Plant growth promoting potential and soil enzyme production of the most abundant Streptomyces spp. from wheat rhizosphere

Reshaping the root endophytic microbiota in plants to combat mercury-induced stress

Emerging evidence suggests that plants experiencing abiotic stress actively seek help from soil microbes. However, the empirical evidence supporting this strategy is limited, especially in response to heavy metal stress. We used integrated microbial community profiling and culture-based methods to investigate the interaction between mercury (Hg) stress, the entophytic root microbiome, and maize seedlings. The results of the pot experiment showed that soil Hg (20 mg/kg) strongly inhibited maize growth, indicating its strong phytotoxicity. Furthermore, Hg stress significantly altered the structure of the bacterial and fungal communities and enriched the potentially pathogenic Fusarium sp., suggesting that soil Hg stress may enhance the bio-stress induced by Fusarium species in maize. Additionally, soil Hg also led to the enrichment of beneficial bacterial members of Streptomyces, Lysobacter, and Sphingomonas (defined as differential species), which were also identified as keystone species in the Hg treatment by the analysis of co-occurrence networks. Therefore, it can be postulated that the members of Streptomyces, Lysobacter, and Sphingomonas function as stress-alleviating microbes. We successfully isolated the representatives of these stress-alleviating microbes. As expected, these strains mitigated the detrimental effects of Hg stess for the maize seedlings, suggesting that plants recruit the stress-alleviated microbiota to combat Hg stress. This study provides insights into the potential of manipulating the root microbiome to enhance plant growth in polluted environments.

Synergistic effects of biofilm-producing PGPR strains on wheat plant colonization, growth and soil resilience under drought stress

Drought stress substantially impedes crop productivity throughout the world. Microbial based approaches have been considered a potential possibility and are under study. Based on our prior screening examination, two distinct and novel biofilm-forming PGPR strains namely Bacillus subtilis-FAB1 and Pseudomonas azotoformans-FAP3 are encompassed in this research. Bacterial biofilm development on glass surface, microtiter plate and seedling roots were assessed and characterized quantitatively and qualitatively by light and scanning electron microscopy. Above two isolates were further evaluated for their consistent performance by inoculating on wheat plants in a pot-soil system under water stresses. Bacterial moderate tolerance to ten-day drought was recorded on the application of individual strains with wheat plants; however, the FAB1 + FAP3 consortium expressively improved wheat survival during drought. The strains FAB1 and FAP3 displayed distinct and multifunctional plant growth stimulating attributes as well as effective roots and rhizosphere colonization in combination which could provide sustained wheat growth during drought. FAB1 and FAP3-induced alterations cooperatively conferred improved plant drought tolerance by controlling physiological traits (gs, Ci, E, iWUE and P_N), stress indicators (SOD, CAT, GR, proline and MDA content) and also maintained physico-chemical attributes and hydrolytic enzymes including DHA, urease, ALP, protease, ACP and β glucosidase in the soil. Our findings could support future efforts to enhance plant drought tolerance by engineering the rhizobacterial biofilms and associated attributes which requires in-depth exploration and exploiting potential native strains for local agricultural application.

Microbial chitinases and their relevance in various industries

Chitin, the second most abundant biopolymer on earth after cellulose, is composed of β-1,4-N-acetylglucosamine (GlcNAc) units. It is widely distributed in nature, especially as a structural polysaccharide in the cell walls of fungi, the exoskeletons of crustaceans, insects, and nematodes. However, the principal commercial source of chitin is the shells of marine or freshwater invertebrates. Microbial chitinases are largely responsible for chitin breakdown in nature, and they play an important role in the ecosystem's carbon and nitrogen balance. Several microbial chitinases have been characterized and are gaining prominence for their applications in various sectors. The current review focuses on chitinases of microbial origin, their diversity, and their characteristics. The applications of chitinases in several industries such as agriculture, food, the environment, and pharmaceutical sectors are also highlighted.

Diversity, mechanisms and beneficial features of phosphate-solubilizing Streptomyces in sustainable agriculture: A review

Currently, the use of phosphate (P) biofertilizers among many bioformulations has attracted a large amount of interest for sustainable agriculture. By acting as growth promoters, members of the Streptomyces genus can positively interact with plants. Several studies have shown the great potential of this bacterial group in supplementing P in a soluble, plant-available form by several mechanisms. Furthermore, some P-solubilizing Streptomyces (PSS) species are known as plant growth-promoting rhizobacteria that are able to promote plant growth through other means, such as increasing the availability of soil nutrients and producing a wide range of antibiotics, phytohormones, bioactive compounds, and secondary metabolites other than antimicrobial compounds. Therefore, the use of PSS with multiple plant growth-promoting activities as an alternative strategy appears to limit the negative impacts of chemical fertilizers in agricultural practices on environmental and human health, and the potential effects of these PSS on enhancing plant fitness and crop yields have been explored. However, compared with studies on the use of other gram-positive bacteria, studies on the use of Streptomyces as P solubilizers are still lacking, and their results are unclear. Although PSS have been reported as potential bioinoculants in both greenhouse and field experiments, no PSS-based biofertilizers have been commercialized to date. In this regard, this review provides an overview mainly of the P solubilization activity of Streptomyces species, including their use as P biofertilizers in competitive agronomic practices and the mechanisms through which they release P by solubilization/mineralization, for both increasing P use efficiency in the soil and plant growth. This review further highlights and discusses the beneficial association of PSS with plants in detail with the latest developments and research to expand the knowledge concerning the use of PSS as P biofertilizers for field applications by exploiting their numerous advantages in improving crop production to meet global food demands.

Exploring the Plant Growth-Promotion of Four Streptomyces Strains from Rhizosphere Soil to Enhance Cucumber Growth and Yield

The genus Streptomyces is the most abundant and essential microbes in the soil microbial community. Streptomyces are familiar and have great potential to produce a large variety of bioactive compounds. This genus considers an efficient biofertilizer based on its plant growth-promoting activities. Based on their ability to produce a wide varieties of bioactive molecules, the present study aimed to explore the potential plant growth promotion of four Streptomyces strains and their role in enhancing cucumber growth and yield under greenhouse conditions. Streptomyces sp. strain HM2, Streptomyces thinghirensis strain HM3, Streptomyces sp. strain HM8, and Streptomyces tricolor strain HM10 were chosen for the current study. Plant growth-promoting (PGP) features, i.e., indole acetic acid (IAA) production, siderophore excretion, and solubilizing phosphate, were evaluated in vitro. All four strains produced IAA, siderophore, and immobilized inorganic phosphate. Following 4 days of incubation at 30 °C, strains HM2, HM3, HM8, and HM10 produced copious amounts of IAA (18, 22, 62, and 146 µg/mL, respectively) and siderophores (42.59, 40.01, 16.84, 64.14% SU, respectively). At the same time, P solubilization efficacy scored 64.3%, 84.4%, 57.2%, and 81.6% with the same frequency. During in planta evaluation, selected Streptomyces strains combined with rock phosphate were assessed as biofertilizers on the growth and yield of cucumber plants. Under all treatments, positive and significant differences in studied traits were manifested except dry stem matter (SDM), net assimilation rate (NAR), relative growth rate (RGR), and fruit firmness (FF). Treatment T4 (rock phosphate + strain HM3) followed by T5 (rock phosphate + strain HM8) revealed the best results for plant height (PH), number of leaves per plant (NLPP), root length (RL), number of fruits per plant (NFPP), fruit length (FL), fruit diameter (FD), fruit fresh weight per plant (FFWPP), soil P (SP) after 21 DAT, and soil P at the end of the experiment. Notably, T6 (rock phosphate + strain HM10) caused a considerable increase in leaf area (LA). Plant growth-promoting bacteria enhance plant growth and yield through phosphorus solubilizing, improve nutrient availability, produce phytohormones, and support plant growth under abiotic stress. These features are important for sustainable agriculture and reducing environmental pollution with chemical fertilizers and pesticides.

Microbial endophytes: application towards sustainable agriculture and food security

Microbial endophytes are ubiquitous and exist in each recognised plant species reported till date. Within the host plant, the entire community of microbes lives non-invasively within the active internal tissues without causing any harm to the plant. Endophytes interact with their host plant via metabolic communication enables them to generate signal molecules. In addition, the host plant's genetic recombination with endophytes helps them to imitate the host's physicochemical functions and develop identical active molecules. Therefore, when cultured separately, they begin producing the host plant phytochemicals. The fungal species Penicillium chrysogenum has portrayed the glory days of antibiotics with the invention of the antibiotic penicillin. Therefore, fungi have substantially supported social health by developing many bioactive molecules utilised as antioxidant, antibacterial, antiviral, immunomodulatory and anticancerous agents. But plant-related microbes have emanated as fountainheads of biologically functional compounds with higher levels of medicinal perspective in recent years. Researchers have been motivated by the endless need for potent drugs to investigate alternate ways to find new endophytes and bioactive molecules, which tend to be a probable aim for drug discovery. The current research trends with these promising endophytic organisms are reviewed in this review paper. KEY POINTS: • Identified 54 important bioactive compounds as agricultural relevance • Role of genome mining of endophytes and "Multi-Omics" tools in sustainable agriculture • A thorough description and graphical presentation of agricultural significance of plant endophytes.

Exploring plant growth-promoting, biocatalytic, and antimicrobial potential of salt tolerant rhizospheric Georgenia soli strain TSm39 for sustainable agriculture

To explore the in vivo and in vitro plant growth promoting activities, biocatalytic potential, and antimicrobial activity of salt tolerance rhizoactinobacteria, rhizospheric soil of a halotolerant plant Saueda maritima L. was collected from Rann of Tiker, near Little Rann of Kutch, Gujarat (India). The morphology analysis of the isolated strain TSm39 revealed that the strain belonged to the phylum actinobacteria, as it was stained Gram-positive, displayed filamentous growth, showed spore formation and red pigment production on starch casein agar (SCA). It was identified as Georgenia soli based on 16S rRNA gene sequencing. The Georgenia soli strain TSm39 secreted extracellular amylase, pectinase, and protease. It showed in vitro plant growth-promoting (PGP) activities such as indole acetic acid (IAA) production, siderophore production, ammonia production, and phosphate solubilization. In vivo plant growth-promoting traits of strain TSm39 revealed 30% seed germination on water agar and vigor index 374.4. Additionally, a significant increase (p ≤ 0.05) was found in growth parameters such as root length (16.1 ± 0.22), shoot length (15.2 ± 0.17), the fresh weight (g), and dry weight (g) of the roots (0.43 ± 0.42 and 0.32 ± 0.12), shoots (0.62 ± 0.41 and 0.13 ± 0.03), and leaves (0.42 ± 0.161 and 0.14 ± 0.42) in treated seeds of Vigna radiata L. plant with the strain TSm39 compared to control. The antibiotic susceptibility profile revealed resistance of the strain TSm39 to erythromycin, ampicillin, tetracycline, and oxacillin, while it displayed maximum sensitivity to vancomycin (40 ± 0.72), chloramphenicol (40 ± 0.61), clarithromycin (40 ± 1.30), azithromycin (39 ± 0.42), and least sensitivity to teicoplanin (15 ± 0.15). Moreover, the antimicrobial activity of the strain TSm39 was observed against Gram's positive and Gram's negative microorganisms such as Shigella, Proteus vulgaris, and Bacillus subtilis. These findings indicated that the Georgenia soli strain TSm39 has multiple plant-growth-promoting properties and biocatalytic potential that signifies its agricultural applications in the enhancement of crop yield and quality and would protect the plant against plant pathogens.

Inoculation with Native Actinobacteria May Improve Desert Plant Growth and Survival with Potential Use for Restoration Practices

Soil microorganisms, together with water, play a key role in arid ecosystems, being responsible for the nutrient cycle, facilitating nutrient incorporation into plants, influencing plant drought tolerance, and enhancing their establishment. Therefore, their use for restoration practices is promising. We tested the potential of native strains of Actinobacteria from Monte Desert as growth promoters of native vegetation, isolating them from two substrates from their habitat (bare soil and leaf-cutting ant refuse dumps). Strains were inoculated into the soil where seedlings of three native plant species (Atriplex lampa, Grindelia chiloensis, Gutierrezia solbrigii) were growing. Seedlings were grown following a full factorial design experiment under greenhouse and field conditions comparing native Actinobacteria effects with a known growth-promoting strain, Streptomyces sp. (BCRU-MM40 GenBank accession number: FJ771041), and control treatments. Seedlings survived greenhouse condition but species survival and growth were different among treatments at field conditions, varying over time. The highest survival was observed in a native soil strain (S20) while the lowest in MM40. The low survival in MM40 and in the other treatments may be explained by the higher herbivory observed in those seedlings compared to control ones, suggesting a higher nutritional status in inoculated plants. Strains from refuse dumps were the best at enhancing seedling growth, while strains from soil were the best at maintaining their survival. Native Actinobacteria studied may increase plant species survival and growth by improving their nutritional status, suggesting their potential to facilitate vegetation establishment and, therefore, being good candidates for restoration practices. Furthermore, plant species respond differently to different strains, highlighting the importance of microorganism diversity for ecosystem functioning.

Interactions between soil compositions and the wheat root microbiome under drought stress: From an in silico to in planta perspective

As wheat (Triticum aestivum) is an important staple food across the world, preservation of stable yields and increased productivity are major objectives in breeding programs. Drought is a global concern because its adverse impact is expected to be amplified in the future due to the current climate change. Here, we analyzed the effects of edaphic, environmental, and host factors on the wheat root microbiomes collected in soils from six regions in Belgium. Amplicon sequencing analysis of unplanted soil and wheat root endosphere samples indicated that the microbial community variations can be significantly explained by soil pH, microbial biomass, wheat genotype, and soil sodium and iron levels. Under drought stress, the biodiversity in the soil decreased significantly, but increased in the root endosphere community, where specific soil parameters seemingly determine the enrichment of bacterial groups. Indeed, we identified a cluster of drought-enriched bacteria that significantly correlated with soil compositions. Interestingly, integration of a functional analysis further revealed a strong correlation between the same cluster of bacteria and β-glucosidase and osmoprotectant proteins, two functions known to be involved in coping with drought stress. By means of this in silico analysis, we identified amplicon sequence variants (ASVs) that could potentially protect the plant from drought stress and validated them in planta. Yet, ASVs based on 16S rRNA sequencing data did not completely distinguish individual isolates because of their intrinsic short sequences. Our findings support the efforts to maintain stable crop yields under drought conditions through implementation of root microbiome analyses.

The Impact of Growth-Promoting Streptomycetes Isolated from Rhizosphere and Bulk Soil on Oilseed Rape (Brassica napus L.) Growth Parameters

Inoculation of Streptomyces to improve oilseed rape (Brassica napus L.) yields and minimise the use of chemical fertilisers is a promising sustainable strategy. In this study, we isolated 72 actinobacterial strains from rhizosphere of oilseed rape and maize and from bulk soil for screening and characterising their antimicrobial activity. Nine promising strains, identified as Streptomyces sp. by morphology, physiological characteristics, and 16S rRNA gene sequencing, were selected for their plant growth-promoting traits and in planta experiments. The actinobacterial strains were positive for IAA production, siderophore production, and HCN production. In planta experiments were conducted by soaking the oilseed rape seeds in the actinobacterial suspension, followed by plant growth under controlled conditions in a cultivate chamber (22–28 °C, 8 h dark/16 h light, constant humidity 80%). We recorded root and shoot length (cm) and seedling fresh weight (g). For most of the abovementioned parameters, a significant enhancement was observed with strain KmiRC20A118 treatment. The length of the root increased by 53.14%, the shoot length increased by 65.6%, and the weight of the fresh plant by 60% compared to the control. The integrated application of PGPS (Plant Growth Promoting Streptomyces) from the rhizosphere of oilseed rape is a promising strategy to improve the growth of oilseed rape.

Defining the wheat microbiome: Towards microbiome-facilitated crop production

Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.

Actinomycetes Enrich Soil Rhizosphere and Improve Seed Quality as well as Productivity of Legumes by Boosting Nitrogen Availability and Metabolism

The use of actinomycetes for improving soil fertility and plant production is an attractive strategy for developing sustainable agricultural systems due to their effectiveness, eco-friendliness, and low production cost. Out of 17 species isolated from the soil rhizosphere of legume crops, 4 bioactive isolates were selected and their impact on 5 legumes: soybean, kidney bean, chickpea, lentil, and pea were evaluated. According to the morphological and molecular identification, these isolates belong to the genus Streptomyces. Here, we showed that these isolates increased soil nutrients and organic matter content and improved soil microbial populations. At the plant level, soil enrichment with actinomycetes increased photosynthetic reactions and eventually increased legume yield. Actinomycetes also increased nitrogen availability in soil and legume tissue and seeds, which induced the activity of key nitrogen metabolizing enzymes, e.g., glutamine synthetase, glutamate synthase, and nitrate reductase. In addition to increased nitrogen-containing amino acids levels, we also report high sugar, organic acids, and fatty acids as well as antioxidant phenolics, mineral, and vitamins levels in actinomycete treated legume seeds, which in turn improved their seed quality. Overall, this study shed the light on the impact of actinomycetes on enhancing the quality and productivity of legume crops by boosting the bioactive primary and secondary metabolites. Moreover, our findings emphasize the positive role of actinomycetes in improving the soil by enriching its microbial population. Therefore, our data reinforce the usage of actinomycetes as biofertilizers to provide sustainable food production and achieve biosafety.

Purification of the phytase enzyme from Lactobacillus plantarum: The effect on pansy growth and macro-micro element content

In the present study, the phytase enzyme was purified from Lactobacillus plantarum with a 3.08% recovery, 9.57-purification fold, and with a specific activity of 278.82 EU/mg protein. Then, the effects of the 5 EU and 10 EU purified phytase was determined on the plant growth, quality, the macro-micro nutrient content of pansy (Viola × wittrockiana), which is of great importance in ornamental plants industry. The research was established under greenhouse conditions with natural light in 2017. The pansy seeds were coated with phytase enzyme solution, sown in a peat environment, and transferred to pots at the seedling period. In general, the 5 EU and 10 EU applications increase plant height, the number of leaves per plant, the number of side branches per plant, and flower height parameters compared to control. Also, micro- and macronutrient values in soil and plant samples were examined. According to the results, the phytase application on pansy cultivation positively affected the properties and yielded high quality of plants.

The Nexus Between Plant and Plant Microbiome: Revelation of the Networking Strategies

The diversity of plant-associated microbes is enormous and complex. These microbiomes are structured and form complex interconnected microbial networks that are important in plant health and ecosystem functioning. Understanding the composition of the microbiome and their core function is important in unraveling their networking strategies and their potential influence on plant performance. The network is altered by the host plant species, which in turn influence the microbial interaction dynamics and co-evolution. We discuss the plant microbiome and the complex interplay among microbes and between their host plants. We provide an overview of how plant performance is influenced by the microbiome diversity and function.

P-Solubilizing Streptomyces roseocinereus MS1B15 With Multiple Plant Growth-Promoting Traits Enhance Barley Development and Regulate Rhizosphere Microbial Population

Phosphate-solubilizing bacteria (PSB) have been reported to increase phosphate (P) content and plant growth. Their application in agricultural systems is an eco-friendly alternative strategy for limiting negative environmental impact of chemical fertilizers and increasing costs. Therefore, the aim of this study was to isolate and characterize new putative PSB to use as inoculum to enhance plant growth and increase P bioavailability in soil. Sixteen bacteria were isolated from Moroccan oat rhizosphere and were screened for their putative P-solubilization by semi-quantitative agar spot method. The two strains MS1B15 and MS1B13, identified as Streptomyces roseocinereus and Streptomyces natalensis, respectively, showed the maximum phosphate solubilization index (PSI = 1.75 and PSI = 1.63). After quantitative assay to determine phosphate solubilization activity, S. roseocinereus MS1B15 was selected for evaluating its putative plant growth promotion activities including production of siderophores, indole-3-acetic acid (IAA) and amino-cyclopropane-1-carboxylate (ACC) deaminase, nitrogen fixation and antimicrobial activity against soil-borne plant pathogens. Under greenhouse condition, barley plants inoculated with S. roseocinereus MS1B15 significantly increased shoot and ear length as well as available phosphorus in ears and leaves and P and N contents in the soil. Overall results showed that the selected strain S. roseocinereus MS1B15 could represent a potential candidate as biofertilizer to increase plant growth as well as P uptake.

In Vitro Assessment of Biocontrol Effects on Fusarium Head Blight and Deoxynivalenol (DON) Accumulation by DON-Degrading Bacteria

Fusarium head blight (FHB) of cereals is a severe disease caused by the Fusarium graminearum species complex. It leads to the accumulation of the mycotoxin deoxynivalenol (DON) in grains and other plant tissues and causes substantial economic losses throughout the world. DON is one of the most troublesome mycotoxins because it is a virulence factor to host plants, including wheat, and exhibits toxicity to plants and animals. To control both FHB and DON accumulation, a biological control approach using DON-degrading bacteria (DDBs) is promising. Here, we performed a disease control assay using an in vitro petri dish test composed of germinated wheat seeds inoculated with F. graminearum (Fg) and DDBs. Determination of both grown leaf lengths and hyphal lesion lengths as a measure of disease severity showed that the inoculation of seeds with the DDBs Devosia sp. strain NKJ1 and Nocardioides spp. strains SS3 or SS4 were protective against the leaf growth inhibition caused by Fg. Furthermore, it was as effective against DON accumulation. The inoculation with strains SS3 or SS4 also reduced the inhibitory effect on leaves treated with 10 µg mL^-1 DON solution (without Fg). These results indicate that the DDBs partially suppress the disease by degrading DON.

Plant growth promoting Streptomyces strains are selectively interacting with the wheat cultivars especially in saline conditions

Plant growth promoting (PGP) effect of Streptomyces on wheat growth in different conditions has been mostly reported although mechanisms which caused wheat cultivars differently response to a PGP Streptomyces has been less studied. In this study, the effect of two Streptomyces strains, previously reported as PGPR, on the growth of four salt-sensitive commercial wheat cultivars under normal and saline conditions was investigated. Strain C-2012 differently affected the growth of the cultivars in the normal and stress conditions. Cultivars Gonbad with the highest (63%) and Zarin without increased dry biomass upon C-2012 treatments were selected for further study. Salinity significantly decreased seedling fresh and dry weight, K⁺ and chlorophyll content and glutathione S-transferase activity. Moreover, the stress increased proline and Na⁺ content and peroxidase (POX) and ascorbate peroxidase (APX) activity in both cultivars. Strain C-2012, generally, ameliorated the negative effect of the stress with increased chlorophyll and carotenoid and reduced Na⁺ content and APX and SOD activity in both cultivars, however, its effect on biomass was different. Increase in SOD, APX and POX activities in bacterial inoculated-Zarin, but not Gonbad, under normal conditions suggested that this cultivar may recognize strain C-2012 as a gentle stressor and not as a PGPR. These results showed that the responses of the wheat cultivars to a defined PGPR is different in the physiological, phenotypic and molecular level. Based on the results, the evaluation of the effect of a bio-fertilizer on each wheat cultivar is necessary prior to use in a commercial field.

Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils with a similar particle size fraction. Field experiments were performed on the area of the Iławski Lake District (north-eastern Poland) at the Production and Experimental Station ‘Bałcyny’ (53°35′49″ N, 19°51′20″ E). In soil samples counts, organotrophic bacteria and actinobacteria were quantified, and the colony development index (CD) and ecophysiological diversity index (EP) were computed. In addition, a 16S amplicon sequencing encoding gene was conducted based on the hypervariable region V3–V4. Further analyses included an evaluation of the basic physiochemical properties of the soil and the activities of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Analyses carried out in the study demonstrated that the rhizosphere of Triticum aestivum had a more beneficial effect on bacteria development than those of Brassica napus and Pisum sativum ssp. arvense, as indicated by the values of the ecophysiological diversity index (EP) and OTU abundance calculated for individual taxa in the soils in which the studied crops were grown. More OTUs of the taxa Alphaproteobacteria, Gammaproteobacteria, Clostridia, Sphingomonadales, Rhodospirillales, Xanthomonadales, Streptomycetaceae, Pseudonocardiaceae, Acetobacteraceae, Solibacteraceae, Kaistobacter, Cohnella, Azospirillum, Cryptosporangium, Rhodoplanes, and Saccharopolyspora were determined in the bacteriome structure of the soil from Triticum aestivum cultivation than in the soils from the cultivation of Brassica napus and Pisum sativum ssp. arvense. Also, the activities of most of the analyzed enzymes, including urease, catalase, alkaline phosphatase, β-glucosidase, and arylsulfatase, were the higher in the soil sown with Triticum aestivum than in those with the other two plant species.

Actinobacteria from Extreme Niches in Morocco and Their Plant Growth-Promoting Potentials

The objectives of this study were to assess actinobacterial diversity in five Moroccan extreme habitats and to evaluate their plant growth-promoting (PGP) activities. The soil samples were collected from different locations, including soils contaminated with heavy metals, from a high altitude site, from the desert, and from a marine environment. In total, 23 actinobacteria were isolated, 8 from Merzouga sand soil; 5 from Cannabis sativa rhizospheric soil; 5 from Toubkal mountain; 4 from a Draa sfar mining site; and 1 from marine soil. Based on their genotypic classification using 16S rRNA gene sequences, 19 of all belonged to the genus Streptomyces (82%) while the rest are the members of the genera Nocardioides (4.5%), Saccharomonospora (4.5%), Actinomadura (4.5%), and Prauserella (4.5%). Isolates Streptomyces sp. TNC-1 and Streptomyces sp. MNC-1 showed the highest level of phosphorus solubilization activity with 12.39 and 8.56 mg/mL, respectively. All 23 isolates were able to solubilize potassium, and 91% of them could grow under nitrogen-free conditions. The ability of the isolated actinobacteria to form indole-3-acetic acid (IAA) ranged from 6.70 to 75.54 μg/mL with Streptomyces sp. MNC-1 being the best IAA producer. In addition, all of the actinobacteria could produce siderophores, with Saccharomonospora sp. LNS-1 synthesizing the greatest amount (138.92 μg/mL). Principal coordinate analysis revealed that Streptomyces spp. MNC-1, MNT-1, MNB-2, and KNC-5; Saccharomonospora sp. LNS-1; and Nocardioides sp. KNC-3 each showed a variety of high-level plant growth-promoting activities. The extreme environments in Morocco are rich with bioactive actinobacteria that possess a variety of plant growth-promoting potentials that can further benefit green and sustainable agriculture.

Utilization of actinobacteria to enhance the production and quality of date palm (Phoenix dactylifera L.) fruits in a semi-arid environment

Actinobacteria have received much attention due to their capacity for plant growth promotion, a promising approach in sustainable development of agriculture. Date palm (Phoenix dactylifera L.) is an important crop, particularly in semi-arid regions of the world, due to the high nutritional and health-promoting values of its fruits. The present study was conducted to investigate the utilization of actinobacteria as an approach to support soil fertility and enhance production and functional food value of date palm fruits in a semi-arid environment. To achieve this purpose, actinobacterial strains were isolated from palm rhizosphere, characterized and screened for bioactivity. Then the potent isolates, based on plant growth promoting assays, were inoculated into the soil rhizosphere of five-target palms (Ajwa, Sokary, Khodry, Rashodia and Saffawy) before flowering and during fruiting stages in two successive seasons. Interestingly, the actinobacterial inoculants increased soil fertility and improved fruit yield of the tested palms. The treated date fruits accumulated higher levels of valuable phytochemicals such as sugars, organic acids, essential amino acids, unsaturated fatty acids, phenolic acids, flavonoids, vitamins and minerals, as compared with the untreated ones. Moreover, actinobacterial treatment induced the biological activities (antioxidant, antibacterial, antifungal and anticancer) of the produce dates. Conclusively, results presented herein suggest the promising application of actinobacteria for supporting the production and functional food value of date palms in semi-arid regions.

Plant growth promotion and chilli anthracnose disease suppression ability of rhizosphere soil actinobacteria

AIM

The aim of this study was to screen potential plant growth promoting rhizobacterial (PGPR) actinobacterial isolate with effective inhibition against anthracnose causing fungal pathogen Colletotrichum capsici.

METHODS AND RESULTS

In this study, actinobacterias were isolated from rhizosphere soil using dilution plate method and tested for antagonistic potential against pathogenic fungi C. capsici. In primary and secondary screening tests, the actinobacterial isolate BS-26 displayed high antagonistic activity against the fungal pathogen. Isolate BS-26 was identified as Streptomyces violaceoruber based on 16S rDNA sequencing. Furthermore, indole acetic acid production, phosphate solubilization and ammonia production have been confirmed in the S. violaceoruber that suggest their potential to be used as PGPR bacteria. A green house experiment showed that application of S. violaceoruber fermentation broth reduced the incidence of the chilli anthracnose and promoted the growth of chilli seedlings with a significant increase in germination %, total plant height, fresh weight and chlorophyll content when compared to controls.

CONCLUSION

Streptomyces violaceoruber can be applied as a biofertilizer and biocontrol agent for growing chillies against the attack of fungal pathogen C. capsici.

SIGNIFICANCE OF IMPACT OF THE STUDY

The damage caused by anthracnose disease is an issue of concern, affecting negatively the economy involved in chilli cultivation. As chemical methods of control have serious disadvantages, biocontrol approach using beneficial (PGPR) micro-organisms shall be a better alternative to control crop diseases.

Rotations with Indian Mustard and Wild Rocket Suppressed Cucumber Fusarium Wilt Disease and Changed Rhizosphere Bacterial Communities

Crop monocropping usually results in an enrichment of soil-borne pathogens in soil. Crop rotation is an environmentally friendly method for controlling soil-borne diseases. Plant rhizosphere microorganisms, especially plant-beneficial microorganisms, play a major role in protecting plants from pathogens, but responses of these microorganisms to crop rotation remain unclear. Here, we evaluated the effects of rotations with Indian mustard (Brassica juncea) and wild rocket (Diplotaxis tenuifolia (L.) DC.) on cucumber Fusarium wilt disease caused by Fusarium oxysporum f.sp. cucumerinum (FOC). Cucumber rhizosphere bacterial community composition was analyzed by high-throughput amplicon sequencing. Bacteria, Pseudomonas spp., 2,4-diacetylphloroglucinol (an antifungal secondary metabolite) producer and FOC abundances were estimated by real-time PCR. Rotations with Indian mustard and wild rocket suppressed cucumber Fusarium wilt disease and cucumber rhizosphere FOC abundance. Crop rotations increased cucumber rhizosphere bacteria, Pseudomonas spp. and 2,4-diacetylphloroglucinol producer abundances. Moreover, crop rotations changed cucumber rhizosphere bacterial community composition and increased bacterial community diversity. However, crop rotations decreased soil inorganic nitrogen content and inhibited cucumber seedling growth. Overall, rotations with Indian mustard and wild rocket suppressed cucumber Fusarium wilt disease, which might be linked to the increased rhizosphere bacterial diversity and abundances of potential plant-beneficial microorganisms (such as Pseudomonas spp. and 2,4-diacetylphloroglucinol producer).

Exploring the potential of actinomycetes in improving soil fertility and grain quality of economically important cereals

The search for environment-friendly, economical and healthy alternatives to agrochemicals tempted us to evaluate the potential of naturally occurring actinomycetes to improve soil properties, plant growth and photosynthesis, grain yield and chemical composition of economically important cereals (wheat, barley, oat, maize and sorghum). To this end, actinomycetes were isolated from soils of local cereals fields, then their biological activities, namely antibacterial, antiprotozoal, antioxidant, and phenolic and flavonoid contents were evaluated. The four most active isolates (9, 16, 24 and 26) were selected and used for enriching the soils until seed set. Each isolate was separately applied. Seeds of the selected cereals were grown in the actinomycete-enriched soils. The soils were analyzed for their electrical conductivity, pH values, total phenolics, organic matter and mineral content. At the vegetative stage, chlorophyll content and gas exchange rates were measured. Mature seeds were then harvested, the yield was evaluated and the seeds were analyzed for their primary and secondary metabolites. The selected isolates improved the grain yield in all tested cereals and most noticeably in barley and maize as compared to control counterparts. These positive effects were probably a result of increased carbon gain due to higher chlorophyll and photosynthetic rate. Isolate 26 showed the highest effect on grains composition profiles followed by the isolate 16. Phenolics and sugars of all grains increased by treatment with the tested isolates. Isolate 26 was the most effective in this regard. All isolates generally improved vitamins, amino acids and organic acids contents in grains. However, fatty acids profile showed a decrease in the content of all measured fatty acids by isolate 26 and an increase in the contents by isolate 16. These results emphasize the potential of actinomycete enrichment as an alternative to agrochemicals and strongly suggest that they can be used in organic farming.

Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China

Actinobacteria from special habitats are of interest due to their producing of bioactive compounds and diverse ecological functions. However, little is known of the diversity and functional traits of actinobacteria inhabiting coastal salt marsh soils. We assessed actinobacterial diversity from eight coastal salt marsh rhizosphere soils from Jiangsu Province, China, using culture-based and 16S rRNA gene high throughput sequencing (HTS) methods, in addition to evaluating their plant growth-promoting (PGP) traits of isolates. Actinobacterial sequences represented 2.8%-43.0% of rhizosphere bacterial communities, as determined by HTS technique. The actinobacteria community comprised 34 families and 79 genera. In addition, 196 actinobacterial isolates were obtained, of which 92 representative isolates were selected for further 16S rRNA gene sequencing and phylogenetic analysis. The 92 strains comprised seven suborders, 12 families, and 20 genera that included several potential novel species. All representative strains were tested for their ability of producing indole acetic acid (IAA), siderophores, 1-aminocyclopropane-1-carboxylate deaminase (ACCD), hydrolytic enzymes, and phosphate solubilization. Based on the presence of multiple PGP traits, two strains, Streptomyces sp. KLBMP S0051 and Micromonospora sp. KLBMP S0019 were selected for inoculation of wheat seeds grown under salt stress. Both strains promoted seed germination, and KLBMP S0019 significantly enhanced seedling growth under NaCl stress. Our study demonstrates that coastal salt marsh rhizosphere soils harbor a diverse reservoir of actinobacteria that are potential resources for the discovery of novel species and functions. Moreover, several of the isolates identified here are good candidates as PGP bacteria that may contribute to plant adaptions to saline soils.

Plant Growth Promoting and Biocontrol Activity of Streptomyces spp. as Endophytes

There has been many recent studies on the use of microbial antagonists to control diseases incited by soilborne and airborne plant pathogenic bacteria and fungi, in an attempt to replace existing methods of chemical control and avoid extensive use of fungicides, which often lead to resistance in plant pathogens. In agriculture, plant growth-promoting and biocontrol microorganisms have emerged as safe alternatives to chemical pesticides. Streptomyces spp. and their metabolites may have great potential as excellent agents for controlling various fungal and bacterial phytopathogens. Streptomycetes belong to the rhizosoil microbial communities and are efficient colonizers of plant tissues, from roots to the aerial parts. They are active producers of antibiotics and volatile organic compounds, both in soil and in planta, and this feature is helpful for identifying active antagonists of plant pathogens and can be used in several cropping systems as biocontrol agents. Additionally, their ability to promote plant growth has been demonstrated in a number of crops, thus inspiring the wide application of streptomycetes as biofertilizers to increase plant productivity. The present review highlights Streptomyces spp.-mediated functional traits, such as enhancement of plant growth and biocontrol of phytopathogens.

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions

Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S. scabrisporus NF3 genome is larger than the average Streptomyces genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that S. scabrisporus NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of S. scabrisporus mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions.

Plant growth-promoting actinobacteria: a new strategy for enhancing sustainable production and protection of grain legumes

Grain legumes are a cost-effective alternative for the animal protein in improving the diets of the poor in South-East Asia and Africa. Legumes, through symbiotic nitrogen fixation, meet a major part of their own N demand and partially benefit the following crops of the system by enriching soil. In realization of this sustainability advantage and to promote pulse production, United Nations had declared 2016 as the "International Year of pulses". Grain legumes are frequently subjected to both abiotic and biotic stresses resulting in severe yield losses. Global yields of legumes have been stagnant for the past five decades in spite of adopting various conventional and molecular breeding approaches. Furthermore, the increasing costs and negative effects of pesticides and fertilizers for crop production necessitate the use of biological options of crop production and protection. The use of plant growth-promoting (PGP) bacteria for improving soil and plant health has become one of the attractive strategies for developing sustainable agricultural systems due to their eco-friendliness, low production cost and minimizing consumption of non-renewable resources. This review emphasizes on how the PGP actinobacteria and their metabolites can be used effectively in enhancing the yield and controlling the pests and pathogens of grain legumes.

Streptomyces cameroonensis sp. nov., a Geldanamycin Producer That Promotes Theobroma cacao Growth

The taxonomy of an actinobacterial strain, designated JJY4^T, was established using a polyphasic approach. JJY4^T was isolated from the rhizosphere of Chromolaena odorata in Yaoundé (Cameroon) during a project for the selection of biological control agents. Strain JJY4^T exhibited antimicrobial activities against bacteria, fungi, and oomycetes. Strain JJY4^T also exhibited the traits of plant growth-promoting rhizobacteria such as the solubilization of inorganic phosphate, production of siderophores and indole-3-acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase activity. In planta assays performed on cocoa plantlets confirmed that strain JJY4^T exhibited strong abilities to promote plant growth and protect against Phytophthora megakarya, the main causal agent of cocoa pod rot. The formation of rugose-ornamented spores in spiral spore chains by strain JJY4^T is a typical feature of members found in the Streptomyces violaceusniger clade and, similar to some members of the clade, strain JJY4^T produces geldanamycin. A phylogenetic analysis based on 16S rRNA gene sequences confirmed this classification and suggests that strain JJY4^T be added to the subclade constituted of the type strains Streptomyces malaysiensis DSM 41697^T and Streptomyces samsunensis DSM 42010^T. However, DNA-DNA relatedness and physiological characteristics allowed for the differentiation of strain JJY4^T from its closest phylogenetic relatives. Based on these results, strain JJY4^T (=NRRL B-65369, =NBRC 112705) appears to represent a novel species in the S. violaceusniger clade for which the proposed name is Streptomyces cameroonensis sp. nov.

Selection of Streptomyces against soil borne fungal pathogens by a standardized dual culture assay and evaluation of their effects on seed germination and plant growth

Background

In the search for new natural resources for crop protection, streptomycetes are gaining interest in agriculture as plant growth promoting bacteria and/or biological control agents. Because of their peculiar life cycle, in which the production of secondary metabolites is synchronized with the development of aerial hyphae and sporulation, the commonly used methods to screen for bacterial antagonists need to be adapted.

Results

The dual culture assay was standardized in terms of inoculation timing of Streptomyces antagonist and pathogen, and growth rate of different fungal pathogens. In case of fast-growing fungi, inoculation of the antagonist 2 or 3 days prior to the pathogen resulted in significantly stronger inhibition of mycelium growth. One hundred and thirty Streptomyces strains were evaluated against six destructive soil borne pathogens. The activity of strains varied from broad-spectrum to highly specific inhibition of individual pathogens. All strains inhibited at least one tested pathogen. Three strains, which combined the largest broad-spectrum with the highest inhibition activity, were selected for further characterization with four vegetable species. All of them were able to colonize seed surface of all tested vegetable crops. They mostly improved radicle and hypocotyl growth in vitro, although no statistically significant enhancement of biomass weight was observed in vivo. Occasionally, transient negative effects on germination and plant growth were observed.

Conclusions

The adapted dual culture assay allowed us to compare the inhibition of individual Streptomyces strains against six fungal soil borne pathogens. The best selected strains were able to colonize the four vegetable crops and have a potential to be developed into biocontrol products. Although they occasionally negatively influenced plant growth, these effects did not persist during the further development. Additional in vivo studies are needed to confirm their potential as biological control or plant growth promoting agents.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0886-1) contains supplementary material, which is available to authorized users.

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria

Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.

Mechanism of phosphate solubilization and antifungal activity of Streptomyces spp. isolated from wheat roots and rhizosphere and their application in improving plant growth

The application of plant-growth-promoting rhizobacteria (PGPR) at field scale has been hindered by an inadequate understanding of the mechanisms that enhance plant growth, rhizosphere incompetence and the inability of bacterial strains to thrive in different soil types and environmental conditions. Actinobacteria with their sporulation, nutrient cycling, root colonization, bio-control and other plant-growth-promoting activities could be potential field bio-inoculants. We report the isolation of five rhizospheric and two root endophytic actinobacteria from Triticum aestivum (wheat) plants. The cultures exhibited plant-growth-promoting activities, namely phosphate solubilization (1916 mg l−1), phytase (0.68 U ml−1), chitinase (6.2 U ml−1), indole-3-acetic acid (136.5 mg l−1) and siderophore (47.4 mg l−1) production, as well as utilizing all the rhizospheric sugars under test. Malate (50–55 mmol l−1) was estimated in the culture supernatant of the highest phosphate solublizer, Streptomyces mhcr0816. The mechanism of malate overproduction was studied by gene expression and assays of key glyoxalate cycle enzymes – isocitrate dehydrogenase (IDH), isocitrate lyase (ICL) and malate synthase (MS). The significant increase in gene expression (ICL fourfold, MS sixfold) and enzyme activity (ICL fourfold, MS tenfold) of ICL and MS during stationary phase resulted in malate production as indicated by lowered pH (2.9) and HPLC analysis (retention time 13.1 min). Similarly, the secondary metabolites for chitinase-independent biocontrol activity of Streptomyces mhcr0817, as identified by GC-MS and 1H-NMR spectra, were isoforms of pyrrole derivatives. The inoculation of actinobacterial isolate mhce0811 in T. aestivum (wheat) significantly improved plant growth, biomass (33 %) and mineral (Fe, Mn, P) content in non-axenic conditions. Thus the actinobacterial isolates reported here were efficient PGPR possessing significant antifungal activity and may have potential field applications.

Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.)

The soil microbial community acts as a reservoir of microbes that directly influences the structure and composition of the aboveground plant community, promotes plant growth, increases stress tolerance and mediates local patterns of nutrient cycling. Direct interactions between plants and rhizosphere-dwelling microorganisms occur at, or near, the surface of the root. Upon introduction and establishment, invasive plants modify the soil microbial communities and soil biochemistry affecting bioremediation efforts and future plant communities. Here, we used tag-encoded FLX amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and fungal community diversity in the rhizosphere of Berberis thunbergii DC. (Japanese barberry) from invasive stands in coastal Maine to investigate effects of soil type, soil chemistry and surrounding plant cover on the soil microbial community structure. Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia were the dominant bacterial phyla, whereas fungal communities were comprised mostly of Ascomycota and Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes. Bulk soil chemistry had more effect on the bacterial community structure than the fungal community. An effect of geographic location was apparent in the rhizosphere microbial communities, yet it was less significant than the effect of surrounding plant cover. These data demonstrate a high degree of spatial variation in the rhizosphere microbial communities of Japanese barberry with apparent effects of soil chemistry, location and canopy cover on the microbial community structure.