Draft genome sequence of Paraburkholderia tropica Ppe8 strain, a sugarcane endophytic diazotrophic bacterium

Designing and validation of specific primers for the quantitative detection of bacteria in sugarcane inoculant

Endophytic diazotrophic plant growth-promoting bacteria Herbaspirillum rubrisubalbicans (HCC103), Herbaspirillum seropedicae (HRC54), Paraburkholderia tropica (Ppe8T), Gluconacetobacter diazotrophicus (Pal5T), and Nitrospirillum amazonense (CBAmC) have been used as inoculants for sugarcane. The genome sequences of these strains were used to design a set of specific primers for the real-time PCR (qPCR) assay. Primer specificity was confirmed by conventional PCR using the genomic DNAs of 25 related bacterial species and the five target strains. The qPCR assays were conducted using root and shoot samples from two sugarcane varieties (RB867515 and RB92579). These samples were collected both with and without inoculation, using the target strains specified in this study. The sugarcane plants were grown in a greenhouse, utilizing a substrate composed of sterile sand and vermiculite in a 2:1 ratio, for a duration of 55 days. The primers designed for this study successfully amplified target DNA fragments from each of the bacterial species, enabling their differentiation at the species level. The total bacterial population present in the sugarcane quantified using qPCR was on average 105.2 cells g-1 of fresh tissue. Across both evaluated varieties, it was observed that the population of inoculated bacteria tended to decrease over time and became more concentrated in the sugarcane roots compared to the aerial parts. The qPCR results suggest that both the host and the microbes influence the endophytic population and the bacterial number decreases with plant age.

Survival of five diazotrophic bacterial strains in different substrates used in sugarcane seedling propagation

An inoculant containing selected bacterial strains can be easily applied during the nursery please process, but in this case, substrate composition can affect its survival and, in consequence, bacterial colonization. The aim of this study was to evaluate the survival of five diazotrophic bacterial strains/species applied individually on 13 different substrates used in sugarcane seedling nurseries considering an active population higher than 105 cells g-1. In addition, one experiment was performed using two commercial substrates, coconut fiber, and Multiplant™, inoculated or not with a mixture of five bacterial strains to evaluate plant growth after 30 days. These strains are combined inoculants selected for sugarcane acting as plant growth promoters. Bacterial counts were determined every seven days using the Most Probable Number technique with four different semi-solid N-free media specific for each strain tested over 35 days. The survival order, independent of the substrate tested, was: Paraburkholderia tropica Pt-PPe8T > Nitrospirillum amazonense Na-CBAMc > Herbaspirillum seropedicae Hs-HRC54 = H. rubrisubalbicans Hr-HCC103 > Gluconacetobacter diazotrophicus Gd-PAL5T. All tested substrates influenced the bacterial survival, especially after 21 days of incubation. The population size can be partially controlled by the substrate pH and stimulated by the addition of slow-release fertilizer. Besides the differences in the bacterial population present in the two commercial substrates, plant growth was found to be stimulated by the inoculated bacteria, depending on the substrate and its sugarcane cultivar tested. The selection of a substrate used to produce new plantlets of sugarcane can contribute to bacterial survival and improve bacterial colonization.

Prevalence of Deltaproteobacterial sequences in nifH gene pools associated with the rhizosphere of native switchgrass from Tall Grass Prairie (Oklahoma, USA)

The potential nitrogen-fixing bacterial diversity in the rhizospheric soil of the native switchgrass (Panicum virgatum L.) from Tall Grass Prairies of Northern Oklahoma was studied using a partial region of nitrogenase structural gene-nifH. Eleven clone libraries constructed from nifH amplicons gave 407 good-quality sequences. More than 70% of sequences showed similarity of nifH with uncultured bacteria (< 98%). The dominance of sequences affiliated with Deltaproteobacterial nifH was observed, followed by Betaproteobacterial nifH sequences. The nifH gene library was dominated by the genera Geobacter, Rhizobacter, Paenibacillus, and Azoarcus. Sequences affiliated with rhizobia, such as Bradyrhizobium, Methylocystis, Ensifer, etc., were also in the rhizosphere in small numbers. From Deltaproteobacteria, five genera, namely Geobacter, Pelobacter, Geomonas, Desulfovibrio, and Anaeromyxobacter, contributed to 48% of the total sequences suggesting the dominance of group Deltaproteobacteria in the rhizosphere of native switchgrass. Considering the percent similarity of the nifH sequences with cultivated bacteria, this study demonstrated the presence of novel bacterial species in switchgrass rhizospheric soil from Tall Grass Prairie.

First Study on profiling of gut microbiome in wild and captive Sumatran orangutans (Pongo abelii)

Background and Aim

Orangutans are an "umbrella species" for conserving tropical forests in Sumatra and Kalimantan. There are remarkable changes between the gut microbiomes of wild and captive Sumatran orangutans. This study aimed to profile gut microbiota of wild and captive Sumatran orangutans.

Materials and Methods

Nine fecal samples collected from wild orangutans and nine fecal samples collected from captive orangutans were divided into three replicates. Each replicate randomly combined three pieces and were analyzed on the Illumina platform. A bioinformatics study of 16S rRNA according to Qiime2 (Version 2021.4) and microbiome profiling analysis was conducted.

Results

The relative abundance of different microbial taxa varied significantly between wild and captive Sumatran orangutans. Among the operational taxonomic units, various proportions of Firmicutes, Proteobacteria, Bacteroidetes, Euryarchaeota, Acidobacteria, Actinobacteria and Verrucomicrobia predominated. Solobacterium was found only in 19% of captive orangutans. Methanobrevibacter was identified to be prevalent among wild orangutans (16%). Analysis of the core microbiome from the combined wild and captive data revealed seven species as cores. According to linear discriminant analysis effect size, Micrococcus luteus, Bacteroidescaccae, Lachnospiraceae bacterium, Ruthenibacterium lactatiformans, Haemophilus haemolyticus, and Chishuiella spp. were microbiome biomarkers in captive orangutans, whereas Roseburia inulinivorans, Collinsella aerofaciens, Oscillibacter spp., and Eubacterium hallii were microbiome biomarkers in wild orangutans.

Conclusion

There were differences in the microbiome biomarkers of wild and captive Sumatran orangutans. This study is important for understanding the role of gut bacteria in the health of Sumatran orangutans.

Paraburkholderia bengalensis sp. nov. isolated from roots of Oryza sativa, IR64

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 STM815^T (98.5% identity), P. terrae KMY02^T (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 17164^T, P. terrae DSM 17804^T, P. phymatum STM815^T 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.

Molecular characterization of endophytic and ectophytic plant growth promoting bacteria isolated from tomato plants (Solanum lycopersicum L.) grown in different soil types

Background

Successful rhizosphere colonization by plant growth promoting rhizobacteria (PGPR) is of crucial importance to perform the desired plant growth promoting activities. Since rhizocompetence is a dynamic process influenced by surrounding environmental conditions. In the present study, we hypothesized that bacterial isolates obtained from different tomato plant microhabitats (balk soil, rhizosphere, endorhiza, phyllosphere, and endoshoot) grown in different soils (sand, clay, and peat moss) will show different rhizocompetence abilities.

Results

To evaluate this hypothesis, bacterial isolates were obtained from different plant microhabitats and screened for their phosphate solubilizing and nitrogen fixing activates. BOX-PCR fingerprint profiles showed high genotypic diversity among the tested isolates and that same genotypes were shared between different soils and/or plant microhabitats. 16S rRNA gene sequences of 25 PGP isolates, representing different plant spheres and soil types, were affiliated to eight genera: Enterobacter, Paraburkholderia, Klebsiella, Bacillus, Paenibacillus, Stenotrophomonas, Pseudomonas, and Kosakonia. The rhizocompetence of each isolate was evaluated in the rhizosphere of tomato plants grown on a mixture of the three soils. Different genotypes of the same bacterial species displayed different rhizocompetence potentials. However, isolates obtained from the above-ground parts of the plant showed high rhizocompetence. In addition, biological control-related genes, ituD and srfC, were detected in the obtained spore forming bacterial isolates.

Conclusion

This study evaluates, for the first time, the relationship between plant microhabitat and the rhizocompetence ability in tomato rhizosphere. The results indicated that soil type and plant sphere can influence both the genotypic diversity and rhizocompetence ability of the same bacterial species. Bacterial isolates obtained in this study are promising to be used as an environmentally friendly substitution of chemical fertilizers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00361-0.

Functional Investigation of Plant Growth Promoting Rhizobacterial Communities in Sugarcane

Plant microbiota are of great importance for host nutrition and health. As a C₄ plant species with a high carbon fixation capacity, sugarcane also associates with beneficial microbes, though mechanisms underlying sugarcane root-associated community development remain unclear. Here, we identify microbes that are specifically enriched around sugarcane roots and report results of functional testing of potentially beneficial microbes propagating with sugarcane plants. First, we analyzed recruitment of microbes through analysis of 16S rDNA enrichment in greenhouse cultured sugarcane seedlings growing in field soil. Then, plant-associated microbes were isolated and assayed for beneficial activity, first in greenhouse experiments, followed by field trials for selected microbial strains. The promising beneficial microbe SRB-109, which quickly colonized both roots and shoots of sugarcane plants, significantly promoted sugarcane growth in field trials, nitrogen and potassium acquisition increasing by 35.68 and 28.35%, respectively. Taken together, this report demonstrates successful identification and utilization of beneficial plant-associated microbes in sugarcane production. Further development might facilitate incorporation of such growth-promoting microbial applications in large-scale sugarcane production, which may not only increase yields but also reduce fertilizer costs and runoff.

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 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.

Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens

Burkholderia harbors versatile Gram-negative species and is β-Proteobacteria. Recently, it was proposed to split the genus in two main branches: one of animal and plant pathogens and another, Paraburkholderia, harboring environmental and plant-beneficial species. Currently, Paraburkholderia comprises more than 70 species with ability to occupy very diverse environmental niches. Herein, we sequenced and analyzed the genome of Paraburkholderia kururiensis type strain KP23T , and compared to P. kururiensis M130, isolated in Brazil, and P. kururiensis susbp. thiooxydans, from Korea. This study focused on the gene content of the three genomes with special emphasis on their potential of plant-association, biocontrol, and bioremediation. The comparative analyses revealed several genes related to plant benefits, including biosynthesis of IAA, ACC deaminase, multiple efflux pumps, dioxygenases, and degradation of aromatic compounds. Importantly, a range of genes for protein secretion systems (type III, IV, V, and VI) were characterized, potentially involved in P. kururiensis well documented ability to establish endophytic association with plants. These findings shed light onto bacteria-plant interaction mechanisms at molecular level, adding novel information that supports their potential application in bioremediation, biofertilization, and biocontrol of plant pathogens. P. kururiensis emerges as a promising model to investigate adaptation mechanisms in different ecological niches.