Isolation, characterization and selection of bacterial isolates from a suppressive soil with beneficial traits to plants

Backgrounds This study focused on the characterization and selection of bacterial strains obtained from a suppressive soil displaying antifungal activity against the soilborne phytopathogenic fungi Rosellinia necatrix. Bacterial profile from this suppressive soil were first obtained by 16S rRNA gene sequencing, revealing a significant increase in the bacterial class Gammaproteobacteria, especially in some antagonistic representatives of Pseudomonas spp. Objectives To obtain and characterize a collection of 246 bacterial isolates obtained from this suppressive soil, in order to identify new strains with antifungal activity against fungal phytopathogens. Methods To obtain the bacterial collection, we performed an isolation on a selective medium for Pseudomonas-like microorganisms. Further characterization tests were used in order to analyse the bacterial collection, including identification of the general metabolic profile of glucose, the profiling of antifungals produced, including both the putative production of antifungal compounds and lytic exoenzymes, and the evaluation of traits related with beneficial effects on plants. Conclusions A final selection of representative strains resulted in antifungal isolates belonging to the genus Pseudomonas, but also some representatives of the genera Serratia and Stenotrophomonas. These selected strains were tested for plant protection by an in vivo experiment using avocado and wheat plants challenged by the pathogen R. necatrix, showing all of them an antifungal ability and plant disease protection. Pseudomonas-like strains isolated from suppressive soils constitute an excellent source for novel microbial biocontrol agents against soilborne fungal pathogens. This work was supported by grant AGL2014-52518-C2-1-R. Carmen Vida and Sandra Tienda are supported by a PhD fellowship from the FPI program of the Spanish Government.This work was supported by grant AGL2014-52518-C2-1-R. Carmen Vida and Sandra Tienda are supported by a PhD fellowship from the FPI program of the Spanish Government; Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

Background When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures. Results We investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature. Conclusions Our analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions

Bacterial wilt resistance in tomato, eggplant and pepper : genetic resources challenged with the multifaceted Ralstonia solanacearum species complex : [P3-49]

Bacterial wilt caused by strains belonging to the #Ralstonia solanacearum# species complex inflicts severe economic losses in many crops worldwide. Host resistance remains the most effective control strategy against the bacterial wilt. However, interactions among plant, strain and environment often result in overcoming resistance properties due to variation in strain pathogenicity and adaptation. To help breeders circumvent this problem, we assembled a worldwide collection of 30 accessions of Tomato, Eggplant and Pepper (Core-TEP) that are commonly used as sources of resistance to #R. solanacearum# or for mapping QTLs. The Core-TEP lines were challenged with a core collection of 12 pathogen strains (Core-Rs2) representing the phylogenetic diversity of #R. solanacearum#. To our knowledge, this is the first study that investigated bacterial wilt resistance in a set of worldwide genetic resources used as sources of resistance in three solanaceous species (tomato, eggplant, and pepper). Our results showed that none of the Core-TEP accessions, representative of the TEP genetic diversity for resistance, was resistant to all Core-Rs2 strains. Hence, none of them displayed universal resistance. We observed six wilt interaction phenotypes, from highly susceptible to highly resistant. Intermediate phenotype resulted from the ability of plants to tolerate latent infections, i.e. bacterial colonization of vascular elements with limited or no wilting. #R. solanacearum# strains exhibited specific patterns of interaction with Core-TEP accessions. Thanks to several similarities of virulence patterns between strains of Core-Rs2, we defined two working concepts associated with two levels of resolution of the interactions between strains and plant phenotypes. One concept, the "pathoprofile" is based on the interactions for the three solanaceae taken together, and the other, the pathotype is based on the interactions for each plant species taken separately. The 12 Core-Rs2 strains partitioned into four pathotypes on Pepper accessions, five pathotypes on Tomato, six pathotypes on Eggplant, and six pathoprofiles on the whole set of Core-TEP accessions. Neither pathotypes nor pathoprofiles were phylotype-specific. Pathoprofiles with high pathogenicity were mainly found in strains from phylotypes I, IIB and III. One pathoprofile included a strain that overcame almost all resistance sources. (Résumé d'auteur

No evidence for a culturable bacterial tetrodotoxin producer in Pleurobranchaea maculata (Gastropoda: Pleurobranchidae) and Stylochoplana sp. (Platyhelminthes: Polycladida)

Tetrodotoxin (TTX) is a potent neurotoxin found in the tissues of many taxonomically diverse organisms. Its origin has been the topic of much debate, with suggestions including endogenous production, acquisition through diet, and symbiotic bacterial synthesis. Bacterial production of TTX has been reported in isolates from marine biota, but at lower than expected concentrations. In this study, 102 strains were isolated from Pleurobranchaea maculata (Opisthobranchia) and Stylochoplana sp. (Platyhelminthes). Tetrodotoxin production was tested utilizing a recently developed sensitive method to detect the C9 base of TTX via liquid chromatography—mass spectrometry. Bacterial strains were characterized by sequencing a region of the 16S ribosomal RNA gene. To account for the possibility that TTX is produced by a consortium of bacteria, a series of experiments using marine broth spiked with various P. maculata tissues were undertaken. Sixteen unique strains from P. maculata and one from Stylochoplana sp. were isolated, representing eight different genera; Pseudomonadales, Actinomycetales, Oceanospirillales, Thiotrichales, Rhodobacterales, Sphingomonadales, Bacillales, and Vibrionales. Molecular fingerprinting of bacterial communities from broth experiments showed little change over the first four days. No C9 base or TTX was detected in isolates or broth experiments (past day 0), suggesting a culturable microbial source of TTX in P. maculata and Stylochoplana sp. is unlikely

Multistrain models predict sequential multidrug treatment strategies to result in less antimicrobial resistance than combination treatment

Background Combination treatment is increasingly used to fight infections caused by bacteria resistant to two or more antimicrobials. While multiple studies have evaluated treatment strategies to minimize the emergence of resistant strains for single antimicrobial treatment, fewer studies have considered combination treatments. The current study modeled bacterial growth in the intestine of pigs after intramuscular combination treatment (i.e. using two antibiotics simultaneously) and sequential treatments (i.e. alternating between two antibiotics) in order to identify the factors that favor the sensitive fraction of the commensal flora. Growth parameters for competing bacterial strains were estimated from the combined in vitro pharmacodynamic effect of two antimicrobials using the relationship between concentration and net bacterial growth rate. Predictions of in vivo bacterial growth were generated by a mathematical model of the competitive growth of multiple strains of Escherichia coli. Results Simulation studies showed that sequential use of tetracycline and ampicillin reduced the level of double resistance, when compared to the combination treatment. The effect of the cycling frequency (how frequently antibiotics are alternated in a sequential treatment) of the two drugs was dependent upon the order in which the two drugs were used. Conclusion Sequential treatment was more effective in preventing the growth of resistant strains when compared to the combination treatment. The cycling frequency did not play a role in suppressing the growth of resistant strains, but the specific order of the two antimicrobials did. Predictions made from the study could be used to redesign multidrug treatment strategies not only for intramuscular treatment in pigs, but also for other dosing routes

Bacillus based biocontrol on Brassica

Many bacterial strains have been shown to mediate protection to biotic stress and promote growth of plants. Different bacteria can mediate protection in different ways e.g. by inhibition, competition or increasing plant resistance. Examples of bacteria that mediate protection to plants include different Pseudomonas, Serratia and Bacillus strains. Bacillus strains have one major advantage toward other biocontrol strains and that is the ability to form spores that are resilient against chemicals and mechanical damage. I have studied the effect of four closely related Bacillus strains on plants in two different projects, one concerned with oilseed rape (Brassica napus) and the other using Arabidopsis thaliana to allow mechanistic studies of the interaction. The bacterial strains are all classified as Bacillus amyloliquefaciens. These bacterial strains have been tested for phenological effects on plants and for plant protection towards pathogens like Alternaria brassicae, Botrytis cinerea, Leptosphaeria maculans, and Verticillium longisporum. Production of antifungal compounds by the strains and the effects on the different pathogens were investigated. Two potential candidates for biocontrol were identified. Both Bacillus strains were found to provide significant protection of oilseed rape against the four pathogens. The effects of Bacillus treatment on the B. napus transcriptome were studied using the cDNA-AFLP technique. Bacillus priming had strong systemic effects on leaf transcripts but small effects on roots. This far 65 differentially expressed plant genes have been identified due to Bacillus treatment, of which many seem related to metabolism. The effect of Bacillus seed treatment has also been studied on Arabidopsis. Significant protection was achieved also here using the same two strains toward Alternaria and Leptosphaeria as well as Pseudomonas syringae as pathogens. Arabidopsis signalling mutant studies showed that functional jasmonic acid (JA) and ethylene (Et) signalling as well as Npr1 were needed for Bacillus biocontrol. Expression levels of marker genes depending on these signalling pathways showed no increase upon Bacillus treatment, while an increase of the JA dependent marker occurred after Bacillus treated plants were infected by P. syringae. Altogether, Bacillus primed biocontrol seems to be based on induced systemic resistance (ISR)

Phylogenic distribution of the large 55 rRNA from Halococcus morrhuae

Sequence characterizations of bacterial ribonucleic acids are discussed. The phylogeny of various bacterial strains based upon RNA data is presented

Combined endophytic inoculants enhance nickel phytoextraction from serpentine soil in the hyperaccumulator Noccaea caerulescens

This study assesses the effects of specific bacterial endophytes on the phytoextraction capacity of the Ni-hyperaccumulator Noccaea caerulescens, spontaneously growing in a serpentine soil environment. Five metal-tolerant endophytes had already been selected for their high Ni tolerance (6 mM) and plant growth promoting ability. Here we demonstrate that individual bacterial inoculation is ineffective in enhancing Ni translocation and growth of N. caerulescens in serpentine soil, except for specific strains Ncr-1 and Ncr-8, belonging to the Arthrobacter and Microbacterium genera, which showed the highest indole acetic acid production and 1-aminocyclopropane-1-carboxylic acid-deaminase activity. Ncr-1 and Ncr-8 co-inoculation was even more efficient in promoting plant growth, soil Ni removal, and translocation of Ni, together with that of Fe, Co, and Cu. Bacteria of both strains densely colonized the root surfaces and intercellular spaces of leaf epidermal tissue. These two bacterial strains also turned out to stimulate root length, shoot biomass, and Ni uptake in Arabidopsis thaliana grown in MS agar medium supplemented with Ni. It is concluded that adaptation of N. caerulescens in highly Ni-contaminated serpentine soil can be enhanced by an integrated community of bacterial endophytes rather than by single strains; of the former, Arthrobacter and Microbacterium may be useful candidates for future phytoremediation trials in multiple metal-contaminated sites, with possible extension to non-hyperaccumulator plants

Genome sequences of 15 Gardnerella vaginalis strains isolated from the vaginas of women with and without bacterial vaginosis

Gardnerella vaginalis is a predominant species in bacterial vaginosis, a dysbiosis of the vagina that is associated with adverse health outcomes, including preterm birth. Here, we present the draft genome sequences of 15 Gardnerella vaginalis strains (now available through BEI Resources) isolated from women with and without bacterial vaginosis