Bacterial Communities in the Rhizosphere of Amilaceous Maize (Zea mays L.) as Assessed by Pyrosequencing

Abstract

Maize (Zea mays L.) is the staple diet of the native peasants in the Quechua region of the Peruvian Andes who continue growing it in small plots called chacras following ancestral traditions. The abundance and structure of bacterial communities associated with the roots of amilaceous maize has not been studied in Andean chacras. Accordingly, the main objective of this study was to describe the rhizospheric bacterial diversity of amilaceous maize grown either in the presence or the absence of bur clover cultivated in soils from the Quechua maize belt. Three 16S rRNA gene libraries, one corresponding to sequences of bacteria from bulk soil of a chacra maintained under fallow conditions, the second from the rhizosphere of maize-cultivated soils, and the third prepared from rhizospheric soil of maize cultivated in intercropping with bur clover were examined using pyrosequencing tags spanning the V4 and V5 hypervariable regions of the gene. A total of 26031 sequences were found that grouped into 5955 distinct operational taxonomic units which distributed in 309 genera. The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from bulk soil. One hundred ninety seven genera were found in the bulk soil library and 234 and 203 were in those from the maize and maize/bur clover-cultivated soils. Sixteen out of the 309 genera had a relative abundance higher than 0.5% and the were (in decreasing order of abundance) Gp4, Gp6, Flavobacterium, Subdivision3 genera incertae sedis of the Verrucomicrobia phylum, Gemmatimonas, Dechloromonas, Ohtaekwangia, Rhodoferax, Gaiella, Opitutus, Gp7, Spartobacteria genera incertae sedis, Terrimonas, Gp5, Steroidobacter and Parcubacteria genera incertae sedis. Genera Gp4 and Gp6 of the Acidobacteria, Gemmatimonas and Rhodoferax were the most abundant in bulk soil, whereas Flavobacterium, Dechloromonas and Ohtaekwangia were the main genera in the rhizosphere of maize intercropped with bur clover, and Gp4, Subdivision3 genera incertae sedis of phylum Verrucomicrobia, Gp6 and Rhodoferax were the main genera in the rhizosphere of maize plants. Taken together, our results suggest that bur clover produces specific changes in rhizospheric bacterial diversity of amilaceous maize plants.

Comparison of specific endophytic bacterial communities in different developmental stages of Passiflora incarnata using culture‐dependent and culture‐independent analysis

“…Additionally, 15% of the overall sequences from both the vegetative and RS corresponded to unassigned OTUs. A similar undetermined fraction was found in bacterial communities from the rhizosphere of amylaceous maize (Correa‐Galeote, Bedmar, Fernández‐González, Fernández‐López, & Arone, ), which indicates the occurrence of yet uncultured bacterial groups. However, as occurred in the study just cited, the unassigned sequences had no affected clustering (Dohrmann et al, ).…”

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation

“…Altogether, the influence of habitat type and growth stage was less important than the influence of soil type in explaining diversity patterns (Supplementary Figure S5). There are several contrasting reports in the literature relating to whether habitat type (rhizosphere vs bulk soil), plant grow stage, plant species or soil type is the dominant factor in driving biodiversity patterns in soil microbial communities (Berg and Smalla, 2009;Bulgarelli et al, 2015;Chaparro et al, 2014;Correa-Galeote et al, 2016;Donn et al, 2015;Edwards et al, 2015;Peiffer et al, 2013;Schreiter et al, 2014;Tkacz et al, 2015). These results support the concept that soil type is a major factor in shaping microbial community diversity and composition under field conditions, whereas habitat type and plant growth stage seem to have a relatively small impact on these communities.…”

DNA accumulation on ventilation system filters in university buildings in Singapore

“…To our knowledge, genera Gp1, Gp4, Gp6 and Gp16 have not been reported in previous indoor bioaerosol studies. These genera belong to phylum Acidobacteria, which are commonly found in soil or plant roots [29–30]. These bacteria likely originate outdoors.…”