Genus Paraburkholderia Research Articles

Propane Monooxygenases in Soil Associated Metagenomes Align Most Closely to those in the Genera Kribbella, Amycolatopsis, Bradyrhizobium, Paraburkholderia and Burkholderia.

Propanotrophs are a focus of interest because of their ability to degrade numerous environmental contaminants. To explore the phylogeny of microorganisms containing the propane monooxygenase gene cluster (prmABCD), NCBI bacterial genomes and publicly available soil associated metagenomes (from soils, rhizospheres, tree roots) were both examined. Nucleic acid sequences were collected only if all four subunits were located together, were of the expected length and were annotated as propane monooxygenase subunits. In the bacterial genomes, this resulted in data collection only from the phyla Actinomycetota and Pseudomonadota. For the soil associated metagenomes, reads from four studies were subject to quality control, assembly and annotation. Following this, the propane monooxygenase subunit nucleic acid sequences were collected and aligned to the collected bacterial sequences. In total, forty-two propane monooxygenase gene clusters were annotated from the soil associated metagenomes. The majority aligned closely to those from the Actinomycetota, followed by the Alphaproteobacteria, then the Betaproteobacteria. Actinomycetota aligning propane monooxygenase sequences were obtained from all four datasets and most closely aligned to the genera Kribbella and Amycolatopsis. Alphaproteobacteria aligning sequences largely originated from metagenomes associated with miscanthus and switchgrass rhizospheres and primarily aligned with the genera Bradyrhizobium, Acidiphilium and unclassified Rhizobiales. Betaproteobacteria aligning sequences were obtained from only the Red Oak root metagenomes and primarily aligned with the genera Paraburkholderia, Burkholderia and Caballeronia. Interestingly, sequences from the environmental metagenomes were not closely aligned to those from well-studied propanotrophs, such as Mycobacterium and Rhodococcus. Overall, the study highlights the previously unreported diversity of putative propanotrophs in environmental samples. The common occurrence of propane monooxygenase gene clusters has implications for their potential use for contaminant biodegradation.

Paraburkholderia largidicola sp. nov., a gut symbiont of the bordered plant bug Physopelta gutta.

Gram-negative, aerobic, rod-shaped, non-spore-forming, motile bacteria, designated strains F2T and PGU16, were isolated from the midgut crypts of the bordered plant bug Physopelta gutta, collected in Okinawa prefecture, Japan. Although these strains were derived from different host individuals collected at different times, their 16S rRNA gene sequences were identical and showed the highest similarity to Paraburkholderia caribensis MWAP64T (99.3 %). The genome of strain F2T consisted of two chromosomes and two plasmids, and its size and G+C content were 9.28 Mb and 62.4 mol% respectively; on the other hand, that of strain PGU16 consisted of two chromosomes and three plasmids, and its size and G+C content were 9.47 Mb and 62.4 mol%, respectively. Phylogenetic analyses revealed that these two strains are members of the genus Paraburkholderia. The digital DNA-DNA hybridization value between these two strains was 92.4 %; on the other hand, the values between strain F2T and P. caribensis MWAP64T or phylogenetically closely related Paraburkholderia species were 44.3 % or below 49.1 %. The predominant fatty acids of both strains were C16 : 0, C17 : 0 cyclo, summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), and C19 : 0 cyclo ω8c, and their respiratory quinone was ubiquinone 8. Based on the above genotypic and phenotypic characteristics, strains F2T and PGU16 represent a novel species of the genus Paraburkholderia for which the name Paraburkholderia largidicola sp. nov. is proposed. The type strain is F2T (=NBRC 115765T=LMG 32765T).

Paraburkholderia translucens sp. nov. and Paraburkholderia sejongensis sp. nov., isolated from grassland soil and showing plant growth promoting potential.

Two Gram-negative bacterial strains designated MMS20-SJTN17T and MMS20-SJTR3T were isolated from a grassland soil sample, and taxonomically characterized using a polyphasic approach. The 16S rRNA gene sequence analysis indicates that both strains belong to the genus Paraburkholderia of the class Betaproteobacteria, with strain MMS20-SJTN17T being mostly related to Paraburkholderia sprentiae WSM5005T (96.45 % sequence similarity) and strain MMS20-SJTR3T to Paraburkholderia tuberum STM678T (98.59 % sequence similarity). MMS20-SJTN17T could grow at 15-40 °C (optimum, 25-30 °C) and at pH 6.0-8.0 (optimum, pH 6.0-7.0), whereas MMS20-SJTR3T could grow at 10-40 °C (optimum, 30-37 °C) and at pH 6.0-8.0 (optimum, pH 6.0). Both strains tolerated up to 1 % (w/v) NaCl (optimum, 0 %). The major fatty acids of MMS20-SJTN17T were C16 : 0 and C19 : 0 cyclo ω8c, and those of MMS20-SJTR3T were C17 : 0 cyclo and a summed feature comprising C18 : 1 ω7c and/or C18 : 1 ω6c. The major isoprenoid quinone of both strains was ubiquinone-8 and the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Regarding plant growth promoting potential, both strains were capable of producing indole acetic acid, siderophore and 1-aminocyclopropane-1-carboxylic acid deaminase, and also showed phosphate-solubilizing activity. A genome-based comparison using orthologous average nucleotide identity and digital DNA-DNA hybridization values indicates that strain MMS20-SJTN17T shares highest relatedness with Paraburkholderia monticola JC2948T and MMS20-SJTR3T with Paraburkholderia antibiotica G-4-1-8T, with values clearly below the cutoffs for species distinction. Examination of biosynthetic gene clusters responsible for secondary metabolite production reveals unique characteristics distinguishing each strain from closely related Paraburkholderia species. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenomic data, each strain should be classified as a novel species of the genus Paraburkholderia, for which the names Paraburkholderia translucens sp. nov. (=MMS20-SJTN17T=LMG 32366T=KCTC 82783T) and Paraburkholderia sejongensis sp. nov. (=MMS20-SJTR3T=LMG 32367T=KCTC 82784T) are proposed.

The seeds of invasion: a comparison of endophytic seed bacteria of Acacia longifolia between its native and invasive ranges

Acacia longifolia is an aggressive invader in Mediterranean-type ecosystems severely impacting biodiversity and ecosystem functions. The species’ invasiveness has been linked to its ability to thrive in nutrient poor soils, high seed production, and quick establishment after fire. In this study, we identify and compare the bacterial endophytes of A. longifolia seeds collected from populations in the species’ native (Australia) and invasive (Portugal) ranges. For this, we characterised the morphology (length, width, and weight) of seeds from two sites in each range and isolated and cultivated bacteria from seeds. DNA fingerprinting and cluster analyses revealed slightly higher, and distinct, bacterial diversity associated with seeds collected from native range populations in comparison to those collected from invasive populations. Sequencing of the 16S rDNA gene identified 119 bacterial isolates from 15 genera, with Curtobacterium strains being common in both ranges. Several differences in bacterial genera were found among ranges and sites: Dermacoccus, Frigoribacterium, Kocuria, Pantoea and Phyllobacterium taxa were each unique to seeds from the native populations, while Brevundimonas, Microbacterium, Rhizobium and Sphingomonas taxa were only found in the invasive seeds. The genus Paraburkholderia occurred in all invasive-range seeds but was not isolated from the native-range. Bacillus and Paenibacillus co-occurred in seeds collected from all invaded sites, but the simultaneous presence of both taxa was not found in native-range seeds. We propose that the bacterial endophytes present in invasive-range seeds may be important players for the invasiveness of A. longifolia, due to their role as plant growth promoters, providing extra capabilities helping acacia expansion.

Taxonomy-guided selection of Paraburkholderia busanensis sp. nov.: a versatile biocontrol agent with mycophagy against Colletotrichum scovillei causing pepper anthracnose.

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.

Rhizobiome of ‘Ōhi‘a Lehua (Metrosideros polymorpha) Offers Insight into Plant-Microbe-Invertebrate Interactions in the Subsurface

Roots are common features in basaltic lava tube caves on the island of Hawai‘i. For the past 50 years, new species of cave-adapted invertebrates, including cixiid planthoppers, crickets, thread-legged bugs, and spiders, have been discovered from root patches in lava tubes on different volcanoes and across variable climatic conditions. Assessing vegetation on the surface above lava tube passages, as well as genetic characterization of roots from within lava tubes, suggest that most roots belong to the native pioneer tree, ‘ōhi‘a lehua (Metrosideros polymorpha). Planthoppers are the primary consumers of sap at the base of the subsurface food web. However, root physicochemistry and rhizobiome microbial diversity and functional potential have received little attention. This study focuses on characterizing the ‘ōhi‘a rhizobiome, accessed from free-hanging roots inside lava tubes. Using these results, we can begin to evaluate the development and evolution of plant-microbe-invertebrate relationships. We explored lava tubes formed in flows of differing elevations and ages, from about 140 to 3000 years old, on Mauna Loa, Kīlauea, and Hualālai volcanoes on Hawai‘i Island. Invertebrate diversity was evaluated from root galleries and non-root galleries, in situ fluid physicochemistry was measured, and root and bare rock fluids (e.g., water, sap) were collected to determine major ion concentrations, as well as non-purgeable organic carbon (NPOC) and total nitrogen (TN) content. To verify root identity, DNA was extracted, and three sets of primers were used. After screening for only Metrosideros spp., the V4 region of the 16S rRNA gene was sequenced and taxonomy was assigned. Root fluids were viscous and ranged in color from clear to yellow to reddish orange. Root fluids had 2X to 10X higher major ion concentrations compared to rock water. The average root NPOC and TN concentrations were 192 mg/L and 5.2 mg/L, respectively, compared to rock water that had concentrations of 6.8 mg/L and 1.8 mg/L, respectively. Fluids from almost 300 root samples had pH values that ranged from 2.2 to 5.6 (average pH 4.63) and were lower than rock water (average pH 6.39). Root fluid pH was comparable to soil pH from montane wet forests dominated by ‘ōhi‘a (Selmants et al. 2016), which can grow in infertile soil with pH values as low as 3.6. On Hawai‘i, rain water pH averages 5.2 at sea level and systematically decreases with elevation to pH 4.3 at 2500 m (Miller and Yoshinaga 2012), but root fluid pH did not correlate with elevation, temperature, relative humidity, inorganic and organic constituents, or age of flow. Root fluid acidity is likely due to concentrated organic compounds, sourced as root exudates, and this habitat is acidic for the associated invertebrates. From 62 root samples, over 66% were identified to the genus Metrosideros. A few other identifications of roots from lava tube systems where there had been extensive clear-cutting and ranching included monkey pod tree, coconut palm, Ficus spp., and silky oak. The 16S rRNA gene sequence surveys revealed that root bacterial communities were dominated by few groups, including Burkholderiaceae, as well as Acetobacteraceae, Sphingomonadaceae, Acidobacteriaceae, Gemmataceae, Xanthobacteraceae, and Chitinophagaceae. However, most of the reads could not be classified to a specific genus, which suggested that the rhizobiome harbor novel diversity. Diversity was higher from wetter climates. The root communities were distinct from those described previously from ‘ōhi‘a flowers and leaves (Junker and Keller 2015) and lava tube rocky surfaces (Hathaway et al. 2014) where microbial groups were specifically presumed capable of heterotrophy, methanotrophy, diazotrophy, and nitrification. Less can be inferred for the rhizobiome metabolism, although most taxa are likely aerobic heterotrophs. Within the Burkholderiaceae, there were high relative abundances of sequences affiliated with the genus Paraburkholderia, which includes known plant symbionts, as well as the acidophilic genera Acidocella and Acidisoma from the Acetobacteraceae, which were retrieved predominately from caves in the oldest lava flows that also had the lowest root pH values. It is likely that the bacterial groups are capable of degrading exudates and providing nutritional substrates for invertebrate consumers that are not provided by root fluids (i.e., phloem) alone. As details about the biochemistry of ‘ōhi‘a have been missing, characterizing the rhizobiome from lava tubes will help to better understand potential plant-microbe-invertebrate interactions and ecological and evolutionary relationships through time. In particular, the microbial rhizobiome may produce compounds used by invertebrates nutritionally or that affect their behavior, and changes to the rhizobiome in response to environmental conditions may influence invertebrate interactions with the roots, which could be important to combat climate change effects or invasive species introductions.

Paraburkholderia flagellata sp. nov. and Paraburkholderia adhaesiva sp. nov., two novel species isolated from forest soil in Dinghushan Biosphere Reserve in Guangdong, China.

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 9,002,095bp, 62.9% and 6,974,420bp, 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 C18:1 ω7c and/or C18:1 ω6c, 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.

Symbiotic bacteria, immune-like sentinel cells, and the response to pathogens in a social amoeba.

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.

Isolation of new Paraburkholderia strains for polyhydroxybutyrate production.

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).

Paraburkholderia symbionts isolated from Dictyostelium discoideum induce bacterial carriage in other Dictyostelium species.

The social amoeba Dictyostelium discoideum engages in a complex relationship with bacterial endosymbionts in the genus Paraburkholderia, which can benefit their host by imbuing it with the ability to carry prey bacteria throughout its life cycle. The relationship between D. discoideum and Paraburkholderia has been shown to take place across many strains and a large geographical area, but little is known about Paraburkholderia's potential interaction with other dictyostelid species. We explore the ability of three Paraburkholderia species to stably infect and induce bacterial carriage in other dictyostelid hosts. We found that all three Paraburkholderia species successfully infected and induced carriage in seven species of Dictyostelium hosts. While the overall behaviour was qualitatively similar to that previously observed in infections of D. discoideum, differences in the outcomes of different host/symbiont combinations suggest a degree of specialization between partners. Paraburkholderia was unable to maintain a stable association with the more distantly related host Polysphondylium violaceum. Our results suggest that the mechanisms and evolutionary history of Paraburkholderia's symbiotic relationships may be general within Dictyostelium hosts, but not so general that it can associate with hosts of other genera. Our work further develops an emerging model system for the study of symbiosis in microbes.

Changes in Bacterial Communities and Functions Associated with Litter Degradation During Forest Succession Caused by Forest Disease

Forest succession affects aboveground vegetation and belowground microbial community composition, in which litter degradation plays an important role in nutrient cycling. However, limited information is available on how microbial communities change during litter degradation in forests undergoing succession due to disease. In this study, the bacterial communities and functions in litter degradation during the forest succession from pure Pinus forest (PPF), mixed Pinus and Liquidambar forest (MPF and MLF), and pure Liquidambar forest (PLF) were investigated. The results showed that the bacterial community richness and diversity in both needles or leaves and branch litters increased progressively with forest succession. Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were the most abundant bacterial phyla in the litter degradation during forest succession. The abundance of Bacteroidetes in branches increased significantly, while the abundance of genus Paraburkholderia decreased during forest succession. The different forests formed distinct bacterial community structures during litter decomposition. Functionally, chemoheterotrophy was the most abundant functional guild, followed by nitrogen fixation, intracellular parasitism, and urealysis. The abundance of nitrogen fixation decreased significantly during forest succession. Similarly, the different forests formed distinct bacterial functional structures in the needle or leaf during the succession. However, only two functional structures were formed in the branch. These results suggest that the bacterial community and its functions undergo significant changes during forest succession, particularly from the pure-pine to mixed-pine forest. These results provide a clear understanding of the changes in bacterial communities and functions during litter degradation in forests undergoing disease-induced succession.

Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato).

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).

Nitrogen-Fixing Symbiotic Paraburkholderia Species: Current Knowledge and Future Perspectives

A century after the discovery of rhizobia, the first Beta-proteobacteria species (beta-rhizobia) were isolated from legume nodules in South Africa and South America. Since then, numerous species belonging to the Burkholderiaceae family have been isolated. The presence of a highly branching lineage of nodulation genes in beta-rhizobia suggests a long symbiotic history. In this review, we focus on the beta-rhizobial genus Paraburkholderia, which includes two main groups: the South American mimosoid-nodulating Paraburkholderia and the South African predominantly papilionoid-nodulating Paraburkholderia. Here, we discuss the latest knowledge on Paraburkholderia nitrogen-fixing symbionts in each step of the symbiosis, from their survival in the soil, through the first contact with the legumes until the formation of an efficient nitrogen-fixing symbiosis in root nodules. Special attention is given to the strain P. phymatum STM815T that exhibits extraordinary features, such as the ability to: (i) enter into symbiosis with more than 50 legume species, including the agriculturally important common bean, (ii) outcompete other rhizobial species for nodulation of several legumes, and (iii) endure stressful soil conditions (e.g., high salt concentration and low pH) and high temperatures.

Effects of a growth-promoting Paraburkholderia species on nitrogen acquisition by avocado seedlings

The increasing popularity of avocado (Persea americana) fruit has led to a rise in environmental impacts of avocado production. There is an urgent need to adopt sustainable nutrient practices in avocado nurseries and orchards to reduce nitrogen (N) pollution without compromising productivity. However, there is little understanding of how avocado rootstocks respond to different N fertilisation strategies. We investigated the effects of a plant growth-promoting rhizobacterium (PGPR) from the genus Paraburkholderia on growth of Reed avocado seedlings fertilised with either inorganic N fertiliser (iN) or combined inorganic N with organic manure-based fertiliser (iNoN). We studied plant growth and N acquisition, mineral N (NH4+-N and NO3−-N) in leachate, potting-mix physicochemical properties, and rhizosphere microbial communities. PGPR increased N uptake efficiency (NUpE) in seedlings fertilised with iNoN by 23% compared with iNoN without PGPR, 120% compared with iN without PGPR, and 71% compared with iN with PGPR. No significant differences in growth or mineral N leaching were observed between the iNoN and iN treatments. However, both uninoculated and PGPR-inoculated plants with iNoN fertiliser had greater plant N uptake and rhizosphere microbial-biomass N than uninoculated plants with iN fertiliser. Potting medium with iNoN fertiliser had higher N retention than with iN fertiliser, regardless of PGPR inoculation. Our results provide evidence that PGPR effects on N uptake efficiency are regulated by N form and N availability. The beneficial effects of PGPR inoculation when co-applied with a combination of inorganic and organic N fertiliser indicate that PGPR-based technologies can improve nitrogen recovery in avocado nurseries.

Gene expression and metabolite analysis in barley inoculated with net blotch fungus and plant growth-promoting rhizobacteria

Net blotch, caused by the ascomycete Drechslera teres, can compromise barley production. Beneficial bacteria strains are of substantial interest as biological agents for plant protection in agriculture. Belonging to the genus Paraburkholderia, a bacterium, referred to as strain B25, has been identified as protective for barley against net blotch. The strain Paraburkholderia phytofirmans (strain PsJN), which has no effect on the pathogen's growth, has been used as control. In this study, the expression of target genes involved in cell wall-related processes, defense responses, carbohydrate and phenylpropanoid pathways was studied under various conditions (with or without pathogen and/or with or without bacterial strains) at different time-points (0-6-12-48 h). The results show that specific genes were subjected to a circadian regulation and that the expression of most of them increased in barley infected with D. teres and/or bacterized with the strain PsJN. On the contrary, a decreased gene expression was observed in the presence of strain B25. To complement and enrich the gene expression analysis, untargeted metabolomics was carried out on the same samples. The data obtained show an increase in the production of lipid compounds in barley in the presence of the pathogen. In addition, the presence of strain B25 leads to a decrease in the production of defense compounds in this crop. The results contribute to advance the knowledge on the mechanisms occurring at the onset of D. teres infection and in the presence of a biocontrol agent limiting the severity of net blotch in barley.

Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor.

A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA–DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).

Twenty years of paradigm-breaking studies of taxonomy and symbiotic nitrogen fixation by beta-rhizobia, and indication of Brazil as a hotspot of Paraburkholderia diversity.

Twenty years ago, the first members of the genus Burkholderia capable of nodulating and fixing N2 during symbiosis with leguminous plants were reported. The discovery that β-proteobacteria could nodulate legumes represented a breakthrough event because, for over 100years, it was thought that all rhizobia belonged exclusively to the α-Proteobacteria class. Over the past 20years, efforts toward robust characterization of these bacteria with large-scale phylogenomic and taxonomic studies have led to the separation of clinically important and phytopathogenic members of Burkholderia from environmental ones, and the symbiotic nodulating species are now included in the genera Paraburkholderia and Trinickia. Paraburkholderia encompasses the vast majority of β-rhizobia and has been mostly found in South America and South Africa, presenting greater symbiotic affinity with native members of the families Mimosoideae and Papilionoideae, respectively. Being the main center of Mimosa spp. diversity, Brazil is also known as the center of symbiotic Paraburkholderia diversity. Of the 21 symbiotic Paraburkholderia species described to date, 11 have been isolated in Brazil, and others first isolated in different countries have also been found in this country. Additionally, besides the symbiotic N2-fixation capacity of some of its members, Paraburkholderia is considered rich in other beneficial interactions with plants and can promote growth through several direct and indirect mechanisms. Therefore, these bacteria can be considered biological resources employed as environmentally friendly alternatives that could reduce the agricultural dependence on agrochemical inputs.

Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.

We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderia aspalathi, Paraburkholderia madseniana, Paraburkholderia sediminicola, Paraburkholderia caffeinilytica, Paraburkholderia solitsugae and Paraburkholderia elongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA–DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832T (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836T (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837T (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.

The history and distribution of nodulating Paraburkholderia, a potential inoculum for Fynbos forage species

AbstractLegumes 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.

Burkholderia Bacteria Produce Multiple Potentially Novel Molecules that Inhibit Carbapenem-Resistant Gram-Negative Bacterial Pathogens

Antimicrobial resistance in Gram-negative pathogens represents a global threat to human health. This study determines the antimicrobial potential of a taxonomically and geographically diverse collection of 263 Burkholderia (sensu lato) isolates and applies natural product dereplication strategies to identify potentially novel molecules. Antimicrobial activity is almost exclusively present in Burkholderia sensu stricto bacteria and rarely observed in the novel genera Paraburkholderia, Caballeronia, Robbsia, Trinickia, and Mycetohabitans. Fourteen isolates show a unique spectrum of antimicrobial activity and inhibited carbapenem-resistant Gram-negative bacterial pathogens. Dereplication of the molecules present in crude spent agar extracts identifies 42 specialized metabolites, 19 of which represented potentially novel molecules. The known identified Burkholderia metabolites include toxoflavin, reumycin, pyrrolnitrin, enacyloxin, bactobolin, cepacidin, ditropolonyl sulfide, and antibiotics BN-227-F and SF 2420B, as well as the siderophores ornibactin, pyochelin, and cepabactin. Following semipreparative fractionation and activity testing, a total of five potentially novel molecules are detected in active fractions. Given the molecular formula and UV spectrum, two of those putative novel molecules are likely related to bactobolins, and another is likely related to enacyloxins. The results from this study confirm and extend the observation that Burkholderia bacteria present exciting opportunities for the discovery of potentially novel bioactive molecules.