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

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.

Deciphering the rhizobacterial assemblages under the influence of genetically engineered maize carrying mcry genes

Genetically engineered (GE) maize has been thoroughly studied regarding its agro-environmental impact; however, its concerns for the soil environment remain. This work was aimed to decode rhizosphere microbe interactions and potential ecological hazards associated with GE maize. Rhizobacterial communities of field grown transgenic insect-resistant 2A5 maize carrying mcry1Ab and mcry2Ab genes were compared with control Z58 using PacBio sequencing platform. Also full-length 16S rDNA gene sequencing was used to verify the partial (V3-V4) sequencing results obtained in 2017. Measures of α-diversity displayed transgenic 2A5 to be significantly lower in species richness at the flowering stage; however, diversity remained undisturbed. β-diversity was least affected by genetic modifications where similar community profiles were shared by transgenic 2A5 and control Z58. In addition, root exudation patterns were found to drive variations in bacterial assemblages based on developmental stages. For example, genus Massilia successfully colonized the rhizosphere at jointing stage, while Mucilaginobacter showed higher relative abundance in flowering stages of both 2A5 and Z58. These members are known to possess attributes related to plant growth. The impact of dual-transgene insertion on nifH gene abundance was also analyzed where no apparent significant difference in nifH gene copy number was observed. Our results confirmed that full-length 16S rDNA sequencing was sufficient to provide higher taxonomic resolution. Also, results of our 2-year field trials confirmed that there is no significant impact of mcry gene integration on belowground biomasses. Therefore, GE insect-resistant 2A5 maize carrying mcry1Ab and mcry2Ab genes can continue to benefit human populations by increasing crop productivity. In future, further research needs to be catalyzed to analyze the impact of Bt-insertion on microbial community structure across the years for ecosystem sustainability.

The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire

Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.

Nodulation of the neotropical genus Calliandra by alpha or betaproteobacterial symbionts depends on the biogeographical origins of the host species

The neotropical genus Calliandra is of great importance to ecology and agroforestry, but little is known about its nodulation or its rhizobia. The nodulation of several species from two restricted diversity centres with native/endemic species (Eastern Brazil and North-Central America) and species widespread in South America, as well as their nodule structure and the molecular characterization of their rhizobial symbionts based on phylogeny of the 16S rRNA, recA and nodC gene, is reported herein. Species representative of different regions were grown in Brazilian soil, their nodulation observed, and their symbionts characterized. Calliandra nodules have anatomy that is typical of mimosoid nodules regardless of the microsymbiont type. The rhizobial symbionts differed according to the geographical origin of the species, i.e. Alphaproteobacteria (Rhizobium) were the exclusive symbionts from North-Central America, Betaproteobacteria (Paraburkholderia) from Eastern Brazil, and a mixture of both nodulated the widespread species. The symbiont preferences of Calliandra species are the result of the host co-evolving with the "local" symbiotic bacteria that thrive in the different edaphoclimatic conditions, e.g. the acidic soils of NE Brazil are rich in acid-tolerant Paraburkholderia, whereas those of North-Central America are typically neutral-alkaline and harbour Rhizobium. It is hypothesized that the flexibility of widespread species in symbiont choice has assisted in their wider dispersal across the neotropics.

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 100 years, it was thought that all rhizobia belonged exclusively to the α-Proteobacteria class. Over the past 20 years, 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.

Paraburkholderia spp. are the main rhizobial microsymbionts of Mimosa tenuiflora (Willd.) Poir. in soils of the Brazilian tropical dry forests (Caatinga biome)

Mimosa tenuiflora (Willd.) Poir. is widespread in southern and central American drylands, but little information is available concerning its associated rhizobia. Therefore, this study aimed to characterize M. tenuiflora rhizobia from soils of the tropical dry forests (Caatinga) in Pernambuco State, Brazil, at the molecular and symbiotic levels. Soil samples of pristine Caatinga areas in four municipalities were used to grow M. tenuiflora. First, the bacteria from root nodules were subjected to nodC/nifH gene amplification, and the bacteria positive for both genes had the 16S rRNA gene sequenced. Then, ten strains were evaluated using recA, gyrB, and nodC gene sequences, and seven of them had their symbiotic efficiency assessed. Thirty-two strains were obtained and 22 of them were nodC/nifH positive. Twenty strains clustered within Paraburkholderia and two within Rhizobium by 16S rRNA gene sequencing. The beta-rhizobia were similar to P. phenoliruptrix (12) and P. diazotrophica (8). Both alpha-rhizobia were closely related to R. miluonense. The recA + gyrB phylogenetic analysis clustered four and five strains within the P. phenoliruptrix and P. diazotrophica branches, respectively, but they were somewhat divergent to the 16S rRNA phylogeny. For Rhizobium sp. ESA 637, the recA + gyrB phylogeny clustered the strain with R. jaguaris. The nodC phylogeny indicated that ESA 626, ESA 629, and ESA 630 probably represented a new symbiovar branch. The inoculation assay showed high symbiotic efficiency for all tested strains. The results indicated high genetic diversity and efficiency of M. tenuiflora rhizobia in Brazilian drylands and included P. phenoliruptrix-like bacteria in the list of efficient beta-rhizobia in the Caatinga biome.

Phenolic acid-degrading Paraburkholderia prime decomposition in forest soil

Plant-derived phenolic acids are catabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria enhance SOC mineralization in forest soils when primed with 13C-labeled p-hydroxybenzoic acid (pHB). We further tested whether pHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. pHB addition primed significant losses of SOC (3-13 µmols C g-1 dry wt soil over 7 days) compared to glucose, which reduced mineralization (-3 to -8 µmols C g-1 dry wt soil over 7 days). The principal degraders of pHB were Paraburkholderia and Caballeronia in all plantations regardless of tree species or soil type, with one predominant phylotype (RP11ASV) enriched 23-fold following peak pHB respiration. We isolated and confirmed the phenolic degrading activity of a strain matching this phylotype (RP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, Dyp-type peroxidase and aryl-alcohol oxidase. Increased relative abundance of RP11ASV corresponded with higher pHB respiration and expression of pHB monooxygenase (pobA), which was inversely proportional to SOC content among plantations. pobA expression proved a responsive measure of priming activity. We found that stimulating phenolic-acid degrading bacteria can prime decomposition and that this activity, corresponding with differences in tree species, is a potential mechanism in SOC cycling in forests. Overall, this study highlights the ecology and function of Paraburkholderia whose associations with plant roots and capacity to degrade phenolics suggest a role for specialized bacteria in the priming effect.

Paraburkholderia youngii sp. nov. and 'Paraburkholderia atlantica' - Brazilian and Mexican Mimosa-associated rhizobia that were previously known as Paraburkholderia tuberum sv. mimosae

Previous studies have recognized South and Central/Latin American mimosoid legumes in the genera Mimosa, Piptadenia and Calliandra as hosts for various nodulating Paraburkholderia species. Several of these species have been validly named in the last two decades, e.g., P. nodosa, P. phymatum, P. diazotrophica, P. piptadeniae, P. ribeironis, P. sabiae and P. mimosarum. There are still, however, a number of diverse Paraburkholderia strains associated with these legumes that have an unclear taxonomic status. In this study, we focus on 30 of these strains which originate from the root nodules of Brazilian and Mexican Mimosa species. They were initially identified as P. tuberum and subsequently placed into a symbiovar (sv. mimosae) based on their host preferences. A polyphasic approach for the delineation of these strains was used, consisting of genealogical concordance analysis (using atpD, gyrB, acnA, pab and 16S rRNA gene sequences), together with comparisons of Average Nucleotide Identity (ANI), DNA G+C content ratios and phenotypic characteristics with those of the type strains of validly named Paraburkholderia species. Accordingly, these 30 strains were delineated into two distinct groups, of which one is conspecific with 'P. atlantica' CNPSo 3155^T and the other new to Science. We propose the name Paraburkholderia youngii sp. nov. with type strain JPY169^T (= LMG 31411^T; SARCC751^T) for this novel species.

Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana

Two bacterial strains, 1N^T and 5N^T, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1N^T (0.65×1.85 µm) and 5N^T (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5N^T elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1N^T and 5N^T occurred at 25-30 °C, pH 6.5-7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1N^T and 5N^T were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11^T, Paraburkholderia aspalathi LMG 27731^T and Paraburkholderia caffeinilytica CF1^T. The genomes of 1N^T and 5N^T had an average nucleotide identity (91.6 and 91.3%) and in silico DNA-DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1N^T and 5N^T from each other and their closest relatives. The only ubiquinone present in strains 1N^T and 5N^T was Q-8. The major cellular fatty acids were C_{16 : 0}, 3OH-C_{16 : 0}, C_{17 : 0} cyclo, C_{19 : 0} cyclo ω8c and summed features 2 (3OH-C_{14 : 0} / C_{16 : 1} iso I), 3 (C_{16 : 1} ω6c/ω7c) and 8 (C_{18 : 1} ω7c/ω6c). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana. Our polyphasic approach demonstrated that strains 1N^T and 5N^T represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1N^T=DSM 110721^T=LMG 31704^T) and Paraburkholderia elongata sp. nov. (type strain 5N^T=DSM 110722^T=LMG 31705^T) are proposed.

Phylogeny of symbiotic genes reveals symbiovars within legume-nodulating Paraburkholderia species

Bacteria belonging to the genus Paraburkholderia are capable of establishing symbiotic relationships with plants belonging to the Fabaceae (=Leguminosae) family and fixing the atmospheric nitrogen in specialized structures in the roots called nodules, in a process known as biological nitrogen fixation (BNF). In the nodulation and BNF processes several bacterial symbiotic genes are involved, but the relations between symbiotic, core genes and host specificity are still poorly studied and understood in Paraburkholderia. In this study, eight strains of nodulating nitrogen-fixing Paraburkholderia isolated in Brazil, together with described species and other reference strains were used to infer the relatedness between core (16S rDNA, recA) and symbiotic (nod, nif, fix) genes. The diversity of genes involved in the nodulation (nodAC) and nitrogen fixation (nifH) abilities was investigated. Only two groups, one containing three Paraburkholderia species symbionts of Mimosa, and another one with P. ribeironis strains presented similar phylogenetic patterns in the analysis of core and symbiotic genes. In three other groups events of horizontal gene transfer of symbiotic genes were detected. Paraburkholderia strains with available genomes were used in the complementary analysis of nifHDK and fixABC and confirmed well-defined phylogenetic positions of symbiotic genes. In all analyses of nod, nif and fix genes the strains were distributed into five clades with high bootstrap support, allowing the proposal of five symbiovars in nodulating nitrogen-fixing Paraburkholderia, designated as mimosae, africana, tropicalis, atlantica and piptadeniae. Phylogenetic inferences within each symbiovar are discussed.

Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

RP11^T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11^T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3-4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr^-1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731^T, Paraburkholderia fungorum LMG 16225^T and Paraburkholderia caffeinilytica CF1^T. Strain RP11^T is genetically distinct from P. aspalathi, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA-DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11^T from its closest relatives, including growth on phthalic acid. Strain RP11^T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11^T was Q-8, and the major cellular fatty acids were C_16 : 0, 3OH-C_16 : 0, C_17 : 0 cyclo, C_19 : 0 cyclo ω8c, and summed feature 8 (C_18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11^T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11^T (=DSM 110123^T=LMG 31517^T).

Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond

A Gram-stain-negative, strictly aerobic bacterial strain, designated strain S27^T, was isolated from soil near an artificial pond in South Korea. Cells were non-motile short rods showing oxidase- and catalase-positive activities. Growth of strain S27^T was observed at 20-40°C (optimum, 30°C), pH 5.0-7.0 (optimum, pH 6.0), and 0-0.5% (w/v) NaCl (optimum, 0%). Ubiquinone-8 was detected as the sole respiratory quinone and the major fatty acids were C_16:0, cyclo-C_17:0, and cyclo-C_19:0ω8c. The G + C content of the genomic DNA was 62.4 mol%. Phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid were detected as the major polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S27_T formed a clearly distinct phyletic lineage from closely related Paraburkholderia species within the genus Paraburkholderia. Strain S27^T was most closely related to Paraburkholderia rhynchosiae WSM3937^T, Paraburkholderia ginsengiterrae DCY85^T, Paraburkholderia fungorum NBRC 102489^T, and Paraburkholderia graminis C4D1M^T with 98.8%, 98.4%, 98.4%, and 97.7% 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness level between strain S27^T and the type strain of P. rhynchosiae was 36.8 ± 2.6%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain S27^T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia lacunae sp. nov. is proposed. The type strain is S27^T (KACC 19714 ^T = JCM 32721^T).