Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization

Abstract

The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane. CLPP revealed a higher metabolic activity in the rhizosphere compared to bulk soil, and suggested that D-galacturonic acid plays a role in bacterial selection by the plant roots (supported by results of metagenome prediction). Quantification of the 16S rRNA gene confirmed the higher abundance of bacteria in the rhizosphere. Sequence analysis showed that of the 252 classified families sampled, 24 were significantly more abundant in the bulk soil and 29 were more abundant in the rhizosphere. Furthermore, metagenomes predicted from the 16S rRNA gene sequences revealed a significant higher abundance of predicted genes associated with biofilm formation and with horizontal gene transfer (HGT) processes. In sum, this study identified major bacterial groups and their potential abilities to occupy the sugarcane rhizosphere, and indicated that polygalacturonase activity and HGT events may be important features for rhizosphere colonization.

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica

“…In addition, accuracy of the PI-CRUSt predictions was estimated using the Nearest Sequenced Taxon Index (NSTI) values of the two mat samples used in this study. The NSTI value validates the taxonomy-based PICRUSt-predicted KEGG functional categories of the microbial communities (Langille et al, 2013; Staley et al, 2014; Lopes et al, 2016; Kim et al, 2017). Since the output of the functional profiles generated by PICRUSt was not compatible with Tax4Fun, we have written an R script for the comparative analyses of the taxonomy-based metabolic functional predictions of the microbial communities in the two mat samples (Supplementary Materials, S1.1, S1.2, and S2).…”

“…), and surface soil samples from the Austre Lovénbreen glacier in High Arctic (mean NSTI = 0.18 ± 0.03 s.d.) (Langille et al, 2013; Staley et al, 2014; Lopes et al, 2016; Kim et al, 2017). Thus, the mean NSTI values in our study suggest that the predicted metabolic functions of the microbial communities in Lake Obersee mat samples are close to the known microbial reference genome databases, implying higher accuracy of the predictions.…”

Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population

“…For our soil population of P. koreensis , xut + genotypes were selected in the habitat where the capacity to assimilate xylose is advantageous (bulk soil), while the more fit xut − genotypes were possibly selected in the habitat where this capacity is not essential (rhizosphere). In a previous microbiome study of the same sugarcane field, CLPP analysis identified d ‐xylose as a C‐source more highly oxidized by the bulk soil than the rhizosphere microbiome (Lopes et al ., ). Those results suggest that the assimilation of xylose could be a characteristic of other microbial taxa inhabiting bulk soil in addition to the ecotype of P. koreensis here assessed.…”

“…Studies of soil microbial communities have advanced our knowledge in recent years, revealing a different microbiome assemblage in bulk soil compared to the rhizosphere (Berg and Smalla, ; Uroz et al ., ; Mendes et al ., ; Lopes et al ., ), which is enriched in microbes able to promote plant health and growth (Weller et al ., ; Mendes et al ., ; Kwak and Weller, ; Philippot et al ., ). However, little is known about the evolutionary ecology of specific bacterial populations inhabiting these soil compartments.…”

“…A previous study, based on 16S rRNA gene highthroughput sequencing, showed that the microbiomes of sugarcane rhizosphere and bulk soil are distinct (Lopes et al, 2016). Here, we first analysed the OTUs classified as Pseudomonas spp.…”