Prey range characterization, ribotyping, and diversity of soil and rhizosphere Bdellovibrio spp. isolated on phytopathogenic bacteria

Predation and Disturbance Interact to Shape Prey Species Diversity

Though predation, productivity (nutrient richness), spatial heterogeneity, and disturbance regimes are known to influence species diversity, interactions between these factors remain largely unknown. Predation has been shown to interact with productivity and with spatial heterogeneity, but few experimental studies have focused on how predation and disturbance interact to influence prey diversity. We used theory and experiments to investigate how these factors influence diversification of Pseudomonas fluorescens by manipulating both predation (presence or absence of Bdellovibrio bacteriovorus) and disturbance (frequency and intensity of disturbance). Our results show that in a homogeneous environment, predation is essential to promote prey species diversity. However, in most but not all treatments, elevated diversity was transitory, implying that the effect of predation on diversity was strongly influenced by disturbance. Both our experimental and theoretical results suggest that disturbance interacts with predation by modifying the interplay of resource and apparent competition among prey.

A new alpha-proteobacterial clade of Bdellovibrio-like predators: implications for the mitochondrial endosymbiotic theory

Bdellovibrio-and-like organisms (BALOs) are peculiar, ubiquitous, small-sized, highly motile Gram-negative bacteria that are obligatory predators of other bacteria. Typically, these predators invade the periplasm of their prey where they grow and replicate. To date, BALOs constitute two highly diverse families affiliated with the delta-proteobacteria class. In this study, Micavibrio spp., a BALO lineage of epibiotic predators, were isolated from soil. These bacteria attach to digest and grow at the expense of other prokaryotes, much like other BALOs. Multiple phylogenetic analyses based on six genes revealed that they formed a deep branch within the alpha-proteobacteria, not affiliated with any of the alpha-proteobacterial orders. The presence of BALOs deep among the alpha-proteobacteria suggests that their peculiar mode of parasitism maybe an ancestral character in this proteobacterial class. The origin of the mitochondrion from an alpha-proteobacterium endosymbiont is strongly supported by molecular phylogenies. Accumulating data suggest that the endosymbiont's host was also a prokaryote. As prokaryotes are unable to phagocytose, the means by which the endosymbiont gained access into its host remains mysterious. We here propose a scenario based on the BALO feeding-mode to hypothesize a mechanism at play at the origin of the mitochondrial endosymbiosis.

Structure analysis of a soil community of predatory bacteria using culture-dependent and culture-independent methods reveals a hitherto undetected diversity of Bdellovibrio-and-like organisms

Bdellovibrio-and-like organisms (BALOs) are widespread obligatory predators of other Gram-negative bacteria. Their detection by culture-dependent methods is complicated as their replication is totally dependent upon the availability of an appropriate prey. Because BALOs do not form numerically dominant groups within microbial communities, non-specific culture-independent tools also generally fail to detect them. We designed sets of 16S rRNA primers that specifically target BALOs. Polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) were combined, yielding partial 16S rDNA sequences. This simple method that allows specific in situ culture-independent detection of BALOs was applied to the soil environment. Bdellovibrio-and-like organisms were also isolated from the same soil and the phylogeny and prey range of the isolates analysed. Seventeen isolates retrieved using five different potential preys exhibited eight different spectra of prey utilization and formed nine operational taxonomic units (OTUs). These OTUs were affiliated with the Bdellovibrionaceae, Bacteriovorax, Peredibacter or Micavibrio, i.e. the known BALO groups. In comparison, 15 OTUs including 10 that were not detected by the culture-dependent approach were obtained using the specific primers in a PCR-DGGE approach. The occurrence of a complex BALO community suggests that predation occurs on a much wider range of prey than can be detected by the classical culture-dependent technique.

Azospirillum brasilense does not affect population structure of specific rhizobacterial communities of inoculated maize (Zea mays)

Positive response of plant species to plant growth-promoting rhizobacteria have led to an increased interest in their use as bacterial inoculants. However, the introduction of exogenous bacteria into natural ecosystems may perturb bacterial populations within the microbial community and lead to the disruption of indigenous populations performing key functional roles. In this study the effect of Azospirillum brasilense inoculation on maize (Zea mays) rhizosphere Actinobacteria, Bacteroidetes, alpha-Proteobacteria, Pseudomonas and Bdellovibrio spp. was assessed using a polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) approach in conjunction with group-specific primers. The DGGE fingerprints analysis revealed that the introduction of A. brasilense did not alter or disrupt the microbial system at the group-specific level. However, some communities such as the alpha-Proteobacteria and Bdellovibrio were influenced by plant age while the other bacterial groups remained unaffected. Based on these as well as previous data, it can be inferred that inoculation with A. brasilense does not perturb the natural bacterial populations investigated.

Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus

The recently sequenced genome of the predatory delta-proteobacterium Bdellovibrio bacteriovorus provides many insights into its metabolism and evolution. Because its genes are reasonably uniform in G+C content, it was suggested that B. bacteriovorus actively resists recombination with foreign DNA and horizontal transfer of DNA from other bacteria. To investigate this further, we carried out a variety of phylogenetic and comparative genomics analyses using data from >200 microbial genomes, including several published delta-proteobacteria. Although there might be little evidence for the extensive recent transfer of genes, we demonstrate that ancient lateral gene acquisition has shaped the B. bacteriovorus genome to a great extent.

Differential predation by Bdellovibrio bacteriovorus 109J

Bdellovibrio bacteriovorus is a predatory bacterium that can replicate only inside Gram-negative bacteria. We incubated B. bacteriovorus 109J in a mixture of two prey cells present in equal numbers and enumerated prey cells after 3 h of predation. In multiple prey pairings, B. bacteriovorus preferentially lysed on one prey over the other. When prey were individually incubated with B. bacteriovorus, they were preyed on with different efficiencies. Three prey had only 5-8% of cells remaining after Bdellovibrio predation and the other three prey had 37-43% of cells remaining. Timing of attachment of B. bacteriovorus to prey cells also varied with Bdellovibrio attachment to more preferred prey occurring the fastest. These results suggest that B. bacteriovorus 109J does not randomly infect prey cells but infects and kills some prey more readily than others.

Transcriptional Activity of the Host-Interaction Locus and a Putative Pilin Gene of Bdellovibrio bacteriovorus in the Predatory Life Cycle

Bdellovibrio bacteriovorus is a predatory bacterium that grows and replicates within the periplasm of a large variety of Gram-negative bacteria. So far, the host-interaction locus (hit locus) is the only genetic locus that is implicated in the obligate predatory lifestyle. Sequence analysis revealed that upstream of the hit locus, the genomic regions of the two obligate predatory B. bacteriovorus-type strains HD100 and HD114 encode genes for pilus formation. As pili might be involved in the invasion process, the transcriptional activity of the hit locus and of a putative pilin gene (flp1) of the pilus cluster were studied in synchronized cultures of B. bacteriovorus with Escherichia coli K-12 as prey bacteria. Stages of the life cycle were monitored with scanning electronic microscopy and transcriptional analyses were performed by quantitative reverse transcription polymerase chain reaction. Our study revealed an increased expression level of the putative hit and flp1 genes in the attack phase of B. bacteriovorus, whereas the transcriptional activity significantly decreased during the intracellular replication phase.

Diversity and evolution of Bdellovibrio-and-like organisms (BALOs), reclassification of Bacteriovorax starrii as Peredibacter starrii gen. nov., comb. nov., and description of the Bacteriovorax–Peredibacter clade as Bacteriovoracaceae fam. nov

A phylogenetic analysis of Bdellovibrio-and-like organisms (BALOs) was performed. It was based on the characterization of 71 strains and on all consequent 16S rRNA gene sequences available in databases, including clones identified by data-mining, totalling 120 strains from very varied biotopes. Amplified rDNA restriction analysis (ARDRA) accurately reflected the diversity and phylogenetic affiliation of BALOs, thereby providing an efficient screening tool. Extensive phylogenetic analysis of the 16S rRNA gene sequences revealed great diversity within the Bdellovibrio (>14 % divergence) and Bacteriovorax (>16 %) clades, which comprised nine and eight clusters, respectively, exhibiting more than 3 % intra-cluster divergence. The clades diverged by more than 20 %. The analysis of conserved 16S rRNA secondary structures showed that Bdellovibrio contained motifs atypical of the δ-Proteobacteria, suggesting that it is ancestral to Bacteriovorax. While none of the Bdellovibrio strains were of marine origin, Bacteriovorax included separate soil/freshwater and marine-specific groups. On the basis of their extensive diversity and the large distance separating the groups, it is proposed that Bacteriovorax starrii be placed into a new genus, Peredibacter gen. nov., with Peredibacter starrii A3.12T (=ATCC 15145T=NCCB 72004T) as its type strain. Also proposed is a redefinition of the Bdellovibrio and the Bacteriovorax–Peredibacter lineages as two different families, i.e. ‘Bdellovibrionaceae’ and a new family, Bacteriovoracaceae. Also, a re-evaluation of oligonucleotides targeting BALOs is presented, and the implications of the large diversity of these organisms and of their distribution in very different environments are discussed.

Bdellovibrio bacteriovorus strains produce a novel major outer membrane protein during predacious growth in the periplasm of prey bacteria

Bdellovibrio bacteriovorus is a predatory bacterium that is capable of invading a number of gram-negative bacteria. The life cycle of this predator can be divided into a nonreproductive phase outside the prey bacteria and a multiplication phase in their periplasm. It was suggested that during the reproduction phase, B. bacteriovorus reutilizes unmodified components of the prey's cell wall. We therefore examined the outer membranes of B. bacteriovorus strains HD100 (DSM 50701) and HD114 (DSM 50705) by using Escherichia coli, Yersinia enterocolitica, and Pseudomonas putida as prey organisms. The combined sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometric analyses revealed novel and innate major outer membrane proteins (OMPs) of B. bacteriovorus strains. An incorporation of prey-derived proteins into the cell wall of B. bacteriovorus was not observed. The corresponding genes of the B. bacteriovorus strains were elucidated by a reverse-genetics approach, and a leader peptide was deduced from the gene sequence and confirmed by Edman degradation. The host-independent mutant strain B. bacteriovorus HI100 (DSM 12732) growing in the absence of prey organisms possesses an OMP similar to the major OMPs of the host-dependent strains. The similarity of the primary structure of the OMPs produced by the three Bdellovibrio strains is between 67 and 89%. The leader peptides of all OMPs have a length of 20 amino acids and are highly conserved. The molecular sizes of the mature proteins range from 34.9 to 37.6 kDa. Secondary-structure predictions indicate preferential alpha-helices and little beta-barrel structures.

Downregulation of the motA gene delays the escape of the obligate predator Bdellovibrio bacteriovorus 109J from bdelloplasts of bacterial prey cells

Bdellovibrio bacteriovorus is a Gram-negative bacterium that preys on other Gram-negative bacteria. The lifecycle of B. bacteriovorus alternates between an extracellular flagellated and highly motile non-replicative attack-phase cell and a periplasmic non-flagellated growth-phase cell. The prey bacterium containing periplasmic bdellovibrios becomes spherical but osmotically stable, forming a structure known as the bdelloplast. After completing the growth phase, newly formed bdellovibrios regain their flagellum and escape the bdelloplast into the environment, where they encounter more prey bacteria. The obligate predatory nature of B. bacteriovorus imposes a major difficulty to introducing mutations in genes directly involved in predation, since these mutants could be non-viable. This work reports the cloning of the B. bacteriovorus 109J motAB operon, encoding proteins from the flagellar motor complex, and a genetic approach based on the expression of a motA antisense RNA fragment to downregulate motility. Periplasmic bdellovibrios carrying the plasmid expressing antisense RNA displayed a marked delay in escaping from bdelloplasts, while the released attack-phase cells showed altered motility. These observations suggest that a functionally intact flagellar motor is required for the predatory lifecycle of B. bacteriovorus. Also, the use of antisense RNA expression may be a useful genetic tool to study the Bdellovibrio developmental cycle.

Plastic phenotypic resistance to predation by Bdellovibrio and like organisms in bacterial prey

Predation at the lowest trophic level, i.e. between bacteria, is poorly understood, hindering efforts to assess its impact on the structure of bacterial communities. The interaction of Bdellovibrio and Bacteriovorax (Bdellovibrio and like organisms, BLOs), a group of obligate, ubiquitous predatory bacteria, with their Gram-negative bacterial prey results in the multiplication of the predator and in the lysis, but not in the eradication, of the prey. We show that the residual, surviving populations of prey cells exposed to predation stress differ from the populations before exposure, as they exhibit increased resistance to predation. This resistance was demonstrated in a number of Gram-negative prey. Moreover, predation resistance is not specific for the BLO strain experienced by the prey. The phenomenon does not stem from a mutation but is a plastic response associated with a phenotypic change, and it disappears upon removal of the predator. As resistance to predation is not total, this mechanism can ensure survival of both predator and prey.

The obligate predatory Bdellovibrio bacteriovorus possesses a neutral lipid A containing alpha-D-Mannoses that replace phosphate residues: similarities and differences between the lipid As and the lipopolysaccharides of the wild type strain B. bacteriovorus HD100 and its host-independent derivative HI100

Bdellovibrio bacteriovorus are predatory bacteria that penetrate Gram-negative bacteria and grow intraperiplasmically at the expense of the prey. It was suggested that B. bacteriovorus partially degrade and reutilize lipopolysaccharide (LPS) of the host, thus synthesizing an outer membrane containing structural elements of the prey. According to this hypothesis a host-independent mutant should possess a chemically different LPS. Therefore, the lipopolysaccharides of B. bacteriovorus HD100 and its host-independent derivative B. bacteriovorus HI100 were isolated and characterized by SDS-polyacrylamide gel electrophoresis, immunoblotting, and mass spectrometry. LPS of both strains were identified as smooth-form LPS with different repeating units. The lipid As were isolated after mild acid hydrolysis and their structures were determined by chemical analysis, by mass spectrometric methods, and by NMR spectroscopy. Both lipid As were characterized by an unusual chemical structure, consisting of a beta-(1-->6)-linked 2,3-diamino-2,3-dideoxy-d-glucopyranose disaccharide carrying six fatty acids that were all hydroxylated. Instead of phosphate groups substituting position O-1 of the reducing and O-4' of the nonreducing end alpha-d-mannopyranose residues were found in these lipid As. Thus, they represent the first lipid As completely missing negatively charged groups. A reduced endotoxic activity as determined by cytokine induction from human macrophages was shown for this novel structure. Only minor differences with respect to fatty acids were detected between the lipid As of the host-dependent wild type strain HD100 and for its host-independent derivative HI100. From the results of the detailed analysis it can be concluded that the wild type strain HD100 synthesizes an innate LPS.

Engineering bacterial competitiveness and persistence in the phytosphere

Several tactics exist to improve the survival of an introduced microorganism of interest in the plant environment. One, derived from studies on the Agrobacterium-plant interaction and the role of opines in this interaction, proposes to promote growth of the inoculant in the plant environment via the establishment of a bias in the rhizosphere. It is supported by the occurrence of natural biases, such as those generated by opine-like molecules, by calestegins, or by mimosine. Opine-mediated biases have allowed several investigators to favor the growth of opine-degrading bacteria or communities under sterile or axenic environments or in microcosms mimicking near field conditions. Another way to favor a given microbe consists in impeding growth of competing microorganisms. Experiments performed using detergent or bacteriostatic agents as amendments under field or near field conditions yielded promising results. Research perspectives for engineering plant-microbe interactions also include specific engineering of predation and strategies designed to interfere with some of the signals perceived by the microbes, provided these signals control the expression of functions central to microbial fitness. In this respect, quorum-sensing signal molecules, such as N-acyl-homoserine lactones, may be valuable targets for the development of biocontrol agents and procedures.

Taxonomic studies of predatory bdellovibrios based on 16S rRNA analysis, ribotyping and the hit locus and characterization of isolates from the gut of animals

The aim of our study was to obtain data for the molecular characterization of bdellovibrio bacteria, which were recently split into the genus Bdellovibrio and the newly designated genus Bacteriovorax. We determined the 16S rDNA sequences of five reference strains and performed a phylogenetic analysis including published 16S rRNA sequences of bdellovibrios. A comparison of the secondary structure showed significant differences in two regions of the 16S rRNAs of the species Bdellovibrio bacteriovorus, Bacteriovorax starrii, and Bacteriovorax stolpii. In addition, ribotyping techniques gave specific hybridization patterns and revealed that two rRNA operons are present in the investigated strains. A hybridization probe derived from the genetic locus hit, associated with the host independent (HI) phenotype of B. bacteriovorus, was found to be specific for this species. Sequence comparison of the hit locus revealed few base pair changes between host independent (HI) and host dependent (HD) strains. Ribotyping and hybridization experiments using the hit probe were applied to characterize bdellovibrio strains isolated from the gut of animals and humans and one isolate from sewage.

Culture-Independent Detection of Changes in Root-Associated Bacterial Populations of Common Bean (Phaseolus vulgaris L.) Following Nitrogen Depletion

The structure of root-associated bacterial populations in the legume common bean (Phaseolus vulgaris L.), was studied in plants grown under nitrogen sufficiency and under conditions inducing nitrogen deficiency. Similar cell numbers were obtained in the rhizosphere of nitrogen-amended plants as compared to nitrogen-deficient plants and between various root parts-tip, elongation and branching zones-using DAPI staining. In contrast, a higher proportion of DAPI-stained cells from the nitrogen-amended plants hybridized with a fluorescence-labeled EUB338 probe for the Bacteria domain than cells originating from nitrogen-deficient plants. Shifts in the percentages of EUB338-reactive cells-as well as in absolute cell number-hybridizing to fluorescent rRNA-directed probes specific for the a and g Proteobacteria and for high GC content gram-positive bacteria in separated root segments were detected between the treatments. No such differences were found using b and d Proteobacteria or rRNA group I pseudomonad targeted probes. Denaturating gradient gel electrophoresis profiles of PCR products obtained from the same samples and amplified with Bacteria-domain targeted primers supported the results obtained with the whole cell hybridizations. The advantages and drawbacks of the techniques applied are discussed.