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Bacteria can solubilize phosphorus (P) through the secretion of low-molecular-weight organic acids and acidification. However, the genes involved in the production of these organic acids are poorly understood. The objectives of this study were to verify the calcium phosphate solubilization and the production of low-molecular-weight organic acids by diverse genera of phosphate solubilizing bacterial strains (PSBS); to identify the genes related to the synthesis of the organic acids in the genomes of these strains and; to evaluate growth and nutrient accumulation of maize plants inoculated with PSBS and fertilized with Bayóvar rock phosphate. Genomic DNA was extracted for strain identification and annotation of genes related to the organic acids production. A greenhouse experiment was performed with five strains plus 150 mg dm− 3 P2O5 as Bayóvar rock phosphate (BRP) to assess phosphate solubilization contribution to maize growth and nutrition. Paraburkholderia fungorum UFLA 04–21 and Pseudomonas anuradhapurensis UFPI B5-8A solubilized over 60% of Ca phosphate and produced high amounts of citric/maleic and gluconic acids in vitro, respectively. Eleven organic acids were identified in total, although not all strains produced all acids. Besides, enzymes related to the organic acids production were found in all bacterial genomes. Plants inoculated with strains UFPI B5-6 (Enterobacter bugandensis), UFPI B5-8A, and UFLA 03–10 (Paenibacillus peoriae) accumulated more biomass than the plants fertilized with BRP only. Strains UFLA 03–10 and UFPI B5-8A increased the accumulation of most macronutrients, including P. Collectively, the results show that PSBS can increase maize growth and nutrient accumulation based on Bayóvar rock phosphate fertilization. [ABSTRACT FROM AUTHOR]

Symbiotic interactions may change depending on third parties like predators or prey. Third-party interactions with prey bacteria are central to the symbiosis between Dictyostelium discoideum social amoeba hosts and Paraburkholderia bacterial symbionts. Symbiosis with inedible Paraburkholderia allows host D. discoideum to carry prey bacteria through the dispersal stage where hosts aggregate and develop into fruiting bodies that disperse spores. Carrying prey bacteria benefits hosts when prey are scarce but harms hosts when prey bacteria are plentiful, possibly because hosts leave some prey bacteria behind while carrying. Thus, understanding benefits and costs in this symbiosis requires measuring how many prey bacteria are eaten, carried and left behind by infected hosts. We found that Paraburkholderia infection makes hosts leave behind both symbionts and prey bacteria. However, the number of prey bacteria left uneaten was too small to explain why infected hosts produced fewer spores than uninfected hosts. Turning to carried bacteria, we found that hosts carry prey bacteria more often after developing in prey-poor environments than in prey-rich ones. This suggests that carriage is actively modified to ensure hosts have prey in the harshest conditions. Our results show that multi-faceted interactions with third parties shape the evolution of symbioses in complex ways. [ABSTRACT FROM AUTHOR]

Paraburkholderia ultramafica STM10279T is a metal-tolerant rhizobacterium that promotes plant growth. It was isolated from the roots of Tetraria arundinaceae, a pioneer endemic tropical herb growing on ultramafic soils in New Caledonia. We have recently shown that the main mechanism of metal tolerance of P. ultramafica is related to the production of an acidic exopolysaccharide (EPS). To explore the potential role of this EPS in the plant's environmental adaptation, we first elucidated its structure by employing a combination of chromatography and mass spectrometry techniques. These analyses revealed that the EPS is highly branched and composed of galactosyl (35.8%), glucosyl (33.2%), rhamnosyl (19.5%), mannosyl (7.2%), and glucuronosyl residues (4.4%), similar to the EPS of the Burkholderia cepacia complex known as cepacian. We subsequently conducted greenhouse experiments on Tetraria comosa plantlets inoculated with P. ultramafica or a solution of its EPS during transplanting onto ultramafic substrate. The data showed that the dry weight of T. comosa shoots was 2.5 times higher in the plants treated with the EPS compared to the unexposed plants. In addition, inductively coupled plasma-optical emission spectrometry (ICP-OES) analysis revealed that exposure to the EPS significantly increased Ca, Mg, K, and P uptake as well as K content in roots. In vitro experiments using the Pikovskaya method showed that the EPS was able to solubilize phosphorus. Consistent with the retention of metals in roots and a reduction in shoots, our data revealed a significant decrease in metal translocation factors (TFs) in the plants inoculated with the EPS. These results suggest a beneficial effect of the rhizobacterial EPS on plant growth and abiotic stress mitigation. In addition, the data suggest that the reduced levels of trace metals in plants exposed to P. ultramafica STM10279T are due to metal chelation by the EPS. Further investigations are needed to firmly demonstrate whether this EPS could be used as a biostimulant for plant growth and adaptation to ultramafic soils. [ABSTRACT FROM AUTHOR]

All non-Mimosoid nodulated genera in the legume subfamily Caesalpinioideae confine their rhizobial symbionts within cell wall-bound 'fixation threads' (FTs). The exception is the large genus Chamaecrista in which shrubs and subshrubs house their rhizobial bacteroids more intimately within symbiosomes, whereas large trees have FTs. This study aimed to unravel the evolutionary relationships between Chamaecrista growth habit, habitat, nodule bacteroid type, and rhizobial genotype. The growth habit, bacteroid anatomy, and rhizobial symbionts of 30 nodulated Chamaecrista species native to different biomes in the Brazilian state of Bahia, a major centre of diversity for the genus, was plotted onto an ITS- trnL-F -derived phylogeny of Chamaecrista. The bacteroids from most of the Chamaecrista species examined were enclosed in symbiosomes (SYM-type nodules), but those in arborescent species in the section Apoucouita , at the base of the genus, were enclosed in cell wall material containing homogalacturonan (HG) and cellulose (FT-type nodules). Most symbionts were Bradyrhizobium genotypes grouped according to the growth habits of their hosts, but the tree, C. eitenorum , was nodulated by Paraburkholderia. Chamaecrista has a range of growth habits that allow it to occupy several different biomes and to co-evolve with a wide range of (mainly) bradyrhizobial symbionts. FTs represent a less intimate symbiosis linked with nodulation losses, so the evolution of SYM-type nodules by most Chamaecrista species may have (i) aided the genus-wide retention of nodulation, and (ii) assisted in its rapid speciation and radiation out of the rainforest into more diverse and challenging habitats. [ABSTRACT FROM AUTHOR]

The evolution of symbiotic interactions may be affected by unpredictable conditions. However, a link between prevalence of these conditions and symbiosis has not been widely demonstrated. We test for these associations using Dictyostelium discoideum social amoebae and their bacterial endosymbionts. D. discoideum commonly hosts endosymbiotic bacteria from three taxa: Paraburkholderia, Amoebophilus and Chlamydiae. Three species of facultative Paraburkholderia endosymbionts are the best studied and give hosts the ability to carry prey bacteria through the dispersal stage to new environments. Amoebophilus and Chlamydiae are obligate endosymbiont lineages with no measurable impact on host fitness. We tested whether the frequency of both single infections and coinfections of these symbionts were associated with the unpredictability of their soil environments by using symbiont presence-absence data from D. discoideum isolates from 21 locations across the eastern United States. We found that symbiosis across all infection types, symbiosis with Amoebophilus and Chlamydiae obligate endosymbionts, and symbiosis involving coinfections were not associated with any of our measures. However, unpredictable precipitation was associated with symbiosis in two species of Paraburkholderia, suggesting a link between unpredictable conditions and symbiosis. [ABSTRACT FROM AUTHOR]

Paraburkholderia ultramafica STM10279T is a metal-tolerant rhizobacterium that promotes plant growth. It was isolated from the roots of Tetraria arundinaceae, a pioneer endemic tropical herb growing on ultramafic soils in New Caledonia. We have recently shown that the main mechanism of metal tolerance of P. ultramafica is related to the production of an acidic exopolysaccharide (EPS). To explore the potential role of this EPS in the plant’s environmental adaptation, we first elucidated its structure by employing a combination of chromatography and mass spectrometry techniques. These analyses revealed that the EPS is highly branched and composed of galactosyl (35.8%), glucosyl (33.2%), rhamnosyl (19.5%), mannosyl (7.2%), and glucuronosyl residues (4.4%), similar to the EPS of the Burkholderia cepacia complex known as cepacian. We subsequently conducted greenhouse experiments on Tetraria comosa plantlets inoculated with P. ultramafica or a solution of its EPS during transplanting onto ultramafic substrate. The data showed that the dry weight of T. comosa shoots was 2.5 times higher in the plants treated with the EPS compared to the unexposed plants. In addition, inductively coupled plasma–optical emission spectrometry (ICP-OES) analysis revealed that exposure to the EPS significantly increased Ca, Mg, K, and P uptake as well as K content in roots. In vitro experiments using the Pikovskaya method showed that the EPS was able to solubilize phosphorus. Consistent with the retention of metals in roots and a reduction in shoots, our data revealed a significant decrease in metal translocation factors (TFs) in the plants inoculated with the EPS. These results suggest a beneficial effect of the rhizobacterial EPS on plant growth and abiotic stress mitigation. In addition, the data suggest that the reduced levels of trace metals in plants exposed to P. ultramafica STM10279T are due to metal chelation by the EPS. Further investigations are needed to firmly demonstrate whether this EPS could be used as a biostimulant for plant growth and adaptation to ultramafic soils.

The evolution of symbiotic interactions may be affected by unpredictable conditions. However, a link between prevalence of these conditions and symbiosis has not been widely demonstrated. We test for these associations using Dictyostelium discoideum social amoebae and their bacterial endosymbionts. D. discoideum commonly hosts endosymbiotic bacteria from three taxa: Paraburkholderia, Amoebophilus and Chlamydiae. Three species of facultative Paraburkholderia endosymbionts are the best studied and give hosts the ability to carry prey bacteria through the dispersal stage to new environments. Amoebophilus and Chlamydiae are obligate endosymbiont lineages with no measurable impact on host fitness. We tested whether the frequency of both single infections and coinfections of these symbionts were associated with the unpredictability of their soil environments by using symbiont presence-absence data from D. discoideum isolates from 21 locations across the eastern United States. We found that symbiosis across all infection types, symbiosis with Amoebophilus and Chlamydiae obligate endosymbionts, and symbiosis involving coinfections were not associated with any of our measures. However, unpredictable precipitation was associated with symbiosis in two species of Paraburkholderia, suggesting a link between unpredictable conditions and symbiosis.

Cyanobacterial blooms in freshwater bodies are mainly attributed to the excess loading of nutrients. The microbes in sediments may affect nutrient migration and transformation during the growth of cyanobacteria. This study focused on the role of Paraburkholderia disturbance in affecting the sediment nutrient conditions and further contributing to cyanobacterial community succession in Meiliang Bay, Lake Taihu. The dissolving phosphorus and fixing nitrogen of Paraburkholderia with different concentration and characteristic capabilities, as well as the impact on nutrients (nitrogen (N), phosphorus (P), iron (Fe), etc.) in eutrophic lakes were determined. The results indicated that the various forms of phosphorus in the sediments showed total phosphorus (TP) > inorganic phosphorus (IP) > iron/aluminum-bound phosphate (NaOH-P) > algal-available phosphorus (AAP) > organic phosphorus (OP) > calcium-bound phosphate (HCl-P). Additionally, it was observed that with higher values of Paraburkholderia (OD600), the higher the corresponding risk of endogenous nutrient release from the sediments into the overlying water (but more is not always better), especially for the solubilization of HCl-P. The diffusion fluxes of TP, total nitrogen (TN) and Fe at the sediment–water interface (SWI) were all positive in the bacteria only experiment, with maximum values of 0.64, 15.0 and 5.02 mg/(m2d), respectively. Additionally, it was interesting that Paraburkholderia were able to produce organic acids, causing a decrease in pH. Furthermore, glucose levels can seriously affect water quality, especially the reduction in dissolved oxygen (DO) (down to 0.01 mg/L), leading to a series of side effects that have a huge impact on cyanobacterial community succession. These results provide a theoretical basis for the microbial ecological factors in eutrophic lakes. [ABSTRACT FROM AUTHOR]

Main conclusion: Extracellular traps in the primary root of Pinus densiflora contribute to root-associated bacterial colonization. Trapped rhizobacteria induce the production of reactive oxygen species in root-associated, cap-derived cells. Ectomycorrhizal (ECM) woody plants, such as members of Pinaceae and Fagaceae, can acquire resistance to biotic and abiotic stresses through the formation of mycorrhiza with ECM fungi. However, germinated tree seedlings do not have mycorrhizae and it takes several weeks for ectomycorrhizae to form on their root tips. Therefore, to confer protection during the early growth stage, bare primary roots require defense mechanisms other than mycorrhization. Here, we attempted to visualize root extracellular traps (RETs), an innate root defense mechanism, in the primary root of Pinus densiflora and investigate the interactions with root-associated bacteria isolated from ECM and fine non-mycorrhizal roots. Histological and histochemical imaging and colony-forming unit assays demonstrated that RETs in P. densiflora, mainly consisting of root-associated, cap-derived cells (AC-DCs) and large amounts of root mucilage, promote bacterial colonization in the rhizosphere, despite also having bactericidal activity via extracellular DNA. Four rhizobacterial strains retarded the mycelial growth of a pathogenic strain belonging to the Fusarium oxysporum species complex in dual culture assay. They also induced the production of reactive oxygen species (ROS) from host tree AC-DCs without being excluded from the rhizosphere of P. densiflora. Applying three Paraburkholderia strains, especially PM O-EM8 and PF T-NM22, showed significant differences in the ROS levels from the control group. These results reveal the indirect contributions of rhizobacteria to host root defense and suggest that root-associated bacteria could be a component of RETs as a first line of defense against root pathogens in the early growth stage of ECM woody plants. [ABSTRACT FROM AUTHOR]

Glucose and xylose are fermentable sugars readily available from lignocellulosic biomass, and are a sustainable carbon substrate supporting industrial biotechnology. Three strains were assessed in this work – Paraburkholderia sacchari , Hydrogenophaga pseudoflava , and Bacillus megaterium – for their ability to uptake both C 5 and C 6 sugars contained in a hardwood hydrolysate produced via a thermomechanical pulping-based process with concomitant production of poly(3-hydroxyalkanoate) (PHA) biopolymers. In batch conditions, B. megaterium showed poor growth after 12 h, minimal uptake of xylose throughout the cultivation, and accumulated a maximum of only 25 % of the dry biomass as PHA. The other strains simultaneously utilized both sugars, although glucose uptake was faster than xylose. From hardwood hydrolysate, P. sacchari accumulated 57 % of its biomass as PHA within 24 h, whereas H. pseudoflava achieved an intracellular PHA content of 84 % by 72 h. The molecular weight of the PHA synthesized by H. pseudoflava (520.2 kDa) was higher than that of P. sacchari (265.5 kDa). When the medium was supplemented with propionic acid, the latter was rapidly consumed by both strains and incorporated as 3-hydroxyvalerate subunits into the polymer, demonstrating the potential for production of polymers with improved properties and value. H. pseudoflava incorporated 3-hydroxyvalerate subunits with at least a 3-fold higher yield, and produced polymers with higher 3-hydroxyvalerate content than P. sacchari. Overall, this work has shown that H. pseudoflava can be an excellent candidate for bioconversion of lignocellulosic sugars to PHA polymers or copolymers as part of an integrated biorefinery. [Display omitted] • Three strains were evaluated to convert hardwood hydrolysate into PHA biopolymers. • Hydrogenophaga pseudoflava accumulated up to 84 % of its cell mass as PHA. • This strain also synthesized at least two-fold higher molecular weight polymers. • The strain displayed three-fold higher propionate-to-3-hydroxyvalerate yields. • H. pseudoflava may be promising for PHA production in an integrated biorefinery. [ABSTRACT FROM AUTHOR]

Two Gram-stain-negative, aerobic, motile and short rod strains, designated 4D117T and ZD32-2T, were isolated from the forest soils. Strains 4D117T and ZD32-2T grew optimally at pH 4.0–6.5, 20–33 °C and pH 4.5–7.0, 33 °C, respectively, and both at 0.5% (w/v) NaCl concentration. Strains 4D117T and ZD32-2T shared the highest 16S rRNA gene sequence similarity with P. acidiphila 7Q-K02T (99.1%) and P. ferrariae NBRC 106233T (98.7%), respectively. The genome size and G + C contents of strains 4D117T and ZD32-2T were 9,002,095 bp, 62.9% and 6,974,420 bp, 61.7%, respectively. The dDDH and ANI values between strains 4D117T, ZD32-2T and closely related Paraburkholderia species were in the ranges of 21.9–51.6% and 82.9–94.4%, and 81.7% and 25.4% between themself, respectively. Functional genomic analysis showed both strains were capable of degrading contaminants, such as benzoate, anthranilic acid and catechol for 4D117T, and benzene and catechol for ZD32-2T, indicating that they may have potentials for soil pollutant treatment. The main polar lipids of strains 4D117T and ZD32-2T were phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain 4D117T contained C16:0, C19:0 cyclo ω8c and C18:1ω7c and/or C18:1ω6c, while strain ZD32-2T had C16:0 and C17:0 cyclo as their major cellular fatty acids (> 10%). Based on the phenotypic characters and genomic data, strains 4D117T and ZD32-2T represent two novel species of genus Paraburkholderia, for which the names Paraburkholderia flagellata sp. nov. (type strain 4D117T = GDMCC 1.2617T = NBRC 115278T) and Paraburkholderia adhaesiva sp. nov. (type strain ZD32-2T = GDMCC 1.2622T = NBRC 115282T) are proposed. [ABSTRACT FROM AUTHOR]

ABSTRACT This study introduces a novel approach based on the taxonomy-guided selection of bacterial biocontrol agents from a known beneficial taxonomic group. Following 16S rRNA screening, we focused on the genus Paraburkholderia, which harbors strains with large genomes and versatile benefits to plants. A strain designated P39 was selected, identified, and characterized for its biocontrol activity against Colletotrichum scovillei. Strain P39 exhibited antagonism against C. scovillei by producing compounds, including volatiles, with antifungal activity, both in vitro and on pepper fruits. Genomic, physiological, and biochemical analyses revealed that the selected strain represents a novel species, named Paraburkholderia busanensis. Genomic analyses provided insights into the fitness and biocontrol activities of the selected strains. Moreover, P39 displays mycophagy, consuming fungal mycelia and transforming them into bacterial biomass, particularly in nutrient-poor media supplemented with fungal mycelia. The genome harbored chitin and N-acetylglucosamine utilization genes, suggesting a proposed pathway for the utilization of fungal cells as a nutrient source. Microscopic observations further supported the ability of this strain to rupture and damage fungal hyphae, depriving them of their cellular constituents. This study successfully demonstrated the implementation of a taxonomy-guided approach for the selection of bacterial strains for biocontrol. These findings contribute to our understanding of biocontrol strategies, bacteria-fungi interactions, and the identification of Paraburkholderia busanensis sp. nov. as a potential candidate for the biocontrol of pepper anthracnose. Additionally, this strain serves as a valuable resource for antifungal compounds and volatiles, and for the study of bacteria-fungal interactions and mycophagy. IMPORTANCE Traditional control methods for postharvest diseases rely on fungicides, which cause human health and environmental concerns. This study introduces a taxonomy-guided strategy for selecting biocontrol agents. By focusing on Paraburkholderia group, which harbors diverse plant-beneficial strains, the inadvertent selection of harmful strains was circumvented, thereby obviating the need for laborious in vitro screening assays. A highly promising candidate, strain P39, has been identified, exhibiting remarkable biocontrol activity against Colletotrichum scovillei. Through comprehensive genomic, physiological, and biochemical analyses, P39 was characterized as a novel species within the Paraburkholderia genus and designated Paraburkholderia busanensis. Moreover, these findings deepen our understanding of bacterial-fungal interactions, as they elucidate a potential pathway for the utilization of fungal chitin, thereby enhancing our understanding of bacterial mycophagy. P. busanensis is a promising source of antifungal volatiles and putative novel secondary metabolites.

Abstract The taxonomy of Burkholderia sensu lato (s.l.) has been revisited using genome-based tools, which have helped differentiate closely related species. Many species from this group are indistinguishable through phenotypic traits and 16S rRNA gene sequence analysis. Furthermore, they also exhibit whole-genome Average Nucleotide Identity (ANI) values in the twilight zone for species circumscription (95-96%), which may impair their correct classification. In this work, we provided an updated Burkholderia s.l. taxonomy focusing on closely related species and give other recommendations for those developing genome-based taxonomy studies. We showed that a combination of ANI and digital DNA-DNA hybridization (dDDH) applying the universal cutoff values of 95% and 70%, respectively, successfully discriminates Burkholderia s.l. species. Using genome metrics with this pragmatic criterion, we demonstrated that i) Paraburkholderia insulsa should be considered a later heterotypic synonym of Paraburkholderia fungorum; ii) Paraburkholderia steynii differs from P. terrae by harboring symbiotic genes; iii) some Paraburkholderia are indeed different species based on dDDH values, albeit sharing ANI values close to 95%; iv) some Burkholderia s.l. indeed represent new species from the genomic viewpoint; iv) some genome sequences should be evaluated with care due to quality concerns.

Little is currently known about the metabolism of the industrial pollutant 2,4-dinitrophenol (DNP), particularly among gram-negative bacteria. In this study, we identified two non-contiguous genetic loci spanning 22 kb of Paraburkholderia (formerly Burkholderia) sp. strain KU-46. Additionally, we characterized four key initial genes (dnpA , dnpB , and dnpC1C2) responsible for DNP degradation, providing molecular and biochemical evidence for the degradation of DNP via the formation of 4-nitrophenol (NP), a pathway that is unique among DNP utilizing bacteria. Reverse transcription polymerase chain reaction (PCR) analysis indicated that dnpA , which encodes the initial hydride transferase, and dnpB which encodes a nitrite-eliminating enzyme, were induced by DNP and organized in an operon. Moreover, we purified DnpA and DnpB from recombinant Escherichia coli to demonstrate their effect on the transformation of DNP to NP through the formation of a hydride-Meisenheimer complex of DNP, designated as H−-DNP. The function of DnpB appears new since all homologs of the DnpB sequences in the protein database are annotated as putative nitrate ABC transporter substrate-binding proteins. The gene cluster responsible for the degradation of DNP after NP formation was designated dnpC1C2DXFER , and DnpC1 and DnpC2 were functionally characterized as the FAD reductase and oxygenase components of the two-component DNP monooxygenase, respectively. By elucidating the hqdA1A2BCD gene cluster, we are now able to delineate the final degradation pathway of hydroquinone to β-ketoadipate before it enters the tricarboxylic acid cycle. [ABSTRACT FROM AUTHOR]

Polyhydroxyalkanoates (PHAs) are bioplastics that can serve as substitutes for petroleum-based plastics with the advantages of being biodegradable, biocompatible, and biobased. The microbial production of polyhydroxyalkanoates is generally conducted in the presence of sugar mixes rich in monosaccharides. In this study, molecular and cultural approaches based on forest soils enriched with hydrocarbon complexes led to the identification and isolation of microbial strains affiliated with Paraburkholderia sp. that dominated the microbial communities that are recognized among the top polyhydroxyalkanoates producers. The genome sequencing of those isolated affiliated strains showed that compared to the reference type strain of their species, they harbored more gene copies of the enzymes involved in PHB synthesis. The microbial conversion of sugar mixes for the newly isolated strains showed a higher PHB production (g/L) and content (%) than was exhibited by the reference strain type of that genus Paraburkholderia for PHB production (P. sacchari LMG 19450T). [ABSTRACT FROM AUTHOR]

The compound 3-chlorobenzoate (3-CBA) is a hazardous industrial waste product that can harm human health and the environment. This study investigates the physiological and genetic potential for 3-chlorobenzoate (3-CBA) degradation. Six 3-CBA Gram-negative degraders with different degradation properties belonging to the genera Caballeronia, Paraburkholderia and Cupriavidus were isolated from the soil. The representative strains Caballeronia 19CS4-2 and Paraburkholderia 19CS9-1 showed higher maximum specific growth rates (µmax, h−1) than Cupriavidus 19C6 and degraded 5 mM 3-CBA within 20–28 h. Two degradation products, chloro-cis,cis-muconate and maleylacetate, were detected in all isolates using high-performance liquid chromatography and mass spectrometry. Genomic analyses revealed the presence of cbe and tfd gene clusters in strains 19CS4-2 and 19CS9-1, indicating that they probably metabolized the 3-CBA via the chlorocatechol ortho-cleavage pathway. Strain 19C6 possessed cbe genes, but not tfd genes, suggesting it might have a different chlorocatechol degradation pathway. Putative genes for the metabolism of 3-hydroxybenzoate via gentisate were found only in 19C6, which utilized the compound as a sole carbon source. 19C6 exhibited distinct characteristics from strains 19CS4-2 and 19CS9-1. The results confirm that bacteria can degrade 3-CBA and improve our understanding of how they contribute to environmental 3-CBA biodegradation. [ABSTRACT FROM AUTHOR]

Keypoints P. aromaticivorans AR20-38 differentially regulates three main enzymes for the bioconversion of ferulic acid to vanillic acid. ATP binding cassette transporters, major facilitator superfamily transporters and outer membrane vesicles are putative transport routes for catabolic enzymes. Regulated degradation enzymes indicate xenobiotic degradation potential

Bacterial endosymbionts can provide benefits for their eukaryotic hosts, but it is often unclear if endosymbionts benefit from these relationships. The social amoeba Dictyostelium discoideum associates with three species of Paraburkholderia endosymbionts, including P. agricolaris and P. hayleyella. These endosymbionts can be costly to the host but are beneficial in certain contexts because they allow D. discoideum to carry prey bacteria through the dispersal stage. In experiments where no other species are present, P. hayleyella benefits from D. discoideum while P. agricolaris does not. However, the presence of other species may influence this symbiosis. We tested if P. agricolaris and P. hayleyella benefit from D. discoideum in the context of resource competition with Klebsiella pneumoniae , the typical laboratory prey of D. discoideum. Without D. discoideum, K. pneumoniae depressed the growth of both Paraburkholderia symbionts, consistent with competition. P. hayleyella was more harmed by interspecific competition than P. agricolaris. We found that P. hayleyella was rescued from competition by D. discoideum , while P. agricolaris was not. This may be because P. hayleyella is more specialized as an endosymbiont; it has a highly reduced genome compared to P. agricolaris and may have lost genes relevant for resource competition outside of its host. [ABSTRACT FROM AUTHOR]

A multifunctional, Gram-stain-negative, aerobic, motile by flagella, short-rod shaped bacteria, designated strain RG36T was isolated from roots of marigold plant (Tagetes patula) sampled at Dongguk University, Republic of Korea. A 16S rRNA sequences indicated that the closest phylogenetic neighbors were Paraburkholderia acidiphila 7Q-K02T (99.0%) and Paraburkholderia sacchari IPT101T (98.9%) of the family Burkholderiaceae. The draft genome size was 8.52 Mb (63.7% GC). The genome contained 7,381 coding sequences. Digital DNA--DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strain RG36T with its most closely related species were only 83.1-88.7 and 27.6-36.7%, respectively. Strain RG36T contained Q-8 as the major respiratory quinone and its main fatty acids (>10%) were C16:0, C17:0 cyclo, C19:0 cyclo ω8c, and summed feature 8 (comprising C18:1 ω7c and/or C18V1 ω6c). Strain RG36T accumulates polyhydroxybutyrates (PHB) and exhibits multiple plant growth-promoting properties including production of indole-3-acetic acid (IAA), siderophores, protease, phosphate solubilization, and harboring gene clusters for its multifunctional properties. A pot experiment was conducted to evaluate the effect of PGPR on the growth of Solanum lycopersicum L. (Tomato). Result also confirmed the ability of strain RG36T to promote tomato plant growth, especially it increases the yield of tomatoes. Structural assessment of the bioplastic by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and GC-MS spectroscopy, which confirmed the structure of the polymer as PHB. Our study revealed the potential of strain RG36T to promote the growth of tomato plant and fruit yield by stimulating the various phytohormones, which could be use as bio-fertilizers to reduce the use of chemical fertilizers and promotes sustainable agricultural production. The phenotypic, chemotaxonomic and phylogenetic data, and genome analysis showed that strain RG36T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia tagetis sp. nov. is proposed. The type strain is RG36T (=KACC 22685T D TBRC 15696T). [ABSTRACT FROM AUTHOR]

Some endosymbionts living within a host must modulate their hosts' immune systems in order to infect and persist. We studied the effect of a bacterial endosymbiont on a facultatively multicellular social amoeba host. Aggregates of the amoeba Dictyostelium discoideum contain a subpopulation of sentinel cells that function akin to the immune systems of more conventional multicellular organisms. Sentinel cells sequester and discard toxins from D. discoideum aggregates and may play a central role in defence against pathogens. We measured the number and functionality of sentinel cells in aggregates of D. discoideum infected by bacterial endosymbionts in the genus Paraburkholderia. Infected D. discoideum produced fewer and less functional sentinel cells, suggesting that Paraburkholderia may interfere with its host's immune system. Despite impaired sentinel cells, however, infected D. discoideum were less sensitive to ethidium bromide toxicity, suggesting that Paraburkholderia may also have a protective effect on its host. By contrast, D. discoideum infected by Paraburkholderia did not show differences in their sensitivity to two non-symbiotic pathogens. Our results expand previous work on yet another aspect of the complicated relationship between D. discoideum and Paraburkholderia, which has considerable potential as a model for the study of symbiosis.

"Burkholderia dabaoshanensis" was described in 2012. Although the name was effectively published, it could not be validly published, because the description provided in the original paper did not comply with the Rule 27 (2) (c) of the Bacterial Code. The Code requiresthat the properties of the taxon form part of the protologue. As the name of this species does not have standing in nomenclature, the recently published new combination Trinickia dabaoshanensis could also not be validly published. The current proposal attempts to rectify the situation by providing the information required to meet the criteria stipulated in Rule 27 for valid publication.

A multifunctional, Gram-stain-negative, aerobic, motile by flagella, short-rod shaped bacteria, designated strain RG36T was isolated from roots of marigold plant (Tagetes patula) sampled at Dongguk University, Republic of Korea. A 16S rRNA sequences indicated that the closest phylogenetic neighbors were Paraburkholderia acidiphila 7Q-K02T (99.0%) and Paraburkholderia sacchari IPT101T (98.9%) of the family Burkholderiaceae. The draft genome size was 8.52 Mb (63.7% GC). The genome contained 7,381 coding sequences. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strain RG36T with its most closely related species were only 83.1–88.7 and 27.6–36.7%, respectively. Strain RG36T contained Q-8 as the major respiratory quinone and its main fatty acids (>10%) were C16:0, C17:0 cyclo, C19:0 cyclo ω8c, and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). Strain RG36T accumulates polyhydroxybutyrates (PHB) and exhibits multiple plant growth-promoting properties including production of indole-3-acetic acid (IAA), siderophores, protease, phosphate solubilization, and harboring gene clusters for its multifunctional properties. A pot experiment was conducted to evaluate the effect of PGPR on the growth of Solanum lycopersicum L. (Tomato). Result also confirmed the ability of strain RG36T to promote tomato plant growth, especially it increases the yield of tomatoes. Structural assessment of the bioplastic by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and GC-MS spectroscopy, which confirmed the structure of the polymer as PHB. Our study revealed the potential of strain RG36T to promote the growth of tomato plant and fruit yield by stimulating the various phytohormones, which could be use as bio-fertilizers to reduce the use of chemical fertilizers and promotes sustainable agricultural production. The phenotypic, chemotaxonomic and phylogenetic data, and genome analysis showed that strain RG36T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia tagetis sp. nov. is proposed. The type strain is RG36T (=KACC 22685T = TBRC 15696T).

Background and Aims: Free living, non-symbiotic nitrogen-fixing bacteria (diazotrophs) that inhabit plant rhizosphere substantially contribute to nitrogen input in forest ecosystems. Different plant species provide heterogeneous habitats for rhizosphere diazotrophs by releasing root exudates containing potential resources for microbial utilization, but the ecological processes of diazotrophic community assembly and association with plant species are not fully understood. Methods: We investigated the diazotrophic abundance (as assessed by real-time quantitative PCR), diversity, and composition of rhizosphere diazotrophic communities (based on nifH-amplicon sequencing) for four non-leguminous broadleaf tree species and three conifer tree species in a forest ecosystem. Results: The analysis revealed that the rhizosphere of four broadleaf tree species harbored higher diazotrophic abundance and diversity by 239% and 50.0% respectively, as compared to the conifer tree species. Further, phylogenetic distance between the seven tree species was positively correlated (Mantel r = 0.482, P < 0.001) with the dissimilarity of diazotrophic community assembly, thus determining rhizosphere potential nitrogen fixation indicated by nifH gene abundance. Of the top 20 genera (ranked by percentage increase in Mean Squared Error) that contribute to potential nitrogen fixation, 11 rare genera were at low relative abundances (< 1%). Network analysis further showed the central position of rare genera in the diazotrophic co-occurrence network of four broadleaf tree species, as the closeness centrality of rare genera was significantly higher than that of abundant genera. Conclusion: Overall, the study suggested that the identity of tree species impresses the assembly of diazotrophic communities in its rhizosphere. Possible implication of our findings for forest management is discussed for maintaining nitrogen sustainability in forest ecosystems. [ABSTRACT FROM AUTHOR]

Abstract Symbiotic interactions change with environmental context. Measuring these context‐dependent effects in hosts and symbionts is critical to determining the nature of symbiotic interactions. We investigated context dependence in the symbiosis between social amoeba hosts and their inedible Paraburkholderia bacterial symbionts, where the context is the abundance of host food bacteria. Paraburkholderia have been shown to harm hosts dispersed to food‐rich environments, but aid hosts dispersed to food‐poor environments by allowing hosts to carry food bacteria. Through measuring symbiont density and host spore production, we show that this food context matters in three other ways. First, it matters for symbionts, who suffer a greater cost from competition with food bacteria in the food‐rich context. Second, it matters for host‐symbiont conflict, changing how symbiont density negatively impacts host spore production. Third, data‐based simulations show that symbiosis often provides a long‐term fitness advantage for hosts after rounds of growth and dispersal in variable food contexts, especially when conditions are harsh with little food. These results show how food context can have many consequences for the Dictyostelium‐Paraburkholderia symbiosis and that both sides can frequently benefit.

Neotropical Beta-rhizobia have a particular affinity to the large legume (Fabaceae) genus Mimosa and some of its relatives in the tribe Mimosae of the Caesalpinioideae subfamily. However, little is still known about the ecology of this interaction, especially the relationship between the rhizobia of "widespread" pan-tropical Mimosa species like M. pudica and the rhizobia that nodulate endemic Mimosa species that are very restricted in their habitats. The objective of this study was to examine the microsymbionts of Mimosa spp. and other mimosoids in climates ranging from tropical to subtropical, humid to semi-arid, with varied soil characteristics and altitudes, with the aim of testing the hypothesis that widespread species have more cosmopolitan symbiont preferences than endemic ones. Nodules were sampled from >30 Mimosa spp. and related taxa in 13 Brazilian states covering all five national regions; many of the species were endemics or biome-restricted, but particular attention was also paid to sample nodules from the widespread species M. pudica at all locations. The Mimosa symbionts comprised 21 potential 16S rRNA and recA groups at the species level, with 17 belonging to the genus Paraburkholderia , including four lineages that may represent new species. The remaining genotypes consisted of 14 strains in two lineages of Cupriavidus that were mainly isolated from M. pudica growing at low altitudes, and a single lineage of Rhizobium also from M. pudica. In addition, a strain of Trinickia symbiotica was isolated from M. misera. It is concluded that diverse genotypes of Paraburkholderia dominate as symbionts of Mimosa in the acidic soils of its main center of radiation in Central Brazil but that Cupriavidus and Rhizobium comprise a significant minority of symbionts of widespread Mimosa spp., especially M. pudica , in lowland or disturbed areas with less acidic soils. Mimosa symbiont selection is thus driven either by edapho-climatic characteristics for widespread species and/or by co-evolution of the symbiotic partners for endemic species. • A survey of Mimosa -nodulating symbionts was conducted in thirteen Brazilian states. • Endemic Mimosa spp. are almost exclusively nodulated by Paraburkholderia strains. • Genomic comparisons indicate that these include several potential new species. • Widespread Mimosa spp. are also nodulated with Cupriavidus and Rhizobium strains. • The selection of symbionts by widespread Mimosa spp. depends on edaphic characters. [ABSTRACT FROM AUTHOR]

This study provided evidence at the first time showing that root inoculation with the plant growth-promoting rhizobacteria Paraburkholderia sp. GD17 improved the growth and tolerance to Cd stress in Chinese cabbage seedlings. Under normal conditions, the shoot fresh and dry weight of GD17-inoculated 30-day-old plants increased by about 29 % and 33 %, and their root fresh and dry weight by 104 % and 67 %, respectively, compared with their non-inoculated partners. The GD17-mediated growth promotion could be attributed to its facilitating influence on plant acquisition of nutrient elements and photosynthetic efficiency, and decreasing abscisic acid production. Under Cd stress, an effective alleviation in Cd-induced growth inhibition was observed in GD17 plants relative to non-inoculated control, suggesting that the root inoculation with GD17 played a systemic protective role. The Cd concentration in plant aerial tissues was comparable between GD17 plants and non-inoculated ones, but it was substantially decreased in GD17 plant roots. In response to Cd, GD17-inoculated plants generally showed a stronger ability to absorb and transport nutrient elements to shoots. The GD17-conferred plant tolerance to Cd was also associated with an increased antioxidative capacity companied by declined oxidative damage, optimal levels of phytohormones, increased flavonoid synthesis as indicated by significantly upregulated expression of related genes and activity of phenylalanine ammonia-lyase. Additionally, root inoculation with GD17 effectively mitigated the Cd-induced decline in photosynthetic efficiency. Collectively, this study firstly showed that GD17-conferred growth-promotion and Cd-tolerance in Chinese cabbage was correlated with multiple regulatory roles in plant metabolism, which, in most cases, was involved in the regulation at the transcription levels of relevant genes. • GD17 strain improves Chinese cabbage seedling growth. • GD17 strain promotes Cd tolerance in Chinese cabbage seedlings. • GD17 regulates the Cd absorption and intracellular chelation, nutrient element acquisition and root-shoot transport. • GD17 regulates antioxidative defense, phytohormone contents, flavonoid synthesis and photosynthetic efficiency. [ABSTRACT FROM AUTHOR]

Cyanobacterial blooms in freshwater bodies are mainly attributed to the excess loading of nutrients. The microbes in sediments may affect nutrient migration and transformation during the growth of cyanobacteria. This study focused on the role of Paraburkholderia disturbance in affecting the sediment nutrient conditions and further contributing to cyanobacterial community succession in Meiliang Bay, Lake Taihu. The dissolving phosphorus and fixing nitrogen of Paraburkholderia with different concentration and characteristic capabilities, as well as the impact on nutrients (nitrogen (N), phosphorus (P), iron (Fe), etc.) in eutrophic lakes were determined. The results indicated that the various forms of phosphorus in the sediments showed total phosphorus (TP) > inorganic phosphorus (IP) > iron/aluminum-bound phosphate (NaOH-P) > algal-available phosphorus (AAP) > organic phosphorus (OP) > calcium-bound phosphate (HCl-P). Additionally, it was observed that with higher values of Paraburkholderia (OD600), the higher the corresponding risk of endogenous nutrient release from the sediments into the overlying water (but more is not always better), especially for the solubilization of HCl-P. The diffusion fluxes of TP, total nitrogen (TN) and Fe at the sediment–water interface (SWI) were all positive in the bacteria only experiment, with maximum values of 0.64, 15.0 and 5.02 mg/(m2d), respectively. Additionally, it was interesting that Paraburkholderia were able to produce organic acids, causing a decrease in pH. Furthermore, glucose levels can seriously affect water quality, especially the reduction in dissolved oxygen (DO) (down to 0.01 mg/L), leading to a series of side effects that have a huge impact on cyanobacterial community succession. These results provide a theoretical basis for the microbial ecological factors in eutrophic lakes.

Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4⁻7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into Burkholderia, Caballeronia, Paraburkholderia, and Robbsia is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of Burkholderia s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in Paraburkholderia (which also includes all the N₂-fixing legume symbionts) and Caballeronia, while most of the human and animal pathogens are retained in Burkholderia sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related Paraburkholderia rhizoxinica and Paraburkholderia endofungorum, which are both symbionts of the fungal phytopathogen Rhizopus microsporus. The second group comprises the Mimosa-nodulating bacterium Paraburkholderia symbiotica, the phytopathogen Paraburkholderia caryophylli, and the soil bacteria Burkholderia dabaoshanensis and Paraburkholderia soli. In order to clarify their positions within Burkholderia sensu lato, a phylogenomic approach based on a maximum likelihood analysis of conserved genes from more than 100 Burkholderia sensu lato species was carried out. Additionally, the average nucleotide identity (ANI) and amino acid identity (AAI) were calculated. The data strongly supported the existence of two distinct and unique clades, which in fact sustain the description of two novel genera Mycetohabitans gen. nov. and Trinickia gen. nov. The newly proposed combinations are Mycetohabitans endofungorum comb. nov., Mycetohabitansrhizoxinica comb. nov., Trinickia caryophylli comb. nov., Trinickiadabaoshanensis comb. nov., Trinickia soli comb. nov., and Trinickiasymbiotica comb. nov. Given that the division between the genera that comprise Burkholderia s.l. in terms of their lifestyles is often complex, differential characteristics of the genomes of these new combinations were investigated. In addition, two important lifestyle-determining traits-diazotrophy and/or symbiotic nodulation, and pathogenesis-were analyzed in depth i.e., the phylogenetic positions of nitrogen fixation and nodulation genes in Trinickia via-à-vis other Burkholderiaceae were determined, and the possibility of pathogenesis in Mycetohabitans and Trinickia was tested by performing infection experiments on plants and the nematode Caenorhabditis elegans. It is concluded that (1) T. symbiotica nif and nod genes fit within the wider Mimosa-nodulating Burkholderiaceae but appear in separate clades and that T. caryophyllinif genes are basal to the free-living Burkholderia s.l. strains, while with regard to pathogenesis (2) none of the Mycetohabitans and Trinickia strains tested are likely to be pathogenic, except for the known phytopathogen T. caryophylli.

[This corrects the article on p. 1154 in vol. 8, PMID: 28694797.].

The importance and need of renewable-based, sustainable feedstocks increased in recent years. Lignin-derived monomers have high potential, energetic and economic value in the microbial bioconversion to valuable biomolecules. The bacterium Paraburkholderia aromaticivorans AR20-38 produces a remarkable yield of vanillic acid from ferulic acid at moderate and low temperatures and is therefore a good candidate for biotechnological applications. To understand this bioconversion process on a molecular level, a transcriptomic study during the bioconversion process was conducted to elucidate gene expression patterns. Differentially expressed genes, cellular transporters as well as transcriptional factors involved in the bioconversion process could be described. Additional enzymes known for xenobiotic degradation were differentially expressed and a potential membrane vesicle mechanism was detected. The bioconversion mechanism on a transcriptional level of P. aromaticivorans could be elucidated and results can be used for strain optimization. Additionally, the transcriptome study showed the high potential of the strain for other degradation applications. Keypoints: P. aromaticivorans AR20-38 differentially regulates three main enzymes for the bioconversion of ferulic acid to vanillic acid. ATP binding cassette transporters, major facilitator superfamily transporters and outer membrane vesicles are putative transport routes for catabolic enzymes. Regulated degradation enzymes indicate xenobiotic degradation potential [ABSTRACT FROM AUTHOR]

The relationship between the social amoeba Dictyostelium discoideum and its endosymbiotic bacteria Paraburkholderia provides a model system for studying the development of symbiotic relationships. Laboratory experiments have shown that any of three species of the Paraburkholderia symbiont allow D. discoideum food bacteria to persist through the amoeba life cycle and survive in amoeba spores rather than being fully digested. This phenomenon is termed "farming," as it potentially allows spores dispersed to food-poor locations to grow their own. The occurrence and impact of farming in natural populations, however, have been a challenge to measure. Here, we surveyed natural D. discoideum populations and found that only one of the three symbiont species, Paraburkholderia agricolaris, remained prevalent. We then explored the effect of Paraburkholderia on the amoeba microbiota, expecting that by facilitating bacterial food carriage, it would diversify the microbiota. Contrary to our expectations, Paraburkholderia tended to infectiously dominate the D. discoideum microbiota, in some cases decreasing diversity. Similarly, we found little evidence for Paraburkholderia facilitating the carriage of particular food bacteria. These findings highlight the complexities of inferring symbiont function in nature and suggest the possibility that Paraburkholderia could be playing multiple roles for its host. [ABSTRACT FROM AUTHOR]

Paraburkholderia tropica MTo‐293 was applied as an experimental bio‐input to Solanum lycopersicum (tomato) cv. Platense. Different plant growth systems and inoculation strategies were tested to evaluate P. tropica plant colonization at the seedling stage (growth chamber) using culture‐dependent and ‐independent techniques. The effect of P. tropica on plant growth was evaluated in the growth chamber and greenhouse (productive stage) by biomass accumulation and fruit production, respectively. P. tropica was able to colonize the surface and inner root and stem of tomato seedlings regardless of the inoculation strategy—at sowing and/or before transplanting—showing the competitive nature of P. tropica in nonsterile substrate systems. A nested polymerase chain reaction was validated to track P. tropica in tomato plants even in the inner stem with endophytic P. tropica populations of less than 102 CFU g–1 of fresh weight. Efficient colonization of P. tropica correlated with a positive effect on tomato growth when applied at sowing and/or before transplanting: plant growth promotion was observed not only at the seedling stage but also at productive stages improving crop yield in two different seasons. To our knowledge, this report is the first to track and evaluate the plant growth‐promoting effect of P. tropica MTo‐293 in tomato plants grown in nonsterile substrate systems. [ABSTRACT FROM AUTHOR]

Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+Paraburkholderia clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but also for studying the evolution of this assemblage of medically, industrially and agriculturally important species.

The compound 3-chlorobenzoate (3-CBA) is a hazardous industrial waste product that can harm human health and the environment. This study investigates the physiological and genetic potential for 3-chlorobenzoate (3-CBA) degradation. Six 3-CBA Gram-negative degraders with different degradation properties belonging to the genera Caballeronia, Paraburkholderia and Cupriavidus were isolated from the soil. The representative strains Caballeronia 19CS4-2 and Paraburkholderia 19CS9-1 showed higher maximum specific growth rates (µmax, h−1) than Cupriavidus 19C6 and degraded 5 mM 3-CBA within 20–28 h. Two degradation products, chloro-cis,cis-muconate and maleylacetate, were detected in all isolates using high-performance liquid chromatography and mass spectrometry. Genomic analyses revealed the presence of cbe and tfd gene clusters in strains 19CS4-2 and 19CS9-1, indicating that they probably metabolized the 3-CBA via the chlorocatechol ortho-cleavage pathway. Strain 19C6 possessed cbe genes, but not tfd genes, suggesting it might have a different chlorocatechol degradation pathway. Putative genes for the metabolism of 3-hydroxybenzoate via gentisate were found only in 19C6, which utilized the compound as a sole carbon source. 19C6 exhibited distinct characteristics from strains 19CS4-2 and 19CS9-1. The results confirm that bacteria can degrade 3-CBA and improve our understanding of how they contribute to environmental 3-CBA biodegradation.

Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas , for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential. [Display omitted] • Quartzite caves are rare subterranean environments with still unexplored microbiology. • Eighty isolates were obtained from pristine and remote quartzite caves on tepuis. • More than half of microbial isolates showed enzymatic and/or metabolic activities. • Genome analysis allowed BGCs prediction and phylogenomics of two bioactive strains. • MEM_CA187 isolate belongs to a novel species of Sphingomonas. [ABSTRACT FROM AUTHOR]

Paraburkholderia bengalensis sp. nov. strain IR64_4_BI was isolated from rice roots cultivated in Madhyamgram field station of Bose Institute, West Bengal, India. IR64_4_BI is a Gram-negative, motile, nitrate-reducing, nitrogen-fixing bacterium. Whole-cell fatty acid analyses of IR64_4_BI show C16:0, summed feature 8 (comprising C18:1ω7c and/or C18:1 ω 6c) and summed feature 3(C16:1 w7c/C16:1 w6c or C16:1 ω 7c/C16:1 ω 6c) were the predominant fatty acids. 16S rRNA phylogeny showed that it was most similar to P. phymatum STM815T (98.5% identity), P. terrae KMY02T (98.44% identity) and P. hospita LMG 20598T (98.32% identity). The Average Nucleotide Identity-BLAST (ANIb) of P. bengalensis IR64_4_BI with P. hospita DSM 17164T, P. terrae DSM 17804T, P. phymatum STM815T and P. hospita LMG 20598T was 83.11, 83.52, 84.5 and 83.12% respectively. Comparison of genome sequence of IR64_4_BI with other species of Paraburkholderia using the Multi-locus species tree software show that P. bengalensis IR64_4_BI is a novel species. The ability of P. bengalensis IR64_4_BI to survive on nitrogen-free medium under microaerophilic conditions and the abundance of nitrogen metabolism-related genes makes this strain a potential candidate for developing a nitrogen-fixing system in rice. Based on genotypic, phenotypic and chemotaxonomic studies, we propose that IR64_4_BI (= MTCC 13051 = JCM 34777) is a new species of Paraburkholderia which has been assigned as Paraburkholderia bengalensis sp.nov. [ABSTRACT FROM AUTHOR]

Symbiotic interactions change with environmental context. Measuring these context‐dependent effects in hosts and symbionts is critical to determining the nature of symbiotic interactions. We investigated context dependence in the symbiosis between social amoeba hosts and their inedible Paraburkholderia bacterial symbionts, where the context is the abundance of host food bacteria. Paraburkholderia have been shown to harm hosts dispersed to food‐rich environments, but aid hosts dispersed to food‐poor environments by allowing hosts to carry food bacteria. Through measuring symbiont density and host spore production, we show that this food context matters in three other ways. First, it matters for symbionts, who suffer a greater cost from competition with food bacteria in the food‐rich context. Second, it matters for host‐symbiont conflict, changing how symbiont density negatively impacts host spore production. Third, data‐based simulations show that symbiosis often provides a long‐term fitness advantage for hosts after rounds of growth and dispersal in variable food contexts, especially when conditions are harsh with little food. These results show how food context can have many consequences for the Dictyostelium‐Paraburkholderia symbiosis and that both sides can frequently benefit. [ABSTRACT FROM AUTHOR]

Burkholderia sensu lato species are prominent for their diversity of hosts. The type 3 secretion system (T3SS) is a major mechanism impacting the interactions between bacteria and eukaryotic hosts. Besides the human pathogenic species Burkholderia pseudomallei and closely affiliated species, the T3SS has received little attention in this genus as in taxonomically and evolutionary close genera Paraburkholderia , Caballeronia , Trinickia , and Mycetohabitans. We proceeded to identify and characterize the diversity of T3SS types using the genomic data from a subset of 145 strains representative of the species diversity found in the Burkholderia s.l. group. Through an analysis of their phylogenetic distribution, we identified two new T3SS types with an atypical chromosomal organization and which we propose to name BCI (Burkholderia cepacia complex Injectisome) and PSI (Paraburkholderia Short Injectisome). BCI is the dominant T3SS type found in Burkholderia sensu stricto (s.s.) species and PSI is mostly restricted to the Paraburkholderia genus. By correlating their distribution with the ecology of their strains of origin, we propose a role in plant interaction for these T3SS types. Experimentally, we demonstrated that a BCI deficient B. vietnamiensis LMG10929 mutant was strongly affected in its rice colonization capacity. [ABSTRACT FROM AUTHOR]

Background and aims: The plant growth promoting rhizobacteria have been extensively implicated in plant responses to changing environments. However, the action mechanisms still need to be elucidated. This study addressed the effect of Paraburkholderia sp. GD17 on rice seedlings in responses to salt stress. Methods: The experiment consisted of GD17-inoculated and non-inoculated plants, with or without NaCl treatment. Physiological and biochemical parameters, and gene expression were analyzed. Results: GD17 efficiently colonized inside roots, and provided a protection against salt stress. Following exposure to 68 mM of NaCl for 48 h, although the accumulation of Na+ was not affected in GD17-inoculated (+ GD17) roots relative to non-inoculated ones, its concentration was substantially reduced in + GD17 shoots. The contents of K and other mineral elements were higher in + GD17 plants. The expression of Na+ and K+ transporter-encoding genes generally presented a higher level in + GD17 plants. The antioxidative defense especially related to the removal of H2O2 was more strongly activated in + GD17 plants. Correspondingly, salt-induced oxidative damage was significantly ameliorated. A substantial increase in proline content and gene expression was observed in + GD17 plants. Additionally, the cell wall invertase-encoding gene displayed a dramatically higher expression level in + GD17 plants. Conclusions: GD17 efficiently improved rice seedling tolerance to salt stress. The possible mechanisms might be associated with the absorption and redistribution of mineral elements, the vacuolar sequestration of Na+ as well as exclusion of Na+, antioxidative defense, the production of proline, and the sucrose catabolism in apoplast. [ABSTRACT FROM AUTHOR]

Here, we report the draft genome of Paraburkholderia sp. XV. This strain was isolated from the rhizosphere of mango (Mangifera indica L.). Its genome consists of 9,189 coding DNA sequences, 60 tRNAs, a single copy of the 16S rRNA, 5S rRNA, and 23S rRNA gene, and 1 tmRNA. The GC content is 62.6%.

Burkholderia sensu lato species are prominent for their diversity of hosts. The type 3 secretion system (T3SS) is a major mechanism impacting the interactions between bacteria and eukaryotic hosts. Besides the human pathogenic species Burkholderia pseudomallei and closely affiliated species, the T3SS has received little attention in this genus as in taxonomically and evolutionary close genera Paraburkholderia, Caballeronia, Trinickia, and Mycetohabitans. We proceeded to identify and characterize the diversity of T3SS types using the genomic data from a subset of 145 strains representative of the species diversity found in the Burkholderia s.l. group. Through an analysis of their phylogenetic distribution, we identified two new T3SS types with an atypical chromosomal organization and which we propose to name BCI (Burkholderia cepacia complex Injectisome) and PSI (Paraburkholderia Short Injectisome). BCI is the dominant T3SS type found in Burkholderia sensu stricto (s.s.) species and PSI is mostly restricted to the Paraburkholderia genus. By correlating their distribution with the ecology of their strains of origin, we propose a role in plant interaction for these T3SS types. Experimentally, we demonstrated that a BCI deficient B. vietnamiensis LMG10929 mutant was strongly affected in its rice colonization capacity.

Abstract Background A major facilitator superfamily transporter Dehp2 was recently shown to be playing an important role in transport and biodegradation of haloacids in Paraburkholderia caribensis MBA4, and Dehp2 is phylogenetically conserved in Burkholderia sensu lato. Results We designed both Burkholderia sensu stricto-specific and Paraburkholderia-specific qPCR assays based on dehp2 and 16S rRNA, and validated the qPCR assays in 12 bacterial strains. The qPCR assays could detect single species of Burkholderia sensu stricto or Paraburkholderia with high sensitivity and discriminate them in mixtures with high specificity over a wide dynamic range of relative concentrations. At relatively lower cost compared with sequencing-based approach, the qPCR assays will facilitate discrimination of Burkholderia sensu stricto and Paraburkholderia in a large number of samples. Conclusions For the first time, we report the utilization of a haloacids transporter gene for discriminative purpose in Burkholderia sensu lato. This enables not only quick decision on proper handling of putative pathogenic samples in Burkholderia sensu stricto group but also future exploitation of relevant species in Paraburkholderia group for haloacids biodegradation purposes.

Plant-beneficial microbes have drawn wide attention due to their potential application as bio-control agents and bio-fertilizers. Moso bamboo, which is among the monocots with the highest growth rate, lives perennially with abundant microbes that may benefit annually growing crops. Genome information of moso bamboo associated bacteria remains underexplored. We isolated and identified a novel Paraburkholderia strain Suichang626 from moso bamboo roots. Growth promoting effects of Suichang626 on both moso bamboo and seedlings of the model dicot Arabidopsis thaliana were documented in laboratory conditions. To gain insight into the genetic basis of this growth promotion effect, we sequenced the genome of Suichang626. Evidenced by genome-wide phylogeny data, we propose that Suichang626 is a novel strain of Paraburkholderia sacchari. Gene homologs encoding biosynthesis of the plant growth-promoting chemicals, acetoin and 2,3-butanediol, were identified in the genome of Suichang626. Comparative genomics was further performed with plant-beneficial and plant/animal pathogenic species of Paraburkholderia and Burkholderia. Genes related to volatile organic compounds, nitrogen fixation, and auxin biosynthesis were discovered specifically in the plant growth-promoting species of both genera.

Plant-beneficial microbes have drawn wide attention due to their potential application as bio-control agents and bio-fertilizers. Moso bamboo, which is among the monocots with the highest growth rate, lives perennially with abundant microbes that may benefit annually growing crops. Genome information of moso bamboo associated bacteria remains underexplored. We isolated and identified a novel Paraburkholderia strain Suichang626 from moso bamboo roots. Growth promoting effects of Suichang626 on both moso bamboo and seedlings of the model dicot Arabidopsis thaliana were documented in laboratory conditions. To gain insight into the genetic basis of this growth promotion effect, we sequenced the genome of Suichang626. Evidenced by genome-wide phylogeny data, we propose that Suichang626 is a novel strain of Paraburkholderia sacchari. Gene homologs encoding biosynthesis of the plant growth-promoting chemicals, acetoin and 2,3-butanediol, were identified in the genome of Suichang626. Comparative genomics was further performed with plant-beneficial and plant/animal pathogenic species of Paraburkholderia and Burkholderia. Genes related to volatile organic compounds, nitrogen fixation, and auxin biosynthesis were discovered specifically in the plant growth-promoting species of both genera. [ABSTRACT FROM AUTHOR]

Legumes in the Fynbos vegetation of the Western Cape of South Africa have emerged as candidates for domestication, particularly for their adaptation to acidic and infertile soils. However, South African rhizobia have been shown to be very diverse and unique, and a detailed understanding of them is essential to success in forage breeding programs that seek to exploit these "new" legumes. Symbionts of legumes in South Africa that belong to traditional rhizobial genera have been shown to have a unique origin for their symbiotic loci in comparison to members sampled from other regions of the world. Some of the legume tribes in the Fynbos have also been shown to associate predominantly with unique species in the Betaproteobacterial genus Paraburkholderia. The rhizobial members of this genus have two main centres of diversity, of which South Africa is one. In this centre, the legume hosts are principally from the Papilionoideae subfamily while hosts from the mimosoid clade (now in the Caesalpinioideae) are abundant in the South American centre. Not only do these rhizobia differ in terms of host, but their symbiotic loci also show separate origins. The dominance and uniqueness of the Paraburkholderia symbionts, in the context of indigenous South African legumes, makes understanding the history and factors that affect the distribution of this genus essential if successful adaptation and effective nodulation of these legumes in Agriculture are to be achieved globally. [ABSTRACT FROM AUTHOR]

Paraburkholderia terrae strain KU-46 has been studied for its capability to degrade 2,4-dinitrophenol. Here, we present the complete 10,833,180bp genome of this microorganism, comprising five circular chromosomes housing 9,797 protein-coding sequences. The genes responsible for 2,4-dinitrophenol and 4-nitrophenol degradation are located on chromosome 2., Competing Interests: The authors declare no conflict of interest.

Paraburkholderia ultramafica STM10279 T is a metal-tolerant rhizobacterium that promotes plant growth. It was isolated from the roots of Tetraria arundinaceae , a pioneer endemic tropical herb growing on ultramafic soils in New Caledonia. We have recently shown that the main mechanism of metal tolerance of P. ultramafica is related to the production of an acidic exopolysaccharide (EPS). To explore the potential role of this EPS in the plant's environmental adaptation, we first elucidated its structure by employing a combination of chromatography and mass spectrometry techniques. These analyses revealed that the EPS is highly branched and composed of galactosyl (35.8%), glucosyl (33.2%), rhamnosyl (19.5%), mannosyl (7.2%), and glucuronosyl residues (4.4%), similar to the EPS of the Burkholderia cepacia complex known as cepacian. We subsequently conducted greenhouse experiments on Tetraria comosa plantlets inoculated with P. ultramafica or a solution of its EPS during transplanting onto ultramafic substrate. The data showed that the dry weight of T. comosa shoots was 2.5 times higher in the plants treated with the EPS compared to the unexposed plants. In addition, inductively coupled plasma-optical emission spectrometry (ICP-OES) analysis revealed that exposure to the EPS significantly increased Ca, Mg, K, and P uptake as well as K content in roots. In vitro experiments using the Pikovskaya method showed that the EPS was able to solubilize phosphorus. Consistent with the retention of metals in roots and a reduction in shoots, our data revealed a significant decrease in metal translocation factors (TFs) in the plants inoculated with the EPS. These results suggest a beneficial effect of the rhizobacterial EPS on plant growth and abiotic stress mitigation. In addition, the data suggest that the reduced levels of trace metals in plants exposed to P. ultramafica STM10279 T are due to metal chelation by the EPS. Further investigations are needed to firmly demonstrate whether this EPS could be used as a biostimulant for plant growth and adaptation to ultramafic soils., Competing Interests: Author EC is employed by BIOTECAL, Marine Biotechnology Company, New Caledonia. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Bourles, Pierre, Amir, Le Floc’h, Chalkiadakis, Médevielle, Jourand, Michaud, Burtet-Sarramégna and Guentas.)