Colonization by endophytic Ochrobactrum anthropi Mn1 promotes growth of Jerusalem artichoke

The Roles of Plant-Growth-Promoting Rhizobacteria (PGPR)-Based Biostimulants for Agricultural Production Systems

The application of biostimulants has been proven to be an advantageous tool and an appropriate form of management towards the effective use of natural resources, food security, and the beneficial effects on plant growth and yield. Plant-growth-promoting rhizobacteria (PGPR) are microbes connected with plant roots that can increase plant growth by different methods such as producing plant hormones and molecules to improve plant growth or providing increased mineral nutrition. They can colonize all ecological niches of roots to all stages of crop development, and they can affect plant growth and development directly by modulating plant hormone levels and enhancing nutrient acquisition such as of potassium, phosphorus, nitrogen, and essential minerals, or indirectly via reducing the inhibitory impacts of different pathogens in the forms of biocontrol parameters. Many plant-associated species such as Pseudomonas, Acinetobacter, Streptomyces, Serratia, Arthrobacter, and Rhodococcus can increase plant growth by improving plant disease resistance, synthesizing growth-stimulating plant hormones, and suppressing pathogenic microorganisms. The application of biostimulants is both an environmentally friendly practice and a promising method that can enhance the sustainability of horticultural and agricultural production systems as well as promote the quantity and quality of foods. They can also reduce the global dependence on hazardous agricultural chemicals. Science Direct, Google Scholar, Springer Link, CAB Direct, Scopus, Springer Link, Taylor and Francis, Web of Science, and Wiley Online Library were checked, and the search was conducted on all manuscript sections in accordance with the terms Acinetobacter, Arthrobacter, Enterobacter, Ochrobactrum, Pseudomonas, Rhodococcus, Serratia, Streptomyces, Biostimulants, Plant growth promoting rhizobactera, and Stenotrophomonas. The aim of this manuscript is to survey the effects of plant-growth-promoting rhizobacteria by presenting case studies and successful paradigms in various agricultural and horticultural crops.

Bottom-up construction and screening of algae-bacteria consortia for pollutant biodegradation

Microbial communities have been used as important biological tools for a variety of purposes associated with agriculture, the food industry and human health. Artificial engineering of microbial communities is an emerging field of research motivated by finding stable and efficient microbial systems. However, the successful design of microbial communities with desirable functions not only requires profound understanding of microbial activities, but also needs efficient approaches to piece together the known microbial traits to give rise to more complex systems. This study demonstrates the bottom-up integration of environmentally isolated phototrophic microalgae and chemotrophic bacteria as artificial consortia to bio-degrade selected volatile organic compounds (VOCs). A high throughput screening method based on 96-well plate format was developed for discovering consortia with bioremediation potential. Screened exemplar consortia were verified for VOCs degradation performance, among these, certain robust consortia were estimated to have achieved efficiencies of 95.72% and 92.70% and near 100% removal (7 days) of benzene, toluene, and phenol, respectively, with initial concentrations of 100 mg/L. VOCs degradation by consortia was mainly attributed to certain bacteria including Rhodococcus erythropolis, and Cupriavidus metallidurans, and directly contributed to the growth of microalgae Coelastrella terrestris (R = 0.82, p < 0.001). This work revealed the potential of converting VOCs waste into algal biomass by algae-bacteria consortia constructed through a bottom-up approach. The screening method enables rapid shortlisting of consortia combinatorial scenarios without prior knowledge about the individual strains or the need for interpreting complex microbial interactions.

Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max

BACKGROUND

Plant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbiome of native plants was demonstrated to harbour a more diverse microbiota and shared a common core microbiome with modern cultivars. In this study the composition of the seed-associated bacteria of Glycine clandestina is compared to seed-associated bacteria of Glycine max (soybean).

RESULTS

The seed microbiome of the native legume Glycine clandestina (crop wild relative; cwr) was more diverse than that of the domesticated Glycine max and was dominated by the bacterial class Gammaproteobacteria. Both the plant species (cwr vs domesticated) and individual seed accessions were identified as the main driver for this diversity and composition of the microbiota of all Glycine seed lots, with the effect of factor "plant species" exceeded that of "geographical location". A core microbiome was identified between the two Glycine species. A high percentage of the Glycine microbiome was unculturable [G. clandestina (80.8%) and G. max (75.5%)] with only bacteria of a high relative abundance being culturable under the conditions of this study.

CONCLUSION

Our results provided novel insights into the structure and diversity of the native Glycine clandestina seed microbiome and how it compares to that of the domesticated crop Glycine max. Beyond that, it also increased our knowledge of the key microbial taxa associated with the core Glycine spp. microbiome, both wild and domesticated. The investigation of this commonality and diversity is a valuable and essential tool in understanding the use of native Glycine spp. for the discovery of new microbes that would be of benefit to domesticated Glycine max cultivars or any other economically important crops. This study has isolated microbes from a crop wild relative that are now available for testing in G. max for beneficial phenotypes.

Microbiome structure and function in rhizosphere of Jerusalem artichoke grown in saline land

The improvement and development of saline-alkali soils is currently a hot economic and scientific issue, and exploring the correlation between rhizosphere microorganisms of plants growing on saline-alkali soils and their salt tolerance has become the key point of related research. In our study, the community structure of microorganism and various properties of saline soils were characterized in which Jerusalem artichoke grown along a soil salinity gradient. A variety of basic soil properties were measured and the amplicon was performed as well as metagenomic sequencing on coastal saline soils using various techniques (such as RDA analysis and the assembly of genomes) to evaluate microbial functions. In addition, WGCNA (Weighted gene coexpression network analysis) method was used to identify the species related to salt stress and the sequence binning to assemble two enriched putative bacterial genomes. The research showed the cultivation of Jerusalem artichoke on saline soil changed soil physico-chemical and enzymatic properties; most of the rapidly changing as well as the long-term stable properties differed significantly between the rhizosphere and bulk soils. The amplicon and metagenomic sequencing revealed the function and structure of microorganisms varied between the rhizosphere and bulk soils, with greater microbial diversity in the rhizosphere. Catalase activity and the moisture content were the factors with the greatest impact on microorganisms. The putative genomes of two species of microorganisms (belong to Nitrospira and Gemmatimonas) were assembled, identified microbial species that were highly responsive to salt stress and that may play a key role in saline soil, stressed the important role of archaea in microbial communities in response to salt stress. The study provides a comprehensive understanding of the microbial community structure in the rhizosphere of Jerusalem artichoke to enable the improvement and economic development of saline land.

Drought tolerant Ochrobactrum sp. inoculation performs multiple roles in maintaining the homeostasis in Zea mays L. subjected to deficit water stress

Plant growth-promoting rhizobacteria (PGPR) improve plant health under various biotic and abiotic stresses. However, the underlying mechanisms of the protective effects of PGPR in deficit water stress (WS) remain less explored. This study aimed to characterize the role of Ochrobactrum sp. NBRISH6 inoculation on maize (Zea mays "Maharaja") under WS conditions using multiple approaches such as physiological, anatomical, metabolic, and molecular. The effect of NBRISH6 inoculation using maize as a host plant was characterized under greenhouse conditions in deficit water stress. Results from this study demonstrated that NBRISH6 significantly lowered the expression of genes involved in the abscisic acid cycle, deficit water stress-response, osmotic stress, and antioxidant enzyme activity (superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, and polyphenol oxidase). Phytohormones, i.e. indole acetic acid (IAA) and salicylic acid (SA) levels, intercellular CO₂ concentration, metabolites such as simple sugars, amino acids, aliphatic hydrocarbons, and the number of shrunken pith cells modulated in maize roots inoculated with NBRISH6. The NBRISH6 inoculation also improved the plant vegetative properties (root length, 33.80%; shoot length, 20.68%; root dry weight, 39.21%; shoot dry weight, 61.95%), shoot nutrients, xylem cells, root hairs, vapor pressure deficit (75%), intrinsic water-use efficiency (41.67%), photosynthesis rate (83.33%), and total chlorophyll (16.15%) as compared to the respective stress controls. This study provides valuable insights into mechanistic functions of PGPR in WS amelioration and promoting plant physiological response.

Bacterial endophyte mediated plant tolerance to salinity: growth responses and mechanisms of action

Salinity stress is one of the key constraints for sustainable crop production. It has gained immense importance in the backdrop of climate change induced imbalanced terrestrial water budgets. The traditional agronomic approaches and breeding salt-tolerant genotypes have often proved insufficient to alleviate salinity stress. Newer approaches like the use of bacterial endophytes associated with agricultural crops have occupied center place recently, owing to their advantageous role in improving crop growth, health and yield. Research evidences have revealed that bacterial endophytes can promote plant growth by accelerating availability of mineral nutrients, helping in production of phytohormones, siderophores, and enzymes, and also by activating systemic resistance against insect pest and pathogens in plants. These research developments have opened an innovative boulevard in agriculture for capitalizing bacterial endophytes, single species or consortium, to enhance plant salt tolerance capabilities, and ultimately lead to translational refinement of crop-production business under salty environments. This article reviews the latest research progress on the identification and functional characterization of salt tolerant endophytic bacteria and illustrates various mechanisms triggered by them for plant growth promotion under saline environment.

Functional Fungal Endophytes in Coleus forskohlii Regulate Labdane Diterpene Biosynthesis for Elevated Forskolin Accumulation in Roots

Coleus forskohlii is a perennial medicinal shrub cultivated mainly for its forskolin content. The plant has been used since ancient times in ayurvedic traditional medicines for the treatment of hypertension, glaucoma, asthma, congestive heart failures, obesity, and cancer. Use of endophytic microorganisms presents a special interest for the development of value-added bioactive compounds through agriculture. Limited investigations have been undertaken on in planta enhancement of forskolin content using endophytic fungus in sustainable agriculture. Here we report specific roles of three fungal endophytes, Fusarium redolens (RF1), Phialemoniopsis cornearis (SF1), and Macrophomina pseudophaseolina (SF2), functionally acting as plant probiotic fungus, regulating secondary metabolite (forskolin) biosynthesis in C. forskohlii. The root endophyte, RF1, and shoot endophytes, SF1 and SF2, were found to enhance forskolin content by 52 to 88% in pot and 60 to 84% in field experiments as compared to uninoculated control plants. The three endophytes also enhanced total biomass owing to plant growth promoting properties. The expression of diterpene synthases (CfTPSs) like CfTPS1, CfTPS2, CfTPS3, and CfTPS4 were significantly upregulated in endophyte-treated C. forskohlii plants. Elevated expression of key diterpene synthases (CfTPS2) in the forskolin biosynthesis pathway, exclusively present in the root cork of C. forskohlii, was observed following SF2 endophyte treatment. Furthermore, endophyte treatments conferred a variety of antagonistic activity against nematode galls (80%) and plant pathogens like Fusarium oxysporum, Colletotricum gloeosporioides, and Sclerotium rolfsii. RF1 and SF1 fungal endophytes showed positive for IAA production; however, SF1 also indicated phosphate solubilization activity. Overall, the qualitative and quantitative improvement of in planta forskolin enhancement represents an area of high commercial interest, and hence, our work focused on novel insights for the application of three fungal endophytes for in planta enhancement of forskolin content for C. forskohlii cultivation by a sustainable approach.

Ochrobactrum cytisi IPA7.2 promotes growth of potato microplants and is resistant to abiotic stress

Bacteria in natural associations with agricultural crops are promising for use in the improvement of clonal micropropagation of plants. We clarified the taxonomic position of Ochrobactrum cytisi strain IPA7.2 and investigated its tolerance for salinity, high temperature, and glyphosate pollution. We also tested the strain's potential to promote the growth of potato (Solanum tuberosum L.) microplants. Using the IPA7.2 draft genome (no. NZ_MOEC00000000), we searched for housekeeping genes and also for the target genes encoding glyphosate tolerance and plant-growth-promoting ability. A multilocus sequence analysis of the gap, rpoB, dnaK, trpE, aroC, and recA housekeeping genes led us to identify isolate IPA7.2 as O. cytisi. The strain tolerated temperatures up to 50 °C and NaCl concentrations up to 3-4%, and it produced 8 µg ml-1 of indole-3-acetic acid. It also tolerated 6 mM glyphosate owing to the presence of type II 5-enolpyruvylshikimate-3-phosphate synthase. Finally, it was able to colonize the roots and tissues of potato microplants, an ability preserved by several generations after subculturing. We identified the development phase of potato microplants that was optimal for inoculation with O. cytisi IPA7.2. Inoculation of in vitro-grown 15-day-old microplants increased the mitotic index of root meristem cells (by 50%), the length of shoots (by 34%), the number of leaves (by 7%), and the number of roots (by 16%). Under ex vitro conditions, the inoculated plants had a greater leaf area (by 77%) and greater shoot and root dry weight (by 84 and 61%, respectively) than did the control plants. We recommend O. cytisi IPA 7.2 for use in the growing of potato microplants to improve the production of elite seed material.

Morphological responses to nitrogen stress deficiency of a new heterotrophic isolated strain of Ebro Delta microbial mats

Microorganisms living in hypersaline microbial mats frequently form consortia under stressful and changing environmental conditions. In this paper, the heterotrophic strain DE2010 from a microalgae consortium (Scenedesmus sp. DE2009) from Ebro Delta microbial mats has been phenotypically and genotypically characterized and identified. In addition, changes in the morphology and biomass of this bacterium in response to nitrogen deficiency stress have been evaluated by correlative light and electron microscopy (CLEM) combining differential interference contrast (DIC) microscopy and transmission electron microscopy (TEM) and scanning electron microscopy (SEM). These isolated bacteria are chemoorganoheterotrophic, gram-negative, and strictly aerobic bacteria that use a variety of amino acids, organic acids, and carbohydrates as carbon and energy sources, and they grow optimally at 27 °C in a pH range of 5 to 9 and tolerate salinity from 0 to 70‰ NaCl. The DNA-sequencing analysis of the 16S rRNA and nudC and fixH genes and the metabolic characterization highlight that strain DE2010 corresponds to the species Ochrobactrum anthropi. Cells are rod shaped, 1-3 μm in length, and 0.5 μm wide, but under deprived nitrogen conditions, cells are less abundant and become more round, reducing their length and area and, consequently, their biomass. An increase in the number of pleomorphic cells is observed in cultures grown without nitrogen using different optical and electron microscopy techniques. In addition, the amplification of the fixH gene confirms that Ochrobactrum anthropi DE2010 has the capacity to fix nitrogen, overcoming N₂-limiting conditions through a nifH-independent mechanism that is still unidentified.

Effect of microorganisms on reducing cadmium uptake and toxicity in rice (Oryza sativa L.)

This study analyzed the application of three microorganism inoculums, including Bacillus subtilis, Bacillus cereus, and commercial effective microorganism (EM) solution in order to determine cadmium (Cd) reduction in rice (Oryza sativa L.) and rice growth promotion. Rice was grown in Cd-contaminated soil (120 mg/kg) and selected microorganisms were inoculated. Cd concentration and rice weight were measured at 45 and 120 days of the experiment. The result showed that B. subtilis inoculation into rice can highly reduce Cd accumulation in every part of rice roots and shoots (45 days), and grains (120 days). This species can effectively absorb Cd compared to other inoculums, which might be the main mechanism to reduce Cd transportation in rice plants. Interestingly, plants that were inoculated with bacterial species individually harbored higher calcium (Ca) and magnesium (Mg) accumulation; B. subtilis-inoculated plants had the highest levels of Ca and Mg compared to other inoculated ones. Moreover, inoculating rice plants with these microorganisms could increase the dry weight of the plant and protect them from Cd stress because all the inoculums presented the ability to solubilize phosphate, produce indole-3-acetic acid (IAA), and control ethylene levels by 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. After 120 days, quantification of each inoculum by quantitative polymerase chain reaction (qPCR) confirmed the root colonization of bacterial species, with B. subtilis showing higher 16S rRNA gene copy numbers than the other species. B. subtilis was classified as a non-human pathogenic strain, reassuring the safe application of this plant growth-promoting bacterium as a crop inoculum.

Role of plant growth-promoting Ochrobactrum sp. MC22 on triclocarban degradation and toxicity mitigation to legume plants

Triclocarban (TCC) is an emerging and persistent pollutant once released into environment. In this study, TCC-degrading Ochrobactrum sp. MC22, was isolated and characterized. This is the first report on plant-growth promoting bacterium with versatile capability of TCC degradation under aerobic and anaerobic conditions. The aerobic degradation of TCC occurred completely of which the kinetic analysis revealed a non-self-inhibitive substrate effect, and broad-concentration-range degradation efficiency (ranging from 0.16-30mgL-1). Anaerobic TCC degradation was feasible, but was significantly enhanced up to 40-50% when ferric, or acetate was provided as electron donor, or acceptor, respectively. TCC biodegradation under both conditions was proposed to initially occur through hydrolysis leading to transient accumulation of chloroanilines, which could be completely metabolized and detoxified. With concern on TCC adverse effect to plants, role of MC22 on toxicity mitigation was investigated using two legume plants: Vigna radiata and Glycine max (L.) Merr. Upon TCC exposure, damage of both plant structures, especially root system was observed, but was substantially mitigated by MC22 bioaugmentation. This study not only provides thorough TCC degradation characteristic and kinetics of MC22, but also suggests a potential role of this bacterial strain for a rhizoremediation in crop area with TCC contamination.

Characterisation of Pseudomonas spp. and Ochrobactrum sp. isolated from volcanic soil

Soil bacteria may have properties of plant growth promotion but not be sufficiently beneficial for plants under stress conditions. This challenge has led researchers to extend their searches into extreme environments for potential soil bacteria with multiple plant beneficial traits as well as abiotic stress tolerance abilities. In the current study, an attempt was made to evaluate soil bacteria from an extreme environment, volcano soils, based on plant growth promoting and abiotic stress mitigating characteristics. The screening led to the isolation of eight (NBRISH4, NBRISH6, NBRISH10, NBRISH11, NBRISH13, NBRISH14, NBRISH16 and NBRISH26) bacterial isolates capable of withstanding stresses, namely temperature (up to 45 °C), salt (up to 2 M NaCl) and drought (up to 60% Poly Ethylene Glycol 6000) in vitro. Further, the selected isolates were notable for their in vitro temporal performance with regards to survival (in terms of colony count), phosphate solubilisation, biofilm formation, auxin, alginate and exo-polysaccharide production abilities under abiotic stresses i.e. 40 °C temperature; 500 mM NaCl salt and drought (PEG) conditions. In vivo seed treatments of individual selected bacteria to maize plants resulted into significant enhancement in root and shoot length, root and shoot fresh and dry weight and number of leaves per plant. Overall, the plant growth promoting and abiotic stress tolerance ability was most evident for bacterial isolate NBRISH6 which was identified as an Ochrobactrum sp. using 16S rRNA based phylogenetic analysis.

Endophytic cultivable bacterial community obtained from the Paullinia cupana seed in Amazonas and Bahia regions and its antagonistic effects against Colletotrichum gloeosporioides

Guarana (Paullinia cupana var. sorbilis) is a plant from the Amazonas region with socio-economic importance. However, guarana production has been increasingly affected by unfavorable conditions resulting from anthracnose, caused by the Colletotrichum fungal genus, which primarily affects mainly the Amazonas region. The aim of the present study was to isolate bacterial endophytes from the seeds of guarana plants obtained from Amazonas region and the Northeast state of Bahia, a region where this disease is not a problem for guarana plantations. The number of bacterial Colony Forming Units (CFU/g seeds) was 2.4 × 10(4) from the Bahia and 2.9 × 10(4) from the Amazonas region. One hundred and two isolated bacteria were evaluated in vitro against the phytopathogenic strain Colletotrichum gloeosporioides L1. These isolates were also analyzed for the enzymatic production of amylase, cellulase, protease, pectinase, lipase and esterase. Approximately 15% of isolates, showing high antagonistic activity, and the production of at least one enzyme were identified through the partial sequencing of 16S rDNA. The genus Bacillus was the most frequently observed, followed by Paenibacillus, Ochrobactrum, Microbacterium and Stenotrophomonas. Proteolytic activity was observed in 24 isolates followed by amylolytic, pectinolytic and cellulolytic activities. No esterase and lipase production was detected. Most of the isolates, showing antagonistic effects against C. gloeosporioides and high enzymatic activities, were isolated from the anthracnose-affected region. A biocontrol method using the endophytes from guarana seeds could be applied in the future, as these bacteria are vertically transferred to guarana seedlings.