Hanene Cherif

Thuricin 7: a novel bacteriocin produced by Bacillus thuringiensis BMG1.7, a new strain isolated from soil

Aims: Detection and identification of new antagonistic activities towards Bacillus cereus and relatives.

Potential for Plant Growth Promotion of Rhizobacteria Associated with Salicornia Growing in Tunisian Hypersaline Soils

Soil salinity and drought are among the environmental stresses that most severely affect plant growth and production around the world. In this study the rhizospheres of Salicornia plants and bulk soils were collected from Sebkhet and Chott hypersaline ecosystems in Tunisia. Depiction of bacterial microbiome composition by Denaturing Gradient Gel Electrophoresis unveiled the occurrence of a high bacterial diversity associated with Salicornia root system. A large collection of 475 halophilic and halotolerant bacteria was established from Salicornia rhizosphere and the surrounding bulk soil, and the bacteria were characterized for the resistance to temperature, osmotic and saline stresses, and plant growth promotion (PGP) features. Twenty Halomonas strains showed resistance to a wide set of abiotic stresses and were able to perform different PGP activities in vitro at 5% NaCl, including ammonia and indole-3-acetic acid production, phosphate solubilisation, and potential nitrogen fixation. By using a gfp-labelled strain it was possible to demonstrate that Halomonas is capable of successfully colonising Salicornia roots in the laboratory conditions. Our results indicated that the culturable halophilic/halotolerant bacteria inhabiting salty and arid ecosystems have a potential to contribute to promoting plant growth under the harsh salinity and drought conditions. These halophilic/halotolerant strains could be exploited in biofertilizer formulates to sustain crop production in degraded and arid lands.

Oasis desert farming selects environment-specific date palm root endophytic communities and cultivable bacteria that promote resistance to drought

Oases are desert-farming agro-ecosystems, where date palm (Phoenix dactylifera L.) plays a keystone role in offsetting the effects of drought and maintaining a suitable microclimate for agriculture. At present, abundance, diversity and plant growth promotion (PGP) of date palm root-associated bacteria remain unknown. Considering the environmental pressure determined by the water scarcity in the desert environments, we hypothesized that bacteria associated with date palm roots improve plant resistance to drought. Here, the ecology of date palm root endophytes from oases in the Tunisian Sahara was studied with emphasis on their capacity to promote growth under drought. Endophytic communities segregated along a north-south gradient in correlation with geo-climatic parameters. Screening of 120 endophytes indicated that date palm roots select for bacteria with multiple PGP traits. Bacteria rapidly cross-colonized the root tissues of different species of plants, including the original Tunisian date palm cultivar, Saudi Arabian cultivars and Arabidopsis. Selected endophytes significantly increased the biomass of date palms exposed to repeated drought stress periods during a 9-month greenhouse experiment. Overall, results indicate that date palm roots shape endophytic communities that are capable to promote plant growth under drought conditions, thereby contributing an essential ecological service to the entire oasis ecosystem.

Plant-associated microbiomes in arid lands: diversity, ecology and biotechnological potential

BackgroundAridification is a worldwide serious threat directly affecting agriculture and crop production. In arid and desert areas, it has been found that microbial diversity is huge, built of microorganisms able to cope with the environmental harsh conditions by developing adaptation strategies. Plants growing in arid lands or regions facing prolonged abiotic stresses such as water limitation and salt accumulation have also developed specific physiological and molecular stress responses allowing them to thrive under normally unfavorable conditions.ScopeUnder such extreme selection pressures, special root-associated bacterial assemblages, endowed with capabilities of plant growth promotion (PGP) and extremophile traits, are selected by the plants. In this review, we provide a general overview on the microbial diversity in arid lands and deserts versus specific microbial assemblages associated with plants. The ecological drivers that shape this diversity, how plant-associated microbiomes are selected, and their biotechnological potential are discussed.ConclusionsSelection and recruitment of the plant associated bacterial assemblages is mediated by the combination of the bio-pedo-agroclimatic conditions and the plant species or varieties. Diversity and functional redundancy of these associated PGPR makes them very active in supporting plant improvement, health and resistance to drought, salt and related stresses. Implementing proper biotechnological applications of the arid and desert-adapted PGPR constitute the challenge to be raised.

Effects of municipal solid waste compost application on the microbial biomass of cultivated and non-cultivated soil in a semi-arid zone

The aim of this study was to assess whether soil microbial biomass could be used as an indicator of environmental changes following the application of organic residue (compost of municipal solid waste and farmyard manure) or mineral fertilizers (N and P) into cultivated or uncultivated loam—clayey soil, for three consecutive years. The carbon and nitrogen of the microbial biomass (BC and BN) were studied using the fumigation-extraction method. For the two cultivated and uncultivated plots, BN and BC were more important in the superficial profile (0—20 cm) than in the deep one (20— 40 cm). In the uncultivated soil, we observed a good linear relation between BC and BN at the level of upper soil horizon during the wet season with r coefficients of 0.95, 0.71 and 0.80 for the consecutive years 2000, 2001 and 2002, respectively. Microbial biomasses C and N increased during the rainy season and decreased during the dry season. Microbial biomass C and N showed the higher content with compost and farmyard manure at 40 tonnes ha—1. Moreover, the results showed that at the beginning of the experiment, the microbial biomass was higher in the ploughed wheat-cultivated plot than in the uncultivated one. Microbial biomass C and N in the cultivated plot amended with compost at 40 tonnes ha—1 were significantly different in comparison with the soil microbial biomass amended with farmyard manure. The combining of chemical fertilizer with the organic fertilizer, such as compost at 40 or 80 tonnes ha—1 and farmyard manure, increased the microbial biomasses C and N after 1 and 2 years. In the cultivated or uncultivated plots the results revealed that the best application rate of the compost was 40 tonnes ha—1 and when the compost rate was increased from 40 to 80 tonnes ha—1 both BC and BN decreased significantly.

Municipal solid waste compost dose effects on soil microbial biomass determined by chloroform fumigation-extraction and DNA methods

We evaluated the relationship between microbial biomass C and N (BC and BN) as estimated by the chloroform fumigation-extraction (CFE) method and microbial biomass DNA concentration in a loam-clayey wheat cultivated soil. The soil received municipal solid waste compost at rates of 40 or 80 t ha−1 and farmyard manure at 40 t ha−1. Microbial biomasses C and N and DNA concentration centration showed the highest values for microorganisms counts with compost and farmyard manure at 40 t ha−1. Compost applications at 40 t ha−1 improve the micro-organisms growth than that of 80 t ha−1. Moreover a significant decrease of soil microbial biomass was noted after fertilisation for three years. The presence of humic acid and proteins impurities in DNA extracts; even in important level as in F-treated soil; did not affect the microbial biomass. The decrease of microbial biomass was due to heavy metals content elevation in compost at 80 t ha−1 treated soil. Thus the highest rate of municipal solid waste compost induced the lowest ratio of biomass C to soil organic carbon and the lowest ratio of biomass N to soil organic nitrogen. There was a positive relationship between BC, BN and DNA concentration. DNA concentration was significantly and positively correlated with BC and with BN. However there was a negative correlation between either micro-organisms numbers and DNA concentration, or BC and BN. The comparison of the two used methods DNA extraction and CFE showed the lowest coefficient of variation (cv %) with DNA extraction method. This last method can be used as an alternative method to measure the microbial biomass in amended soils.

The Date Palm Tree Rhizosphere Is a Niche for Plant Growth Promoting Bacteria in the Oasis Ecosystem

In arid ecosystems environmental factors such as geoclimatic conditions and agricultural practices are of major importance in shaping the diversity and functionality of plant-associated bacterial communities. Assessing the influence of such factors is a key to understand (i) the driving forces determining the shape of root-associated bacterial communities and (ii) the plant growth promoting (PGP) services they provide. Desert oasis environment was chosen as model ecosystem where agriculture is possible by the microclimate determined by the date palm cultivation. The bacterial communities in the soil fractions associated with the root system of date palms cultivated in seven oases in Tunisia were assessed by culture-independent and dependent approaches. According to 16S rRNA gene PCR-DGGE fingerprinting, the shapes of the date palm rhizosphere bacterial communities correlate with geoclimatic features along a north-south aridity transect. Despite the fact that the date palm root bacterial community structure was strongly influenced by macroecological factors, the potential rhizosphere services reflected in the PGP traits of isolates screened in vitro were conserved among the different oases. Such services were exerted by the 83% of the screened isolates. The comparable numbers and types of PGP traits indicate their importance in maintaining the plant functional homeostasis despite the different environmental selection pressures.

Isolation and characterization of facultative mixotrophic ammonia-oxidizing bacteria from constructed wetlands

Autotrophic ammonia-oxidizing bacteria (AOB) have been widely studied in constructed wetlands systems, while mixotrophic AOB have been less thoroughly examined. Heterotrophic bacteria were isolated from wastewater and rhizospheres of macrophytes of constructed wetlands, and then cultivated in a mixotrophic medium containing ammonium and acetic acid. A molecular characterization was accomplished using ITS-PCR amplification, and phylogenetic analysis based on 16S rRNA gene sequences. Results showed the presence of 35 bacteria, among 400 initially heterotrophic isolates, that were able to remove ammonia. These 35 isolates were classified into 10 genetically different groups based on ITS pattern. Then, a collection of 10 isolates were selected because of their relatively high ammonia removal efficiencies (ARE > or = 80%) and their phylogenetic diversity. In conditions of mixotrophy, these strains were shown to be able to grow (increase of optical density OD660 during incubation with assimilation of nitrogen into cellular biomass) and to oxidize ammonia (important ammonia oxidation efficiencies, AOE between 79% and 87%). Among these facultative mixotrophic AOB, four isolates were genetically related to Firmicutes (Bacillus and Exiguobacterium), three isolates were affiliated to Actinobacteria (Arthrobacter) and three other isolates were associated with Proteobacteria (Pseudomonas, Ochrobactrum and Bordetella).

Isolation and characterization of microbial communities from a constructed wetlands system: A case study in Tunisia

Constructed wetlands (CWs) have received increasing attention in the last decade due to their high potential for wastewater treatment. The nitrogen removal performance is always the main focus when evaluating the treatment ability of CWs. In this work, we aimed to isolate and identify the heterotrophic bacteria using the 16S rRNA gene sequencing method and to characterize the microbial communities removing nitrogen from wastewater and rhizosphere of constructed wetlands and quantified the heterotrophic nitrification on a microtiter plate by applying a spectrofluorometric assay. A number of 35 isolates within the obtained bacterial collection (380 isolates), were selected for molecular classification based on their genetic patterns after amplification of ITS fragments. Results obtained from the PCR amplification of the 16S-23S rDNA gene followed by the partial sequencing of the 16S rDNA genes confirmed the affiliation of the isolates to γ-Proteobacteria, Firmictes, α-Proteobacteria, Actinobacteria and δ-Proteobacteria. Batch tests were carried out to investigate the capacity for heterotrophic nitrification in the pure culture. The batch test results indicate that nitrifying bacteria can utilize the organic carbon as the source of assimilation when it grows on glucose and ammonium chloride medium accompanying the formation of NO2- (nitrified products > 80%). Quantification of bacterial biofilms grown on microtiter plate showed that six strains were strongly adhesive to polystyrene microtiter plate with an OD595 ranging between 3.031 and 4.0368 and only one strain was weak biofilm forming. These bacteria might be used to activate nitrifying bioreactor for a tertiary domestic wastewaters treatment. Key words: Wastewater treatment, 16S-23S intergenic spacer, nitrifying heterotrophic bacteria, Biofilm.

Diagnosis of Biodiversity of Rhizobium Leguminosarum Nodulating Pea (Pisum Sativum L.) in Differents Soils of Tunisia

Pulses such as peas (Pisum sativum L.) are essential components of the human diet. They are an important source of protein, energy, minerals, vitamins and other nutrients. They are recognized by their symbiosis with soil bacteria of the genus Rhizobium, fixing atmospheric nitrogen. However, the areas reserved for legumes in Tunisia are in constant decline, leading to a decrease in production particularly for peas production. The extension of this culture is limited by its extreme sensitivity to biotic and abiotic stresses. To resolve these problems, farmers resorted to the excessive use of fertilizers and pesticides, which is harmful to the environment. Therefore, sustainable alternative practices for pea production should be developed. Among the abiotic constraints, the absence of efficient and specific rhizobial strains for the cultivation of pea was noted.