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Wallner A, Antonielli L, Mesguida O, Rey P, Compant S. Genomic diversity in Paenibacillus polymyxa: unveiling distinct species groups and functional variability. BMC Genomics 2024; 25:720. [PMID: 39054421 PMCID: PMC11271205 DOI: 10.1186/s12864-024-10610-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Paenibacillus polymyxa is a bacterial species of high interest, as suggested by the increased number of publications on its functions in the past years. Accordingly, the number of described strains and sequenced genomes is also on the rise. While functional diversity of P. polymyxa has been suggested before, the available genomic data is now sufficient for robust comparative genomics analyses. RESULTS Using 157 genomes, we found significant disparities among strains currently affiliated to P. polymyxa. Multiple taxonomic groups were identified with conserved predicted functions putatively impacting their respective ecology. As strains of this species have been reported to exhibit considerable potential in agriculture, medicine, and bioremediation, it is preferable to clarify their taxonomic organization to facilitate reliable and durable approval as active ingredients. CONCLUSIONS Strains currently affiliated to P. polymyxa can be separated into two major species groups with differential potential in nitrogen fixation, plant interaction, secondary metabolism, and antimicrobial resistance, as inferred from genomic data.
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Affiliation(s)
- Adrian Wallner
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Konrad Lorenz Str. 24, Tulln, 3430, Austria.
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Konrad Lorenz Str. 24, Tulln, 3430, Austria
| | - Ouiza Mesguida
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, 64000, France
- GreenCell, Biopôle Clermont-Limagne, Saint Beauzire, 63360, France
| | - Patrice Rey
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, 64000, France
| | - Stéphane Compant
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Konrad Lorenz Str. 24, Tulln, 3430, Austria
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Lebano I, Fracchetti F, Vigni ML, Mejia JF, Felis G, Lampis S. MALDI-TOF as a powerful tool for identifying and differentiating closely related microorganisms: the strange case of three reference strains of Paenibacillus polymyxa. Sci Rep 2024; 14:2585. [PMID: 38297004 PMCID: PMC10831075 DOI: 10.1038/s41598-023-50010-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/14/2023] [Indexed: 02/02/2024] Open
Abstract
Accurate identification and typing of microbes are crucial steps in gaining an awareness of the biological heterogeneity and reliability of microbial material within any proprietary or public collection. Paenibacillus polymyxa is a bacterial species of great agricultural and industrial importance due to its plant growth-promoting activities and production of several relevant secondary metabolites. In recent years, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an alternative rapid tool for identifying, typing, and differentiating closely related strains. In this study, we investigated the diversity of three P. polymyxa strains. The mass spectra of ATCC 842T, DSM 292, and DSM 365 were obtained, analysed, and compared to select discriminant peaks using ClinProTools software and generate classification models. MALDI-TOF MS analysis showed inconsistent results in identifying DSM 292 and DSM 365 as belonging to P. polimixa species, and comparative analysis of mass spectra revealed the presence of highly discriminatory biomarkers among the three strains. 16S rRNA sequencing and Average Nucleotide Identity (ANI) confirmed the discrepancies found in the proteomic analysis. The case study presented here suggests the enormous potential of the proteomic-based approach, combined with statistical tools, to predict and explore differences between closely related strains in large microbial datasets.
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Affiliation(s)
- Ilaria Lebano
- Syngenta Biologicals (Valagro SpA), 66041, Atessa, CH, Italy.
| | | | - Mario Li Vigni
- Syngenta Biologicals (Valagro SpA), 66041, Atessa, CH, Italy
| | | | - Giovanna Felis
- Department of Biotechnology and VUCC-DBT Verona University Culture Collection, University of Verona, 37154, Verona, VR, Italy
| | - Silvia Lampis
- Department of Biotechnology and VUCC-DBT Verona University Culture Collection, University of Verona, 37154, Verona, VR, Italy.
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Pacher N, Burtscher J, Johler S, Etter D, Bender D, Fieseler L, Domig KJ. Ropiness in Bread-A Re-Emerging Spoilage Phenomenon. Foods 2022; 11:3021. [PMID: 36230100 PMCID: PMC9564316 DOI: 10.3390/foods11193021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
As bread is a very important staple food, its spoilage threatens global food security. Ropy bread spoilage manifests in sticky and stringy degradation of the crumb, slime formation, discoloration, and an odor reminiscent of rotting fruit. Increasing consumer demand for preservative-free products and global warming may increase the occurrence of ropy spoilage. Bacillus amyloliquefaciens, B. subtilis, B. licheniformis, the B. cereus group, B. pumilus, B. sonorensis, Cytobacillus firmus, Niallia circulans, Paenibacillus polymyxa, and Priestia megaterium were reported to cause ropiness in bread. Process hygiene does not prevent ropy spoilage, as contamination of flour with these Bacillus species is unavoidable due to their occurrence as a part of the endophytic commensal microbiota of wheat and the formation of heat-stable endospores that are not inactivated during processing, baking, or storage. To date, the underlying mechanisms behind ropy bread spoilage remain unclear, high-throughput screening tools to identify rope-forming bacteria are missing, and only a limited number of strategies to reduce rope spoilage were described. This review provides a current overview on (i) routes of entry of Bacillus endospores into bread, (ii) bacterial species implicated in rope spoilage, (iii) factors influencing rope development, and (iv) methods used to assess bacterial rope-forming potential. Finally, we pinpoint key gaps in knowledge and related challenges, as well as future research questions.
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Affiliation(s)
- Nicola Pacher
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Johanna Burtscher
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Sophia Johler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstr. 272, 8057 Zurich, Switzerland
| | - Danai Etter
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstr. 272, 8057 Zurich, Switzerland
| | - Denisse Bender
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Lars Fieseler
- Institute of Food and Beverage Innovation, ZHAW Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Konrad J. Domig
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
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Paenibacillus mellifer sp. nov., isolated from gut of the honey bee Apis mellifera. Arch Microbiol 2022; 204:558. [PMID: 35974114 DOI: 10.1007/s00203-022-03178-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 11/02/2022]
Abstract
An isolate, designated MBLB2552T, was isolated from the gut of the honey bees (Apis mellifera L.) and identified as a member of the genus Paenibacillus based on the sequences of the 16S rRNA gene sequences. The most closely related species to strain MBLB2552T were Paenibacillus timonensis 2301032 T, Paenibacillus barengoltzii NBRC 101215 T, and Paenibacillus macerans IAM 12467 T, with similarity values of 98.1, 97.21 and 97.0%, respectively, based on 16S rRNA gene sequences. The genome size and G + C content of MBLB2552T were 5.2 Mb and 52.4%, respectively. The Ortho average nucleotide identity (OrthoANI) and in silico DNA-DNA hybridization (isDDH) values between strain MBLB2552T and the type strains of the closest species were below the species delineation threshold. Comparative genomic analysis showed that most core POGs of strain MBLB2552T and other related taxa were related to translation, ribosomal structure and biogenesis (J) and carbohydrate metabolism in the COG category and KEGG pathways, respectively. Strain MBLB2552T was Gram stain-positive, spore-forming, rod-shaped, facultative anaerobic, motile, and grew at 20‒45 °C in 0‒2% (w/v) NaCl at pH 6.0‒9.0. The major polar lipids identified were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylserine, unidentified polar lipids, and an unidentified glycolipid. We propose that strain MBLB2552T represents the type strain of the genus Paenibacillus and its name Paenibacillus mellifer sp. nov. is proposed. The type of strain was MBLB2552T (= JCM 35371 T = KCTC 43386 T).
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Costa A, Corallo B, Amarelle V, Stewart S, Pan D, Tiscornia S, Fabiano E. Paenibacillus sp. Strain UY79, Isolated from a Root Nodule of Arachis villosa, Displays a Broad Spectrum of Antifungal Activity. Appl Environ Microbiol 2022; 88:e0164521. [PMID: 34757818 PMCID: PMC8788682 DOI: 10.1128/aem.01645-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
A nodule-inhabiting Paenibacillus sp. strain (UY79) isolated from wild peanut (Arachis villosa) was screened for its antagonistic activity against diverse fungi and oomycetes (Botrytis cinerea, Fusarium verticillioides, Fusarium oxysporum, Fusarium graminearum, Fusarium semitectum, Macrophomina phaseolina, Phomopsis longicolla, Pythium ultimum, Phytophthora sojae, Rhizoctonia solani, Sclerotium rolfsii, and Trichoderma atroviride). The results obtained show that Paenibacillus sp. UY79 was able to antagonize these fungi/oomycetes and that agar-diffusible compounds and volatile compounds (different from HCN) participate in the antagonism exerted. Acetoin, 2,3-butanediol, and 2-methyl-1-butanol were identified among the volatile compounds produced by strain UY79 with possible antagonistic activity against fungi/oomycetes. Paenibacillus sp. strain UY79 did not affect symbiotic association or growth promotion of alfalfa plants when coinoculated with rhizobia. By whole-genome sequence analysis, we determined that strain UY79 is a new species of Paenibacillus within the Paenibacillus polymyxa complex. Diverse genes putatively involved in biocontrol activity were identified in the UY79 genome. Furthermore, according to genome mining and antibiosis assays, strain UY79 would have the capability to modulate the growth of bacteria commonly found in soil/plant communities. IMPORTANCE Phytopathogenic fungi and oomycetes are responsible for causing devastating losses in agricultural crops. Therefore, there is enormous interest in the development of effective and complementary strategies that allow the control of the phytopathogens, reducing the input of agrochemicals in croplands. The discovery of new strains with expanded antifungal activities and with a broad spectrum of action is challenging and of great future impact. Diverse strains belonging to the P. polymyxa complex have been reported to be effective biocontrol agents. Results presented here show that the novel discovered strain of Paenibacillus sp. presents diverse traits involved in antagonistic activity against a broad spectrum of pathogens and is a potential and valuable strain to be further assessed for the development of biofungicides.
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Affiliation(s)
- Andrés Costa
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Belén Corallo
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Vanesa Amarelle
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Silvina Stewart
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa Cultivos de Secano. Estación Experimental La Estanzuela, Colonia, Uruguay
| | - Dinorah Pan
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Susana Tiscornia
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Elena Fabiano
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
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Sun R, Vermeulen A, Wieme AD, Vandamme P, Devlieghere F. Identification and characterization of acid-tolerant spore-forming spoilage bacteria from acidified and low-acid pasteurized sauces. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Ali MA, Lou Y, Hafeez R, Li X, Hossain A, Xie T, Lin L, Li B, Yin Y, Yan J, An Q. Functional Analysis and Genome Mining Reveal High Potential of Biocontrol and Plant Growth Promotion in Nodule-Inhabiting Bacteria Within Paenibacillus polymyxa Complex. Front Microbiol 2021; 11:618601. [PMID: 33537018 PMCID: PMC7848036 DOI: 10.3389/fmicb.2020.618601] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Bacteria belonging to the genus Paenibacillus were frequently isolated from legume nodules. The nodule-inhabiting Paenibacillus as a resource of biocontrol and plant growth-promoting endophytes has rarely been explored. This study explored the nodule-inhabiting Paenibacillus' antifungal activities and biocontrol potentials against broad-spectrum important phytopathogenic fungi. We collected strains which were isolated from nodules of Robinia pseudoacacia, Dendrolobium triangulare, Ormosia semicastrata, Cicer arietinum, Acacia crassicarpa, or Acacia implexa and belong to P. peoriae, P. kribbensis, P. endophyticus, P. enshidis, P. puldeungensis, P. taichungensis, or closely related to P. kribbensis, or P. anseongense. These nodule-inhabiting Paenibacillus showed diverse antagonistic activities against five phytopathogenic fungi (Fusarium graminearum, Magnaporthe oryzae, Rhizoctonia solani, Sclerotinia sclerotiorum, and Botrytis cinerea). Six strains within the P. polymyxa complex showed broad-spectrum and potent activities against all the five pathogens, and produced multiple hydrolytic enzymes, siderophores, and lipopeptide fusaricidins. Fusaricidins are likely the key antimicrobials responsible for the broad-spectrum antifungal activities. The nodule-inhabiting strains within the P. polymyxa complex were able to epiphytically and endophytically colonize the non-host wheat plants, produce indole acetic acids (IAA), and dissolve calcium phosphate and calcium phytate. P. peoriae strains RP20, RP51, and RP62 could fix N2. P. peoriae RP51 and Paenibacillus sp. RP31, which showed potent plant colonization and plant growth-promotion competence, effectively control fungal infection in planta. Genome mining revealed that all strains (n = 76) within the P. polymyxa complex contain ipdC gene encoding indole-3-pyruvate decarboxylase for biosynthesis of IAA, 96% (n = 73) contain the fus cluster for biosynthesis of fusaricidins, and 43% (n = 33) contain the nif cluster for nitrogen fixation. Together, our study highlights that endophytic strains within the P. polymyxa complex have a high probability to be effective biocontrol agents and biofertilizers and we propose an effective approach to screen strains within the P. polymyxa complex.
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Affiliation(s)
- Md. Arshad Ali
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yang Lou
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Rahila Hafeez
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xuqing Li
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Afsana Hossain
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Ting Xie
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Li Lin
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Bin Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yanni Yin
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jianli Yan
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qianli An
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
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