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

Abstract

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 rRNAbased 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.

Effects of Compound Microbial Fertilizer on Soil Characteristics and Yield of Wheat (Triticum aestivum L.)

“…Acuña et al (2020) found that in the rhizobiome of wheat, Proteobacteria and Acidobacteria were the most dominant phyla (Smit et al 2001). Proteobacteria responded quickly to unstable carbon and phosphorus nutrients and showed the ability to grow rapidly and adapt to diverse plant rhizosphere environments (Acuña et al 2020). In this study, we observed that Proteobacteria occupied higher abundance in all the bacteria during the whole wheat growth period and has little change.…”

“…The phylum Proteobacteria, which is metabolically versatile and genetically diverse, comprises the largest fraction of the bacterial community in soil ecosystems and is more dominant than the phylum Acidobacteria (Smit et al 2001;Wu et al 2013). Acuña et al (2020) found that in the rhizobiome of wheat, Proteobacteria and Acidobacteria were the most dominant phyla (Smit et al 2001). Proteobacteria responded quickly to unstable carbon and phosphorus nutrients and showed the ability to grow rapidly and adapt to diverse plant rhizosphere environments (Acuña et al 2020).…”

Microbial Diversity of Psychrotolerant Bacteria Isolated from Wild Flora of Andes Mountains and Patagonia of Chile towards the Selection of Plant Growth-Promoting Bacterial Consortia to Alleviate Cold Stress in Plants

“…in association with the lichen Usnea sp., Haplopappus sp., and Gaultheria sp. The low bacterial number can be partly explained due to the antimicrobial activities of some of these wild plants and the lichen [ 75 , 76 , 77 , 78 , 79 , 80 , 81 , 82 ], and the low recovery rates of culturable bacteria from the rhizosphere and phyllosphere of plants [ 83 , 84 ] under the conditions used in this study.…”

CRISPR loci-PCR as Tool for Tracking Azospirillum sp. Strain B510

“…After standardization, fingerprint analyses were performed using genomic DNA from other two culture collection Azospirillum sp. CRISPR-harboring strains, as well as nine other native Azospirillum spp., and 38 native strains of different taxa previously isolated from wheat rhizosphere and root endosphere from the Region de La Araucanía [ 10 , 11 ].…”

“…strain B506 (WGS: BADK01000001:BADK01001143) [ 8 ], both harboring CRISPR loci, were also acquired from JCM-RIKEN and used as control strains for PCR specificity assays. Additional control strains consisted of Azospirillum strains isolated from the wheat rhizosphere in Chile [ 10 ], and strains from the genera Bacillus , Microbacterium , Chitinophaga , Arthrobacter , Georgenia , Psychrobacillus , Roseomonas , Bosea and Leifsonia previously isolated from the wheat rhizosphere (20 strains), and endosphere (18 strains) [ 11 ]. All bacteria used in this study are listed in Table 1 .…”