In Situ Cultivation Approach to Increase the Culturable Bacterial Diversity in the Rhizobiome of Plants

Acuna, Jacquelinne J.
Marileo, Luis G.
Araya, Macarena A.
Rilling, Joaquin I.
Larama, Giovanni A.
Mora, Maria Luz
Epstein, Slava
Jorquera, Milko A.
Datos de publicación:
The use of high-throughput DNA sequencing (HTS) has revealed the great diversity of rhizobacteria in plant rhizospheres; however, only a minor portion (<= 1%) of rhizobacteria belonging to few taxa can be cultured under laboratory conditions. In recent years, in situ cultivation has opened a window to explore a greater diversity of bacterial taxa in the environment. Here, we explored the total and culturable rhizobacterial communities associated with the rhizosphere of wheat plants by using 16S rRNA-based HTS and in situ cultivation with microwell chambers (MWCs), respectively. Results by HTS revealed to phyla Proteobacteria (29-39%), Acidobacteria (17%), Actinobacteria (11-15%), and Bacteroidetes (5-12%) as the most abundant rhizobacterial taxa in rhizosphere samples. A total of 206 isolates (26 genera) were obtained with MWCs, where coincidentally with HTS, the most abundant phyla were Proteobacteria (70.4%), Firmicutes (24%), Actinobacteria (4%), and Bacteroidetes (1.5%). At the genus level, the most of isolates (72%) belonged to Pseudomonas, followed by Bacillus, Stenotrophomonas, Delftia, and Herbaspirillum. Members of rare taxa (Lelliottia, Rhodococcus, Micrococcus, Variovorax, and Bosea) also were isolated by MWCs. In addition, a high proportion (82%) of isolates showed high similarity with plant beneficial and environmental non-pathogenic bacteria whereas a minor proportion (18%) of isolates showed high similarity to human and plant pathogenic bacteria. This study demonstrates that in situ cultivation represents a useful tool to isolate a greater number of rhizobacterial taxa, which can be investigated under laboratory conditions in bioprospecting (e.g., plant growth-promoting bacteria) and public health (e.g., human opportunist and plant pathogens) studies.