Darine Trabelsi

Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

Effect of on-field inoculation of Phaseolus vulgaris with rhizobia on soil bacterial communities

The aim of this study was to assess the impact of inoculation of Phaseolus vulgaris with two indigenous rhizobia strains on plant growth promotion, nitrogen turnover processes, richness and structure of the Rhizobiaceae and total bacterial communities in the bulk soil. Both strains used induced a significant increase in nodulation and grain yield. Analysis of bulk soil fertility showed positive, negative and strain-dependent effects of inoculation on nitrate, phosphorus and ammonium, respectively. Terminal-restriction fragment length polymorphism profiling demonstrated that inoculation significantly increased the phylotype richness of the bacterial communities. No significant difference in richness between the strains used and no additive effect of co-inoculation were observed. However, differences between both inoculants and a clear additive effect of co-inoculation on heterogeneity were found. This work gives original insights into the effect of rhizobial inoculation outside the restricted rhizospheric area. Effects on bacterial structure and diversity are clearly sensed in the neighbourhood of 25 cm and in a limited time course. Both Alpha- and Gammaproteobacteria, together with Firmicutes and Actinobacteria, were enhanced by inoculation, No evidence of terminal-restriction fragment inhibition was found. However, it remains to be answered how the impact on taxonomic groups can be related to effects on functional capabilities of soil microbial communities.

Development of real-time PCR assay for detection and quantification of Sinorhizobium meliloti in soil and plant tissue.

Aims:  Sinorhizobium meliloti is a nitrogen‐fixing alpha‐proteobacterium present in soil and symbiotically associated with root nodules of leguminous plants. To date, estimation of bacterial titres in soil is achieved by most‐probable‐number assays based on the number of nodules on the roots of test plants. Here, we report the development of two real‐time PCR (qPCR) assays to detect the presence of S. meliloti in soil and plant tissues by targeting, in a species‐specific fashion, the chromosomal gene rpoE1 and the pSymA gene nodC.

Genetic diversity and salt tolerance of bacterial communities from two Tunisian soils

Microbial ecology studies on arid soils are particularly important for the analysis of biological functions during desertification. Although much is known about the arid saline flora, few researches have directly compared the bacterial communities of saline arid soils with cultivated soils in Northern Africa. Bacterial communities present in two soils from Soliman (north of Tunisia), one salty and neglected, and the other cultivated, were investigated by using both cultivation dependent and independent approaches. The first approach was used to assess the presence of salt tolerant bacteria and the relationships among salt (NaCl) resistance phenotype, soil characteristics and phylogenetic assignment of strains. Total community analysis, performed by T-RFLP on total DNA, was carried out to investigate the relationships between total community fingerprinting with cultivated isolates diversity. The cultivated isolates from salty soil were more genetically diverse, harbouring strains that can grow at high salt concentration. Moreover, the salt resistance of isolates was found not to be related to any particular phylogenetic group, being widespread among isolates belonging to different bacterial subdivisions. Ribotype richness, evaluated as number of different T-RFLP bands (TRFs), was shown to be higher in the agricultural soil than in the salty soil and several agricultural soil-specific TRFs were detected.

Effect of Glyphosate on Enzymatic Activities, Rhizobiaceae and Total Bacterial Communities in an Agricultural Tunisian Soil

The effect of glyphosate on richness and structure of the Rhizobiaceae and total bacterial communities in an agricultural soil after different treatments was studied. The herbicide was applied on the soil in the presence or the absence of Medicago sativa plants with or without inoculation with the Sinorhizobium meliloti reference strain RCR2011. Terminal-restriction fragment length polymorphism (T-RFLP) profiling showed that this agricultural soil has a high total microbial and rhizobial genetic diversity. To investigate the impact of the herbicide on microbial activity, fluorescein diacetate (FDA) and a panel of three enzymes (phosphatase, catalase, and protease BAA) were assessed. Depending on the type of enzyme tested, the enzymatic activities responded differently to the action of glyphosate, the presence of M. sativa, and the inoculation with RCR2011. The present work gives original insights into the effect of the herbicide on the rhizospheric area of M. sativa with or without rhizobial inoculation by the fact that glyphosate changes microbial diversity and affects soil enzymatic activities.

Development of a cultivation-independent approach for the study of genetic diversity of Sinorhizobium meliloti populations.

The development of a species‐specific marker for the analysis of the genetic polymorphism of the nitrogen‐fixing symbiotic bacterium Sinorhizobium meliloti directly from environmental DNA is reported. The marker is based on terminal‐restriction fragment length polymorphism (T‐RFLP) methodology targeting specifically the 16S‐23S Ribosomal Intergenic Spacer of S. meliloti. Species‐specificity and polymorphism of the marker were tested on DNA extracted from soil samples and from a collection of 130 S. meliloti bacterial isolates. These primers and the T‐RFLP approach proved useful for the detection and analysis of polymorphism of S. meliloti populations.