Abstract
This study combined culture-dependent (strain isolation plus molecular identification) and culture-independent (metabarcoding) approaches to characterize the diversity of microbiota on wheat and oilseed rape residues. The goal was to develop a methodology to culture microorganisms with the aim of being able to establish synthetic crop residue microbial communities for further study, i.e., testing potential interactions within these communities and characterizing groups of beneficial taxa that could be used as biological control agents against plant pathogens. We generated community-based culture collections. We adapted the isolation strategy to the potential differences in the spatial and temporal distribution of diversity between bacteria and fungi. We performed (i) a high-throughput isolation from few samples with no a priori for bacteria and (ii) a low-throughput isolation from several samples with a priori—i.e., morphotype selection—for fungi. Although isolation using a single medium did not allow us to characterize the microbiome as precisely as metabarcoding, the bacterial diversity (158 ASVs, 36 genera) was relatively higher than the fungal diversity (131 ASVs, 17 genera) known to be limited by competition for growth on non-selective solid media. Isolation and metabarcoding provided consistent and complementary information: they revealed several common but also specific ASVs, leading to close microbial community profiles of the most abundant fungal and bacterial taxa in residues. Finally, by empirically comparing the different profiles, we assessed the cultivability of the most abundant fungal and bacterial taxa obtained in metabarcoding.
Highlights
Crop residues are the decaying parts of the crop plant that are not harvested [1].They were recently described as an ‘ecotone’ by Kerdraon et al [2], i.e., a boundary compartment between two biomes, the plant, and the soil
We developed an integrated approach tailored to the ‘residue sphere’: (i) that modulates the sample size considering potential differences in the spatial and temporal distribution of diversity between bacteria and fungi [5], with a dedicated way of isolating on a single medium; and (ii) that allows us to test, by comparing different microbial assemblage profiles, whether the most abundant taxa obtained in metabarcoding [5] could be isolated
Bacterial and fungal strains were treated sepasampled was cut in two lengthwise, with one half used for microbial isolation and the rately: for bacteria, reduced sampling effort was coupled with high-throughput isolation, other half for metabarcoding (Figure 1)
Summary
Crop residues are the decaying parts of the crop plant that are not harvested [1] They were recently described as an ‘ecotone’ by Kerdraon et al [2], i.e., a boundary compartment between two biomes, the plant, and the soil. These residues, as a transient half-plant/half-soil compartment, constitute a key fully fledged microbial ecosystem worthy of the attention of microbiologists and plant disease epidemiologists. They are the main support for the phytopathogenic agents responsible for residue-borne plant diseases, but they host several plant-beneficial microorganisms and make a significant contribution to agrosystem stability [3,4,5]. The cultures of fungal and bacterial species from different ecological niches within a specific ecosystem is still indispensable: it complements molecular databases for taxonomic identification through a single-strain approach, making it possible to test whether the interactions between micro-organisms predicted by metagenomic sequencing (e.g., through the analysis of interaction networks [8])
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