Biology subjects

Benucci, G. M. N.

Publications and source records attributed to Benucci, G. M. N..

4 recordsLinked to original sources

bioRxiv2025

Developmentally-specific physiological and metabolic responses support drought resilience in switchgrass and constrains biofuel yield

Switchgrass (Panicum virgatum) is a promising bioenergy crop due in part to its resilience to drought stress. However, the significance of drought timing remains poorly understood, both from a plant biology perspective and its impact on downstream biofuel production. This study determines the developmental stage-specific physiological and metabolic responses of switchgrass to drought stress and its implications for biofuel production using a custom-built programmable irrigation system. Vegetative, flowering, and senescence-stage drought significantly reduced CO2 assimilation, and stomatal conductance without affecting biomass yield. Metabolic profiling revealed significant accumulation of glucose, fructose, quinic acid, shikimate and GABA during vegetative-stage drought, while flowering and senescence stages exhibited limited metabolic changes. Similarly, specialized metabolites also displayed distinct developmental patterns, with vegetative-stage drought driving the most pronounced metabolic alterations. Thermochemically-treated and hydrolyzed switchgrass biomass from vegetative-stage drought showed elevated lignocellulose-derived compounds and saponins with the latter most positively correlating with fermentation lag times. Conversely, senescence-stage drought enhanced ethanol yields while lowering saponin levels in the hydrolysates. While vegetative-stage drought enhanced physiological resilience, it compromises downstream biofuel production by introducing fermentation inhibitors, particularly saponins.

plant biology↗

bioRxiv2024

Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (Panicum virgatum L.) significantly impacts plant microbiomes

Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remains unclear. To address this, wildtype and QsuB engineered switchgrass were grown in switchgrass field soils and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wildtype, QsuB engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB engineered plants had a lower abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both organismal groups similarly, or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing non-target impacts of engineered plant traits on the plant microbiome.

microbiology↗

bioRxiv2021

Host genetic control of succession in the switchgrass leaf fungal microbiome

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across three additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association mapping and RNA-sequencing to show that three cysteine-rich receptor-like kinases were linked to a genetic locus associated with microbiome structure. These genes were more highly expressed in genotypes susceptible to fungal pathogens, which were central to microbial covariance networks, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

ecology↗

bioRxiv2021

CONSTAX2: Improved taxonomic classification of environmental DNA markers

CONSTAX - the CONSensus TAXonomy classifier - was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicons and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 can be used to classify prokaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable, command line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases, new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability and ImplementationCONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/.

bioinformatics↗