Статті в журналах: "Collimonas"

1

Höppener-Ogawa, Sachie, Johan H. J. Leveau, Wiecher Smant, Johannes A. van Veen, and Wietse de Boer. "Specific Detection and Real-Time PCR Quantification of Potentially Mycophagous Bacteria Belonging to the Genus Collimonas in Different Soil Ecosystems†." Applied and Environmental Microbiology 73, no. 13 (May 4, 2007): 4191–97. http://dx.doi.org/10.1128/aem.00387-07.

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ABSTRACT The bacterial genus Collimonas has the remarkable characteristic that it grows at the expense of living fungal hyphae under laboratory conditions. Here, we report the first field inventory of the occurrence and abundance of Collimonas in soils (n = 45) with naturally different fungal densities, which was performed in order to test the null hypothesis that there is a relationship between the presence of Collimonas and fungal biomass. Estimates of fungal densities were based on ergosterol measurements. Each soil was also characterized in terms of its physical and chemical properties and vegetation and management types. Culturable Collimonas was identified in plate-spread soil samples by its ability to clear colloidal chitin, in combination with a Collimonas-specific restriction fragment length polymorphism analysis of 16S rRNA PCR amplified from individual colonies. Using this approach, we found culturable collimonads only in (semi)natural grasslands. A real-time PCR assay for the specific quantification of Collimonas 16S rRNA in total soil DNA was developed. Collimonas was detectable in 80% of the soil samples, with densities up to 105 cells g−1 (dry weight) soil. The numbers of Collimonas cells per gram of soil were consistently lowest in fungus-poor arable soils and, surprisingly, also in fungus-rich organic layers of forest soils. When all soils were included, no significant correlation was observed between the number of Collimonas cells and ergosterol-based soil fungal biomass. Based on this result, we rejected our null hypothesis, and possible explanations for this were addressed.

2

Zhang, De-Chao, Mersiha Redzic, Franz Schinner, and Rosa Margesin. "Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite." International Journal of Systematic and Evolutionary Microbiology 61, no. 9 (September 1, 2011): 2186–90. http://dx.doi.org/10.1099/ijs.0.028001-0.

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Strains Cr9-30T and Cr9-12 were isolated from alpine glacier cryoconite. Both strains were Gram-negative-staining, non-motile, rod-shaped and psychrophilic, showing good growth over the temperature range 1–20 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that the two strains formed a distinct branch within the family Oxalobacteraceae and were most closely related to members of the genus Collimonas. The 16S rRNA gene sequence similarity between strains Cr9-30T and Cr9-12 was 99.0 %. The two strains showed highest 16S rRNA gene sequence pairwise similarity with Collimonas pratensis LMG 23965T (96.6 and 96.1 % for strains Cr9-30T and Cr9-12, respectively), Collimonas arenae LMG 23964T (96.5 and 96.3 %, respectively) and Collimonas fungivorans LMG 21973T (96.4 and 96.2 %, respectively). The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The DNA G+C content of strain Cr9-30T was 51.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strains Cr9-30T and Cr9-12 represent a novel species in a new genus of the family Oxalobacteraceae, for which the name Glaciimonas immobilis gen. nov., sp. nov. is proposed. The type strain of Glaciimonas immobilis is Cr9-30T ( = DSM 23240T = LMG 25547T).

3

Hoppener-Ogawa, S., W. de Boer, J. H. J. Leveau, J. A. van Veen, E. de Brandt, E. Vanlaere, H. Sutton, D. J. Dare, and P. Vandamme. "Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-)natural grassland soils." INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 58, no. 2 (February 1, 2008): 414–19. http://dx.doi.org/10.1099/ijs.0.65375-0.

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4

Lee, Soon Dong. "Collimonas antrihumi sp. nov., isolated from a natural cave and emended description of the genus Collimonas." International Journal of Systematic and Evolutionary Microbiology 68, no. 8 (August 1, 2018): 2448–53. http://dx.doi.org/10.1099/ijsem.0.002855.

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5

de Boer, Wietse, Johan H. J. Leveau, George A. Kowalchuk, Paulien J. A. Klein Gunnewiek, Edwin C. A. Abeln, Marian J. Figge, Klaas Sjollema, Jaap D. Janse, and Johannes A. van Veen. "Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae." International Journal of Systematic and Evolutionary Microbiology 54, no. 3 (May 1, 2004): 857–64. http://dx.doi.org/10.1099/ijs.0.02920-0.

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A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. DNA G+C contents were 57–62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98·6 % sequence similarity) and could be assigned to the β-Proteobacteria, family ‘Oxalobacteraceae’, order ‘Burkholderiales’. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95·9–96·7 % (Herbaspirillum species) and 94·3–95·6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6T (=NCCB 100033T=LMG 21973T).

6

Doan, Hung K., Nilesh N. Maharaj, Kaitlyn N. Kelly, Eugene M. Miyao, R. Michael Davis, and Johan H. J. Leveau. "Antimycotal Activity of Collimonas Isolates and Synergy-Based Biological Control of Fusarium Wilt of Tomato." Phytobiomes Journal 4, no. 1 (January 2020): 64–74. http://dx.doi.org/10.1094/pbiomes-05-19-0027-r.

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In a continued effort to discover microorganisms with plant-protective properties, we characterized a collection of bacterial isolates from multiple geographic origins and belonging to the genus Collimonas, for their ability to inhibit in vitro the growth of a wide range of plant-pathogenic fungi and oomycetes. Isolate Collimonas arenae Cal35 showed the greatest all-round performance and was the single-best inhibitor of several of the tested pathogens, including Fusarium oxysporum f. sp. lycopersici, the causal agent of Fusarium wilt of tomato. In greenhouse trials, neither C. arenae Cal35 nor the control treatment, i.e., the commercially available Bacillus-based biofungicide Serenade Soil, was able to prevent symptom formation on tomato plants challenged with F. oxysporum f. sp. lycopersici. However, a mixture of Cal35 and Serenade Soil (referred to as Collinade) significantly reduced vascular discoloration and F. oxysporum f. sp. lycopersici-induced loss of shoot dry weight. In replicated field experiments, a Collinade application reduced vascular symptoms as well as the relative abundance of F. oxysporum in the root endosphere of F. oxysporum f. sp. lycopersici-challenged plants. We discuss the emerging property of “biocombicontrol” by Collimonas and Bacillus in the context of synergy-based formulations for the protection of crops against pathogens.

7

Ballhausen, Max-Bernhard, Peter Vandamme, and Wietse de Boer. "Trait Differentiation within the Fungus-Feeding (Mycophagous) Bacterial Genus Collimonas." PLOS ONE 11, no. 6 (June 16, 2016): e0157552. http://dx.doi.org/10.1371/journal.pone.0157552.

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8

Fritsche, Kathrin, Wietse De Boer, Saskia Gerards, Marlies Van Den Berg, Johannes A. Van Veen, and Johan H. J. Leveau. "Identification and characterization of genes underlying chitinolysis in Collimonas fungivorans Ter331." FEMS Microbiology Ecology 66, no. 1 (October 2008): 123–35. http://dx.doi.org/10.1111/j.1574-6941.2008.00547.x.

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9

Lee, Ye-Rim, Robert J. Mitchell, and Kyung-Sook Whang. "Isolation and characterization of antifungal violacein producing bacterium Collimonas sp. DEC-B5." Korean Journal of Microbiology 52, no. 2 (June 30, 2016): 212–19. http://dx.doi.org/10.7845/kjm.2016.6031.

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10

Uroz, S., C. Calvaruso, M. P. Turpault, J. C. Pierrat, C. Mustin, and P. Frey-Klett. "Effect of the Mycorrhizosphere on the Genotypic and Metabolic Diversity of the Bacterial Communities Involved in Mineral Weathering in a Forest Soil." Applied and Environmental Microbiology 73, no. 9 (March 9, 2007): 3019–27. http://dx.doi.org/10.1128/aem.00121-07.

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ABSTRACT To date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. However, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. In this study, we characterized a collection of 61 bacterial strains isolated from Scleroderma citrinum mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. The ability of bacteria to weather biotite was assessed with a new microplate bioassay that measures the pH and the quantity of iron released from this mineral. We showed that weathering bacteria occurred more frequently in the vicinity of S. citrinum than in the bulk soil. Moreover, the weathering efficacy of the mycorrhizosphere bacterial isolates was significantly greater than that of the bulk soil isolates. All the bacterial isolates were identified by partial 16S rRNA gene sequence analysis as members of the genera Burkholderia, Collimonas, Pseudomonas, and Sphingomonas, and their carbon metabolism was characterized by the BIOLOG method. The most efficient isolates belonged to the genera Burkholderia and Collimonas. Multivariate analysis resulted in identification of three metabolic groups, one of which contained mainly bacterial isolates associated with S. citrinum and exhibiting high mineral-weathering potential. Therefore, our results support the hypothesis that by its carbon metabolism this fungus selects in the bulk soil reservoir a bacterial community with high weathering potential, and they also address the question of functional complementation between mycorrhizal fungi and bacteria in the ectomycorrhizal complex for the promotion of tree nutrition.

11

Mela, Francesca, Kathrin Fritsche, Wietse de Boer, Johannes A. van Veen, Leo H. de Graaff, Marlies van den Berg, and Johan H. J. Leveau. "Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger." ISME Journal 5, no. 9 (May 26, 2011): 1494–504. http://dx.doi.org/10.1038/ismej.2011.29.

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12

Uroz, S., C. Calvaruso, M. P. Turpault, A. Sarniguet, W. de Boer, J. H. J. Leveau, and P. Frey-Klett. "Efficient mineral weathering is a distinctive functional trait of the bacterial genus Collimonas." Soil Biology and Biochemistry 41, no. 10 (October 2009): 2178–86. http://dx.doi.org/10.1016/j.soilbio.2009.07.031.

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13

Hakvåg, Sigrid, Espen Fjærvik, Geir Klinkenberg, Sven Even Borgos, Kjell Josefsen, Trond Ellingsen, and Sergey Zotchev. "Violacein-Producing Collimonas sp. from the Sea Surface Microlayer of Costal Waters in Trøndelag, Norway." Marine Drugs 7, no. 4 (November 12, 2009): 576–88. http://dx.doi.org/10.3390/md7040576.

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14

Zhang, Hong, Rong Zheng, Taotao Zhang, Dan Dong, Ting Liu, Juan Zhao, Zhaofeng Tian, Weicheng Liu, Lijin Luo, and Huiling Wu. "Efficient transformation and expression of Vitreoscilla haemoglobin in the biological control bacterium Collimonas pratensis ZL261." Biocontrol Science and Technology 28, no. 8 (July 2, 2018): 786–95. http://dx.doi.org/10.1080/09583157.2018.1493721.

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15

Çelik Doğan, Cansu, Hafize Tuğba Yüksel Dolgun, Serkan İkiz, Şükrü Kırkan, and Uğur Parın. "Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis." Foods 12, no. 19 (September 22, 2023): 3538. http://dx.doi.org/10.3390/foods12193538.

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The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially manufactured fermented liquids live up to their claims by analyzing pathogens and beneficial bacteria using a 16S rRNA sequencing technique called metagenomic analysis. Paenibacillus, Lentibacillus, Bacillus, Enterococcus, Levilactobacillus, and Oenococcus were the most abundant bacterial genera observed as potential probiotics. Pseudomonas stutzeri, Acinetobacter, and Collimonas, which have plant-growth-promoting traits, were also detected. The fact that we encounter biocontroller bacteria that promote plant growth demonstrates that these organisms are widely used in foods and emphasizes the necessity of evaluating them in terms of public health. Their potential applications in agriculture may pose a danger to food hygiene and human health in the long term, so our data suggest that this should be evaluated.

16

Wu, Huiling, Jieqiong Li, Weicheng Liu, Xuelian Bai, Dewen Liu, and Jiewei Zhang. "Identification and characterization of ZL261, a novel Collimonas pratensis strain with antagonistic activity toward Monilinia fructicola." Science China Life Sciences 59, no. 12 (October 12, 2016): 1345–47. http://dx.doi.org/10.1007/s11427-016-0066-9.

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17

Senechkin, Ilya V., Leonard S. van Overbeek, Hong Ling Er, Oscar de Vos, and Ariena H. C. van Bruggen. "Interaction of Collimonas strain IS343 with Rhizoctonia solani at low carbon availability in vitro and in soil." European Journal of Plant Pathology 136, no. 4 (April 11, 2013): 789–802. http://dx.doi.org/10.1007/s10658-013-0207-6.

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18

Kamilova, Faina, Johan H. J. Leveau, and Ben Lugtenberg. "Collimonas fungivorans, an unpredictedin vitrobut efficientin vivobiocontrol agent for the suppression of tomato foot and root rot." Environmental Microbiology 9, no. 7 (June 8, 2007): 1868. http://dx.doi.org/10.1111/j.1462-2920.2007.01348.x.

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19

Kanade, Yogini, Waman Mohan, and Rajashree Patwardhan. "Violacein: A Promising Bacterial Secondary Metabolite." Research Journal of Chemistry and Environment 26, no. 6 (May 25, 2022): 165–77. http://dx.doi.org/10.25303/2606rjce165177.

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Pigment is a secondary metabolite produced by microorganisms. As a natural product, bacterial pigments are being studied for their applications in pharmaceutical, food and cosmetic industry. Purple and blue bacterial pigments are less common. Violacein, a purple pigment is an indole derivative with molecular mass of 343.3. Some bacteria like Pseudoalteromonas sp. 520P1, Chromobacterium violaceum, Janthinobacterium lividum, Duganella violaceinigra, Collimonas and Iodobacter species are reported for violacein production. It is produced by vio operon comprising of vioABCDE genes. Violacein production is beneficial to the bacterial cell as it acts as a respiratory pigment involved in the regulation of tryptophan production, active in defensive mechanism and helps cell survival in stressed conditions. Carbon source, pH, temperature, incubation period and agitation rate are factors affecting violacein production. Violacein has shown antibacterial, antifungal, antiviral, anticancer and antiparasitic activity. It also displayed immunostimulatory, gastroprotective and antioxidant properties. Violacein gained industrial importance as a coloring agent in cosmetic, food and textile industries. This review intended to describe the violacein production by bacteria, its advantages to bacteria producing it, factors affecting its production and its applications.

20

Sharma, Shubhangi, Stéphane Compant, Philipp Franken, Silke Ruppel, and Max-Bernhard Ballhausen. "It Takes Two to Tango: A Bacterial Biofilm Provides Protection against a Fungus-Feeding Bacterial Predator." Microorganisms 9, no. 8 (July 23, 2021): 1566. http://dx.doi.org/10.3390/microorganisms9081566.

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Fungus-bacterium interactions are widespread, encompass multiple interaction types from mutualism to parasitism, and have been frequent targets for microbial inoculant development. In this study, using in vitro systems combined with confocal laser scanning microscopy and real-time quantitative PCR, we test whether the nitrogen-fixing bacterium Kosakonia radicincitans can provide protection to the plant-beneficial fungus Serendipita indica, which inhabits the rhizosphere and colonizes plants as an endophyte, from the fungus-feeding bacterium Collimonas fungivorans. We show that K. radicincitans can protect fungal hyphae from bacterial feeding on solid agar medium, with probable mechanisms being quick hyphal colonization and biofilm formation. We furthermore find evidence for different feeding modes of K. radicincitans and C. fungivorans, namely “metabolite” and “hyphal feeding”, respectively. Overall, we demonstrate, to our knowledge, the first evidence for a bacterial, biofilm-based protection of fungal hyphae against attack by a fungus-feeding, bacterial predator on solid agar medium. Besides highlighting the importance of tripartite microbial interactions, we discuss implications of our results for the development and application of microbial consortium-based bioprotectants and biostimulants.

21

Lyakhovchenko, Nikita S., Tatiana N. Abashina, Valentina N. Polivtseva, Vladislav Yu Senchenkov, Daniil A. Pribylov, Anna A. Chepurina, Ilja A. Nikishin, et al. "A Blue-Purple Pigment-Producing Bacterium Isolated from the Vezelka River in the City of Belgorod." Microorganisms 9, no. 1 (January 5, 2021): 102. http://dx.doi.org/10.3390/microorganisms9010102.

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Violacein is a biotechnologically significant secondary metabolite due to its antibacterial, antifungal, and other properties. Isolation, research, and identification of violacein producing strains are of interest for the development of biotechnological processes, in order to enhance the biosynthesis of this compound. The purpose of the present work was to study the properties of a newly isolated bacterium capable of synthesizing blue-purple pigment. An aboriginal bacterium was isolated from the coastal zone of the Vezelka River in the city of Belgorod. Based on chemical and spectrophotometric studies of the crude ethanol extract, the pigment was identified as violacein, and the isolate was assigned to the group of violacein-forming bacteria, which includes bacteria of the genera Chromobacterium, Iodobacter, Janthinobacterium, Duganella, Collimonas, and Massilia. Based on cultural, morphological, tinctorial, physiological, and biochemical properties, as well as analysis of the 16S rRNA gene sequence, the new isolated strain was assigned to the genus Janthinobacterium. The isolated strain is capable of suppressing the growth of a number of fungal and bacterial phytopathogens. For representatives of the genus Janthinobacterium, their inhibitory influence on cyanobacteria was shown for the first time.

22

Höppener-Ogawa, Sachie, Johan HJ Leveau, Johannes A. van Veen, and Wietse De Boer. "Mycophagous growth of Collimonas bacteria in natural soils, impact on fungal biomass turnover and interactions with mycophagous Trichoderma fungi." ISME Journal 3, no. 2 (October 16, 2008): 190–98. http://dx.doi.org/10.1038/ismej.2008.97.

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23

Mela, F., K. Fritsche, W. de Boer, M. van den Berg, J. A. van Veen, N. N. Maharaj, and J. H. J. Leveau. "Comparative genomics of bacteria from the genus Collimonas: linking (dis)similarities in gene content to phenotypic variation and conservation." Environmental Microbiology Reports 4, no. 4 (March 19, 2012): 424–32. http://dx.doi.org/10.1111/j.1758-2229.2012.00336.x.

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24

Ishani, Isita, and T. Vijayakumar. "Exploitation of Versatile Naturally Derived Blue Colorant Pigment 3-[2-hydroxy-5-(5-hydroxy-1H-indol-3-yl)-1H-pyrrol-3-yl] indol-one." IOP Conference Series: Materials Science and Engineering 1219, no. 1 (December 1, 2021): 012020. http://dx.doi.org/10.1088/1757-899x/1219/1/012020.

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Abstract 3-[2-hydroxy-5-(5-hydroxy-1H-indol-3-yl)-1H-pyrrol-3-yl] indol-one depicts a multifaceted pigment which was discovered in distinct bacteria species like Chromobacterium violaceum, Duganella sp. , Collimonas sp. , D. violaceinigra , Pseudoalteromonas sp. , J. svalbardensis , Janthinobacteriumlividum, etc. 3-[2-hydroxy-5-(5-hydroxy-1H-indol-3-yl)-1H-pyrrol-3-yl] indol-one is liable for the stunning purple pastels which demonstrates a variety of biological behaviors and is reportedly garnering growing popularity in industrial- market segments, for instance, textiles, medicine, cosmetics etc. It is perhaps a novel therapeutic category of drug which is L-tryptophan originated displays anti-cancer along with antibiotic action. The intention of this review was to identify the numerous applications of 3-[2-hydroxy-5-(5-hydroxy-1H-indol-3-yl)-1H-pyrrol-3-yl] indol-one and evaluate its varied biochemical properties in a pharmacological sense, including its antioxidant, antitumor, anti-trypanocidal, antibacterial, anti-ulcerogenic, anticancer and immunomodulatory activities. Additionally, its usage in cosmetics, food, textiles, toys along with insecticides has stemmed as peculiar emerging segments of applications of 3-[2-hydroxy-5-(5-hydroxy-1H-indol-3-yl)-1H-pyrrol-3-yl] indol-one have been reviewed here.

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Woźniak, M., A. Gałązka, J. Grządziel, and M. Głodowska. "The identification and genetic diversity of endophytic bacteria isolated from selected crops." Journal of Agricultural Science 156, no. 4 (May 2018): 547–56. http://dx.doi.org/10.1017/s0021859618000618.

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AbstractA collection of 45 isolates was created based on bacteria isolated from maize, broad bean, wheat, rye and wild plants such as horsetail and burdock. The aim of the current study was to isolate the bacteria, and then identify and assess the degree of genomic diversity. The molecular identification of microsymbionts isolated from the endosphere (root and stem) of plants grown in agricultural soils was performed using 16S rRNA gene sequencing. To evaluate the genomic diversity between strains that occurred in multiple host plants, 18 bacterial isolates representing four species were subjected to denaturing gradient gel electrophoresis. The 16S rDNA analysis assigned all bacterial isolates to ten genera, from whichRhizobiumwas represented by 19 isolates,Delftiaby 11,Agrobacteriumby five,Stenotrophomonasby three,Brevundimonasby two andNovosphingobium,Variovorax, Collimonas, AchromobacterandComamonasby only one isolate. Furthermore, the genomic diversity of the 11 isolates ofDelftiasp. was assessed using the BOX – polymerase chain reaction (BOX-PCR) and enterobacterial repetitive intergenic consensus – PCR (ERIC-PCR) methods. Typing patterns and analysis using BOX-PCR and ERIC-PCR data demonstrated similarities among the tested isolates. In general, the results obtained with BOX-PCR and ERIC-PCR were in good agreement. However, a greater degree of differentiation patterns of the genomic DNA was obtained in the ERIC-PCR method.

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Woźniak, Małgorzata, Anna Gałązka, Renata Tyśkiewicz, and Jolanta Jaroszuk-Ściseł. "Endophytic Bacteria Potentially Promote Plant Growth by Synthesizing Different Metabolites and their Phenotypic/Physiological Profiles in the Biolog GEN III MicroPlateTM Test." International Journal of Molecular Sciences 20, no. 21 (October 24, 2019): 5283. http://dx.doi.org/10.3390/ijms20215283.

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Endophytic bacteria, as the most promising components of effective, biofertilizers biostimulating and biocontrol preparations, should be very intensively obtained from various plants and studied in terms of the conditions determining the potential ability to promote plant growth. For this reason, endophytic bacteria have been isolated from both stems and roots of up to six systematically distant species of vascular plants: one species belonging to the seedless vascular plants (Monilophyta), and five seed plants (Spermatophyta). The 23 isolated strains represented nine genera: Delftia, Stenotrophomonas, Rhizobium, Brevundimonas, Variovorax, Achromobacter, Novosphingobium, Comamonas and Collimonas, notably which were closely related—belonging to the phylum Proteobacteria. Stenotrophomonas sp. strains showed the greatest ability to synthesize indole-3-acetic acid (IAA)-like compounds, while Achromobacter sp. strains produced the highest levels of siderophores. The presence of the nifH gene and nitrogen binding activity was demonstrated for 95% of the strains tested. Stenotrophomonas maltophila (ES2 strain) showed the highest metabolic activity based on Biolog GEN III test. The ability to solubilize phosphate was determined only for three tested strains from genus: Delftia, Rhizobium and Novosphingobium. The presented work demonstrated that the metabolic and phenotypic properties of plant growth-promoting endophytes are correlated with the genus of bacteria and are not correlated with the host plant species or part of plant (stem, root).

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Mela, Francesca, Kathrin Fritsche, Hidde Boersma, Jan D. Van Elsas, Daniela Bartels, Folker Meyer, Wietse De Boer, Johannes A. Van Veen, and Johan H. J. Leveau. "Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331." FEMS Microbiology Ecology 66, no. 1 (October 2008): 45–62. http://dx.doi.org/10.1111/j.1574-6941.2008.00472.x.

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28

Kamilova, Faina, Johan H. J. Leveau, and Ben Lugtenberg. "Collimonas fungivorans, an unpredicted in vitro but efficient in vivo biocontrol agent for the suppression of tomato foot and root rot." Environmental Microbiology 9, no. 6 (June 2007): 1597–603. http://dx.doi.org/10.1111/j.1462-2920.2007.01263.x.

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Chung, Ana Paula, Igor Tiago, M. Fernanda Nobre, António Veríssimo, and Paula V. Morais. "Glaciimonas singularis sp. nov., isolated from a uranium mine wastewater treatment plant." International Journal of Systematic and Evolutionary Microbiology 63, Pt_6 (June 1, 2013): 2344–50. http://dx.doi.org/10.1099/ijs.0.046581-0.

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A bacterial strain, A2-57T, recovered from a water sample collected in a uranium mine was taxonomically studied in detail. This strain was a Gram-reaction-negative, rod-shaped bacterium that grew optimally at 25 °C and at pH 6.0–7.0 and had a DNA G+C content of 55.0 mol%. Ubiquinone 8 (UQ-8) was the predominant respiratory quinone and the major fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1ω6c and/or ω7c and/or C15 : 0 iso 2-OH) and C18 : 1ω7c. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain A2-57T belonged to the family Oxalobacteraceae and formed a distinct branch with Glaciimonas immobilis Cr9-30T. Strain A2-57T shared approximately 97.3 % 16S rRNA sequence similarity with G. immobilis Cr9-30T and also showed high sequence similarity with members of the genera Herbaspirillum (96.3–97.0 %) and Collimonas (96.2–97.0 %). Although phylogenetically closely related to the type strain of G. immobilis , the low level of DNA–DNA hybridization between the two strains (21.6 %) and several physiological and biochemical properties indicated that the novel strain could be clearly distinguished from G. immobilis LMG 25547T. Therefore, it is concluded that strain A2-57T represents a novel species of the genus Glaciimonas , for which the name Glaciimonas singularis sp. nov. is proposed. The type strain is A2-57T ( = CIP 110539T = LMG 27070T).

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Hamamura, Natsuko, Sarah H. Olson, David M. Ward, and William P. Inskeep. "Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils." Applied and Environmental Microbiology 72, no. 9 (September 2006): 6316–24. http://dx.doi.org/10.1128/aem.01015-06.

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ABSTRACT Soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. Seven soil types obtained from six geographically distinct areas of the United States (Arizona, Oregon, Indiana, Virginia, Oklahoma, and Montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-14C]hexadecane. Microbial populations present during hydrocarbon degradation were analyzed using both 16S rRNA gene sequence analysis and by traditional methods for cultivating hydrocarbon-oxidizing bacteria. After a 50-day incubation, all seven soils showed comparable hydrocarbon depletion, where >80% of added crude oil was depleted and approximately 40 to 70% of added [14C]hexadecane was converted to 14CO2. However, the initial rates of hydrocarbon depletion differed up to 10-fold, and preferential utilization of shorter-chain-length n-alkanes relative to longer-chain-length n-alkanes was observed in some soils. Distinct microbial populations developed, concomitant with crude-oil depletion. Phylogenetically diverse bacterial populations were selected across different soils, many of which were identical to hydrocarbon-degrading isolates obtained from the same systems (e.g., Nocardioides albus, Collimonas sp., and Rhodococcus coprophilus). In several cases, soil type was shown to be an important determinant, defining specific microorganisms responding to hydrocarbon contamination. However, similar Rhodococcus erythropolis-like populations were observed in four of the seven soils and were the most common hydrocarbon-degrading organisms identified via cultivation.

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Herrera, Héctor, Tedy Sanhueza, Alžběta Novotná, Trevor C. Charles, and Cesar Arriagada. "Isolation and Identification of Endophytic Bacteria from Mycorrhizal Tissues of Terrestrial Orchids from Southern Chile." Diversity 12, no. 2 (January 30, 2020): 55. http://dx.doi.org/10.3390/d12020055.

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Endophytic bacteria are relevant symbionts that contribute to plant growth and development. However, the diversity of bacteria associated with the roots of terrestrial orchids colonizing Andean ecosystems is limited. This study identifies and examines the capabilities of endophytic bacteria associated with peloton-containing roots of six terrestrial orchid species from southern Chile. To achieve our goals, we placed superficially disinfected root fragments harboring pelotons on oatmeal agar (OMA) with no antibiotic addition and cultured them until the bacteria appeared. Subsequently, they were purified and identified using molecular tools and examined for plant growth metabolites production and antifungal activity. In total, 168 bacterial strains were isolated and assigned to 8 OTUs. The orders Pseudomonadales, Burkholderiales, and Xanthomonadales of phylum Proteobacteria were the most frequent. The orders Bacillales and Flavobacteriales of the phylla Firmicutes and Bacteroidetes were also obtained. Phosphate solubilization was detected in majority of isolates; however, it was significantly higher in Collimonas pratensis and Chryseobacterium sp. (PSI = 1.505 ± 0.09 and 1.405 ± 0.24, respectively). Siderophore production was recorded only for C. pratensis (0.657 ± 0.14 mm day−1), Dyella marensis (0.131 ± 0.02 mm day−1), and Luteibacter rhizovicinus (0.343 ± 0.12 mm day−1). Indole acetic acid production was highly influenced by the isolate identity; however, the significantly higher activity was recorded for Pseudomonas spp. (ranging from 5.507 ± 1.57 µg mL−1 to 7.437 ± 0.99 µg mL−1). Additionally, six bacterial isolates were able to inhibit the growth of some potential plant pathogenic fungi. Our findings demonstrate the potential for plant growth promoting capabilities and some antifungal activities of endophytic bacteria inhabiting the mycorrhizal tissue of terrestrial orchids, which may contribute especially at early developmental stages of orchid seedlings.

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Wu, Rongrong, Quratulain Sabih, Masanori Oshi, Takashi Ishikawa, Li Yan, and Kazuaki Takabe. "Abstract 3061: Elevated bile acid metabolism is associated with breast cancer microbiome, less cell proliferation, and better survival." Cancer Research 82, no. 12_Supplement (June 15, 2022): 3061. http://dx.doi.org/10.1158/1538-7445.am2022-3061.

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Abstract BACKGROUND: Bile acids are generated and secreted by hepatocytes and are involved in intestinal circulation. Recently it has been reported that specific bile acids are accumulated in the breast cancer tumor microenvironment (TME), leading to a favorable prognosis for patients and reducing the aggressiveness and metastatic potential of the cancer. We hypothesized that breast cancers with increased bile acid metabolism may have a favorable clinical outcome due to the suppression of cancer cell proliferation. MATERIALS AND METHODS: We analyzed total of 6285 patients from three independent breast cancer cohorts with TCGA as an exploring cohort and METABRIC, GSE96058 as validation cohorts. We divided each cohort into "high" and "low" groups by the top and bottom quartiles of the score following the previous reports. RESULTS: High bile acid metabolism breast cancer enriched multiple metabolic pathway gene sets such as fatty acid and xenobiotic metabolism, as well as adipogenesis and protein secretion by gene set enrichment analysis (GSEA). Adipocytes and preadipocytes were significantly infiltrated in the high score group. Considering the possibility that activation of bile acid metabolism is due to accumulation of microbiome-derived bile acids in breast cancer, we identified that four microorganisms (Anaerococcus, Collimonas, Gammaretrovirus and Hymenobacter) significantly correlated with the bile acid metabolism using TCGA 16s RNA seq data. Surprisingly, protein secretion gene set was significantly enriched to tumors that are abundant in three out of four of these bacterial species. This may suggest that bile acid metabolism are elevated in response to bile acids secreted by the microbiome present in breast cancer TME. The bile acid metabolism was highest in ER+HER2- and lowest in triple-negative, the most aggressive form of breast cancer. The score was negatively correlated with Ki67 gene expression and histological grade, consistent with previous reports that breast cancers with high bile acid accumulation were less proliferative. In agreement, breast cancers with low bile acid metabolism was associated with significantly high silent and non-silent mutation rates, Intratumor Heterogeneity, Proliferation score and Homologous Recombination Defects, and enriched G2M checkpoint gene set. Finally, survival analysis showed that high bile acid metabolism group had significantly better disease free, disease specific and overall survival. CONCULUSIONS: Bile acid metabolism was associated with involvement of microbiome in TME, the suppression of cell proliferation, and better prognosis in breast cancer. Citation Format: Rongrong Wu, Quratulain Sabih, Masanori Oshi, Takashi Ishikawa, Li Yan, Kazuaki Takabe. Elevated bile acid metabolism is associated with breast cancer microbiome, less cell proliferation, and better survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3061.

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Kai, Kenji, Mai Sogame, Fumie Sakurai, Norihiro Nasu, and Makoto Fujita. "Collimonins A–D, Unstable Polyynes with Antifungal or Pigmentation Activities from the Fungus-Feeding BacteriumCollimonas fungivoransTer331." Organic Letters 20, no. 12 (May 24, 2018): 3536–40. http://dx.doi.org/10.1021/acs.orglett.8b01311.

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34

Picard, L., M.-P. Turpault, P. M. Oger, and S. Uroz. "Identification of a novel type of glucose dehydrogenase involved in the mineral weathering ability of Collimonas pratensis strain PMB3(1)." FEMS Microbiology Ecology, November 17, 2020. http://dx.doi.org/10.1093/femsec/fiaa232.

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Abstract The exact molecular mechanisms as well as the genes involved in the mineral weathering (MW) process by bacteria remain poorly characterized. To date, a single type of glucose dehydrogenase (GDH) depending on a particular co-factor named pyrroloquinoline quinone (PQQ) is known. These enzymes allow the production of gluconic acid through the oxidation of glucose. However, it remains to be determined how bacteria missing PQQ-dependent GDH and/or the related pqq biogenesis genes weather minerals. In this study, we considered the very effective mineral weathering bacterial strain PMB3(1) of Collimonas pratensis. Genome analysis revealed that it does not possess the PQQ based system. The use of random mutagenesis, gene complementation and functional assays allowed us to identify mutants impacted in their ability to weather mineral. Among them, three mutants were strongly altered on their acidification and biotite weathering abilities (58 to 75% of reduction compared to WT) and did not produce gluconic acid. The characterization of the genomic regions allowed noticeably to the identification of a Glucose/Methanol/Choline oxidoreductase. This region appeared very conserved among collimonads and related genera. This study represents the first demonstration of the implication of a PQQ-independent GDH in the mineral weathering process and explains how Collimonas weather minerals.

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Li, Jiali, Mingkai Pan, Xianjiao Zhang, Yang Zhou, Guang-Da Feng, and Honghui Zhu. "Collimonas silvisoli sp. nov. and Collimonas humicola sp. nov., two novel species isolated from forest soil." International Journal of Systematic and Evolutionary Microbiology 71, no. 10 (October 22, 2021). http://dx.doi.org/10.1099/ijsem.0.005061.

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Three aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria, designated strains RXD178T, RXD172-2 and RLT1W51T, were isolated from two forest soil samples of Nanling National Nature Reserve in Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that they belonged to the genus Collimonas , and were most closely related to four validly published species with similarities ranging from 99.4 to 98.2 %. The genomic DNA G+C contents of strains RXD178T, RXD172-2 and RLT1W51T were 57.1, 59.5 and 59.4 mol%, respectively. The genome-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the novel strains and closely related type species were below 37.90 and 89.34 %, respectively. Meanwhile, the ANI and dDDH values between strains RXD172-2 and RLT1W51T were 98.27 and 83.50 %, respectively. The three novel strains contained C16 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) as the major fatty acids, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) comprised a relative higher proportion in strain RXD178T than in other strains. Both strains RXD172-2 and RLT1W51T had phosphatidylglycerol (PG), phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG) and an unidentified aminophospholipid (APL) as the main polar lipids while only PE and APL were detected in strain RXD178T. Ubiquinone 8 was the predominant quinone. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, strain RXD178T should be considered as representing one novel species within the genus Collimonas and strains RXD172-2 and RLT1W51T as another one, for which the names Collimonas silvisoli sp. nov. and Collimonas humicola sp. nov. are proposed, with RXD178T (=GDMCC 1.1925T=KACC 21987T) and RLT1W51T (=GDMCC 1.1923T=KACC 21985T) as the type strains, respectively.

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Wu, Je-Jia, Victor C. L. de Jager, Wen-Ling Deng, and Johan H. J. Leveau. "Finished Genome Sequence of Collimonas arenae Cal35." Genome Announcements 3, no. 1 (January 8, 2015). http://dx.doi.org/10.1128/genomea.01408-14.

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37

Picard, Laura, Philippe Oger, Marie-Pierre Turpault, and Stéphane Uroz. "Draft Genome Sequence of Collimonas pratensis Strain PMB3(1), an Effective Mineral-Weathering and Chitin-Hydrolyzing Bacterial Strain." Microbiology Resource Announcements 9, no. 37 (September 10, 2020). http://dx.doi.org/10.1128/mra.00601-20.

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ABSTRACT We announce the draft genome sequence of Collimonas pratensis PMB3(1), isolated from the Scleroderma citrinum mycorrhizosphere. In addition to its mineral-weathering effectiveness and antifungal activity, this strain is characterized by genomic features that give it great potential as a biocontrol and plant growth-promoting agent in nutrient-poor soils.

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Song, Chunxu, Ruth Schmidt, Victor de Jager, Dorota Krzyzanowska, Esmer Jongedijk, Katarina Cankar, Jules Beekwilder, et al. "Exploring the genomic traits of fungus-feeding bacterial genus Collimonas." BMC Genomics 16, no. 1 (December 2015). http://dx.doi.org/10.1186/s12864-015-2289-3.

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39

Picard, Laura, Cédric Paris, Tiphaine Dhalleine, Emmanuelle Morin, Philippe Oger, Marie‐Pierre Turpault, and Stéphane Uroz. "The mineral weathering ability of Collimonas pratensis PMB3(1) involves a Malleobactin‐mediated iron acquisition system." Environmental Microbiology, April 21, 2021. http://dx.doi.org/10.1111/1462-2920.15508.

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40

Mosquera, Sandra, Johan H. J. Leveau, and Ioannis Stergiopoulos. "Repeated Exposure of Aspergillus niger Spores to the Antifungal Bacterium Collimonas fungivorans Ter331 Selects for Delayed Spore Germination." Applied and Environmental Microbiology 87, no. 12 (May 26, 2021). http://dx.doi.org/10.1128/aem.00233-21.

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The use of antagonistic bacteria for managing fungal diseases is becoming increasingly popular, and thus there is a need to understand the implications of their long-term use against fungi. Most efforts have so far focused on characterizing the antifungal properties and mode of action of the bacterial antagonists, but the possible outcomes of the persisting interaction between antagonistic bacteria and fungi are not well understood.

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Picard, Laura, Cintia Blanco Nouche, Carine Cochet, Marie-Pierre Turpault, and Stéphane Uroz. "Mineral weathering by Collimonas pratensis PMB3(1) as a function of mineral properties, solution chemistry and carbon substrate." npj Materials Degradation 7, no. 1 (September 23, 2023). http://dx.doi.org/10.1038/s41529-023-00396-9.

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AbstractWhile the role of mineral weathering (MWe) bacteria in nutrient cycling and plant growth promotion is established, our understanding of the molecular mechanisms involved and how their contribution to MWe varies according to the mineral properties and the environmental conditions remain poorly documented. In this study, we investigate how the type of mineral, the source of carbon and the buffering capacity of the medium impacted the effectiveness at weathering of the strain PMB3(1) of Collimonas pratensis and the molecular mechanisms involved. Using abiotic and biotic weathering tests, we characterised the weatherability of the different minerals considered (i.e., biotite, olivine, garnet, hematite, apatite). We reveal that the model PMB3(1) strain is able to weather all the minerals tested and that its effectiveness is related to the weatherability of each mineral in poorly buffered condition, but not in buffered condition. Using single and double mutants affected in their Glucose-Methanol-Choline oxidoreductase activity and/or the biosynthesis of siderophore, we identify which mechanism the strain PMB3(1) uses to weather minerals in each condition. Our results indicate that the effectiveness at weathering of bacteria depends more strongly on the environmental conditions (carbon source, buffering capacity) than on the mineral type.

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Nicolitch, O., M. Feucherolles, J. L. Churin, L. Fauchery, M. P. Turpault, and S. Uroz. "A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability." Scientific Reports 9, no. 1 (October 7, 2019). http://dx.doi.org/10.1038/s41598-019-50730-y.

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Abstract The access and recycling of the base cations are essential processes for the long-lasting functioning of forest ecosystems. While the role of soil bacterial communities has been demonstrated in mineral weathering and tree nutrition, our understanding of the link between the availability of base cations and the functioning of these communities remains limited. To fill this gap, we developed a microcosm approach to investigate how an increase in key base cations (potassium or magnesium) impacted the taxonomic and functional structures of the bacterial communities. During a 2-month period after fertilization with available potassium or magnesium, soil properties, global functions (metabolic potentials and respiration) as well as mineral weathering bioassays and 16S rRNA amplicon pyrosequencing were monitored. Our analyses showed no or small variations in the taxonomic structure, total densities and global functions between the treatments. In contrast, a decrease in the frequency and effectiveness of mineral weathering bacteria was observed in the fertilized treatments. Notably, quantitative PCR targeting specific genera known for their mineral weathering ability (i.e., Burkholderia and Collimonas) confirmed this decrease. These new results suggest that K and Mg cation availability drives the distribution of the mineral weathering bacterial communities in forest soil.

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Futagawa, Kei, Donglin Tang, Yugo Kato, Koji Nagata, and Michio Suzuki. "Structural Analyses of DP‐1, a Protein with the Ability to Keep the Gold Nanoparticles, using Nuclear Magnetic Resonance." ChemBioChem, October 4, 2023. http://dx.doi.org/10.1002/cbic.202300554.

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Gold nanoparticles (AuNPs) consisting of metallic gold are applied in various fields owing to their characteristic physical properties. Collimonas sp. D‐25 (D‐25) is a Gram‐negative bacterium obtained from soil, compost, and other environmental materials in the Akita Prefecture. DP‐1 is a water‐soluble protein found in D‐25 that binds specifically to AuNPs and retains the nano‐sized AuNPs with high stability. This study aimed to identify the part of DP‐1 interacting with AuNPs and determine its 3D structure in solution using nuclear magnetic resonance (NMR). The peptide fragments obtained by trypsin digestion were examined for their AuNP‐binding capacity to determine the key Au‐binding domain of DP‐1. A fragment consisting of 16 amino acid residues (GHAATPEQYGVVTANK) was identified as the peptide with the highest binding activity. Structural analyses of this peptide indicated that the main chain was elongated, and negatively charged residues in the side chain were exposed on the surface by incorporating AuNPs. These results suggest that DP‐1 interacts with AuNPs via negatively charged residues and extended hydrophobic residues for protein‐protein interactions. The structural data also provide new insights into biomimetic technologies.

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Tang, Donglin, Yugo Kato, Dingkun Zhang, Lumi Negishi, Hitoshi Kurumizaka, Takafumi Hirata, Makoto Nakakido, et al. "Dispersion function of a protein, DP‐1, identified in Collimonas sp. D‐25, for the synthesis of gold nanoparticles." ChemBioChem, May 26, 2023. http://dx.doi.org/10.1002/cbic.202300221.

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Hu, Dong, Shuhong Li, Ying Li, Jieli Peng, Xiaoyan Wei, Jia Ma, Cuimian Zhang, Nan Jia, Entao Wang, and Zhanwu Wang. "Streptomyces sp. strain TOR3209: a rhizosphere bacterium promoting growth of tomato by affecting the rhizosphere microbial community." Scientific Reports 10, no. 1 (November 18, 2020). http://dx.doi.org/10.1038/s41598-020-76887-5.

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AbstractAiming at revealing the possible mechanism of its growth promoting effect on tomato, the correlations among Streptomyces sp. TOR3209 inoculation, rhizobacteriome, and tomato growth/production traits were investigated in this study. By analyses of Illumina sequencing and plate coating, differences in rhizosphere microbial communities were found in different growth stages and distinct inoculation treatments. The plant biomass/fruit yields and relative abundances of families Flavobacteriaceae, Sphingobacteriaceae, Polyangiaceae and Enterobacteriaceae in treatments T (tomato inoculated with TOR3209) and TF (tomato inoculated with TOR3209 + organic fertilizer) were higher than that in the controls (CK and CK+ organic fertilizer), respectively. The analysis of Metastats and LEfSe revealed that the genera Flavobacterium and Sorangium in seedling stage, Klebsiella in flowering stage, Collimonas in early fruit setting stage, and genera Micrococcaceae, Pontibacte and Adhaeribacter in late fruit setting stage were the most representative rhizobacteria that positively responded to TOR3209 inoculation. By cultivation method, five bacterial strains positively correlated to TOR3209 inoculation were isolated from rhizosphere and root endosphere, which were identified as tomato growth promoters affiliated to Enterobacter sp., Arthrobacter sp., Bacillus subtilis, Rhizobium sp. and Bacillus velezensis. In pot experiment, TOR3209 and B. velezensis WSW007 showed joint promotion to tomato production, while the abundance of inoculated TOR3209 was dramatically decreased in rhizosphere along the growth of tomato. Conclusively, TOR3209 might promote the tomato production via changing of microbial community in rhizosphere. These findings provide a better understanding of the interactions among PGPR in plant promotion.

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Akum, Fidele N., Ravi Kumar, Gary Lai, Catherine H. Williams, Hung K. Doan, and Johan H. J. Leveau. "Identification of Collimonas gene loci involved in the biosynthesis of a diffusible secondary metabolite with broad‐spectrum antifungal activity and plant‐protective properties." Microbial Biotechnology, December 21, 2020. http://dx.doi.org/10.1111/1751-7915.13716.

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Webster, Gordon, Alex J. Mullins, Yoana D. Petrova, and Eshwar Mahenthiralingam. "Polyyne-producing Burkholderia suppress Globisporangium ultimum damping-off disease of Pisum sativum (pea)." Frontiers in Microbiology 14 (August 25, 2023). http://dx.doi.org/10.3389/fmicb.2023.1240206.

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Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. Burkholderia were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits. However, their potential for opportunistic pathogenicity led to a moratorium on their registration as biopesticides. Subsequently, Burkholderia were shown to produce multiple specialised metabolites including potent antimicrobial polyynes. Cepacin A, a polyyne produced by Burkholderia ambifaria biopesticide strains was shown to be an important metabolite for the protection of germinating peas against Globisporangium ultimum (formerly Pythium) damping-off disease. Recently, there has been an expansion in bacterial polyyne discovery, with the metabolites and their biosynthetic gene pathways found in several bacterial genera including Burkholderia, Collimonas, Trinickia, and Pseudomonas. To define the efficacy of these bacterial polyyne producers as biopesticidal agents, we systematically evaluated metabolite production, in vitro microbial antagonism, and G. ultimum biocontrol across a panel of 30 strains representing four bacterial genera. In vitro polyyne production and antimicrobial activity was demonstrated for most strains, but only Burkholderia polyyne producers were protective within the in vivo G. ultimum damping-off pea protection model. B. ambifaria was the most effective cepacin-expressing biopesticide, and despite their known potential for plant pathogenicity Burkholderia gladioli and Burkholderia plantarii were uniquely shown to be protective as caryoynencin-producing biopesticides. In summary, Burkholderia are effective biopesticides due to their suite of antimicrobials, but the ability to deploy polyyne metabolites, caryoynencin and cepacin, is strain and species dependent.Graphical Abstract

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Grzesiak, Jakub, Małgorzata Marta Rogala, Jan Gawor, Xenie Kouřilová, and Stanislav Obruča. "Polyhydroxyalkanoate involvement in stress-survival of two psychrophilic bacterial strains from the High Arctic." Applied Microbiology and Biotechnology 108, no. 1 (March 23, 2024). http://dx.doi.org/10.1007/s00253-024-13092-8.

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Abstract An ever-growing body of literature evidences the protective role of polyhydroxyalkanoates (PHAs) against a plethora of mostly physical stressors in prokaryotic cells. To date, most of the research done involved bacterial strains isolated from habitats not considered to be life-challenging or extremely impacted by abiotic environmental factors. Polar region microorganisms experience a multitude of damaging factors in combinations rarely seen in other of Earth’s environments. Therefore, the main objective of this investigation was to examine the role of PHAs in the adaptation of psychrophilic, Arctic-derived bacteria to stress conditions. Arctic PHA producers: Acidovorax sp. A1169 and Collimonas sp. A2191, were chosen and their genes involved in PHB metabolism were deactivated making them unable to accumulate PHAs (ΔphaC) or to utilize them (Δi-phaZ) as a carbon source. Varying stressors were applied to the wild-type and the prepared mutant strains and their survival rates were assessed based on CFU count. Wild-type strains with a functional PHA metabolism were best suited to survive the freeze–thaw cycle — a common feature of polar region habitats. However, the majority of stresses were best survived by the ΔphaC mutants, suggesting that the biochemical imbalance caused by the lack of PHAs induced a permanent cell-wide stress response thus causing them to better withstand the stressor application. Δi-phaZ mutants were superior in surviving UV irradiation, hinting that PHA granule presence in bacterial cells is beneficial despite it being biologically inaccessible. Obtained data suggests that the ability to metabolize PHA although important for survival, probably is not the most crucial mechanism in the stress-resistance strategies arsenal of cold-loving bacteria. Key points • PHA metabolism helps psychrophiles survive freezing • PHA-lacking psychrophile mutants cope better with oxidative and heat stresses • PHA granule presence enhances the UV resistance of psychrophiles

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Lang, Ming, Haoming Li, Prakash Lakshmanan, Yuanxue Chen, and Xinping Chen. "phoD-harboring bacterial community composition dominates organic P mineralization under long-term P fertilization in acid purple soil." Frontiers in Microbiology 13 (November 24, 2022). http://dx.doi.org/10.3389/fmicb.2022.1045919.

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IntroductionA better understanding of the regulatory role of microorganisms on soil phosphorous (P) mobilization is critical for developing sustainable fertilization practices and reducing P resource scarcity. The phoD genes regulate soil organic P (Po) mobilization.MethodsBased on the long-term P application experiments in acid purple soil of maize system in Southwest China (started in 2010), the experiment included five P levels: 0, 16, 33, 49, and 65.5 kg P hm–2 (P0, P16, P33, P49, and P65.5, respectively). The molecular speciation of organic P in soil was determined by 31P-nuclear magnetic resonance (NMR), high-throughput sequencing technology, and real-time qPCR were used to analyze the bacterial community and abundance of phoD-harboring bacterial genes, exploring the bacterial community and abundance characteristics of phoD gene and its relationship with the forms of Po and alkaline phosphatase (ALP) activity in the soil.ResultsThe results showed that the orthophosphate monoesters (OM) were the main Po speciation and varied by P fertilization in acid purple soil. ALP activity decreased as P fertilization increased. Co-occurrence network analysis identified the overall network under five P fertilizations. The keystone taxon base on the network showed that Collimonas, Roseateles, Mesorhizobium, and Cellulomonas positively correlated with both OM and Po. The random forest showed that Cellulomonas, Roseateles, and Rhodoplanes were the key predictors for ALP activity. The keystone taxon was a more important predictor than the dominant taxon for ALP, OM, and Po. The structural equation model (SEM) showed that soil organic matter (SOM), available P (AP), and OM were the main factors influencing the ALP by reshaping phoD-harboring bacteria alpha diversity, community composition, and phoD abundance.DiscussionThe phoD-harboring bacterial community composition especially the keystone taxon rather than alpha diversity and abundance dominated the ALP activity, which could promote P utilization over an intensive agroecosystem. These findings improve the understanding of how long-term gradient fertilization influences the community composition and function of P-solubilizing microorganisms in acid purple soil.

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Colin, Y., O. Nicolitch, M. P. Turpault, and S. Uroz. "Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities." Applied and Environmental Microbiology 83, no. 5 (December 21, 2016). http://dx.doi.org/10.1128/aem.02684-16.

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ABSTRACT Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.

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