Biology subjects

Estera-Molina, K.

Publications and source records attributed to Estera-Molina, K..

11 recordsLinked to original sources

bioRxiv2026

Drought Dominates Engineered Lipid Sink Effects on Sorghum Physiology and Carbon Allocation

Determining the environmental limits that govern how engineered metabolic traits control whole-plant carbon (C) allocation is essential for developing climate-resilient bioenergy systems. Oil-enhanced sorghum offers a promising strategy to boost aboveground energy density, yet its system-wide effects on root C investment and soil C delivery, particularly under drought, are largely uncharacterized. Here, we provide the first comprehensive assessment of these interactions using whole-plant 13CO2 continuous labeling, depth-specific sampling of roots and rhizosphere soil, and coordinated measurements of photosynthesis, stomatal anatomy, tissue nitrogen, and root non-structural carbohydrates (NSCs). Under well-watered conditions, oil enhancement produced distinct aboveground physiological changes, including slightly longer stomata, lower stomatal density, significantly higher leaf nitrogen concentration and biomass, and greater leaf 13C enrichment. Importantly, these aboveground changes did not translate into detectable shifts in the allocation of recent photosynthate to belowground pools. In contrast, drought acted as a dominant regulatory factor, reorganizing C flow across both genotypes by suppressing photosynthesis and leaf water status, increasing root nitrogen and NSC reserves, and significantly promoting the retention of recent assimilates in shallow root systems. Depth-specific 13C patterns showed that drought reduced new C incorporation into deep roots while increasing 13C enrichment in deep rhizosphere soil, suggesting that drought altered the balance between C investment in root growth and rhizodeposit C inputs at depth. Ultimately, soil moisture availability was an overriding determinant of belowground C partitioning and vertical C delivery, superseding the influence of the engineered lipid sink. These findings provide new mechanistic insight into the environmental constraints on C flow in an engineered bioenergy crop and identify moisture-driven limitations as the primary bottleneck for translating synthetic metabolic innovations into robust, ecosystem-level C outcomes.

ecology↗

bioRxiv2025

Spatial and depth structuring predominate over temporal variation in Mediterranean grassland soil viral communities

Viruses have the potential to influence microbial community structure and elemental cycling in soils, but it remains unclear how these communities are distributed across space and time, which can shape how they respond to environmental change and impact ecosystem processes. Mediterranean grasslands, with their pronounced seasonal moisture fluctuations, offer an ideal system to examine viral biogeography. While previous studies hint at spatial structuring and moisture controls on viral communities, temporal responses to seasonal moisture shifts have not been comprehensively investigated in situ. Here, we generated 59 viromes and leveraged 89 metagenomes from two Mediterranean grasslands to measure soil viral communities across horizontal space (sampling zone), depth, and key seasonal stages of the Mediterranean water year (e.g. plant productivity, dry down and wetup). Sampling zone was the dominant driver of viral community composition in viromes, with time secondarily explaining variation in viral communities. In contrast, viral richness and DNA yields varied primarily across time. Spatial structuring also emerged in viruses recovered from metagenomes, with depth having the strongest effect, followed by sampling zone. Environmental variables and predicted host distributions partially explained these patterns, but substantial variation remained unaccounted for, suggesting a role for dispersal limitation. Overall, soil viral communities were primarily structured by spatial factors, with temporal and environmental influences acting secondarily, highlighting the importance of fine-scale spatial dynamics in understanding viral ecology. Future studies should explicitly examine the role of dispersal limitation and fine-scale host-environment interactions to fully resolve drivers of soil viral biogeography.

ecology↗

bioRxiv2025

Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland

Changes in global patterns can leave a lasting legacy in semi-arid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn--a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H218O, and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux; measured microbial growth and mortality via quantitative 18O stable isotope probing and 16S rRNA gene amplicon sequencing; and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes. We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by [~]1 order of magnitude, yielding decreased community growth efficiency (CGE = gross community growth/net respiration), and microbial mortality declined by [~]2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover), this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low-CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth. Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting. Persistent decreases in CGE due to reduced winter rainfall result in consistent carbon loss as CO2, which, if sustained over multiple years, could ultimately lead to a net decline in total soil organic carbon.

microbiology↗

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↗

bioRxiv2024

The active subset of grassland soil microbiomes changes with soil depth, water availability and prominently features predatory bacteria and episymbionts

Mediterranean grasslands, vital natural and agricultural ecosystems, experience seasonal variation in water content that likely affect microbial activity. We used metagenomics-informed stable isotope probing to investigate how the activities of microorganisms in Angelo Reserve (2160 mm rainfall) and Hopland (956 mm rainfall) soil change over depth and the seasons. At both sites, we find that the relative abundances of organisms in shallow soil changes relatively little but the most abundant organisms vary greatly with soil depth. Notably the highest levels of isotope incorporation, indicative of growth, occurs in deep soils. The active part of the 0-10 cm soil community varies over time, especially in Hopland soils during the fall rewetting. We defined a large, novel clade of Actinomycetota with notable capacity for thiosulfate oxidation whose representatives are prevalent and active in deep soils (>20 cm) across both ecosystems. Active Saccharibacteria unexpectedly encode nucleotide synthesis genes that enabled isotope incorporation while growing in shallow Angelo soils over all time periods. In contrast to predicted episymbiotic lifestyles of Saccharibacteria, other highly active bacteria are predicted predators. Obligately predatory Pseudobdellovibrio are active in intermediate depth Hopland soils whereas bacteria of the order Haliangiales are active in shallow Angelo soils. Supporting predatory lifestyles of Haliangiales, we used in silico structure prediction to assemble a large protein complex that we identify as a contractile injection system. Overall, the results indicate the potential for active carbon turnover in deep grassland soil and strong seasonal changes in the active members of microbial communities, despite relatively minor shifts in community composition.

bioinformatics↗

bioRxiv2024

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

In soils, the first rain after a prolonged dry period greatly impacts soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils--however this is often through measurements in culture. Here, we used metagenome-assembled genomes in combination with metatranscriptomics and 18O- water stable isotope probing to track genomic traits associated with transcriptional activity and growth of soil microorganisms over the course of one week following rewetting of a grassland soil. We found that the codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also observed higher growth rates in bacteria with smaller genomes, demonstrating that reduced genome size contributes to bacterial growth responses to sudden changes in water or nutrient availability--potentially explaining why smaller genomes are more prevalent in arid and carbon poor systems. High levels of codon bias corresponded to faster transcriptional upregulation of ribosomal protein genes. In early transcribing taxa, nucleotides requiring less energy to produce were more common at synonymous substitution sites--where nucleotide substitutions did not change the encoded amino acid. We found several of these relationships also existed within a phylum, suggesting that association between genomic traits and activity could be a generalized characteristic of soil bacteria. These results provide in situ evidence that following rewetting, certain genomic characteristics affect soil microbial growth rate and transcription, and points towards the fitness advantages that these traits might pose for bacteria under changing conditions in soil.

microbiology↗

bioRxiv2023

Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter

O_LIArbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for other soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for six weeks and measured. the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. C_LIO_LINanoSIMS imaging, IRMS, 13C NMR, and SOM density fractionation showed hyphae and roots had similar 13C enrichment. AMF transferred 0.77 mg C per g of soil (increasing total C by 2%); 33% was found in occluded or mineral-associated pools, primarily as carbohydrates. C_LIO_LIIn the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (>20 atom%). Mapping 13C-enriched metagenome-assembled genomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. C_LIO_LIOur results illustrate the quantitative impact of hyphal C transport on the formation of potentially protective SOM pools and indicate microbial roles in the AMF hyphosphere soil food web. C_LI

microbiology↗

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

Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands

Although soil viral abundance, diversity, and potential roles in microbial community dynamics and biogeochemical cycling are beginning to be appreciated1-5, little is known about the patterns and drivers of soil viral community composition that underlie their contributions to terrestrial ecology. Here, we analyzed 43 soil viromes from a precipitation manipulation experiment in a Mediterranean grassland in California, USA. We recovered 5,315 viral population sequences (vOTUs), and viral community composition exhibited a highly significant distance-decay relationship within the 18 m long field. This pattern was recapitulated in the microheterogeneity of 130 prevalent vOTUs (detected in >=90% of the viromes), which tended to exhibit significant negative correlations between genomic similarity of their predominant allelic variants and distance. Although spatial turnover was also observed in the bacterial and archaeal communities from the same soils, the signal was dampened relative to the viromes, suggesting differences in assembly drivers at local scales for viruses and their microbial hosts and/or differences in the temporal scales captured by viromes and total DNA. Despite the overwhelming spatial signal, vOTUs responsive to a decrease in soil moisture were significantly enriched in a predicted protein-sharing subnetwork of 326 vOTUs linked to 191 known actinobacteriophages, suggesting a genomically cohesive viral response to soil moisture evocative of environmental filtering, potentially by way of actinobacterial hosts. Overall, soil viral ecological processes appear to be highly constrained in space and tightly coupled to the heterogeneous, dynamic soil environment and thus fundamentally different from those of their well-mixed and more thoroughly studied marine counterparts.

microbiology↗

bioRxiv2021

Belowground allocation and dynamics of recently fixed plant carbon in a California annual grassland soil

Plant roots and the organisms that surround them are a primary source for stabilized organic C, particularly in grassland soils, which have a large capacity to store organic carbon belowground. To quantify the flow and fate of plant fixed carbon (C) in a Northern California annual grassland, we tracked plant carbon from a five-day 13CO2 pulse field labeling for the following two years. Soil and plant samples were collected immediately after the pulse labeling, and again at three days, four weeks, six months, one year, and two years. Soil organic matter was fractionated using a sodium polytungstate density gradient to separate the free-light fraction (FLF), occluded-light fraction (OLF), and heavy fraction (HF). Using isotope ratio mass spectrometry, we measured 13C enrichment and total C content for plant shoots, roots, soil, soil dissolved organic carbon (DOC), and the FLF, OLF, and HF. The HF was further analyzed by solid state 13C NMR spectroscopy. At the end of the labeling period, the largest amount of 13C was recovered in plant shoots (60%), but a substantial amount (40%) was already found belowground in roots, soil, and soil DOC. Density fractionation of 4-week soil samples (from which living roots were removed) indicated that the highest isotope enrichment was in the mineral-rich heavy fraction, with similar enrichment of the FLF and OLF. At the 6-month sampling, after the dry summer period during which plants senesced and died, the amount of label in the FLF increased such that it was equal to that in the HF. By the 1-year sampling, 13C in the FLF had declined substantially and continued to decline by the 2-year sampling. 13C recovery in the OLF and HF, however, was qualitatively stable between sampling times. By the end of the 2-year experiment, 69% of remaining label was in the HF, 18% in the FLF and 13% in the OLF. While the total 13C content of the HF did not change significantly from the 4-week to the 2-year sample time, 13C NMR spectroscopic analysis of spring HF samples from 2018, 2019, and 2020 suggests that the relative proportion of aliphatic/alkyl functional groups declined in the newly formed SOC over the 2-year period. Simultaneously, aromatic and carbonyl functional groups increased, and the proportion of carbohydrate groups remained relatively constant. In summary, our results indicate that initial associations between minerals and root-derived organic matter are significant and form rapidly; by 4 weeks, a substantial amount (17%) of the total plant-derived 13C had become associated with the heavy fraction (HF) of soil. While the majority of annual C input cycles rapidly (<2-year timescale), a sizeable proportion ([~]12% of the original inputs) persisted for 2 years.

biochemistry↗