Falsochrobactrum shanghaiense sp. nov., isolated from paddy soil and emended description of the genus Falsochrobactrum

Ochrobactrum chromiisoli sp. nov., Isolated from Chromium-Contaminated Soil

A Gram-stain-negative, non-spore-forming, flagellated, motile, aerobic, rod-shaped bacteria strain, designated YY2XT, was isolated from chromium-contaminated soil. Phylogenetic analysis based on 16S rRNA gene, recA gene, and whole genome indicated that the strain represented a new member of the genus Ochrobactrum, family Brucellaceae, class Alphaproteobacteria. The phylogenetic trees based on 16 s rRNA gene, revealed that Falsochrobactrum ovis DSM26720T (96.7%), Ochrobactrum gallinifaecis DSM15295T (96.2%), and Pseudochrobactrum asaccharolyticum DSM25619T (96.2%) are the most closely related phylogenetic neighbors of strain YY2XT. The draft genome of YY2XT was approximately 4,650,646 bp in size with a G + C content of 53.0 mol%. Average nucleotide identity and digital DNA-DNA hybridization values among strain YY2XT and the selected Brucellaceae species were 71.4-83.1% and 13.5-42.7%, which are below the recommended cut-off values for species delineation. Growth of strain YY2XT occurred within pH 5-10 (optimum, pH 7-8), 4 ℃-42 °C (optimum, 30 °C), and NaCl concentrations of 0.0-6.0% (optimum, 1.0%). Major quinone system was ubiquinone 10, the major fatty acids were C16:0, C18:1ω7c, and C16:1ω7c and the major polyamines were spermidine and putrescine. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, and four undefined lipids. On the basis of the phenotypic, genotypic and chemotaxonomic traits, strain YY2XT was considered to represent a novel species of the genus Ochrobactrum, for which the name Ochrobactrum chromiisoli sp. nov. is proposed. The type strain is YY2XT (= CCTCC AB 2023035T = JCM 36000T).

Falsochrobactrum tianjinense sp. nov., a New Petroleum-Degrading Bacteria Isolated from Oily Soils

The microbial remediation technology had great potential and attracted attention to total petroleum hydrocarbon pollution (TPH) remediation, but its efficiency is limited by its application in the field. In this study, a new TPH-degrading strain, TDYN1, was isolated from contaminated oil soil in Dagang Oilfield in Tianjin, China, and identified as Falsochrobactrum sp. by 16S rRNA sequence analysis. The physiological characterization of the isolate was observed. The orthogonal experiment was carried out for the optimum degradation conditions to improve its biodegradation efficiency. The strain was the gram-stain-negative, short rod-shaped, non-spore-forming, designated Falsochrobactrum tianjinense sp. nov (strain TDYN1); it had 3.51 Mb, and the DNA G + C content of the strain was 56.0%. The degradation rate of TDYN1 was 69.95% after 7 days of culture in optimal degradation conditions (temperature = 30 °C, pH = 8, salinity = 10 g L^-1, petroleum concentration = 1 g L^-1, and the inoculation dose of strain TDYN1 = 6%) and also reached more than 30% under other relatively extreme conditions. It suggested that the TDYN1 has great potential for TPH remediation in the soils of North China.

Brucella and Its Hidden Flagellar System

Brucella, a Gram-negative bacterium with a high infective capacity and a wide spectrum of hosts in the animal world, is found in terrestrial and marine mammals, as well as amphibians. This broad spectrum of hosts is closely related to the non-classical virulence factors that allow this pathogen to establish its replicative niche, colonizing epithelial and immune system cells, evading the host's defenses and defensive response. While motility is the primary role of the flagellum in most bacteria, in Brucella, the flagellum is involved in virulence, infectivity, cell growth, and biofilm formation, all of which are very important facts in a bacterium that to date has been described as a non-motile organism. Evidence of the expression of these flagellar proteins that are present in Brucella makes it possible to hypothesize certain evolutionary aspects as to where a free-living bacterium eventually acquired genetic material from environmental microorganisms, including flagellar genes, conferring on it the ability to reach other hosts (mammals), and, under selective pressure from the environment, can express these genes, helping it to evade the immune response. This review summarizes relevant aspects of the presence of flagellar proteins and puts into context their relevance in certain functions associated with the infective process. The study of these flagellar genes gives the genus Brucella a very high infectious versatility, placing it among the main organisms in urgent need of study, as it is linked to human health by direct contact with farm animals and by eventual transmission to the general population, where flagellar genes and proteins are of great relevance.

Performance and Microbial Community Analysis of an Electrobiofilm Reactor Enhanced by Ferrous-EDTA

The biological reduction of ferrous ethylenediaminetetraacetic acid (EDTA-Fe^II-NO and EDTA-Fe^III) is an important process in the integrated electrobiofilm reduction method, and it has been regarded as a promising alternative method for removing NO _x from industrial boiler flue gas. EDTA-Fe^II-NO and EDTA-Fe^III are crucial substrates that should be biologically reduced at a high rate. However, they inhibit the reduction processes of one another when these two substrates are presented together, which might limit further promotion of the integrated method. In this study, an integrated electrobiofilm reduction system with high reduction rates of EDTA-Fe^II-NO and EDTA-Fe^III was developed. The dynamic changes of microbial communities in the electrobiofilms were mainly investigated to analyze the changes during the reduction of these two substrates under different conditions. The results showed that compared to the conventional chemical absorption-biological reduction system, the reduction system exhibited better performance in terms of resistance to substrate shock loading and high microbial diversities. High-throughput sequencing analysis showed that Alicycliphilus, Enterobacteriaceae, and Raoultella were the dominant genera (>25% each) during the process of EDTA-Fe^II-NO reduction. Chryseobacterium had the ability to endure the shock loading of EDTA-Fe^III, and the relative abundance of Chryseobacterium under abnormal operation conditions was up to 30.82%. Ochrobactrum was the main bacteria for reducing nitrate by electrons and the relative abundance still exhibited 16.11% under shock loading. Furthermore, higher microbial diversity and stable reactor operation were achieved when the concentrations of EDTA-Fe^II-NO and EDTA-Fe^III approached the same value (9 mmol·L^-1).

Long-lasting effects of antibiotics on bacterial communities of adult flies

Insect symbionts benefit their host and their study requires large spectrum antibiotic use like tetracycline to weaken or suppress symbiotic communities. While antibiotics have a negative impact on insect fitness, little is known about antibiotic effects on insect microbial communities and how long they last. We characterized the bacterial communities of adult cabbage root fly Delia radicum in a Wolbachia-free population and evaluated the effect of tetracycline treatment on these communities over several generations. Three D. radicum generations were used: the first- and second-generation flies either ingested tetracycline or not, while the third-generation flies were untreated but differed with their parents and/or grandparents that had or had not been treated. Fly bacterial communities were sequenced using a 16S rRNA gene. Tetracycline decreased fly bacterial diversity and induced modifications in both bacterial abundance and relative frequencies, still visible on untreated offspring whose parents and/or grandparents had been treated, therefore demonstrating long-lasting transgenerational effects on animal microbiomes after antibiotic treatment. Flies with an antibiotic history shared bacterial genera, potentially tetracycline resistant and heritable. Next, the transmission should be investigated by comparing several insect development stages and plant compartments to assess vertical and horizontal transmissions of D. radicum bacterial communities.

Application of Whole Genome Sequencing and Pan-Family Multi-Locus Sequence Analysis to Characterize Relationships Within the Family Brucellaceae

The bacterial family Brucellaceae is currently composed of seven genera, including species of the genus Brucella, a number of which are significant veterinary and zoonotic pathogens. The bacteriological identification of pathogenic Brucella spp. may be hindered by their close phenotypic similarity to other members of the Brucellaceae, particularly of the genus Ochrobactrum. Additionally, a number of novel atypical Brucella taxa have recently been identified, which exhibit greater genetic diversity than observed within the previously described species, and which share genomic features with organisms outside of the genus. Furthermore, previous work has indicated that the genus Ochrobactrum is polyphyletic, raising further questions regarding the relationship between the genus Brucella and wider Brucellaceae. We have applied whole genome sequencing (WGS) and pan-family multi-locus sequence analysis (MLSA) approaches to a comprehensive panel of Brucellaceae type strains, in order to characterize relationships within the family. Phylogenies based on WGS core genome alignments were able to resolve phylogenetic relationships of 31 non-Brucella spp. type strains from within the family, alongside type strains of twelve Brucella species. A phylogeny based on concatenated pan-family MLSA data was largely consistent with WGS based analyses. Notably, recently described atypical Brucella isolates were consistently placed in a single clade with existing species, clearly distinct from all members of the genus Ochrobactrum and wider family. Both WGS and MLSA methods closely grouped Brucella spp. with a sub-set of Ochrobactrum species. However, results also confirmed that the genus Ochrobactrum is polyphyletic, with seven species forming a separate grouping. The pan-family MLSA scheme was subsequently applied to a panel of 50 field strains of the family Brucellaceae, isolated from a wide variety of sources. This analysis confirmed the utility of the pan-Brucellaceae MLSA scheme in placing field isolates in relation to recognized type strains. However, a significant number of these isolates did not cluster with currently identified type strains, suggesting the existence of additional taxonomic diversity within some members of the Brucellaceae. The WGS and pan-family MLSA approaches applied here provide valuable tools for resolving the identity and phylogenetic relationships of isolates from an expanding bacterial family containing a number of important pathogens.

Taxonomic Organization of the Family Brucellaceae Based on a Phylogenomic Approach

Deciphering the evolutionary history of pathogenic bacteria and their near neighbors may help to understand the genetic or ecological bases which led to their pathogenic behavior. The Brucellaceae family comprises zoonotic pathogenic species belonging to the genus Brucella as well as the environmental genus Ochrobactrum for which some species are considered as opportunistic pathogens. Here, we used a phylogenomic approach including a set of 145 Brucellaceae genomes representative of the family diversity and more than 40 genomes of the order Rhizobiales to infer the taxonomic relationships between the family’s species. Our results clarified some unresolved phylogenetic ambiguities, conducting to the exclusion of Mycoplana spp. out of the family Brucellaceae and the positioning of all Brucella spp. as a single genomic species within the current Ochrobactrum species diversity. Additional analyses also revealed that Ochrobactrum spp. separate into two clades, one comprising mostly environmental species while the other one includes the species considered as pathogens (Brucella spp.) or opportunistic pathogens (mainly O. anthropi, O. intermedium, and O. pseudintermedium). Finally, we show that O. intermedium is undergoing a beginning of genome reduction suggestive of an ongoing ecological niche specialization, and that some lineages of O. intermedium and O. anthropi may shift toward an adaption to the human host.