-
Seminars in Respiratory and Critical... Dec 2019Although survival of individuals with cystic fibrosis (CF) has been continuously improving for the past 40 years, respiratory failure secondary to recurrent pulmonary... (Review)
Review
Although survival of individuals with cystic fibrosis (CF) has been continuously improving for the past 40 years, respiratory failure secondary to recurrent pulmonary infections remains the leading cause of mortality in this patient population. Certain pathogens such as , methicillin-resistant , and species of the complex continue to be associated with poorer clinical outcomes including accelerated lung function decline and increased mortality. In addition, other organisms such as anaerobes, viruses, and fungi are increasingly recognized as potential contributors to disease progression. Culture-independent molecular methods are also being used for diagnostic purposes and to examine the interaction of microorganisms in the CF airway. Given the importance of CF airway infections, ongoing initiatives to promote understanding of the epidemiology, clinical course, and treatment options for these infections are needed.
Topics: Bacterial Infections; Burkholderiaceae; Cystic Fibrosis; Humans; Methicillin-Resistant Staphylococcus aureus; Microbiota; Mycoses; Pseudomonas aeruginosa; Respiratory Tract Infections; Virus Diseases
PubMed: 31887768
DOI: 10.1055/s-0039-1698464 -
Applied and Environmental Microbiology Mar 2021Mucoromycota representatives are known to harbor two types of endohyphal bacteria (EHB)--related endobacteria (BRE) and -related endobacteria (MRE). While both BRE and...
Mucoromycota representatives are known to harbor two types of endohyphal bacteria (EHB)--related endobacteria (BRE) and -related endobacteria (MRE). While both BRE and MRE occur in fungi representing all subphyla of Mucoromycota, their distribution is not well studied. Therefore, it is difficult to resolve the evolutionary history of these associations in favor of one of the following two alternative hypotheses explaining their origin: "early invasion" and "late invasion." Our main goal was to fill this knowledge gap by surveying Mucoromycota fungi for the presence of EHB. We screened 196 fungal strains from 16 genera using a PCR-based approach to detect bacterial 16S rRNA genes, complemented with fluorescence hybridization (FISH) imaging to confirm the presence of bacteria within the hyphae. We detected in ca. 20% of fungal strains. Some of these bacteria clustered phylogenetically with previously described BRE clades, whereas others grouped with free-living Importantly, the latter were detected in Umbelopsidales, which previously were not known to harbor endobacteria. Our results suggest that this group of EHB is recruited from the environment, supporting the late invasion scenario. This pattern complements the early invasion scenario apparent in the BRE clade of EHB. Bacteria living within fungal hyphae present an example of one of the most intimate relationships between fungi and bacteria. Even though there are several well-described examples of such partnerships, their prevalence within the fungal kingdom remains unknown. Our study focused on early divergent terrestrial fungi in the phylum Mucoromycota. We found that ca. 20% of the strains tested harbored bacteria from the family Not only did we confirm the presence of bacteria from previously described endosymbiont clades, we also identified a new group of endohyphal representing the genus We established that more than half of the screened strains were positive for bacteria from this new group. We also determined that, while previously described BRE codiverged with their fungal hosts, symbionts did not.
Topics: Burkholderiaceae; Fungi; Hyphae; In Situ Hybridization, Fluorescence; Polymerase Chain Reaction; RNA, Bacterial; RNA, Ribosomal, 16S
PubMed: 33483310
DOI: 10.1128/AEM.02707-20 -
Molecular Plant Pathology Sep 2013Ralstonia solanacearum is a soil-borne bacterium causing the widespread disease known as bacterial wilt. Ralstonia solanacearum is also the causal agent of Moko disease... (Review)
Review
UNLABELLED
Ralstonia solanacearum is a soil-borne bacterium causing the widespread disease known as bacterial wilt. Ralstonia solanacearum is also the causal agent of Moko disease of banana and brown rot of potato. Since the last R. solanacearum pathogen profile was published 10 years ago, studies concerning this plant pathogen have taken a genomic and post-genomic direction. This was pioneered by the first sequenced and annotated genome for a major plant bacterial pathogen and followed by many more genomes in subsequent years. All molecular features studied now have a genomic flavour. In the future, this will help in connecting the classical field of pathology and diversity studies with the gene content of specific strains. In this review, we summarize the recent research on this bacterial pathogen, including strain classification, host range, pathogenicity determinants, regulation of virulence genes, type III effector repertoire, effector-triggered immunity, plant signalling in response to R. solanacearum, as well as a review of different new pathosystems.
TAXONOMY
Bacteria; Proteobacteria; β subdivision; Ralstonia group; genus Ralstonia.
DISEASE SYMPTOMS
Ralstonia solanacearum is the agent of bacterial wilt of plants, characterized by a sudden wilt of the whole plant. Typically, stem cross-sections will ooze a slimy bacterial exudate. In the case of Moko disease of banana and brown rot of potato, there is also visible bacterial colonization of banana fruit and potato tuber.
DISEASE CONTROL
As a soil-borne pathogen, infected fields can rarely be reused, even after rotation with nonhost plants. The disease is controlled by the use of resistant and tolerant plant cultivars. The prevention of spread of the disease has been achieved, in some instances, by the application of strict prophylactic sanitation practices.
USEFUL WEBSITES
Stock centre: International Centre for Microbial Resources-French Collection for Plant-associated Bacteria CIRM-CFBP, IRHS UMR 1345 INRA-ACO-UA, 42 rue Georges Morel, 49070 Beaucouzé Cedex, France, http://www.angers-nantes.inra.fr/cfbp/. Ralstonia Genome browser: https://iant.toulouse.inra.fr/R.solanacearum. GMI1000 insertion mutant library: https://iant.toulouse.inra.fr/R.solanacearumGMI1000/GenomicResources. MaGe Genome Browser: https://www.genoscope.cns.fr/agc/microscope/mage/viewer.php?
Topics: Genomics; Host Specificity; Phylogeny; Plant Diseases; Plants; Ralstonia solanacearum
PubMed: 23718203
DOI: 10.1111/mpp.12038 -
Microbiology Spectrum Feb 2022Chromids (secondary chromosomes) in bacterial genomes that are present in addition to the main chromosome appear to be evolutionarily conserved in some specific...
Chromids (secondary chromosomes) in bacterial genomes that are present in addition to the main chromosome appear to be evolutionarily conserved in some specific bacterial groups. In rare cases among these groups, a small number of strains from and were shown to possess a naturally fused single chromosome that was reported to have been generated through intragenomic homologous recombination between repeated sequences on the chromosome and chromid. Similar examples have never been reported in the family , a well-documented group that conserves chromids. Here, an in-depth genomic characterization was performed on a bacterium that was isolated from a soil bacterial consortium maintained on diesel fuel and mutagenic benzo[]pyrene. This organism, Cupriavidus necator strain KK10, was revealed to carry a single chromosome with unexpectedly large size (>6.6 Mb), and results of comparative genomics with the genome of C. necator N-1 indicated that the single chromosome of KK10 was generated through fusion of the prototypical chromosome and chromid at the rRNA operons. This fusion hypothetically occurred through homologous recombination with a crossover between repeated rRNA operons on the chromosome and chromid. Some metabolic functions that were likely expressed from genes on the prototypical chromid region were indicated to be retained. If this phenomenon-the bacterial chromosome-chromid fusion across the rRNA operons through homologous recombination-occurs universally in prokaryotes, the multiple rRNA operons in bacterial genomes may not only contribute to the robustness of ribosome function, but also provide more opportunities for genomic rearrangements through frequent recombination. A bacterial chromosome that was naturally fused with the secondary chromosome, or "chromid," and presented as an unexpectedly large single replicon was discovered in the genome of Cupriavidus necator strain KK10, a biotechnologically useful member of the family . Although is a well-documented group that conserves chromids in their genomes, this chromosomal fusion event has not been previously reported for this family. This fusion has hypothetically occurred through intragenomic homologous recombination between repeated rRNA operons and, if so, provides novel insight into the potential of multiple rRNA operons in bacterial genomes to lead to chromosome-chromid fusion. The harsh conditions under which strain KK10 was maintained-a genotoxic hydrocarbon-enriched milieu-may have provided this genotype with a niche in which to survive.
Topics: Burkholderiaceae; Chromosomes, Bacterial; Genome, Bacterial; Genomics; RNA, Bacterial; Recombination, Genetic; Replicon; rRNA Operon
PubMed: 34985328
DOI: 10.1128/spectrum.02225-21 -
Applied and Environmental Microbiology May 2022Microbial symbionts are critical for the development and survival of many eukaryotes. Recent research suggests that the genes enabling these relationships can be...
Microbial symbionts are critical for the development and survival of many eukaryotes. Recent research suggests that the genes enabling these relationships can be localized in horizontally transferred regions of microbial genomes termed "symbiotic islands." Recently, a putative symbiotic island was found that may facilitate symbioses between true bugs and numerous species, based on analysis of five symbionts. We expanded on this work by exploring the putative island's prevalence, origin, and association with colonization across the bacterial family . We performed a broad comparative analysis of 229 genomes, including 8 new genomes of insect- or soil-associated sequenced for this study. We detected the region in 23% of the genomes; these were located solely within two clades. Our analyses suggested that the contiguous region arose at the common ancestor of plant- and insect-associated clades, but the genes themselves are ancestral. Although the region was initially discovered on plasmids and we did detect two likely instances of horizontal transfer within , we found that the region is almost always localized to a chromosome and does not possess any of the mobility elements that typify genomic islands. Finally, to attempt to deduce the region's function, we combined our data with information on several strains' abilities to colonize the insect's symbiotic organ. Although the region was associated with improved colonization of the host, this relationship was confounded with, and likely driven by, clade membership. These findings advance our understanding of the genomic underpinnings of a widespread insect-microbe symbiosis. Many plants and animals form intricate associations with bacteria. These pairings can be mediated by genomic islands, contiguous regions containing numerous genes with cohesive functionality. Pathogen-associated islands are well described, but recent evidence suggests that mutualistic islands, which benefit both host and symbiont, may also be common. Recently, a putative symbiosis island was found in symbionts of insects. We determined that this genomic region is located in only two clades of (the plant- and insect-associated species) and that although it has undergone horizontal transfer, it is most likely a symbiosis-associated region rather than a true island. This region is associated with improved host colonization, although this is may be due to specific clades' abilities to colonize rather than presence of the region. By studying the genomic basis of the insect- symbiosis, we can better understand how mutualisms evolve in animals.
Topics: Animals; Burkholderia; Burkholderiaceae; Genomics; Heteroptera; Insecta; Prevalence; Symbiosis
PubMed: 35435710
DOI: 10.1128/aem.02502-21 -
Microbes and Environments 2020Bacterial endosymbionts inhabit diverse fungal lineages. Although the number of studies on bacteria is increasing, the mechanisms by which bacteria affect their fungal...
Bacterial endosymbionts inhabit diverse fungal lineages. Although the number of studies on bacteria is increasing, the mechanisms by which bacteria affect their fungal hosts remain unclear. We herein examined the homothallic isolate, Mortierella sugadairana YTM39, harboring a Burkholderiaceae-related endobacterium, which did not produce sexual spores. We successfully eliminated the bacterium from fungal isolates using ciprofloxacin treatment and asexual spore isolation for germinated asexual spores. Sexual spore formation by the fungus was restored by eliminating the bacterium from isolates. These results indicate that sexual reproduction by the fungus was inhibited by the bacterium. This is the first study on the sexual spore infertility of fungal hosts by endofungal bacteria.
Topics: Biological Evolution; Burkholderiaceae; Ciprofloxacin; Mortierella; Mycelium; Reproduction; Spores, Fungal; Symbiosis
PubMed: 32295978
DOI: 10.1264/jsme2.ME19167 -
Archives of Microbiology Nov 2022CRISPR-Cas systems are composed of repeated sequences separated by non-repeated sequences that are near genes coding for Cas proteins, which are involved in the function...
CRISPR-Cas systems are composed of repeated sequences separated by non-repeated sequences that are near genes coding for Cas proteins, which are involved in the function of these systems. Their function has been mostly related to "genetic immunity" against foreign genetic material, among other roles. Interest in them increased after their use in genetic manipulation was uncovered and surveys to find and classify them have been done in several bacterial groups. To determine the presence of these genetic elements in the Burkholderiaceae family members, a bioinformatic approach was followed. Attention in this family comes as it is formed by a great diversity of microorganisms that include opportunistic and true pathogens, and symbiotic and saprophytic organisms, among others. Results show that, in contrast to other bacterial groups, only 8.4% of family members harbor complete CRISPR-Cas systems and the rest either do not have one or have remains or sections of one. Analyses of the spacer sequences indicated that most of them have identity to sections of the same genomes they were found, while a few had identities with either plasmids or phages. The genus with the higher proportion of self-directed spacers is Ralstonia, and their possible roles are discussed. Most of the systems (60%) belong to the class I subtype I-E and a few to subtypes I-C (13.3%), I-F (18.3%), II-C (5%), IV-A (1.7%) and V-C (1.7%). To the best of our knowledge, this is the first study to uncover the CRISPR-Cas system for the whole Burkholderiaceae family.
Topics: CRISPR-Cas Systems; Burkholderiaceae; Plasmids; Computational Biology; Bacteriophages; Bacteria
PubMed: 36370236
DOI: 10.1007/s00203-022-03312-y -
Trends in Microbiology Jan 2024is a Gram negative, facultative intracellular bacterium that resides in the rhizosphere of tropical soils. causes melioidosis, which is transmitted by cutaneous entry,...
is a Gram negative, facultative intracellular bacterium that resides in the rhizosphere of tropical soils. causes melioidosis, which is transmitted by cutaneous entry, ingestion, or inhalation of contaminated soil or water. Infection with can cause a wide array of clinical symptoms such as pneumonia, bone, joint, skin, genitourinary, and central nervous system infections, as well as parotid abscesses in children. Mammalian virulence is linked to the intracellular life cycle, which begins with attachment and internalization by host cells. can infect a wide range of eukaryotic cells, including macrophages, monocytes, and neutrophils, as well as nonphagocytic cells. Once internalized, a type 3 secretion system (T3SS) facilitates escape from the phagosome, and the bacteria replicate in the cytoplasm. Autotransporter protein BimA mediates actin polymerization, enabling to spread, cell to cell, using actin-based motility. This process, coupled with the activity of a type 6 secretion system (T6SS-5), results in host membrane fusion and the formation of multinucleated giant cells. Capsule polysaccharides also contribute to virulence and evasion of host innate immunity. Treatment of infections is complicated by the organism’s intrinsic resistance to multiple classes of antimicrobials, largely due to an abundance of efflux pumps and reduced outer membrane permeability. While is commonly associated with endemic ‘hotspots’ in southeast Asia and northern Australia, there is increasing evidence that it is likely endemic in a large range of tropical and subtropical areas, including regions in Africa, South America, the Middle East, Central America, and the Caribbean. Soil and climate conditions favorable for survival are also found in additional areas worldwide. Consequently, it is important for clinical and public health laboratories located outside of high-endemicity areas to be aware of , as well as for improved diagnostic and reporting methods.
Topics: Burkholderia pseudomallei; Burkholderia
PubMed: 37634974
DOI: 10.1016/j.tim.2023.07.008 -
The ISME Journal Sep 2018Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of...
Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of soils suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392-3, 2016), but the mechanisms and microbial species involved in the soil suppressiveness are largely unknown. Previous taxonomic and metatranscriptome analyses of a soil suppressive to the fungal root pathogen Rhizoctonia solani revealed that members of the Burkholderiaceae family were more abundant and more active in suppressive than in non-suppressive soils. Here, isolation, phylogeny, and soil bioassays revealed a significant disease-suppressive activity for representative isolates of Burkholderia pyrrocinia, Paraburkholderia caledonica, P. graminis, P. hospita, and P. terricola. In vitro antifungal activity was only observed for P. graminis. Comparative genomics and metabolite profiling further showed that the antifungal activity of P. graminis PHS1 was associated with the production of sulfurous volatile compounds encoded by genes not found in the other four genera. Site-directed mutagenesis of two of these genes, encoding a dimethyl sulfoxide reductase and a cysteine desulfurase, resulted in a loss of antifungal activity both in vitro and in situ. These results indicate that specific members of the Burkholderiaceae family contribute to soil suppressiveness via the production of sulfurous volatile compounds.
Topics: Antibiosis; Burkholderiaceae; Carbon-Sulfur Lyases; Ecosystem; Fungi; Iron-Sulfur Proteins; Microbial Consortia; Oxidoreductases; Phylogeny; Plant Diseases; Soil; Soil Microbiology; Sulfur
PubMed: 29899517
DOI: 10.1038/s41396-018-0186-x -
Molecular Biology and Evolution Mar 2019Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely... (Comparative Study)
Comparative Study
Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipartite genomes. Almost all essential secondary replicons (chromids) of the β-proteobacteria are found in the family Burkholderiaceae. These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes. On average, Burkholderiaceae genera with multipartite genomes had a larger total genome size, but smaller chromosome, than genera without secondary replicons. Pangenome-level functional enrichment analyses suggested that interreplicon functional biases are partially driven by the enrichment of secondary replicons in the accessory pangenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicon's pangenome indicated a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also overrepresented on the chromosomes of the environmental genera (Paraburkholderia and Cupriavidus) compared with the pathogenic genera (Burkholderia and Ralstonia). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in replicons enriched in genes associated with adaptation to novel environments.
Topics: Adaptation, Biological; Burkholderiaceae; Gene Transfer, Horizontal; Genome Size; Genome, Bacterial; Replicon; Selection, Genetic
PubMed: 30608550
DOI: 10.1093/molbev/msy248