Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota

Phenotype microarray-based assessment of metabolic variability in plant protoplasts

BACKGROUND

Productivity and fitness of cultivated plants are influenced by genetic heritage and environmental interactions, shaping certain phenotypes. Phenomics is the -omics methodology providing applicative approaches for the analysis of multidimensional phenotypic information, essential to understand and foresee the genetic potential of organisms relevant to agriculture. While plant phenotyping provides information at the whole organism level, cellular level phenotyping is crucial for identifying and dissecting the metabolic basis of different phenotypes and the effect of metabolic-related genetic modifications. Phenotype Microarray (PM) is a high-throughput technology developed by Biolog™ for metabolic characterization studies at cellular level, which is based on colorimetric reactions to monitor cellular respiration under different conditions. Nowadays, PM is widely used for bacteria, fungi, and mammalian cells, but a procedure for plant cells characterization has not yet been developed, due to difficulties linked in identifying a suitable reporter of cell activities.

RESULTS

Here, we tested for the first time, PM technology on plant cells using protoplasts as a means of evaluating metabolic activity. Indeed, studying the metabolism of plant protoplasts can be a valuable method for predicting the inherent metabolic potential of an entire plant organism. Protoplasts are indeed valuable tools in plant research and biotechnology because they offer a simplified, isolated cellular system where researchers can focus on intracellular processes without interference from the cell wall. As a proof-of-principle, we used protoplasts of Solanum tuberosum L. as model system. Protoplasts were isolated from leaf tissue of in vitro-grown plants, purified and then diluted until desired concentration. Microplates were inoculated with protoplasts suspension and various markers of redox potential as indicators of cell activity were tested. After identifying the optimal conditions for PM testing, metabolic tests were extended to protoplasts from S. lycopersicum L., evaluating plant response to different NaCl concentrations and some of the toxic compounds present in pre-configured Biolog™ microplates.

CONCLUSIONS

The standardized high-throughput system developed was effective for the metabolic characterization of plant protoplasts. This method lays the foundation for plant cell metabolic phenotype studies enabling comparative studies at cellular level among cultivars, species, wild-type organisms, and genome-edited plants.

Role of metabolism, resistance, and/or antagonism as drivers of endomicrobiomes assemblage in Origanum heracleoticum L

The understanding of selective forces driving the compartmentalization of microbiota in plants remains limited. In this study, we performed a phenotypic characterization of bacterial endophytes isolated from the medicinal plant Origanum heracleoticum, together with the determination of the antibiotic resistance profiles and the antagonistic interactions of communities within and across different plant organs. Results revealed organ-related differences in the metabolic capabilities of bacteria, with those associated with stems displaying the highest metabolic activity for carbon sources. Contrarily, the patterns of antibiotic resistance appeared closely aligned with the taxonomical classification of the endophytes. The presence of antagonistic interactions, likely spurred by resource limitations, favor bacteria exhibiting greater metabolic plasticity. In conclusion, this research advances our comprehension of the intricate dynamics between plants and their associated microbiota, indicating that its composition is mainly influenced by forces contributing to the selection of distinct functions and phenotypic traits.

Organic Matter Composition as a Driver of Soil Bacterial Responses to Pig Carcass Decomposition in a Canadian Continental Climate

Organic by-products are released into the surrounding soil during the terrestrial decomposition of animal remains. The affected area, known as the Cadaver Decomposition Island (CDI), can undergo biochemical changes that contribute to landscape heterogeneity. Soil bacteria are highly sensitive to labile inputs, but it is unknown how they respond to shifts in dissolved organic matter (DOM) quantity and quality resulting from animal decomposition. We aimed to evaluate the relationship between soil DOM composition and bacterial activity/function in CDIs under a Canadian temperate continental climate. This was studied in soils surrounding adult pig carcasses (n = 3) that were surface deposited within a mixed forested environment (Trois-Rivières, Québec) in June 2019. Using fluorescence spectroscopy and dissolved organic carbon analyses, we detected a pulse of labile protein-like DOM during the summer season (day 55). This was found to be an important driver of heightened soil bacterial respiration, cell abundance and potential carbohydrate metabolism. These bacterial disturbances persisted into the cooler autumn season (day 156) and led to the gradual transformation of labile DOM inputs into microbially sourced humic-like compounds. By the spring (day 324), DOM quantities and bacterial measures almost recovered, but DOM quality remained distinct from surrounding vegetal humic signals. All observed effects were spatially constrained to the topsoil (A-horizon) and within 20 cm laterally from the carcasses. These findings provide valuable insight into CDI organic matter cycling within a cold-climate ecosystem. Repeated CDI studies will however be required to capture the changing dynamics resulting from increasing global temperatures.