Frateuria defendens sp. nov., bacterium isolated from the yellows grapevine's disease vector Hyalesthes obsoletus

Investigating the lignocellulolytic gut microbiome of huhu grubs (Prionoplus reticularis) using defined diets and dietary switch

The huhu beetle (Prionoplus reticularis) is the largest endemic beetle found throughout Aotearoa New Zealand, and is characterised by feeding on wood during its larval stage. It has been hypothesised that its gut microbiome plays a fundamental role in the degradation of wood. To explore this idea we examined the fungal and bacterial community composition of huhu grubs' frass, using amplicon sequencing. Grubs were reared on an exclusive diet of either a predominantly cellulose source (cotton) or lignocellulose source (pine) for 4 months; subsequently a diet switch was performed and the grubs were grown for another 4 months. The fungal community of cellulose-reared huhu grubs was abundant in potential cellulose degraders, contrasting with the community of lignocellulose-reared grubs, which showed abundant potential soft rot fungi, yeasts, and hemicellulose and cellulose degraders. Cellulose-reared grubs showed a less diverse fungal community, however, diet switch from cellulose to lignocellulose resulted in a change in community composition that showed grubs were still capable of utilising this substrate. Conversely, diet seemed to have a limited influence on huhu grub gut bacterial communities.

Frateuria soli sp. nov. and Frateuria edaphi sp. nov., isolated from greenhouse soil

Two bacterial strains, designated 5GH9-11^T and 5GH9-34^T, were isolated from greenhouse soil sampled in Wanju-gun, Jeollabuk-do, Republic of Korea. Both strains formed yellow colonies and were aerobic, rod-shaped and flagellated. The 16S rRNA gene sequence similarity between 5GH9-11^T and 5GH9-34^T was 98.6 %. Strain 5GH9-11^T showed the highest sequence similarities to Dyella thiooxydans ATSB10^T (98.1 %) and Frateuria aurantia DSM 6220^T (97.7 %) while strain 5GH9-34^T revealed the highest sequence similarity to F. aurantia DSM 6220^T (98.3 %) and D. thiooxydans ATSB10^T (98.3 %). Phylogenetic analysis on the basis of the 16S rRNA gene sequence showed that strains 5GH9-11^T and 5GH9-34^T formed a robust cluster with Frateuria flava MAH-13^T and Frateuria terrea NBRC 104236^T. The phylogenomic tree also showed that strains 5GH9-11^T and 5GH9-34^T formed a robust cluster with F. terrea DSM 26515^T and F. flava MAH-13^T. Strain 5GH9-11^T showed the highest orthologous average nucleotide identity (OrthoANI; 88.5 %) and digital DNA-DNA hybridization (dDDH) values (35.5 %) with F. flava MAH-13^T, and strain 5GH9-34^T revealed highest OrthoANI (88.1 %) and dDDH (34.2 %) values with F. flava MAH-13^T. The orthoANI and dDDH values between strain 5GH9-11^T and 5GH9-34^T were 87.7 and 33.9 %, respectively. Their major respiratory quinone was ubiquinone 8, and the major cellular fatty acids were iso-C_16 : 0, summed feature 9 (iso-C_17 : 1 ω9c and/or C_16 : 0 10-methyl) and iso-C_15 : 0. The major polar lipids of both strains were composed of large or moderate amounts of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and an unidentified aminophospholipid. Based on these data, strains 5GH9-11^T and 5GH9-34^T should represent two independent novel species of Frateuria, for which the names Frateuria soli sp. nov. (type strain 5GH9-11^T=KACC 16943^T=JCM 35197^T) and Frateuria edaphi sp. nov. (type strain 5GH9-34^T=KACC 16945^T=JCM 35198^T) are proposed.

Evaluation of the biocontrol activity of Frateuria defendens-derived metabolites against mollicutes

Frateuria defendens is a candidate biocontrol agent that has been shown to reduce phytoplasma-related disease symptoms in grapevines and periwinkle plants. While a crude filtrate prepared from F. defendens can inhibit mollicute growth, the specific growth parameters for this bacterium, necessary to enhance this protective inhibitory response, remain unknown. Moreover, the separation of filtrate preparations from bacterial cells via centrifugation and filtration is laborious and time-consuming. As such, the present study was conducted to define the optimal growth conditions associated with maximal inhibitory activity of F. defendens and to establish a better approach to separating these bacterial cells from their secreted metabolites. To conduct these analyses, F. defendens was cultured in a range of media types, while associated inhibitory effects were tested in vitro using Spiroplasma melliferum as a model mollicute bacterium, and in planta using phytoplasma-infected periwinkle plantlets. These analyses revealed F. defendens growth patterns change based upon media composition, with filtrates prepared from a specific rich medium (S-medium) exhibiting beneficial activities, including the inhibition of S. melliferum and enhanced plant growth. When F. defendens cells were grown within semi-permeable, membrane-coated Small Bioreactor Platform (SBP) capsules, they could be more readily separated from the secreted metabolite fraction, obviating the need for filtration and/or centrifugation. This study is the first to have reported the use of SBP capsules to separate bacterial cells from their secreted metabolites under sterile conditions while retaining the ability of these metabolites to inhibit S. melliferum growth and to benefit the host plant. The results highlight promising new approaches to the effective biocontrol of phytoplasma-driven diseases in grapevines and other economically important plant species.

Frateuria flava sp. nov., isolated from soil

A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAH-13^T, was isolated from a soil sample. The colonies were observed to be yellow-coloured, smooth, spherical and 1.8-3.0 mm in diameter when grown on nutrient agar medium for 2 days. Strain MAH-13^T was found to be able to grow at 20-40 °C, at pH 5.0-10.0 and with 0-1.0% NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria-Bertani agar, nutrient agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of casein, starch, DNA and l-tyrosine. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Frateuria and to be closely related to Frateuria terrea DSM 26515^T (98.2% similarity), Dyella thiooxydans ATSB10^T (98.2 %), Frateuria defendens HyOG^T (97.9 %), Rhodanobacter glycinis MO64^T (97.8 %) and Frateuria aurantia DSM 6220^T (97.8 %). The novel strain MAH-13^T has a draft genome size of 3 682 848 bp (40 contigs), annotated with 3172 protein-coding genes, 49 tRNA genes and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAH-13^T and five closely related type strains were in the range of 73.7-85.5 % and 20.7-30.1%, respectively. The genomic DNA G+C content was determined to be 68.0 mol%. The predominant isoprenoid quinone was ubiquinone 8. The major fatty acids were identified as iso-C_15:0, iso-C_16:0 and summed feature 9 (iso-C_17 : 1 ω9c and/or C_16:0 10-methyl). On the basis of dDDH and ANI values, genotypic analysis, and chemotaxonomic and physiological data, strain MAH-13^T represents a novel species within the genus Frateuria, for which the name Frateuria flava sp. nov. is proposed, with MAH-13^T (=KACC 19743^T=CGMCC 1.13655^T) as the type strain.

Antimicrobial Activity of Metabolites Secreted by the Endophytic Bacterium Frateuria defendens

Candidatus Phytoplasma, the causative agent of yellows disease, inflicts substantial damage on several hundred plant species including perennials and annual plants. The endophytic bacterium Frateuria defendens reduces the symptoms of yellows disease in a number of agricultural crops. One possible mode of action is that the bacterium secretes antimicrobial metabolites. To test this hypothesis, the substances secreted by the endophyte during 10 days of growth in an artificial medium were identified by GC-MS (gas chromatography-mass spectrometry). Synthetic analogues to these substances were then used on periwinkle, a nurse culture plant infected by phytoplasma. Phytoplasma quantities were evaluated by quantitative PCR, and disease symptoms were monitored and recorded. It was found that specific compounds identified by the biochemical analysis caused a significant reduction in both the titer of phytoplasma and the disease symptoms in periwinkle when compared to untreated infected plants. Further research is required to examine the potential of these compounds as an effective treatment against yellows disease.