RNA sequencing. We observe differences in the transcriptome across all conditions analyzed. A larger number of genes are differentially expressed as matric potential increases; however, many of the transcripts differentially expressed as osmotic pressure increases covary with those observed as the matrix potential increases.

systems biology↗

bioRxiv2023

Using methyl bromide for interspecies cell-cell signaling and as a reporter in a model soil consortium

Soil microbial communities with reduced complexity are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five member MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that Variovorax beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are [≥]24-fold higher than all other MSC members across a range of environmentally-relevant hydration conditions. We find that methyl halide production can report on a MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. These tools will be useful for future studies that investigate how MSC respond to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.

synthetic biology↗

bioRxiv2023

Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface

Microbes can be found in abundance many kilometers underground. While microbial metabolic capabilities have been examined across different geochemical settings, it remains unclear how changes in subsurface niches affect microbial needs to sense and respond to their environment. To address this question, we examined how two component systems (TCS) vary across metagenomes in the Deep Mine Microbial Observatory (DeMMO). TCSs were found at all six subsurface sites, the service water control, and the surface site, with an average of 0.88 sensor histidine kinases (HKs) per 100 genes across all sites. Abundance was greater in subsurface fracture fluids compared with surface-derived fluids, and candidate phyla radiation (CPR) bacteria presented the lowest HK frequencies. Measures of microbial diversity, such as the Shannon diversity index, revealed that HK abundance is inversely correlated with microbial diversity (r2 = 0.81). Among the geochemical parameters measured, HK frequency correlated the strongest with variance in dissolved organic carbon (DOC) (r2 = 0.82). Taken together, these results implicate the abiotic and biotic properties of an ecological niche as drivers of sensor needs, and they suggest that microbes in environments with large fluctuations in organic nutrients (e.g., lacustrine, terrestrial, and coastal ecosystems) may require greater TCS diversity than ecosystems with low nutrients (e.g., open ocean). IMPORTANCEThe ability to detect environmental conditions is a fundamental property of all life forms. However, organisms do not maintain the same environmental sensing abilities during evolution. To better understand the controls on microbial sensor abundance, which remain poorly understood, we evaluated how two-component sensor systems evolved within the deep Earth across sampling sites where abiotic and biotic properties vary. We quantify the relative abundances of sensor proteins and find that sensor systems remain abundant in microbial consortia as depth below the Earths surface increases. We also observe correlations between sensor system abundances and abiotic (dissolved organic carbon variation) and biotic (consortia diversity) properties across the DeMMO sites. These results suggest that multiple environmental properties drive sensor protein evolution and diversification and highlight the importance of studying metagenomic and geochemical data in parallel to understand the drivers of microbial sensor evolution.

microbiology↗

bioRxiv2022

Non-destructive chemical sensing within bulk soil using 1000 biosensors per gram of matrix

Gene expression can be monitored in hard-to-image environmental materials using gas-reporting biosensors, but these outputs have only been applied in autoclaved matrices that are hydrated with rich medium. To better understand the compatibility of indicator gas reporting with environmental samples, we evaluated how matrix hydration affects the gas signal of an engineered microbe added to a sieved soil. A gas-reporting microbe presented a gas signal in a forest soil (Alfisol) when hydrated to an environmentally-relevant osmotic pressure. When the gas signal was concentrated prior to analysis, a biosensor titer of 103 cells/gram soil produced a significant signal when soil was supplemented with halides. A signal was also observed without halide amendment, but a higher cell titer (106 cells/gram soil) was required. A sugar-regulated gas biosensor was able to report with a similar level of sensitivity when added to an unsterilized soil matrix, illustrating how gas concentration enables biosensing within a soil containing environmental microbes. These results establish conditions where engineered microbes can report on gene expression in living environmental matrices with minimal perturbation, using biosensor titers that are orders of magnitude lower than the number of cells typically observed in a gram of soil.

synthetic biology↗

bioRxiv2022

Artificial soils reveal individual factor controls on microbial processes

Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil recipe and used these materials to study the abiotic mechanisms driving soil microbial growth and communication. When we used standardized matrices with varying textures to culture gas-reporting biosensors, we found that Gram-negative bacteria grew best in synthetic silt soils, remaining active over a wide range of soil matric potentials, while Gram-positive bacteria preferred sandy soils, sporulating at a low water potentials. Soil texture, mineralogy, and alkalinity all attenuated the bioavailability of an acyl-homoserine lactone (AHL) signaling molecule that controls community-level microbial behaviors. Texture controlled the timing of AHL sensing, while AHL bioavailability was decreased [~]105-fold by mineralogy and [~]103-fold by alkalinity. Finally, we built artificial soils with a range of complexities that converge on the properties of one Mollisol. As artificial soil complexity increased to more closely resemble the Mollisol, microbial behaviors approached those occurring in the natural soil, with the notable exception of organic matter. Properties that behaved additively were soil texture, pH, and mineralogy, while organic matter did not, suggesting that its soil behavior is an emergent property. IMPORTANCEUnderstanding environmental controls on soil microbes is difficult because many abiotic parameters vary simultaneously and uncontrollably when different natural soils are compared, preventing mechanistic determination of any individual soil parameters effect on microbial behaviors. We describe how soil texture, mineralogy, pH, and organic matter content can be varied individually within artificial soils to study their effects on soil microbes. Using microbial biosensors that report by producing a rare indicator gas, we identify soil properties that control microbial growth and attenuate the bioavailability of a diffusible chemical used to control community-level behaviors. We find that artificial soils differentially affect signal bioavailability and the growth of Gram-negative and Gram-positive microbes. We show that some soil properties have additive effects on signal bioavailability, while others exhibit emergent properties. These artificial soils are useful for studying the mechanisms that underlie soil controls on microbial fitness, signaling, and gene transfer.

systems biology↗

bioRxiv2020

A split methyl halide transferase AND gate that reports by synthesizing an indicator gas

It is challenging to detect microbial reactions in highly opaque or autofluorescent environments like soils, seawater, and wastewater. To develop a simple approach for monitoring post-translational reactions within microbes situated in environmental matrices, we designed a methyl halide transferase (MHT) fragment complementation assay that reports by synthesizing an indicator gas. We show that backbone fission within regions of high sequence variability in the Rossmann-fold domain yields split MHT (sMHT) AND gates whose fragments cooperatively associate to synthesize CH3Br. Additionally, we identify a sMHT whose fragments require fusion to pairs of interacting partner proteins for maximal activity. We also show that sMHT fragments fused to FKBP12 and the FKBP-rapamycin binding domain of mTOR display significantly enhanced CH3Br production in the presence of rapamycin. This gas production is reversed in the presence of the competitive inhibitor of FKBP12/FKPB dimerization, indicating that sMHT is a reversible reporter of post-translational reactions. This sMHT represents the first genetic AND gate that can report on protein-protein interactions via an indicator gas. Because indicator gases can be measured in the headspaces of complex environmental samples, this protein fragment complementation assay should be useful for monitoring the dynamics of diverse molecular interactions within microbes situated in hard-to-image marine and terrestrial matrices.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗