Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing

Abstract

In this study, we designed a microcosm experiment to explore the composition of the bacterial community in the rhizosphere of maize and bulk soil by sequencing the V3-V4 region of the 16S rRNA gene on the Illumina system. 978–1239 OTUs (cut off level of 3%) were found in rhizosphere and bulk soil samples. Rhizosphere shared features with the bulk soil, such as predominance of Acidobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes and TM7. At genus level, many of the dominant rhizosphere genera (Chitinophaga, Nitrospira, Flavobacterium, etc.) displayed different patterns of temporal changes in the rhizosphere as opposed to the bulk soil, showing rhizosphere has more impact on soil microorganisms. Besides, we found that significant growth-related dynamic changes in bacterial community structure were mainly associated with phylum Bacteroidetes, Proteobacteria and Actinobacteria (mainly genera Burkholderia, Flavisolibacter and Pseudomonas), indicating that different growth stages affected the bacterial community composition in maize soil. Furthermore, some unique genera in especial Plant-Growth Promoting Rhizobacteria (PGPR) such as Nonomuraea, Thiobacillus and Bradyrhizobium etc., which were beneficial for the plant growth appeared to be more abundant in the rhizosphere than bulk soil, indicating that the selectivity of root to rhizosphere microbial is an important mechanism leading to the differences in the bacteria community structure between rhizosphere and bulk soil.

Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions

“…The plants selected for distinct rhizomicrobiomes at each field site, still the community composition as indicated by the relative abundance of phyla, subphyla, and classes was similar to those described in other studies [52,53]. While the self-organized process of the formation of the rhizosphere microbial community indicated by the consistent occurrence of the same taxonomic groups across different 490 geographical zones is still a matter of research, it appears that the genetic modification did not interfere with this process.…”

Bacterial community diversity in the rhizosphere of nickel hyperaccumulator species of Halmahera Island (Indonesia)

“…In our study, Proteobacteria was the most well represented phylum in all rhizosphere soils sampled. Bacteria belonging to this phylum have been defined as copiotrophic (Fierer et al, 2007;Lienhard et al, 2014), which are fast-growing organisms that prefer carbon-rich environments, such as in the rhizosphere (Yang et al, 2017). In our study, among the sixteen sampled sites, the average organic matter content was 84 ± 18 g kg−1 (ranging from 18.5 to 136 g kg −1 in the soil of the site B and I, respectively).…”

“…Currently, many reports employ NGS to reveal fundamental and new understanding of the rhizomicrobiome structure and diversity (Metzker, 2010;Mendes et al, 2013;Knief, 2014;Lopez et al, 2017). Among bacteria and whatever the soil type studied, whether contaminated with metals (Kim et al, 2006) or non-contaminated (Smalla et al, 2001;Miethling et al, 2003), the phylum Proteobacteria generally represents the dominant members of the rhizosphere microbiome (Uroz et al, 2010;Johnston-Monje et al, 2016;Yang et al, 2017) followed by other phyla such as Actinobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia and Planctomycetes (Buée et al, 2009b;Turner et al, 2013;Prashar et al, 2014;Yang et al, 2017). In the ultramafic soils of Halmahera, the microbial community composition consisted of high proportions of Proteobacteria and Acidobacteria phyla that are abundant in many other soil types (Janssen, 2006;Lauber et al, 2009;Yang et al, 2017).…”

“…Among bacteria and whatever the soil type studied, whether contaminated with metals (Kim et al, 2006) or non-contaminated (Smalla et al, 2001;Miethling et al, 2003), the phylum Proteobacteria generally represents the dominant members of the rhizosphere microbiome (Uroz et al, 2010;Johnston-Monje et al, 2016;Yang et al, 2017) followed by other phyla such as Actinobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia and Planctomycetes (Buée et al, 2009b;Turner et al, 2013;Prashar et al, 2014;Yang et al, 2017). In the ultramafic soils of Halmahera, the microbial community composition consisted of high proportions of Proteobacteria and Acidobacteria phyla that are abundant in many other soil types (Janssen, 2006;Lauber et al, 2009;Yang et al, 2017). Indeed, Proteobacteria and Acidobacteria are generally the numerically dominant phyla in soil, with members of the Bacteroidetes and Firmicutes phyla being less common (Dunbar et al, 1999;Chow et al, 2002;Zhou et al, 2003).…”

Bacterial community diversity in the rhizosphere of nickel hyperaccumulator plant species from Borneo Island (Malaysia)

“…Many studies suggest that Proteobacteria and Actinobacteria are the most common phyla in the rhizosphere of many plant species (Green and Bohannan, ; Singh et al ., ; Kaiser et al ., ) and bacteria belonging to these two phyla have been defined as copiotrophic (Fierer et al ., ; Kopecky et al ., ; Lienhard et al ., ). Moreover, it is currently accepted that copiotrophic bacteria are known to prefer carbon‐rich environments, such as rhizospheres (Semenov et al ., ; Buée et al ., ; Yang et al ., ). Consequently, the positive correlations between Proteobacteria and both total C and organic C contents underline the adaptability of this phylum to the rhizosphere, which is known to content a wide variety of substances such as rhizodeposits.…”