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Suphannarot A, Butdee W, Suriyachadkun C, Duangmal K, Mingma R. Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov., two novel actinobacteria isolated from mangrove sediments and leaves of halophyte Sesuvium portulacastrum in Thailand. Int J Syst Evol Microbiol 2024; 74. [PMID: 38805028 DOI: 10.1099/ijsem.0.006401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024] Open
Abstract
A polyphasic approach was used to characterize two novel actinobacterial strains, designated PKS22-38T and LSe1-13T, which were isolated from mangrove soils and leaves of halophyte Sesuvium portulacastrum (L.), respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that they belonged to the genus Gordonia and were most closely related to three validly published species with similarities ranging from 98.6 to 98.1 %. The genomic DNA G+C contents of strains PKS22-38T and LSe1-13T were 67.3 and 67.2 mol%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 93.3 and 54.9 %, respectively, revealing that they are independent species. Meanwhile, the ANI and dDDH values between the two novel strains and closely related type strains were below 80.5 and 24.0 %, respectively. Strains PKS22-38T and LSe1-13T contained C16 : 0, C18 : 1 ω9c and C18 : 0 10-methyl (TBSA) as the major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the main phospholipids. The predominant menaquinone was MK-9(H2). Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strains PKS22-38T and LSe1-13T are considered to represent two novel species within the genus Gordonia, for which the names Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov. are proposed, with strain PKS22-38T (=TBRC 17540T=NBRC 116256T) and strain LSe1-13T (=TBRC 17706T=NBRC 116396T) as the type strains, respectively.
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Affiliation(s)
- Aekasit Suphannarot
- Division of Microbiology, Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
| | - Waranya Butdee
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Chanwit Suriyachadkun
- BIOTEC Culture Collection, Biodiversity and Biotechnological Resource Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Kannika Duangmal
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Ratchanee Mingma
- Division of Microbiology, Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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Liu W, Xing X, Dong Q, Liu X, Li W. Isolation and identification of the alga-symbiotic bacterium Gordonia and characterisation of its exopolysaccharide. Nat Prod Res 2024; 38:523-529. [PMID: 36102747 DOI: 10.1080/14786419.2022.2123477] [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: 05/09/2022] [Accepted: 09/07/2022] [Indexed: 10/14/2022]
Abstract
An exopolysaccharide (EPS)-producing bacterium TD18, isolated from the culture broth of green alga Scenedesmus obliquus, was identified as Gordonia terrae based on the 100% identity of 16S rRNA sequences and designated Gordonia terrae TD18. The results of compositional and structural analyses and physiochemical tests show that (1) the exopolysaccharide produced by G. terrae TD18 (TD18-EPS) is an acidic hetero-polysaccharide with a molecular weight of 23 kDa, consisting of glucose, mannose, galactose and glucuronic acid, and (2) TD18-EPS is of high thermal stability with a degradation temperature of 308 °C, the solution of which is non-Newtonian pseudoplastic fluid exhibiting good emulsifying properties over a wide range of temperatures, pH and NaCl concentrations. Hence, Gordonia terrae TD18 is the first alga-symbiotic Gordonia strain identified thus far, while TD18-EPS is unique in terms of composition and structure, different from the known Gordonia EPS, with excellent physiochemical properties and thus has potential applications in industry.
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Affiliation(s)
- Wang Liu
- Department of Bioengineering, School of Chemical Engineering, Hebei University of Technology, Tianjin, China
| | - Xiangying Xing
- Department of Applied Chemistry, School of Chemical Engineering, Hebei University of Technology, Tianjin, China
| | - Qinglin Dong
- Department of Bioengineering, School of Chemical Engineering, Hebei University of Technology, Tianjin, China
| | - Xiaohang Liu
- Department of Bioengineering, School of Chemical Engineering, Hebei University of Technology, Tianjin, China
| | - Wenna Li
- Department of Bioengineering, School of Chemical Engineering, Hebei University of Technology, Tianjin, China
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Wang H, Guan F, Zhu Y, Pan Y, Liu Q, Liu Q, He W, Gong D, Tian J, Han D. Biofilm formation promoted biodegradation of polyethylene in Gordonia polyisoprenivorans B251 isolated from bacterial enrichment acclimated by hexadecane for two years. CHEMOSPHERE 2023; 344:140383. [PMID: 37832891 DOI: 10.1016/j.chemosphere.2023.140383] [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: 02/15/2023] [Revised: 08/31/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Polyethylene (PE) mulch films have been widely used in agriculture and led to a significant pollution in cultivated soils. It is desirable to develop the sustainable method for the degradation of PE. As an environment friendly approach, microbial or enzymatic degradation of PE could meet this demanding. Thus, more microbial strains are required for illustrating biodegrading pathway and developing efficient biological method. In this study, Gordonia polyisoprenivorans B251 capable of degrading PE was isolated from bacterial enrichment with hexadecane as a sole carbon source for two years, in which genus Gordonia had dominated. As revealed by microbial growth curve, the strain B251 had the highest growth rate than other tested strains in the mediums either with hexadecane or PE particles as sole carbon source. The formation of biofilms in both enriched culture and G. polyisoprenivorans B251 pure culture attached to PE film was observed. The capability for PE degradation of individual strain was screened by 30-day incubation with PE film and confirmed by the presence of hydroxyl, carbonyl, carbon-carbon double bond and ether groups in FT-IR analysis and cracks on the surface of PE film observed by scanning electron microscopy (SEM). Therefore, Gordonia polyisoprenivorans, reported as their degradation of environmental contaminants in previous study, were also identified in current study as a candidate for polyethylene biodegradation.
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Affiliation(s)
- Hongzhe Wang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan Zhu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Yanshuo Pan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qi Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qin Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenqing He
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Daozhi Gong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Tian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Dongfei Han
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
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De Filippis F, Bonelli M, Bruno D, Sequino G, Montali A, Reguzzoni M, Pasolli E, Savy D, Cangemi S, Cozzolino V, Tettamanti G, Ercolini D, Casartelli M, Caccia S. Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions. MICROBIOME 2023; 11:205. [PMID: 37705113 PMCID: PMC10500907 DOI: 10.1186/s40168-023-01649-0] [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: 10/26/2022] [Accepted: 07/16/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic waste management. Although many analyses based on 16S rRNA gene sequencing are available, an in-depth analysis of the insect gut microbiome to identify genes with plastic-degrading potential is still lacking. RESULTS In the present work, we aim to fill this gap using Black Soldier Fly (BSF) as insect model. BSF larvae have proven capability to efficiently bioconvert a wide variety of organic wastes but, surprisingly, have never been considered for plastic degradation. BSF larvae were reared on two widely used plastic polymers and shotgun metagenomics was exploited to evaluate if and how plastic-containing diets affect composition and functions of the gut microbial community. The high-definition picture of the BSF gut microbiome gave access for the first time to the genomes of culturable and unculturable microorganisms in the gut of insects reared on plastics and revealed that (i) plastics significantly shaped bacterial composition at species and strain level, and (ii) functions that trigger the degradation of the polymer chains, i.e., DyP-type peroxidases, multicopper oxidases, and alkane monooxygenases, were highly enriched in the metagenomes upon exposure to plastics, consistently with the evidences obtained by scanning electron microscopy and 1H nuclear magnetic resonance analyses on plastics. CONCLUSIONS In addition to highlighting that the astonishing plasticity of the microbiota composition of BSF larvae is associated with functional shifts in the insect microbiome, the present work sets the stage for exploiting BSF larvae as "bioincubators" to isolate microbial strains and enzymes for the development of innovative plastic biodegradation strategies. However, most importantly, the larvae constitute a source of enzymes to be evolved and valorized by pioneering synthetic biology approaches. Video Abstract.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Marco Bonelli
- Department of Biosciences, University of Milan, Milan, Italy
| | - Daniele Bruno
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Aurora Montali
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marcella Reguzzoni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Davide Savy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Silvana Cangemi
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Vincenza Cozzolino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Gianluca Tettamanti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
| | - Morena Casartelli
- Department of Biosciences, University of Milan, Milan, Italy.
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy.
| | - Silvia Caccia
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
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Silva NM, Romagnoli CL, Santiago CRDN, de Lacerda JPA, Leão SC, Digiampietri LA, Viana-Niero C. Multi-Approach Characterization of Novel Pyrene-Degrading Mycolicibacterium austroafricanum Isolates Lacking nid Genes. Microorganisms 2023; 11:1413. [PMID: 37374915 DOI: 10.3390/microorganisms11061413] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/21/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are chemical compounds that are widespread in the environment, arising from the incomplete combustion of organic material, as well as from human activities involving petrol exploitation, petrochemical industrial waste, gas stations, and environmental disasters. PAHs of high molecular weight, such as pyrene, have carcinogenic and mutagenic effects and are considered pollutants. The microbial degradation of PAHs occurs through the action of multiple dioxygenase genes (nid), which are localized in genomic island denominate region A, and cytochrome P450 monooxygenases genes (cyp) dispersed in the bacterial genome. This study evaluated pyrene degradation by five isolates of Mycolicibacterium austroafricanum using 2,6-dichlorophenol indophenol (DCPIP assay), gas chromatography/mass spectrometry (CG/MS), and genomic analyses. Two isolates (MYC038 and MYC040) exhibited pyrene degradation indexes of 96% and 88%, respectively, over a seven-day incubation period. Interestingly, the genomic analyses showed that the isolates do not have nid genes, which are involved in PAH biodegradation, despite their ability to degrade pyrene, suggesting that degradation may occur due to the presence of cyp150 genes, or even genes that have not yet been described. To the best of our knowledge, this is the first report of isolates without nid genes demonstrating the ability to degrade pyrene.
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Affiliation(s)
- Natalia Maria Silva
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | - Camila Lopes Romagnoli
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | | | - João Paulo Amorim de Lacerda
- Laboratory of Chemistry and Manufactured Products, Institute of Technological Research, São Paulo 05508-901, Brazil
| | - Sylvia Cardoso Leão
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | | | - Cristina Viana-Niero
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo 04023-901, Brazil
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Frantsuzova E, Bogun A, Solomentsev V, Vetrova A, Streletskii R, Solyanikova I, Delegan Y. Whole Genome Analysis and Assessment of the Metabolic Potential of Gordonia rubripertincta Strain 112, a Degrader of Aromatic and Aliphatic Compounds. BIOLOGY 2023; 12:biology12050721. [PMID: 37237534 DOI: 10.3390/biology12050721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023]
Abstract
The application of Gordonia strains in biotechnologies of environmental purification as degraders of pollutants of different chemical structures is an interesting research topic. The strain Gordonia rubripertincta 112 (IEGM112) is capable of utilizing diesel fuel, alkanes, and aromatic compounds. The aim of this work was to study the potential of G. rubripertincta 112 as a degrader of aromatic and aliphatic compounds and analyze its complete genome in comparison with other known G. rubripertincta strains. The genome had a total length of 5.28 Mb and contained 4861 genes in total, of which 4799 were coding sequences (CDS). The genome contained 62 RNA genes in total, of which 50 were tRNAs, three were ncRNAs, and nine were rRNAs. The strain bears plasmid elements with a total length of 189,570 nucleotides (plasmid p1517). The strain can utilize 10.79 ± 1.17% of hexadecane and 16.14 ± 0.16% of decane over 3 days of cultivation. In the genome of the strain, we have found metabolic pathways of alkane (cytochrome P450 hydroxylases) and catechol (ortho- and meta-pathways) degradation. These results will help us to further approach the fundamental study of the processes occurring in the strain cells and to enrich our knowledge of the catabolic capabilities of G. rubripertincta.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Viktor Solomentsev
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Rostislav Streletskii
- Laboratory of Ecological Soil Science, Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Inna Solyanikova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- Regional Microbiological Center, Belgorod State University, 308015 Belgorod, Russia
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
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Use of Shotgun Metagenomics to Assess the Microbial Diversity and Hydrocarbons Degrading Functions of Auto-Mechanic Workshops Soils Polluted with Gasoline and Diesel Fuel. Microorganisms 2023; 11:microorganisms11030722. [PMID: 36985295 PMCID: PMC10059880 DOI: 10.3390/microorganisms11030722] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
Bioaugmentation is a valuable technique for oil recovery. This study investigates the composition and functions of microbial communities in gasoline- and diesel-contaminated soils of garages Matoko (SGM) and Guy et Paul (SGP) originating from auto mechanic workshops as well as the concentration of soil enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase. The work aimed to evaluate the presence of petroleum-hydrocarbon-degrading bacteria for the development of foreseen bioremediation of oil-contaminated soils. Microbial diversity, as given by shotgun metagenomics, indicated the presence of 16 classes, among which Actinobacteria and Gammaproteobacteria dominated, as well as more than 50 families, including the dominant Gordoniaceae (26.63%) in SGM and Pseudomonadaceae (57.89%) in SGP. The dominant bacterial genera in the two soils were, respectively, Gordonia (26.7%) and Pseudomonas (57.9%). The exploration of the bacterial metabolic abilities using HUMANn2 allowed to detect genes and pathways involved in alkanes and aromatic hydrocarbons in the two contaminated soils. Furthermore, enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase were found in high concentrations ranging between 90.27 ± 5.3 and 804.17 ± 20.5 µg pN/g soil/h, which indicated active microbial metabolism. The high diversity of microorganisms with a hydrocarbon degradation genetic package revealed that the bacteria inhabiting the two soils are likely good candidates for the bioaugmentation of oil-contaminated soils.
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Gordonia species as a rare pathogen isolated from milk of dairy cows with mastitis. Sci Rep 2022; 12:6028. [PMID: 35411009 PMCID: PMC9001696 DOI: 10.1038/s41598-022-09340-4] [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: 06/06/2021] [Accepted: 03/21/2022] [Indexed: 11/24/2022] Open
Abstract
While Gordonia species have long been known to cause severe inflammation in humans, the pathogenic effects of Gordonia species in veterinary medicine have rarely been described. Between 2010 and 2019, we collected microorganisms of the genus Gordonia isolated from milk samples from dairy cows with mastitis. We describe the growth properties of these microorganisms and their prevalence, virulence factors and susceptibility to antimicrobial agents. From 31,534 quarter milk samples processed by standard culture methods, 27 isolates of Gordonia species (0.086% prevalence) were identified by a molecular phenotyping method. The isolates originated from 17 farms in 12 districts of the Czech Republic. Twenty-one isolates were tested for susceptibility to 7 antimicrobials by the disc diffusion method. Notably, 100% of these isolates were susceptible to streptomycin and neomycin, 85.7% to cefovecin and tetracycline, 76.2% to penicillin G, 47.6% to trimethoprim/sulfamethoxazole and 0% to clindamycin. The species was determined to be Gordonia paraffinivorans by whole genome sequencing for 9 isolates (from 8 farms in 7 districts). These isolates showed the highest similarity to two reference strains from the environment. In all these isolates, we identified genes encoding virulence factors that are very similar to genes encoding virulence factors expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis. However, genome analysis revealed 61 unique genes in all 9 sequenced isolates.
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Ahmed IB, Nwaichi EO, Ugwoha E, Ugbebor JN, Arokoyu SB. Cost reduction strategies in the remediation of petroleum hydrocarbon contaminated soil. OPEN RESEARCH AFRICA 2022; 5:21. [PMID: 36561538 PMCID: PMC9718438 DOI: 10.12688/openresafrica.13383.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/04/2022] [Indexed: 12/25/2022]
Abstract
Petroleum hydrocarbon spill on land pollutes soil and reduces its ecosystem. Hydrocarbon transport in the soil is aided by several biological, physical, and chemical processes. However, pore characteristics play a major role in the distribution within the soil matrix. Restoring land use after spills necessitates remediation using cost-effective technologies. Several remediation technologies have been demonstrated at different scales, and research is ongoing to improve their performances towards the reduction of treatment costs. The process of removing the contaminants in the soil is through one or a combination of containment, separation, and degradation methods under the influence of biological, physical, chemical, and electrically-dominated processes. Generally, performance improvement is achieved through the introduction of products/materials and/or energy. Nevertheless, the technologies can be categorized based on effectiveness period as short, medium, and long term. The treatment cost of short, medium, and long-term technologies are usually in the range of $39 - 331/t (/tonne), $22 - 131/t, and $8 - 131/t, respectively. However, the total cost depends on other factors such as site location, capital cost, and permitting. This review compiles cost-saving strategies reported for different techniques used in remediating petroleum hydrocarbon polluted soil. We discuss the principles of contaminant removal, performance enhancing methods, and the cost-effectiveness analysis of selected technologies.
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Affiliation(s)
- Ismail B. Ahmed
- Centre for Occupational Health, Safety and Environment, University of Port Harcourt, Choba, Nigeria,National Oil Spill Detection and Response Agency (NOSDRA), Abuja, Nigeria
| | - Eucharia O. Nwaichi
- Department of Biochemistry, University of Port Harcourt, Choba, Nigeria,Exchange & Linkage Programmes Unit, University of Port Harcourt, Choba, Nigeria,
| | - Ejikeme Ugwoha
- Centre for Occupational Health, Safety and Environment, University of Port Harcourt, Choba, Nigeria,Department of Civil & Environmental Engineering, University of Port Harcourt, Choba, Nigeria
| | - John N. Ugbebor
- Centre for Occupational Health, Safety and Environment, University of Port Harcourt, Choba, Nigeria,Department of Civil & Environmental Engineering, University of Port Harcourt, Choba, Nigeria
| | - Samuel B. Arokoyu
- Centre for Research Management and Administration, University of Port Harcourt, Choba, Nigeria,Department of Geography and Environmental Management, University of Port Harcourt, Choba, Nigeria
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Ashfaq MY, Da'na DA, Al-Ghouti MA. Application of MALDI-TOF MS for identification of environmental bacteria: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114359. [PMID: 34959061 DOI: 10.1016/j.jenvman.2021.114359] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 05/22/2023]
Abstract
Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.
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Affiliation(s)
- Mohammad Y Ashfaq
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Dana A Da'na
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar.
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Oliveira VM, Andreote FD, Cortelo PC, Castro-Gamboa I, Costa-Lotufo LV, Polizeli MDLTM, Thiemann OH, Setubal JC. Microorganisms: the secret agents of the biosphere, and their key roles in biotechnology. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract We present a survey of projects that have been funded by FAPESP under the BIOTA-Microorganisms program. These projects generated a wide variety of results, including the identification of novel antibacterial-producing microorganisms, the characterization of novel microbial enzymes for industrial applications, taxonomic classification of novel microorganisms in several environments, investigation of the soil and mangrove microbial ecosystems and its influence on endangered plant species, and the sequencing of novel metagenome-assembled genomes. The results surveyed demonstrate the importance of microorganisms in environments that play important roles in human activities as well as the potential that many of these microorganisms have in contributing to biotechnological applications crucial for human survival in the 21st century.
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Braga LPP, Pereira RV, Martins LF, Moura LMS, Sanchez FB, Patané JSL, da Silva AM, Setubal JC. Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. BMC Genomics 2021; 22:652. [PMID: 34507539 PMCID: PMC8434746 DOI: 10.1186/s12864-021-07957-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. RESULTS Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. CONCLUSIONS The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.
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Affiliation(s)
- Lucas Palma Perez Braga
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Livia Maria Silva Moura
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio Beltrame Sanchez
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
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Bodor A, Bounedjoum N, Feigl G, Duzs Á, Laczi K, Szilágyi Á, Rákhely G, Perei K. Exploitation of extracellular organic matter from Micrococcus luteus to enhance ex situ bioremediation of soils polluted with used lubricants. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:125996. [PMID: 33992922 DOI: 10.1016/j.jhazmat.2021.125996] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Chronic pollution by used lubricant oils (ULOs) poses a serious challenge to the environment. Under stress conditions, microorganisms, including potential degraders, can enter a viable but non-culturable (VBNC) state, complicating the bioremediation of ULO-polluted areas. Resuscitation-promoting factors (Rpfs) can reverse this transition and/or enhance the biodegradation performance of both native and augmented strains. Here, Rpf-containing extracellular organic matter (EOM) from Micrococcus luteus was used to enhance the ex situ ULO removal in biostimulated and bioaugmented (with Rhodococcus qingshengii KAG C, R. erythropolis PR4) soils. ULO bioconversion, microbial activity, and CFUs were significantly higher in EOM-treated soils compared to corresponding control soils. After 60 days, the initial ULO concentration (52,500 mg kg-1) was reduced by 37% and 45% with EOM-supplemented biostimulation and bioaugmentation, respectively. Based on high-throughput 16S rRNA analysis, the enhancement was attributable both to the reactivation of EOM-responsive hydrocarbonoclastic bacterial genera (e.g., Pseudomonas, Comamonas, Stenotrophomonas, Gordonia) and to the long-term positive effect of EOM on the degradative efficacy of the introduced rhodococci. Ecotoxicological responses revealed that reduced ULO concentration did not correlate with decreased soil toxicity. Our findings provide an insight into the applicability of EOM in bioremediation and its effects on the soil microbial activity and community composition.
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Affiliation(s)
- Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Feigl
- Department of Plant Biology, University of Szeged, Szeged, Hungary
| | - Ágnes Duzs
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary
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Abstract
Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern and has resulted from the intensification of industrial activities. This has created a serious environmental issue; therefore, there is a need to find solutions, including application of efficient remediation technologies or improvement of current techniques. Rhizoremediation is a green technology that has received global attention as a cost-effective and possibly efficient remediation technique for PHC-polluted soil. Rhizoremediation refers to the use of plants and their associated microbiota to clean up contaminated soils, where plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is complicated because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the current knowledge of rhizoremediation approaches that can accelerate the remediation of PHC-contaminated soil. Recent approaches discussed in this review include (1) selecting plants with desired characteristics suitable for rhizoremediation; (2) exploiting and manipulating the plant microbiome by using inoculants containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms; (3) enhancing the understanding of how the host–plant assembles a beneficial microbiome, and how it functions, under pollutant stress. A better understanding of plant–microbiome interactions could lead to successful use of rhizoremediation for PHC-contaminated soil in the future.
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Baburam C, Feto NA. Mining of two novel aldehyde dehydrogenases (DHY-SC-VUT5 and DHY-G-VUT7) from metagenome of hydrocarbon contaminated soils. BMC Biotechnol 2021; 21:18. [PMID: 33648490 PMCID: PMC7923466 DOI: 10.1186/s12896-021-00677-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/07/2021] [Indexed: 01/20/2023] Open
Abstract
Background Aldehyde dehydrogenases are vital for aerobic hydrocarbon degradation and is involved in the last step of catalysing the oxidation of aldehydes to carboxylic acids. With the global increase in hydrocarbon pollution of different environments, these enzymes have the potential to be used in enzymatic bioremediation applications. Results Fifteen fosmid clones with hydrocarbon degrading potential were functionally screened to identify dehydrogenase enzymes. Accordingly, the fosmid insert of the positive clones were sequenced using PacBio next generation sequencing platform and de novo assembled using CLC Genomic Work Bench. The 1233 bp long open reading frame (ORF) for DHY-SC-VUT5 was found to share a protein sequence similarity of 97.7% to short-chain dehydrogenase from E. coli. The 1470 bp long ORF for DHY-G-VUT7 was found to share a protein sequence similarity of 23.9% to glycine dehydrogenase (decarboxylating) (EC 1.4.4.2) from Caulobacter vibrioides (strain NA1000 / CB15N) (Caulobacter crescentus). The in silico analyses and blast against UNIPROT protein database with the stated similarity show that the two dehydrogenases are novel. Biochemical characterization revealed, that the highest relative activity was observed at substrate concentrations of 150 mM and 50 mM for DHY-SC-VUT5 and DHY-G-VUT7, respectively. The Km values were found to be 13.77 mM with a Vmax of 0.009135 μmol.min− 1 and 2.832 mM with a Vmax of 0.005886 μmol.min− 1 for DHY-SC-VUT5 and DHY-G-VUT7, respectively. Thus, a potent and efficient enzyme for alkyl aldehyde conversion to carboxylic acid. Conclusion The microorganisms overexpressing the novel aldehyde dehydrogenases could be used to make up microbial cocktails for biodegradation of alkanes. Moreover, since the discovered enzymes are novel it would be interesting to solve their structures by crystallography and explore the downstream applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00677-8.
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Affiliation(s)
- Cindy Baburam
- OMICS Research Group, Department of Biotechnology, Faculty of Applied and Computer Sciences, Vaal University of Technology, Vanderbijlpark 1911, South Africa
| | - Naser Aliye Feto
- OMICS Research Group, Department of Biotechnology, Faculty of Applied and Computer Sciences, Vaal University of Technology, Vanderbijlpark 1911, South Africa.
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Das D, Mawlong GT, Sarki YN, Singh AK, Chikkaputtaiah C, Boruah HPD. Transcriptome analysis of crude oil degrading Pseudomonas aeruginosa strains for identification of potential genes involved in crude oil degradation. Gene 2020; 755:144909. [PMID: 32569720 DOI: 10.1016/j.gene.2020.144909] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 12/27/2022]
Abstract
In the microbial world, bacteria are the most effective agents in petroleum hydrocarbons (PHs) degradation, utilization/mineralization and they serve as essential degraders of crude oil contaminated environment. Some genes and traits are involved in the hydrocarbon utilization process for which transcriptome analyses are important to identify differentially expressed genes (DEGs) among different conditions, leading to a new understanding of genes or pathways associated with crude oil degradation. In this work, three crude oil utilizing Pseudomonas aeruginosa strains designated as N002, TP16 and J001 subjected to transcriptome analyses revealed a total of 81, 269 and 137 significant DEGs. Among them are 80 up-regulated genes and one downregulated gene of N002, 121 up- regulated and 148 down-regulated genes of TP16, 97 up-regulated and 40 down-regulated genes of J001 which are involved in various metabolic pathways. TP16 strain has shown more number of DEGs upon crude oil treatment in comparison to the other two strains. Through quantitative real time polymerase chain reaction (qRT-PCR), the selected DEGs of each strain from transcriptome data were substantiated. The results have shown that the up- regulated and down-regulated genes observed by qRT-PCR were consistent with transcriptome data. Taken together, our transcriptome results have revealed that TP16 is a potential P. aeruginosa strain for functional analysis of identified potential DEGs involved in crude oil degradation.
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Affiliation(s)
- Dhrubajyoti Das
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Gabriella T Mawlong
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Yogita N Sarki
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Innovative and Scientific Research (AcSIR), CSIR-NEIST, Jorhat 785006, Assam, India
| | - Anil Kumar Singh
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Innovative and Scientific Research (AcSIR), CSIR-NEIST, Jorhat 785006, Assam, India
| | - Channakeshavaiah Chikkaputtaiah
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Innovative and Scientific Research (AcSIR), CSIR-NEIST, Jorhat 785006, Assam, India
| | - Hari Prasanna Deka Boruah
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Innovative and Scientific Research (AcSIR), CSIR-NEIST, Jorhat 785006, Assam, India.
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