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Cortés-Albayay C, Delgado-Torres M, Larama G, Paredes-Negron C, de la Luz Mora M, Durán P, Barra PJ. Comparative genomics of plant growth promoting phosphobacteria isolated from acidic soils. Antonie Van Leeuwenhoek 2024; 117:76. [PMID: 38705910 DOI: 10.1007/s10482-024-01961-1] [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: 01/25/2024] [Accepted: 03/26/2024] [Indexed: 05/07/2024]
Abstract
Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily locked away in insoluble organic and inorganic forms. Phosphate solubilizing and mineralizing bacteria, also called phosphobacteria, isolated from P-deficient soils have emerged as a promising biofertilizer alternative, capable of converting these recalcitrant P forms into plant-available phosphates. Three such phosphobacteria strains-Serratia sp. RJAL6, Klebsiella sp. RCJ4, and Enterobacter sp. 198-previously demonstrated their particular strength as plant growth promoters for wheat, ryegrass, or avocado under abiotic stresses and P deficiency. Comparative genomic analysis of their draft genomes revealed several genes encoding key functionalities, including alkaline phosphatases, isonitrile secondary metabolites, enterobactin biosynthesis and genes associated to the production of indole-3-acetic acid (IAA) and gluconic acid. Moreover, overall genome relatedness indexes (OGRIs) revealed substantial divergence between Serratia sp. RJAL6 and its closest phylogenetic neighbours, Serratia nematodiphila and Serratia bockelmanii. This compelling evidence suggests that RJAL6 merits classification as a novel species. This in silico genomic analysis provides vital insights into the plant growth-promoting capabilities and provenance of these promising PSRB strains. Notably, it paves the way for further characterization and potential application of the newly identified Serratia species as a powerful bioinoculant in future agricultural settings.
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Affiliation(s)
- Carlos Cortés-Albayay
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Mabel Delgado-Torres
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
| | - Giovanni Larama
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Cecilia Paredes-Negron
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
| | - María de la Luz Mora
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile
| | - Paola Durán
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile.
- Biocontrol Research Laboratory, Universidad de La Frontera, 4811230, Temuco, Chile.
- Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, 4811230, Temuco, Chile.
| | - Patricio Javier Barra
- Centre of Plant and Soil Interaction, Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4811230, Temuco, Chile.
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Diez-Marulanda JC, Brandão PFB. Potential use of two Serratia strains for cadmium remediation based on microbiologically induced carbonate precipitation and their cadmium resistance. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:5319-5330. [PMID: 38114705 DOI: 10.1007/s11356-023-31062-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/11/2023] [Indexed: 12/21/2023]
Abstract
Cadmium (Cd) presence and bioavailability in soils is a serious concern for cocoa producers. Cocoa plants can bioaccumulate Cd that can reach humans through the food chain, thus posing a threat to human health, as Cd is a highly toxic metal. Currently, microbiologically induced carbonate precipitation (MICP) by the ureolytic path has been proposed as an effective technique for Cd remediation. In this work, the Cd remediation potential and Cd resistance of two ureolytic bacteria, Serratia sp. strains 4.1a and 5b, were evaluated. The growth of both Serratia strains was inhibited at 4 mM Cd(II) in the culture medium, which is far higher than the Cd content that can be found in the soils targeted for remediation. Regarding removal efficiency, for an initial concentration of 0.15 mM Cd(II) in liquid medium, the maximum removal percentages for Serratia sp. 4.1.a and 5b were 99.3% and 99.57%, respectively. Their precipitates produced during Cd removal were identified as calcite by X-ray diffraction. Energy dispersive X-ray spectroscopy analysis showed that a portion of Cd was immobilized in this matrix. Finally, the presence of a partial gene from the czc operon, involved in Cd resistance, was observed in Serratia sp. 5b. The expression of this gene was found to be unaffected by the presence of Cd(II), and upregulated in the presence of urea. This work is one of the few to report the use of bacterial strains of the Serratia genus for Cd remediation by MICP, and apparently the first one to report differential expression of a Cd resistance gene due to the presence of urea.
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Affiliation(s)
- Juan C Diez-Marulanda
- Universidad Nacional de Colombia - Sede Bogotá, Facultad de Ciencias, Departamento de Química, Grupo de Estudios para la Remediación y Mitigación de Impactos Negativos al Ambiente (GERMINA), Av. Carrera 30 # 45-03, 111321, Bogotá, Colombia.
| | - Pedro F B Brandão
- Universidad Nacional de Colombia - Sede Bogotá, Facultad de Ciencias, Departamento de Química, Grupo de Estudios para la Remediación y Mitigación de Impactos Negativos al Ambiente (GERMINA), Av. Carrera 30 # 45-03, 111321, Bogotá, Colombia
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Shikov AE, Merkushova AV, Savina IA, Nizhnikov AA, Antonets KS. The man, the plant, and the insect: shooting host specificity determinants in Serratia marcescens pangenome. Front Microbiol 2023; 14:1211999. [PMID: 38029097 PMCID: PMC10656689 DOI: 10.3389/fmicb.2023.1211999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/21/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Serratia marcescens is most commonly known as an opportunistic pathogen causing nosocomial infections. It, however, was shown to infect a wide range of hosts apart from vertebrates such as insects or plants as well, being either pathogenic or growth-promoting for the latter. Despite being extensively studied in terms of virulence mechanisms during human infections, there has been little evidence of which factors determine S. marcescens host specificity. On that account, we analyzed S. marcescens pangenome to reveal possible specificity factors. Methods We selected 73 high-quality genome assemblies of complete level and reconstructed the respective pangenome and reference phylogeny based on core genes alignment. To find an optimal pipeline, we tested current pangenomic tools and obtained several phylogenetic inferences. The pangenome was rich in its accessory component and was considered open according to the Heaps' law. We then applied the pangenome-wide associating method (pan-GWAS) and predicted positively associated gene clusters attributed to three host groups, namely, humans, insects, and plants. Results According to the results, significant factors relating to human infections included transcriptional regulators, lipoproteins, ABC transporters, and membrane proteins. Host preference toward insects, in its turn, was associated with diverse enzymes, such as hydrolases, isochorismatase, and N-acetyltransferase with the latter possibly exerting a neurotoxic effect. Finally, plant infection may be conducted through type VI secretion systems and modulation of plant cell wall synthesis. Interestingly, factors associated with plants also included putative growth-promoting proteins like enzymes performing xenobiotic degradation and releasing ammonium irons. We also identified overrepresented functional annotations within the sets of specificity factors and found that their functional characteristics fell into separate clusters, thus, implying that host adaptation is represented by diverse functional pathways. Finally, we found that mobile genetic elements bore specificity determinants. In particular, prophages were mainly associated with factors related to humans, while genetic islands-with insects and plants, respectively. Discussion In summary, functional enrichments coupled with pangenomic inferences allowed us to hypothesize that the respective host preference is carried out through distinct molecular mechanisms of virulence. To the best of our knowledge, the presented research is the first to identify specific genomic features of S. marcescens assemblies isolated from different hosts at the pangenomic level.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Anastasiya V. Merkushova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
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Alemán-Duarte MI, Aguilar-Uscanga BR, García-Robles G, Ramírez-Salazar FDJ, Benítez-García I, Balcázar-López E, Solís-Pacheco JR. Improvement and Validation of a Genomic DNA Extraction Method for Human Breastmilk. Methods Protoc 2023; 6:mps6020034. [PMID: 37104016 PMCID: PMC10144544 DOI: 10.3390/mps6020034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
The human milk microbiota (HMM) of healthy women can vary substantially, as demonstrated by recent advances in DNA sequencing technology. However, the method used to extract genomic DNA (gDNA) from these samples may impact the observed variations and potentially bias the microbiological reconstruction. Therefore, it is important to use a DNA extraction method that is able to effectively isolate gDNA from a diverse range of microorganisms. In this study, we improved and compared a DNA extraction method for gDNA isolation from human milk (HM) samples to commercial and standard protocols. We evaluated the extracted gDNA using spectrophotometric measurements, gel electrophoresis, and PCR amplifications to assess its quantity, quality, and amplifiability. Additionally, we tested the improved method’s ability to isolate amplifiable gDNA from fungi, Gram-positive and Gram-negative bacteria to validate its potential for reconstructing microbiological profiles. The improved DNA extraction method resulted in a higher quality and quantity of the extracted gDNA compared to the commercial and standard protocols and allowed for polymerase chain reaction (PCR) amplification of the V3–V4 regions of the 16S ribosomal gene in all the samples and the ITS-1 region of the fungal 18S ribosomal gene in 95% of the samples. These results suggest that the improved DNA extraction method demonstrates better performance for gDNA extraction from complex samples such as HM.
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Affiliation(s)
- Mario Iván Alemán-Duarte
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
| | - Blanca Rosa Aguilar-Uscanga
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
| | - Guadalupe García-Robles
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
| | - Felipe de Jesús Ramírez-Salazar
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
| | - Israel Benítez-García
- Unidad Académica de Ingeniería en Biotecnología, Universidad Politécnica de Sinaloa (UPSIN), Carretera Municipal Libre Mazatlán Higueras Km 3 Col. Genaro Estrada, Mazatlán 82199, Mexico
| | - Edgar Balcázar-López
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
- Correspondence: (E.B.-L.); (J.R.S.-P.); Tel.: +52-(33)-1378-59000 (ext. 27648) (J.R.S.-P.)
| | - Josué Raymundo Solís-Pacheco
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
- Correspondence: (E.B.-L.); (J.R.S.-P.); Tel.: +52-(33)-1378-59000 (ext. 27648) (J.R.S.-P.)
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Tshikhudo PP, Ntushelo K, Mudau FN. Sustainable Applications of Endophytic Bacteria and Their Physiological/Biochemical Roles on Medicinal and Herbal Plants: Review. Microorganisms 2023; 11:microorganisms11020453. [PMID: 36838418 PMCID: PMC9967847 DOI: 10.3390/microorganisms11020453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Bacterial endophytes reside within the tissues of living plant species without causing any harm or disease to their hosts. These endophytes can be isolated, identified, characterized, and used as biofertilizers. Moreover, bacterial endophytes increase the plants' resistance against diseases, pests, and parasites, and are a promising source of pharmaceutically important bioactives. For instance, the production of antibiotics, auxins, biosurfactants, cytokinin's, ethylene, enzymes, gibberellins, nitric oxide organic acids, osmolytes, and siderophores is accredited to the existence of various bacterial strains. Thus, this manuscript intends to review the sustainable applications of endophytic bacteria to promote the growth, development, and chemical integrity of medicinal and herbal plants, as well as their role in plant physiology. The study of the importance of bacterial endophytes in the suppression of diseases in medicinal and herbal plants is crucial and a promising area of future investigation.
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Affiliation(s)
- Phumudzo Patrick Tshikhudo
- Department of Agriculture, Land Reform and Rural Development, Directorate Plant Health, Division Pest Risk Analysis, Arcadia, Pretoria 0001, South Africa
- Correspondence:
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Private Bag X6, Florida 1710, South Africa
| | - Fhatuwani Nixwell Mudau
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
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Impact of lead (Pb 2+) on the growth and biological activity of Serratia marcescens selected for wastewater treatment and identification of its zntR gene-a metal efflux regulator. World J Microbiol Biotechnol 2023; 39:91. [PMID: 36752862 DOI: 10.1007/s11274-023-03535-1] [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: 05/02/2022] [Accepted: 01/30/2023] [Indexed: 02/09/2023]
Abstract
Microorganisms isolated from contaminated areas play an important role in bioremediation processes. They promote heavy metal removal from the environment by adsorbing ions onto the cell wall surface, accumulating them inside the cells, or reducing, complexing, or precipitating these substances in the environment. Microorganism-based bioremediation processes can be highly efficient, low-cost and have low environmental impact. Thus, the present study aimed to select Pb2+-resistant bacteria and evaluate the growth rate, biological activity, and the presence of genes associated with metal resistance. Serratia marcescens CCMA 1010, that was previously isolated from coffee processing wastewater, was selected since was able to growth in Pb2+ concentrations of up to 4.0 mM. The growth rate and generation time did not differ from those of the control (without Pb2+), although biological activity decreased in the first hour of exposure to these ions and stabilized after this period. The presence of the zntR, zntA and pbrA genes was analysed, and only zntR was detected. The zntR gene encodes a protein responsible for regulating the production of ZntA, a transmembrane protein that facilitates Pb2+ extrusion out of the cell. S. marcescens CCMA 1010 demonstrated a potential for use as bioindicator that has potential to be used in bioremediation processes due to its resistance to high concentrations of Pb2+, ability to grow until 24 h of exposure, and possession of a gene that indicates the existence of mechanisms associated with resistance to lead (Pb2+).
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Jaiswal S, Singh DK, Shukla P. Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120867. [PMID: 36528203 DOI: 10.1016/j.envpol.2022.120867] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/19/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due to its persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-1, 3300-2800 cm-1 and 785-540 cm-1. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.
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Affiliation(s)
- Shweta Jaiswal
- Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Dileep Kumar Singh
- Soil Microbial Ecology and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Pratyoosh Shukla
- Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India; Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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Manogaran M, Halmi MIE, Othman AR, Yasid NA, Gunasekaran B, Shukor MYA. Decolorization of Reactive Red 120 by a novel bacterial consortium: Kinetics and heavy metal inhibition study. AIMS ENVIRONMENTAL SCIENCE 2023; 10:424-445. [DOI: 10.3934/environsci.2023024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
<abstract><p>Juru River is one of the most polluted rivers in Malaysia. A dye-degrading bacterial consortium has been isolated from the river's sediment. This consortium JR3 consists of <italic>Pseudomonas aeruginosa</italic> MM01, <italic>Enterobacter</italic> sp. MM05 and <italic>Serratia marcescens</italic> MM06, which were able to decolorize up to 700 ppm of the Reactive Red 120 (RR120) dye under optimal conditions with limited substrate available. Substrate inhibition kinetics were investigated, and, based on the best model, Aiba, the maximum growth rate was 0.795 h<sup>–1</sup>, while the saturation constant and inhibitory constant were 0.185% and 0.14%, respectively. In addition, the influence of various metal ions on the growth and decolorization rate of this bacterial consortium on RR120 was investigated. Chromium showed the weakest effect on the decolorization of 200 ppm RR120, with 73.5% removal and bacterial growth of 11.461 log CFU mL<sup>–1</sup>. Zinc yielded the second weakest effect, followed by silver and lead, with percentages of RR120 decolorization of 63.8%, 54.6% and 50.5%, respectively. Meanwhile, cadmium, arsenic and copper reduced the decolorization of RR120 in consortium JR3 by half. Mercury strongly inhibited decolorization by 32.5%. Based on the least inhibited heavy metal in RR120 decolorization activity of consortium JR3, the best inhibitory kinetic model was Levenspiel, with a maximum growth rate of 0.632 h<sup>–1</sup>, while the saturation constant and inhibitory constants were 15.08% and 0.5783%, respectively. The metal-tolerant azo dye-degrading bacterial consortium will be very useful in dye remediation in metal-laden polluted environments.</p></abstract>
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Affiliation(s)
- Motharasan Manogaran
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor D.E., Malaysia
| | - Mohd Izuan Effendi Halmi
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor D.E., Malaysia
| | - Ahmad Razi Othman
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor D.E., Malaysia
| | - Nur Adeela Yasid
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor D.E., Malaysia
| | - Baskaran Gunasekaran
- Faculty of Applied Sciences, UCSI University Kuala Lumpur (South Wing), No.1, Jalan Menara Gading, UCSI Heights 56000 Cheras, Kuala Lumpur, Malaysia
| | - Mohd Yunus Abd Shukor
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor D.E., Malaysia
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Guzmán-Moreno J, García-Ortega LF, Torres-Saucedo L, Rivas-Noriega P, Ramírez-Santoyo RM, Sánchez-Calderón L, Quiroz-Serrano IN, Vidales-Rodríguez LE. Bacillus megaterium HgT21: a Promising Metal Multiresistant Plant Growth-Promoting Bacteria for Soil Biorestoration. Microbiol Spectr 2022; 10:e0065622. [PMID: 35980185 PMCID: PMC9604106 DOI: 10.1128/spectrum.00656-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022] Open
Abstract
The environmental deterioration produced by heavy metals derived from anthropogenic activities has gradually increased. The worldwide dissemination of toxic metals in crop soils represents a threat for sustainability and biosafety in agriculture and requires strategies for the recovery of metal-polluted crop soils. The biorestoration of metal-polluted soils using technologies that combine plants and microorganisms has gained attention in recent decades due to the beneficial and synergistic effects produced by its biotic interactions. In this context, native and heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in the development of strategies for sustainable biorestoration of metal-contaminated soils. In this study, we present a genomic analysis and characterization of the rhizospheric bacterium Bacillus megaterium HgT21 isolated from metal-polluted soil from Zacatecas, Mexico. The results reveal that this autochthonous bacterium contains an important set of genes related to a variety of operons associated with mercury, arsenic, copper, cobalt, cadmium, zinc and aluminum resistance. Additionally, halotolerance-, beta-lactam resistance-, phosphate solubilization-, and plant growth-promotion-related genes were identified. The analysis of resistance to metal ions revealed resistance to mercury (HgII+), arsenate [AsO4]³-, cobalt (Co2+), zinc (Zn2+), and copper (Cu2+). Moreover, the ability of the HgT21 strain to produce indole acetic acid (a phytohormone) and promote the growth of Arabidopsis thaliana seedlings in vitro was also demonstrated. The genotype and phenotype of Bacillus megaterium HgT21 reveal its potential to be used as a model of both plant growth-promoting and metal multiresistant bacteria. IMPORTANCE Metal-polluted environments are natural sources of a wide variety of PGPB adapted to cope with toxic metal concentrations. In this work, the bacterial strain Bacillus megaterium HgT21 was isolated from metal-contaminated soil and is proposed as a model for the study of metal multiresistance in spore-forming Gram-positive bacteria due to the presence of a variety of metal resistance-associated genes similar to those encountered in the metal multiresistant Gram-negative Cupriavidus metallidurans CH34. The ability of B. megaterium HgT21 to promote the growth of plants also makes it suitable for the study of plant-bacteria interactions in metal-polluted environments, which is key for the development of techniques for the biorestoration of metal-contaminated soils used for agriculture.
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Affiliation(s)
- Jesús Guzmán-Moreno
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Luis Fernando García-Ortega
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - Lilia Torres-Saucedo
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Paulina Rivas-Noriega
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Rosa María Ramírez-Santoyo
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Lenin Sánchez-Calderón
- Laboratorio de Genómica Evolutiva, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Iliana Noemi Quiroz-Serrano
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Luz Elena Vidales-Rodríguez
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
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Tanwir K, Shahid M, Abbas S, Ali Q, Akram MS, Chaudhary HJ, Javed MT. Deciphering distinct root exudation, ionomics, and physio-biochemical attributes of Serratia marcescens CP-13 inoculated differentially Cd tolerant Zea mays cultivars. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:71632-71649. [PMID: 35599287 DOI: 10.1007/s11356-022-20945-0] [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: 02/23/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) being a non-essential, mobile, and toxic heavy metal, negatively affects the plant growth and physiology. Current work investigated the impact of Serratia marcescens CP-13 inoculation on root organic acids and nutrient exudates of two maize cultivars varying in Cd tolerance under induced Cd toxicity. Seedlings of Cd-sensitive (Sahiwal-2002) and Cd-tolerant (MMRI-Yellow) cultivars were grown either inoculated or non-inoculated with CP-13 in Petri plates having various Cd stress levels (0, 6, 12, 18, 24, 30 μM). Seedlings were transferred to rhizoboxes for the collection of root exudates and analysis of physio-biochemical traits. Both maize cultivars exuded higher organic acids and nutrient exudates under non-inoculated conditions as compared to inoculated ones. Non-inoculated tolerant cultivar exhibited higher nutrient accumulation, biomass, antioxidants, total chlorophyll, Cd release meanwhile reduced Cd uptake, lipid peroxidation, exudation of organic acids, and nutrients than the sensitive one. However, under CP-13 inoculation, Cd sensitive cultivar exhibited less exudation of organic acids (citric acid, acetic acid, malic acid, glutamic acid, formic acid, succinic acid, and oxalic acid), nutrients mobilization (K, Na, Zn, Ca, and Mg), total chlorophyll, antioxidants (APX, SOD, POD), total soluble sugar, diminished MDA, and Cd uptake. The significant reduction in release of root exudates by both cultivars was likely due to the plant growth promoting traits of CP-13 which confer Cd tolerance. The maximum release of rhizospheric root exudates were documented at 30 μM applied Cd stress. Therefore, the Serratia sp. CP-13 was proposed as a potential inoculant for bioremediation of Cd together with maize cultivars.
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Affiliation(s)
- Kashif Tanwir
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad, 38000, Pakistan
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
| | - Saghir Abbas
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad, 38000, Pakistan
| | - Qasim Ali
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad, 38000, Pakistan
| | - Muhammad Sohail Akram
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad, 38000, Pakistan
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Tariq Javed
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad, 38000, Pakistan.
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11
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Zhu G, Xie L, Tan W, Ma C, Wei Y. Cd2+ Tolerance and Removal Mechanisms of Serratia marcescens KMR-3. J Biotechnol 2022; 359:65-74. [DOI: 10.1016/j.jbiotec.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/30/2022]
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12
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Liu H, Chen GH, Sun JJ, Chen S, Fang Y, Ren JH. Isolation, Characterization, and Tea Growth-Promoting Analysis of JW-CZ2, a Bacterium With 1-Aminocyclopropane-1-Carboxylic Acid Deaminase Activity Isolated From the Rhizosphere Soils of Tea Plants. Front Microbiol 2022; 13:792876. [PMID: 35295310 PMCID: PMC8918981 DOI: 10.3389/fmicb.2022.792876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/24/2022] [Indexed: 11/23/2022] Open
Abstract
One of the major mechanisms underlying plant growth-promoting rhizobacteria (PGPR) is the lowering of ethylene level in plants by deamination of 1-aminocyclopropane-1-carboxylic acid (ACC) in the environment. In the present study, using ACC as the sole nitrogen source, we screened seven ACC deaminase-producing bacterial strains from rhizosphere soils of tea plants. The strain with the highest ACC deaminase activity was identified as Serratia marcescens strain JW-CZ2. Inoculation of this strain significantly increased shoot height and stem diameter of tea seedlings, displaying significant promotive effects. Besides, S. marcescens strain JW-CZ2 displayed high ACC deaminase activities in wide ranges of ACC concentration, pH, and temperature, suggesting the applicable potential of JW-CZ2 as a biofertilizer. Genome sequencing indicated that clusters of orthologous groups of proteins (COG) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of JW-CZ2 mainly included amino acid transport and metabolism, transcription, carbohydrate transport and metabolism, inorganic ion transport and metabolism, and membrane transport. Moreover, genes in relation to phosphate solubilization, indole acetic acid (IAA) production, and siderophore were observed in the genome of JW-CZ2, and further experimental evidence demonstrated JW-CZ2 could promote solubilization of inorganic phosphate, inhibit growth of pathogenic fungi, and produce IAA and siderophore. These aspects might be major reasons underlying the plant growth-promoting function of JW-CZ2. Overall, this study provides a new S. marcescens strain, which has applicable potential as a promising biofertilizer.
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Affiliation(s)
- Hui Liu
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Wuhu, China
- *Correspondence: Hui Liu,
| | - Guang-Hui Chen
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Wuhu, China
| | - Jing-Jing Sun
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Wuhu, China
| | - Shu Chen
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Wuhu, China
| | - Yong Fang
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Jia-Hong Ren
- Department of Life Sciences, Changzhi University, Changzhi, China
- Jia-Hong Ren,
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Li Y, Guo L, Häggblom MM, Yang R, Li M, Sun X, Chen Z, Li F, Su X, Yan G, Xiao E, Zhang H, Sun W. Serratia spp. Are Responsible for Nitrogen Fixation Fueled by As(III) Oxidation, a Novel Biogeochemical Process Identified in Mine Tailings. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2033-2043. [PMID: 35006678 DOI: 10.1021/acs.est.1c06857] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biological nitrogen fixation (BNF) has important environmental implications in tailings by providing bioavailable nitrogen to these habitats and sustaining ecosystem functions. Previously, chemolithotrophic diazotrophs that dominate in mine tailings were shown to use reduced sulfur (S) as the electron donor. Tailings often contain high concentrations of As(III) that might function as an alternative electron donor to fuel BNF. Here, we tested this hypothesis and report on BNF fueled by As(III) oxidation as a novel biogeochemical process in addition to BNF fueled by S. Arsenic (As)-dependent BNF was detected in cultures inoculated from As-rich tailing samples derived from the Xikuangshan mining area in China, as suggested by nitrogenase activity assays, quantitative polymerase chain reaction, and 15N2 enrichment incubations. As-dependent BNF was also active in eight other As-contaminated tailings and soils, suggesting that the potential for As-dependent BNF may be widespread in As-rich habitats. DNA-stable isotope probing identified Serratia spp. as the bacteria responsible for As-dependent BNF. Metagenomic binning indicated that the essential genes for As-dependent BNF [i.e., nitrogen fixation, As(III) oxidation, and carbon fixation] were present in Serratia-associated metagenome-assembled genomes. Over 20 Serratia genomes obtained from NCBI also contained essential genes for both As(III) oxidation and BNF (i.e., aioA and nifH), suggesting that As-dependent BNF may be a widespread metabolic trait in Serratia spp.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Lifang Guo
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick New Jersey 08901, United States
| | - Rui Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark New Jersey 07102, United States
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Xianfa Su
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, P. R. China
| | - Geng Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Enzong Xiao
- Innovation Center and Key Laboratory of Waters Safety & Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, P.R. China
| | - Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Phytoremediation of Cadmium Contaminated Soil Using Sesbania sesban L. in Association with Bacillus anthracis PM21: A Biochemical Analysis. SUSTAINABILITY 2021. [DOI: 10.3390/su132413529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sustainable food production to feed nine to 10 billion people by 2050 is one of the greatest challenges we face in the 21st century. Due to anthropogenic activities, cadmium (Cd) contamination is ubiquitous with deleterious effects on plant and soil microbiota. In the current study, the phytoremediation potential of Sesbania sesban L. was investigated in Cd-spiked soil inoculated with Bacillus anthracis PM21. The Cd-spiked soil drastically reduced important plant attributes; however, inoculation of B. anthracis PM21 significantly (p ≤ 0.05) enhanced root length (17.21%), shoot length (15.35%), fresh weight (37.02%), dry weight (28.37%), chlorophyll a (52.79%), chlorophyll b (48.38%), and total chlorophyll contents (17.65%) at the Cd stress level of 200 mg/kg as compared to the respective control. In addition, bacterial inoculation improved superoxide dismutase (11.98%), peroxidase (12.16%), catalase (25.26%), and relative water content (16.66%) whereas it reduced proline content (16.37%), malondialdehyde content (12.67%), and electrolyte leakage (12.5%). Inoculated plants showed significantly (p ≤ 0.05) higher Cd concentration in the S. sesban root (118.6 mg/kg) and shoot (73.4 mg/kg) with a translocation (0.61) and bioconcentration factor (0.36), at 200 mg/kg Cd. Surface characterization of bacteria through Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) predicted the involvement of various functional groups and cell surface morphology in the adsorption of Cd ions. Amplification of the CzcD gene in strain PM21, improved antioxidant activities, and the membrane stability of inoculated S. sesban plants conferred Cd tolerance of strain PM21. In addition, the evaluated bacterial strain B. anthracis PM21 revealed significant plant growth-promoting potential in S. sesban; thus, it can be an effective candidate for phyto-remediation of Cd-polluted soil.
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Friedrich I, Bodenberger B, Neubauer H, Hertel R, Daniel R. Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog's lettuce (Groenlandia densa). PLoS One 2021; 16:e0259673. [PMID: 34748577 PMCID: PMC8575298 DOI: 10.1371/journal.pone.0259673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Serratia marcescens is a species that belongs to the family of Yersiniaceae. This family comprises taxa representing opportunistic human- and phytopathogens but also plant growth-promoting rhizobacteria (PGPR). This study describes a novel Gram-negative strain (LVF3R) of the species Serratia marcescens. The strain was characterized genomically, morphologically, and physiologically. In addition, the potential of the isolate to act as a host strain to assess the diversity of Serratia associated phages in environmental samples was explored. Average nucleotide identity analysis revealed that LVF3R belongs to the species Serratia marcescens. In silico analysis and ProphageSeq data resulted in the identification of one prophage, which is capable of viral particle formation. Electron microscopy showed cells of a rod-shaped, flagellated morphotype. The cells revealed a length and width of 1-1.6 μm and 0.8 μm, respectively. LVF3R showed optimal growth at 30 C and in the presence of up to 2% (w/v) NaCl. It exhibited resistances to ampicillin, erythromycin, oxacillin, oxytetracycline, rifampicin, tetracycline, and vancomycin. Genome data indicate that strain S. marcescens LVF3R is a potential PGPR strain. It harbors genes coding for indole acetic acid (IAA) biosynthesis, siderophore production, plant polymer degradation enzymes, acetoin synthesis, flagellar proteins, type IV secretion system, chemotaxis, phosphorous solubilization, and biofilm formation.
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Affiliation(s)
- Ines Friedrich
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Bernhard Bodenberger
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Hannes Neubauer
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Robert Hertel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
- FG Synthetic Microbiology, Institute of Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
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16
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Renoz F, Foray V, Ambroise J, Baa-Puyoulet P, Bearzatto B, Mendez GL, Grigorescu AS, Mahillon J, Mardulyn P, Gala JL, Calevro F, Hance T. At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica. Front Cell Infect Microbiol 2021; 11:660007. [PMID: 34268133 PMCID: PMC8275996 DOI: 10.3389/fcimb.2021.660007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/14/2021] [Indexed: 01/10/2023] Open
Abstract
Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial associates of insects that are at the gateway to a host-dependent lifestyle.
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Affiliation(s)
- François Renoz
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Vincent Foray
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
- Institut de Recherche sur la Biologie de l’insecte, UMR 7261, CNRS, Université de Tours, Tours, France
| | - Jérôme Ambroise
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | | | - Bertrand Bearzatto
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Gipsi Lima Mendez
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Luc Gala
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2i, UMR203, F-69621, Villeurbanne, France
| | - Thierry Hance
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
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17
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Diamandas A, Razon MR, Ramirez-Arcos S, Brassinga AKC. The Virulence of S. marcescens Strains Isolated From Contaminated Blood Products Is Divergent in the C. elegans Infection Model. Front Genet 2021; 12:667062. [PMID: 34178032 PMCID: PMC8222908 DOI: 10.3389/fgene.2021.667062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
Bacterial contamination of platelet concentrates (PCs) can occur during blood donation or PC processing, necessitating routine screening to identify contaminated products in efforts to prevent adverse transfusion reactions in recipient patients. Serratia marcescens is a common bacterial contaminant, and its resilient nature coupled with genetic promiscuity imbue this environmental bacterium with resistance to disinfectants and antibiotics enhancing bacterial virulence. In this study, we aim to understand adaptive survival mechanisms through genetic characterization of two S. marcescens strains, CBS11 and CBS12, isolated from PCs by Canadian Blood Services. Genomic analyses of the two strains indicated that CBS11 has one chromosome and one plasmid (pAM01), whereas CBS12 has no plasmids. Phylogenetic analyses show that CBS11 and CBS12 are non-clonal strains, with CBS11 clustering closely with clinical strain CAV1492 and less so with environmental strain PWN146, and CBS12 clustering with a clinical strain AR_0027. Interestingly, pAM01 was most closely related to PWN146p1, a plasmid found in S. marcescens PWN146 strain associated with pinewood nematode Bursaphelenchus xylophilus. Lastly, the genomic diversity of CBS11 and CBS12 was not reflected in the antibiotic resistance profiles as they were remarkably similar to one another, but was reflected in the virulence phenotypes assessed in the Caenorhabditis elegans nematode infection model, with CBS11 being more virulent then CBS12. Taken together, we suggest that S. marcescens environmental isolates that feature evolutionary diverse genomics are better equipped to adapt and thrive in varied environments, such as that of PCs, and therefore is as much of a concern as multi-drug resistance for human infection potential.
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Affiliation(s)
- Alexander Diamandas
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
| | - Mikhail R Razon
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
| | - Sandra Ramirez-Arcos
- Centre for Innovation, Canadian Blood Services, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Ann Karen C Brassinga
- Department of Microbiology, Faculty of Science, University of Manitoba, Winnipeg, MB, Canada
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18
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Bacterial Endophytes: The Hidden Actor in Plant Immune Responses against Biotic Stress. PLANTS 2021; 10:plants10051012. [PMID: 34069509 PMCID: PMC8161118 DOI: 10.3390/plants10051012] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Bacterial endophytes constitute an essential part of the plant microbiome and are described to promote plant health by different mechanisms. The close interaction with the host leads to important changes in the physiology of the plant. Although beneficial bacteria use the same entrance strategies as bacterial pathogens to colonize and enter the inner plant tissues, the host develops strategies to select and allow the entrance to specific genera of bacteria. In addition, endophytes may modify their own genome to adapt or avoid the defense machinery of the host. The present review gives an overview about bacterial endophytes inhabiting the phytosphere, their diversity, and the interaction with the host. Direct and indirect defenses promoted by the plant-endophyte symbiont exert an important role in controlling plant defenses against different stresses, and here, more specifically, is discussed the role against biotic stress. Defenses that should be considered are the emission of volatiles or antibiotic compounds, but also the induction of basal defenses and boosting plant immunity by priming defenses. The primed defenses may encompass pathogenesis-related protein genes (PR family), antioxidant enzymes, or changes in the secondary metabolism.
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19
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Kumar R, Borker SS, Thakur A, Thapa P, Kumar S, Mukhia S, Anu K, Bhattacharya A, Kumar S. Physiological and genomic evidence supports the role of Serratia quinivorans PKL:12 as a biopriming agent for the biohardening of micropropagated Picrorhiza kurroa plantlets in cold regions. Genomics 2021; 113:1448-1457. [PMID: 33744342 DOI: 10.1016/j.ygeno.2021.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/26/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
The medicinal herb, Picrorhiza kurroa Royle ex Benth has become endangered because of indiscriminate over-harvesting. Although micropropagation has been attempted for mass propagation of the plant, survival of in vitro plantlets under green house/open field poses a major challenge. Biopriming of micropropagated plantlets with plant growth-promoting rhizobacteria (PGPR) are among the successful methods to combat this problem. Serratia quinivorans PKL:12 was the best-characterized PGPR from rhizospheric soil of P. kurroa as it increased the vegetative growth and survival of the micropropagated plantlets most effectively. Complete genome (5.29 Mb) predicted genes encoding proteins for cold adaptation and plant growth-promoting traits in PKL:12. Antibiotic and biosynthetic gene cluster prediction supported PKL:12 as a potential biocontrol agent. Comparative genomics revealed 226 unique genes with few genes associated with plant growth-promoting potential. Physiological and genomic evidence supports S. quinivorans PKL:12 as a potential agent for bio-hardening of micropropagated P. kurroa plantlets in cold regions.
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Affiliation(s)
- Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh 201 002, India..
| | - Shruti Sinai Borker
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh 201 002, India
| | - Aman Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh 201 002, India
| | - Pooja Thapa
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Sanjeet Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Srijana Mukhia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Amita Bhattacharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
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20
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Abdullahi S, Haris H, Zarkasi KZ, Amir HG. Complete genome sequence of plant growth-promoting and heavy metal-tolerant Enterobacter tabaci 4M9 (CCB-MBL 5004). J Basic Microbiol 2021; 61:293-304. [PMID: 33491813 DOI: 10.1002/jobm.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/30/2020] [Accepted: 01/10/2021] [Indexed: 11/10/2022]
Abstract
Enterobacter tabaci 4M9 (CCB-MBL 5004) was reported to have plant growth-promoting and heavy metal tolerance traits. It was able to tolerate more than 300 mg/L Cd, 600 mg/L As, and 500 mg/L Pb and still maintained the ability to produce plant growth-promoting substances under metal stress conditions. To explore the genetic basis of these beneficial traits, the complete genome sequencing of 4M9 was carried out using Pacific Bioscience (PacBio) sequencing technology. The complete genome consisted of one chromosome of 4,654,430 bp with a GC content of 54.6% and one plasmid of 51,135 bp with a GC content of 49.4%. Genome annotation revealed several genes involved in plant growth-promoting traits, including the production of siderophore, indole acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase; solubilization of phosphate and potassium; and nitrogen metabolism. Similarly, genes involved in heavy metals (As, Co, Zn, Cu, Mn, Se, Cd, and Fe) tolerance were detected. These support its potential as a heavy metal-tolerant plant growth-promoting bacterium and a good genetic resource that can be employed to improve phytoremediation efficiency of heavy metal-contaminated soil via biotechnological techniques. This, to the best of our knowledge, is the first report on the complete genome sequence of heavy metal-tolerant plant growth-promoting E. tabaci.
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Affiliation(s)
- Saidu Abdullahi
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia.,Department of Botany, Ahmadu Bello University, Zaria, Nigeria
| | - Hazzeman Haris
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia
| | - Kamarul Z Zarkasi
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia
| | - Hamzah G Amir
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia
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21
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Insights into the individual evolutionary origins of Yersinia virulence factor effector proteins. Plasmid 2021; 114:102562. [PMID: 33497686 DOI: 10.1016/j.plasmid.2021.102562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/31/2020] [Accepted: 01/14/2021] [Indexed: 11/22/2022]
Abstract
Pathogenic Yersinia bacteria, including Y. pseudotubuclosis Y. enterocolitica, and Y. pestis, contain the mosaic plasmid pYV that encodes for, among other things, a number of proteinaceous virulence factors. While the evolutionary histories of many of the biovars and strains of pathogenic Yersinia species are well documented, the origins of many of the individual virulence factors have not been comprehensively examined. Here, the evolutionary origins of the genes coding for a set of Yersinia outer protein (Yop) virulence factors were investigated through phylogenetic reconstruction and subsequence analysis. It was found that many of these genes had only a few sequenced homologs and none of the resolved phylogenies recovered the same relationships as was resolved from chromosomal analyses. Many of the evolutionary relationships differ greatly among genes on the plasmid, and variation is also found across different domains of the same gene, which provides evidence of the mosaic nature of the plasmid as well as multiple genes on the plasmid. This mosaic aspect also relates to patterns of selection, which vary among the studied domains.
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22
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Tanwir K, Javed MT, Abbas S, Shahid M, Akram MS, Chaudhary HJ, Iqbal M. Serratia sp. CP-13 alleviates Cd toxicity by morpho-physio-biochemical improvements, antioxidative potential and diminished Cd uptake in Zea mays L. cultivars differing in Cd tolerance. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111584. [PMID: 33396107 DOI: 10.1016/j.ecoenv.2020.111584] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/11/2020] [Accepted: 10/27/2020] [Indexed: 05/13/2023]
Abstract
Cadmium (Cd) is highly toxic for plant metabolic processes even in low concentration due to higher retention rates, longer half-life and non-biodegradable nature. The current study was designed to assess the bioremediation potential of Cd tolerant PGPR, Serratia sp. CP-13 together with two differentially Cd tolerant maize cultivars (MMRI-Yellow, Sahiwal-2002) selected amongst ten cultivars after screening. The maize cultivars were grown under different Cd treatments (0, 6, 12, 18, 24, 30 µM) in Petri plates both with and without Serratia sp. CP-13 inoculation. Treated plants were analyzed for their biomass accumulation, chlorophylls, carotenoids, proline, anthocyanin, protein, malondialdehyde (MDA), H2O2 as well as for antioxidants (POD, SOD, CAT) and mineral elements (Ca, Mg, Zn, K, Fe, Na, Cd). The maize cultivar MMRI-Yellow (tolerant) and Sahiwal-2002 (sensitive) exhibited significant reduction in leaf area, nutrient contents, plant biomass, activity of antioxidants, total proteins, photosynthetic pigments as well as flavonoids with increased production of H2O2, proline, MDA and relative membrane permeability (RMP) under Cd stress. However, this reduction was cultivar specific and recorded higher in cv. Sahiwal-2002 as compared to MMRI-Yellow. Application of Serratia sp. CP-13 significantly augmented plant biomass, photosynthetic pigments, antioxidative machinery, as well as flavonoids and proline while diminishing H2O2, RMP MDA production even under Cd stress in studied cultivars. Furthermore, CP-13 inoculation assisted the Cd stressed plants to sustain an optimal level of essential nutrients (Ca, Mg, Zn, K, Fe) except for Na and Cd which responded antagonistically. It was inferred that both inoculated maize cultivars exhibited better health and metabolism but substantial Cd tolerance was acquired by the sensitive cv. Sahiwal-2002 than the tolerant cv. MMRI-Yellow under applied Cd regimes. Furthermore, studied maize cultivars depicted maximum Cd tolerance in order of 30 < 24 < 18 < 12 < 6 < 0 µM Cd treatments under Serratia sp. CP-13 inoculation. Findings of current work highlighted the importance of Serratia sp. CP-13 and its inoculation impact on morpho-physio-biochemical attributes of maize growth under Cd dominant environment, which is likely an addition towards efficient approaches for bacterially-assisted Cd bioremediation and minimal Cd retention in edible plant parts.
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Affiliation(s)
- Kashif Tanwir
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Tariq Javed
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan.
| | - Saghir Abbas
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Sohail Akram
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Iqbal
- Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan
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Hu X, Wei X, Ling J, Chen J. Cobalt: An Essential Micronutrient for Plant Growth? FRONTIERS IN PLANT SCIENCE 2021; 12:768523. [PMID: 34868165 PMCID: PMC8635114 DOI: 10.3389/fpls.2021.768523] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/29/2021] [Indexed: 05/19/2023]
Abstract
Cobalt is a transition metal located in the fourth row of the periodic table and is a neighbor of iron and nickel. It has been considered an essential element for prokaryotes, human beings, and other mammals, but its essentiality for plants remains obscure. In this article, we proposed that cobalt (Co) is a potentially essential micronutrient of plants. Co is essential for the growth of many lower plants, such as marine algal species including diatoms, chrysophytes, and dinoflagellates, as well as for higher plants in the family Fabaceae or Leguminosae. The essentiality to leguminous plants is attributed to its role in nitrogen (N) fixation by symbiotic microbes, primarily rhizobia. Co is an integral component of cobalamin or vitamin B12, which is required by several enzymes involved in N2 fixation. In addition to symbiosis, a group of N2 fixing bacteria known as diazotrophs is able to situate in plant tissue as endophytes or closely associated with roots of plants including economically important crops, such as barley, corn, rice, sugarcane, and wheat. Their action in N2 fixation provides crops with the macronutrient of N. Co is a component of several enzymes and proteins, participating in plant metabolism. Plants may exhibit Co deficiency if there is a severe limitation in Co supply. Conversely, Co is toxic to plants at higher concentrations. High levels of Co result in pale-colored leaves, discolored veins, and the loss of leaves and can also cause iron deficiency in plants. It is anticipated that with the advance of omics, Co as a constitute of enzymes and proteins and its specific role in plant metabolism will be exclusively revealed. The confirmation of Co as an essential micronutrient will enrich our understanding of plant mineral nutrition and improve our practice in crop production.
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Affiliation(s)
- Xiu Hu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiangying Wei
- Institute of Oceanography, Minjiang University, Fuzhou, China
- Xiangying Wei
| | - Jie Ling
- He Xiangning College of Art and Design, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jianjun Chen
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL, United States
- *Correspondence: Jianjun Chen
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24
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Obi LU, Tekere M, Roopnarain A, Sanko T, Maguvu TE, Bezuidenhout CC, Adeleke RA. Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain. ACTA ACUST UNITED AC 2020; 28:e00542. [PMID: 33102161 PMCID: PMC7569290 DOI: 10.1016/j.btre.2020.e00542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/27/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Serratia marcescens 39_H1 could enhance the hydrolysis of lignocellulosic biomass. Serratia marcescens 39_H1 is a plant growth promoting organism. Genome analysis showed diverse potential biotechnological application of organism. This is an original report on the hydrolytic and acidogenic attributes ofSerratia marcescens 39_H1 for biogas production.
Here, we report a high quality annotated draft genome of Serratia marcescens 39_H1, a Gram-negative facultative anaerobe that was isolated from an anaerobic digester. The strain exhibited hydrolytic/acidogenic properties by significantly improving methane production when used as a single isolate inoculum during anaerobic digestion of water hyacinth and cow dung. The total genome size of the isolate was 5,106,712 bp which corresponds to an N50 of 267,528 and G + C content of 59.7 %. Genome annotation with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) predicted a total of 4,908 genes of which 4,755 were protein coding genes; there were no plasmids detected. A number of genes associated with hydrolytic/acidogenic activities as well as other metabolic activities were identified and discussed.
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Affiliation(s)
- Linda U Obi
- Department of Environmental Sciences, University of South Africa, Johannesburg, South Africa.,Microbiology and Environmental Biotechnology Research Group, Institute for Soil, Climate and Water, Agricultural Research Council, Arcadia, 0083, Pretoria, South Africa
| | - Memory Tekere
- Department of Environmental Sciences, University of South Africa, Johannesburg, South Africa
| | - Ashira Roopnarain
- Microbiology and Environmental Biotechnology Research Group, Institute for Soil, Climate and Water, Agricultural Research Council, Arcadia, 0083, Pretoria, South Africa
| | - Tomasz Sanko
- Unit for Environment Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Tawanda E Maguvu
- Unit for Environment Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Cornelius C Bezuidenhout
- Unit for Environment Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Rasheed A Adeleke
- Microbiology and Environmental Biotechnology Research Group, Institute for Soil, Climate and Water, Agricultural Research Council, Arcadia, 0083, Pretoria, South Africa.,Unit for Environment Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
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25
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Coal-Degrading Bacteria Display Characteristics Typical of Plant Growth Promoting Rhizobacteria. Processes (Basel) 2020. [DOI: 10.3390/pr8091111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Coal mining produces large quantities of discard that is stockpiled in large dumps. This stockpiled material, termed coal discard, poses an environmental threat emphasising the need for appropriate bioremediation. Here, metagenomic analysis of the 16S rRNA from ten coal-degrading strains previously isolated from coal slurry from discard dumps and from the rhizosphere of diesel-contaminated sites was used to establish genetic relatedness to known plant growth-promoting (PGP) bacteria in the NCBI database. Measurement of indole and ammonium production and solubilisation of P and K were used to screen bacteria for PGP characteristics. BLAST analysis revealed ≥ 99% homology of six isolates with reference PGP strains of Bacillus, Escherichia, Citrobacter, Serratia, Exiguobacterium and Microbacterium, while two strains showed 94% and 91% homology with Proteus. The most competent PGP strains were Proteus strain ECCN 20b, Proteus strain ECCN 23b and Serratia strain ECCN 24b isolated from diesel-contaminated soil. In response to L-trp supplementation, the concentration of indolic compounds (measured as indole-3-acetic acid) increased. Production of ammonium and solubilisation of insoluble P by these strains was also apparent. Only Serratia strain ECCN 24b was capable of solubilising insoluble K. Production of indoles increased following exposure to increasing aliquots of coal discard, suggesting no negative effect of this material on indole production by these coal-degrading bacterial isolates and that these bacteria may indeed possess PGP characteristics.
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26
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Reyes-Hernández SJ, Zamora-Briseño JA, Cerqueda-García D, Castaño E, Rodríguez-Zapata LC. Alterations in the sap-associated microbiota of Carica papaya in response to drought stress. Symbiosis 2020. [DOI: 10.1007/s13199-020-00682-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rhizosphere assisted biodegradation of benzo(a)pyrene by cadmium resistant plant-probiotic Serratia marcescens S2I7, and its genomic traits. Sci Rep 2020; 10:5279. [PMID: 32210346 PMCID: PMC7093395 DOI: 10.1038/s41598-020-62285-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/12/2020] [Indexed: 12/02/2022] Open
Abstract
Melia azedarach-rhizosphere mediated degradation of benzo(a)pyrene (BaP), in the presence of cadmium (Cd) was studied, using efficient rhizobacterial isolate. Serratia marcescens S2I7, isolated from the petroleum-contaminated site, was able to tolerate up to 3.25 mM Cd. In the presence of Cd, the isolate S2I7 exhibited an increase in the activity of stress-responsive enzyme, glutathione-S-transferase. Gas Chromatography-Mass spectroscopy analysis revealed up to 59% in -vitro degradation of BaP after 21 days, while in the presence of Cd, the degradation was decreased by 14%. The bacterial isolate showed excellent plant growth-promoting attributes and could enhance the growth of host plant in Cd contaminated soil. The 52,41,555 bp genome of isolate S. marcescens S2I7 was sequenced, assembled and annotated into 4694 genes. Among these, 89 genes were identified for the metabolism of aromatic compounds and 172 genes for metal resistance, including the efflux pump system. A 2 MB segment of the genome was identified to contain operons for protocatechuate degradation, catechol degradation, benzoate degradation, and an IclR type regulatory protein pcaR, reported to be involved in the regulation of protocatechuate degradation. A pot trial was performed to validate the ability of S2I7 for rhizodegradation of BaP when applied through Melia azedarach rhizosphere. The rhizodegradation of BaP was significantly higher when augmented with S2I7 (85%) than degradation in bulk soil (68%), but decreased in the presence of Cd (71%).
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28
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Fang Q, Maglangit F, Mugat M, Urwald C, Kyeremeh K, Deng H. Targeted Isolation of Indole Alkaloids from Streptomyces sp. CT37. Molecules 2020; 25:E1108. [PMID: 32131464 PMCID: PMC7179168 DOI: 10.3390/molecules25051108] [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: 02/02/2020] [Revised: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 12/22/2022] Open
Abstract
Four compounds (1-4) were isolated from the extracts of Streptomyces sp. CT37 using bioassay in conjunction with mass spectrometric molecular networking (MN) driven isolation. Their complete structures were established by high-resolution electrospray ionization mass spectrometry (HR-ESIMS), and 1D and 2D nuclear magnetic resonance (NMR) data. Legonimide 1 was identified as a new alkaloid containing a rare linear imide motif in its structure, while compounds 2-4 were already known and their structures were elucidated as 1H-indole-3-carbaldehyde, actinopolymorphol B, (2R,3R)-1-phenylbutane-2,3-diol, respectively. The biosynthetic pathways of 1-4 were proposed based on the reported biogenesis of indole alkaloids in literature. Bioactivity tests for 1 and 2 revealed moderate growth inhibition activity against Candida albicans ATCC 10231 with MIC95 values of 21.54 µg/mL and 11.47 µg/mL, respectively.
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Affiliation(s)
- Qing Fang
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK; (Q.F.); (F.M.)
| | - Fleurdeliz Maglangit
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK; (Q.F.); (F.M.)
- Department of Biology and Environmental Science, College of Science, University of the Philippines Cebu, Lahug, Cebu City 6000, Philippines
| | - Morgane Mugat
- ENSAIA, 2 avenue de la forêt de Haye, 54505 vandœuvre lès Nancy, France; (M.M.); (C.U.)
| | - Caroline Urwald
- ENSAIA, 2 avenue de la forêt de Haye, 54505 vandœuvre lès Nancy, France; (M.M.); (C.U.)
| | - Kwaku Kyeremeh
- Department of Chemistry, University of Ghana, P.O. Box LG56 Legon-Accra, Ghana;
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK; (Q.F.); (F.M.)
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Adhikari A, Lee KE, Khan MA, Kang SM, Adhikari B, Imran M, Jan R, Lee KMKAIJ, Lee IJ. Effect of Silicate and Phosphate Solubilizing Rhizobacterium Enterobacter ludwigii GAK2 on Oryza sativa L. under Cadmium Stress. J Microbiol Biotechnol 2020; 30:118-126. [PMID: 31650772 PMCID: PMC9728408 DOI: 10.4014/jmb.1906.06010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Silicon and phosphorus are elements that are beneficial for plant growth. Despite the abundant availability of silicate and phosphate in the Earth's crust, crop nutritional requirements for silicon and phosphorus are normally met through the application of fertilizer. However, fertilizers are one of the major causes of heavy metal pollution. In our study, we aimed to assess silicate and phosphate solubilization by the bacteria Enterobacter ludwigii GAK2, in the presence and absence of phosphate [Ca3(PO4)2] or silicate (Mg2O8Si3), to counteract cadmium stress in rice (Oryza sativa L). Our results showed that the GAK2-treated rice plants, grown in soil amended with phosphate [Ca3(PO4)2] or silicate (Mg2O8Si3), had significantly reduced cadmium content, and enhanced plant growth promoting characteristics including fresh shoot and root weight, plant height, and chlorophyll content. These plants showed significant downregulation of the cadmium transporter gene, OsHMA2, and upregulation of the silicon carrier gene, OsLsi1. Moreover, jasmonic acid levels were significantly reduced in the GAK2-inoculated plants, and this was further supported by the downregulation of the jasmonic acid related gene, OsJAZ1. These results indicate that Enterobacter ludwigii GAK2 can be used as a silicon and phosphorus bio-fertilizer, which solubilizes insoluble silicate and phosphate, and mitigates heavy metal toxicity in crops.
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Affiliation(s)
- Arjun Adhikari
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ko-Eun Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Muhammad Aaqil Khan
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sang-Mo Kang
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Bishnu Adhikari
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Muhammad Imran
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Rahmatullah Jan
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Min Kim and In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea,Corresponding author Phone: +82-53-950-5708 Fax: +82-53-953-697 E-mail:
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Serratia marcescens BM1 Enhances Cadmium Stress Tolerance and Phytoremediation Potential of Soybean Through Modulation of Osmolytes, Leaf Gas Exchange, Antioxidant Machinery, and Stress-Responsive Genes Expression. Antioxidants (Basel) 2020; 9:antiox9010043. [PMID: 31947957 PMCID: PMC7023057 DOI: 10.3390/antiox9010043] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 12/23/2019] [Accepted: 12/31/2019] [Indexed: 01/24/2023] Open
Abstract
The heavy metal contamination in plant-soil environment has increased manifold recently. In order to reduce the harmful effects of metal stress in plants, the application of beneficial soil microbes is gaining much attention. In the present research, the role of Serratia marcescens BM1 in enhancing cadmium (Cd) stress tolerance and phytoremediation potential of soybean plants, was investigated. Exposure of soybean plants to two Cd doses (150 and 300 µM) significantly reduced plant growth, biomass, gas exchange attributes, nutrients uptake, antioxidant capacity, and the contents of chlorophyll, total phenolics, flavonoids, soluble sugars, and proteins. Additionally, Cd induced the stress levels of Cd, proline, glycine betaine, hydrogen peroxide, malondialdehyde, antioxidant enzymes (i.e., catalase, CAT; ascorbate peroxidase, APX; superoxide dismutase, SOD; peroxidise, POD), and the expression of stress-related genes (i.e., APX, CAT, Fe-SOD, POD, CHI, CHS, PHD2, VSO, NR, and P5CS) in soybean leaves. On the other hand, inoculation of Cd-stressed soybean plants with Serratia marcescens BM1 significantly enhanced the plant growth, biomass, gas exchange attributes, nutrients uptake, antioxidant capacity, and the contents of chlorophyll, total phenolics, flavonoids, soluble sugars, and proteins. Moreover, Serratia marcescens BM1 inoculation reduced the levels of cadmium and oxidative stress markers, but significantly induced the activities of antioxidant enzymes and the levels of osmolytes and stress-related genes expression in Cd-stressed plants. The application of 300 µM CdCl2 and Serratia marcescens triggered the highest expression levels of stress-related genes. Overall, this study suggests that inoculation of soybean plants with Serratia marcescens BM1 promotes phytoremediation potential and Cd stress tolerance by modulating the photosynthetic attributes, osmolytes biosynthesis, antioxidants machinery, and the expression of stress-related genes.
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Caneschi WL, Sanchez AB, Felestrino ÉB, Lemes CGDC, Cordeiro IF, Fonseca NP, Villa MM, Vieira IT, Moraes LÂG, Assis RDAB, do Carmo FF, Kamino LHY, Silva RS, Ferro JA, Ferro MIT, Ferreira RM, Santos VL, Silva UDCM, Almeida NF, Varani ADM, Garcia CCM, Setubal JC, Moreira LM. Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environments. Sci Rep 2019; 9:18006. [PMID: 31784663 PMCID: PMC6884506 DOI: 10.1038/s41598-019-54601-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/31/2019] [Indexed: 12/02/2022] Open
Abstract
Serratia liquefaciens strain FG3 (SlFG3), isolated from the flower of Stachytarpheta glabra in the Brazilian ferruginous fields, has distinctive genomic, adaptive, and biotechnological potential. Herein, using a combination of genomics and molecular approaches, we unlocked the evolution of the adaptive traits acquired by S1FG3, which exhibits the second largest chromosome containing the largest conjugative plasmids described for Serratia. Comparative analysis revealed the presence of 18 genomic islands and 311 unique protein families involved in distinct adaptive features. S1FG3 has a diversified repertoire of genes associated with Nonribosomal peptides (NRPs/PKS), a complete and functional cluster related to cellulose synthesis, and an extensive and functional repertoire of oxidative metabolism genes. In addition, S1FG3 possesses a complete pathway related to protocatecuate and chloroaromatic degradation, and a complete repertoire of genes related to DNA repair and protection that includes mechanisms related to UV light tolerance, redox process resistance, and a laterally acquired capacity to protect DNA using phosphorothioation. These findings summarize that SlFG3 is well-adapted to different biotic and abiotic stress situations imposed by extreme conditions associated with ferruginous fields, unlocking the impact of the lateral gene transfer to adjust the genome for extreme environments, and providing insight into the evolution of prokaryotes.
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Affiliation(s)
- Washington Luiz Caneschi
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Angélica Bianchini Sanchez
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Érica Barbosa Felestrino
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | | | - Isabella Ferreira Cordeiro
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Natasha Peixoto Fonseca
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Morghana Marina Villa
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Izadora Tabuso Vieira
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Lauro Ângelo Gonçalves Moraes
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | | | | | | | - Robson Soares Silva
- Faculdade de Computação (FACOM), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Jesus Aparecido Ferro
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, SP, Brazil
| | - Maria Inês Tiraboschi Ferro
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, SP, Brazil
| | - Rafael Marini Ferreira
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, SP, Brazil
| | - Vera Lúcia Santos
- Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | | | - Nalvo Franco Almeida
- Faculdade de Computação (FACOM), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Alessandro de Mello Varani
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, SP, Brazil
| | - Camila Carrião Machado Garcia
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
- Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas (ICEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica (DB), Instituto de Química (IQ), Universidade de São Paulo (USP), São Paulo, SP, Brazil
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Leandro Marcio Moreira
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil.
- Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas (ICEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil.
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Shahid M, Javed M, Masood S, Akram M, Azeem M, Ali Q, Gilani R, Basit F, Abid A, Lindberg S. Serratiasp.CP‐13 augments the growth of cadmium (Cd)‐stressedLinum usitatissimumL. by limited Cd uptake, enhanced nutrient acquisition and antioxidative potential. J Appl Microbiol 2019; 126:1708-1721. [DOI: 10.1111/jam.14252] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/24/2019] [Accepted: 03/11/2019] [Indexed: 01/21/2023]
Affiliation(s)
- M. Shahid
- Department of Bioinformatics and Biotechnology Government College University Faisalabad Pakistan
| | - M.T. Javed
- Department of Botany Government College University Faisalabad Pakistan
| | - S. Masood
- Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - M.S. Akram
- Department of Botany Government College University Faisalabad Pakistan
| | - M. Azeem
- Department of Botany Government College University Faisalabad Pakistan
| | - Q. Ali
- Department of Botany Government College University Faisalabad Pakistan
| | - R. Gilani
- Department of Bioinformatics and Biotechnology Government College University Faisalabad Pakistan
- Department of Botany Government College University Faisalabad Pakistan
| | - F. Basit
- Department of Bioinformatics and Biotechnology Government College University Faisalabad Pakistan
| | - A. Abid
- Department of Botany Government College University Faisalabad Pakistan
| | - S. Lindberg
- Department of Ecology, Environment and Plant Sciences Stockholm University Stockholm Sweden
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Qin Y, Wang J, Wang F, Shen L, Zhou H, Sun H, Hao K, Song L, Zhou Z, Zhang C, Wu Y, Yang J. Purification and Characterization of a Secretory Alkaline Metalloprotease with Highly Potent Antiviral Activity from Serratia marcescens Strain S3. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3168-3178. [PMID: 30799619 DOI: 10.1021/acs.jafc.8b06909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In this study we report a secretory protein that was purified from Serratia marcescens strain S3 isolated from soil from the tobacco rhizosphere. Subsequent mass spectrometry and annotation characterized the protein as secretory alkaline metalloprotease (SAMP). SAMP plays a crucial role in inhibiting Tobacco mosaic virus (TMV). Transmission electron microscopy (TEM), dynamic light scattering (DLS), confocal microscopy, and microscale thermophoresis (MST) were employed to investigate the anti-TMV mechanism of SAMP. Our results demonstrated that SAMP, as a hydrolytic metal protease, combined and hydrolyzed TMV coat proteins to destroy the virus particles. This study is the first to investigate the antiviral effects of a S. marcescens metalloprotease, and our finding suggests that S. marcescens-S3 may be agronomically useful as a disease-controlling factor active against Tobacco mosaic virus.
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Affiliation(s)
- Yuanxia Qin
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , P. R. China
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Jie Wang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Lili Shen
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Haixiang Zhou
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Hangjun Sun
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Kaiqiang Hao
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Liyun Song
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , P. R. China
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Zhicheng Zhou
- Hunan Tobacco Science Institute , Changsha 410004 , P. R. China
| | - Chaoqun Zhang
- Jiangxi Institute of Tobacco Leaf Science , Nanchang 330025 , P. R. China
| | - Yuanhua Wu
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , P. R. China
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
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Matteoli FP, Passarelli-Araujo H, Reis RJA, da Rocha LO, de Souza EM, Aravind L, Olivares FL, Venancio TM. Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost. BMC Genomics 2018; 19:750. [PMID: 30326830 PMCID: PMC6192313 DOI: 10.1186/s12864-018-5130-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/27/2018] [Indexed: 01/11/2023] Open
Abstract
Background Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil. Results Here we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5 Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria. Conclusions Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture. Electronic supplementary material The online version of this article (10.1186/s12864-018-5130-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Filipe P Matteoli
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Régis Josué A Reis
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Letícia O da Rocha
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Emanuel M de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Fabio L Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil.
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Żur J, Wojcieszyńska D, Hupert-Kocurek K, Marchlewicz A, Guzik U. Paracetamol - toxicity and microbial utilization. Pseudomonas moorei KB4 as a case study for exploring degradation pathway. CHEMOSPHERE 2018; 206:192-202. [PMID: 29751245 DOI: 10.1016/j.chemosphere.2018.04.179] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Paracetamol, a widely used analgesic and antipyretic drug, is currently one of the most emerging pollutants worldwide. Besides its wide prevalence in the literature only several bacterial strains able to degrade this compound have been described. In this study, we isolated six new bacterial strains able to remove paracetamol. The isolated strains were identified as the members of Pseudomonas, Bacillus, Acinetobacter and Sphingomonas genera and characterized phenotypically and biochemically using standard methods. From the isolated strains, Pseudomonas moorei KB4 was able to utilize 50 mg L-1 of paracetamol. As the main degradation products, p-aminophenol and hydroquinone were identified. Based on the measurements of specific activity of acyl amidohydrolase, deaminase and hydroquinone 1,2-dioxygenase and the results of liquid chromatography analyses, we proposed a mechanism of paracetamol degradation by KB4 strain under co-metabolic conditions with glucose. Additionally, toxicity bioassays and the influence of various environmental factors, including pH, temperature, heavy metals at no-observed-effective-concentrations, and the presence of aromatic compounds on the efficiency and mechanism of paracetamol degradation by KB4 strain were determined. This comprehensive study about paracetamol biodegradation will be helpful in designing a treatment systems of wastewaters contaminated with paracetamol.
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Affiliation(s)
- Joanna Żur
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Danuta Wojcieszyńska
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Katarzyna Hupert-Kocurek
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Ariel Marchlewicz
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Urszula Guzik
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
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Mohamed EAH, Farag AG, Youssef SA. Phosphate Solubilization by <i>Bacillus subtilis</i> and <i>Serratia marcescens</i> Isolated from Tomato Plant Rhizosphere. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/jep.2018.93018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Arsène-Ploetze F, Chiboub O, Lièvremont D, Farasin J, Freel KC, Fouteau S, Barbe V. Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:1470-1483. [PMID: 29090447 DOI: 10.1007/s11356-017-0535-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library. In particular, resistance to antibiotics was observed among five clones carrying four different loci originating from CARN5 and CARN2, two genomes reconstructed from the metagenomic data. Among the three CARN2 loci, two carry genes homologous to those previously proposed to be involved in antibiotic resistance. The third CARN2 locus carries a gene encoding a membrane transporter with an unknown function and was found to confer bacterial resistance to rifampicin, gentamycin, and kanamycin. The genome of Thiomonas delicata DSM 16361 and Thiomonas sp. X19 were sequenced in this study. Homologs of genes carried on these three CARN2 loci were found in these genomes, two of these loci were found in genomic islands. Together, these findings confirm that AMD environments contaminated with several toxic metals also constitute habitats for bacteria that function as reservoirs for antibiotic resistance genes.
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Affiliation(s)
- Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France.
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Olfa Chiboub
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Didier Lièvremont
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
- Institut de Chimie de Strasbourg, UMR7177 CNRS-Université de Strasbourg, Strasbourg, France
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Kelle C Freel
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Stephanie Fouteau
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
| | - Valérie Barbe
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
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