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

Rhizobium laguerreae sp. nov. nodulates Vicia faba in several continents

Several fast-growing strains nodulating Vicia faba in Peru, Spain and Tunisia formed a cluster related to Rhizobium leguminosarum. The 16S rRNA gene sequences were identical to that of R. leguminosarum USDA 2370 T , whereas rpoB, recA and atpD gene sequences were phylogenetically distant, with sequence similarities of less than 96 %, 97 % and 94 %, respectively. DNA-DNA hybridization analysis showed a mean relatedness value of 43 % between strain FB206 T and R. leguminosarum USDA 2370 T . Phenotypic characteristics of the novel strains also differed from those of the closest related species of the genus Rhizobium. Therefore, based on genotypic and phenotypic data obtained in this study, we propose to classify this group of strains nodulating Vicia faba as a novel species of the genus Rhizobium named Rhizobium laguerreae sp. nov. The type strain is FB206 T (5LMG 27434 T 5CECT 8280 T )

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

Microbial inoculants and their impact on soil microbial communities: a review. Biomed Res Int 2013; 2013: 863240

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

Characterization of rhizobia nodulating chickpea in Tunisia

One hundred and fifty rhizobia nodulating chickpea (Cicer arietinum L.) were isolated from soils sampled in different regions of Tunisia. Variability in the time at which nodules appeared after plant inoculation was observed among these isolates. Five isolates induced nodules two weeks after inoculation, whereas, with the remaining 145 isolates, nodules were observed after more than four weeks. On the basis of PCR/RFLP analysis of 16S rDNA, isolates from the first group were classified as Mesorhizobium mediterraneum, and isolates from the second group as Sinorhizobium medicae. The respective taxonomic position of both types of isolates was confirmed by their symbiotic properties. M. mediterraneum isolates did not nodulate Medicago sativa and formed effective nodules on C. arietinum while S. medicae isolates were able to form effective nodules on M. sativa but formed ineffective nodules on C. arietinum, as did reference strains of the species.Caractérisation des rhizobia nodulant le pois chiche en Tunisie. Cent cinquante rhizobia nodulant le pois chiche (Cicer arietinum L.) ont été isolés à partir de sols échantillonnés dans différentes régions de Tunisie. L'inoculation de la plante hôte avec ces isolats montre une variabilité dans le temps d'apparition des premières nodosités. Cinq isolats induisent des nodosités deux semaines après inoculation alors que pour les 145 isolats restants les nodosités ne sont observées qu'après au moins quatre semaines. L'étude par PCR/RFLP de l'ADNr 16S a permis de rattacher les isolats du premier groupe à l'espèce Mesorhizobium mediterraneum et ceux du second groupe à l'espèce Sinorhizobium medicae. La position taxonomique des isolats a été confirmée par leurs propriétés symbiotiques. Les isolats de M. mediterraneum ne nodulent pas Medicago sativa mais forment une symbiose fixatrice avec C. arietinum, ceux de S. medicae, comme les souches références de l'espèce, forment des nodosités efficientes avec M. sativa et inefficientes avec C. arietinum

Sinorhizobium meliloti can protect Medicago truncatula against Phoma medicaginis attack

The Sinorhizobium meliloti microsymbiont of Medicago spp. was used in an antibiosis test against Phoma medicaginis and in bioprotection assays of Medicago truncatula JA17 from the pathogen. Among 17 S. meliloti strains isolated from root nodules of M. truncatula and Medicago laciniata grown in Tunisian soils, six showed up to 60% growth inhibition of five P. medicaginis strains isolated from infected field-grown M. truncatula. Two S. meliloti strains with differing in vitro effects on P. medicaginis, 10.16/R6 antagonist and 5M6 non antagonist, were used in a bioprotection assay of M. truncatula JA17 from the pathogen. The inoculation of P. medicaginis caused complete root and stem rotting, and the mortality of all treated plantlets. Inoculation of the antagonist S. meliloti strain 10.16/R6 to M. truncatula JA17 infected with P. medicaginis was associated with a significant 65% decrease of vegetative rotting length, an 80% decrease of plant mortality, an increase of root length, and enhancement of root and shoot biomass comparatively to control plantlets treated with P. medicaginis. The inoculation of the non antagonistic S. meliloti strain 5M6 slightly decreased disease and slightly increased plant growth parameters

<I>Sinorhizobium meliloti</I> can protect <I>Medicago truncatula</I> against <I>Phoma medicaginis</I> attack

The Sinorhizobium meliloti microsymbiont of Medicago spp. was used in an antibiosis test against Phoma medicaginis and in bioprotection assays of Medicago truncatula JA17 from the pathogen. Among 17 S. meliloti strains isolated from root nodules of M. truncatula and Medicago laciniata grown in Tunisian soils, six showed up to 60% growth inhibition of five P. medicaginis strains isolated from infected field-grown M. truncatula. Two S. meliloti strains with differing in vitro effects on P. medicaginis, 10.16/R6 antagonist and 5M6 non antagonist, were used in a bioprotection assay of M. truncatula JA17 from the pathogen. The inoculation of P. medicaginis caused complete root and stem rotting, and the mortality of all treated plantlets. Inoculation of the antagonist S. meliloti strain 10.16/R6 to M. truncatula JA17 infected with P. medicaginis was associated with a significant 65% decrease of vegetative rotting length, an 80% decrease of plant mortality, an increase of root length, and enhancement of root and shoot biomass comparatively to control plantlets treated with P. medicaginis. The inoculation of the non antagonistic S. meliloti strain 5M6 slightly decreased disease and slightly increased plant growth parameters

Rhizobium gallicum as an efficient symbiont for bean cultivation

Rhizobia are soil bacteria that fix atmospheric nitrogen in symbiosis with legumes in specialized organs called nodules. The legumes thus acquire the autonomy to grow in nitrogen-deficient soils. When nitrogen fixation by indigenous rhizobia is limited, field inoculation with efficient and competitive strains is an economically feasible way to increase production. When the inoculant is made from native strains of rhizobia the success of inoculation should be increased, since local strains are better adapted than commercial inoculants. Here, a Rhizobium gallicum strain, 8a3, previously selected for its competitiveness and symbiotic effectiveness with common bean under laboratory conditions, was tested in field trials in Tunisia. The experiments were conducted in six fields using three common bean cultivars. The majority of the fields showed a low density of the native rhizobia and inefficient nodulation by Sinorhizobium meliloti, a known symbiont of Medicago. Our results show that inoculation with R. gallicum strain 8a3 induced an increase in nodule numbers accompanied by a more than twofold increase in shoot dry yield. Monitoring of the nodulation occupancy through the fingerprinting of the repetitive extragenic palindromic sequences (REP-PCR) showed that strain 8a3 was competitive even in the soil showing a high population density of indigenous R. gallicum, and occupied more than 40% of the nodules. Moreover, in vitro antibiosis assays indicated that strain 8a3 produces antimicrobial activity on agar medium against indigenous common bean rhizobia, including the inefficient strains of S. meliloti. These results point out the benefits that could be achieved by selecting efficient and competitive strains among natural populations of rhizobia

Colonization of Phaseolus vulgaris nodules by Agrobacterium-like strains

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699International audienceNon-nodulating Agrobacterium-like strains identified among root nodule isolates of common bean were labeled with gusA, a reporter gene encoding β-glucuronidase (GUS). Bean plants were then co-inoculated with an infective Rhizobium strain and labeled transconjugants of Agrobacterium-like strains. Blue staining of nodules showed that Agrobacterium-like strains were able to colonize these symbiotic organs. Isolation and characterization by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes revealed a mixed population of Rhizobium and Agrobacterium-like strains in all nodules showing GUS activity. PCR amplification of the nifH gene and nodulation tests did not show any evidence of acquisition of symbiotic gene by lateral transfer from Rhizobium to Agrobacterium-like strains. Moreover, these strains were able to invade mature nodules. Based on sequencing of the 16S rRNA gene, one of these Agrobacterium-like strains showed 99.4% sequence similarity with Agrobacterium bv. 1 reference strains and 99% similarity with an Agrobacterium bv. 1 strain isolated from Acacia mollisima in Senegal. Agrobacterium tumefaciens C58 and the disarmed variant AT123 did not show any ability to colonize nodules. Co-inoculation of bean seeds with Agrobacterium and Rhizobium strains did not enhance nodulation and plant yield under controlled conditions

Salt-tolerant rhizobia isolated from a Tunisian oasis that are highly effective for symbiotic N-2-fixation with Phaseolus vulgaris constitute a novel biovar (bv. mediterranense) of Sinorhizobium meliloti

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699International audienceNodulation of common bean was explored in six oases in the south of Tunisia. Nineteen isolates were characterized by PCR-RFLP of 16S rDNA. Three species of rhizobia were identified, Rhizobium etli, Rhizobium gallicum and Sinorhizobium meliloti. The diversity of the symbiotic genes was then assessed by PCR-RFLP of nodC and nifH genes. The majority of the symbiotic genotypes were conserved between oases and other soils of the north of the country. Sinorhizobia isolated from bean were then compared with isolates from Medicago truncatula plants grown in the oases soils. All the nodC types except for nodC type p that was specific to common bean isolates were shared by both hosts. The four isolates with nodC type p induced N-2-fixing effective nodules on common bean but did not nodulate M. truncatula and Medicago sativa. The phylogenetic analysis of nifH and nodC genes showed that these isolates carry symbiotic genes different from those previously characterized among Medicago and bean symbionts, but closely related to those of S. fredii Spanish and Tunisian isolates effective in symbiosis with common bean but unable to nodulate soybean. The creation of a novel biovar shared by S. meliloti and S. fredii, bv. mediterranense, was propose