Trinickia dabaoshanensis sp. nov., a new name for a lost species Abstract “Burkholderia dabaoshanensis” was described in 2012. Although the name was effectively published, it could not be validly published, because the description provided in the original paper did not comply with the Rule 27 (2) (c) of the Bacterial Code. The Code requiresthat the properties of the taxon form part of the protologue. As the name of this species does not have standing in nomenclature, the recently published new combination Trinickia dabaoshanensis could also not be validly published. The current proposal attempts to rectify the situation by providing the information required to meet the criteria stipulated in Rule 27 for valid publication.

Bacteriocinogenic Lactococcus lactis subsp. lactis 3MT isolated from freshwater Nile Tilapia: isolation, safety traits, bacteriocin characterisation, and application for biopreservation in fish pâté Abstract This work was aimed to screen bacteriocin-producing LAB from freshwater fish, select a prominent strain and evaluate its safety, characterise the bacteriocin produced, and evaluate its potential to be used as biopreservatives. Isolate 3MT showed the ability to produce bacteriocin-like substances and was identified as Lactococcus lactis subsp. lactis. This strain proved to be free from virulence factors as well as biogenic amine production and antibiotic resistance patterns. The bacteriocin produced displayed high resistance to heat, pH, detergents, and its partial purification led to a 4.35-fold increase in specific activity. Moreover, this bacteriocin showed the ability to inhibit the growth of Vibrio sp. 1T1 in fish pâté stored at 10 °C for 20 days, without altering its sensory properties. The bacteriocin can be used successfully as a preservative to improve the hygienic quality and enhance the shelf life of fish paté in particular and food products in general. Lactococcus lactis subsp. lactis strain 3MT can also be safely used as a protective culture.

Genomic analysis of a novel Rhodococcus ( Prescottella ) equi isolate from a bovine host Abstract Rhodococcus (Prescottella) equi causes pneumonia-like infections in foals with high mortality rates and can also infect a number of other animals. R. equi is also emerging as an opportunistic human pathogen. In this study, we have sequenced the genome of a novel R. equi isolate, B0269, isolated from the faeces of a bovine host. Comparative genomic analyses with seven other published R. equi genomes, including those from equine or human sources, revealed a pangenome comprising of 6876 genes with 4141 genes in the core genome. Two hundred and 75 genes were specific to the bovine isolate, mostly encoding hypothetical proteins of unknown function. However, these genes include four copies of terA and five copies of terD genes that may be involved in responding to chemical stress. Virulence characteristics in R. equi are associated with the presence of large plasmids carrying a pathogenicity island, including genes from the vap multigene family. A BLAST search of the protein sequences from known virulence-associated plasmids (pVAPA, pVAPB and pVAPN) revealed a similar plasmid backbone on two contigs in bovine isolate B0269; however, no homologues of the main virulence-associated genes, vapA, vapB or vapN, were identified. In summary, this study confirms that R. equi genomes are highly conserved and reports the presence of an apparently novel plasmid in the bovine isolate B0269 that needs further characterisation to understand its potential involvement in virulence properties.

Isolation and identification of the Raoultella ornithinolytica -ZK4 degrading pyrethroid pesticides within soil sediment from an abandoned pesticide plant Abstract We examined how Raoultella ornithinolytica-ZK4 degraded pyrethroid pesticides within soil sediment from an abandoned pesticide plant. Lambda-cypermethrin and deltamethrin are two pyrethroid insecticides with high insecticidal activity and a wide range of applications. However, their increased use has raised concerns regarding toxicity and accumulation. We isolated a strain of ZK4 (Raoultella ornithinolytica-ZK4) from soil taken from a channel that surrounded a pesticide plant. We used enzyme localization to study degrading bacteria ZK4. The ZK4 strain underwent intracellular enzyme degradation. The degradation rates of lambda-cyhalothrin and deltamethrin were 55% and 53%, respectively. The optimum pH of the two kinds of pyrethroids in ZK4 was 6.5, and their optimum temperature was 37 °C. The intracellular degradation of the crude enzyme produced by the ZK4 strain had a pH of 6.0–8.0 and a temperature of 20–42 °C. The ZK4 strain genome contained 5310 genes with a total length of 4,864,494 bp. Sugar metabolism and exogenous chemical metabolism accounted for the largest proportion of metabolic activities. We used the clusters of orthologous groups (COG) alignment and found numbers for 4686 protein sequences, accounting for 88.25% of the total predicted protein. ZK4 degraded lambda-cyhalothrin and deltamethrin, and may serve as a reference for the preparation of future degrading microbial agents to assist with environmental restoration efforts.

Proteomics-based discrimination of differentially expressed proteins in antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium, Klebsiella pneumoniae , and Staphylococcus aureus Abstract This study was designed to compare the differentially expressed proteins between antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium, Klebsiella pneumonia, and Staphylococcus aureus. The susceptibilities of wild-type (WT), ciprofloxacin (CIP) and/or oxacillin (OXA)-induced, and clinically isolated resistant (CCARM) S. Typhimurium (STWT, STCIP, and STCCARM), K. pneumoniae (KPWT, KPCIP, and KPCCARM), and S. aureus (SAWT, SACIP, SAOXA, and SACCARM) to antibiotics were determined using broth microdilution assay. STCIP was highly resistant to piperacillin (MIC > 512 μg/ml), KPCIP was resistant to chloramphenicol (128 μg/ml) and norfloxacin (16 μg/ml), SACIP was resistant to fluoroquinolones (32 μg/ml), and SAOXA was resistant to ceftriaxone (32 μg/ml). The protein profiles of antibiotic-sensitive and antibiotic-resistant strains were determined using 2-DE analysis followed by LC–MS/MS. The commonly expressed proteins of STWT–STCIP, STWT–STCCARM, KPWT–KPCIP, KPWT–KPCCARM, SAWT–SACIP, SAWT–SAOXA, and SAWT–SACCARM were 763, 677, 677, 469, 261, 259, and 226, respectively. The unique protein spots were observed 57 (6.5%), 80 (11.5%), and 68 (13.9%), respectively, for STCCARM, KPCCARM, and SACCARM. The highly up-regulated protein, PrsA (10-fold), was observed in STCIP resistant to ciprofloxacin (128-fold), levofloxacin (32-fold), norfloxacin (64-fold), and piperacillin (> 16-fold). The up-regulated proteins (YadC, FimA, and RplB) in KPCIP resistant to chloramphenicol (> 32-fold), ciprofloxacin (32-fold), levofloxacin (6-fold), norfloxacin (128-fold), and sparfloxacin (64-fold). AcrB and RpoB were up-regulated in SACCARM resistant to multiple antibiotics. The differentially expressed proteins were related to the antibiotic resistance of STWT, STCIP, STCCARM, KPWT, KPCIP, KPCCARM, SAWT, SACIP, SAOXA, and SACCARM. The resistance-associated proteins could be useful biomarkers for detecting antibiotic-resistant pathogens.

Diversity and nodulation effectiveness of rhizobia and mycorrhizal presence in climbing dry beans grown in Prespa lakes plain, Greece Abstract The Prespa lakes plain is an isolated area where about 1000 ha are seeded to Phaseolus vulgaris L. and Phaseolus coccineus L. Nodulation, arbuscular mycorrhizal fungal (AMF) presence and the genetic diversity of rhizobia were evaluated by 16S-ITS-23S-RFLP patterns and by sequencing. The bean rhizobial population in the region was diverse, despite its geographic isolation. No biogeographic relationships were detected, apart from a Rhizobium tropici-related strain that originated from an acidic soil. No clear pattern was detected in clustering with bean species and all isolates formed nodules with both bean species. Most strains were related to Rhizobium leguminosarum and a number of isolates were falling outside the already characterized species of genus Rhizobium. Application of heavy fertilization has resulted in high soil N and P levels, which most likely reduced nodulation and AMF spore presence. However, considerable AMF root length colonization was found in most of the fields.

Investigation of the effect of different environmental conditions on biofilm structure of Salmonella enterica serotype Virchow via FTIR spectroscopy Abstract This study aims to describe the content of polymeric matrix components under different incubation temperatures and pH levels. Optimal biofilm production of 15 S. Virchow isolates occurred following the incubation in LB−NaCl for 72 h, at pH 6.6 and 20 °C. The expression of csgA, csgD, adrA and bcsA genes at 20 °C, 25 °C and 30 °C in S. Virchow DMC18 was analyzed, and it was discovered that the maximum production of cellulose and curli fimbriae occurred at 20 °C. The physical characteristics of pellicle structure of S. Virchow DMC18 was determined as rigid at 20 °C, while becoming fragile at higher temperatures. FTIR analyses confirmed the obtained molecular findings. The intensities of the 16 different peaks originating from carbohydrate, protein, and nucleic acid in the spectra of biofilm samples significantly diminished (p < 0.05) with the increasing temperature. The highest intensities of lipids and carbohydrates were observed at 20 °C indicating the changes in cell surface properties.

Response of soil bacterial community structure to different reclamation years of abandoned salinized farmland in arid China Abstract In recent years, understanding the impact of reclamation of abandoned salinized field on microbial community structure is of great importance for ecosystem restoration in arid regions. The aim of this work was to investigate the effects of reclamation years on soil properties, bacterial community composition and diversity based on field sampling and llumina MiSeq sequencing. The five reclamation years are: unreclaimed salinized and reclaimed (1, 5, 10, and 15 years) fields. The results showed soil properties are significantly altered by abandoned salinized field. In particular, reclamation significantly decreased soil electrical conductivity, Cl−, SO42−, Na+, and Ca2+, during 5 years of reclamation. In addition, reclamation increased the richness and diversity of the bacterial community, except for the 1-year field soils. There was a large difference in the abundant bacterial phyla in 1-year field soils compared with other field soils. Proteobacteria were the most abundant in all of the field soils. Principal coordinates analysis showed that the abandoned and 1-year field soils exhibited specific differences in bacterial community structures compared with other field soils. Statistical analyses showed that available phosphorus, SO42−, Mg2+, and Ca2+ were the main physicochemical properties affecting the soil bacterial communities. Overall, reclamation improved soil physicochemical properties and altered the structure and composition of soil bacterial communities compared with unreclaimed salinized soil.

First insights into salt tolerance improvement of Stevia by plant growth-promoting Streptomyces species Abstract The present study aimed to investigate the potential of plant growth-promoting rhizobacteria (PGPR) to improve the salt stress and alleviate its impact on Stevia crop plant under different levels of salt concentration. Two Streptomyces spp. isolated from the rhizosphere of halophytic plants (Cucumis sativus L. and Salicornia europaea L.) have shown potential for plant growth promotion in Stevia plant. The streptomycetes isolates were identified by classical microbiological techniques and partial sequencing of 16S rRNA gene as Streptomyces variabilis (4NC) and S. fradiae (8PK). The results have shown that inoculation of Stevia plant by these isolates has enhanced plant growth parameters under applied salt stress. Moreover, total cellular proteins were extracted from the two Streptomyces isolates and SDS-PAGE technique was conducted. Mass spectrometric analysis has identified unique polypeptide of the elongation factor thermos unstable (EF-Tu) indicating the elevation of ribosomal RNA and ribosomal protein genes transcription. On the same context, alleviation of salt stress in Stevia plants inoculated with the two Streptomyces isolates has potentially promoted the accumulation of the major pronounced RuBisCO large subunit protein band detected approximately at 53 kDa. These results may give novel insights and accretion our understanding of salinity tolerance mechanisms using PGP streptomycetes to develop resistant sugar crops of highly important economic value. This study has presented the integration of microbiological, biochemical, and molecular techniques to evaluate the effect of salt stress and to assess the level of stress amelioration using PGPR on proteostasis of sugar crops in Egypt.

Construction and in vitro characterisation of aroA defective ( aroA Δ) mutant Salmonella Infantis Abstract Poultry vaccine programs are important for control of Salmonella infections. Although there are vaccines for Salmonella Enteritidis, Salmonella Typhimurium and Salmonella Typhi, there are no vaccines for Salmonella Infantis which has an increased rate in the world. In this study, it was aimed to generate aroA gene deleted mutant bacteria for the constitution of S. Infantis vaccine prototype and the in vitro characterisation of this bacterium. S. Infantis auxotrophic mutant which has a block at any step of chorismate pathway has been constituted for the first time in the world and it was determined that this bacterium gets susceptibility against some antibiotics and antimicrobial substances. It was also observed that the adhesion and invasion rate of mutant strain tenfold decreased in comparison with the field strain in cell culture assay. It is understood from the in vitro evaluation of this mutant strain that it can be used as a vaccine candidate in further vaccine development studies.