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Ribeiro IDA, Paes JA, Wendisch VF, Ferreira HB, Passaglia LMP. Proteome profiling of Paenibacillus sonchi genomovar Riograndensis SBR5 T under conventional and alternative nitrogen fixation. J Proteomics 2024; 294:105061. [PMID: 38154550 DOI: 10.1016/j.jprot.2023.105061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/30/2023]
Abstract
Paenibacillus sonchi SBR5T is a Gram-positive, endospore-forming facultative aerobic diazotrophic bacterium that can fix nitrogen via an alternative Fe-only nitrogenase (AnfHDGK). In several bacteria, this alternative system is expressed under molybdenum (Mo)-limiting conditions when the conventional Mo-dependent nitrogenase (NifHDK) production is impaired. The regulatory mechanisms, metabolic processes, and cellular functions of N2 fixation by alternative and/or conventional systems are poorly understood in the Paenibacillus genus. We conducted a comparative proteomic profiling study of P. sonchi SBR5T grown under N2-fixing conditions with and without Mo supply through an LC-MS/MS and label-free quantification analysis to address this gap. Protein abundances revealed overrepresented processes related to anaerobiosis growth adaption, Fe-S cluster biosynthesis, ammonia assimilation, electron transfer, and sporulation under N2-fixing conditions compared to non-fixing control. Under Mo limitation, the Fe-only nitrogenase components were overrepresented together with the Mo-transporter system, while the dinitrogenase component (NifDK) of Mo‑nitrogenase was underrepresented. The dinitrogenase reductase component (NifH) and accessory proteins encoded by the nif operon had no significant differential expression, suggesting post-transcriptional regulation of nif gene products in this strain. Overall, this was the first comprehensive proteomic analysis of a diazotrophic strain from the Paenibacillaceae family, and it provided insights related to alternative N2-fixation by Fe-only nitrogenase. SIGNIFICANCE: In this work, we try to understand how the alternative nitrogen fixation system, presented by some diazotrophic bacteria, works. For this, we used the SBR5 lineage of P. sonchi, which presents the alternative system in which the nitrogenase cofactor is composed only of iron. In addition, we tried to unravel the proteome of this strain in different situations of nitrogen fixation, since, for Gram-positive bacteria, these systems are little known. The results achieved, through LC-MS/MS and label-free quantitative analysis, showed an overrepresentation of proteins related to different processes involved with growth under stressful conditions in situations of nitrogen deficiency, in addition to suggesting that some encoded proteins by the nif operon may be regulated at post-transcriptional levels. Our findings represent important steps toward the elucidation of nitrogen fixation systems in Gram-positive diazotrophic bacteria.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil
| | - Jéssica Andrade Paes
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Volker F Wendisch
- Institute for Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil.
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Wendisch VF, Brito LF, Passaglia LM. Genome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T. Genet Mol Biol 2024; 46:e20230115. [PMID: 38224489 PMCID: PMC10789242 DOI: 10.1590/1678-4685-gmb-2023-0115] [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: 04/21/2023] [Accepted: 11/20/2023] [Indexed: 01/17/2024] Open
Abstract
Paenibacillus sonchi genomovar Riograndensis SBR5T is a plant growth-promoting rhizobacterium (PGPR) isolated in the Brazilian state of Rio Grande do Sul from the rhizosphere of Triticum aestivum. It fixes nitrogen, produces siderophores as well as the phytohormone indole-3-acetic acid, solubilizes phosphate and displays antagonist activity against Listeria monocytogenes and Pectobacterium carotovorum. Comprehensive omics analysis and the development of genetic tools are key to characterizing and engineering such non-model microorganisms. Therefore, the complete genome of SBR5T was sequenced, and shown to encode 6,705 proteins, 87 tRNAs, and 27 rRNAs and it enabled a landscape transcriptome analysis that unveiled conserved transcriptional and translational patterns and characterized operon structures and riboswitches. The pangenome of P. sonchi species is open with a stable core pangenome. At the same time, the analysis of genes coding for nitrogenases revealed that the trait of nitrogen fixation is sparse within the Paenibacillaceae family and the presence of Fe-only nitrogenase in the P. sonchi group was exclusive to SBR5T. The development of genetic tools for SBR5T enabled genetic transformation, plasmid construction for constitutive and inducible gene expression, and gene repression using the CRISPRi system. Altogether, the work with P. sonchi can guide the study of non-model bacteria with economic potential.
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Affiliation(s)
- Volker F. Wendisch
- Bielefeld University, Faculty of Biology, Genetics of Prokaryotes, Bielefeld, Germany
- Bielefeld University, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Luciana F. Brito
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway
| | - Luciane M.P. Passaglia
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Departamento de Genética, Porto Alegre, RS, Brazil
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Xu M, Selvaraj GK, Lu H. Environmental sporobiota: Occurrence, dissemination, and risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161809. [PMID: 36702282 DOI: 10.1016/j.scitotenv.2023.161809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/03/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Spore-forming bacteria known as sporobiota are widespread in diverse environments from terrestrial and aquatic habitats to industrial and healthcare systems. Studies on sporobiota have been mainly focused on food processing and clinical fields, while a large amount of sporobiota exist in natural environments. Due to their persistence and capabilities of transmitting virulence factors and antibiotic resistant genes, environmental sporobiota could pose significant health risks to humans. These risks could increase as global warming and environmental pollution has altered the life cycle of sporobiota. This review summarizes the current knowledge of environmental sporobiota, including their occurrence, characteristics, and functions. An interaction network among clinical-, food-related, and environment-related sporobiota is constructed. Recent and effective methods for detecting and disinfecting environmental sporobiota are also discussed. Key problems and future research needs for better understanding and reducing the risks of environmental sporobiota and sporobiome are proposed.
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Affiliation(s)
- Min Xu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ganesh-Kumar Selvaraj
- Department of Microbiology, St. Peter's Institute of Higher Education and Research, Chennai 600054, Tamil Nadu, India.
| | - Huijie Lu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang, China.
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Rosado-Porto D, Ratering S, Wohlfahrt Y, Schneider B, Glatt A, Schnell S. Elevated atmospheric CO 2 concentrations caused a shift of the metabolically active microbiome in vineyard soil. BMC Microbiol 2023; 23:46. [PMID: 36809988 PMCID: PMC9942357 DOI: 10.1186/s12866-023-02781-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/23/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Elevated carbon dioxide concentrations (eCO2), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO2 enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO2 or ambient CO2 (aCO2). RESULTS Diversity indices and redundancy analysis (RDA) demonstrated that eCO2 changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO2. Moreover, under eCO2 conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N2 fixation and NO2- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO2 conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions. CONCLUSIONS The results of this study demonstrate that eCO2 concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.
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Affiliation(s)
- David Rosado-Porto
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
- Faculty of Basic and Biomedical Sciences, Simón Bolívar University, 080002, Barranquilla, Colombia
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
| | - Yvette Wohlfahrt
- Department of General and Organic Viticulture, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366, Geisenheim, Germany
| | - Bellinda Schneider
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
| | - Andrea Glatt
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University, 35392, Giessen, Germany.
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Ribeiro IDA, Bach E, Passaglia LMP. Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family. Mol Phylogenet Evol 2022; 177:107624. [PMID: 36084857 DOI: 10.1016/j.ympev.2022.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/26/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Evelise Bach
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
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Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola. Mol Genet Genomics 2022; 297:1063-1079. [PMID: 35612623 DOI: 10.1007/s00438-022-01907-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/05/2022] [Indexed: 12/11/2022]
Abstract
Previous genome mining of the strains Bacillus pumilus 7PB, Bacillus safensis 1TAz, 8Taz, and 32PB, and Priestia megaterium 16PB isolated from canola revealed differences in the profile of antimicrobial biosynthetic genes when compared to the species type strains. To evaluate not only the similarities among B. pumilus, B. safensis, and P. megaterium genomes but also the specificities found in the canola bacilli, we performed comparative genomic analyses through the pangenome evaluation of each species. Besides that, other genome features were explored, especially focusing on plant-associated and biotechnological characteristics. The combination of the genome metrics Average Nucleotide Identity and digital DNA-DNA hybridization formulas 1 and 3 adopting the universal thresholds of 95 and 70%, respectively, was suitable to verify the identification of strains from these groups. On average, core genes corresponded to 45%, 52%, and 34% of B. pumilus, B. safensis, and P. megaterium open pangenomes, respectively. Many genes related to adaptations to plant-associated lifestyles were predicted, especially in the Bacillus genomes. These included genes for acetoin production, polyamines utilization, root exudate chemoreceptors, biofilm formation, and plant cell-wall degrading enzymes. Overall, we could observe that strains of these species exhibit many features in common, whereas most of their variable genome portions have features yet to be uncovered. The observed antifungal activity of canola bacilli might be a result of the synergistic action of secondary metabolites, siderophores, and chitinases. Genome analysis confirmed that these species and strains have biotechnological potential to be used both as agricultural inoculants or hydrolases producers. Up to our knowledge, this is the first work that evaluates the pangenome features of P. megaterium.
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Bender KS, Madigan MT, Williamson KL, Mayer MH, Parenteau MN, Jahnke LL, Welander PV, Sanguedolce SA, Brown AC, Sattley WM. Genomic Features of the Bundle-Forming Heliobacterium Heliophilum fasciatum. Microorganisms 2022; 10:microorganisms10050869. [PMID: 35630314 PMCID: PMC9147875 DOI: 10.3390/microorganisms10050869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
Eight species of heliobacteria have had their genomes sequenced. However, only two of these genomes have been analyzed in detail, those from the thermophilic Heliomicrobium (Hmi.) modesticaldum and the alkaliphilic Heliorestis (Hrs.) convoluta. Here we present analyses of the draft genome sequence of a species of heliobacterium that grows optimally at a moderate temperature and neutral pH. The organism, Heliophilum (Hph.) fasciatum, is phylogenetically unique among cultured heliobacteria and was isolated from rice soil, a common habitat for heliobacteria. The Hph. fasciatum genome contains 3.14 Mbp—similar to that of other reported heliobacteria—but has a G+C base ratio that lies between that of Hmi. modesticaldum and Hrs. convoluta. Many of the genomic features of Hmi. modesticaldum and Hrs. convoluta, such as the absence of genes encoding autotrophic pathways, the presence of a superoperonal cluster of photosynthesis-related genes, and genes encoding endospore-specific proteins, are also characteristic of the Hph. fasciatum genome. However, despite the fact that Hph. fasciatum is diazotrophic, classical nif genes encoding the alpha and beta subunits of dinitrogenase (nifDK) present in other heliobacteria could not be identified. Instead, genes encoding several highly divergent NifDK homologs were present, at least one of which likely encodes a functional dinitrogenase and another a methylthio-alkane reductase (MarDK) for sulfur assimilation. A classical NifH (dinitrogenase reductase) homolog was also absent in Hph. fasciatum, but a related protein was identified that likely carries out this function as well as electron delivery to MarDK. The N2-fixing system of Hph. fasciatum is therefore distinct from that of other heliobacteria and may have unusual properties.
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Affiliation(s)
- Kelly S. Bender
- Microbiology Program, School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.); (K.L.W.)
| | - Michael T. Madigan
- Microbiology Program, School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.); (K.L.W.)
| | - Kyleigh L. Williamson
- Microbiology Program, School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.); (K.L.W.)
| | - Marisa H. Mayer
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; (M.H.M.); (M.N.P.); (L.L.J.)
| | - Mary N. Parenteau
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; (M.H.M.); (M.N.P.); (L.L.J.)
| | - Linda L. Jahnke
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; (M.H.M.); (M.N.P.); (L.L.J.)
| | - Paula V. Welander
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA;
| | - Sophia A. Sanguedolce
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (S.A.S.); (A.C.B.)
| | - Abigail C. Brown
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (S.A.S.); (A.C.B.)
| | - W. Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (S.A.S.); (A.C.B.)
- Correspondence: ; Tel.: +1-765-677-2128
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Hoke AK, Reynoso G, Smith MR, Gardner MI, Lockwood DJ, Gilbert NE, Wilhelm SW, Becker IR, Brennan GJ, Crider KE, Farnan SR, Mendoza V, Poole AC, Zimmerman ZP, Utz LK, Wurch LL, Steffen MM. Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere. PLoS One 2021; 16:e0257017. [PMID: 34550975 PMCID: PMC8457463 DOI: 10.1371/journal.pone.0257017] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 11/18/2022] Open
Abstract
Microbial interactions in harmful algal bloom (HAB) communities have been examined in marine systems, but are poorly studied in fresh waters. To investigate HAB-microbe interactions, we isolated bacteria with close associations to bloom-forming cyanobacteria, Microcystis spp., during a 2017 bloom in the western basin of Lake Erie. The genomes of five isolates (Exiguobacterium sp. JMULE1, Enterobacter sp. JMULE2, Deinococcus sp. JMULE3, Paenibacillus sp. JMULE4, and Acidovorax sp. JMULE5.) were sequenced on a PacBio Sequel system. These genomes ranged in size from 3.1 Mbp (Exiguobacterium sp. JMULE1) to 5.7 Mbp (Enterobacter sp. JMULE2). The genomes were analyzed for genes relating to critical metabolic functions, including nitrogen reduction and carbon utilization. All five of the sequenced genomes contained genes that could be used in potential signaling and nutrient exchange between the bacteria and cyanobacteria such as Microcystis. Gene expression signatures of algal-derived carbon utilization for two isolates were identified in Microcystis blooms in Lake Erie and Lake Tai (Taihu) at low levels, suggesting these organisms are active and may have a functional role during Microcystis blooms in aggregates, but were largely missing from whole water samples. These findings build on the growing evidence that the bacterial microbiome associated with bloom-forming algae have the functional potential to contribute to nutrient exchange within bloom communities and interact with important bloom formers like Microcystis.
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Affiliation(s)
- Alexa K. Hoke
- James Madison University, Harrisonburg, VA, United States of America
| | - Guadalupe Reynoso
- James Madison University, Harrisonburg, VA, United States of America
- Virginia Tech, Blacksburg, VA, United States of America
| | - Morgan R. Smith
- James Madison University, Harrisonburg, VA, United States of America
- Texas A&M University, College Station, TX, United States of America
| | - Malia I. Gardner
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Naomi E. Gilbert
- James Madison University, Harrisonburg, VA, United States of America
- University of Tennessee, Knoxville, TN, United States of America
| | | | | | - Grant J. Brennan
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Shannon R. Farnan
- James Madison University, Harrisonburg, VA, United States of America
| | - Victoria Mendoza
- James Madison University, Harrisonburg, VA, United States of America
| | - Alison C. Poole
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Lucy K. Utz
- James Madison University, Harrisonburg, VA, United States of America
| | - Louie L. Wurch
- James Madison University, Harrisonburg, VA, United States of America
| | - Morgan M. Steffen
- James Madison University, Harrisonburg, VA, United States of America
- * E-mail:
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Ribeiro IDA, Bach E, da Silva Moreira F, Müller AR, Rangel CP, Wilhelm CM, Barth AL, Passaglia LMP. Antifungal potential against Sclerotinia sclerotiorum (Lib.) de Bary and plant growth promoting abilities of Bacillus isolates from canola (Brassica napus L.) roots. Microbiol Res 2021; 248:126754. [PMID: 33848783 DOI: 10.1016/j.micres.2021.126754] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/28/2021] [Accepted: 03/27/2021] [Indexed: 10/21/2022]
Abstract
Endophytic bacteria show important abilities in promoting plant growth and suppressing phytopathogens, being largely explored in agriculture as biofertilizers or biocontrol agents. Bacteria from canola roots were isolated and screened for different plant growth promotion (PGP) traits and biocontrol of Sclerotinia sclerotiorum. Thirty isolates belonging to Bacillus, Paenibacillus, Lysinibacillus, and Microbacterium genera were obtained. Several isolates produced auxin, siderophores, hydrolytic enzymes, fixed nitrogen and solubilized phosphate. Five isolates presented antifungal activity against S. sclerotiorum by the dual culture assay and four of them also inhibited fungal growth by volatile organic compounds production. All antagonistic isolates belonged to the Bacillus genus, and had their genomes sequenced for the search of biosynthetic gene clusters (BGC) related to antimicrobial metabolites. These isolates were identified as Bacillus safensis (3), Bacillus pumilus (1), and Bacillus megaterium (1), using the genomic metrics ANI and dDDH. Most strains showed several common BGCs, including bacteriocin, polyketide synthase (PKS), and non-ribosomal peptide synthetase (NRPS), related to pumilacidin, bacillibactin, bacilysin, and other antimicrobial compounds. Pumilacidin-related mass peaks were detected in acid precipitation extracts through MALDI-TOF analysis. The genomic features demonstrated the potential of these isolates in the suppression of plant pathogens; however, some aspects of plant-bacterial interactions remain to be elucidated.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970, Porto Alegre, RS, Brazil
| | - Evelise Bach
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970, Porto Alegre, RS, Brazil
| | - Fernanda da Silva Moreira
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970, Porto Alegre, RS, Brazil
| | - Aline Reis Müller
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970, Porto Alegre, RS, Brazil
| | - Caroline Pinto Rangel
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970, Porto Alegre, RS, Brazil
| | - Camila Mörschbächer Wilhelm
- LABRESIS - Laboratório de Pesquisa em Resistência Bacteriana, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos 2350, Porto Alegre, RS, 90.035-903, Brazil
| | - Afonso Luis Barth
- LABRESIS - Laboratório de Pesquisa em Resistência Bacteriana, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos 2350, Porto Alegre, RS, 90.035-903, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970, Porto Alegre, RS, Brazil.
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Brito LF, López MG, Straube L, Passaglia LMP, Wendisch VF. Inorganic Phosphate Solubilization by Rhizosphere Bacterium Paenibacillus sonchi: Gene Expression and Physiological Functions. Front Microbiol 2020; 11:588605. [PMID: 33424789 PMCID: PMC7793946 DOI: 10.3389/fmicb.2020.588605] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Due to the importance of phosphorus (P) in agriculture, crop inoculation with phosphate-solubilizing bacteria is a relevant subject of study. Paenibacillus sonchi genomovar Riograndensis SBR5 is a promising candidate for crop inoculation, as it can fix nitrogen and excrete ammonium at a remarkably high rate. However, its trait of phosphate solubilization (PS) has not yet been studied in detail. Here, differential gene expression and functional analyses were performed to characterize PS in this bacterium. SBR5 was cultivated with two distinct P sources: NaH2PO4 as soluble phosphate source (SPi) and hydroxyapatite as insoluble phosphate source (IPi). Total RNA of SBR5 cultivated in those two conditions was isolated and sequenced, and bacterial growth and product formation were monitored. In the IPi medium, the expression of 68 genes was upregulated, whereas 100 genes were downregulated. Among those, genes involved in carbon metabolism, including those coding for subunits of 2-oxoglutarate dehydrogenase, were identified. Quantitation of organic acids showed that the production of tricarboxylic acid cycle-derived organic acids was reduced in IPi condition, whereas acetate and gluconate were overproduced. Increased concentrations of proline, trehalose, and glycine betaine revealed active osmoprotection during growth in IPi. The cultivation with hydroxyapatite also caused the reduction in the motility of SBR5 cells as a response to Pi depletion at the beginning of its growth. SBR5 was able to solubilize hydroxyapatite, which suggests that this organism is a promising phosphate-solubilizing bacterium. Our findings are the initial step in the elucidation of the PS process in P. sonchi SBR5 and will be a valuable groundwork for further studies of this organism as a plant growth-promoting rhizobacterium.
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Affiliation(s)
- Luciana F. Brito
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marina Gil López
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Lucas Straube
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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do Carmo Dias B, da Mota FF, Jurelevicius D, Seldin L. Genetics and regulation of nitrogen fixation in Paenibacillus brasilensis PB24. Microbiol Res 2020; 243:126647. [PMID: 33290933 DOI: 10.1016/j.micres.2020.126647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 12/23/2022]
Abstract
Biological nitrogen fixation (BNF), performed by diazotrophic prokaryotes, is responsible for reducing dinitrogen (N2) present in the biosphere into biologically available forms of nitrogen. Paenibacillus brasilensis PB24 is a diazotrophic Gram-positive bacterium and is considered ecologically and industrially important because it is able to produce antimicrobial substances and 2,3-butanediol. However, the genetics and regulation of its nitrogen fixing (nif) genes have never been assessed so far. Therefore, the present study aimed to (i) identify the structural and regulatory genes related to BNF in the PB24 genome, (ii) perform comparative genomics analysis of the nif operon among different Paenibacillus species and (iii) study the expression of these genes in the presence and absence of NH4. Strain PB24 showed a nif operon composed of nine genes (nifBHDKENXhesAV), with a conserved synteny (with small variations) among the Paenibacillus species evaluated. BNF regulatory genes, glnK and amtB (encoding GlnK signal transduction protein and AmtB transmembrane protein, respectively) and glnR and glnA genes (encoding the transcription factor GlnR and glutamine synthetase) were found in the PB24 genome. Primers were designed for qPCR amplification of the nitrogenase structural (nifH, nifD and nifK) and regulatory (glnA and amtB) BNF genes. The structural gene expression in PB24 was up- and downregulated in the absence and presence of NH4, respectively. The gene expression levels indicated a GlnR-mediated repression of genes associated with ammonium import (amtBglnK) and BNF (nif genes). Additionally, the regulatory mechanism of GlnR in P. brasilensis PB24 differed from the other Paenibacillus evaluated, considering the different distribution of binding sites recognized by GlnR.
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Affiliation(s)
- Beatriz do Carmo Dias
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Diogo Jurelevicius
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Brito LF, Schultenkämper K, Passaglia LMP, Wendisch VF. CRISPR interference-based gene repression in the plant growth promoter Paenibacillus sonchi genomovar Riograndensis SBR5. Appl Microbiol Biotechnol 2020; 104:5095-5106. [PMID: 32274563 PMCID: PMC7229006 DOI: 10.1007/s00253-020-10571-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 03/20/2020] [Indexed: 12/16/2022]
Abstract
Gene repression using the endonucleolytically deactivated dCas9 protein and sgRNAs (CRISPR interference or CRISPRi) is a useful approach to study gene functions. Here, we established CRISPRi in Paenibacillus sonchi genomovar Riograndensis SBR5, a plant growth promoting bacterium. CRISPRi system with sgRNAs targeting SBR5 endogenous genes spo0A, yaaT and ydjJ and plasmid-borne gfpUV was constructed and analyzed. Flow cytometry analysis revealed a significant decrease of reporter protein GFPUV signal in P. sonchi strains expressing gfpUV sgRNA in comparison with non-targeting controls. CRISPRi-based repression of chromosomal genes for regulation of sporulation spo0A and yaaT decreased sporulation and increased biofilm formation in SBR5. Repression of the sorbitol catabolic gene ydjJ revealed decreased specific activity of YdjJ in crude cell extracts and reduced biomass formation from sorbitol in growth experiments. Our work on CRISPRi-based gene repression serves as basis for gene function studies of the plant growth promoter P. sonchi SBR5. To our knowledge, the present study presents the first tool for gene repression established in Paenibacillus species.Key points• CRISPRi toward gene repression was applied for the first time in Paenibacillus.• CRISPRi of spo0A and yaaT depleted spores and increased biofilms in SBR5.• CRISPRi-based ydjJ repression decreased specific activity of sorbitol dehydrogenase.
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Affiliation(s)
- Luciana F Brito
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
- Department of Biotechnology and Food Science, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kerstin Schultenkämper
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Luciane M P Passaglia
- Department of Genetics UFRGS, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany.
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Genomic characterization of methylotrophy of Oharaeibacter diazotrophicus strain SM30T. J Biosci Bioeng 2018; 126:667-675. [DOI: 10.1016/j.jbiosc.2018.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/22/2018] [Accepted: 05/28/2018] [Indexed: 11/21/2022]
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Brito LF, Irla M, Kalinowski J, Wendisch VF. Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology. BMC Genomics 2017; 18:846. [PMID: 29100491 PMCID: PMC5670726 DOI: 10.1186/s12864-017-4235-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The plant growth promoting rhizobacterium Paenibacillus riograndensis SBR5 is a promising candidate to serve as crop inoculant. Despite its potential in providing environmental and economic benefits, the species P. riograndensis is poorly characterized. Here, we performed for the first time a detailed transcriptome analysis of P. riograndensis SBR5 using RNA-seq technology. RESULTS RNA was isolated from P. riograndensis SBR5 cultivated under 15 different growth conditions and combined together in order to analyze an RNA pool representing a large set of expressed genes. The resultant total RNA was used to generate 2 different libraries, one enriched in 5'-ends of the primary transcripts and the other representing the whole transcriptome. Both libraries were sequenced and analyzed to identify the conserved sequences of ribosome biding sites and translation start motifs, and to elucidate operon structures present in the transcriptome of P. riograndensis. Sequence analysis of the library enriched in 5'-ends of the primary transcripts was used to identify 1082 transcription start sites (TSS) belonging to novel transcripts and allowed us to determine a promoter consensus sequence and regulatory sequences in 5' untranslated regions including riboswitches. A putative thiamine pyrophosphate dependent riboswitch upstream of the thiamine biosynthesis gene thiC was characterized by translational fusion to a fluorescent reporter gene and shown to function in P. riograndensis SBR5. CONCLUSIONS Our RNA-seq analysis provides insight into the P. riograndensis SBR5 transcriptome at the systems level and will be a valuable basis for differential RNA-seq analysis of this bacterium.
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Affiliation(s)
- Luciana Fernandes Brito
- Department of Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Marta Irla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Volker F Wendisch
- Department of Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany. .,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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Fernandes GDC, Hauf K, Sant'Anna FH, Forchhammer K, Passaglia LMP. Glutamine synthetase stabilizes the binding of GlnR to nitrogen fixation gene operators. FEBS J 2017; 284:903-918. [DOI: 10.1111/febs.14021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/22/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Gabriela de C. Fernandes
- Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre RS Brazil
- Interfaculty Institute for Microbiology and Infection Medicine University of Tuebingen Germany
| | - Ksenia Hauf
- Interfaculty Institute for Microbiology and Infection Medicine University of Tuebingen Germany
| | - Fernando H. Sant'Anna
- Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre RS Brazil
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine University of Tuebingen Germany
| | - Luciane M. P. Passaglia
- Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre RS Brazil
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Grady EN, MacDonald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016; 15:203. [PMID: 27905924 PMCID: PMC5134293 DOI: 10.1186/s12934-016-0603-7] [Citation(s) in RCA: 445] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/24/2016] [Indexed: 12/11/2022] Open
Abstract
Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.
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Affiliation(s)
- Elliot Nicholas Grady
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Jacqueline MacDonald
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, Dental Science Building Rm. 3014, London, ON N6A 5C1 Canada
| | - Linda Liu
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Alex Richman
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ze-Chun Yuan
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, Dental Science Building Rm. 3014, London, ON N6A 5C1 Canada
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Brito LF, Irla M, Walter T, Wendisch VF. Magnesium aminoclay-based transformation of Paenibacillus riograndensis and Paenibacillus polymyxa and development of tools for gene expression. Appl Microbiol Biotechnol 2016; 101:735-747. [DOI: 10.1007/s00253-016-7999-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/30/2016] [Accepted: 11/05/2016] [Indexed: 11/25/2022]
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How to transform a recalcitrant Paenibacillus strain: From culture medium to restriction barrier. J Microbiol Methods 2016; 131:135-143. [PMID: 27780731 DOI: 10.1016/j.mimet.2016.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/11/2016] [Accepted: 10/21/2016] [Indexed: 11/20/2022]
Abstract
Paenibacillus riograndensis SBR5T is a plant growth-promoting bacterium isolated from the wheat rhizosphere. Its recalcitrance to genetic manipulation is a major bottleneck for molecular studies, as has been reported for other Paenibacillus environmental isolates. An efficient electroporation protocol was established by evaluating diverse parameters and optimizing the culture medium, culture growth phase, electroporation solution, recovery medium, DNA input, and electric field strength. Efficiencies of approximately 2.8×104transformantsμg-1 of plasmid DNA were obtained. The optimized protocol was tested with other Paenibacillus species, and the relevance of bypassing the restriction DNA defense system to transform Paenibacillus was highlighted. This protocol is the tool needed to deepen molecular studies with this strain and will aid in the manipulation of other new environmental isolates that also exhibit recalcitrant transformation difficulties.
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Brito LF, Bach E, Kalinowski J, Rückert C, Wibberg D, Passaglia LM, Wendisch VF. Complete genome sequence of Paenibacillus riograndensis SBR5T, a Gram-positive diazotrophic rhizobacterium. J Biotechnol 2015; 207:30-1. [PMID: 25959170 DOI: 10.1016/j.jbiotec.2015.04.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 04/27/2015] [Indexed: 10/23/2022]
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