Biology subjects

Klonowska, A.

Publications and source records attributed to Klonowska, A..

3 recordsLinked to original sources

bioRxiv2022

Quantification of the diversity sampling bias resulting from rice root bacterial isolation on popular and nitrogen-free culture media, using 16S amplicon barcoding

Culturing bacteria from plant material is well known to introduce a strong bias compared to the real diversity present in the original samples. This bias is related to cultivability of bacteria, the chemical composition of media and culture conditions. The bias of recovery is often observed but was never quantified on different media using an amplicon barcoding approach comparing plant microbiota DNA extractions versus DNA extracted from serial dilutions of the same plant tissues grown on bacterial culture media. In this study, we i) quantified the culturing diversity bias using 16S amplicon barcode sequencing by comparing a culture-dependent approach (CDA) on rice roots on four popular bacterial media (Tryptone Soybean Agar-TSA-at two concentrations, 10% and 50%; a plant-based media with rice flour; Norris Glucose Nitrogen Free Medium-NGN; and Nitrogen Free -NFb) versus a culture-independent approach (CIA) assessed from DNA extracted directly on root and rhizosphere samples; ii) assessed enriched and missing taxa detected on the different media; iii) use biostatistics functional predictions to predict which metabolic profiles are enriched in the CDA and CIA. A comparative analysis of the two approaches revealed that among the 22 phyla present in the microbiota of the studied rice root samples, only five were present on the culture media approach (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicrobia). The Proteobacteria phylum was the most abundant in all cultured media samples, showing a high enrichment of gamma-Proteobacteria. The diversity of the combined culture media represented about 1/3 of the diversity of the total microbiota, and its genus diversity and frequency was documented. The functional prediction tool (PiCrust2) detected an enrichment of nitrogenase enzyme in bacterial taxa sampled from Nitrogen-free media, validating its predictive capacity. Further functional predictions also showed that the CDA missed mostly anaerobic, methylotrophic, methanotrophic and photosynthetic bacteria compared to the culture independent approach, delivering valuable insights to design ad-hoc culture media and conditions to increase cultivability of the rice-associated microbiota.

microbiology↗

bioRxiv2022

Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species

Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the Burkholderia and Paraburkholderia genera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species, Burkholderia are often studied for their human opportunistic traits. Here, we used root exudate stimulation on three Burkholderia and three Paraburkholderia strains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling.

microbiology↗

bioRxiv2022

The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso

As a consequence of its potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmers fields from irrigated and rainfed lowlands in western Burkina Faso, using an amplicon metabarcoding approach 16S (Prokaryotes, three plant sample per field) and ITS (fungi, one sample per field). In addition to the expected structure according to the root compartment (root vs. rhizosphere) and geographical zones, we show that the rice production system is a major driver of microbiome structure, both for prokaryotes and fungi. In irrigated systems, we found a higher diversity of prokaryotic communities from rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands. Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae and Bradyrhizobiaceae families in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, phylotypes assigned to putative phytobeneficial and pathogen species were found. Mycorrhizal fungi Glomeromycetes abundance was higher in rainfed lowlands. Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for potential microbial engineering applications.

microbiology↗