Статті в журналах: "Caballeronia"

1

Stoy, Kayla S., Joselyne Chavez, Valeria De Las Casas, Venkat Talla, Aileen Berasategui, Levi T. Morran, and Nicole M. Gerardo. "Evaluating coevolution in a horizontally transmitted mutualism." Evolution 77, no. 1 (December 8, 2022): 166–85. http://dx.doi.org/10.1093/evolut/qpac009.

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Abstract Many interspecific interactions are shaped by coevolution. Transmission mode is thought to influence opportunities for coevolution within symbiotic interactions. Vertical transmission maintains partner fidelity, increasing opportunities for coevolution, but horizontal transmission may disrupt partner fidelity, potentially reducing opportunities for coevolution. Despite these predictions, the role of coevolution in the maintenance of horizontally transmitted symbioses is unclear. Leveraging a tractable insect–bacteria symbiosis, we tested for signatures of pairwise coevolution by assessing patterns of host–symbiont specialization. If pairwise coevolution defines the interaction, we expected to observe evidence of reciprocal specialization between hosts and their local symbionts. We found no evidence for local adaptation between sympatric lineages of Anasa tristis squash bugs and Caballeronia spp. symbionts across their native geographic range. We also found no evidence for specialization between three co-localized Anasa host species and their native Caballeronia symbionts. Our results demonstrate generalist dynamics underlie the interaction between Anasa insect hosts and their Caballeronia symbionts. We predict that selection from multiple host species may favor generalist symbiont traits through diffuse coevolution. Alternatively, selection for generalist traits may be a consequence of selection by hosts for fixed cooperative symbiont traits without coevolution.

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Quan, Xiao-Tian, Qing-Zhen Liu, Muhammad Zubair Siddiqi, and Wan-Taek Im. "Caballeronia ginsengisoli sp. nov., isolated from ginseng cultivating soil." Archives of Microbiology 201, no. 4 (October 4, 2018): 443–49. http://dx.doi.org/10.1007/s00203-018-1577-0.

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3

Uroz, S., and P. Oger. "Caballeronia mineralivorans sp. nov., isolated from oak- Scleroderma citrinum mycorrhizosphere." Systematic and Applied Microbiology 40, no. 6 (September 2017): 345–51. http://dx.doi.org/10.1016/j.syapm.2017.05.005.

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Kim, Jae Hwan, So-Jeong Kim, and In-Hyun Nam. "Effect of Treating Acid Sulfate Soils with Phosphate Solubilizing Bacteria on Germination and Growth of Tomato (Lycopersicon esculentum L.)." International Journal of Environmental Research and Public Health 18, no. 17 (August 25, 2021): 8919. http://dx.doi.org/10.3390/ijerph18178919.

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Acid sulfate soils contain sulfide minerals that have adverse environmental effects because they can lead to acidic drainage and prevent the establishment of vegetation. The current study examined the effect of a novel method for the restoration of these soils and the promotion of germination and plant growth. Thus, we isolated two strains of phosphate solubilizing bacteria, Methylobacterium sp. PS and Caballeronia sp. EK, characterized their properties, and examined their effects in promoting the growth of tomato plants (Lycopersicon esculentum L.) in acid sulfate soil. Compared with untreated control soil, treatment of acid sulfate soils with these bacterial strains led to increased seed germination, growth of plants with more leaves, and plants with greater levels of total-adenosine tri-phosphate (tATP). Relative to the untreated control soil, the addition of Caballeronia sp. EK led to a 60% increase in seed germination after 52 days, growth of plants with more than 3 times as many leaves, and a 45.2% increase in tATP after 50 days. This strain has potential for use as a plant biofertilizer that promotes vegetation growth in acid sulfate soils by improving the absorption of phosphorous.

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Verstraete, Brecht, Steven Janssens, Petra De Block, Pieter Asselman, Gabriela Méndez, Serigne Ly, Perla Hamon, and Romain Guyot. "Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes." PeerJ 11 (August 4, 2023): e15778. http://dx.doi.org/10.7717/peerj.15778.

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Background Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in the African plant genera Empogona and Tricalysia and, if present, to establish their identity. Methods Total DNA was extracted from the leaves of four species of the Coffeeae tribe (Empogona congesta, Tricalysia hensii, T. lasiodelphys, and T. semidecidua) and sequenced. Bacterial reads were filtered out and assembled. Phylogenetic analysis of the endophytes was used to reveal their identity and their relationship with known symbionts. Results All four species have non-nodulated leaf endophytes, which are identified as Caballeronia. The endophytes are distinct from each other but related to other nodulated and non-nodulated endophytes. An apparent phylogenetic or geographic pattern appears to be absent in endophytes or host plants. Caballeronia endophytes are present in the leaves of Empogona and Tricalysia, two genera not previously implicated in leaf symbiosis. This interaction is likely to be more widespread, and future discoveries are inevitable.

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Kim, Junghee, Kae Kyoung Kwon, Byung Kwon Kim, Soon Gyu Hong, and Hyun-Myung Oh. "Genome sequence of Caballeronia sordidicola strain PAMC 26592 isolated from an arctic lichen species." Korean Journal of Microbiology 53, no. 1 (March 31, 2017): 64–66. http://dx.doi.org/10.7845/kjm.2017.7008.

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Ara, Ifat, Ryota Moriuchi, Hideo Dohra, Kazuhide Kimbara, Naoto Ogawa, and Masaki Shintani. "Isolation and Genomic Analysis of 3-Chlorobenzoate-Degrading Bacteria from Soil." Microorganisms 11, no. 7 (June 28, 2023): 1684. http://dx.doi.org/10.3390/microorganisms11071684.

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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.

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8

Jiang, Yanbing, Hao Fu, Meng Li, and Changtao Wang. "Characterization of Functional Microorganisms in Representative Traditional Fermented Dongcai from Different Regions of China." Foods 12, no. 9 (April 23, 2023): 1753. http://dx.doi.org/10.3390/foods12091753.

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Dongcai is loved for its delicious flavor and nutritional value. The microorganisms in Dongcai play a vital role in their flavor, quality, and safety, and the microbial communities of Dongcai vary greatly from region to region. However, it remains unknown what the predominant microorganisms are in different traditional Dongcai and how they affect its flavor. The objective of this study is to explore the microbial diversity of traditional fermented Dongcai in three representative Chinese regions (Tianjin, Sichuan, and Guangzhou) and further assess their microbial functions. The microbial diversity of fermented Dongcai in Guangdong has the lowest diversity compared to fermented Dongcai in Sichuan, which has the highest. The distribution of the main genera of fermented Dongcai varies from region to region, but Carnimonas, Staphylococcus, Pseudomonas, Sphingomonas, Burkholderia-Caballeronia-Paraburkholderia, and Rhodococcus are the dominant genera in common. In addition, halophilic bacteria (HAB, i.e., Halomonas Bacillus, Virgibacillus, etc.) and lactic acid bacteria (LAB, i.e., Weissella and Lactobacillus) are also highly abundant. Of these, Burkholderia-Caballeronia-Paraburkholderia, Rhodococcus, Sphingomonas, Ralstonia, and Chromohalobacter are dominant in the Sichuan samples. In the Tianjin samples, Lactobacillus, Weissella, Virgibacillus, Enterobacter, Klebsiella, and Pseudomonas are the most abundant. Predictions of microbial metabolic function reveal that carbohydrates, amino acids, polyketides, lipids, and other secondary metabolites are abundantly available for biosynthesis. In addition, the different flavors of the three types of Dongcai may be due to the fact that the abundance of HAB and LAB shows a significant positive correlation with the amounts of important metabolites (e.g., salt, acid, amino nitrogen, and sugar). These results contribute to our understanding of the link between the distinctive flavors of different types of Dongcai and the microorganisms they contain and will also provide a reference for the relationship between microbial communities and flavor substances in semi-fermented pickles.

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9

Sadauskas, Mikas, Roberta Statkevičiūtė, Justas Vaitekūnas, and Rolandas Meškys. "Bioconversion of Biologically Active Indole Derivatives with Indole-3-Acetic Acid-Degrading Enzymes from Caballeronia glathei DSM50014." Biomolecules 10, no. 4 (April 24, 2020): 663. http://dx.doi.org/10.3390/biom10040663.

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A plant auxin hormone indole-3-acetic acid (IAA) can be assimilated by bacteria as an energy and carbon source, although no degradation has been reported for indole-3-propionic acid and indole-3-butyric acid. While significant efforts have been made to decipher the Iac (indole-3-acetic acid catabolism)-mediated IAA degradation pathway, a lot of questions remain regarding the mechanisms of individual reactions, involvement of specific Iac proteins, and the overall reaction scheme. This work was aimed at providing new experimental evidence regarding the biodegradation of IAA and its derivatives. Here, it was shown that Caballeronia glathei strain DSM50014 possesses a full iac gene cluster and is able to use IAA as a sole source of carbon and energy. Next, IacE was shown to be responsible for the conversion of 2-oxoindole-3-acetic acid (Ox-IAA) intermediate into the central intermediate 3-hydroxy-2-oxindole-3-acetic acid (DOAA) without the requirement for IacB. During this reaction, the oxygen atom incorporated into Ox-IAA was derived from water. Finally, IacA and IacE were shown to convert a wide range of indole derivatives, including indole-3-propionic acid and indole-3-butyric acid, into corresponding DOAA homologs. This work provides novel insights into Iac-mediated IAA degradation and demonstrates the versatility and substrate scope of IacA and IacE enzymes.

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Li, Shengnan, Ziwei Chen, Wenli Zhang, Cuie Guang, and Wanmeng Mu. "Characterization of a d-tagatose 3-epimerase from Caballeronia fortuita and its application in rare sugar production." International Journal of Biological Macromolecules 138 (October 2019): 536–45. http://dx.doi.org/10.1016/j.ijbiomac.2019.07.112.

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Uroz, Stéphane, Laura Picard, Marie‐Pierre Turpault, Lucas Auer, Jean Armengaud, and Phil Oger. "Dual transcriptomics and proteomics analyses of the early stage of interaction between Caballeronia mineralivorans PML1 (12) and mineral." Environmental Microbiology 22, no. 9 (September 2020): 3838–62. http://dx.doi.org/10.1111/1462-2920.15159.

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12

Dobritsa, Anatoly P., and Mansour Samadpour. "Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies." International Journal of Systematic and Evolutionary Microbiology 69, no. 7 (July 1, 2019): 2057–63. http://dx.doi.org/10.1099/ijsem.0.003431.

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13

Uroz, S., and P. Oger. "Corrigendum to “Caballeronia mineralivorans sp. nov., isolated from oak-Scleroderma citrinum mycorrhizosphere” [Syst. Appl. Microbiol. 40 (2017) 345–351]." Systematic and Applied Microbiology 42, no. 3 (May 2019): 423–24. http://dx.doi.org/10.1016/j.syapm.2019.03.001.

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Grill, Birgit, Maximilian Glänzer, Helmut Schwab, Kerstin Steiner, Daniel Pienaar, Dean Brady, Kai Donsbach, and Margit Winkler. "Functional Expression and Characterization of a Panel of Cobalt and Iron-Dependent Nitrile Hydratases." Molecules 25, no. 11 (May 28, 2020): 2521. http://dx.doi.org/10.3390/molecules25112521.

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Nitrile hydratases (NHase) catalyze the hydration of nitriles to the corresponding amides. We report on the heterologous expression of various nitrile hydratases. Some of these enzymes have been investigated by others and us before, but sixteen target proteins represent novel sequences. Of 21 target sequences, 4 iron and 16 cobalt containing proteins were functionally expressed from Escherichia coli BL21 (DE3) Gold. Cell free extracts were used for activity profiling and basic characterization of the NHases using the typical NHase substrate methacrylonitrile. Co-type NHases are more tolerant to high pH than Fe-type NHases. A screening for activity on three structurally diverse nitriles was carried out. Two novel Co-dependent NHases from Afipia broomeae and Roseobacter sp. and a new Fe-type NHase from Gordonia hydrophobica were very well expressed and hydrated methacrylonitrile, pyrazine-carbonitrile, and 3-amino-3-(p-toluoyl)propanenitrile. The Co-dependent NHases from Caballeronia jiangsuensis and Microvirga lotononidis, as well as two Fe-dependent NHases from Pseudomonades, were—in addition—able to produce the amide from cinnamonitrile. Summarizing, seven so far uncharacterized NHases are described to be promising biocatalysts.

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Wu, Wei, Zhuochen Wang, Boyang Xu, Jing Cai, Jianghua Cheng, Dongdong Mu, Xuefeng Wu, and Xingjiang Li. "Exploring Core Microbiota Based on Characteristic Flavor Compounds in Different Fermentation Phases of Sufu." Molecules 27, no. 15 (August 3, 2022): 4933. http://dx.doi.org/10.3390/molecules27154933.

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Sufu, a Chinese traditional fermented soybean product, has a characteristic foul smell but a pleasant taste. We determined the core functional microbiota and their metabolic mechanisms during sufu fermentation by examining relationships among bacteria, characteristic flavor compounds, and physicochemical factors. Flavor compounds in sufu were detected through headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry, and the microbial community structure was determined through high-throughput 16S rRNA sequencing. The results showed that the fermentation process of sufu could be divided into early and late stages. The early stage was critical for flavor development. Seven microbiota were screened based on their abundance, microbial relevance, and flavor production capacity. Five microbes were screened in the early stage: Pseudomonas, Tetragenococcus, Lysinibacillus, Pantoea, and Burkholderia–Caballeronia–Paraburkholderia. Three microbes were screened in the late stage: Exiguobacterium, Bacillus, and Pseudomonas. Their metabolic profiles were predicted. The results provided a reference for the selection of enriched bacterial genera in the fermentation process and controlling applicable process conditions to improve the flavor of sufu.

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Estrada-de los Santos, Paulina, Marike Palmer, Belén Chávez-Ramírez, Chrizelle Beukes, Emma Steenkamp, Leah Briscoe, Noor Khan, et al. "Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae." Genes 9, no. 8 (August 1, 2018): 389. http://dx.doi.org/10.3390/genes9080389.

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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.

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Zhang, Mingzhu, Chao Peng, Wentao Sun, Rui Dong, and Jun Hao. "Effects of Variety, Plant Location, and Season on the Phyllosphere Bacterial Community Structure of Alfalfa (Medicago sativa L.)." Microorganisms 10, no. 10 (October 13, 2022): 2023. http://dx.doi.org/10.3390/microorganisms10102023.

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Plant phyllosphere bacteria are vital for plant health and productivity and are affected by both abiotic and biotic factors. In this study, we surveyed the structure of the phyllosphere bacterial community associated with alfalfa. For two varieties of alfalfa, forty-eight samples of phyllosphere communities were collected at two locations over four seasons in 2020. Proteobacteria and actinobacteria were associated with the dominating phylum in the bacterial communities of the alfalfa phyllosphere. Sphingomonas was the most abundant genus-level bacteria, followed by Methylobacterium, Burkholderia-Caballeronia-Paraburkholderia, and Pseudomonas. Sampling time had a greater affect than site and variety on alfalfa surface microorganisms. The variation in phyllosphere bacterial community assembly was mostly explained by the season–site interaction (43%), season–variety interaction (35%), and season (28%). Variety, site–variety interaction, and season–site–variety interactions did not have a meaningful effect on phyllosphere bacterial diversity and community structure. The bacterial community in the phyllosphere of alfalfa showed seasonal changes over time. The environmental factors that contributed most to the phyllosphere bacterial community of alfalfa were temperature and sunshine duration, which were significantly positively correlated with most of the dominant bacterial genera in the alfalfa phyllosphere.

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Nadifah, Fitri, Wayan Tunas Artama, Budi Setiadi Daryono, and Endah Retnaningrum. "Characterization of the urogenital microbiome in patients with urinary tract infections." Indonesian Journal of Biotechnology 27, no. 3 (September 30, 2022): 142. http://dx.doi.org/10.22146/ijbiotech.69212.

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Standard microbiological culture techniques can only identify a fraction of the urogenital microbiome. Meanwhile, identifying and characterizing infectious microorganisms are very important for the success of diagnosis and treatments, especially for Urinary Tract Infection (UTI) patients. This study aimed to characterize the urogenital microbiome of UTI patients using 16S rRNA gene sequencing. We sequenced two pooled DNA samples from voided urine of UTI patients (21 females and 13 males). To determine the structure and composition of taxa in the samples, 16S rRNA gene sequencing was performed using the Illumina Mi‐Seq paired‐end platform. The most abundant genera were Burkholderia‐Caballeronia‐Paraburkholderia (71%) followed by Prevotella (33%), Escherichia‐Shigella (24%), Klebsiella (23%) and Sneathia (10%). The female microbiome was dominated by Prevotella bivia (28%), Escherichia coli (24%), Sneathia sanguinegens (7%) and Klebsiella pneumoniae (4%). On the other hand, the male microbiome was dominated by K. pneumoniae (23%) and E. coli (2%). K. pneumoniae and E. coli were the most abundant species found in both microbiomes. The 16S rRNA gene sequencing used in this study successfully uncovered the composition of the urogenital microbiome, which might not have been possible with conventional culture methods.

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Gonçalves, Ana C., Fernando Sánchez-Juanes, Sara Meirinho, Luís R. Silva, Gilberto Alves, and José David Flores-Félix. "Insight into the Taxonomic and Functional Diversity of Bacterial Communities Inhabiting Blueberries in Portugal." Microorganisms 10, no. 11 (November 4, 2022): 2193. http://dx.doi.org/10.3390/microorganisms10112193.

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Vaccinium myrtillus is a dwarf shrub of the Ericaceae family with a Palearctic distribution, associated with temperate and cold humid climates. It is widespread on the European continent; on the Iberian Peninsula it is located on Atlantic climate mountains and glacial relicts. In Portugal, we find scattered and interesting populations; however, the majority of them are threatened by climate change and wildfires. Given that, the objective of this study is to determine the rhizospheric and root bacterial communities of this plant in the southernmost regions, and, consequently, its potential range and ability to be used as a biofertilizer. In this work, metabarcoding of 16S rRNA gene showed that the endophytic bacterial diversity is dependent on the plant and selected by it according to the observed alpha and beta diversity. Moreover, a culturomic approach allowed 142 different strains to be isolated, some of them being putative new species. Additionally, some strains belonging to the genera Bacillus, Paenibacillus, Pseudomonas, Paraburkholderia, and Caballeronia showed significant potential to be applied as multifunctional biofertilizers since they present good plant growth-promoting (PGP) mechanisms, high colonization capacities, and an increase in vegetative parameters in blueberry and tomato plants.

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Yang, Yuehua, Fangkui Wang, Jialin Jiang, and Ling Jiang. "Inhibition of Citrus Huanglongbing Disease by Paenibacillus polymyx KN-03 and Analysis with Transcriptome and Microflora." Agronomy 13, no. 12 (November 30, 2023): 2958. http://dx.doi.org/10.3390/agronomy13122958.

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Soil drench treatment using Paenibacillus polymyxa strain KN-03 was applied to citrus plants infected with Candidatus Liberibacter asiaticus (CLas). The infection status was assessed using PCR and a real-time quantitative PCR detection system (qPCR). The application of KN-03 resulted in a notable reduction in CLas levels in citrus plants. Specifically, by the 257th day post treatment commencement, following 24 KN-03 applications, the negative rates of CLas in the vein, root tip, and shoot tip were 50%, 0%, and 50%, respectively. After 24 cycles, KN-03 application significantly enhanced plant growth and stimulated reactive oxygen production in citrus leaves compared to control plants. Transcriptome analysis identified specific upregulated pathways. Furthermore, flora analysis revealed an increased abundance of microorganisms possessing potential utilization value, including Burkholderia-Caballeronia-Paraburkholderia, uncultured_bacterium_o_Acidobacteriales, uncultured_bacterium_f_Gemmatimonadaceae, and Rhodanobacter, in the root zone. Moreover, the BugBase analysis indicated that KN-03 treatment increased the abundance of beneficial rhizosphere bacteria associated with biofilm formation, element mobilization, and stress tolerance. These findings support the utility of Paenibacillus polymyxa KN-03 as an effective plant-growth-promoting bacterium for CLas management, with additional benefits for plant growth and soil health, specifically offering detoxification resources for shoot tip grafting.

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Dobritsa, Anatoly P., Elena V. Linardopoulou, and Mansour Samadpour. "Transfer of 13 species of the genus Burkholderia to the genus Caballeronia and reclassification of Burkholderia jirisanensis as Paraburkholderia jirisanensis comb. nov." International Journal of Systematic and Evolutionary Microbiology 67, no. 10 (October 1, 2017): 3846–53. http://dx.doi.org/10.1099/ijsem.0.002202.

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Depoorter, Eliza, Evelien De Canck, Tom Coenye, and Peter Vandamme. "Burkholderia Bacteria Produce Multiple Potentially Novel Molecules that Inhibit Carbapenem-Resistant Gram-Negative Bacterial Pathogens." Antibiotics 10, no. 2 (February 2, 2021): 147. http://dx.doi.org/10.3390/antibiotics10020147.

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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.

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Han, Gil, Mohamed Mannaa, Namgyu Kim, Hee Won Jeon, Hyejung Jung, Hyun-Hee Lee, Junheon Kim, et al. "Response of Pine Rhizosphere Microbiota to Foliar Treatment with Resistance-Inducing Bacteria against Pine Wilt Disease." Microorganisms 9, no. 4 (March 26, 2021): 688. http://dx.doi.org/10.3390/microorganisms9040688.

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In this study, two bacterial strains, IRP7 and IRP8, were selected to induce resistance against pine wilt disease (PWD). Foliar application with these strains to nematode-inoculated pine seedlings significantly reduced PWD severity. The effect of nematode inoculation and bacterial treatment on the rhizosphere bacterial community was investigated. The results indicated that the rhizosphere of nematode-inoculated seedlings contained a lower relative abundance of beneficial microbes such as Paraburkholderia, Bradyrhizobium, Rhizobacter, Lysobacter, and Caballeronia. Bacterial treatment resulted in significant changes in the microbes that were represented in relatively low relative abundance. Treatment with IRP7 resulted in an increase in the relative abundance of Nitrospirillum, Bacillus, and Luteibacter, which might be useful for protection against infection. Treatment with IRP8 resulted in an increase in the relative abundance of obligate bacterial predators of the Bdellovibrio genus that were previously shown to control several bacterial phytopathogens and may have a role in the management of nematode-carried bacteria. The selected bacteria were identified as Pseudomonas koreensis IRP7 and Lysobacter enzymogenes IRP8 and are suggested as a potential treatment for induced resistance against PWD. To our knowledge, this is the first report on the effect of foliar treatment with resistance-inducing bacteria on the rhizosphere microbiota.

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Shang, Shuai, Liangyu Li, Xiaoxue Liu, Jun Wang, and Xuexi Tang. "Bacterial Community in the Gut of Neanthes japonica and Its Association with Surrounding Environment." Diversity 14, no. 7 (June 25, 2022): 514. http://dx.doi.org/10.3390/d14070514.

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Neanthes japonica has high commercial value. The gut microbes in N. japonica can maintain the normal biological functions of the host. However, information on the gut bacterial community of N. japonica and its relationship with the surrounding environment is unclear. In this study, we used high-throughput sequencing technology to investigate the bacterial communities in the gut of N. japonica and soil. The results showed that the bacterial community diversity and structure differed obviously between the gut and soil samples. Bacterial richness and diversity in the gut samples decreased considerably compared to soil samples. In addition, dominant bacterial taxa varied significantly between the gut and soil samples. The dominant phyla in the gut and soil samples were Proteobacteria, Bacteroidota and Planctomycetota. The dominant genus in the gut was Burkholderia-Caballeronia-Paraburkholderia, while the dominant genera in the soil were Woeseia and Subgroup_23. In conclusion, the similarity between the bacterial communities in soil and the gut of N. japonica was small, indicating that soil had little effect on the establishment of the gut bacterial community. This study provides a better understanding of the gut bacterial community in N. japonica and the influence of the external environment on the colonization of the gut bacterial community.

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Walker, Madison Blake, Matthew Patrick Holton, Todd Riley Callaway, Jeferson Menezes Lourenco, and Pedro Levy Piza Fontes. "Differences in Microbial Community Composition between Uterine Horns Ipsilateral and Contralateral to the Corpus Luteum in Beef Cows on Day 15 of the Estrous Cycle." Microorganisms 11, no. 8 (August 20, 2023): 2117. http://dx.doi.org/10.3390/microorganisms11082117.

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This study evaluated differences in uterine microbiota composition between uterine horns ipsilateral and contralateral to the corpus luteum of beef cows on day 15 of the estrous cycle. Cows (n = 23) were exposed to an estrus synchronization protocol to exogenously induce synchronized ovulation. Cows were then euthanized on day 15 of the estrous cycle, and individual swabs were collected from uterine horns ipsilateral and contralateral to the corpus luteum using aseptic techniques. DNA was extracted, and the entire (V1–V9 hypervariable regions) 16s rRNA gene was sequenced. Sequences were analyzed, and amplicon sequence variants (ASVs) were determined. Across all samples, 2 bacterial domains, 24 phyla, and 265 genera were identified. Butyribirio, Cutibacterium, BD7-11, Bacteroidales BS11 gut group, Ruminococcus, Bacteroidales RF16 group, and Clostridia UCG-014 differed in relative abundances between uterine horns. Rikenellaceae RC9 gut group, Bacteroidales UCG-001, Lachnospiraceae AC2044 group, Burkholderia-Caballeronia-Paraburkholderia, Psudobutyribibrio, and an unidentified genus of the family Chitinophagaceae and dgA-11 gut group differed between cows that expressed estrus and those that did not. The composition of the microbial community differed between the ipsilateral and contralateral horns and between cows that expressed estrus and cows that failed to express estrus, indicating that the uterine microbiota might play a role in cow fertility.

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Zhang, Xiaoxiao, Wei Zhao, Yuming Lin, Bin Shan, and Shanshan Yang. "Identification of Meloidogyne panyuensis (Nematoda: Meloidogynidae) infecting Orah (Citrus reticulata Blanco) and its impact on rhizosphere microbial dynamics: Guangxi, China." PeerJ 12 (November 6, 2024): e18495. http://dx.doi.org/10.7717/peerj.18495.

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Root-knot nematode disease severely affects the yield and quality of the mandarin variety Citrus reticulata Blanco “Orah” in Guangxi, China. Nevertheless, the pathogen and the effects of this disease on microbial communities remain inadequately understood. This study identified the root-knot nematode Meloidogyne panyuensis in the rhizosphere of infected Orah using morphological and molecular biological methods. Soil chemical properties indicated that organic matter, total nitrogen (TN), total phosphorus (TP), available phosphorus (AP), total potassium (TK), and available potassium (AK) were significantly higher in the rhizosphere soil of M. panyuensis-infected Orah than in that of healthy plants. The relative abundance of the bacteria Bacillus, Sphingomonas, and Burkholderia-Caballeronia-Paraburkholderia, as well as the fungi Lycoperdon, Fusarium, Neocosmospora, Talaromyces, and Tetragoniomyces, was elevated in the rhizosphere soil of M. panyuensis-infected plants. Furthermore, organic matter, TN, available nitrogen (AN), TP, AP, TK, and AK exhibited positive correlationswith these bacteria and fungi in the rhizosphere soil of M. panyuensis-infected Orah. Potential biocontrol strains, such as Burkholderia spp., were identified by comparing the differences in rhizosphere microbial composition between healthy Orah and M. panyuensis-infected Orah. Our findings provide a foundation for the early warning and prevention of root-knot nematode disease in Orah.

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Roslan, Muhamad Aidilfitri Mohamad, Zulfazli M. Sobri, Ali Tan Kee Zuan, and Nor Aini Abdul Rahman. "Okra Growth, Yield and Rhizosphere Microbiome Responses to the Encapsulated Bioinoculant Application under Reduced Fertilization Regime." Biology 11, no. 8 (July 25, 2022): 1107. http://dx.doi.org/10.3390/biology11081107.

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There is limited evidence that Enterobacter hormaechei can improve plant physiology and yield through soil phosphate (P) and potassium (K) amelioration. This study unraveled the effect of different soil inoculation methods i.e., free-cell and encapsulated (alginate bead containing sugar-protein hydrolysate and molasses) E. hormaechei 40a with different rates of PK-fertilization on okra P and K uptake, and soil rhizosphere bacterial community. The results revealed that 3HB (half-dose PK-fertilizer + encapsulated strain 40a) had the highest soil available P (SAP) and K (SAK), as well as P and K uptake for all plant organs, followed by 3F (full-dose PK-fertilizer), 3HI (half-dose PK-fertilizer + free-cell strain 40a), and 3H (half-dose PK-fertilizer), and improved yield by up to 75.6%. Both inoculated and full-dose fertilizer treatments produced larger pods (>15 cm) compared to 3H. We discovered increased bacterial richness and diversity in both 3HB and 3HI samples compared to uninoculated treatments. Both 3HB and 3F treatments were positively correlated with the increasing abundance of Acidobacteriales, Burkholderia caballeronia paraburkholderia, Gemmataceae, and Sphingomonas along with the SAP and SAK. The plant-beneficial effect of one-time 3HB treatment on okra growth and yield was comparable to biweekly inoculation in 3HI, suggesting a new cost-effective farming approach in precision agriculture.

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Takeshita, Kazutaka, and Yoshitomo Kikuchi. "Genomic Comparison of Insect Gut Symbionts from Divergent Burkholderia Subclades." Genes 11, no. 7 (July 3, 2020): 744. http://dx.doi.org/10.3390/genes11070744.

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Stink bugs of the superfamilies Coreoidea and Lygaeoidea establish gut symbioses with environmentally acquired bacteria of the genus Burkholderia sensu lato. In the genus Burkholderia, the stink bug-associated strains form a monophyletic clade, named stink bug-associated beneficial and environmental (SBE) clade (or Caballeronia). Recently, we revealed that members of the family Largidae of the superfamily Pyrrhocoroidea are associated with Burkholderia but not specifically with the SBE Burkholderia; largid bugs harbor symbionts that belong to a clade of plant-associated group of Burkholderia, called plant-associated beneficial and environmental (PBE) clade (or Paraburkholderia). To understand the genomic features of Burkholderia symbionts of stink bugs, we isolated two symbiotic Burkholderia strains from a bordered plant bug Physopellta gutta (Pyrrhocoroidea: Largidae) and determined their complete genomes. The genome sizes of the insect-associated PBE (iPBE) are 9.5 Mb and 11.2 Mb, both of which are larger than the genomes of the SBE Burkholderia symbionts. A whole-genome comparison between two iPBE symbionts and three SBE symbionts highlighted that all previously reported symbiosis factors are shared and that 282 genes are specifically conserved in the five stink bug symbionts, over one-third of which have unknown function. Among the symbiont-specific genes, about 40 genes formed a cluster in all five symbionts; this suggests a “symbiotic island” in the genome of stink bug-associated Burkholderia.

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South, Kaylee A., Nathan P. Nordstedt, and Michelle L. Jones. "Identification of Plant Growth Promoting Rhizobacteria That Improve the Performance of Greenhouse-Grown Petunias under Low Fertility Conditions." Plants 10, no. 7 (July 9, 2021): 1410. http://dx.doi.org/10.3390/plants10071410.

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The production of greenhouse ornamentals relies on high fertilizer inputs to meet scheduling deadlines and quality standards, but overfertilization has negative environmental impacts. The goals of this study were to identify plant-growth-promoting rhizobacteria (PGPR) that can improve greenhouse ornamental crop performance with reduced fertilizer inputs, and to identify the best measurements of plant performance for assessing the beneficial impact of PGPR on ornamentals. A high-throughput greenhouse trial was used to identify 14 PGPR isolates that improved the flower/bud number and shoot dry weight of Petunia × hybrida ‘Picobella Blue’ grown under low fertility conditions in peat-based media. These 14 PGPR were then applied to petunias grown under low fertility conditions (25 mg L−1 N). PGPR-treated plants were compared to negative (untreated at 25 mg L−1 N) and positive (untreated at 50, 75, 100, and 150 mg L−1 N) controls. Multiple parameters were measured in the categories of flowering, vegetative growth, and vegetative quality to determine the best measurements to assess improvements in ornamental plant performance. Caballeronia zhejiangensis C7B12-treated plants performed better in almost all parameters and were comparable to untreated plants fertilized with 50 mg L−1 N. Genomic analysis identified genes that were potentially involved in plant growth promotion. Our study identified potential PGPR that can be used as biostimulants to produce high-quality greenhouse ornamentals with lower fertilizer inputs.

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Han, Gil, Mohamed Mannaa, Hyoseong Jeon, Hyejung Jung, Jin-Cheol Kim, Ae Ran Park, and Young-Su Seo. "Dysbiosis in the Rhizosphere Microbiome of Standing Dead Korean Fir (Abies koreana)." Plants 11, no. 7 (April 5, 2022): 990. http://dx.doi.org/10.3390/plants11070990.

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The Korean fir (Abies koreana), a native coniferous tree species mainly found on Mt. Halla in Jeju, South Korea, is suffering from continuous population decline and has been declared an endangered species. Research efforts have focused on the possible abiotic causes behind this worrying decline. However, the potential link between tree vitality and the rhizosphere microbiome remains unclear. In this study, a comparative metagenomic 16S rRNA sequence analysis was used to investigate the composition of the rhizosphere microbiota of samples collected from healthy and die-back-affected trees on Mt. Halla. The results indicated a significant reduction in the richness and diversity of microbiota in the rhizosphere of die-back-affected trees. Moreover, the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes were significantly higher in healthy trees than in standing dead trees. Many bacterial genera were significantly more abundant in the rhizosphere of healthy trees, including those known for promoting plant growth and tolerance to biotic and abiotic stresses (e.g., Bradyrhizobium, Rhizomicrobium, Caulobacter, Nitrosospira, Rhizobacter, Paraburkholderia, Rhizobium, Devosia, Caballeronia, Niveispirillum, Dyella, Herbaspirillum, Frankia, Streptomyces, Actinoallomurus, Lysobacter, Luteibacter, Mucilaginibacter, and Variovorax). To our knowledge, this is the first report on rhizosphere bacterial microbiome dysbiosis in die-back-affected Korean fir trees, suggesting that the influence of rhizosphere microbiota should be considered to save this endangered species by investigating possible intervention strategies in future work.

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Chen, Jason Z., Zeeyong Kwong, Nicole M. Gerardo, and Nic M. Vega. "Ecological drift during colonization drives within-host and between-host heterogeneity in an animal-associated symbiont." PLOS Biology 22, no. 4 (April 25, 2024): e3002304. http://dx.doi.org/10.1371/journal.pbio.3002304.

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Specialized host–microbe symbioses canonically show greater diversity than expected from simple models, both at the population level and within individual hosts. To understand how this heterogeneity arises, we utilize the squash bug, Anasa tristis, and its bacterial symbionts in the genus Caballeronia. We modulate symbiont bottleneck size and inoculum composition during colonization to demonstrate the significance of ecological drift, the noisy fluctuations in community composition due to demographic stochasticity. Consistent with predictions from the neutral theory of biodiversity, we found that ecological drift alone can account for heterogeneity in symbiont community composition between hosts, even when 2 strains are nearly genetically identical. When acting on competing strains, ecological drift can maintain symbiont genetic diversity among different hosts by stochastically determining the dominant strain within each host. Finally, ecological drift mediates heterogeneity in isogenic symbiont populations even within a single host, along a consistent gradient running the anterior-posterior axis of the symbiotic organ. Our results demonstrate that symbiont population structure across scales does not necessarily require host-mediated selection, as it can emerge as a result of ecological drift acting on both isogenic and unrelated competitors. Our findings illuminate the processes that might affect symbiont transmission, coinfection, and population structure in nature, which can drive the evolution of host–microbe symbioses and microbe–microbe interactions within host-associated microbiomes.

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Zhang, Jianfeng, Hengfei Zhang, Shouyang Luo, Libo Ye, Changji Wang, Xiaonan Wang, Chunjie Tian, and Yu Sun. "Analysis and Functional Prediction of Core Bacteria in the Arabidopsis Rhizosphere Microbiome under Drought Stress." Microorganisms 12, no. 4 (April 12, 2024): 790. http://dx.doi.org/10.3390/microorganisms12040790.

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The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.

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Lin, Xinru, Da Yang, Xinyan Zhou, Xun Wei, Yuanyuan Xie, and Shangdong Yang. "Response of the Endophytic Microbial Composition in Amaranthus Roots to Different Fertilization Treatments." Agronomy 14, no. 5 (May 3, 2024): 965. http://dx.doi.org/10.3390/agronomy14050965.

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To explore how endophytic microbial compositions in amaranth roots are influenced by various fertilization methods and to determine whether these microbes are associated with amaranthin formation, we conducted an analysis of the endophytic microbial community structure. The roots of amaranth plants subjected to different fertilization treatments—conventional fertilization without potassium (NP), conventional fertilization without phosphorus (NK), conventional fertilization without nitrogen (PK), and balanced fertilization (NPK)—were examined. The results showed that the proportions of Streptomyces, Actinospica, and Burkholderia-Caballeronia-Paraburkholderia in the amaranth roots under the balanced fertilization (NPK) treatment were all greater than those in the amaranth roots under the nitrogen (PK), phosphorus (NK), and potassium (NP) deficiency fertilization treatments. In contrast, the proportions of Phenylobacterium, Acrocalymma, Neocosmospora, Fusarium, Acidovorax, Gibellulopsis, Cladosporium, Dactylonectria, and Gibberella in the amaranth roots under the nutrient deficiency fertilization (NP, NK, and PK) treatments were higher than those in the amaranth roots under the balanced fertilization treatment. Additionally, a significantly positive correlation was found between Streptomyces and the amaranthin content. Furthermore, Acrocalymma, Neocosmospora, and Fusarium exhibited significantly negative correlations with the amaranthin content. The above results suggested that endophytes could easily colonize in amaranth roots as beneficial microorganisms under balanced fertilization conditions. In other words, the balanced fertilization (N, P and K fertilizers are 188.0, 53.0 and 50.0 kg·hm−2, respectively) could recruit more beneficial endogenous microorganisms in amaranth roots for improving their growth and quality.

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Aleynova, Olga A., Alexey A. Ananev, Nikolay N. Nityagovsky, Andrey R. Suprun, Nursaule Zh Zhanbyrshina, Alina A. Beresh, Zlata V. Ogneva, Alexey P. Tyunin, and Konstantin V. Kiselev. "Endophytic Bacteria and Fungi Associated with Polygonum cuspidatum in the Russian Far East." Plants 13, no. 18 (September 19, 2024): 2618. http://dx.doi.org/10.3390/plants13182618.

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Polygonum cuspidatum, alternatively known as Fallopia japonica or Reynoutria japonica, is a perennial herb belonging to the Polygonaceae family. Commonly called Japanese knotweed or Asian knotweed, this plant is native to East Asia, particularly in regions such as Korea, China, and Japan. It has successfully adapted to a wide range of habitats, resulting in it being listed as a pest and invasive species in several countries in North America and Europe. This study focuses on analysing the composition of the bacterial and fungal endophytic communities associated with Japanese knotweed growing in the Russian Far East, employing next-generation sequencing (NGS) and a cultivation-based method (microbiological sowing). The NGS analysis showed that the dominant classes of endophytic bacteria were Alphaproteobacteria (28%) and Gammaproteobacteria (28%), Actinobacteria (20%), Bacteroidia (15%), and Bacilli (4%), and fungal classes were Agaricomycetes (40%), Dothideomycetes (24%), Leotiomycetes (10%), Tremellomycetes (9%), Pezizomycetes (5%), Sordariomycetes (3%), and Exobasidiomycetes (3%). The most common genera of endophytic bacteria were Burkholderia-Caballeronia-Parabukholderia, Sphingomonas, Hydrotalea, Methylobacterium-Metylorubrum, Cutibacterium, and Comamonadaceae, and genera of fungal endophytes were Marasmius, Tuber, Microcyclosporella, Schizothyrium, Alternaria, Parastagonospora, Vishniacozyma, and Cladosporium. The present data showed that the roots, leaves, and stems of P. cuspidatum have a greater number and diversity of endophytic bacteria and fungi compared to the flowers and seeds. Thus, the biodiversity of endophytic bacteria and fungi of P. cuspidatum was described and analysed for the first time in this study.

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Ohbayashi, Tsubasa, Raynald Cossard, Gaëlle Lextrait, Takahiro Hosokawa, Vincent Lesieur, Kazutaka Takeshita, Kanako Tago, Peter Mergaert, and Yoshitomo Kikuchi. "Intercontinental Diversity of <i>Caballeronia</i> Gut Symbionts in the Conifer Pest Bug <i>Leptoglossus occidentalis</i>." Microbes and Environments 37, no. 3 (2022): n/a. http://dx.doi.org/10.1264/jsme2.me22042.

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GE, WEI, ZHI-YUAN ZHANG, CHUN-BO DONG, YAN-FENG HAN, SUNIL K. DESHMUKH, and ZONG-QI LIANG. "Bacterial Community Analysis and Potential Functions of Core Taxa in Different Parts of the Fungus Cantharellus cibarius." Polish Journal of Microbiology 70, no. 3 (September 2021): 373–85. http://dx.doi.org/10.33073/pjm-2021-035.

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Cantharellus cibarius is a widely distributed, popular, edible fungus with high nutritional and economic value. However, significant challenges persist in the microbial ecology and artificial cultivation of C. cibarius. Based on the 16S rRNA sequencing data, this study analyzed bacterial community structures and diversity of fruit bodies and rhizomorph parts of C. cibarius and mycosphere samples (collected in the Wudang District, Guiyang, Guizhou Province, China). It explored the composition and function of the core bacterial taxa. The analyzed results showed that the rhizomorph bacterial community structure was similar to mycosphere, but differed from the fruit bodies. Members of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex had the highest abundance in the fruit bodies. However, they were either absent or low in abundance in the rhizomorphs and mycosphere. At the same time, members of the Burkholderia-Caballeronia-Paraburkholderia complex were abundant in the fruit bodies and rhizomorphs parts of C. cibarius, as well as mycosphere. Through functional annotation of core bacterial taxa, we found that there was an apparent trend of potential functional differentiation of related bacterial communities in the fruit body and rhizomorph: potential functional groups of core bacterial taxa in the fruit bodies centered on nitrogen fixation, nitrogen metabolism, and degradation of aromatic compounds, while those in rhizomorphs focused on aerobic chemoheterotrophy, chemoheterotrophy, defense against soil pathogens, decomposition of complex organic compounds, and uptake of insoluble inorganic compounds. The analysis of functional groups of bacteria with different structures is of great significance to understand that bacteria promote the growth and development of C. cibarius.

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Madhaiyan, Munusamy, Wah-Seng See-Too, Robson Ee, Venkatakrishnan Sivaraj Saravanan, Joseph S. Wirth, Tan Hian Hwee Alex, Cai Lin, et al. "Chitinasiproducens palmae gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from leaf tissues of oil palm (Elaeis guineensis Jacq.)." International Journal of Systematic and Evolutionary Microbiology 70, no. 4 (April 1, 2020): 2640–47. http://dx.doi.org/10.1099/ijsem.0.004084.

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A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23T, was isolated from surface-sterilized leaf tissue of an oil palm grown in Singapore and was investigated by polyphasic taxonomy. Phylogenetic analyses based on 16S rRNA gene sequences and 180 conserved genes in the genome of several members of Burkholderiaceae revealed that strain JS23T formed a distinct evolutionary lineage independent of other taxa within the family Burkholderiaceae . The predominant ubiquinone was Q-8. The primary polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminophospholipid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c /C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c /C18 : 1 ω6c). The size of the genome is 5.36 Mbp with a DNA G+C content of 66.2 mol%. Genomic relatedness measurements such as average nucleotide identity, genome-to-genome distance and digital DNA–DNA hybridization clearly distinguished strain JS23T from the closely related genera Burkholderia , Caballeronia , Mycetohabitans , Mycoavidus , Pandoraea , Paraburkholderia , Robbsia and Trinickia . Furthermore, average amino acid identity values and the percentages of conserved proteins, 56.0–68.4 and 28.2–45.5, respectively, were well below threshold values for genus delineation and supported the assignment of JS23T to a novel genus. On the basis of the phylogenetic, biochemical, chemotaxonomic and phylogenomic evidence, strain JS23T is proposed to represent a novel species of a new genus within the family Burkholderiaceae , for which the name Chitinasiproducens palmae gen. nov., sp. nov., is proposed with the type strain of JS23T (= DSM 27307T=KACC 17592T).

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Dobritsa, Anatoly P., and Mansour Samadpour. "Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia." International Journal of Systematic and Evolutionary Microbiology 66, no. 8 (August 1, 2016): 2836–46. http://dx.doi.org/10.1099/ijsem.0.001065.

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Shi, Shuai, Huiqian Zhang, Shuai Zhang, Lijin Yi, Gulijiazi Yeerkenbieke, and Xiaoxia Lu. "Degradation of Benzo[a]pyrene and 2,2′,4,4′-Tebrabrominated Diphenyl Ether in Cultures Originated from an Agricultural Soil." Toxics 12, no. 1 (January 1, 2024): 33. http://dx.doi.org/10.3390/toxics12010033.

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Benzo[a]pyrene (BaP) and 2,2′,4,4′-tetrabrominated diphenyl ether (BDE-47) are common contaminants in the environment, posing a threat to the ecosystems and human health. Currently, information on the microbial metabolism of BaP and BDE-47 as well as the correlated bacteria is still limited. This research aimed to study the degradation of BaP and BDE-47 by enriched cultures originated from an agricultural soil in Tianjin (North China) and characterize the bacteria involved in the degradation. Two sets of experiments were set up with BaP and BDE-47 (2 mg/L) as the sole carbon source, respectively. The degradation of BaP and BDE-47 occurred at rate constants of 0.030 /d and 0.026 /d, respectively. For BaP, the degradation products included benzo[a]pyrene-9,10-dihydrodiol or its isomers, ben-zo(a)pyrene-7,8-dihydrodiol-9,10-epoxide, and cis-4 (8-hydroxypyrenyl-7)-2-oxo-3-butenoic acid. For BDE-47, the degradation products included 2,2′,4-tribrominated diphenyl ether (BDE-17), 2,4-dibrominated diphenyl ether (BDE-7), and hydroxylated dibromodiphenyl ether. The bacterial community structures in the original soil, the BaP culture, and the BDE-47 culture were quite different. The richness and diversity of bacteria in the two cultures were much lower than that in the original soil, and the BaP culture had higher richness and diversity than the BDE-47 culture. In the BaP culture, multiple species such as Niabella (23.4%), Burkholderia-Caballeronia-Paraburkholderia (13.7%), Cupriavidus (8.3%), and Allorhizobi-um-Neorhizobium-Pararhizobium-Rhizobium (8.0%) were dominant. In the BDE-47 culture, an unassigned species in the Rhizobiaceae was dominant (82.3%). The results from this study provide a scientific basis for the risk assessment and bioremediation of BaP and/or BDE-47 in a contaminated environment.

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Lozano, Mauricio Javier, Ezequiel Gerdardo Mogro, and Walter Omar Draghi. "Phylogenomic analysis supports the reclassification of Burkholderia novacaledonica as Caballeronia novacaledonica comb. nov." International Journal of Systematic and Evolutionary Microbiology 71, no. 6 (June 24, 2021). http://dx.doi.org/10.1099/ijsem.0.004843.

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Burkholderia novacaledonica is a Betaproteobacterial species isolated from ultramafic soils in New Caledonia. The characterization and classification of this species into the Burkholderia genus was done simultaneously with the proposal of the new genus Caballeronia , initially composed of closely related Burkholderia glathei -like species. Thereafter, some reports based on the use of phylogenetic marker genes suggested that B. novacaledonica forms part of Caballeronia genus. Lacking a formal validation, and with the availability of its genome sequence, a genome-based phylogeny of B. novacaledonica was obtained to unravel its taxonomic position in Burkholderia sensu lato. A partial gyrB gene phylogeny, extended multilocus sequence typing on homologous protein sequences, and genomic distance-based phylogeny, all support the placement of this species in the Caballeronia genus. Therefore, the reclassification of B. novacaledonica to Caballeronia novacaledonica comb. nov. is proposed.

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Jouan, Romain, Gaëlle Lextrait, Joy Lachat, Aya Yokota, Raynald Cossard, Delphine Naquin, Tatiana Timchenko, Yoshitomo Kikuchi, Tsubasa Ohbayashi, and Peter Mergaert. "Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiont Caballeronia insecticola." ISME Communications 4, no. 1 (January 1, 2024). http://dx.doi.org/10.1093/ismeco/ycad001.

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Abstract Caballeronia insecticola is a bacterium belonging to the Burkholderia genus sensu lato, which is able to colonize multiple environments like soils and the gut of the bean bug Riptortus pedestris. We constructed a saturated Himar1 mariner transposon library and revealed by transposon-sequencing that 498 protein-coding genes constitute the essential genome of Caballeronia insecticola for growth in free-living conditions. By comparing essential gene sets of Caballeronia insecticola and seven related Burkholderia s.l. strains, only 120 common genes were identified, indicating that a large part of the essential genome is strain-specific. In order to reproduce specific nutritional conditions that are present in the gut of Riptortus pedestris, we grew the mutant library in minimal media supplemented with candidate gut nutrients and identified several condition-dependent fitness-defect genes by transposon-sequencing. To validate the robustness of the approach, insertion mutants in six fitness genes were constructed and their growth deficiency in media supplemented with the corresponding nutrient was confirmed. The mutants were further tested for their efficiency in Riptortus pedestris gut colonization, confirming that gluconeogenic carbon sources, taurine and inositol, are nutrients consumed by the symbiont in the gut. Thus, our study provides insights about specific contributions provided by the insect host to the bacterial symbiont.

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42

Mendiola, Sandra Y., Jason Z. Chen, Ben Lukubye, David J. Civitello, Nic M. Vega, and Nicole M. Gerardo. "Differential gene expression in the insect vector Anasa tristis in response to symbiont colonization but not infection with a vectored phytopathogen." Frontiers in Ecology and Evolution 12 (May 22, 2024). http://dx.doi.org/10.3389/fevo.2024.1390625.

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Many insects selectively associate with specific microbes in long-term, symbiotic relationships. Maintaining these associations can be vital for the insect hosts’ development, but insects must also contend with potential coinfections from other microbes in the environment. Fending off microbial threats while maintaining mutualistic microbes has resulted in many insects developing specialized symbiotic organs to house beneficial microbes. Though locally concentrated in these organs, symbiont establishment can have global consequences for the insect, including influence over the success of coinfecting microbes in colonizing the insect host. We use a transcriptomic approach to examine how the mutualistic symbiosis between the agricultural pest Anasa tristis and bacteria in the genus Caballeronia affects insect gene expression locally within the symbiotic organs and in the insect host at large. We simultaneously determine whether Caballeronia colonization impacts insect host responses to infection with the plant pathogen Serratia marcescens, which it vectors to plants. We found that no significant differential gene expression was elicited by infection with S. marcescens. This was a surprising finding given previous work indicating that symbiotic A. tristis clear S. marcescens infection rapidly compared to aposymbiotic individuals. Our results indicate that symbiotic and nonsymbiotic tissues in A. tristis differ greatly in their gene expression, particularly following successful symbiont colonization. We found evidence for local downregulation of host immunity and upregulation of cell communication within the symbiotic organs, functions which can facilitate the success of the A. tristis-Caballeronia symbiosis.

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Hetz, Stefanie A., Anja Poehlein, and Marcus A. Horn. "Whole-Genome Sequences of Two New Caballeronia Strains Isolated from Cryoturbated Peat Circles of the Permafrost-Affected Eastern European Tundra." Microbiology Resource Announcements 9, no. 31 (July 30, 2020). http://dx.doi.org/10.1128/mra.00731-20.

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ABSTRACT Annotated genomes of Caballeronia strains SBC1 and SBC2 from acidic permafrost suggest a new species with a facultative lifestyle via oxygen and nitrate respiration. Thus, a contribution to nitrogen cycling in cold and low-pH environments is anticipated.

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44

Yamamoto-Tamura, Kimiko, Ryota Moriuchi, and Naoto Ogawa. "Complete Genome Sequence of Caballeronia sp. Strain NK8 (MAFF311271), a Chlorobenzoate-Degrading Bacterium." Microbiology Resource Announcements 10, no. 31 (August 5, 2021). http://dx.doi.org/10.1128/mra.00416-21.

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Caballeronia sp. strain NK8 grows on 3-chlorobenzoate and shows chemotaxis toward 3-chlorobenzoate and its degradation products, such as chlorocatechols. Complete genome sequencing revealed a 9.2-Mb genome consisting of three chromosomes and four plasmids. The genes for degradation of chlorobenzoate and chlorocatechols were located on plasmids pNK81 and pNK84, respectively.

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Gook, Do-Hun, Minhyung Jung, Soowan Kim, and Doo-Hyung Lee. "Species diversity of environmentally-transmitted bacteria colonizing Riptortus pedestris (Hemiptera: Alydidae) and symbiotic effects of the most dominant bacteria." Scientific Reports 13, no. 1 (September 13, 2023). http://dx.doi.org/10.1038/s41598-023-42419-0.

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AbstractRiptortus pedestris (Hemiptera: Alydidae) establish endosymbiosis with specific bacteria from extremely diverse microbiota in soil. To better understand ecology and evolution of the symbiosis, it is important to characterize bacterial species diversity colonizing R. pedestris and evaluate their symbiotic effects. Nonetheless, previous research was limited to a few bacteria strains such as Caballeronia insecticola. In this study, second-instar nymphs were provided with field soils and reared to adult. Then, bacteria colonizing the midgut M4 region of R. pedestris were analyzed for bacterial species identification based on the 16S rRNA gene. First, a total of 15 bacterial species were detected belonging to Burkholderiaceae. Most of R. pedestris were found to harbor single bacterial species, whereas several insects harbored at most two bacterial species simultaneously. Among the total insects harboring single bacterial species, 91.2% harbored genus Caballeronia. The most dominant species was C. jiangsuensis, not previously documented for symbiotic associations with R. pedestris. Second, in laboratory conditions, C. jiangsuensis significantly enhanced the development, body size, and reproductive potentials of R. pedestris, compared to individuals with no symbiotic bacteria. These results add novel information to better understand symbiotic bacteria community establishing in R. pedestris and symbiotic effects on the host insects.

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46

Zou, Dulei, Xiuhai Lu, Fangying Song, Xiaowei Zhong, Huabo Chen, Ju Zhang, Yabin Tian, et al. "Characteristics of bacterial community in eyelashes of patients with Demodex blepharitis." Parasites & Vectors 17, no. 1 (February 14, 2024). http://dx.doi.org/10.1186/s13071-024-06122-x.

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Abstract Background Demodex blepharitis (DB) is a common disease of the ocular surface. The characteristics of the bacterial community in eyelash roots after Demodex infestation are still unknown. Knowledge of the characteristics of the bacterial community of eyelash follicles in patients with DB can provide valuable insights for guiding the diagnosis and treatment of DB. Methods Twenty-five patients with DB (DB group) and 21 non-DB volunteers (control group) were enrolled in the study. Eyelashes from the upper eyelid of the right eye were sampled, and 16S ribosomal DNA (rDNA) sequencing was performed to determine the V3-V4 regions of the microbial 16S rDNA gene within 1 month of infestation. The sequencing data of the two groups were analyzed and compared. The effect of the bacterium Burkholderia on the survival of Demodex mites was evaluated using Demodex obtained from 12 patients with DB other that the patients in the DB group. Results A total of 31 phyla and 862 genera were identified in the DB and control groups. The five most abundant phyla in the two groups were Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Cyanobacteria. The abundance of Actinomycetes was significantly higher in the DB group than in the control group. At the genus level, the five most abundant genera in the two groups were Pseudomonas, Burkholderia-Caballeronia-Paraburkholderia, Rolstonia and Acinetobacter; Clostridium sensu stricto 1 was abundant in the control group and Corynebacterium_1 was abundant in the DB group. Compared with the control group, the abundance of Burkholderia-Caballeronia-Paraburkholderia was 2.36-fold lower in the DB group. Linear discriminant analysis Effect Size (LEfSe) analysis revealed Burkholderia-Caballeronia-Paraburkholderia, SC_I_84_unclassified, Nonmyxobacteria and Succinvibrio to be the major biomarkers in the control group and Catenibacterium and Lachnospiraceae NK4A136 group to be the major biomarkers in the DB group. To explore the performance of these optimal marker models, receiver operational characteristic curve analysis was performed, and the average area under the curve value of Burkholderia-Caballeronia-Paraburkholderia was 0.7448. Burkholderia cepacia isolated from normal human eyelashes was fermented, and the Demodex mites isolated from patient eyelashes were cultured together with its fermented supernatant. The results showed that the fermentation supernatant could significantly reduce the survival time of the Demodex mites, suggesting the potential therapeutic value of this bacterium against Demodex. Conclusions The composition of the bacterial community in the eyelashes of DB patients differed from that in eyelashes of healthy volunteers, revealing a decrease in bacterial diversity in infested eyelashes. This decrease may be related to the occurrence and development of DB. The supernatant of Burkholderia cepacia culture medium was found to inhibit the growth of Demodex in eyelash hair follicles, providing a new insight with potential applications for the clinical treatment of Demodex infestation. Graphical Abstract

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Fergusson, Claire H., Julienne M. F. Coloma, Mercia C. Valentine, F. P. Jake Haeckl, and Roger G. Linington. "Custom Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometric Database for Identification of Environmental Isolates of the Genus Burkholderia and Related Genera." Applied and Environmental Microbiology 86, no. 11 (April 3, 2020). http://dx.doi.org/10.1128/aem.00354-20.

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ABSTRACT Success of discovery programs for microbial natural products is dependent on quick and concise discrimination between isolates from diverse environments. However, laboratory isolation and identification of priority genera using current 16S rRNA PCR-based methods are both challenging and time-consuming. An emerging strategy for rapid isolate discrimination is protein fingerprinting via matrix-assisted laser desorption ionization (MALDI) mass spectrometry. Using our in-house environmental isolate repository, we have created a main spectral (MSP) library for the Bruker Biotyper MALDI mass spectrometer that contains 95 entries, including Burkholderia, Caballeronia, Paraburkholderia, and other environmentally related genera. The library creation required the acquisition of over 2,250 mass spectra, which were manually reviewed for quality control and consolidated into a single reference library using a commercial software platform. We tested the effectiveness of the reference library by analyzing 49 environmental isolate strains using two different sample preparation methods. Overall, this approach correctly identified all strains to the genus level provided that suitable reference spectra were present in the MSP library. In this study, we present a fast, accurate method for taxonomic assignment of environmentally derived bacteria from the order Burkholderiales, providing a valuable alternative to traditional PCR-based methods. The MSP library described in the manuscript is available for use. IMPORTANCE The Gram-negative proteobacterial order Burkholderiales has emerged as a promising source of novel natural products in recent years. This order includes the genus Burkholderia and the newly defined genera Caballeronia and Paraburkholderia. However, development of this resource has been hampered by difficulties with rapid and selective isolation of Burkholderiales strains from the environment. Environmental metagenome sequencing has revealed that the potential for natural products is not evenly distributed throughout the microbial world. Thus, large but targeted microbial isolate libraries are needed to effectively explore the chemical potential of natural products. To study these organisms efficiently, methods to quickly identify isolates to the genus level are required. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is already used in clinical settings to reliably identify unknown bacterial pathogens. We have adapted similar methodology using the MALDI Biotyper instrument to rapidly identify environmental isolates of Burkholderia, Caballeronia, and Paraburkholderia for downstream natural product discovery.

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Blanco Nouche, Cintia, Cédric Paris, Tiphaine Dhalleine, Philippe Oger, Marie-Pierre Turpault, and Stéphane Uroz. "The non-ribosomal peptide synthetase-independent siderophore (NIS) rhizobactin produced by Caballeronia mineralivorans PML1(12) confers the ability to weather minerals." Applied and Environmental Microbiology, October 6, 2023. http://dx.doi.org/10.1128/aem.00453-23.

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ABSTRACT To mobilize nutrients entrapped into minerals and rocks, heterotrophic bacteria living in nutrient-poor environments have developed different mechanisms based mainly on acidolysis and chelation. However, the genetic bases of these mechanisms remain unidentified. To fill this gap, we considered the model strain Caballeronia mineralivorans PML1(12) known to be effective at weathering. Based on its transcriptomics and proteomics responses in Fe-depleted conditions, we pointed a cluster of genes differentially expressed and putatively involved in the production of siderophores. In this study, we report the characterization of this gene region coding for the production of a non-ribosomal peptide synthetase-independent siderophore (NIS). Targeted mutagenesis associated with functional assays and liquid chromatography coupled to high-resolution tandem mass spectrometry demonstrated the production of a single siderophore, identified as rhizobactin. This siderophore represents the first NIS containing malic acid in its structure. The evidence for the implication of rhizobactin in mineral weathering was demonstrated during a hematite dissolution assay. This study provides the first demonstration of the synthesis of a NIS in the genus Caballeronia and its involvement in mineral weathering. Our conclusions reinforce the idea that strain PML1(12) is particularly well adapted to nutrient-poor environments. IMPORTANCE This work deciphers the molecular and genetic bases used by strain PML1(12) of Caballeronia mineralivorans to mobilize iron and weather minerals. Through the combination of bioinformatics, chemical, and phylogenetic analyses, we characterized the siderophore produced by strain PML1(12) and the related genes. This siderophore was identified as rhizobactin and classified as a non-ribosomal peptide synthetase-independent siderophore (NIS). Contrary to the previously identified NIS synthetases that form siderophores containing citric acid, α-ketoglutarate, or succinic acid, our analyses revealed that rhizobactin contains malic acid in its structure, representing, therefore, the first identified NIS with such an acid and probably a new NIS category. Last, this work demonstrates for the first time the effectiveness at weathering minerals of a siderophore of the NIS family. Our findings offer relevant information for different fields of research, such as environmental genomics, microbiology, chemistry, and soil sciences.

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Acevedo, Tarik S., Gregory P. Fricker, Justine R. Garcia, Tiffanie Alcaide, Aileen Berasategui, Kayla S. Stoy, and Nicole M. Gerardo. "The Importance of Environmentally Acquired Bacterial Symbionts for the Squash Bug (Anasa tristis), a Significant Agricultural Pest." Frontiers in Microbiology 12 (October 4, 2021). http://dx.doi.org/10.3389/fmicb.2021.719112.

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Most insects maintain associations with microbes that shape their ecology and evolution. Such symbioses have important applied implications when the associated insects are pests or vectors of disease. The squash bug, Anasa tristis (Coreoidea: Coreidae), is a significant pest of human agriculture in its own right and also causes damage to crops due to its capacity to transmit a bacterial plant pathogen. Here, we demonstrate that complete understanding of these insects requires consideration of their association with bacterial symbionts in the family Burkholderiaceae. Isolation and sequencing of bacteria housed in the insects’ midgut crypts indicates that these bacteria are consistent and dominant members of the crypt-associated bacterial communities. These symbionts are closely related to Caballeronia spp. associated with other true bugs in the superfamilies Lygaeoidea and Coreoidea. Fitness assays with representative Burkholderiaceae strains indicate that the association can significantly increase survival and decrease development time, though strains do vary in the benefits that they confer to their hosts, with Caballeronia spp. providing the greatest benefit. Experiments designed to assess transmission mode indicate that, unlike many other beneficial insect symbionts, the bacteria are not acquired from parents before or after hatching but are instead acquired from the environment after molting to a later developmental stage. The bacteria do, however, have the capacity to escape adults to be transmitted to later generations, leaving the possibility for a combination of indirect vertical and horizontal transmission.

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Ge, Si-Xun, Feng-Ming Shi, Jia-He Pei, Ze-Hai Hou, Shi-Xiang Zong, and Li-Li Ren. "Gut Bacteria Associated With Monochamus saltuarius (Coleoptera: Cerambycidae) and Their Possible Roles in Host Plant Adaptations." Frontiers in Microbiology 12 (June 21, 2021). http://dx.doi.org/10.3389/fmicb.2021.687211.

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Monochamus saltuarius (Coleoptera: Cerambycidae) is an important native pest in the pine forests of northeast China and a dispersing vector of an invasive species Bursaphelenchus xylophilus. To investigate the bacterial gut diversity of M. saltuarius larvae in different host species, and infer the role of symbiotic bacteria in host adaptation, we used 16S rRNA gene Illumina sequencing and liquid chromatography-mass spectrometry metabolomics processing to obtain and compare the composition of the bacterial community and metabolites in the midguts of larvae feeding on three host tree species: Pinus koraiensis, Pinus sylvestris var. mongolica, and Pinus tabuliformis. Metabolomics in xylem samples from the three aforementioned hosts were also performed. Proteobacteria and Firmicutes were the predominant bacterial phyla in the larval gut. At the genus level, Klebsiella, unclassified_f__Enterobacteriaceae, Lactococcus, and Burkholderia–Caballeronia–Paraburkholderia were most dominant in P. koraiensis and P. sylvestris var. mongolica feeders, while Burkholderia–Caballeronia–Paraburkholderia, Dyella, Pseudoxanthomonas, and Mycobacterium were most dominant in P. tabuliformis feeders. Bacterial communities were similar in diversity in P. koraiensis and P. sylvestris var. mongolica feeders, while communities were highly diverse in P. tabuliformis feeders. Compared with the other two tree species, P. tabuliformis xylems had more diverse and abundant secondary metabolites, while larvae feeding on these trees had a stronger metabolic capacity for secondary metabolites than the other two host feeders. Correlation analysis of the association of microorganisms with metabolic features showed that dominant bacterial genera in P. tabuliformis feeders were more negatively correlated with plant secondary metabolites than those of other host tree feeders.

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