Endophytic colonization of rice by a diazotrophic strain of Serratia marcescens

Stigmas of holoparasitic Phelipanche arenaria (Orobanchaceae) - a suitable ephemeric flower habitat for development unique microbiome

BACKGROUND

Microbial communities have occasionally been observed in part of the ephemeric reproductive structure of floral stigmas, but their prevalence, phylogenetic diversity and ecological roles are understudied. This report describes the first study of bacterial and fungal communities in immature and mature stigma tissue of the endangered holoparasitic plant Phelipanche arenaria. Culture-dependent methods coupled with next-generation sequencing indicated that a small surface of the flower stigma was an unexpectedly rich and diverse microhabitat for colonization of microbial. We also compared the enzymatic activity of the bacterial communities between immature and mature stigmas samples.

RESULTS

Using high-throughput sequencing methods, we identified and classified 39 to over 51 OTUs per sample for bacterial OTUs represented by Pantoea agglomerans and P. ananatis, comprising 50.6%, followed by Pseudomonas, Luteibacter spp., Sphingomonas spp. with 17% of total frequency. The bacterial profile of immature stigmas of P. arenaria contained unique microorganisms (21 of the most numerous OTUs) that were not confirmed in mature stigmas. However, the enzymatic activity of bacteria in mature stigmas of P. arenaria showed more activity than observed in immature stigmas. In the fungal profile, we recorded even 80 OTUs in mature stigmas, consisting of Capnodiales 45.03% of the total abundance with 28.27% of frequency was created by Alternaria eichhorniae (10.55%), Mycosphaerella tassiana (9.69%), and Aureobasidium pullulans (8.03%). Additionally, numerous putative plant growth-promoting bacteria, fungal pathogens and pathogen-antagonistic yeasts were also detected.

CONCLUSIONS

Our study uncovered that P. arenaria stigmas host diverse bacterial and fungal communities. These microorganisms are well known and have been described as beneficial for biotechnological and environmental applications (e.g., production of different enzymes and antimicrobial compounds). This research provided valuable insight into the parasitic plant-microbe interactions.

Characterization and genomics identification of key genes involved in denitrification-DNRA-nitrification pathway of plant growth-promoting rhizobacteria (Serratia marcescens OK482790)

BACKGROUND

A wide variety of microorganisms, including bacteria, live in the rhizosphere zone of plants and have an impact on plant development both favorably and adversely. The beneficial outcome is due to the presence of rhizobacteria that promote plant growth (PGPR).

RESULTS

In this study, a bacterial strain was isolated from lupin rhizosphere and identified genetically as Serratia marcescens (OK482790). Several biochemically and genetically characteristics were confirmed in vitro and in vivo to determine the OK482790 strain ability to be PGPR. The in vitro results revealed production of different lytic enzymes (protease, lipase, cellulase, and catalase), antimicrobial compounds (hydrogen cyanide, and siderophores), ammonia, nitrite, and nitrate and its ability to reduce nitrate to nitrite. In silico and in vitro screening proposed possible denitrification-DNRA-nitrification pathway for OK482790 strain. The genome screening indicated the presence of nitrite and nitrate genes encoding Nar membrane bound sensor proteins (NarK, NarQ and NarX). Nitrate and nitrite reductase encoding genes (NarI, NarJ, NarH, NarG and NapC/NirT) and (NirB, NirC, and NirD) are also found in addition to nitroreductases (NTR) and several oxidoreductases. In vivo results on wheat seedlings confirmed that seedlings growth was significantly improved by soil inoculation of OK482790 strain.

CONCLUSIONS

This study provides evidence for participation of S. marcescens OK482790 in nitrogen cycling via the denitrification-DNRA-nitrification pathway and for its ability to produce several enzymes and compounds that support the beneficial role of plant-microbe interactions to sustain plant growth and development for a safer environment.

Characterization of Growth-Promoting Activities of Consortia of Chlorpyrifos Mineralizing Endophytic Bacteria Naturally Harboring in Rice Plants-A Potential Bio-Stimulant to Develop a Safe and Sustainable Agriculture

Eighteen pesticide-degrading endophytic bacteria were isolated from the roots, stems, and leaves of healthy rice plants and identified through 16S rRNA gene sequencing. Furthermore, biochemical properties, including enzyme production, dye degradation, anti-bacterial activities, plant-growth-promoting traits, including N-fixation, P-solubilization, auxin production, and ACC-deaminase activities of these naturally occurring endophytic bacteria along with their four consortia, were characterized. Enterobacter cloacae HSTU-ABk39 and Enterobacter sp. HSTU-ABk36 displayed inhibition zones of 41.5 ± 1.5 mm, and 29 ± 09 mm against multidrug-resistant human pathogenic bacteria Staphylococcus aureus and Staphylococcus epidermidis, respectively. FT-IR analysis revealed that all eighteen isolates were able to degrade chlorpyrifos pesticide. Our study confirms that pesticide-degrading endophytic bacteria from rice plants play a key role in enhancing plant growth. Notably, rice plants grown in pots containing reduced urea (30%) mixed with either endophytic bacterial consortium-1, consortium-2, consortium-3, or consortia-4 demonstrated an increase of 17.3%, 38.6%, 18.2%, and 39.1% yields, respectively, compared to the control plants grown in pots containing 100% fertilizer. GC-MS/MS analysis confirmed that consortia treatment caused the degradation of chlorpyrifos into different non-toxic metabolites, including 2-Hydroxy-3,5,6 trichloropyridine, Diethyl methane phosphonate, Phorate sulfoxide, and Carbonochloridic. Thus, these isolates could be deployed as bio-stimulants to improve crop production by creating a sustainable biological system.

Non-rhizobial nodule endophytes improve nodulation, change root exudation pattern and promote the growth of lentil, for prospective application in fallow soil

Non-rhizobial endophytes (NREs) are active colonizers inhabiting the root nodules. Though their active role in the lentil agroecosystem is not well defined, here we observed that these NREs might promote the growth of lentils, modulate rhizospheric community structure and could be used as promising organisms for optimal use of rice fallow soil. NREs from root nodules of lentils were isolated and examined for plant growth-promoting traits, exopolysaccharide (EPS) and biofilm production, root metabolites, and the presence of nifH and nifK elements. The greenhouse experiment with the chosen NREs, i.e., Serratia plymuthica 33GS and Serratia sp. R6 significantly increased the germination rate, vigour index, development of nodules (in non-sterile soil) and fresh weight of nodules (33GS 94%, R6 61% growth) and length of the shoot (33GS 86%, R6 51.16%) as well as chlorophyll levels when compared to the uninoculated control. Scanning Electron Microscopy (SEM) revealed that both isolates could successfully colonize the roots and elicit root hair growth. The inoculation of the NREs resulted in specific changes in root exudation patterns. The plants with 33GS and R6 treatment significantly stimulated the exudation of triterpenes, fatty acids, and their methyl esters in comparison to the uninoculated plants, altering the rhizospheric microbial community structure. Proteobacteria dominated the rhizospheric microbiota in all the treatments. Treatment with 33GS or R6 also enhanced the relative abundance of other favourable microbes, including Rhizobium, Mesorhizobium, and Bradyrhizobium. The correlation network analysis of relative abundances resulted in numerous bacterial taxa, which were in cooperation with each other, having a possible role in plant growth promotion. The results indicate the significant role of NREs as plant growth promoters, which also includes their role in root exudation patterns, enhancement of soil nutrient status and modulation of rhizospheric microbiota, suggesting their prospects in sustainable, and bio-based agriculture.

Comparative Physiology and Genomics of Hydrogen-Producing Vibrios

The Hyf-type formate hydrogen lyase (FHL) complex was first proposed based on sequence comparisons in Escherichia coli in 1997 (Andrews et al. in Microbiology 143:3633-3647, 1997). The hydrogenase in the Hyf-type FHL was estimated to be a proton-translocating energy-conserving [NiFe]-hydrogenase. Although the structure of FHL is similar to that of complex I, silent gene expression in E. coli has caused delays in unveiling the genetic and biochemical features of the FHL. The entire set of genes required for Hyf-type FHL synthesis has also been found in the genome sequences of Vibrio tritonius in 2015 (Matsumura et al. in Int J Hydrog Energy 40:9137-9146, 2015), which produces more hydrogen (H₂) than E. coli. Here we investigate the physiological characteristics, genome comparisons, and gene expressions to elucidate the genetic backgrounds of Hyf-type FHL, and how Hyf-type FHL correlates with the higher H₂ production of V. tritonius. Physiological comparisons among the seven H₂-producing vibrios reveal that V. porteresiae and V. tritonius, grouped in the Porteresiae clade, show greater capacity for H₂ production than the other species. The structures of FHL-Hyp gene clusters were closely related in both Porteresiae species, but differed from those of the other species with the presence of hupE, a possible nickel permease gene. Interestingly, deeper genome comparisons revealed the co-presence of nickel ABC transporter genes (nik) with the Hyf-type FHL gene only on the genome of the Porteresiae clade species. Therefore, active primary Ni transport might be one of the key factors characterizing higher H₂ production in V. tritonius. Furthermore, the expression of FHL gene cluster was significantly up-regulated in V. tritonius cells stimulated with formate, indicating that formate is likely to be a control factor for the gene expression of V. tritonius FHL in a similar way to the formate regulon encoding the E. coli FHL.

Characterization of a novel chitinolytic Serratia marcescens strain TC-1 with broad insecticidal spectrum

The Gram-negative rod-shaped bacterium Serratia marcescens is an opportunistic pathogen of many organisms, including insects. We report the identification and optimal in vitro chitinase production conditions of a novel chitinolytic S. marcescens strain TC-1 isolated from a naturally infected white grub (Anomala corpulenta) collected from a peanut field at Nanyang city, Henan province, China. Strain identification was conducted by morphological, physiological, biochemical and molecular analyses. The amplified 16S rRNA gene of TC-1 showed a similarity greater than 99% with multiple strains of S. marcescens. Based on Neighbor-joining phylogenetic tree analysis of bacterial 16S rRNA gene sequences, TC-1 formed a clade with S. marcescens, clearly separated from other Serratia spp. The strain TC-1 showed larvicidal activities against five insect species (A. corpulenta, Plutella xylostella, Spodoptera exigua, Helicoverpa armigera, Bombyx mori) and the nematode Caenorhabditis elegans, but not against S. litura. The operating parameters of chitinase production by TC-1 were optimized by response surface methodology using a three-factor, three-level Box-Behnken experimental design. The effects of three independent variables i.e. colloidal chitin concentration (7–13 g l⁻¹), incubation time (24–72 h) and incubation temperature (24–32 °C) on chitinase production by TC-1 were investigated. A regression model was proposed to correlate the independent variables for an optimal chitinase activity predicted as 20.946 U ml⁻¹, using a combination of colloidal chitin concentration, incubation time and incubation temperature of 9.06 g l⁻¹, 63.83 h and 28.12 °C, respectively. The latter agreed well with a mean chitinase activity of 20.761 ± 0.102 U ml⁻¹ measured in the culture supernatants of TC-1 grown under similar conditions with a colloidal chitin concentration, incubation time and incubation temperature of 9 g l⁻¹, 64 h and 28 °C, respectively. Our study revealed the S. marcescens strain TC-1 with potential as a biocontrol agent of insect pests and nematodes and demonstrated the proposed regression model's potential to guide chitinase production by this strain.

Authentication of putative competitive bacterial endophytes of rice by re-isolation and DNA fingerprinting assay

AIM

The plant-growth-promoting putative competitive endophytes offer significant benefits to sustainable agriculture. The unworthy opportunistic and passenger endophytes are inevitable during the isolation of putative competitive endophytes. This study aimed to discriminate the putative competitive endophytes undoubtedly from the opportunistic and passenger endophytes.

METHODS AND RESULTS

The newly-isolated endophytes from field-grown rice were inoculated to 5-days old rice seedlings under gnotobiotic conditions. Re-isolation of the inoculated strains from the root surface, inner tissues of the whole plant, root, and shoot was performed after 5-days. All the re-isolated colonies were compared with native isolate for the homology by BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) and enterobacterial repetitive intergenic consensus (ERIC-PCR) DNA fingerprints. The results revealed that the putative competitive endophyte (RE25 and RE10) showed positive for re-isolation and BOX and ERIC fingerprints for the whole plant, root, and shoot. The opportunistic (RE27 and RE8) and passenger endophytes (RE44 and RE18) failed in re-isolation either from root or shoot. The epiphytes (ZSB15 and Az204) showed negative for endophytic re-isolation and positive for surface colonization.

CONCLUSION

This modified procedure can discriminate the putative competitive endophytes from others.

SIGNIFICANCE AND IMPACT OF THE STUDY

Eliminating the opportunistic and passenger endophytes and epiphytes early by this method would help develop endophytic inoculants to enhance rice productivity.

Diverse responses of pqqC- and phoD-harbouring bacterial communities to variation in soil properties of Moso bamboo forests

Phosphate‐mobilizing bacteria (PMB) play a critical role in the regulation of phosphorus availability in the soil. The microbial genes pqqC and phoD encode pyrroloquinoline quinone synthase and bacterial alkaline phosphatase, respectively, which regulate inorganic and organic phosphorus mobilization, and are therefore used as PMB markers. We examined the effects of soil properties in three Moso bamboo forest sites on the PMB communities that were profiled using high‐throughput sequencing. We observed differentiated responses of pqqC‐ and phoD‐harbouring PMB communities to various soil conditions. There was significant variation among the sites in the diversity and structure of the phoD‐harbouring community, which correlated with variation in phosphorus levels and non‐capillary porosity; soil organic carbon and soil water content also affected the structure of the phoD‐harbouring community. However, no significant difference in the diversity of pqqC‐harbouring community was observed among different sites, while the structure of the pqqC‐harbouring bacteria community was affected by soil organic carbon and soil total nitrogen, but not soil phosphorus levels. Overall, changes in soil conditions affected the phoD‐harbouring community more than the pqqC‐harbouring community. These findings provide a new insight to explore the effects of soil conditions on microbial communities that solubilize inorganic phosphate and mineralize organic phosphate.

Serratia spp. Are Responsible for Nitrogen Fixation Fueled by As(III) Oxidation, a Novel Biogeochemical Process Identified in Mine Tailings

Biological nitrogen fixation (BNF) has important environmental implications in tailings by providing bioavailable nitrogen to these habitats and sustaining ecosystem functions. Previously, chemolithotrophic diazotrophs that dominate in mine tailings were shown to use reduced sulfur (S) as the electron donor. Tailings often contain high concentrations of As(III) that might function as an alternative electron donor to fuel BNF. Here, we tested this hypothesis and report on BNF fueled by As(III) oxidation as a novel biogeochemical process in addition to BNF fueled by S. Arsenic (As)-dependent BNF was detected in cultures inoculated from As-rich tailing samples derived from the Xikuangshan mining area in China, as suggested by nitrogenase activity assays, quantitative polymerase chain reaction, and ¹⁵N₂ enrichment incubations. As-dependent BNF was also active in eight other As-contaminated tailings and soils, suggesting that the potential for As-dependent BNF may be widespread in As-rich habitats. DNA-stable isotope probing identified Serratia spp. as the bacteria responsible for As-dependent BNF. Metagenomic binning indicated that the essential genes for As-dependent BNF [i.e., nitrogen fixation, As(III) oxidation, and carbon fixation] were present in Serratia-associated metagenome-assembled genomes. Over 20 Serratia genomes obtained from NCBI also contained essential genes for both As(III) oxidation and BNF (i.e., aioA and nifH), suggesting that As-dependent BNF may be a widespread metabolic trait in Serratia spp.

The endophytic bacterial entomopathogen Serratia marcescens promotes plant growth and improves resistance against Nilaparvata lugens in rice

Entomopathogenic bacteria are commonly used as biological agents to control different insect pests. However, little is known about the role of bacterial entomopathogens as endophytes in regulating both plant growth and resistance against insect pests. Here, we applied the entomopathogenic bacterium Serratia marcescens S-JS1 via rice seed inoculation and evaluated its effects on host plant growth and resistance against the rice pest Nilaparvata lugens. Furthermore, the induction of defense-related secondary metabolites by the bacterium was assessed by GC-MS/MS. We showed that S-JS1 was able to endophytically colonize the roots and shoots of rice seedlings following seed inoculation. Colonized plants showed increased seed germination (9.4-13.3 %), root (8.2-36.4 %) and shoot lengths (4.1-22.3 %), and root (26.7-69.3 %) and shoot fresh weights (19.0-49.0 %) compared to plants without inoculation. We also identified the production of indole-3-acetic acid by S-JS1, which is likely involved in enhancing rice plant growth. In a two-choice test, N. lugens adults preferred to feed on untreated control plants than on plants treated with S-JS1. In the no-choice feeding tests, the survival of N. lugens nymphs that fed on S-JS1-treated plants was significantly lower than that of nymphs that fed on untreated plants. Additionally, seeds treated with 10⁹ cfu/mL S-JS1 resulted in elevated levels of secondary metabolites, which may be associated with N. lugens resistance in rice plants. Therefore, we suggest that the entomopathogenic bacterium S. marcescens be considered a potentially promising endophyte for use in an innovative strategy for the integrated management of insect pests.

Isolation and characterization of endophytic bacteria from tomato foliage and their in vitro efficacy against root-knot nematodes

Fifteen endophytic bacteria were isolated from leaves and stems of Solanum lycopersicum and Solanum pimpinellifolium collected from different locations of the Jorhat district of Assam and characterized by morphological, cultural, biochemical and molecular approaches. An in vitro study was carried out to evaluate their potentiality as biological control agents against second stage juvenile of the root-knot nematode, Meloidogyne incognita race2. Thirty second stage juveniles (J₂) of M. incognita race 2 were exposed to cell free culture filtrates of all the 15 bacterial endophytes in a sterile cavity block at a concentration of S(100%), S/2(50%), S/4(25%), S/6(17%) and S/10(10%) for a duration of 6, 12, 24, and 48 hr. The results revealed that all the isolates had the potentiality to significantly increase the mortality of the second stage juveniles (J₂). The percent mortality was directly proportional to the duration of exposure time and the concentration of the culture filtrate. The isolate BETL2 showed the best result with 81.47% mortality of juveniles followed by isolates BETL4 (81.43%), BETLI (79.07%), BETS2 (78.87%), and BETL6 (78.17%). The 16S rRNA sequence amplification results indicated that these isolates were Bacillus marisflavi (BETL2), Bacillus altitudinis (BETL4), Microbacterium arborescens (BETL1), Exiguobacterium indicum (BETS2), and Bacillus marisflavi (BETL6). The four most efficient isolates were structurally analyzed using a scanning electron microscope and this revealed that the length and breadth of isolates—BETLI, BETL2, BETL4, and BETS2 were 701.70 nm × 348.30 nm, 954.10 nm × 303.10 nm, 984.10 nm × 332.90 nm and 1422.00 nm × 742.00 nm, respectively. The result of the present study indicated that the above four novel strains of endophytic bacterial isolates enhance the mortality of J₂ of M. incognita race2 and has the potentiality as biological control agents against M. incognita.

Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.

Bacterial and Fungal Microbiome Profiling in Chilhuacle Negro Chili (Capsicum annuum L.) Associated With Fruit Rot Disease

Chilhuacle negro chili (Capsicum annuum L.) is an ancient Mexican landrace that is deeply linked to the culinary heritage of the country. Because of the high profitability and uniqueness of this crop, the Universidad Autónoma del Estado de Morelos is exploring its production in controlled environments. In the crop cycles of 2018 to 2019, the production of chilhuacle negro plants was seriously affected by an unidentified pathogen causing fruit rot, which reduced its quality, yield, and market value. Therefore, the main objective of this work was to study and characterize the fruit microbiota, which could help reveal the causal agent of this disease. Using DNA metabarcoding coupled with Illumina and nanopore sequencing technologies, we collected and analyzed both healthy and infected chili fruit, along with greenhouse bioaerosols. We also explored the bacterial and fungal microbiota by using microbiological techniques to isolate some of the culturable bacterial and fungal species. Our results suggest that the seedborne fungus Alternaria alternata is activated during the maturation stage of chilhuacle negro fruit, triggering a microbiome imbalance, which may in turn enable the establishment of other opportunistic pathogenic fungi during fruit decay, such as Mucor sp. To our knowledge, this is the first study of the chilhuacle negro chili microbiome, which can shed some light on our understanding of one of the main diseases that affect this valuable crop.

The Role of Plant Growth-Promoting Bacteria in Alleviating the Adverse Effects of Drought on Plants

Plant growth-promoting bacteria play an essential role in enhancing the physical, chemical and biological characters of soils by facilitating nutrient uptake and water flow, especially under abiotic stress conditions, which are major constrains to agricultural development and production. Drought is one of the most harmful abiotic stress and perhaps the most severe problem facing agricultural sustainability, leading to a severe shortage in crop productivity. Drought affects plant growth by causing hormonal and membrane stability perturbations, nutrient imbalance and physiological disorders. Furthermore, drought causes a remarkable decrease in leaf numbers, relative water content, sugar yield, root yield, chlorophyll a and b and ascorbic acid concentrations. However, the concentrations of total phenolic compounds, electrolyte leakage, lipid peroxidation, amounts of proline, and reactive oxygen species are considerably increased because of drought stress. This negative impact of drought can be eliminated by using plant growth-promoting bacteria (PGPB). Under drought conditions, application of PGPB can improve plant growth by adjusting hormonal balance, maintaining nutrient status and producing plant growth regulators. This role of PGPB positively affects physiological and biochemical characteristics, resulting in increased leaf numbers, sugar yield, relative water content, amounts of photosynthetic pigments and ascorbic acid. Conversely, lipid peroxidation, electrolyte leakage and amounts of proline, total phenolic compounds and reactive oxygen species are decreased under drought in the presence of PGPB. The current review gives an overview on the impact of drought on plants and the pivotal role of PGPB in mitigating the negative effects of drought by enhancing antioxidant defense systems and increasing plant growth and yield to improve sustainable agriculture.

Genomic Analysis of Serratia plymuthica MBSA-MJ1: A Plant Growth Promoting Rhizobacteria That Improves Water Stress Tolerance in Greenhouse Ornamentals

Water stress decreases the health and quality of horticulture crops by inhibiting photosynthesis, transpiration, and nutrient uptake. Application of plant growth promoting rhizobacteria (PGPR) can increase the growth, stress tolerance, and overall quality of field and greenhouse grown crops subjected to water stress. Here, we evaluated Serratia plymuthica MBSA-MJ1 for its ability to increase plant growth and quality of Petunia × hybrida (petunia), Impatiens walleriana (impatiens), and Viola × wittrockiana (pansy) plants recovering from severe water stress. Plants were treated weekly with inoculum of MBSA-MJ1, and plant growth and quality were evaluated 2 weeks after recovery from water stress. Application of S. plymuthica MBSA-MJ1 increased the visual quality and shoot biomass of petunia and impatiens and increased the flower number of petunia after recovery from water stress. In addition, in vitro characterizations showed that MBSA-MJ1 is a motile bacterium with moderate levels of antibiotic resistance that can withstand osmotic stress. Further, comprehensive genomic analyses identified genes putatively involved in bacterial osmotic and oxidative stress responses and the synthesis of osmoprotectants and vitamins that could potentially be involved in increasing plant water stress tolerance. This work provides a better understanding of potential mechanisms involved in beneficial plant-microbe interactions under abiotic stress using a novel S. plymuthica strain as a model.

Motility, Adhesion and c-di-GMP Influence the Endophytic Colonization of Rice by Azoarcus sp. CIB

Proficient crop production is needed to ensure the feeding of a growing global population. The association of bacteria with plants plays an important role in the health state of the plants contributing to the increase of agricultural production. Endophytic bacteria are ubiquitous in most plant species providing, in most cases, plant promotion properties. However, the knowledge on the genetic determinants involved in the colonization of plants by endophytic bacteria is still poorly understood. In this work we have used a genetic approach based on the construction of fliM, pilX and eps knockout mutants to show that the motility mediated by a functional flagellum and the pili type IV, and the adhesion modulated by exopolysaccarides are required for the efficient colonization of rice roots by the endophyte Azoarcus sp. CIB. Moreover, we have demonstrated that expression of an exogenous diguanylate cyclase or phophodiesterase, which causes either an increase or decrease of the intracellular levels of the second messenger cyclic di-GMP (c-di-GMP), respectively, leads to a reduction of the ability of Azoarcus sp. CIB to colonize rice plants. Here we present results demonstrating the unprecedented role of the universal second messenger cyclic-di-GMP in plant colonization by an endophytic bacterium, Azoarcus sp. CIB. These studies pave the way to further strategies to modulate the interaction of endophytes with their target plant hosts.

Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India

Bacterial endophytes are found in the internal tissues of plants and have intimate associations with their host. However, little is known about the diversity of medicinal plant endophytes (ME) or their capability to produce specialised metabolites that may contribute to therapeutic properties. We isolated 75 bacterial ME from 24 plant species of the Western Ghats, India. Molecular identification by 16S rRNA gene sequencing grouped MEs into 13 bacterial genera, with members of Gammaproteobacteria and Firmicutes being the most abundant. To improve taxonomic identification, 26 selected MEs were genome sequenced and average nucleotide identity (ANI) used to identify them to the species-level. This identified multiple species in the most common genus as Bacillus. Similarly, identity of the Enterobacterales was also distinguished within Enterobacter and Serratia by ANI and core-gene analysis. AntiSMASH identified non-ribosomal peptide synthase, lantipeptide and bacteriocin biosynthetic gene clusters (BGC) as the most common BGCs found in the ME genomes. A total of five of the ME isolates belonging to Bacillus, Serratia and Enterobacter showed antimicrobial activity against the plant pathogen Pectobacterium carotovorum. Using molecular and genomic approaches we have characterised a unique collection of endophytic bacteria from medicinal plants. Their genomes encode multiple specialised metabolite gene clusters and the collection can now be screened for novel bioactive and medicinal metabolites.

Plant Growth Promoting Potentials of Beneficial Endophytic Escherichia coli USML2 in Association with Rice Seedlings

An endophytic Escherichia coli USML2 originally isolated from the inner part of an oil palm (Elaeis guineensis Jacq.) leaf tissue was inoculated to rice seedlings to investigate its ability in colonising plant inner tissues and promoting growth. Infection of E. coli USML2 was initiated by colonisation on the root surface, invasion of the interior root system followed by endophytic spreading. Inoculation of E. coli USML2 in the rice rhizosphere zone resulted in a significant increase in leaf numbers (33.3%), chlorophyll content (33.3%), shoot height (34.8%) and plant dry weight (90.4%) of 42 days old rice seedlings as compared to the control. These findings also demonstrated the ability of E. coli USML2 to spread endophytically which serves as a beneficial strategy for the bacterium to colonise the host plant and gain protection against adverse soil conditions. The genome of E. coli USML2 had also revealed predicted genes essential for endophytic bacterial colonisation and plant growth promotion which further proven potentials of E. coli USML2 as Plant Growth Promoting Endophyte (PGPE).

Plant-Growth Endophytic Bacteria Improve Nutrient Use Efficiency and Modulate Foliar N-Metabolites in Sugarcane Seedling

Beneficial plant–microbe interactions lead to physiological and biochemical changes that may result in plant-growth promotion. This study evaluated the effect of the interaction between sugarcane and endophytic bacterial strains on plant physiological and biochemical responses under two levels of nitrogen (N) fertilization. Six strains of endophytic bacteria, previously selected as plant growth-promoting bacteria (PGPB), were used to inoculate sugarcane mini stalks, with and without N fertilization. After 45 days, biomass production; shoot nutrient concentrations; foliar polyamine and free amino acid profiles; activities of nitrate reductase and glutamine synthase; and the relative transcript levels of the GS1, GS2, and SHR5 genes in sugarcane leaves were determined. All six endophytic strains promoted sugarcane growth, increasing shoot and root biomass, plant nutritional status, and the use efficiency of most nutrients. The inoculation-induced changes at the biochemical level altered the foliar free amino acid and polyamine profiles, mainly regarding the relative concentrations of citrulline, putrescine, glycine, alanine, glutamate, glutamine, proline, and aspartate. The transcription of GS1, GS2, and SHR5 was higher in the N fertilized seedlings, and almost not altered by endophytic bacterial strains. The endophytic strains promoted sugarcane seedlings growth mainly by improving nutrient efficiency. This improvement could not be explained by their ability to induce the production of amino acid and polyamine composts, or GS1, GS2, and SHR5, showing that complex interactions may be associated with enhancement of the sugarcane seedlings’ performance by endophytic bacteria. The strains demonstrated biotechnological potential for sugarcane seedling production.

Bio-Organic Fertilizer: A Green Technology to Reduce Synthetic N and P Fertilizer for Rice Production

Decomposed organic materials, in combination with plant growth-promoting bacteria (PGPB), are environmentally friendly and reduce synthetic fertilizer use in rice production. A bio-organic fertilizer (BoF) was prepared using kitchen waste (79%), chita-dhan (unfilled rice grain) biochar (15%), rock phosphate (5%), and a consortium of 10 PGPB (1%) to supplement 30% nitrogen and to replace triple superphosphate (TSP) fertilizer in rice production with an improvement of soil health. PGPB were local isolates and identified using 16S ribosomal RNA partial gene sequences as Bacillus mycoides, Proteus sp., Bacillus cereus, Bacillus subtilis, Bacillus pumilus, Paenibacillus polymyxa, and Paenibacillus spp. Isolates could fix N₂ by 0.7-1.4 g kg^-1, solubilize 0.1-1.2 g kg^-1 phosphate, and produce 0.1-40 g kg^-1 indoleacetic acid. The performance of BoF was evaluated by 16 field experiments and 18 farmers' field demonstration trials during the year 2017-2020 in different parts of Bangladesh. Performances of BoF were evaluated based on control (T₁), full synthetic fertilizer dose of N, P, and K (T₂), BoF (2 t ha^-1) + 70% N as urea + 100% K as muriate of potash (T₃), 70% N as urea + 100% P as TSP + 100% K as muriate of potash (T₄), and 2 t ha^-1 BoF (T₅) treatments. At the research station, average grain yield improved by 10-13% in T₃ compared with T₂ treatment. Depending on seasons, higher agronomic N use efficiency (19-30%), physiological N use efficiency (8-18%), partial factor productivity (PFP)_N (114-150%), recovery efficiency (RE)_N (3-31%), N harvest index (HI_N) (14-24%), agronomic P use efficiency (22-25%), partial factor productivity of P (9-12%), ARE_P (15-23%), and HI_P (3-6%) were obtained in T₃ compared with T₂ treatment. Research results were reflected in farmers' field, and significant (P < 0.05) higher plant height, tiller, panicle, grain yield, partial factor productivity of N and P were obtained in the same treatment. Application of BoF improved soil organic carbon by 6-13%, along with an increased number of PGPB as compared with full synthetic fertilizer dose. In conclusion, tested BoF can be considered as a green technology to reduce 30% synthetic N and 100% TSP requirements in rice production with improved soil health.

Ambigols from the Cyanobacterium Fischerella ambigua Increase Prodigiosin Production in Serratia spp

When a library of 573 cyanobacteria extracts was screened for inhibition of the quorum sensing regulated prodigiosin production of Serratia marcescens, an extract of the cyanobacterium Fischerella ambigua (Näg.) Gomont 108b was found to drastically increase prodigiosin production. Bioactivity-guided isolation of the active compounds resulted in the two new natural products ambigol D and E along with the known ambigols A and C. Ambigol C treatment increased prodiginine production of Serratia sp. ATCC 39006 (S39006) by a factor of 10, while ambigols A and D were found to have antibiotic activity against this strain. The RNA-Seq of S39006 treated with ambigol C and subsequent differential gene expression and functional enrichment analyses indicated a significant downregulation of genes associated with the translation machinery and fatty acid biosynthesis in Serratia, as well as increased expression of genes related to the uptake of l-proline. These results suggest that the ambigols increase prodiginine production in S39006 not by activating the SmaIR quorum sensing system but possibly by increasing the precursor supply of l-proline and malonyl-CoA.

Endophytic microbes: biodiversity, plant growth-promoting mechanisms and potential applications for agricultural sustainability

Endophytic microbes are known to live asymptomatically inside their host throughout different stages of their life cycle and play crucial roles in the growth, development, fitness, and diversification of plants. The plant-endophyte association ranges from mutualism to pathogenicity. These microbes help the host to combat a diverse array of biotic and abiotic stressful conditions. Endophytic microbes play a major role in the growth promotion of their host by solubilizing of macronutrients such as phosphorous, potassium, and zinc; fixing of atmospheric nitrogen, synthesizing of phytohormones, siderophores, hydrogen cyanide, ammonia, and act as a biocontrol agent against wide array of phytopathogens. Endophytic microbes are beneficial to plants by directly promoting their growth or indirectly by inhibiting the growth of phytopathogens. Over a long period of co-evolution, endophytic microbes have attained the mechanism of synthesis of various hydrolytic enzymes such as pectinase, xylanases, cellulase, and proteinase which help in the penetration of endophytic microbes into tissues of plants. The effective usage of endophytic microbes in the form of bioinoculants reduce the usage of chemical fertilizers. Endophytic microbes belong to different phyla such as Actinobacteria, Acidobacteria, Bacteroidetes, Deinococcus-thermus, Firmicutes, Proteobacteria, and Verrucomicrobia. The most predominant and studied endophytic bacteria belonged to Proteobacteria followed by Firmicutes and then by Actinobacteria. The most dominant among reported genera in most of the leguminous and non-leguminous plants are Bacillus, Pseudomonas, Fusarium, Burkholderia, Rhizobium, and Klebsiella. In future, endophytic microbes have a wide range of potential for maintaining health of plant as well as environmental conditions for agricultural sustainability. The present review is focused on endophytic microbes, their diversity in leguminous as well as non-leguminous crops, biotechnological applications, and ability to promote the growth of plant for agro-environmental sustainability.

Microgreen nutrition, food safety, and shelf life: A review

Microgreens have gained increasing popularity as food ingredients in recent years because of their high nutritional value and diverse sensorial characteristics. Microgreens are edible seedlings including vegetables and herbs, which have been used, primarily in the restaurant industry, to embellish cuisine since 1996. The rapidly growing microgreen industry faces many challenges. Microgreens share many characteristics with sprouts, and while they have not been associated with any foodborne illness outbreaks, they have recently been the subject of seven recalls. Thus, the potential to carry foodborne pathogens is there, and steps can and should be taken during production to reduce the likelihood of such incidents. One major limitation to the growth of the microgreen industry is the rapid quality deterioration that occurs soon after harvest, which keeps prices high and restricts commerce to local sales. Once harvested, microgreens easily dehydrate, wilt, decay and rapidly lose certain nutrients. Research has explored preharvest and postharvest interventions, such as calcium treatments, modified atmopsphere packaging, temperature control, and light, to maintain quality, augment nutritional value, and extend shelf life. However, more work is needed to optimize both production and storage conditions to improve the safety, quality, and shelf life of microgreens, thereby expanding potential markets.

In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes

Endophytes live inside plants and are often beneficial. Kosakonia is a novel bacterial genus that includes many diazotrophic plant-associated isolates. Plant-bacteria studies on two rice endophytic Kosakonia beneficial strains were performed, including comparative genomics, secretome profiling, in planta tests, and a field release trial. The strains are efficient rhizoplane and root endosphere colonizers and localized in the root cortex. Secretomics revealed 144 putative secreted proteins, including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizoplane and endosphere colonization ability. A field trial using rice seed inoculated with Kosakonia spp. showed no effect on plant growth promotion upon nitrogen stress and microbiome studies revealed that Kosakonia spp. were significantly more present in the inoculated rice. Comparative genomics indicated that several protein domains were enriched in plant-associated Kosakonia spp. This study highlights that Kosakonia is an important, recently classified genus involved in plant-bacteria interaction.

Draft Genome Sequence of a Serratia marcescens Strain Isolated from the Pitcher Fluids of a Sarracenia Pitcher Plant

The genome of a Serratia marcescens strain (C7) that was found in the pitcher fluids of a Sarracenia rosea pitcher plant was sequenced using the Illumina platform. A 5,543,750-bp genome assembly was obtained. A total of 6,278 coding sequences are predicted from this assembly.

The genome of a Serratia marcescens strain (C7) that was found in the pitcher fluids of a Sarracenia rosea pitcher plant was sequenced using the Illumina platform. A 5,543,750-bp genome assembly was obtained. A total of 6,278 coding sequences are predicted from this assembly.

Pangenome of Serratia marcescens strains from nosocomial and environmental origins reveals different populations and the links between them

Serratia marcescens is a Gram-negative bacterial species that can be found in a wide range of environments like soil, water and plant surfaces, while it is also known as an opportunistic human pathogen in hospitals and as a plant growth promoting bacteria (PGPR) in crops. We have used a pangenome-based approach, based on publicly available genomes, to apply whole genome multilocus sequence type schemes to assess whether there is an association between source and genotype, aiming at differentiating between isolates from nosocomial sources and the environment, and between strains reported as PGPR from other environmental strains. Most genomes from a nosocomial setting and environmental origin could be assigned to the proposed nosocomial or environmental MLSTs, which is indicative of an association between source and genotype. The fact that a few genomes from a nosocomial source showed an environmental MLST suggests that a minority of nosocomial strains have recently derived from the environment. PGPR strains were assigned to different environmental types and clades but only one clade comprised strains accumulating a low number of known virulence and antibiotic resistance determinants and was exclusively from environmental sources. This clade is envisaged as a group of promissory MLSTs for selecting prospective PGPR strains.

Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

Background

Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil.

Results

Here we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5 Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria.

Conclusions

Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5130-y) contains supplementary material, which is available to authorized users.

Endogenous microbial contamination of melons (Cucumis melo) from international trade: an underestimated risk for the consumer?

BACKGROUND

Fruits and vegetables have increasingly been related to foodborne outbreaks. Besides surface contamination, a possible internalization of microorganisms into edible parts of plants during growth has already been observed. To examine an actual risk for the consumer, microbial contamination of the rind and pulp of 147 muskmelons from international trade was assessed using cultural and biochemical methods, polymerase chain reaction and matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

RESULTS

One hundred percent of the rind samples [3.69-8.92 log colony forming units (CFU) g^-1 ] and 89.8% of the pulp samples (maximum load 3.66 log CFU g^-1 ) were microbiologically contaminated. Among the 432 pulp isolates, opportunistic and potentially pathogenic bacteria were identified, mainly Staphylococcus spp. (48.9%), Clostridium spp. (42.9%) and Enterobacteriaceae (27.9%). Salmonella spp., Escherichia coli and isolates of the Bacillus cereus group were found on the rind (1.4%, 0.7% and 42.9%, respectively) and in the pulp (0.7%, 1.4% and 4.7%). Clostridium perfringens was isolated from the rind of seven melons.

CONCLUSION

The present study revealed a regularly occurring internal contamination of melons. Possible health risks for consumers because of an occurrence of microorganisms in melon pulp should be considered in future food safety assessments. © 2018 Society of Chemical Industry.

Larvicidal potential of Skermanella sp. against rice leaf folder (Cnaphalocrosis medinalis Guenee) and pink stem borer (Sesamia inferens Walker)

Insect pests in the rice agroecosystem, particularly the leaf folder, Cnaphalocrosis medinalis (Guenee) and stem borer, Sesamia inferens (Walker), cause significant yield losses. These pests are generally managed by farmers by application of insecticides and a few biocontrol agents. As a component of integrated pest management, biocontrol agents play a dynamic role in pest control. Although diverse microbial communities are available in the rice ecosystem, bacterial genera such as Bacillus and Pseudomonas spp. are broadly used as biocontrol agents. Therefore, an attempt was made to identify other effective entomopathogenic bacteria to manage the above mentioned pests. In this study, the two entomopathogenic bacteria isolated from diseased pink stem borer (S. inferens Walker) larvae collected from rice fields were identified as Skermanella sp. (KX611462) and Serratia sp. (KX761232). The larvicidal activity of these two bacteria was evaluated against third instar larvae of C. medinalis and S. inferens in in vitro assays and on potted rice plants (Oryza sativa var. TN1). The results of this study demonstrated 50% (LC₅₀) larval mortality of C. medinalis at 2.95 × 10³ and 5.88 × 10³ colony forming units (CFU) ml^-1 for Skermanella sp. and Serratia sp., respectively, under in vitro conditions, 2.57 × 10⁴ and 3.38 × 10⁴ CFU ml^-1, respectively, in whole plant assays. Similarly, the LC₅₀ value for Skermanella sp. was 3.80 × 10⁴ CFU ml^-1 and Serratia sp. was 2.29 × 10⁵ CFU ml^-1 for S. inferens larvae. Our study reports the larvicidal activity of Skermanella sp. against C. medinalis and S. inferens.

Microscopic study on colonization and antimicrobial property of endophytic bacteria associated with ethnomedicinal plants of Meghalaya

Microscopic visualization using transmission electron microscopy (TEM) can provide a better understanding of endophytic colonization within ethnomedicinal plants. Bacterial endophytes were found attached to the host cell wall colonizing the aerenchyma and intercellular spaces of the epidermis and outer cortex except the vascular system. Colonization was non-uniform as single cells, doublets or in the form of microcolonies. Analysis of in vivo antibacterial action of the methanolic extracts of the isolated endophytic bacteria against Gram-positive, Streptococcus pyogenes MTCC 1925 and Gram-negative, Salmonella enterica ser. paratyphi MTCC735 pathogens has revealed the morphological damages in the tested pathogens respectively, under scanning electron microscopy (SEM). Detached cell wall and cell burst were observed in Streptococcus pyogenes where as, cell blisters were shown in Salmonella enterica ser. paratyphi. The study on bacterial endophyte colonization process is important to better predict how endophytes interact with their host and establish themselves in the plant environment by procuring biocontrol activity.

Evaluation of the biocontrol efficacy of a Serratia marcescens strain indigenous to tea rhizosphere for the management of root rot disease in tea

The aim of the present study is to evaluate plant growth promoting and biocontrol efficacy of a Serratia marcescens strain ETR17 isolated from tea rhizosphere for the effective management of root rot disease in tea. Isolated bacterial culture ETR17 showed significant level of in vitro antagonism against nine different foliar and root pathogens of tea. The phenotypic and molecular characterization of ETR17 revealed the identity of the bacterium as Serratia marcescens. The bacterium was found to produce several hydrolytic enzymes like chitinase, protease, lipase, cellulase and plant growth promoting metabolites like IAA and siderophore. Scanning electron microscopic studies on the interaction zone between pathogen and antagonistic bacterial isolate revealed severe deformities in the fungal mycelia. Spectral analyses (LC-ESI-MS, UV-VIS spectrophotometry and HPLC) and TLC indicated the presence of the antibiotics pyrrolnitrin and prodigiosin in the extracellular bacterial culture extracts. Biofilm formation by ETR17 on polystyrene surface was also observed. In vivo application of talc-based formulations prepared with the isolate ETR17 in tea plantlets under green house conditions revealed effective reduction of root-rot disease as well as plant growth promotion to a considerable extent. Viability studies with the ETR17 talc formulation showed the survivability of the isolate up to six months at room temperature. The sustenance of ETR17 (concentration of 8-9x108 cfu g-1) in the soil after the application of talc formulation was recorded by ELISA. Safety studies revealed that ETR17 did not produce hemolysin as observed in pathogenic Serratia strains. The biocontrol strain reported in this study can be used for field application in order to minimize the use of chemical fungicides for disease control in tea gardens.

The expression of an exogenous ACC deaminase by the endophyte Serratia grimesii BXF1 promotes the early nodulation and growth of common bean

Ethylene acts as an inhibitor of the nodulation process of leguminous plants. However, some bacteria can decrease deleterious ethylene levels by the action of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase which degrades ACC, the ethylene precursor in all higher plants. Co-inoculation of rhizobia with endophytes enhances the rhizobial symbiotic efficiency with legumes, improving both nodulation and nitrogen fixation. However, not much is understood about the mechanisms employed by these endophytic bacteria. In this regard, the role of ACC deaminase from endophytic strains in assisting rhizobia in this process has yet to be confirmed. In this study, the role of ACC deaminase in an endophyte's ability to increase Rhizobium tropici nodulation of common bean was evaluated. To assess the effect of ACC deaminase in an endophyte's ability to promote rhizobial nodulation, the endophyte Serratia grimesii BXF1, which does not encode ACC deaminase, was transformed with an exogenous acdS gene. The results obtained indicate that the ACC deaminase-overexpressing transformant strain increased common bean growth, and enhanced the nodulation abilities of R. tropici CIAT899, in both cases compared to the wild-type non-transformed strain. Furthermore, plant inoculation with the ACC deaminase-overproducing strain led to an increased level of plant protection against a seed-borne pathogen.

SIGNIFICANCE AND IMPACT OF THE STUDY

In this work, we studied the effect of ACC deaminase production by the bacterial endophyte Serratia grimesi BXF1, and its impact on the nodulation process of common bean. The results obtained indicate that ACC deaminase is an asset to the synergetic interaction between rhizobia and the endophyte, positively contributing to the overall legume-rhizobia symbiosis by regulating inhibitory ethylene levels that might otherwise inhibit nodulation and overall plant growth. The use of rhizobia together with an ACC deaminase-producing endophyte is, therefore, an important strategy for the development of new bacterial inoculants with increased performance.

Reduction of cadmium uptake in rice endophytically colonized with the cadmium-tolerant bacterium Cupriavidus taiwanensis KKU2500-3

The effects of the cadmium (Cd)-tolerant bacterium Cupriavidus taiwanensis KKU2500-3 on the growth, yield, and Cd concentration in rice grains were investigated in the rice variety Phitsanulok 2 (PL2), which was cultivated in a hydroponic greenhouse. The numbers of Cd-tolerant bacteria isolated from the roots and shoots of plants under the RB (rice with bacteria) and RBC (rice with bacteria and Cd) treatments ranged from 2.60 to 9.03 and from 3.99 to 9.60 log cfu·g−1 of PL2, respectively. This KKU2500-3 strain was successfully colonized in rice, indicating that it was not only nontoxic to the plants but also became distributed and reproduced throughout the plants. Scanning electron microscopy analysis revealed attachment of the bacterium to the root surface, whereas the internally colonized bacteria were located in the vascular tissue, cell wall, and intercellular space. Although the Cd contents found in PL2 were very high (189.10 and 79.49 mg·kg−1 in the RC (rice with Cd) and RBC roots, respectively), the Cd accumulated inside the rice seeds at densities of only 3.10 and 1.31 mg·kg−1, respectively; thus, the bacteria reduced the Cd content to 57.74% of the control content. Therefore, the colonizing bacteria likely acted as an inhibitor of Cd translocation in PL2.

Bacterial Endophyte Colonization and Distribution within Plants

The plant endosphere contains a diverse group of microbial communities. There is general consensus that these microbial communities make significant contributions to plant health. Both recently adopted genomic approaches and classical microbiology techniques continue to develop the science of plant-microbe interactions. Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant. The use of these natural symbionts offers an opportunity to maximize crop productivity while reducing the environmental impacts of agriculture. Endophytes promote plant growth through nitrogen fixation, phytohormone production, nutrient acquisition, and by conferring tolerance to abiotic and biotic stresses. Colonization by endophytes is crucial for providing these benefits to the host plant. Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant. Lately, plant microbiome research has gained considerable attention but the mechanism allowing plants to recruit endophytes is largely unknown. This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes.

Mutualism between Klebsiella SGM 81 and Dianthus caryophyllus in modulating root plasticity and rhizospheric bacterial density

AIMS

Dianthus caryophyllus is a commercially important ornamental flower. Plant growth promoting rhizobacteria are increasingly applied as bio-fertilisers and bio-fortifiers. We studied the effect of a rhizospheric isolate Klebsiella SGM 81 strain to promote D. caryophyllus growth under sterile and non-sterile conditions, to colonise its root system endophytically and its impact on the cultivatable microbial community. We identified the auxin indole-3-acetic acid (IAA) production of Klebsiella SGM 81 as major bacterial trait most likely to enhance growth of D. caryophyllus.

METHODS

ipdC dependent IAA production of SGM 81 was quantified using LC-MS/MS and localised proximal to D. caryophyllus roots and correlated to root growth promotion and characteristic morphological changes. SGM 81 cells were localised on and within the plant root using 3D rendering confocal microscopy of gfp expressing SGM 81. Using Salkowski reagent IAA production was quantified and localised proximal to roots in situ. The effect of different bacterial titres on rhizosphere bacterial population was CFU enumerated on nutrient agar. The genome sequence of Klebsiella SGM 81 (accession number PRJEB21197) was determined to validate PGP traits and phylogenic relationships.

RESULTS

Inoculation of D. caryophyllus roots with Klebsiella SGM 81 drastically promoted plant growth when grown in agar and soil, concomitant with a burst in root hair formation, suggesting an increase in root auxin activity. We sequenced the Klebsiella SGM 81 genome, identified the presence of a canonical ipdC gene in Klebsiella SGM 81, confirmed bacterial production and secretion of IAA in batch culture using LC-MS/MS and localised plant dependent IAA production by SGM 81 proximal to roots. We found Klebsiella SGM 81 to be a rhizoplane and endophytic coloniser of D. caryophyllus roots in a dose dependent manner. We found no adverse effects of SGM 81 on the overall rhizospheric microbial population unless supplied to soil in very high titres.

CONCLUSION

Klebsiella SGM 81 effectively improves root traits of D. caryophyllus in a dose dependent manner, likely through tryptophan dependent IAA production in the rhizoplane and potentially within the intercellular spaces of root tissue. Under optimal plant growth promoting conditions in non-sterile soil, the high total microbial titre in the rhizosphere supports a mutualistic relationship between Klebsiella SGM 81 and carnation that potentially extends to the wider rhizosphere microbiota.

Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L

Two yellow-pigmented isolates, S5-249^T and L9-754^T, originating from surface-sterilized plant tissues of Jatropha curcas L. (Jatropha) cultivars were characterized using a polyphasic taxonomic approach. Strains S5-249^T and L9-754^T had 16S rRNA genes sharing 94.2 % sequence similarity with each other and 91.6-97.2 % sequence similarity with those of other species in the genus Sphingomonas, suggesting that they represent two potentially novel species. The 16S rRNA gene sequences of strains S5-249^T and L9-754^T shared the highest similarity to that of Sphingomonas sanguinis NBRC 13937^T (96.1 and 97.2 %, respectively). The genomic DNA G+C contents of strains S5-249^T and L9-754^T were 66.9 and 68.5 mol%, respectively. The respiratory quinone was determined to be Q-10, and the major polyamine was homospermidine. Strains S5-249^T and L9-754^T contained summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), C16 : 1, C14 : 0 2-OH and summed feature 4 (C16 : 1ω7t, iso-C15 : 0 2-OH and C16 : 1ω7c) as the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The average nucleotide identity (ANI) values between S. sanguinis NBRC 13937^T and the two type strains (S5-249^T and L9-754^T) were 72.31 and 77.73 %, respectively. Digital DNA-DNA hybridization (dDDH) studies between the novel strains (S5-249^T and L9-754^T) and other species of the genus Sphingomonas were well below the thresholds used to discriminate between bacterial species. The results of dDDH and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the species of the genus Sphingomonas with validly published names. These data strongly support the classification of the strains as representatives of novel species, for which we propose the names Sphingomonas jatrophae sp. nov. (type strain S5-249^T=DSM 27345^T=KACC 17593^T) and Sphingomonas carotinifaciens sp. nov. (type strain L9-754^T=DSM 27347^T=KACC 17595^T).

Bioprospecting endophytic diazotrophic Lysinibacillus sphaericus as biocontrol agents of rice sheath blight disease

The present study tried to explore the possible in vitro biocontrol mechanisms of Lysinibacillus sphaericus, a diazotrophic endophyte from rice against the rice sheath blight pathogen Rhizoctonia solani. The in vivo biocontrol potential of the isolate and the induction of systemic resistance under greenhouse conditions have also been experimented employing different treatments with positive control carbendazim, the chemical fungicide. The endophytic isolate showed 100% growth inhibition of the fungal pathogen via volatile organic compound production and was positive for the production of siderophores, biosurfactants, HCN, and ammonia. Under greenhouse conditions, foliar and soil application of L. sphaericus significantly decreased the percentage of disease incidence. All bacterized treatments are superior to chemical fungicide treatment. Application of L. sphaericus in single and combination treatments induces systemic resistance as evident from the significant accumulation of defense enzymes such as peroxides, polyphenol oxides and phenylalanine ammonia in addition to the increase of phenolic compounds. The results biologically prospect endophytic diazotroph L. sphaericus as a potent plant growth promoter with excellent biocontrol efficiency.

The oil-contaminated soil diazotroph Azoarcus olearius DQS-4T is genetically and phenotypically similar to the model grass endophyte Azoarcus sp. BH72

The genome of Azoarcus olearius DQS-4^T , a N₂ -fixing Betaproteobacterium isolated from oil-contaminated soil in Taiwan, was sequenced and compared with other Azoarcus strains. The genome sequence showed high synteny with Azoarcus sp. BH72, a model endophytic diazotroph, but low synteny with five non-plant-associated strains (Azoarcus CIB, Azoarcus EBN1, Azoarcus KH32C, A. toluclasticus MF63^T and Azoarcus PA01). Average Nucleotide Identity (ANI) revealed that DQS-4^T shares 98.98% identity with Azoarcus BH72, which should now be included in the species A. olearius. The genome of DQS-4^T contained several genes related to plant colonization and plant growth promotion, such as nitrogen fixation, plant adhesion and root surface colonization. In accordance with the presence of these genes, DQS-4^T colonized rice (Oryza sativa) and Setaria viridis, where it was observed within the intercellular spaces and aerenchyma mainly of the roots. Although they promote the growth of grasses, the mechanism(s) of plant growth promotion by A. olearius strains is unknown, as the genomes of DQS-4^T and BH72 do not contain genes for indole acetic acid (IAA) synthesis nor phosphate solubilization. In spite of its original source, both the genome and behaviour of DQS-4^T suggest that it has the capacity to be an endophytic, nitrogen-fixing plant growth-promoting bacterium.

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

Isolation and Identification of Phyllospheric Bacteria Possessing Antimicrobial Activity from Astragalus obtusifolius, Prosopis juliflora, Xanthium strumarium and Hippocrepis unisiliqousa

BACKGROUND

The widespread utilization of antimicrobial compounds has caused emergence of resistant microorganisms in the world. Hence, the research to probe the products with antimicrobial features has led to finding natural habitats and discovering new pharmaceutical products.

METHODS

In this study, an attempt was made to explore the niche of novel habitat to isolate pyllospheric bacteria from the above ground parts (stems and leaves) of Astragalus obtusifolius, Prosopis juliflora, Xanthium strumarium, and Hippocrepis unisiliqousa to evaluate their antimicrobial features. The inhibitory effects of these strains on the growth of two fungi (Aspergillus niger, Aspergillus fumigatus), two yeasts (Saccharomyces cerevisiae, Candida albicans) and six bacteria (Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Bacillus subtilis, Salmonella typhi, Streptococcus pyogenes) were tested.

RESULTS

In total, 113 bacterial strains were isolated. Twenty five bacterial strains (B-1 to B-25) indicated promising antimicrobial (antibacterial and antifungal) activities against aforementioned pathogens. The identification of the bacterial strains was ascertained by morphological, physiological, biochemical tests and two strains with the strongest antimicrobial activities were further characterized based on 16s rRNA sequencing. These two strains were identified as Bacillus amyloliquefaciens.

CONCLUSION

Our results provide evidence that phyllospheric microorganisms are capable of producing some compounds with antimicrobial properties.

Diversity of Serratia marcescens Strains Associated with Cucurbit Yellow Vine Disease in Georgia

Cucurbit yellow vine disease (CYVD), caused by the squash bug (Anasa tristis)-transmitted bacterium Serratia marcescens, was first identified in Oklahoma and Texas in 1988 and in Georgia in 2012. S. marcescens is a highly diverse species found in many ecological niches. In previous studies, CYVD strains of S. marcescens formed a closely related group separate from non-CYVD strains based on biological and molecular characterization techniques. Multilocus sequence analysis (MLSA) of six housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using the BOX and ERIC primers were used to assess the genetic diversity of CYVD strains of S. marcescens collected in Georgia together with a strain from Texas and seven non-CYVD strains of S. marcescens. rep-PCR results revealed genetic diversity among CYVD strains while MLSA results showed a 100% similarity across the six loci for all but one of the CYVD strains, which differed at the icd locus by five polymorphisms. For both methods, CYVD strains clustered separately from nonplant-pathogenic S. marcescens strains and were most similar to a rice endophyte strain. One CYVD strain isolated from a squash bug shared genetic similarities with non-CYVD strains, and may be the result of a recombination event between CYVD and non-CYVD strains.

Chryseobacterium endophyticum sp. nov., isolated from a maize leaf

A Gram-stain-negative, aerobic, yellow-pigmented, flexirubin-producing, rod-shaped and endophytic bacterium, designated strain CC-YTH209^T, was isolated from a maize leaf and subjected to a taxonomic study. Strain CC-YTH209^T was found to grow at 15-40 °C (optimal 30 °C), at pH 6.0-8.0 (optimal pH 7.0) and in the presence of 0-2 % (optimal 1 %) (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain CC-YTH209^T appeared to belong to the genus Chryseobacterium within the class Flavobacteriia, and was closely related to Chryseobacterium rigui CJ16^T (97.5 % similarity) and Chryseobacterium taeanense PHA3-4^T (96.9 %). The level of DNA-DNA relatedness between strain CC-YTH209^T and Chryseobacterium rigui CJ16^T was 14.4 % (reciprocal, 13.0 %). Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-YTH209^T within the clade that accommodated Chryseobacterium species. The DNA G+C content was 37.2 mol%. Strain CC-YTH209^T contained menaquinone MK-6 as the predominant respiratory quinone and sym-homospermidine as the major polyamine. The major cellular fatty acids of the isolate were iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω6c/C16 : 1ω7c. The polar lipid profile comprised phosphatidylethanolamine and five aminolipids, three lipids, one glycolipid, one aminophospholipid and one phospholipid, which are presently uncharacterized. On the basis of evidence presented in this study, strain CC-YTH209^T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium endophyticum sp. nov. is proposed. The type strain is CC-YTH209^T (=BCRC 80938^T=JCM 31226^T).

A rhamnose-deficient lipopolysaccharide mutant of Rhizobium sp. IRBG74 is defective in root colonization and beneficial interactions with its flooding-tolerant hosts Sesbania cannabina and wetland rice

Rhizobium sp. IRBG74 develops a classical nitrogen-fixing symbiosis with the aquatic legume Sesbania cannabina (Retz.). It also promotes the growth of wetland rice (Oryza sativa L.), but little is known about the rhizobial determinants important for these interactions. In this study, we analyzed the colonization of S. cannabina and rice using a strain of Rhizobium sp. IRBG74 dually marked with β-glucuronidase and the green fluorescent protein. This bacterium colonized S. cannabina by crack entry and through root hair infection under flooded and non-flooded conditions, respectively. Rhizobium sp. IRBG74 colonized the surfaces of wetland rice roots, but also entered them at the base of lateral roots. It became endophytically established within intercellular spaces in the rice cortex, and intracellularly within epidermal and hypodermal cells. A mutant of Rhizobium sp. IRBG74 altered in the synthesis of the rhamnose-containing O-antigen exhibited significant defects, not only in nodulation and symbiotic nitrogen fixation with S. cannabina, but also in rice colonization and plant growth promotion. Supplementation with purified lipopolysaccharides from the wild-type strain, but not from the mutant, restored the beneficial colonization of rice roots, but not fully effective nodulation of S. cannabina Commonalities and differences in the rhizobial colonization of the roots of wetland legume and rice hosts are discussed.