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Salinity stress is among the key challenges for sustainable food production. It is continuously increasing against the backdrop of constant climate change and anthropogenic practices leading to a huge drop in soil, water, and cultivated crop quality and productivity. Halotolerant plants represent hot spots for endophytic bacteria which may have mechanisms to overcome salt stress. This research initiative aims to highlight the possible exploitation of bacterial endophytes as a microbial biotechnology tool in the productive success of plants exposed to saline stress. We started by solely studying the mechanisms of stress tolerance by plants and halotolerant bacteria. After that, we focused on the beneficial mechanisms of endophytic bacteria in salt stress mitigation. On one side, potent bacterium works by promoting plant performances by facilitating the plant’s nutrient uptake (P, K, Zn, N, and Fe) and by promoting the production of growth hormones (IAA and CKs). On the other side, they balance stress phytohormones (ABA, JA, GA, and ACC) produced by plants in case of soil salt augmentation. The selected potent endophytic bacteria could be exploited and applied to ameliorate the production and salt tolerance of food crops. Lastly, we elucidated deeper advanced technologies including (i) genomics unveiling the plant’s culture-dependent and culture-independent microbiomes, (ii) metabolomics focusing on genes’ metabolic pathways to discover novel secondary metabolites, (iii) transcriptomics studying gene expression, and (iv) proteomics delimiting proteins expressed in stress alleviation. These technologies have been used to understand the plant–bacterial mechanisms of interaction to combat salt stress.

Safflower is known as a tolerant plant to abiotic stress factors. This study was conducted to introduce some physiological indices to improve drought-tolerant safflower genotypes for cultivation in marginal and arid areas. Six safflower genotypes were studied for two years (2017–2019) in the East Azarbaijan Agricultural and Natural Resources Research and Education Centre of Iran under non-stressed and low-water conditions from flowering to seed maturity. The occurrence of water deficits led to a significant decrease in relative water content (RWC), stomatal conductance (gs), osmotic adjustment (Oadj), water potential (WP) and agronomic water use efficiency (WUEa) and an increase in the water stress index (CWSI). In addition, the values of these traits differed significantly between the safflower genotypes. The correlations between the physiological traits and seed yield were significant. The regression relationships between seed yield and the above traits showed that CWSI, WP and WUEa had a strong relationship with seed yield under normal (R2 = 0.854, 0.801 and 0.856, respectively) and water deficit conditions (R2 = 0.931, 0.877 and 0.900, respectively). It can be concluded that the CWSI, WP and WUEa indices are able to select high-yielding and drought-tolerant safflower genotypes for the late season. Among the components of seed yield, the number of capitula per plant (r = 0.86) and seeds per capitula (r = 0.92), which were positively and significantly correlated with seed yield, played the main roles in the formation of seed yield. The Golemehr and Mec.295 genotypes achieved higher seed yields under normal (4676 and 4961 kg h−1, respectively) and water deficit conditions (3211 and 3385 kg h−1, respectively) and can be recommended for cultivation in marginal and arid areas.

Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.

In addition to changing global demography and global warming, agricultural production systems around the world are threatened by intensive agricultural practices (overuse of land and excessive use of chemical fertilizers and pesticides) that deplete soils by affecting their dynamics and their fertility, pollute the environment, lower production, and alter biodiversity on a large scale. The use of bioformulations based on PGPMs (plant growth-promoting microorganisms) seems to be a promising and sustainable strategy to overcome these threats, thanks to their tolerance to various biotic and abiotic stresses and via their beneficial effects in promising plant growth, pest protection, bioremediation, and restoration of degraded lands. In recent years, particular attention has been paid to encapsulated formulations because they offer several advantages over conventional bioformulation (liquid and solid) related to shelf life, problems of survival and viability in the environment, and the efficiency of rhizospheric colonization. This review focuses on the types of encapsulations and the different technologies used in this process as well as the most commonly used substrates and additives. It also provides an overview on the application of encapsulated bioformulations as biofertilizers, biopesticides, or other biostimulators and summarizes the knowledge of the scientific literature on the development of nanoencapsulation in this sector.

Natural dyes have been used from ancient times for multiple purposes, most importantly in the field of textile dying. The increasing demand and excessive costs of natural dye extraction engendered the discovery of synthetic dyes from petrochemical compounds. Nowadays, they are dominating the textile market, with nearly 8 × 105 tons produced per year due to their wide range of color pigments and consistent coloration. Textile industries consume huge amounts of water in the dyeing processes, making it hard to treat the enormous quantities of this hazardous wastewater. Thus, they have harmful impacts when discharged in non-treated or partially treated forms in the environment (air, soil, plants and water), causing several human diseases. In the present work we focused on synthetic dyes. We started by studying their classification which depended on the nature of the manufactured fiber (cellulose, protein and synthetic fiber dyes). Then, we mentioned the characteristics of synthetic dyes, however, we focused more on their negative impacts on the ecosystem (soil, plants, water and air) and on humans. Lastly, we discussed the applied physical, chemical and biological strategies solely or in combination for textile dye wastewater treatments. Additionally, we described the newly established nanotechnology which achieves complete discharge decontamination.

Diverse vegetable oils are extracted from oleagenic trees and plants all over the world. In particular, olive oil represents a strategic socio-economic branch in the Mediterranean countries. These countries use either two or three-phase olive oil extraction systems. In this work, we focus on the by-products from three-phase olive oil extraction, which are the liquid olive mill wastewater (OMW) and the solid olive mill pomace (OMP) rejected in evaporative ponds. The disposal of this recalcitrant waste poses environmental problems such as the death of different species of insects and animals. In-depth ICP-OES analysis of the heavy metal composition of OMW and OMP revealed the presence of many metals ranging from non-toxic to highly toxic. The LC-HRMS characterization of these by-products indicated the presence of several secondary metabolites harmful to humans or to the environment. Thus, we aimed to identify OMW and OMP indigenous microbiota through metagenomics. The bacterial population was dominated by the Acetobacter (49.7%), Gluconobacter (17.3%), Gortzia (13.7%) and Nardonalla (5.3%) genera. The most abundant fungal genera were Nakazawaea, Saccharomyces, Lachancea and Candida. These microbial genera are responsible for OMW, OMP and soil toxicity alleviation.

There is a great interest in mitigating soil salinity that limits plant growth and productivity. In this study, eighty-nine strains were isolated from the rhizosphere and endosphere of two halophyte species (Suaeda mollis and Salsola tetrandra) collected from three chotts in Algeria. They were screened for diverse plant growth-promoting traits, antifungal activity and tolerance to different physico-chemical conditions (pH, PEG, and NaCl) to evaluate their efficiency in mitigating salt stress and enhancing the growth of Arabidopsis thaliana and durum wheat under NaCl–stress conditions. Three bacterial strains BR5, OR15, and RB13 were finally selected and identified as Bacillus atropheus. The Bacterial strains (separately and combined) were then used for inoculating Arabidopsis thaliana and durum wheat during the seed germination stage under NaCl stress conditions. Results indicated that inoculation of both plant spp. with the bacterial strains separately or combined considerably improved the growth parameters. Three soils with different salinity levels (S1 = 0.48, S2 = 3.81, and S3 = 2.80 mS/cm) were used to investigate the effects of selected strains (BR5, OR15, and RB13; separately and combined) on several growth parameters of wheat plants. The inoculation (notably the multi-strain consortium) proved a better approach to increase the chlorophyll and carotenoid contents as compared to control plants. However, proline content, lipid peroxidation, and activities of antioxidant enzymes decreased after inoculation with the plant growth-promoting rhizobacteria (PGPR) that can attenuate the adverse effects of salt stress by reducing the reactive oxygen species (ROS) production. These results indicated that under saline soil conditions, halotolerant PGPR strains are promising candidates as biofertilizers under salt stress conditions.

The phosphogypsum (PG) endogenous bacterial community and endophytic bacterial communities of four plants growing in phosphogypsum-contaminated sites, Suaeda fruticosa (SF), Suaeda mollis (SM), Mesembryanthmum nodiflorum (MN) and Arthrocnemum indicum (AI) were investigated by amplicon sequencing. Results highlight a more diverse community of phosphogypsum than plants associated endophytic communities. Additionally, the bacterial culturable communities of phosphogypsum and associated plant endophytes were isolated and their plant-growth promotion capabilities, bioremediation potential and stress tolerance studied. Most of plant endophytes were endowed with plant growth-promoting (PGP) activities and phosphogypsum communities and associated plants endophytes proved highly resistant to salt, metal and antibiotic stress. They also proved very active in bioremediation of phosphogypsum and other organic and inorganic environmental pollutants. Genome sequencing of five members of the phosphogypsum endogenous community showed that they belong to the recently described species Bacillus albus (BA). Genome mining of BA allowed the description of pollutant degradation and stress tolerance mechanisms. Prevalence of this tool box in the core, accessory and unique genome allowed to conclude that accessory and unique genomes are critical for the dynamics of strain acquisition of bioremediation abilities. Additionally, secondary metabolites (SM) active in bioremediation such as petrobactin have been characterized. Taken together, our results reveal hidden untapped valuable bacterial actors for waste remediation.

Oomycete and fungal pathogens, mainly Phytophthora and Fusarium species, are notorious causal agents of huge economic losses and environmental damages. For instance, Phytophthora ramorum, Phytophthora cryptogea, Phytophthora plurivora and Fusarium solani cause significant losses in nurseries and in forest ecosystems. Chemical treatments, while harmful to the environment and human health, have been proved to have little or no impact on these species. Recently, biocontrol bacterial species were used to cope with these pathogens and have shown promising prospects towards sustainable and eco-friendly agricultural practices. Olive trees prone to Phytophthora and Fusarium disease outbreaks are suitable for habitat-adapted symbiotic strategies, to recover oomycetes and fungal pathogen biocontrol agents. Using this strategy, we showed that olive trees-associated microbiome represents a valuable source for microorganisms, promoting plant growth and healthy benefits in addition to being biocontrol agents against oomycete and fungal diseases. Isolation, characterization and screening of root microbiome of olive trees against numerous Phytophthora and other fungal pathogens have led to the identification of the Bacillus velezensis OEE1, with plant growth promotion (PGP) abilities and strong activity against major oomycete and fungal pathogens. Phylogenomic analysis of the strain OEE1 showed that B. velezensis suffers taxonomic imprecision that blurs species delimitation, impacting their biofertilizers’ practical use. Genome mining of several B. velezensis strains available in the GenBank have highlighted a wide array of plant growth promoting rhizobacteria (PGPR) features, metals and antibiotics resistance and the degradation ability of phytotoxic aromatic compounds. Strain OEE1 harbours a large repertoire of secreted and volatile secondary metabolites. Rarefaction analysis of secondary metabolites richness in the B. velezenis genomes, unambiguously documented new secondary metabolites from ongoing genome sequencing efforts that warrants more efforts in order to assess the huge diversity in the species. Comparative genomics indicated that B. velezensis harbours a core genome endowed with PGP features and accessory genome encoding diverse secondary metabolites. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of OEE1 Volatile Organic Compounds (VOCs) and Liquid Chromatography High Resolution Mass Spectrometry (LC-HRMS) analysis of secondary metabolites identified numerous molecules with PGP abilities that are known to interfere with pathogen development. Moreover, B. velezensis OEE1 proved effective in protecting olive trees against F. solani in greenhouse experiments and are able to inhabit olive tree roots. Our strategy provides an effective means for isolation of biocontrol agents against recalcitrant pathogens. Their genomic analysis provides necessary clues towards their efficient implementation as biofertilizers.

Halophyte Limoniastrum monopetalum, an evergreen shrub inhabiting the Mediterranean region, has well-documented phytoremediation potential for metal removal from polluted sites. It is also considered to be a medicinal halophyte with potent activity against plant pathogens. Therefore, L. monopetalum may be a suitable candidate for isolating endophytic microbiota members that provide plant growth promotion (PGP) and resistance to abiotic stresses. Selected for biocontrol abilities, these endophytes may represent multifaceted and versatile biocontrol agents, combining pathogen biocontrol in addition to PGP and plant protection against abiotic stresses. In this study 117 root culturable bacterial endophytes, including Gram-positive (Bacillus and Brevibacillus), Gram-negative (Proteus, Providencia, Serratia, Pantoea, Klebsiella, Enterobacter and Pectobacterium) and actinomycete Nocardiopsis genera have been recovered from L. monopetalum. The collection exhibited high levels of biocontrol abilities against bacterial (Agrobacterium tumefaciens MAT2 and Pectobacterium carotovorum MAT3) and fungal (Alternaria alternata XSZJY-1, Rhizoctonia bataticola MAT1 and Fusarium oxysporum f. sp. radicis lycopersici FORL) pathogens. Several bacteria also showed PGP capacity and resistance to antibiotics and metals. A highly promising candidate Bacillus licheniformis LMRE 36 with high PGP, biocontrol, metal and antibiotic, resistance was subsequently tested in planta (potato and olive trees) for biocontrol of a collection of 14 highly damaging Fusarium species. LMRE 36 proved very effective against the collection in both species and against an emerging Fusarium sp. threatening olive trees culture in nurseries. These findings provide a demonstration of our pyramiding strategy. Our strategy was effective in combining desirable traits in biocontrol agents towards broad-spectrum resistance against pathogens and protection of crops from abiotic stresses. Stacking multiple desirable traits into a single biocontrol agent is achieved by first, careful selection of a host for endophytic microbiota recovery; second, stringent in vitro selection of candidates from the collection; and third, application of the selected biocontrol agents in planta experiments. That pyramiding strategy could be successfully used to mitigate effects of diverse biotic and abiotic stresses on plant growth and productivity. It is anticipated that the strategy will provide a new generation of biocontrol agents by targeting the microbiota of plants in hostile environments.

To explore proteolytic activity of endophytic fungi inhabiting date palm roots, a Penicillium bilaiae isolate, displaying the highest level of protease production, has been recovered. Response surface methodology (RSM) was applied to optimize culture conditions for protease production by the fungus. Plackett-Burman design allowed for screening of variables effective in protease production. Results indicated that temperature, initial pH and glucose concentration dramatically affect protease yield. These factors were further optimized using a Box-Behnken design and RSM. A combination of initial pH (6.26), temperature (24.5 °C), glucose (13.75 g/L), NaNO3 (1.5 g/L), MgSO4 (0.2 g/L), KH2PO4 (0.5 g/L) and KCl (0.5 g/L) were optimum for maximum production of protease. A 1086-fold enhancement of protease production was gained after optimization. Biochemical properties of fungal protease including the effect of pH and temperature on the activity and the stability of proteolytic enzyme were determined. Moreover, the influence of carbon and nitrogen sources, metal ions, detergents as well as enzyme inhibitors was investigated. Our results highlighted that protease of Penicillium bilaiae isolate TDPEF30 could be considered as a promising candidate for industrial applications.