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Culturable microorganisms of substrates of terrestrial plant communities of the maritime Antarctic (Galindez Island, Booth Island). Polar Biol 2022. [DOI: 10.1007/s00300-022-03103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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2
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Rosas-Díaz J, Escobar-Zepeda A, Adaya L, Rojas-Vargas J, Cuervo-Amaya DH, Sánchez-Reyes A, Pardo-López L. Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance. Front Microbiol 2021; 12:713702. [PMID: 34413843 PMCID: PMC8369764 DOI: 10.3389/fmicb.2021.713702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Paenarthrobacter sp. GOM3, which is a strain that represents a new species-specific context within the genus Paenarthrobacter, is clearly a branched member independent of any group described thus far. This strain was recovered from marine sediments in the Gulf of Mexico, and despite being isolated from a consortium capable of growing with phenanthrene as a sole carbon source, this strain could not grow successfully in the presence of this substrate alone. We hypothesized that the GOM3 strain could participate in the assimilation of intermediate metabolites for the degradation of aromatic compounds. To date, there are no experimental reports of Paenarthrobacter species that degrade polycyclic aromatic hydrocarbons (PAHs) or their intermediate metabolites. In this work, we report genomic and experimental evidence of metabolic benzoate, gentisate, and protocatechuate degradation by Paenarthrobacter sp. GOM3. Gentisate was the preferred substrate with the highest volumetric consumption rate, and genomic analysis revealed that this strain possesses multiple gene copies for the specific transport of gentisate. Furthermore, upon analyzing the GOM3 genome, we found five different dioxygenases involved in the activation of aromatic compounds, suggesting its potential for complete remediation of PAH-contaminated sites in combination with strains capable of assimilating the upper PAH degradation pathway. Additionally, this strain was characterized experimentally for its pathogenic potential and in silico for its antimicrobial resistance. An overview of the potential ecological role of this strain in the context of other members of this taxonomic clade is also reported.
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Affiliation(s)
- Jaime Rosas-Díaz
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Alejandra Escobar-Zepeda
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Libertad Adaya
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Jorge Rojas-Vargas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Diego Humberto Cuervo-Amaya
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Ayixon Sánchez-Reyes
- Cátedras Conacyt – Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
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Christakis CA, Daskalogiannis G, Chatzaki A, Markakis EA, Mermigka G, Sagia A, Rizzo GF, Catara V, Lagkouvardos I, Studholme DJ, Sarris PF. Endophytic Bacterial Isolates From Halophytes Demonstrate Phytopathogen Biocontrol and Plant Growth Promotion Under High Salinity. Front Microbiol 2021; 12:681567. [PMID: 34017321 PMCID: PMC8129196 DOI: 10.3389/fmicb.2021.681567] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023] Open
Abstract
Halophytic endophytes potentially contribute to the host's adaptation to adverse environments, improving its tolerance against various biotic and abiotic stresses. Here, we identified the culturable endophytic bacteria of three crop wild relative (CWR) halophytes: Cakile maritima, Matthiola tricuspidata, and Crithmum maritimum. In the present study, the potential of these isolates to improve crop adaptations to various stresses was investigated, using both in vitro and in-planta approaches. Endophytic isolates were identified by their 16S rRNA gene sequence and evaluated for their ability to: grow in vitro in high levels of NaCl; inhibit the growth of the economically important phytopathogens Verticillium dahliae, Ralstonia solanacearum, and Clavibacter michiganensis and the human pathogen Aspergillus fumigatus; provide salt tolerance in-planta; and provide growth promoting effect in-planta. Genomes of selected isolates were sequenced. In total, 115 endophytic isolates were identified. At least 16 isolates demonstrated growth under increased salinity, plant growth promotion and phytopathogen antagonistic activity. Three showed in-planta suppression of Verticillium growth. Furthermore, representatives of three novel species were identified: two Pseudomonas species and one Arthrobacter. This study provides proof-of-concept that the endophytes from CWR halophytes can be used as "bio-inoculants," for the enhancement of growth and stress tolerance in crops, including the high-salinity stress.
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Affiliation(s)
- Christos A Christakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | | | - Anastasia Chatzaki
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA, Heraklion, Greece
| | - Emmanouil A Markakis
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA, Heraklion, Greece
| | - Glykeria Mermigka
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | - Angeliki Sagia
- Department of Biology, University of Crete, Heraklion, Greece
| | - Giulio Flavio Rizzo
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Ilias Lagkouvardos
- ZIEL-Institute for Food and Health, Technical University of Munich, Freising, Germany
| | | | - Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece.,Biosciences, University of Exeter, Exeter, United Kingdom
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Katsoula A, Vasileiadis S, Sapountzi M, Karpouzas DG. The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: accelerated biodegradation or toxicity? FEMS Microbiol Ecol 2020; 96:5813261. [PMID: 32221586 DOI: 10.1093/femsec/fiaa056] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/23/2020] [Indexed: 12/30/2022] Open
Abstract
Pesticides interact with microorganisms in various ways with the outcome being negative or positive for the soil microbiota. Pesticides' effects on soil microorganisms have been studied extensively in soil but not in other pesticides-exposed microbial habitats like the phyllosphere. We tested the hypothesis that soil and phyllosphere support distinct microbial communities, but exhibit a similar response (accelerated biodegradation or toxicity) to repeated exposure to the fungicide iprodione. Pepper plants received four repeated foliage or soil applications of iprodione, which accelerated its degradation in soil (DT50_1st = 1.23 and DT50_4th = 0.48 days) and on plant leaves (DT50_1st > 365 and DT50_4th = 5.95 days). The composition of the epiphytic and soil bacterial and fungal communities, determined by amplicon sequencing, was significantly altered by iprodione. The archaeal epiphytic and soil communities responded differently; the former showed no response to iprodione. Three iprodione-degrading Paenarthrobacter strains were isolated from soil and phyllosphere. They hydrolyzed iprodione to 3,5-dichloraniline via the formation of 3,5-dichlorophenyl-carboxiamide and 3,5-dichlorophenylurea-acetate, a pathway shared by other soil-derived arthrobacters implying a phylogenetic specialization in iprodione biotransformation. Our results suggest that iprodione-repeated application could affect soil and epiphytic microbial communities with implications for the homeostasis of the plant-soil system and agricultural production.
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Affiliation(s)
- A Katsoula
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
| | - S Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
| | - M Sapountzi
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
| | - Dimitrios G Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
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Sáenz de Miera LE, Pinto R, Gutierrez-Gonzalez JJ, Calvo L, Ansola G. Wildfire effects on diversity and composition in soil bacterial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138636. [PMID: 32320886 DOI: 10.1016/j.scitotenv.2020.138636] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
In recent years, the Mediterranean area has witnessed an increase of both the frequency and severity of large fires, which appears to be intimately associated with climate and land use changes. To measure the impact of wildfires on living organisms, diverse indicators have been proposed. These indicators of fire severity traditionally rely on quantifying the damage caused to the vegetal component of ecosystems. However, the use of bacterial communities as severity indicators has received less attention. Here, we studied the differences between bacterial communities of three different Mediterranean ecosystems, two shrubby and one arboreal, two months after a large wildfire. Two levels of severity were compared to a control unburnt soil. The results showed that greater fire severity triggers a reduction in the diversity of soil bacterial communities. In high-severity fires, this reduction reached 40.6 and 58.6% of the control values for richness and Shannon's diversity, respectively. We also found that the greatest differences between communities could be attributed first to the severity of the fire, and second to the ecosystem from which they originated. Importantly, species of just five families of bacteria: Oxalobacteraceae, Micrococcaceae, Paenibacillaceae, Bacillaceae and Planococcaceae, became dominant in all three ecosystems. The average frequency increase for particular species was 100 times. However, due to random uncontrolled factors, the species that became dominant in each community were not always the same.
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Affiliation(s)
- Luis E Sáenz de Miera
- Departamento de Biología Molecular, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain.
| | - Rayo Pinto
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | | | - Leonor Calvo
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain.
| | - Gemma Ansola
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain.
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Yu Y, Yang J, Zheng LY, Sheng Q, Li CY, Wang M, Zhang XY, McMinn A, Zhang YZ, Song XY, Chen XL. Diversity of D-Amino Acid Utilizing Bacteria From Kongsfjorden, Arctic and the Metabolic Pathways for Seven D-Amino Acids. Front Microbiol 2020; 10:2983. [PMID: 31998270 PMCID: PMC6965332 DOI: 10.3389/fmicb.2019.02983] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022] Open
Abstract
D-amino acids (DAAs) are an important component of the refractory dissolved organic matter pool in the ocean. Microbes play a vital role in promoting the recycling of DAAs in the ocean. However, the diversity of marine DAA-utilizing bacteria and how they metabolize DAAs are seldom studied. Here, by enrichment culture with DAAs as the sole nitrogen source, bacteria of 12 families from three phyla were recovered from surface seawater and sediment from Kongsfjorden, Arctic, and seven DAA-utilizing bacterial strains were isolated. These strains have different DAA-utilizing abilities. Of the seven DAAs used, Halomonas titanicae SM1922 and Pseudoalteromonas neustonica SM1927 were able to utilize seven and five of them, respectively, while the other strains were able to utilize only one or two. Based on genomic, transcriptional and biochemical analyses, the key genes involved in DAA metabolism in each strain were identified and the metabolic pathways for the seven DAAs in these marine bacteria were identified. Conversion of DAAs into α-keto acids is generally the main pathway in marine DAA-utilizing bacteria, which is performed by several key enzymes, including DAA oxidoreductases/dehydrogenases, D-serine ammonia-lyases, D-serine ammonia-lyase DSD1s and DAA transaminases. In addition, conversion of DAAs into LAAs is another pathway, which is performed by amino acid racemases. Among the identified key enzymes, D-serine ammonia-lyase DSD1 and Asp racemase are first found to be employed by bacteria for DAA utilization. These results shed light on marine DAA-utilizing bacteria and the involved DAA metabolism pathways, offering a better understanding of the DAA recycling in the ocean.
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Affiliation(s)
- Yang Yu
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jie Yang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Li-Yuan Zheng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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Saccà ML, Manici LM, Caputo F, Frisullo S. Changes in rhizosphere bacterial communities associated with tree decline: grapevine esca syndrome case study. Can J Microbiol 2019; 65:930-943. [DOI: 10.1139/cjm-2019-0384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An investigation was carried out on rhizosphere bacteria to determine if they may be associated with perennial crops affected by nonspecific decline, a phenomenon that is difficult to diagnose and prevent. Esca disease of grapevine was chosen for this case study because of its easy foliar symptom identification. Ribosomal DNA fingerprint analysis by polymerase chain reaction – denaturing gradient gel electrophoresis (PCR–DGGE), quantitative PCR (qPCR), and rDNA amplicon sequencing by next-generation sequencing (NGS) were adopted to investigate the bacterial communities associated with grapevines, which were selected for the presence and absence of external foliar symptoms in 11 vineyards. According to PCR–DGGE and qPCR, bacterial communities differed in site of origin (vineyards), but not between symptomatic and asymptomatic plants, whereas qPCR gave a significantly higher presence of total bacteria and Pseudomonas spp. in asymptomatic plants. NGS confirmed no difference between symptomatic and asymptomatic plants, apart from a few minor genera (<0.5%) such as Salinibacterium, Flavobacterium, Nocardia, and Janthinobacterium, which were, in all cases, higher in asymptomatic plants and whose functional role should be the object of further investigation. The fact that total bacteria and Pseudomonas were more abundant in the rhizosphere of asymptomatic grapevines and that some bacterial genera were associated with the latter, represents a new element when investigating the multiple-origin phenomenon such as esca disease of grapevine.
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Affiliation(s)
- Maria Ludovica Saccà
- Council for Agricultural Research and Economics, Agriculture and Environment Research Center, Bologna, Italy
| | - Luisa Maria Manici
- Council for Agricultural Research and Economics, Agriculture and Environment Research Center, Bologna, Italy
| | - Francesco Caputo
- Council for Agricultural Research and Economics, Agriculture and Environment Research Center, Bologna, Italy
| | - Salvatore Frisullo
- University of Foggia, Department of the Sciences of Agriculture, Food and Environment, Foggia, Italy
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Romero IA, van Dillewijn P, Nesme J, Sørensen SJ, Romero E. Improvement of pesticide removal in contaminated media using aqueous extracts from contaminated biopurification systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:749-759. [PMID: 31325872 DOI: 10.1016/j.scitotenv.2019.07.087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/02/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Despite certain limitations, bioaugmentation enhances the efficiency of bioremediation systems. In this study, three aqueous extracts (APE, ACE and APE) from aged residual biomixtures in three biopurification systems (BPSs) exposed to pesticides at a pilot scale were found to improve pesticide removal. The addition of ACEs and AVEs to solutions containing the model compound diuron increased removal rates 6- and 17-fold, respectively, as compared to APEs. These extracts also increased the removal of the metabolite 3,4-dichloroaniline, while AVEs, in particular, were found to remove all pesticides within 9 days. Three metabolites less hazardous than 3,4-dichloroaniline were identified by SPME/GC/MS. AVEs, which also enhance linuron removal in liquid media, were found to increase diuron removal 6-fold in BPSs. We observed an increase in the relative abundance of taxa, such as Chloroflexi, Acidobacteria, Gemmatimonadetes, Firmicutes, Deinococcus-Thermus and especially Proteobacteria (10%), in AV biomixtures, as well as an enrichment of γ-proteobacteria and the actinobacterial genus Dokdonella in AVEs with respect to initial noncontaminated IV biomixture. We demonstrate that extracts containing a pollutant-acclimatized microbiome could be used as part of a bioaugmentation strategy to improve the functioning of on-farm BPSs and contaminated systems.
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Affiliation(s)
- Inés Aguilar Romero
- Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
| | - Pieter van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Esperanza Romero
- Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
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Gurusinghe S, Brooks TL, Barrow RA, Zhu X, Thotagamuwa A, Dennis PG, Gupta VVSR, Vanniasinkam T, Weston LA. Technologies for the Selection, Culture and Metabolic Profiling of Unique Rhizosphere Microorganisms for Natural Product Discovery. Molecules 2019; 24:molecules24101955. [PMID: 31117282 PMCID: PMC6571749 DOI: 10.3390/molecules24101955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 02/04/2023] Open
Abstract
Small molecule discovery has benefitted from the development of technologies that have aided in the culture and identification of soil microorganisms and the subsequent analysis of their respective metabolomes. We report herein on the use of both culture dependent and independent approaches for evaluation of soil microbial diversity in the rhizosphere of canola, a crop known to support a diverse microbiome, including plant growth promoting rhizobacteria. Initial screening of rhizosphere soils showed that microbial diversity, particularly bacterial, was greatest at crop maturity; therefore organismal recovery was attempted with soil collected at canola harvest. Two standard media (Mueller Hinton and gellan gum) were evaluated following inoculation with soil aqueous suspensions and compared with a novel “rhizochip” prototype buried in a living canola crop rhizosphere for microbial culture in situ. Following successful recovery and identification of 375 rhizosphere microbiota of interest from all culture methods, isolates were identified by Sanger sequencing and/or characterization using morphological and biochemical traits. Three bacterial isolates of interest were randomly selected as case studies for intensive metabolic profiling. After successful culture in liquid media and solvent extraction, individual extracts were subjected to evaluation by UHPLC-DAD-QToF-MS, resulting in the rapid characterization of metabolites of interest from cultures of two isolates. After evaluation of key molecular features, unique or unusual bacterial metabolites were annotated and are reported herein.
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Affiliation(s)
- Saliya Gurusinghe
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
| | - Tabin L Brooks
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
| | - Russell A Barrow
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
- Plus 3 Australia Pty Ltd, P.O. Box 4345, Hawker, ACT 2614, Australia.
| | - Xiaocheng Zhu
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
| | - Agasthya Thotagamuwa
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | | | - Thiru Vanniasinkam
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
| | - Leslie A Weston
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
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Agunbiade MO, Van Heerden E, Pohl CH, Ashafa AT. Flocculating performance of a bioflocculant produced by Arthrobacter humicola in sewage waste water treatment. BMC Biotechnol 2017; 17:51. [PMID: 28606076 PMCID: PMC5469021 DOI: 10.1186/s12896-017-0375-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/07/2017] [Indexed: 11/14/2022] Open
Abstract
Background The discharge of poorly treated effluents into the environment has far reaching, consequential impacts on human and aquatic life forms. Thus, we evaluated the flocculating efficiency of our test bioflocculant and we report for the first time the ability of the biopolymeric flocculant produced by Arthrobacter humicola in the treatment of sewage wastewater. This strain was isolated from sediment soil sample at Sterkfontein dam in the Eastern Free State province of South Africa. Results Basic Local Alignment Search Tool (BLAST) analysis of the nucleotide sequence of the 16S rDNA revealed the bacteria to have 99% similarity to Arthrobacter humicola strain R1 and the sequence was deposited in the Gene bank as Arthrobacter humicola with accession number KC816574.1. Flocculating activity was enhanced with the aid of divalent cations, pH 12, at a dosage concentration of 0.8 mg/mL. The purified bioflocculant was heat stable and could retain more than 78% of its flocculating activity after heating at 100 °C for 25 min. Fourier Transform Infrared Spectroscopy analysis demonstrated the presence of hydroxyl and carboxyl moieties as the functional groups. The thermogravimetric analysis was used to monitor the pyrolysis profile of the purified bioflocculant and elemental composition revealed C: O: Na: P: K with 13.90: 41.96: 26.79: 16.61: 0.74 weight percentage respectively. The purified bioflocculant was able to remove chemical oxygen demand, biological oxygen demand, suspended solids, nitrate and turbidity from sewage waste water at efficiencies of 65.7%, 63.5%, 55.7%, 71.4% and 81.3% respectively. Conclusions The results of this study indicate the possibility of using the bioflocculant produced by Arthrobacter humicola as a potential alternative to synthesized chemical flocculants in sewage waste water treatment and other industrial waste water.
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Affiliation(s)
- Mayowa Oladele Agunbiade
- Phytomedicine and Phytopharmacology Research Group, Department of Plant Sciences, University of the Free State, Qwaqwa Campus, P. Bag X13, Phuthaditjabha, 9866, South Africa. .,Department of Microbial, Biochemical & Food Biotechnology, University of the Free State, P.O. Box 339, Nelson Mandela Drive, Bloemfontein, 9301, South Africa.
| | - Esta Van Heerden
- Department of Microbial, Biochemical & Food Biotechnology, University of the Free State, P.O. Box 339, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
| | - Carolina H Pohl
- Department of Microbial, Biochemical & Food Biotechnology, University of the Free State, P.O. Box 339, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
| | - Anofi Tom Ashafa
- Phytomedicine and Phytopharmacology Research Group, Department of Plant Sciences, University of the Free State, Qwaqwa Campus, P. Bag X13, Phuthaditjabha, 9866, South Africa
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11
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Deng Y, Mao Y, Li B, Yang C, Zhang T. Aerobic Degradation of Sulfadiazine by Arthrobacter spp.: Kinetics, Pathways, and Genomic Characterization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:9566-9575. [PMID: 27477918 DOI: 10.1021/acs.est.6b02231] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Two aerobic sulfadiazine (SDZ) degrading bacterial strains, D2 and D4, affiliated with the genus Arthrobacter, were isolated from SDZ-enriched activated sludge. The degradation of SDZ by the two isolates followed first-order decay kinetics. The half-life time of complete SDZ degradation was 11.3 h for strain D2 and 46.4 h for strain D4. Degradation kinetic changed from nongrowth to growth-linked when glucose was introduced as the cosubstrate, and accelerated biodegradation rate was observed after the adaption period. Both isolates could degrade SDZ into 12 biodegradation products via 3 parallel pathways, of which 2-amino-4-hydroxypyrimidine was detected as the principal intermediate product toward the pyrimidine ring cleavage. Compared with five Arthrobacter strains reported previously, D2 and D4 were the only Arthrobacter strains which could degrade SDZ as the sole carbon source. The draft genomes of D2 and D4, with the same completeness of 99.7%, were compared to other genomes of related species. Overall, these two isolates shared high genomic similarities with the s-triazine-degrading Arthrobacter sp. AK-YN10 and the sulfonamide-degrading bacteria Microbacterium sp. C448. In addition, the two genomes contained a few significant regions of difference which may carry the functional genes involved in sulfonamide degradation.
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Affiliation(s)
- Yu Deng
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
| | - Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
| | - Bing Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
| | - Chao Yang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
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12
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Hu QW, Chu X, Xiao M, Li CT, Yan ZF, Hozzein WN, Kim CJ, Zhi XY, Li WJ. Arthrobacter deserti sp. nov., isolated from a desert soil sample. Int J Syst Evol Microbiol 2016; 66:2035-2040. [PMID: 26908080 DOI: 10.1099/ijsem.0.000986] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-motile, rod-shaped, catalase-positive and oxidase-negative bacterium, designated YIM CS25T, was isolated from a soil sample collected from Turpan desert in Xinjiang Uyghur Autonomous Region, north-western China. The isolate grew at 15-40 °C, at pH 6.0-8.0 and with 0-6 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain YIM CS25T belonged to the genus Arthrobacter and was closely related to Arthrobacter halodurans JSM 078085T (95.89 % similarity). The peptidoglycan type contained lysine, alanine and glutamic acid. The major whole-cell sugars were galactose, glucose and ribose. The isolate contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the major polar lipids and MK-9 (H2) as the predominant menaquinone. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and anteiso-C17 : 1ω9c. The genomic DNA G+C content was 68.3 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain YIM CS25T is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter deserti sp. nov. is proposed. The type strain is YIM CS25T ( = KCTC 39544T = CGMCC 1.15091T).
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Affiliation(s)
- Qing-Wen Hu
- Yunnan Institute of Microbiology, Yunnan University,Kunming, 650091, PRChina
| | - Xiao Chu
- Yunnan Institute of Microbiology, Yunnan University,Kunming, 650091, PRChina
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University,Guangzhou, 510275, PRChina
| | - Chang-Tian Li
- College of Chinese Medicinal Materials, Jilin Agricultural University,Changchun, 130118, PRChina
| | - Zheng-Fei Yan
- College of Chinese Medicinal Materials, Jilin Agricultural University,Changchun, 130118, PRChina
| | - Wael N Hozzein
- Bioproducts Research Chair (BRC), College of Science, King Saud University,Riyadh 11451,Kingdom of Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Beni-Suef University,Beni-Suef, 62511,Egypt
| | - Chang-Jin Kim
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology,Daejeon 305-806,Republic of Korea
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Yunnan University,Kunming, 650091, PRChina
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences,Ürümqi 830011, PRChina.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University,Guangzhou, 510275, PRChina.,Yunnan Institute of Microbiology, Yunnan University,Kunming, 650091, PRChina
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Busse HJ. Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus. Int J Syst Evol Microbiol 2015; 66:9-37. [PMID: 26486726 DOI: 10.1099/ijsem.0.000702] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this paper, the taxonomy of the genus Arthrobacter is discussed, from its first description in 1947 to the present state. Emphasis is given to intrageneric phylogeny and chemotaxonomic characteristics, concentrating on quinone systems, peptidoglycan compositions and polar lipid profiles. Internal groups within the genus Arthrobacter indicated from homogeneous chemotaxonomic traits and corresponding to phylogenetic grouping and/or high 16S rRNA gene sequence similarities are highlighted. Furthermore, polar lipid profiles and quinone systems of selected species are shown, filling some gaps concerning these chemotaxonomic traits. Based on phylogenetic groupings, 16S rRNA gene sequence similarities and homogeneity in peptidoglycan types, quinone systems and polar lipid profiles, a description of the genus Arthrobacter sensu lato and an emended description of Arthrobacter roseus are provided. Furthermore, reclassifications of selected species of the genus Arthrobacter into novel genera are proposed, namely Glutamicibacter gen. nov. (nine species), Paeniglutamicibacter gen. nov. (six species), Pseudoglutamicibacter gen. nov. (two species), Paenarthrobacter gen. nov. (six species) and Pseudarthrobacter gen. nov. (ten species).
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Affiliation(s)
- Hans-Jürgen Busse
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz, 1A-1210 Vienna, Austria
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Dsouza M, Taylor MW, Turner SJ, Aislabie J. Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils. BMC Genomics 2015; 16:36. [PMID: 25649291 PMCID: PMC4326396 DOI: 10.1186/s12864-015-1220-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/02/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Members of the bacterial genus Arthrobacter are both readily cultured and commonly identified in Antarctic soil communities. Currently, relatively little is known about the physiological traits that allow these bacteria to survive in the harsh Antarctic soil environment. The aim of this study is to investigate if Antarctic strains of Arthrobacter owe their resilience to substantial genomic changes compared to Arthrobacter spp. isolated from temperate soil environments. RESULTS Quantitative PCR-based analysis revealed that up to 4% of the soil bacterial communities were comprised of Arthrobacter spp. at four locations in the Ross Sea Region. Genome analysis of the seven Antarctic Arthrobacter isolates revealed several features that are commonly observed in psychrophilic/psychrotolerant bacteria. These include genes primarily associated with sigma factors, signal transduction pathways, the carotenoid biosynthesis pathway and genes induced by cold-shock, oxidative and osmotic stresses. However, these genes were also identified in genomes of seven temperate Arthrobacter spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. Phenotypic characterisation revealed that Antarctic Arthrobacter isolates demonstrate significantly lower metabolic versatility and a narrower salinity tolerance range compared to temperate Arthrobacter species. Comparative analyses also revealed fewer protein-coding sequences and a significant decrease in genes associated with transcription and carbohydrate transport and metabolism in four of the seven Antarctic Arthrobacter isolates. Notwithstanding genome incompleteness, these differences together with the decreased metabolic versatility are indicative of genome content scaling. CONCLUSIONS The genomes of the seven Antarctic Arthrobacter isolates contained several features that may be beneficial for growth and survival in the Antarctic soil environment, although these features were not unique to the Antarctic isolates. These genome sequences allow further investigations into the expression of physiological traits that enable survival under extreme conditions and, more importantly, into the ability of these bacteria to respond to future perturbations including climate change and human impacts.
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Affiliation(s)
- Melissa Dsouza
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Michael W Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Susan J Turner
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
- BioDiscovery New Zealand Limited, Parnell, Auckland, New Zealand.
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Park Y, Kook M, Ngo HTT, Kim KY, Park SY, Mavlonov GT, Yi TH. Arthrobacter bambusae sp. nov., isolated from soil of a bamboo grove. Int J Syst Evol Microbiol 2014; 64:3069-3074. [DOI: 10.1099/ijs.0.064550-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, motile by gliding, rod-shaped bacterial strain, THG-GM18T, was isolated from soil of a bamboo grove. Strain THG-GM18T was able to grow in the presence of up to 6.0 % (w/v) NaCl, at 4–37 °C and at pH 7.0–10.0 in R2A medium. Based on 16S rRNA gene sequence similarity, strain THG-GM18T was closely related to species of the genus
Arthrobacter
. The most closely related strains to strain THG-GM18T are
Arthrobacter ramosus
CCM 1646T (98.5 % similarity),
Arthrobacter nitroguajacolicus
G2-1T (98.4 %),
Arthrobacter nicotinovorans
DSM 420T (98.2 %),
Arthrobacter aurescens
DSM 20116T (98.1 %) and
Arthrobacter chlorophenolicus
A6T (98.0 %). Strain THG-GM18T possessed chemotaxonomic properties consistent with those of members of the genus
Arthrobacter
, such as peptidoglycan type A3α (l-Lys–l-Ala–l-Thr–l-Ala), MK-9 as major menaquinone and anteiso- and iso-branched compounds (anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0) as major cellular fatty acids. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, unidentified phospholipids, unidentified aminolipids, an unidentified glycolipid and unidentified lipids. The G+C content of the genomic DNA was 61.0 mol%. The DNA–DNA relatedness values between strain THG-GM18T and its closest phylogenetic neighbours were below 26.0 %. The results of physiological and biochemical tests allowed the differentiation of strain THG-GM18T from species of the genus
Arthrobacter
with validly published names. Arthrobacter bambusae sp. nov. is the proposed name, and the type strain is THG-GM18T ( = KACC 17531T = JCM 19335T).
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Affiliation(s)
- YongJin Park
- College of Life science, Kyung Hee University, Yongin, Gyeonggi 446-701, Republic of Korea
| | - MooChang Kook
- Department of Marine Biotechnology, Anyang University, Incheon 417-833, Republic of Korea
| | - Hien T. T. Ngo
- College of Life science, Kyung Hee University, Yongin, Gyeonggi 446-701, Republic of Korea
| | - Ki-Young Kim
- College of Life science, Kyung Hee University, Yongin, Gyeonggi 446-701, Republic of Korea
| | - Sang-Yong Park
- College of Life science, Kyung Hee University, Yongin, Gyeonggi 446-701, Republic of Korea
| | - Gafurjon T. Mavlonov
- College of Life science, Kyung Hee University, Yongin, Gyeonggi 446-701, Republic of Korea
| | - Tae-Hoo Yi
- College of Life science, Kyung Hee University, Yongin, Gyeonggi 446-701, Republic of Korea
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Fuhshuku KI, Watanabe S, Nishii T, Ishii A, Asano Y. Efficient preparation of both enantiomers of 3,3,3-trifluoro-2-hydroxy-2-methylpropanoic acid catalyzed by Shinella sp. R-6 and Arthrobacter sp. S-2. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Muturi EJ, Orindi BO, Kim CH. Effect of leaf type and pesticide exposure on abundance of bacterial taxa in mosquito larval habitats. PLoS One 2013; 8:e71812. [PMID: 23940789 PMCID: PMC3733839 DOI: 10.1371/journal.pone.0071812] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/03/2013] [Indexed: 10/29/2022] Open
Abstract
Lentic freshwater systems including those inhabited by aquatic stages of mosquitoes derive most of their carbon inputs from terrestrial organic matter mainly leaf litter. The leaf litter is colonized by microbial communities that provide the resource base for mosquito larvae. While the microbial biomass associated with different leaf species in container aquatic habitats is well documented, the taxonomic composition of these microbes and their response to common environmental stressors is poorly understood. We used indoor aquatic microcosms to determine the abundances of major taxonomic groups of bacteria in leaf litters from seven plant species and their responses to low concentrations of four pesticides with different modes of action on the target organisms; permethrin, malathion, atrazine and glyphosate. We tested the hypotheses that leaf species support different quantities of major taxonomic groups of bacteria and that exposure to pesticides at environmentally relevant concentrations alters bacterial abundance and community structure in mosquito larval habitats. We found support for both hypotheses suggesting that leaf litter identity and chemical contamination may alter the quality and quantity of mosquito food base (microbial communities) in larval habitats. The effect of pesticides on microbial communities varied significantly among leaf types, suggesting that the impact of pesticides on natural microbial communities may be highly complex and difficult to predict. Collectively, these findings demonstrate the potential for detritus composition within mosquito larval habitats and exposure to pesticides to influence the quality of mosquito larval habitats.
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Affiliation(s)
- Ephantus J Muturi
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Illinois, United States of America.
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Scheublin TR, Leveau JHJ. Isolation of Arthrobacter species from the phyllosphere and demonstration of their epiphytic fitness. Microbiologyopen 2013; 2:205-13. [PMID: 23355506 PMCID: PMC3584225 DOI: 10.1002/mbo3.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 11/12/2012] [Accepted: 11/13/2012] [Indexed: 11/08/2022] Open
Abstract
Bacteria of the genus Arthrobacter are common inhabitants of the soil environment, but can also be recovered from leaf surfaces (the phyllosphere). Using enrichment cultures on 4-chlorophenol, we succeeded in specifically isolating Arthrobacter bacteria from ground cover vegetation in an apple orchard. Based on 16S rRNA gene sequencing, the isolates were found to belong to at least three different species of Arthrobacter. Compared to the model bacterial epiphyte Pantoea agglomerans, the Arthrobacter isolates performed as well or even better in a standardized laboratory test of phyllosphere fitness. A similar performance was observed with the well-characterized soil isolate Arthrobacter chlorophenolicus A6. These findings suggest that the frequently reported presence of Arthrobacter strains on plant foliage can be explained by the capacity to multiply and persist in the phyllosphere environment. As bacteria from the genus Arthrobacter are known for their ability to degrade a wide variety of organic pollutants, their high phyllosphere competency marks them as a promising group for future studies on phyllosphere-based bioremediation, for example, as foliar bioaugmentation on ground cover or buffer-zone vegetation to prevent pesticides from reaching soil, surface-, or groundwater.
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Affiliation(s)
- Tanja R Scheublin
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
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The PaaX-type repressor MeqR2 of Arthrobacter sp. strain Rue61a, involved in the regulation of quinaldine catabolism, binds to its own promoter and to catabolic promoters and specifically responds to anthraniloyl coenzyme A. J Bacteriol 2012; 195:1068-80. [PMID: 23275246 DOI: 10.1128/jb.01547-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The genes coding for quinaldine catabolism in Arthrobacter sp. strain Rue61a are clustered on the linear plasmid pAL1 in two upper pathway operons (meqABC and meqDEF) coding for quinaldine conversion to anthranilate and a lower pathway operon encoding anthranilate degradation via coenzyme A (CoA) thioester intermediates. The meqR2 gene, located immediately downstream of the catabolic genes, codes for a PaaX-type transcriptional repressor. MeqR2, purified as recombinant fusion protein, forms a dimer in solution and shows specific and cooperative binding to promoter DNA in vitro. DNA fragments recognized by MeqR2 contained a highly conserved palindromic motif, 5'-TGACGNNCGTcA-3', which is located at positions -35 to -24 of the two promoters that control the upper pathway operons, at positions +4 to +15 of the promoter of the lower pathway genes and at positions +53 to +64 of the meqR2 promoter. Disruption of the palindrome abolished MeqR2 binding. The dissociation constants (K(D)) of MeqR2-DNA complexes as deduced from electrophoretic mobility shift assays were very similar for the four promoters tested (23 nM to 28 nM). Anthraniloyl-CoA was identified as the specific effector of MeqR2, which impairs MeqR2-DNA complex formation in vitro. A binding stoichiometry of one effector molecule per MeqR2 monomer and a K(D) of 22 nM were determined for the effector-protein complex by isothermal titration calorimetry (ITC). Quantitative reverse transcriptase PCR analyses suggested that MeqR2 is a potent regulator of the meqDEF operon; however, additional regulatory systems have a major impact on transcriptional control of the catabolic operons and of meqR2.
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Niewerth H, Schuldes J, Parschat K, Kiefer P, Vorholt JA, Daniel R, Fetzner S. Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. Rue61a. BMC Genomics 2012; 13:534. [PMID: 23039946 PMCID: PMC3534580 DOI: 10.1186/1471-2164-13-534] [Citation(s) in RCA: 52] [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: 07/14/2012] [Accepted: 10/01/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Bacteria of the genus Arthrobacter are ubiquitous in soil environments and can be considered as true survivalists. Arthrobacter sp. strain Rue61a is an isolate from sewage sludge able to utilize quinaldine (2-methylquinoline) as sole carbon and energy source. The genome provides insight into the molecular basis of the versatility and robustness of this environmental Arthrobacter strain. RESULTS The genome of Arthrobacter sp. Rue61a consists of a single circular chromosome of 4,736,495 bp with an average G + C content of 62.32%, the circular 231,551-bp plasmid pARUE232, and the linear 112,992-bp plasmid pARUE113 that was already published. Plasmid pARUE232 is proposed to contribute to the resistance of Arthrobacter sp. Rue61a to arsenate and Pb2+, whereas the linear plasmid confers the ability to convert quinaldine to anthranilate. Remarkably, degradation of anthranilate exclusively proceeds via a CoA-thioester pathway. Apart from quinaldine utilization, strain Rue61a has a limited set of aromatic degradation pathways, enabling the utilization of 4-hydroxy-substituted aromatic carboxylic acids, which are characteristic products of lignin depolymerization, via ortho cleavage of protocatechuate. However, 4-hydroxyphenylacetate degradation likely proceeds via meta cleavage of homoprotocatechuate. The genome of strain Rue61a contains numerous genes associated with osmoprotection, and a high number of genes coding for transporters. It encodes a broad spectrum of enzymes for the uptake and utilization of various sugars and organic nitrogen compounds. A. aurescens TC-1 is the closest sequenced relative of strain Rue61a. CONCLUSIONS The genome of Arthrobacter sp. Rue61a reflects the saprophytic lifestyle and nutritional versatility of the organism and a strong adaptive potential to environmental stress. The circular plasmid pARUE232 and the linear plasmid pARUE113 contribute to heavy metal resistance and to the ability to degrade quinaldine, respectively.
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Affiliation(s)
- Heiko Niewerth
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149, Münster, Germany
| | - Jörg Schuldes
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, 37077, Göttingen, Germany
| | - Katja Parschat
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149, Münster, Germany
- Present address: Jennewein Biotechnologie GmbH, 53619, Rheinbreitbach, Germany
| | - Patrick Kiefer
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, 37077, Göttingen, Germany
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149, Münster, Germany
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Ganzert L, Bajerski F, Mangelsdorf K, Lipski A, Wagner D. Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil. Int J Syst Evol Microbiol 2011; 61:979-984. [DOI: 10.1099/ijs.0.021022-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel cold-tolerant, Gram-stain-positive, motile, facultatively anaerobic bacterial strains, LI2T and LI3T, were isolated from moss-covered soil from Livingston Island, Antarctica, near the Bulgarian station St Kliment Ohridski. A rod–coccus cycle was observed for both strains. 16S rRNA gene sequence analysis revealed an affiliation to the genus Arthrobacter, with the highest similarity to Arthrobacter stackebrandtii and Arthrobacter psychrochitiniphilus for strain LI2T (97.8 and 97.7 % similarity to the respective type strains) and to Arthrobacter kerguelensis and Arthrobacter psychrophenolicus for strain LI3T (97.4 and 97.3 % similarity to the respective type strains). The growth temperature range was −6 to 28 °C for LI2T and −6 to 24 °C for LI3T, with an optimum at 16 °C for both strains. Growth occurred at 0–10 % (w/v) NaCl, with optimum growth at 0–1 % (w/v) for LI2T and 0.5–3 % (w/v) for LI3T. The pH range for growth was pH 4–9.5 with an optimum of pH 8 for LI2T and pH 6.5 for LI3T. The predominant fatty acids were anteiso-C15 : 0, C18 : 0 and anteiso-C17 : 0 for LI2T and anteiso-C15 : 0 and C18 : 0 for LI3T. Physiological and biochemical tests clearly differentiated strain LI2T from A. stackebrandtii and A. psychrochitiniphilus and strain LI3T from A. kerguelensis and A. psychrophenolicus. Therefore, two novel species within the genus Arthrobacter are proposed: Arthrobacter livingstonensis sp. nov. (type strain LI2T = DSM 22825T = NCCB 100314T) and Arthrobacter cryotolerans sp. nov. (type strain LI3T = DSM 22826T = NCCB 100315T).
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Affiliation(s)
- Lars Ganzert
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany
| | - Felizitas Bajerski
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany
| | - Kai Mangelsdorf
- Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Section 4.3, Organic Geochemistry, Telegrafenberg B 423, 14473 Potsdam, Germany
| | - André Lipski
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Dirk Wagner
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany
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Salwan R, Gulati A, Kasana RC. Phylogenetic diversity of alkaline protease-producing psychrotrophic bacteria from glacier and cold environments of Lahaul and Spiti, India. J Basic Microbiol 2010; 50:150-9. [PMID: 20082368 DOI: 10.1002/jobm.200800400] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The diversity of proteolytic bacteria associated with a glacier and cold environment soils from three different locations in Lahaul and Spiti, India was investigated. Two hundred seventeen bacterial strains were isolated in pure culture. Subsequently these strains were screened for protease-production and one hundred nine showed protease production. From these protease producing psychrotrophic bacteria twenty showing high enzyme production at low temperature and alkaline pH were characterized and identified. The 16S rRNA phylogenetic analysis revealed that none of the strains showed 100% identity with the validly published species of various genera. Isolates belonged to three classes i.e. Actinobacteria, Gammaproteobacteria and Alphaproteobacteria, and were affiliated with the genera Acinetobacter, Arthrobacter, Mycoplana, Pseudomonas, Pseudoxanthomonas, Serratia and Stenotrophomonas. The optimal growth temperature ranged from 10 to 28 degrees C and interestingly, high levels of enzyme productions were measured at growth temperatures between 15 and 25 degrees C, for most of the isolates in plate assay. Most of the isolates were found to produce at least two other hydrolytic enzymes along with protease. The crude protease from one strain was active over broad range of temperature and pH with optima at 30 degrees C and 7.5, respectively. The protease activity was enhanced by Ca(2+), dithiothreitol and beta-mercaptoethanol. While Na(+), Hg(2+), Zn(2+), Mn(2+), phenylmethanesulfonyl fluoride and ethylenediaminetetraacetic acid did not showed much effect on protease activity. The results enrich our knowledge on the psychrotrophic bacterial diversity and biogeographic distribution of enzyme producing bacteria in western Himalaya.
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Affiliation(s)
- Richa Salwan
- Institute of Himalayan Bioresource Technology (CSIR), Palampur (HP)-176061, India
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Baik KS, Park SC, Kim EM, Bae KS, Ahn JH, Ka JO, Chun J, Seong CN. Diversity of bacterial community in freshwater of Woopo wetland. J Microbiol 2008; 46:647-55. [PMID: 19107393 DOI: 10.1007/s12275-008-0135-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 09/03/2008] [Indexed: 11/28/2022]
Abstract
Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones. Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher than that of isolated bacteria.
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Affiliation(s)
- Keun Sik Baik
- Department of Biology, Sunchon National University, Suncheon, 540-742, Republic of Korea
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24
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Mages IS, Frodl R, Bernard KA, Funke G. Identities of Arthrobacter spp. and Arthrobacter-like bacteria encountered in human clinical specimens. J Clin Microbiol 2008; 46:2980-6. [PMID: 18650355 PMCID: PMC2546711 DOI: 10.1128/jcm.00658-08] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 05/07/2008] [Accepted: 07/11/2008] [Indexed: 11/20/2022] Open
Abstract
After the initial description of Arthrobacter spp. isolated from clinical specimens in the mid-1990s, very few further reports on Arthrobacter spp. have appeared in the clinical microbiology literature. The aim of the present study was to elucidate the distribution of Arthrobacter spp. and Arthrobacter-like bacteria encountered in clinical specimens by studying 50 consecutively isolated or received strains of large-colony-forming, whiteish-grayish, non-cheese-like-smelling, nonfermentative gram-positive rods by applying phenotypic methods as well as 16S rRNA gene sequencing. We observed a very heterogenous distribution, with the 50 strains belonging to 20 different taxa and each of 13 strains as a single representative of its particular taxon. Thirty-eight strains represented true Arthrobacter strains, 7 strains belonged to the genus Brevibacterium, 2 were Microbacterium species, and each of 3 single strains was a member of the rarely encountered genera Pseudoclavibacter, Leucobacter, and Brachybacterium, respectively. A. cumminsii (n = 14) and A. oxydans (n = 11) were the most frequently found species. The present report describes the first three A. aurescens strains isolated from human clinical specimens. Comprehensive antimicrobial susceptibility data are given for the 38 Arthrobacter isolates.
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Affiliation(s)
- Irene S Mages
- Department of Medical Microbiology and Hygiene, Gärtner & Colleagues Laboratories, Ravensburg, Germany
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25
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Del Giudice L, Massardo DR, Pontieri P, Bertea CM, Mombello D, Carata E, Tredici SM, Talà A, Mucciarelli M, Groudeva VI, De Stefano M, Vigliotta G, Maffei ME, Alifano P. The microbial community of Vetiver root and its involvement into essential oil biogenesis. Environ Microbiol 2008; 10:2824-41. [PMID: 18662308 DOI: 10.1111/j.1462-2920.2008.01703.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vetiver is the only grass cultivated worldwide for the root essential oil, which is a mixture of sesquiterpene alcohols and hydrocarbons, used extensively in perfumery and cosmetics. Light and transmission electron microscopy demonstrated the presence of bacteria in the cortical parenchymatous essential oil-producing cells and in the lysigen lacunae in close association with the essential oil. This finding and the evidence that axenic Vetiver produces in vitro only trace amounts of oil with a strikingly different composition compared with the oils from in vivo Vetiver plants stimulated the hypothesis of an involvement of these bacteria in the oil metabolism. We used culture-based and culture-independent approaches to analyse the microbial community of the Vetiver root. Results demonstrate a broad phylogenetic spectrum of bacteria, including alpha-, beta- and gamma-Proteobacteria, high-G+C-content Gram-positive bacteria, and microbes belonging to the Fibrobacteres/Acidobacteria group. We isolated root-associated bacteria and showed that most of them are able to grow by using oil sesquiterpenes as a carbon source and to metabolize them releasing into the medium a large number of compounds typically found in commercial Vetiver oils. Several bacteria were also able to induce gene expression of a Vetiver sesquiterpene synthase. These results support the intriguing hypothesis that bacteria may have a role in essential oil biosynthesis opening the possibility to use them to manoeuvre the Vetiver oil molecular structure.
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Affiliation(s)
- Luigi Del Giudice
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', Consiglio Nazionale delle Ricerche, via Pietro Castellino 111, 80131 Naples, Italy
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26
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Arthrobacter soli sp. nov., a novel bacterium isolated from wastewater reservoir sediment. J Microbiol 2008; 46:40-4. [DOI: 10.1007/s12275-007-0239-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Ferreira MIM, Marchesi JR, Janssen DB. Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1. Appl Microbiol Biotechnol 2008; 78:709-17. [PMID: 18228015 PMCID: PMC2266783 DOI: 10.1007/s00253-008-1343-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 12/26/2007] [Accepted: 12/30/2007] [Indexed: 11/25/2022]
Abstract
A Gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-FP) as the sole source of carbon and energy was isolated by selective enrichment from soil samples collected near an industrial site. The organism, designated strain IF1, was identified as a member of the genus Arthrobacter on the basis of 16S ribosomal RNA gene sequence analysis. Arthrobacter strain IF1 was able to mineralize 4-FP up to concentrations of 5 mM in batch culture. Stoichiometric release of fluoride ions was observed, suggesting that there is no formation of halogenated dead-end products during 4-FP metabolism. The degradative pathway of 4-FP was investigated using enzyme assays and identification of intermediates by gas chromatography (GC), GC-mass spectrometry (MS), high-performance liquid chromatography, and liquid chromatography-MS. Cell-free extracts of 4-FP-grown cells contained no activity for catechol 1,2-dioxygenase or catechol 2,3-dioxygenase, which indicates that the pathway does not proceed through a catechol intermediate. Cells grown on 4-FP oxidized 4-FP, hydroquinone, and hydroxyquinol but not 4-fluorocatechol. During 4-FP metabolism, hydroquinone accumulated as a product. Hydroquinone could be converted to hydroxyquinol, which was further transformed into maleylacetic acid and beta-ketoadipic acid. These results indicate that the biodegradation of 4-FP starts with a 4-FP monooxygenase reaction that yields benzoquinone, which is reduced to hydroquinone and further metabolized via the beta-ketoadipic acid pathway.
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Affiliation(s)
- Maria Isabel M. Ferreira
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, NL-9747 AG Groningen, The Netherlands
| | - Julian R. Marchesi
- Department of Microbiology/Alimentary Pharmabiotic Centre, University College Cork, College Road, Cork, Ireland
| | - Dick B. Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, NL-9747 AG Groningen, The Netherlands
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28
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Tvrzová L, Schumann P, Spröer C, Sedláček I, Páčová Z, Šedo O, Zdráhal Z, Steffen M, Lang E. Pseudomonas moraviensis sp. nov. and Pseudomonas vranovensis sp. nov., soil bacteria isolated on nitroaromatic compounds, and emended description of Pseudomonas asplenii. Int J Syst Evol Microbiol 2007; 56:2657-2663. [PMID: 17082407 DOI: 10.1099/ijs.0.63988-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Two strains of Gram-negative bacteria isolated from soil by selective enrichment with nitroaromatics were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence analysis, the two strains were found to belong to the genus Pseudomonas, within the Gammaproteobacteria. Strain 1B4T shared the highest sequence similarity with Pseudomonas koreensis DSM 16610T (99.5%) and Pseudomonas jessenii CCM 4840T (99.3%), and strain 2B2T with Pseudomonas asplenii DSM 17133T (98.9%), Pseudomonas fuscovaginae DSM 7231T (98.9%) and Pseudomonas putida DSM 291T (98.7%). On the basis of phylogenetic analysis, DNA-DNA hybridization and phenotype, including chemotaxonomic characteristics, two novel species, Pseudomonas moraviensis sp. nov. with the type strain 1B4T (=CCM 7280T=DSM 16007T) and Pseudomonas vranovensis sp. nov. with the type strain 2B2T (=CCM 7279T=DSM 16006T), are proposed. The description of P. asplenii was emended on the basis of additional data obtained in this study.
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Affiliation(s)
- Ludmila Tvrzová
- Department of Microbiology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, 602 00 Brno, Czech Republic
| | - Peter Schumann
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Ivo Sedláček
- CCM - Czech Collection of Microorganisms, Institute of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, 602 00 Brno, Czech Republic
| | - Zdena Páčová
- CCM - Czech Collection of Microorganisms, Institute of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, 602 00 Brno, Czech Republic
| | - Ondrej Šedo
- Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, 602 00 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, 602 00 Brno, Czech Republic
| | - Maike Steffen
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Elke Lang
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
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29
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Paul D, Pandey G, Meier C, van der Meer JR, Jain RK. Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation. FEMS Microbiol Ecol 2006; 57:116-27. [PMID: 16819955 DOI: 10.1111/j.1574-6941.2006.00103.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The introduction of culture-independent molecular screening techniques, especially based on 16S rRNA gene sequences, has allowed microbiologists to examine a facet of microbial diversity not necessarily reflected by the results of culturing studies. The bacterial community structure was studied for a pesticide-contaminated site that was subsequently remediated using an efficient degradative strain Arthrobacter protophormiae RKJ100. The efficiency of the bioremediation process was assessed by monitoring the depletion of the pollutant, and the effect of addition of an exogenous strain on the existing soil community structure was determined using molecular techniques. The 16S rRNA gene pool amplified from the soil metagenome was cloned and restriction fragment length polymorphism studies revealed 46 different phylotypes on the basis of similar banding patterns. Sequencing of representative clones of each phylotype showed that the community structure of the pesticide-contaminated soil was mainly constituted by Proteobacteria and Actinomycetes. Terminal restriction fragment length polymorphism analysis showed only nonsignificant changes in community structure during the process of bioremediation. Immobilized cells of strain RKJ100 enhanced pollutant degradation but seemed to have no detectable effects on the existing bacterial community structure.
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Affiliation(s)
- Debarati Paul
- Institute of Microbial Technology, Chandigarh, India
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30
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Tvrzová L, Prokop Z, Navrátilová J, Müllerová R, Neca J. Development of a microtiter plate-based method for determination of degradation profile of nitrophenolic compounds. J Microbiol Methods 2006; 65:551-6. [PMID: 16289394 DOI: 10.1016/j.mimet.2005.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 09/30/2005] [Accepted: 09/30/2005] [Indexed: 11/15/2022]
Abstract
A microtiter plate-based assay was developed for the automatic monitoring of degradation profile of the yellow-coloured nitrophenolic compounds. The method enables to reduce the intervals between measurements of substrate concentration to minutes and to overcome the problem of discontinuity of sampling typical for conventional methods. The concentrations of nitrophenolic compounds were calculated from the absorbance values determined automatically by BIOSCREEN C. Verification of the method was based on the comparison of results with the conventional HPLC method results. The values of the rate and saturation constants were comparable for both the microtiter plate-based assay and the conventional HPLC method. The automatic method described here seems to be efficient for the screening degradation studies, which requires the treatment of quantity of samples.
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Affiliation(s)
- Ludmila Tvrzová
- Department of Microbiology, Faculty of Science, Masaryk University Brno, Czech Republic.
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31
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Tvrzová L, Schumann P, Spröer C, Sedláček I, Verbarg S, Kroppenstedt RM, Páčová Z. Polyphasic taxonomic study of strain CCM 2783 resulting in the description of Arthrobacter stackebrandtii sp. nov. Int J Syst Evol Microbiol 2005; 55:805-808. [PMID: 15774666 DOI: 10.1099/ijs.0.63428-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain CCM 2783, previously classified as representing Arthrobacter aurescens, was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis and chemotaxonomic characteristics such as peptidoglycan type A3α Lys–Ala2, major menaquinone MK-9(H2) and fatty acid composition confirmed assignment of the strain to the genus Arthrobacter. The results of phylogenetic analysis, DNA–DNA relatedness experiments and physiological and chemotaxonomic characteristics indicate that CCM 2783 differs from its nearest phylogenetic relative Arthrobacter psychrolactophilus and from other recognized Arthrobacter species. Therefore, a novel species, Arthrobacter stackebrandtii sp. nov., is proposed with the type strain CCM 2783T (=DSM 16005T).
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Affiliation(s)
- Ludmila Tvrzová
- Department of Microbiology, Faculty of Science, Masaryk University Brno, Tvrdého 14, 602 00 Brno, Czech Republic
| | - Peter Schumann
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Ivo Sedláček
- CCM - Czech Collection of Microorganisms, Masaryk University Brno, Tvrdého 14, 602 00 Brno, Czech Republic
| | - Susanne Verbarg
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Reiner M Kroppenstedt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Zdena Páčová
- CCM - Czech Collection of Microorganisms, Masaryk University Brno, Tvrdého 14, 602 00 Brno, Czech Republic
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32
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Huang Y, Zhao N, He L, Wang L, Liu Z, You M, Guan F. Arthrobacter scleromae sp. nov. isolated from human clinical specimens. J Clin Microbiol 2005; 43:1451-5. [PMID: 15750131 PMCID: PMC1081264 DOI: 10.1128/jcm.43.3.1451-1455.2005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 10/07/2004] [Accepted: 11/02/2004] [Indexed: 11/20/2022] Open
Abstract
A gram-positive, coryneform bacterium was isolated from swollen scleromata of a dermatosis patient. An analysis of its phenotypic, chemotaxonomic, and genotypic characteristics showed that this bacterium is closely associated with Arthrobacter oxydans and Arthrobacter polychromogenes but that it belongs to a distinct species, for which the name Arthrobacter scleromae sp. nov. is proposed.
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Affiliation(s)
- Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People's Republic of China.
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