Publications

4857

A taxonomic study was conducted on four bacterial strains isolated from the soil of a coking plant. Phylogenetic analysis showed that the four strains belonged to three families: Comamonadaceae, Micrococcaceae and Roseiarcaceae. Identification of the 16S rRNA gene exhibited that their sequence similarities were between 94.96 and 98.98% when compared to known and validly nominated species. Their genomes ranged from 3.4 to 7.2 Mb, with DNA G+C molar contents varying from 62.3 to 67.2%. The average nucleotide identities ranged from 71.4 to 92.3%, and digital DNA–DNA hybridization values were 19.7–47.0% when comparing them with closely related type species, supporting the classification of these four strains. Functional analysis demonstrated that strain H3Y2-7T was robustly resistant to chromate (VI) and arsenite (III) and was able to grow on aromatic compounds including naphthalene as carbon sources even in the presence of chromate (VI). These features reflect its ability to treat combined pollutants and adapt to a polluted environment. Based on the analysis of polyphasic taxonomy, we propose the four bacterial strains representing novel species, namely Curvibacter soli sp. nov. (type strain H39-3-26T=JCM 36178T=CGMCC 1.61344T), Extensimonas soli sp. nov. (type strain H3M7-6T=JCM 36176T=CGMCC 1.61336T), Pseudarthrobacter naphthalenicus sp. nov. (type strain H3Y2-7T=JCM 36482T=CGMCC 1.61323T) and Terripilifer ovatus gen. nov., sp. nov. (type strain H3SJ34-1T=JCM 36465T=CGMCC 1.61333T).

A motile, rod-shaped and anaerobic strain WK13T was isolated from a secondary root canal infection of a human tooth. WK13T cells were Gram-stain-negative, catalase-positive and oxidase-negative. The major fatty acids (≥ 5.0%) were C16 : 0, C18 : 0, C16 : 1  ω7c, C18 : 1  ω9c and C18 : 2  ω6,9c. The DNA G+C content was 57.94 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol, phosphatidylcholine and lysophosphatidylcholine. There were no respiratory quinones detectable. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WK13T belongs to the class Betaproteobacteria. WK13T showed a 93.6% and 93.5% 16S rRNA gene sequence similarity to the most closely related cultured species, Propionivibrio pelophilus strain DSM 12018T and Propionivibrio dicarboxylicus strain DSM 5885T, respectively. On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class Betaproteobacteria, for which we propose the name Dentiradicibacter hellwigii gen. nov., sp. nov. The type strain is WK13T (=DSM 112713T=NCTC 14938T).

This study describes a Gram-stain-negative, rod-shaped, facultatively anaerobic bacterial species isolated from the octocoral Litophyton sp. inhabiting the live coral aquarium at Oceanário de Lisboa in Portugal. Four strains, NE35, NE40T, NE41 and NE43, were classified into the genus Endozoicomonas by means of 16S rRNA gene and whole-genome sequence homologies. We then performed phylogenetic, phylogenomic and biochemical analyses to examine their novel species status within the Endozoicomonas genus, based on comparisons with the designated novel type strain NE40T. The closest 16S rRNA gene relatives to strain NE40T are Endozoicomonas montiporae CL-33T (98.2%), Endozoicomonas euniceicola EF212T (97.6%) and Endozoicomonas gorgoniicola PS125T (97.2%). The four strains show genome-wide average nucleotide identity scores above the species level cut-off (95%) with one another and below the cut-off with all Endozoicomonas type strains with publicly available genomes. Digital DNA–DNA hybridization further supported the classification of the strains as a novel species, showing values below 70% when compared with other Endozoicomonas type strains. The DNA G+C content of NE40T was 49.0 mol%, and its genome size was 5.45 Mb. Strain NE40T grows from 15 to 37 °C, with 1–5% (w/v) NaCl, and between pH 6.0 and 8.0 in marine broth and shows optimal growth at 28–32 °C, 2–3% NaCl and pH 7.0–8.0. The predominant cellular fatty acids are summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), C16 :0 and C14 :0. Strain NE40T presents oxidase, catalase and β-galactosidase activities and can reduce nitrates to nitrites and degrade cellulose, chitin, agarose and xylan. Based on the polyphasic approach employed in this study, we propose the novel species name Endozoicomonas lisbonensis sp. nov. (type strain NE40T=DSM 118084T=UCCCB 212T).

Understanding the characteristics of microbes during long-term space missions is essential for safeguarding the health of astronauts and maintaining the functionality of spacecraft. In this study, a Gram-positive, aerobic, spore-forming, rod-shaped strain JL1B1071T was isolated from the surface of hardware on the China Space Station. This strain belongs to the genus Niallia, with its closest relative being Niallia circulans ATCC 4513T. The genome of JL1B1071T is 5 166 230 bp in size, with a G+C content of 35.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between JL1B1071T and N. circulans ATCC 4513T are 83.3 and 27.5%, respectively, both below the recommended thresholds for species delineation. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0. The major quinone was menaquinone-7 (MK-7). Notably, strain JL1B1071T demonstrates a unique ability to hydrolyse gelatin, suggesting that it can utilize gelatin as a substrate in nutrient-limited environments. Genomic analysis of JL1B1071T revealed two conserved signature indels in the GAF domain-containing protein and DNA ligase D protein, which are specific to the genus Niallia. Additionally, structural and functional differences in proteins BshB1 and SplA were identified, which may enhance biofilm formation, oxidative stress response and radiation damage repair, thereby aiding its survival in the space environment. Based on phenotypic, physiological and chemotaxonomic characteristics, as well as genome annotation, strain JL1B1071T was considered a novel species within the genus Niallia and is proposed to be named Niallia tiangongensis sp. nov. The type strain is JL1B1071T (=GDMCC 1.4642=KCTC 43715).

The occurrence of ‘Candidatus Liberibacter’ spp. and ‘Ca. Phytoplasma’ spp. associated with blotchy mottle symptoms poses challenges to huanglongbing (HLB) diagnosis using molecular techniques. The ability to detect multiple targets simultaneously and specifically is a key aspect met by quantitative PCR (qPCR). A set of primers and hydrolysis probes useful in either single or multiplex reactions for the detection and quantification of HLB-associated bacteria were developed. Sequences from conserved genes of the ribosomal proteins for Liberibacter and phytoplasma circumvent the lack of specificity and cross-reactivity problems related to 16Sr DNA gene amplification, allowing precise and specific detection of HLB-associated bacteria in citrus and in the Liberibacter vector, Diaphorina citri. The triplex reaction exhibited high quality and precision as a robust tool for quantifying ‘Ca. L. asiaticus’ (CLas), ‘Ca. L. americanus’ (CLam), and 16Sr IX phytoplasma. Triplex qPCR showed consistent results and comparable sensitivity to the ribonuclease reductase test, although quantification cycle (Cq) values were higher when compared with 16SrDNA qPCR. Detection tests using field samples indicate that the qPCR triplex can identify HLB-associated bacteria in samples with varying levels of symptoms, ranging from typical to asymptomatic. Assessment of field samples from growers indicated more than 78.6% had Cq lower than 35.0, below the cutoff established for qPCR reactions used in this work. qPCR triplex is a safe, specific, and sufficiently sensitive technique for detecting CLas, CLam, and 16Sr IX phytoplasma simultaneously, in both citrus and D. citri samples. Its application is of importance in assisting growers in making decisions for HLB management.

Abstract In 2022, EFSA was mandated by the European Commission's Directorate‐General for Health and Food Safety (M‐2022‐00070) to provide technical assistance on the list of Union quarantine pests qualifying as priority pests, as specified in Article 6(2) of Regulation (EU) 2016/2031 on protective measures against plant pests. As part of Task C, EFSA conducted comprehensive expert knowledge elicitations for candidate priority pests on the lag period, rate of expansion and impact on production (yield and quality losses) and the environment. This report provides the rationale for the dataset on the three Candidatus Liberibacter species associated with citrus greening disease, delivered to the European Commission's Joint Research Centre, to feed into the Impact Indicator for Priority Pest (I2P2) model and complete the pest prioritisation ranking exercise.

AbstractBACKGROUNDThe brown marmorated stink bug Halyomorpha halys has become an invasive insect pest of many crops. A promising control strategy to manage the proliferation of H. halys is based on the suppression of its obligate and vertically transmitted uncultivated symbiotic bacterium Candidatus Pantoea carbekii through surface‐sterilization of H. halys eggs. Indeed, the application of antimicrobial formulations on the eggs of H. halys could cause mortality of endosymbiont and consequently of newly emerged nymphs.In this study, a microbial live/dead assay was applied directly on H. halys eggs to evaluate Ca. P. carbekii loss of viability after treatments with seven commercial formulations including fungicides (copper hydroxide, sulphur, sweet orange essential oil) and plant biostimulants (flavonoids and chestnut tannin extract) compared with two disinfectants for civil and industrial use (sodium hypochlorite/hydrated sodium/tetraborate decahydrate and peracetic acid/hydrogen peroxide). Impact of mode of application was also evaluated, as surface treatment of egg masses was performed through spraying and dipping in laboratory conditions. Antimicrobial activity data were finally complemented with observations of egg hatching and vitality of the nymphs.RESULTSThe optimization of live/dead staining is useful for evaluating Ca. P. carbekii mortality directly on eggs, providing a rapid and reliable culture‐independent approach. Sodium hypochlorite, copper, sulphur, tannins and sweet orange essential oil showed an antimicrobial effect against Ca. P. carbekii and a H. halys egg hatching reduction and nymph's vitality.CONCLUSIONSThe antimicrobial and insecticidal effects of these commercial products should be further studied to assess their in‐field efficiency as well as the impact of these substances on non‐target organisms. The approach followed in this study could be considered a robust pipeline of analyses to evaluate the effectiveness of antimicrobial eco‐friendly compounds in symbiotic control of H. halys. © 2024 Society of Chemical Industry.