Caister Academic Press


Metagenomics: Current Advances and Emerging Concepts
Edited by: Diana Marco
Cutting-edge and emerging conceptual and methodological tools used in metagenomics
Adapted from Eshwar Mahenthiralingam and Tom Coenye writing in Burkholderia: From Genomes to Function


Burkholderia is an enigmatic Gram-negative bacterial genus that has attracted researchers from multiple disciplines. Burkholderia species possess considerable genetic and metabolic versatility allowing them to exist in a wide range of environmental settings as free-living or host-associated microorganisms. From a research standpoint, their interactions can be divided into either those that are beneficial or those that are problematic, often with the same Burkholderia species capable of both functions. The beneficial traits of Burkholderia are largely environmental and include their ability to promote plant growth, kill pest organisms, fix nitrogen, and degrade man-made pollutants. Pathogenicity towards multiple host organisms is the fundamental negative attribute for which Burkholderia have been widely researched, however, new problematic areas such as industrial contamination are emerging. Advances in the biology of Burkholderia bacteria are a result of greatly improved genomic and molecular resources for these bacteria (Coenye and Mahenthiralingam, 2014).

Since 2007, multiple Burkholderia genome sequences have been obtained and analysis of these bacteria has truly moved into the postgenomic era, prompting a focus on genomic, gene and protein functions. The first genome sequence that was publicly available for researchers to access was that of the epidemic cystic fibrosis (CF) pathogen Burkholderia cenocepacia J2315. The sequencing project carried out by the Wellcome Trust Sanger Institute, was initiated in 2000, with partial sequence data released on their website shortly thereafter, enabling researchers to begin genomic analysis of this pathogen. The B. cenocepacia J2315 genome was completed in 2003 facilitating the design of a microarray to enable global gene expression analysis and finally published in 2009. The first published genome within the genus was that of Burkholderia xenovorans LB400, a strain that was capable of degrading polychlorinated biphenyl pollutants. Over 100 Burkholderia genome sequences have now been determined and multiple complete genomes can be accessed at online databases (Coenye and Mahenthiralingam, 2014).

Burkholderia: multidisciplinary research

Burkholderia are multifaceted bacteria with considerable genetic diversity and very versatile lifestyles. As a result they make very compelling model species to study in relation to various microbial, molecular and biochemical functions. The ability to survive in harsh, competitive, environments is a key aspect of Burkholderia lifestyles. They are widely distributed in terrestrial habitats including soil, especially around or on plant roots at the rhizosphere, where they interact with many biotic and abiotic factors. They may form very close interactions with higher organisms such as fungi, plants and insects, ranging from surface or internal associations, through to fully endosymbiotic relationships. For the most part their environmental lifestyles play beneficial roles, prompting researchers to examine their biopesticidal, bioremedial and plant growth promotion activities. However, plant pathogenic Burkholderia and species that cause human or animal infections represent major areas of study, and other traits, such as their ability to cause industrial contamination or mediate insecticide resistance represent emerging fields where they play a problematic role. With such a polarity of attributes, researchers studying Burkholderia may move between multiple disciplines ranging from their natural ecology through to molecular pathogenesis. This breadth of investigation allows researchers to gain unique insights into the microbiology of these Gram-negative bacteria.

Taxonomy, identification and typing

The systematic classification and re-classification of Burkholderia species continues, but now with well developed molecular and genomic tools to assist in the accurate taxonomic identification of these bacteria (Coenye and Mahenthiralingam, 2014). Major advances in taxonomy to date are (i) the formal naming of 17 species within the B. cepacia complex; (ii) the formal naming of over 74 validly described Burkholderia species; and (iii) the observation that at least two major phylogenetic groups are present within the genus. Regarding this latter observation, it has been suggested that there are considerable ecological differences between both major lineages (with one including human, animal and plant pathogenic species while the other cluster is mainly composed of saprophytic and plantassociated species) and it has been suggested that a subdivision of the genus Burkholderia would be appropriate. However, sequence-based phylogenetic analyses have indicated that several Burkholderia species occupy intermediate positions between the two major phylogenetic groups. In addition, considering the opportunistic nature of many of the 'pathogenic' Burkholderia species involved (including members of the Bcc) it seems ill-advised at this moment to put too much emphasis on the ecological differences to distinguish both groups and it is clear that more work is required before major taxonomic changes are made.

Below the species level the characterization of Burkholderia strains has benefited considerably from a well-developed multilocus sequence typing (MLST) scheme and a searchable online database; a number of other typing methods can also be efficiently applied to characterize isolates and trace outbreaks. Burkholderia strain analysis has now also been taken to the level of mapping genomic evolution using next-generation sequencing platforms with the analysis of the Burkholderia dolosa outbreak of CF infection that occurred in Boston, USA.

In terms of emerging non-genetic tools for bacterial species identification, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) has been successfully applied to assist with Burkholderia species identification. MALDI-TOF was able to distinguish Bcc from non-Bcc species, as well as resolved the majority of Bcc species except Burkholderia anthina and Burkholderia pyrrocinia. A different phenotypic identification system based on a protein microarray has also been developed for B. pseudomallei to enable rapid serodiagnosis of this pathogen. A panel of genes encoding predicted immunogenic and surface proteins were amplified by PCR, cloned by recombination into plasmid vectors and expressed in vitro, prior to being printed onto glass microarray slides. From a starting array containing 1205 B. pseudomallei proteins, 49 were identified as being most predictive of patients with active meliodosis infection as a result of serum cross-reactivity. The microarray also identified 59 candidate antigens that were equally cross-reactive across both infected and healthy individuals, and may serve as proteins suitable for a B. pseudomallei vaccine.

Burkholderia virulence traits

Virulence has arguably been the leading Burkholderia research area for the last three decades with these organisms possessing a diverse range of pathogenicity functions. In particular, there is now an overwhelming body of experimental evidence that supports the intracellular survival of Burkholderia bacteria in single cell organisms such as amoebae and cell types such as macrophages. Moreover, the development of a zebra fish embryo model of infection also showed that B. cenocepacia was able to survive and multiply within macrophages of a multicellular vertebrate host for the first time. Burkholderia have evolved mechanisms that can delay acidification of mammalian macrophage vacuoles and also block intracellular degradation pathways in plant host cells. For example, Burkholderia possesses proteasome inhibitors such as glidobactin which are part of a family of well-characterized bacterial syringolin toxins produced by hybrid non-ribosomal peptide–polyketide synthetase (NRPS) genes in other well-characterized plant pathogens such as Pseudomonas syringae. In addition to zebra fish, a wide range of surrogate infection models have now been applied and tested on Burkholderia bacteria. Comparative analysis infection models using the nematode Caenorhabditis elegans, wax moth larvae, Galleria mellonella, alfalfa plants, and mice or rats has also demonstrated that many of the previously characterized Burkholderia virulence factors are model specific in terms of active function (Uehlinger et al., 2009). Of the virulence determinants screened, quorum sensing, iron acquisition via siderophores and lipopolysaccharide biosynthesis were the only factors required for full pathogenicity in all models. The soil-living amoeba Dictyostelium discoideum has been used to identify B. pseudomallei transposon mutants with diminished virulence Vial and colleagues used this amoebae model as well as the model fly, Drosophila melanogaster, to demonstrate that a spontaneously emerging Burkholderia ambifaria phase variant colony type was less virulent than the wild type (Coenye and Mahenthiralingam, 2014).

While full Burkholderia virulence is clearly multifactorial, type VI secretion has recently been identified as a major Burkholderia virulence factor. It has been shown to be critically important for full pathogenesis of B. pseudomallei and of primary importance the control of biofilm formation in B. cenocepacia. Overall, the availability of multiple genome sequences and molecular strategies to pinpoint genes of interest, excellent tools for gene mutation and several easy to use infection models, will greatly enhance the rate of Burkholderia virulence factor identification and characterization.

Functionality and evolution in biofilms

The ability to form biofilms is common trait possessed by all Burkholderia species and recent studies have begun to take a much more detailed look at the evolution that occurs during this sessile lifestyle. Clonal diversity evolves within a B. cenocepacia biofilm model. Using polystyrene beads to grow and then passage biofilms through multiple generations, the emergence of three colony morphotypes was followed. The functional role of each colony type, studded, ruffled spreader and wrinkly, in biofilm formation was also characterized. Although the wrinkly colony type was the best biofilm former when tested in isolation, biofilms that evolved naturally from the wild type were composed predominantly of the studded morphotype, which, in contrast was the least efficient at biofilm formation. The ruffled colony type was second in dominance among the sessile cells and the wrinkly colony type only made up a minority of the evolved biofilm.

To characterize the molecular basis for the emergence of the colony morphotypes, next generation sequencing and metagenomic analysis was used to identify the mutations that emerged during biofilm formation and growth passage over 1050 generations (Coenye and Mahenthiralingam, 2014). The majority of mutations fell into five functional classes that altered metabolism of cyclic diguanosine monophosphate, lipolysaccharide production, central metabolism within the tricarboxylic acid cycle, global transcription, and the ability to acquire iron. Interestingly, many of the mutations overlapped with those identified in B. dolosa and P. aeruginosa isolates that have adapted during chronic CF lung infection, showing that the abiotic polystyrene bead model of biofilm formation enabled the modelling of evolution during infection.

Loss of replicons and insights derived from complete genome sequences from endosymbionts

The multireplicon structure of Burkholderia genomes has long been noted as an unusual feature of their genomes. Since each of the larger replicons encode ribosomal RNA (rrn) operons and other essential genes, they have been referred to as chromosomes. Genome sequence analysis revealed that the smaller replicons of B. xenovorans, B. pseudomallei and B. cenocepacia had partition (parA and parB) and replication (repA) genes that were plasmid-like. Subsequent phylogenetic comparison also demonstrated that these regions were indeed distinct from those encoded on the largest replicon. These data suggest that the smaller Burkholderia replicons were acquired as megaplasmids and had become genomically stabilized as a result of the transfer of essential genes. Building on these observations, Agnoli and colleagues were recently able to prove that the third replicon in Bcc bacteria was not an essential chromosomal element and could actually be cured from strains.

Loss of the third chromosome (c3) resulted in viable cells despite the loss of over 1 Mb of DNA and the one rrn operon encoded on this replicon. The major functions lost by the c3-minus derivatives were virulence, antifungal activity and several secondary metabolism pathways that were not essential for primary growth. It is quite amazing that a microorganism can tolerate such large loss of its genomic DNA content. This seminal finding of replicon loss (Agnoli et al., 2012) adds weight to the hypothesis that Burkholderia species follow two major evolutionary paths. One path is based on the acquisition of new functionality associated with accessory DNA and the parallel increase in genome size that results. The other evolutionary route is based on rearrangement and loss of DNA as seen in the highly specific horse pathogen Burkholderia mallei (< 6.0 Mb genome) which has clonally emerged from Burkholderia pseudomallei that has a larger genome (> 7 Mb). Within the Burkholderia genus, the Bcc group seems to be unique in having a third replicon encoding an rrn operon. Other Burkholderia species have two major replicons, with the second largest often encoding up to three rrn and multiple tRNAs, as seen in the Burkholderia xenovorans genome (Chain et al., 2006). It will be interesting to see whether in these Burkholderia species as well as the Bcc, the second replicon can be cured.

In addition to adaptation to pathogenic niches as seen with B. mallei, genome size may frequently become reduced when organisms adopt an endosymbiotic lifestyle. Many Burkholderia species form very close interactions with a variety of multicellular host organisms and one of the most intriguing to be recently characterized was that of Burkholderia rhizoxinica. B. rhizoxinica is an endofungal bacterium that was originally identified within the plant pathogenic fungus, Rhizopus, which causes rice seedling blight disease. Rhizopus infection causes swelling of plant tissue due to the production of a polyketide phytotoxin, rhizoxin, which was originally thought to be produced by the fungus. However, detailed characterization of Rhizopus demonstrated that it harboured an intracellular Burkholderia species, and that it was these bacterial cells that were producing the rhizoxin toxin.

Full characterization of the B. rhizoxinica genome has shown that it has all the hallmarks of an endosymbiotic bacterial species; it is one of the smallest Burkholderia genomes to be characterized to date, with a total genome size of only 3.75 Mb. Interestingly it only has one large chromosomal replicon of 2.75 Mb that encodes all three rrn operons. Its GC content, 60.7%, is also considerably lower than the average within the Burkholderia genus (approximately 67%); this low GC content may reflect B. rhizoxinica's evolution towards an intracellular endofungal lifestyle. In addition to the rhizoxin biosynthesis gene cluster, which constitutes a hybrid NRPS and polyketide synthase (PKS) system encoded on the large chromosome, the entire B. rhizoxinica genome was found to contain an additional 14 NRPS gene clusters, devoting nearly 9% of its genome to this form of secondary metabolite production. Since B. rhizoxinica lacks a second chromosomal replicon it is provocative to postulate that it has evolved through replicon loss, rather than the small genome reflecting the ancestral state of this species.

Another major group of symbiotic Burkholderia are the nodulating species (Burkholderia mimosarum, Burkholderia nodosa, Burkholderia sabiae and Burkholderia phymatum), which are the first diazotropic non-alpha-proteobacteria capable of nitrogen fixation within leguminous plants. These Burkholderia species have very large genomes (8.64 Mb and 8.67 Mb, for B. mimosarum and B. phymatum, respectively) and they show no evidence of genome decay as a result of their close, endosymbiotic interactions with leguminous plants. This is probably because they are facultatively endosymbiotic in terms of nodule formation, and several of these species may also be found as free-living bacteria within bulk soil. Endophytic Burkholderia species such as Burkholderia phytofirmans that live within plant tissues without causing any negative effects on their hosts, also possess large genomes (B. phytofirmans PsJN, 8.21 Mb). Overall, this suggests that for close interactions with plants, a large genome size can be tolerated and is actually beneficial for both the bacterium and host plant in terms of the additional functionality it brings.

Burkholderia and cystic fibrosis

The last decade has seen a number of changes in the epidemiology of Burkholderia in CF infection (LiPuma, 2010). The major switch has been the reduction in the prevalence of B. cenocepacia infection, probably as a result of the greatly improved surveillance and infection control that has been widely implemented across CF populations. B. multivorans is now the most dominant Bcc species seen in several CF populations, with B. cenocepacia generally second in dominance. Although this is the major trend seen in the molecular epidemiology of Bcc bacteria, regional and centre specific differences in the prevalence of certain Burkholderia species are still apparent. For example, B. cepacia has dominated at a large Portuguese CF centre in Lisbon (85% of Bcc infected patients); however, this is due to the presence of two major strains which were also found as contaminants of non-sterile saline solutions and were the primary cause of this Bcc infection outbreak. Burkholderia contaminans is the dominant Bcc species seen in Argentinian CF individuals treated at multiple centre. While clonal strains and potential patient-topatient transmission were observed in this study, there was also evidence of genetically distinct B. contaminans strains, suggesting that the dominance of this species may also reflect differences in environmental prevalence of Bcc in Argentina. Outside the Bcc, Burkholderia gladioli, has also emerged as an important cause of CF infection in the US, where it is now the third most prevalent species (accounting for 15% of Burkholderia infections). With B. gladioli infecting over 300 CF patients in the US, it will become increasingly important to begin to characterize the molecular pathogenicity of this species and why it is able to cause chronic lung infection.

The application of cultivation independent techniques to examine microbial diversity in CF infection also represents a major advance in this disease area that has occurred over the last 10 years. Molecular studies have shown that (i) the infected CF lung has a diverse bacterial community and high prevalence of anaerobic species, which are distinct from those present in the oral cavity ; (ii) microaerophillic species, such as the Streptococcus milleri group (SMG), constitute novel pathogens in CF; (iii) cultivation-based diagnostic microbiology is limited when compared with cultivation-independent analysis; and (iv) increased diversity in the CF microbiota is associated with patient stability, while low diversity is associated with increased severity of infection. Although these studies have detected Burkholderia species as key components of the CF microbiota in parallel with what has been seen in conventional cultivation-based analysis (Rogers et al., 2003), no study has yet focused on the effect of this genus on the composition of the microbiota in CF infection. Since Bcc bacteria are known to produce a wide range of antagonistic metabolites that can inhibit other CF pathogens, it will be very interesting to see if they reduce or specifically alter the diversity of infection when they are present.

Novel therapies for CF infection

A number of potential therapies for the treatment of highly antibiotic-resistant Burkholderia infections have also emerged in the last few years. Brackman and colleagues demonstrated that quorum-sensing inhibitors such as baicalin hydrate and cinnamaldehyde were effective in reducing biofilm formation by Bcc bacteria when used in combination with tobramycin. The combination of tobramycin and baicalin hydrate also greatly improved the clearance of B. cenocepacia in a mouse model of infection. Another promising new small molecule therapy for infection is the use of antisense phosphorodiamidate morpholino oligomers (PMO) to block the expression of essential Burkholderia genes. A PMO directed against the start site of acpP gene was selected as this gene encodes an essential component of bacterial fatty acid biosynthesis. When conjugated to a cell-penetrating peptide to form a peptide-PMO (PPMO), enhanced neutrophil killing of B. mutlivorans was seen in vitro. Treatment of B. multivorans-infected mice also resulted in increased survival and reduced inflammation within the spleen and lymph nodes indicating that successful modelling of morpholino therapy could be performed in vivo.

Phage therapy is now being widely investigated as an alternative to the use of antibiotics especially for multidrug resistant Gram-negative pathogens. The successful clinical trials of a phage formulation for chronic ear infections caused by Pseudomonas aeruginosa heralds a promising future for these agents in the topical treatment of infections. The wider genomic biology of Burkholderia phages has been discussed in detail, however, it is also promising to see that inhaled phage formulations have been successfully tested in animal models of infection paving the way for the development of phage therapies for CF respiratory infection (Borysowski et al., 2014).

Two other recent findings point to simple therapies for Burkholderia infection. The drug glyburide is a potassium ATP channel and ATPbinding cassette (ABC) transporter inhibitor that is used to treat type 2 diabetes. It has a wide range of anti-inflammatory effects and when it was administered to B. pseudomallei infected individuals, it reduced the mortality associated with diabetic individuals with B. pseudomallei infection. When white blood cell gene expression was examined in this group of patients, it was clear that the glyburide had reduced the expression of multiple inflammatory genes, consistent with its general anti-inflammatory properties.

Another potentially very simple therapy that could reduce the minimal inhibitory concentration of antibiotics in B. cenocepacia was noted after a global gene expression analysis of spontaneous antibiotic resistant mutants in this pathogen. It was observed that mutants with high-level resistance to beta-lactam antibiotics also showed increased expression of genes involved in phenylacetic acid degradation. It is well known that adding glucose often leads to repression of such alternate metabolic pathways, and indeed when the glucose concentration was increased to 20mM, the expression of genes involved in the phenylacetic acid pathway was decreased and the minimal inhibitory concentration of several antibiotics (meropenem, ceftazidime, tetracycline and chloramphenicol) were considerably reduced in the pan resistant B. cenocepacia J2315 strain. Glucose (dextrose) is a widely used clinical agent; however, whether it could be incorporated into antibiotic formulations and delivered as an inhaled therapy remains to be determined.

Novel Burkholderia niches: insects

In addition to the expansion of research on plant and fungal interactions, a study characterizing insect symbionts found that Burkholderia were carried at high density in the mid-guts of stink bugs, Riptortus clavatus. When the researchers examined the phylogeny of the Burkholderia endosymbionts they found that it did not map onto that of the host insects. In addition, when they examined the stink bug eggs from insects reared in the laboratory they did not find any evidence of the bacteria, suggesting the Burkholderia were not transmitted vertically. However, rearing of the sterile insects in soil led to successful colonization suggesting the Burkholderia was environmentally acquired at an early stage in the insects development.

Follow up to this work led to the intriguing finding that insecticide resistance was one of the functions the Burkholderia endosymbionts was able to confer on the host insects. The ability to degrade a wide variety of man-made organic compounds and pollutants such as polychlorinated biphenyls is a well known Burkholderia trait. It was demonstrated that the organophosphate insecticide, fenitrothion, could be degraded by Burkholderia that were carried within the stink bug pest, Riptortus pedestris. In agricultural fields where fenitrothion had been intensively used to protect sugarcane crops, resident stink bugs were shown to have a gut community that was highly enriched for Burkholderia species that could degrade this insecticide. Although other functions of the Burkholderia symbionts in these insects have not been well characterized, it is amazing that an anthropogenic activity such as insecticide use can drive the evolution of a novel interaction between Burkholderia bacteria that is beneficial to its insect host.

Novel Burkholderia niches: an ability to survive in microaerophilic environments

Resilience and broad environmental fitness traits enable Burkholderia to grow in a number of harsh environments. Classical traits such as metabolic versatility, antibiotic resistance, production of multiple virulence factors and the ability to form biofilms which enable Burkholderia to colonize various environments have already been investigated in some depth. However, one attribute that is not widely studied in the context of aerobic bacteria is the influence of oxygen, and in particular what happens when its concentration is reduced. The majority of Burkholderia species are considered to be aerobic and unable to grow without oxygen. Those species that fix nitrogen, an oxygen-sensitive process, must do so in an anoxic environment such as within the nodules of leguminous plants, suggesting that these species must have the capability to survive without oxygen. Microbial diversity analysis of CF sputum has shown that anaerobic bacteria are present in high number, confirming that the concentration of oxygen in sputum can be close to zero. Therefore, for Bcc bacteria to be such successful CF pathogens, they must have the ability to tolerate low levels of oxygen and grow microaerophilically.

Other than the ability of Burkholderia to grow in biofilms where oxygen can become limited, little is known about how they grow microaerophilically. Sass et al. (2013) examined B. cenocepacia global gene expression under a variety of environmental conditions pertinent to the CF lung, with one of the conditions being a reduction in oxygen concentration to 6% compared with the atmospheric level of 21%. This was a convenient level to produce experimentally using a commercial gas-pack sachet optimized for growth of facultatively anaerobic Campylobacter species. The effect of reduced oxygen concentration on gene expression was staggering, with 1987 of the 7251 (27%) of the coding sequences (CDS) on the B. cenocepacia J2315 microarray altered in expression. The only other growth condition to alter expression of a larger number of genes was growth at stationary phase in a minimal medium, where 29% of the CDS altered in expression. The low oxygen level also resulted in the induction of a novel regulon of genes, the majority of which clustered in one unique 50 Kb gene cluster that was designated the low oxygen activated locus (lxa). The intact lxa region was only found in B. cenocepacia with other Burkholderia species possessing only fragments of this region as small gene clusters or individual homologous genes. The gene content of the lxa cluster was also highly unusual with poorly characterized predicted functions in metabolism, transport, stress (six universal stress proteins) and gene regulation. Overall, the discovery of the lxa locus suggests that Burkholderia have evolved mechanisms to cope with anoxia and that because microaerophilic environments probably reflect 'reality' for most aerobic bacteria, we should be doing more to model this growth parameter.

Undesirable presence of Burkholderia: contamination

In addition to infection, an increasing number of studies are reporting the presence of Burkholderia bacteria as undesirable contaminants of man-made products. Historical outbreaks of infection due to the contamination of disinfectants and medical solutions have been well characterized, but the wider prevalence of Burkholderia as contaminants was not revealed until it was reported that Burkholderia cepacia was the most frequently isolated microbial species in product recalls is logged by the US Food and Drug Agency. It was present in 22% of non-sterile product recalls and 2.5% of sterile product contaminations. A major problem with many of these reports of contamination was the fact that accurate identification of the contaminating Burkholderia species was often not performed. Recent studies have begun to systematically identify the species involved in microbial fouling and have shown that a wide range of Burkholderia have the capability to cause industrial contamination.

MLST analysis of clonal sequence types associated with infection and the environment had demonstrated that Burkholderia stabilis was associated with contamination of shampoo and albuterol inhaler solutions. The formal name given to B. contaminans had reflected the fact that the organism was linked to multiple, globally distributed instances of contamination and opportunistic infection. Burkholderia species may even contaminate fuels with Burkholderia vietnamiensis, B. lata and novel Bcc species found at a single oil refinery site. A recent systematic survey of 60 Burkholderia industrial process contaminants demonstrated that Burkholderia lata and B. cenocepacia were the two most common species in this collection (25% and 18%, respectively); Burkholderia vietnamiensis, Burkholderia arboris, B. stabilis, B. cepacia, B. multivorans, B. contaminans, B. ambifaria and potentially novel Bcc species made up the remaining contaminating isolates). The key features which allow Burkholderia to survive in such harsh anthropogenic environments include (i) their innate resistance to antimicrobials, with efflux shown to mediate preservative resistance, and (ii) their metabolic diversity to grow on a range of substrates including complex hydrocarbons found in fuels.

Future perspectives

With such wide diversity in terms of biological functionality it is not hard to see why there has been increased interest in the study of Burkholderia. Not many bacteria can be used to study both infection and positive environmental interactions at the same time. With the increased availability and reduced costs of next generation sequencing technologies, it will become technically feasible to dissect the complex functions encoded by large Burkholderia genomes. But what are the gaps in our understanding of these bacteria to which these tools can be applied? We can certainly continue to probe their disease-causing ability in more detail to developing new therapies for infection. However, it is probably their vast and varied environmental interactions that represent the greatest challenge. There is no doubt that Burkholderia bacteria bring considerable benefit to many natural interactions especially in terms of their plant growth promotion capabilities. Understanding how to harness these positive environmental properties without tipping the balance towards Burkholderia pathogenicity will be a major future challenge (Coenye and Mahenthiralingam, 2014).


Further reading