Biology subjects

Sokol, N.

Publications and source records attributed to Sokol, N..

6 recordsLinked to original sources

bioRxiv2025

Drought reduces formation, but enhances persistence, of mineral-associated organic matter in a grassland soil

Drought effects are pervasive in many terrestrial ecosystems, yet little is known about the impact of drought on the transformation of plant C inputs to mineral-associated organic matter (MAOM) - the largest and slowest-cycling pool of organic carbon (C) on land. Using 13C-CO2 greenhouse labeling chambers, we tracked the formation of 13C-MAOM derived from Avena barbata living root inputs (13C-rhizodeposits) versus A. barbata decaying root inputs (13C-root detritus) under normal moisture and spring drought conditions in a semi-arid grassland soil, and then tested the durability of this 13C-MAOM in a subsequent persistence assay. Overall, drought reduced formation of MAOM - both per gram of soil and across the entire soil profile. Notably, drought conditions enhanced the persistence of MAOM derived from root detritus, though not of MAOM derived from rhizodeposition. Drought had the most pronounced effect on MAOM accrual from rhizodeposition late in plant development (week 12) whereas it had the most pronounced effect on MAOM accrual from root detritus early in root decomposition (week 4). These temporal responses were associated with distinct trajectories in microbial community-level growth rates, the average mass of OM compounds, and the number of unique metabolites within each habitat. Our results provide mechanistic evidence that drought reduces overall formation of MAOM but can enhance its persistence in a grassland soil.

ecology↗

bioRxiv2025

Specialist Generalist Trade Offs in Microbial Growth Rates Across Soil Habitats

Microbial ecological strategies are shaped by a fundamental trade-off: is it better to specialize and thrive in a narrow niche or generalize and persist across diverse environments? In soils, this trade-off is particularly relevant in the rhizosphere and detritusphere, where microorganisms encounter distinct resource inputs from living and decaying roots. Using H {superscript 1} O quantitative stable isotope probing (qSIP), we measured in situ bacterial and fungal growth rates in the rhizosphere, the root detritusphere, and in the combined presence of rhizosphere + root detritus to test whether specialists--microbes growing in a single habitat--grow faster than generalists that persist across multiple environments. Specialists grew consistently faster than generalists, suggesting a trade-off between the breadth of environmental conditions a microorganism can tolerate and its ability to grow quickly in a specific habitat. This cost to broad niche adaptation was apparent for bacteria, but growth rates of fungal saprotrophs varied little between specialists and generalists, reflecting how fundamental differences in life-history strategies between bacteria and fungi can shape microbial responses to resource availability and habitat heterogeneity. Net relatedness and nearest taxon indices indicated total bacterial communities were phylogenetically clustered while specialist and generalist communities were phylogenetically random, suggesting that functional traits, not lineage, best predict ecological strategy. In annual grassland soils, fast-growing specialists may dominate ecosystem processes when resources abound, and slow-growing generalists may sustain element transformations when conditions shift; understanding this interplay is key to predicting soil-carbon trajectories.

microbiology↗

bioRxiv2023

Improved characterization of soil organic matter by integrating FTICR-MS, liquid chromatography tandem mass spectrometry and molecular networking: a case study of root litter decay under drought conditions

Knowledge of the type of carbon contained in soils is important for predicting carbon fluxes in a warming climate, yet most soil organic matter (SOM) components are unknown. We used an integrated three-part approach to characterize SOM from decaying root-detritus microcosms subject to either drought or normal conditions. To observe broad differences in SOM compositions we employed direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FTICR-MS). We complemented this with liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify components by library matching. Since libraries contain only a small fraction of SOM components, we also used fragment spectra cosine similarity scores to relate unknowns and library matches through molecular networks. This approach allowed us to corroborate DI-FTICR-MS molecular formulas using library matches and infer structures of unknowns from molecular networks to improve SOM annotation. We found matches to fungal metabolites, and under drought conditions, greater relative amounts of lignin-like vs condensed aromatic polyphenol formulas, and lower average nominal oxidation state of SOM carbon, suggesting reduced decomposition of carbon and/or microbes under stress. We propose this integrated approach as more comprehensive than individual analyses in parallel, with the potential to improve knowledge of the chemical composition and persistence of SOM. SynopsisStructural characterization and identifications are lacking for soil organic matter components. This study integrates molecular formula assignments and structural information from fragment ion spectra into molecular networks to better characterize unknown soil organic matter components. For Table of Contents Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/545455v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@140a98org.highwire.dtl.DTLVardef@1c3b26forg.highwire.dtl.DTLVardef@f7b82aorg.highwire.dtl.DTLVardef@15c012f_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2022

Divergent microbial traits influence the transformation of living versus dead root inputs to soil carbon

Soil microorganisms influence the global carbon cycle by transforming plant inputs into soil organic carbon (SOC), but the microbial traits that facilitate this process are unresolved. While current theory and biogeochemical models suggest microbial carbon-use efficiency and growth rate are positive predictors of SOC, recent observations demonstrate these relationships can be positive, negative, or neutral. To parse these contradictory effects, we used a 13C-labeling experiment to test whether different microbial traits influenced the transformation of plant C into SOC within the microbial habitats surrounding living root inputs (rhizosphere) versus decaying root litter (detritusphere), under both normal soil moisture and droughted conditions. In the rhizosphere, bacterial-dominated communities with fast growth, high carbon-use efficiency, and high production of extracellular polymeric substances formed microbial-derived SOC under normal moisture conditions. However, in the detritusphere - and the rhizosphere under drought - more fungal-dominated communities with slower growth but higher exoenzyme activity formed plant-derived SOC. These findings emphasize that microbial traits linked with SOC accrual are not universal, but contingent on how microorganisms allocate carbon under different resource conditions and environmental stressors.

ecology↗

bioRxiv2022

The RNA binding protein Swm is critical for Drosophila melanogaster intestinalprogenitor cell maintenance

The regulation of stem cell survival, self-renewal, and differentiation is critical for the maintenance of tissue homeostasis. Although the involvement of signaling pathways and transcriptional control mechanisms in stem cell regulation have been extensively investigated, the role of post-transcriptional control is still poorly understood. Here we show that the nuclear activity of the RNA-binding protein Second Mitotic Wave Missing (Swm) is critical for Drosophila intestinal stem cells (ISCs) and their daughter cells, enteroblasts (EBs), to maintain their identity and function. Loss of swm in these intestinal progenitor cells leads ISCs and EBs to lose defined cell identities, fail to proliferate, and detach from the basement membrane, resulting in severe progenitor cell loss. swm loss further causes nuclear accumulation of poly(A)+ RNA in progenitor cells. Swm associates with transcripts involved in epithelial cell maintenance and adhesion, and the loss of swm, while not generally affecting the levels of these Swm-bound mRNAs, leads to elevated expression of proteins encoded by some of them, including the fly orthologs of Filamin and Talin. Taken together, this study indicates a role for Swm in adult stem cell maintenance, and raises the possibility that nuclear post-transcriptional gene regulation plays vital roles in controlling adult stem cell maintenance and function.

genetics↗

bioRxiv2020

Identification of split-GAL4 drivers and enhancers that allow regional cell type manipulations of the Drosophila melanogaster intestine

The Drosophila adult midgut is a model epithelial tissue composed of a few major cell types with distinct regional identities. One of the limitations to its analysis is the lack of tools to manipulate gene expression based on these regional identities. To overcome this obstacle, we applied the intersectional split-GAL4 system to the adult midgut and report 653 driver combinations that label cells by region and cell type. We first identified 424 split-GAL4 drivers with midgut expression from over 7,300 drivers screened, and then evaluated the expression patterns of each of these 424 when paired with three reference drivers that report activity specifically in progenitor cells, enteroendocrine cells, or enterocytes. We also evaluated a subset of the drivers expressed in progenitor cells for expression in enteroblasts using another reference driver. We show that driver combinations can define novel cell populations by identifying a driver that marks a distinct subset of enteroendocrine cells expressing genes usually associated with progenitor cells. The regional cell type patterns associated with the entire set of driver combinations are documented in a freely available website, providing information for the design of thousands of additional driver combinations to experimentally manipulate small subsets of intestinal cells. In addition, we show that intestinal enhancers identified with the split-GAL4 system can confer equivalent expression patterns on other transgenic reporters. Altogether, the resource reported here will enable more precisely targeted gene expression for studying intestinal processes, epithelial cell functions, and diseases affecting self-renewing tissues.

genetics↗