Interaction of Arsenophonus with Wolbachia in Nilaparvata lugens

Background

Co-infection of endosymbionts in the same host is ubiquitous, and the interactions of the most common symbiont Wolbachia with other symbionts, including Spiroplasma, in invertebrate organisms have received increasing attention. However, the interactions between Wolbachia and Arsenophonus, another widely distributed symbiont in nature, are poorly understood. We tested the co-infection of Wolbachia and Arsenophonus in different populations of Nilaparvata lugens and investigated whether co-infection affected the population size of the symbionts in their host.

Results

A significant difference was observed in the co-infection incidence of Wolbachia and Arsenophonus among 5 populations of N. lugens from China, with nearly half of the individuals in the Zhenjiang population harbouring the two symbionts simultaneously, and the rate of occurrence was significantly higher than that of the other 4 populations. The Arsenophonus density in the superinfection line was significantly higher only in the Maanshan population compared with that of the single-infection line. Differences in the density of Wolbachia and Arsenophonus were found in all the tested double-infection lines, and the dominant symbiont species varied with the population only in the Nanjing population, with Arsenophonus the overall dominant symbiont.

Conclusions

Wolbachia and Arsenophonus could coexist in N. lugens, and the co-infection incidence varied with the geographic populations. Antagonistic interactions were not observed between Arsenophonus and Wolbachia, and the latter was the dominant symbiont in most populations.

Background-dependent Wolbachia-mediated insecticide resistance in Laodelphax striatellus

Although facultative endosymbionts are now known to protect insect hosts against pathogens and parasitoids, the effects of endosymbionts on insecticide resistance are still unclear. Here we show that Wolbachia are associated with increased resistance to the commonly used insecticide, buprofezin, in the small brown planthopper (Laodelphax striatellus) in some genetic backgrounds while having no effect in other backgrounds. In three Wolbachia-infected lines from experimental buprofezin-resistant strains and one line from a buprofezin-susceptible line established from Chuxiong, Yunnan province, China, susceptibility to buprofezin increased after removal of Wolbachia. An increase in susceptibility was also evident in a Wolbachia-infected line established from a field population in Rugao, Jiangsu province. However, no increase was evident in two field populations from Nanjing and Fengxian, Jiangsu province, China. When Wolbachia was introgressed into different genetic backgrounds, followed by Wolbachia removal, the data pointed to Wolbachia effects that depend on the nuclear background as well as on the Wolbachia strain. However, there was no relationship between Wolbachia density and the component of buprofezin resistance associated with the symbiont. The results suggest that Wolbachia effects associated with chemical resistance are complex and unpredictable, but also that they can be substantial.

Population Dynamics of Wolbachia in Laodelphax striatellus (Fallén) Under Successive Stress of Antibiotics

Wolbachia are the most common symbionts in arthropods; antibiotic treatment for eliminating the symbionts from their host is necessary to investigate the functions. Tetracycline antibiotics are widely used to remove endosymbiont Wolbachia from insect hosts. However, very little has been known on the effects of tetracycline on population size of Wolbachia in small brown planthopper (SBPH), Laodelphax striatellus (Fallén), an important insect pest of rice in Asia. Here, we investigated the dynamics of Wolbachia population density in females and males of L. striatellus by real-time fluorescent quantitative PCR method. The Wolbachia density in females and males of L. striatellus all declined sharply after treatment with 2 mg/mL tetracycline for one generation, and continued to decrease to a level which could not be detected by both qPCR and diagnostic PCR after treated for another generation, then maintained at 0 in the following three generations with continuous antibiotic treatment. Wolbachia infection did not recover in L. striatellus after stopping tetracycline treatment for ten generations. This is the first report to precisely monitor the population dynamics of Wolbachia in L. striatellus during successive tetracycline treatment and after that. The results provide a useful method for evaluating the efficiency of artificial operation of endosymbionts.

Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an "open" pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc), enterotoxin (cpe), and Perfringolysin O (pfo or pfoA), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet) and anti-defensins genes (mprF) were consistently detected in silico (tet: 75%; mprF: 100%). However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus

In this paper, the taxonomy of the genus Arthrobacter is discussed, from its first description in 1947 to the present state. Emphasis is given to intrageneric phylogeny and chemotaxonomic characteristics, concentrating on quinone systems, peptidoglycan compositions and polar lipid profiles. Internal groups within the genus Arthrobacter indicated from homogeneous chemotaxonomic traits and corresponding to phylogenetic grouping and/or high 16S rRNA gene sequence similarities are highlighted. Furthermore, polar lipid profiles and quinone systems of selected species are shown, filling some gaps concerning these chemotaxonomic traits. Based on phylogenetic groupings, 16S rRNA gene sequence similarities and homogeneity in peptidoglycan types, quinone systems and polar lipid profiles, a description of the genus Arthrobacter sensu lato and an emended description of Arthrobacter roseus are provided. Furthermore, reclassifications of selected species of the genus Arthrobacter into novel genera are proposed, namely Glutamicibacter gen. nov. (nine species), Paeniglutamicibacter gen. nov. (six species), Pseudoglutamicibacter gen. nov. (two species), Paenarthrobacter gen. nov. (six species) and Pseudarthrobacter gen. nov. (ten species).

Multilocus variable-number tandem-repeat genotyping of Renibacterium salmoninarum, a bacterium causing bacterial kidney disease in salmonid fish

Background

Bacterial kidney disease (BKD), caused by Renibacterium salmoninarum, is a bacterial disease of fish, which is both geographically widespread and difficult to control. Previously, application of various molecular typing methods has failed to reliably discriminate between R. salmoninarum isolates originating from different host species and geographic areas. The current study aimed to utilize multilocus variable number tandem repeats (VNTR) to investigate inter-strain variation of R. salmoninarum to establish whether host-specific populations exist in Atlantic salmon and rainbow trout respectively. Such information would be valuable in risk assessment of transmission of R. salmoninarum in a multispecies aquaculture environment.

Results

The present analysis utilizing sixteen VNTRs distinguished 17 different haplotypes amongst 41 R. salmoninarum isolates originating from Atlantic salmon and rainbow trout in Scotland, Norway and the US. The VNTR typing system revealed two well supported groups of R. salmoninarum haplotypes. The first group included R. salmoninarum isolates originating from both Atlantic salmon and rainbow trout circulating in Scottish and Norwegian aquaculture, in addition to the type strain ATCC33209^T originating from Chinook salmon in North America. The second group comprised isolates found exclusively in Atlantic salmon, of mainly wild origin, including isolates NCIB1114 and NCIB1116 associated with the original Dee disease in Scotland.

Conclusions

The present study confirmed that VNTR analysis can be successfully applied to discriminate R. salmoninarum strains. There was no clear distinction between isolates originating from Atlantic salmon and rainbow trout as several haplotypes in group 1 clustered together R. salmoninarum isolates from both species. These findings indicate a potential exchange of pathogens between Atlantic salmon and rainbow trout in Scottish and Norwegian aquaculture during the last 20 years. In a scenario of expansion of rainbow trout farming into the marine environment, appropriate biosecurity measures to minimize disease occurrence are advised. The present results also suggest that R. salmoninarum isolates circulating in European aquaculture over the last 20 years are genetically distant to the wild strains originally causing BKD in the rivers Dee and Spey.

Phylogenetic diversity of alkaline protease-producing psychrotrophic bacteria from glacier and cold environments of Lahaul and Spiti, India

The diversity of proteolytic bacteria associated with a glacier and cold environment soils from three different locations in Lahaul and Spiti, India was investigated. Two hundred seventeen bacterial strains were isolated in pure culture. Subsequently these strains were screened for protease-production and one hundred nine showed protease production. From these protease producing psychrotrophic bacteria twenty showing high enzyme production at low temperature and alkaline pH were characterized and identified. The 16S rRNA phylogenetic analysis revealed that none of the strains showed 100% identity with the validly published species of various genera. Isolates belonged to three classes i.e. Actinobacteria, Gammaproteobacteria and Alphaproteobacteria, and were affiliated with the genera Acinetobacter, Arthrobacter, Mycoplana, Pseudomonas, Pseudoxanthomonas, Serratia and Stenotrophomonas. The optimal growth temperature ranged from 10 to 28 degrees C and interestingly, high levels of enzyme productions were measured at growth temperatures between 15 and 25 degrees C, for most of the isolates in plate assay. Most of the isolates were found to produce at least two other hydrolytic enzymes along with protease. The crude protease from one strain was active over broad range of temperature and pH with optima at 30 degrees C and 7.5, respectively. The protease activity was enhanced by Ca(2+), dithiothreitol and beta-mercaptoethanol. While Na(+), Hg(2+), Zn(2+), Mn(2+), phenylmethanesulfonyl fluoride and ethylenediaminetetraacetic acid did not showed much effect on protease activity. The results enrich our knowledge on the psychrotrophic bacterial diversity and biogeographic distribution of enzyme producing bacteria in western Himalaya.

Cloning of a gene cluster involved in the catabolism of p-nitrophenol by Arthrobacter sp. strain JS443 and characterization of the p-nitrophenol monooxygenase

The npd gene cluster, which encodes the enzymes of a p-nitrophenol catabolic pathway from Arthrobacter sp. strain JS443, was cloned and sequenced. Three genes, npdB, npdA1, and npdA2, were independently expressed in Escherichia coli in order to confirm the identities of their gene products. NpdA2 is a p-nitrophenol monooxygenase belonging to the two-component flavin-diffusible monooxygenase family of reduced flavin-dependent monooxygenases. NpdA1 is an NADH-dependent flavin reductase, and NpdB is a hydroxyquinol 1,2-dioxygenase. The npd gene cluster also includes a putative maleylacetate reductase gene, npdC. In an in vitro assay containing NpdA2, an E. coli lysate transforms p-nitrophenol stoichiometrically to hydroquinone and hydroxyquinol. It was concluded that the p-nitrophenol catabolic pathway in JS443 most likely begins with a two-step transformation of p-nitrophenol to hydroxy-1,4-benzoquinone, catalyzed by NpdA2. Hydroxy-1,4-benzoquinone is reduced to hydroxyquinol, which is degraded through the hydroxyquinol ortho cleavage pathway. The hydroquinone detected in vitro is a dead-end product most likely resulting from chemical or enzymatic reduction of the hypothetical intermediate 1,4-benzoquinone. NpdA2 hydroxylates a broad range of chloro- and nitro-substituted phenols, resorcinols, and catechols. Only p-nitro- or p-chloro-substituted phenols are hydroxylated twice. Other substrates are hydroxylated once, always at a position para to a hydroxyl group.

Arthrobacter scleromae sp. nov. isolated from human clinical specimens

A gram-positive, coryneform bacterium was isolated from swollen scleromata of a dermatosis patient. An analysis of its phenotypic, chemotaxonomic, and genotypic characteristics showed that this bacterium is closely associated with Arthrobacter oxydans and Arthrobacter polychromogenes but that it belongs to a distinct species, for which the name Arthrobacter scleromae sp. nov. is proposed.

Identification and differentiation of species and strains of Arthrobacter and Microbacterium barkeri isolated from smear cheeses with Amplified Ribosmal DNA Restriction Analysis (ARDRA) and pulsed field gel electrophoresis (PFGE)

ARDRA (Amplified Ribosomal-DNA Restriction Analysis) was used to differentiate among species and genera of Arthrobacter and Microbacteria. Species-specific restriction patterns of PCR-products were obtained with NciI for Arthrobacter citreus (DSM 20133T), A. sulfureus (DSM 20167T), A. globiformis (DSM 20124T) and A. nicotianae strains (DSM 20123T, MGE 10D, CA13, CA14, isolate 95293, 95294, and 95299), A. rhombi CCUG 38813T, and CCUG 38812, and Microbacterium barkeri strains (DSM 30123T, MGE 10D, CA12 and CA15, isolate 95292, and isolate 95207). All yellow pigmented coryneforme bacteria isolated from the smear of surface ripened cheeses were identified as either A. nicotianae or M. barkeri strains. Using pulsed field gel electrophoresis (PFGE) strain specific restriction pattern for all Arthrobacter species and Microbacteria tested were obtained with restriction enzymes AscI and SpeI.

Arthrobacter strain VAI-A utilizes acyl-homoserine lactone inactivation products and stimulates quorum signal biodegradation by Variovorax paradoxus

Many Proteobacteria produce acyl-homoserine lactones (acyl-HSLs) and employ them as dedicated cell-to-cell signals in a process known as quorum sensing. Previously, Variovorax paradoxus VAI-C was shown to utilize diverse acyl-HSLs as sole sources of energy and nitrogen. We describe here the properties of a second isolate, Arthrobacter strain VAI-A, obtained from the same enrichment culture that yielded V. paradoxus VAI-C. Although strain VAI-A grew rapidly and exponentially on a number of substrates, it grew only slowly and aberrantly (i.e., linearly) in media amended with oxohexanoyl-HSL as the sole energy source. Increasing the culture pH markedly improved the growth rate in media containing this substrate but did not abolish the aberrant kinetics. The observed growth was remarkably similar to the known kinetics of the pH-influenced half-life of acyl-HSLs, which decay chemically to yield the corresponding acyl-homoserines. Strain VAI-A grew rapidly and exponentially when provided with an acyl-homoserine as the sole energy or nitrogen source. The isolate was also able to utilize HSL as a sole source of nitrogen but not as energy for growth. V. paradoxus, known to release HSL as a product of quorum signal degradation, was examined for the ability to support the growth of Arthrobacter strain VAI-A in defined cocultures. It did. Moreover, the acyl-HSL-dependent growth rate and yield of the coculture were dramatically superior to those of the monocultures. This suggested that the original coenrichment of these two organisms from the same soil sample was not coincidental and that consortia may play a role in quorum signal turnover and mineralization. The fact that Arthrobacter strain VAI-A utilizes the two known nitrogenous degradation products of acyl-HSLs, acyl-homoserine and HSL, begins to explain why none of the three compounds are known to accumulate in the environment.

Variation in the spacer regions separating tRNA genes in Renibacterium salmoninarum distinguishes recent clinical isolates from the same location

A means for distinguishing between clinical isolates of Renibacterium salmoninarum that is based on the PCR amplification of length polymorphisms in the tRNA intergenic spacer regions (tDNA-ILPs) was investigated. The method used primers specific to nucleotide sequences of R. salmoninarum tRNA genes and tRNA intergenic spacer regions that had been generated by using consensus tRNA gene primers. Twenty-one PCR products were sequenced from five isolates of R. salmoninarum from the United States, England, and Scotland, and four complete tRNA genes and spacer regions were identified. Sixteen specific PCR primers were designed and tested singly and in all possible pairwise combinations for their potential to discriminate between isolates from recent clinical outbreaks of bacterial kidney disease (BKD) in the United Kingdom. Fourteen of the isolates were cultured from kidney samples taken from fish displaying clinical signs of BKD on five farms, and some of the isolates came from the same farm and at the same time. The tDNA-ILP profiles separated 22 clinical isolates into nine groups and highlighted that some farms may have had more than one source of infection. The grouping of isolates improved on the discriminatory power of previously reported typing methods based on randomly amplified polymorphic DNA analysis and restriction fragment length profiles developed using insertion sequence IS994. Our method enabled us to make divisions between closely related clinical isolates of R. salmoninarum that have identical exact tandem repeat (ETR-A) loci, rRNA intergenic spacer sequences, and IS994 profiles.

Genetic diversity among Arthrobacter species collected across a heterogeneous series of terrestrial deep-subsurface sediments as determined on the basis of 16S rRNA and recA gene sequences

This study was undertaken in an effort to understand how the population structure of bacteria within terrestrial deep-subsurface environments correlates with the physical and chemical structure of their environment. Phylogenetic analysis was performed on strains of Arthrobacter that were collected from various depths, which included a number of different sedimentary units from the Yakima Barricade borehole at the U.S. Department of Energy's Hanford site, Washington, in August 1992. At the same time that bacteria were isolated, detailed information on the physical, chemical, and microbiological characteristics of the sediments was collected. Phylogenetic trees were prepared from the 39 deep-subsurface Arthrobacter isolates (as well as 17 related type strains) based on 16S rRNA and recA gene sequences. Analyses based on each gene independently were in general agreement. These analyses showed that, for all but one of the strata (sedimentary layers characterized by their own unifying lithologic composition), the deep-subsurface isolates from the same stratum are largely monophyletic. Notably, the layers for which this is true were composed of impermeable sediments. This suggests that the populations within each of these strata have remained isolated under constant, uniform conditions, which have selected for a particular dominant genotype in each stratum. Conversely, the few strains isolated from a gravel-rich layer appeared along several lineages. This suggests that the higher-permeability gravel decreases the degree of isolation of this population (through greater groundwater flow), creating fluctuations in environmental conditions or allowing migration, such that a dominant population has not been established. No correlation was seen between the relationship of the strains and any particular chemical or physical characteristics of the sediments. Thus, this work suggests that within sedimentary deep-subsurface environments, permeability of the deposits plays a major role in determining the genetic structure of resident bacterial populations.

Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments

Forty strains of Gram-positive, aerobic, heterotrophic bacteria isolated from saturated subsurface lacustrine, paleosol and fluvial sediments at the US Department of Energy's Hanford Site in south central Washington State were characterized by phylogenetic analysis of 16S rRNA gene sequences and by determination of selected morphological, physiological and biochemical traits. Phylogenetic analyses of 16S rDNA sequences from subsurface isolates in the context of similar sequences from previously described bacterial species indicated that 38 of the subsurface strains were most closely related to Arthrobacter: The other two strains appeared to be most closely related to Kocuria. The subsurface isolates fell into seven phylogenetically coherent and distinct clusters, indicating that there was a significant degree of diversity among them. Additional diversity was detected by analysis of cellular fatty acids and physiological traits. The general morphological, physiological and biochemical traits of the subsurface strains were consistent with those of Arthrobacter, Micrococcus and genera recently separated from Micrococcus, such as Kocuria. Some of the subsurface strains were phylogenetically closely related to certain species of Arthrobacter. (16S rDNA sequence similarities >99%). However, most of the subsurface isolates did not cluster with previously established species in phylogenetic analyses of 16S rRNA gene sequences or with hierarchical cluster analysis of cellular fatty acid profiles. Moreover, many of the subsurface isolates that were most closely related to Arthrobacter. also differed from all established species of that genus in several of their specific physiological characteristics. Most of the subsurface isolates, then, are likely to be novel strains or species of Arthrobacter.

Molecular differentiation of Renibacterium salmoninarum isolates from worldwide locations

Renibacterium salmoninarum is a genospecies that is an obligate pathogen of salmonid fish and is capable of intracellular survival. Conventional typing systems have failed to differentiate isolates of R. salmoninarum. We used two methods to assess the extent of molecular variation which was present in isolates from different geographic locations. In one analysis we investigated possible polymorphisms in a specific region of the genome, the intergenic spacer (ITS) region between the 16S and 23S rRNA genes. In the other analysis we analyzed differences throughout the genome by using randomly amplified polymorphic DNA (RAPD). We amplified the spacer region of 74 isolates by using PCR and performed a DNA sequence analysis with 14 geographically distinct samples. The results showed that the 16S-23S ribosomal DNA spacer region of R. salmoninarum is highly conserved and suggested that only a single copy of the rRNA operon is present in this slowly growing pathogen. DNA sequencing of the spacer region showed that it was the same length in all 14 isolates examined, and the same nucleotide sequence, sequevar 1, was obtained for 11 of these isolates. Two other sequevars were found. No tRNA genes were found. We found that RAPD analysis allows reproducible differentiation between isolates of R. salmoninarum obtained from different hosts and different geographic regions. By using RAPD analysis it was possible to differentiate between isolates with identical ITS sequences.

Purification and characterization of four catechol 1,2-dioxygenase isozymes from the benzamide-assimilating bacterium Arthrobacter species BA-5-17

When Arthrobacter sp. BA-5-17 was grown on benzamide, the bacterium synthesized four different catechol 1,2-dioxygenase (CD, EC 1.13.11.1) isozymes (CD-I, II, III-1, and III-2). We purified each CD to homogeneity by a series of column chromatography. The molecular masses of the four CDs were between 68 and 72 kDa. The enzymes were made up of two identical subunits each with the molecular mass of 33 kDa. CD-I and II were indistinguishable in enzymatic properties tested. Most properties of CD-III-1 were similar to those of CD-III-2. However, CD-III-1 had a marked adsorption peak at 325 nm, which disappeared in CD-III-2 as well as in CD-I and II. CD-III-1 and III-2 were much more resistant to heating and inhibitors than CD-I and II.

Arthrobacter, Brachybacterium and Planococcus isolates identified from antarctic sea ice brine. Description of Planococcus mcmeekinii, sp. nov

Three facultative psychrophilic Gram-positive bacterial strains were isolated from brine samples from the sea ice community in Antarctica. All strains were coccoid to rod-shaped and exhibited broad salinity and temperature ranges for growth. The three strains were subjected to 16S rDNA sequencing and subsequent phylogenetic analysis. All possess unique 16S rDNA sequences indicating they are new, previously unreported organisms. Phylogenetic analyses coupled with phenotypic characterization indicated that one of the strains is most closely related to the low mol% G + C genus Planococcus for which a new species, P. mcmeekinii, is proposed. The two other strains are members of the high mol% G + C Gram-positive bacteria and most closely related to the genera Arthrobacter and Brachybacterium. This study reports the first phylogenetic evidence that Gram-positive bacteria reside in the marine sea ice brine.

An investigation of the intra-generic structure of Rothia by pyrolysis mass spectrometry

Previous studies of the genus Rothia have indicated that members of the only species, Rothia dentocariosa, are heterogeneous and may form more than one species. To study the intrageneric taxonomic structure of the Rothia taxon eighteen strains identified as R. dentocariosa, including reference organisms from culture collections (3 strains), isolates from healthy subjects (5 strains) and from clinical sources (10 strains) were examined using pyrolysis mass spectrometry. The ordination plots of the pyrolysis data indicated that all the strains clustered in a closely related group, with the exception of three strains which out-grouped. Phenotypic testing and fatty acid data indicated that the latter three strains are probably misclassified in the genus Rothia. Reanalysis of the PyMS data including only the fifteen authentic Rothia strains indicated that ten of these organisms formed a group which included the type strain, R. dentocariosa NCTC 10917. Four out of the remaining five organisms formed a diffuse group; the remaining strain was recovered as a single member cluster. These data indicate that R. dentocariosa is heterogeneous though at present there are no suitable criteria for assigning members of this taxon to more than one species.