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Funnicelli MIG, de Carvalho LAL, Teheran-Sierra LG, Dibelli SC, Lemos EGDM, Pinheiro DG. Unveiling genomic features linked to traits of plant growth-promoting bacterial communities from sugarcane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174577. [PMID: 38981540 DOI: 10.1016/j.scitotenv.2024.174577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
Microorganisms are ubiquitous, and those inhabiting plants have been the subject of several studies. Plant-associated bacteria exhibit various biological mechanisms that enable them to colonize host plants and, in some cases, enhance their fitness. In this study, we describe the genomic features predicted to be associated with plant growth-promoting traits in six bacterial communities isolated from sugarcane. The use of highly accurate single-molecule real-time sequencing technology for metagenomic samples from these bacterial communities allowed us to recover 17 genomes. The taxonomic assignments for the binned genomes were performed, revealing taxa distributed across three main phyla: Bacillota, Bacteroidota, and Pseudomonadota, with the latter being the most representative. Subsequently, we functionally annotated the metagenome-assembled genomes (MAGs) to characterize their metabolic pathways related to plant growth-promoting traits. Our study successfully identified the enrichment of important functions related to phosphate and potassium acquisition, modulation of phytohormones, and mechanisms for coping with abiotic stress. These findings could be linked to the robust colonization of these sugarcane endophytes.
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Affiliation(s)
- Michelli Inácio Gonçalves Funnicelli
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Lucas Amoroso Lopes de Carvalho
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Luis Guillermo Teheran-Sierra
- Agronomy Research Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, Bogotá 111121, Colombia
| | - Sabrina Custodio Dibelli
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Molecular Biology Laboratory, Institute for Research in Bioenergy (IPBEN), São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Daniel Guariz Pinheiro
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil.
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2
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Li C, Chen R, Ouyang W, Xue C, Liu M, Liu H. The response of C/N/S cycling functional microbial communities to redox conditions in shallow aquifers using in-situ sediment as bio-trap matrix. ENVIRONMENTAL TECHNOLOGY 2024; 45:3666-3678. [PMID: 37323025 DOI: 10.1080/09593330.2023.2225704] [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: 12/03/2022] [Accepted: 05/20/2023] [Indexed: 06/17/2023]
Abstract
Microbial communities are fundamental components driving critical biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycles in groundwater ecosystems. The reduction-oxidation (redox) potential is one important environmental factor influencing the microbial community composition. Here, we developed a bio-trap method using in-situ sediment as a matrix to collect aquifer sediment samples and evaluate the response of microbial composition and C/N/S cycling functions to redox variations created by providing sole O2, joint O2 and H2, and sole H2 to three wells. Illumina sequencing analyses showed that the microbial communities in the bio-trap sediment could respond quickly to redox changes in the wells, demonstrating that this bio-trap method is promising for detecting microbial variation in the aquifer sediment. The microbial metabolic functions related to C, N and S cyclings and organic pollutants degradation were predicted by the Kyoto Encyclopedia of Genes and Genomes (KEGG) approach. It was found that the joint O2 and H2 injection produced medium oxidation-reduction potential (ORP -346 and -614 mV) and enhanced more microbial functions than sole O2 or H2, which mainly include oxidative phosphorylation, most carbon source metabolism, various pollutants degradation, and nitrogen and sulfur metabolism. Moreover, the functional genes encoding phenol monooxygenase, dioxygenase, nitrogen fixation, nitrification, aerobic and anaerobic nitrate reductase, nitrite reductase, nitric oxide reductase, and sulfur oxidation increased. These findings tell us the contaminant bioremediation and N, S metabolism can be promoted by adjusting ORP realised by injecting joint O2 and H2.
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Affiliation(s)
- Cui Li
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
- Hubei Ecology Polytechnic College, Wuhan, People's Republic of China
| | - Rong Chen
- School of Environmental and Biological Engineering, Wuhan Technology and Business University, Wuhan, People's Republic of China
| | - Weiwei Ouyang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
| | - Chen Xue
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
| | - Minghui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
| | - Hui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, People's Republic of China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
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3
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Cai Z, Karunakaran E, Pandhal J. Bottom-up construction and screening of algae-bacteria consortia for pollutant biodegradation. Front Microbiol 2024; 15:1349016. [PMID: 38389536 PMCID: PMC10883772 DOI: 10.3389/fmicb.2024.1349016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/17/2024] [Indexed: 02/24/2024] Open
Abstract
Microbial communities have been used as important biological tools for a variety of purposes associated with agriculture, the food industry and human health. Artificial engineering of microbial communities is an emerging field of research motivated by finding stable and efficient microbial systems. However, the successful design of microbial communities with desirable functions not only requires profound understanding of microbial activities, but also needs efficient approaches to piece together the known microbial traits to give rise to more complex systems. This study demonstrates the bottom-up integration of environmentally isolated phototrophic microalgae and chemotrophic bacteria as artificial consortia to bio-degrade selected volatile organic compounds (VOCs). A high throughput screening method based on 96-well plate format was developed for discovering consortia with bioremediation potential. Screened exemplar consortia were verified for VOCs degradation performance, among these, certain robust consortia were estimated to have achieved efficiencies of 95.72% and 92.70% and near 100% removal (7 days) of benzene, toluene, and phenol, respectively, with initial concentrations of 100 mg/L. VOCs degradation by consortia was mainly attributed to certain bacteria including Rhodococcus erythropolis, and Cupriavidus metallidurans, and directly contributed to the growth of microalgae Coelastrella terrestris (R = 0.82, p < 0.001). This work revealed the potential of converting VOCs waste into algal biomass by algae-bacteria consortia constructed through a bottom-up approach. The screening method enables rapid shortlisting of consortia combinatorial scenarios without prior knowledge about the individual strains or the need for interpreting complex microbial interactions.
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Affiliation(s)
- Zongting Cai
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
- Grantham Centre for Sustainable Futures, The University of Sheffield, Sheffield, United Kingdom
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
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4
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Wu Z, Liu G, Ji Y, Li P, Yu X, Qiao W, Wang B, Shi K, Liu W, Liang B, Wang D, Yanuka-Golub K, Freilich S, Jiang J. Electron acceptors determine the BTEX degradation capacity of anaerobic microbiota via regulating the microbial community. ENVIRONMENTAL RESEARCH 2022; 215:114420. [PMID: 36167116 DOI: 10.1016/j.envres.2022.114420] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/06/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Anaerobic degradation is the major pathway for microbial degradation of benzene, toluene, ethylbenzene, and xylenes (BTEX) under electron acceptor lacking conditions. However, how exogenous electron acceptors modulate BTEX degradation through shaping the microbial community structure remains poorly understood. Here, we investigated the effect of various exogenous electron acceptors on BTEX degradation as well as methane production in anaerobic microbiota, which were enriched from the same contaminated soil. It was found that the BTEX degradation capacities of the anaerobic microbiota gradually increased along with the increasing redox potentials of the exogenous electron acceptors supplemented (WE: Without exogenous electron acceptors < SS: Sulfate supplement < FS: Ferric iron supplement < NS: Nitrate supplement), while the complexity of the co-occurring networks (e.g., avgK and links) of the microbiota gradually decreased, showing that microbiota supplemented with higher redox potential electron acceptors were less dependent on the formation of complex microbial interactions to perform BTEX degradation. Microbiota NS showed the highest degrading capacity and the broadest substrate-spectrum for BTEX, and it could metabolize BTEX through multiple modules which not only contained fewer species but also different key microbial taxa (eg. Petrimonas, Achromobacter and Comamonas). Microbiota WE and FS, with the highest methanogenic capacities, shared common core species such as Sedimentibacter, Acetobacterium, Methanobacterium and Smithella/Syntrophus, which cooperated with Geobacter (microbiota WE) or Desulfoprunum (microbiota FS) to perform BTEX degradation and methane production. This study demonstrates that electron acceptors may alter microbial function by reshaping microbial community structure and regulating microbial interactions and provides guidelines for electron acceptor selection for bioremediation of aromatic pollutant-contaminated anaerobic sites.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Guiping Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Yanhan Ji
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Xin Yu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Wenjing Qiao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Ke Shi
- State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Wenzhong Liu
- State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Dong Wang
- Jiangsu Academy of Environmental Science and Technology Co., Ltd, Nanjing, 210095, China
| | - Keren Yanuka-Golub
- The Galilee Society Institute of Applied Research, Shefa-Amr, 20200, Israel
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions. Antonie Van Leeuwenhoek 2022; 115:1113-1128. [PMID: 35841500 PMCID: PMC9363352 DOI: 10.1007/s10482-022-01759-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022]
Abstract
In the present study, the bacterial community structure of enrichment cultures degrading benzene under microaerobic conditions was investigated through culturing and 16S rRNA gene Illumina amplicon sequencing. Enrichments were dominated by members of the genus Rhodoferax followed by Pseudomonas and Acidovorax. Additionally, a pale amber-coloured, motile, Gram-stain-negative bacterium, designated B7T was isolated from the microaerobic benzene-degrading enrichment cultures and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene and whole genome-based phylogenetic analyses revealed that strain B7T formed a lineage within the family Comamonadaceae, clustered as a member of the genus Ideonella and most closely related to Ideonella dechloratans CCUG 30977T. The sole respiratory quinone is ubiquinone-8. The major fatty acids are C16:0 and summed feature 3 (C16:1ω7c/iso-C15:0 2-OH). The DNA G + C content of the type strain is 68.8 mol%. The orthologous average nucleotide identity (OrthoANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain B7T and closest relatives were below the threshold values for species demarcation. The genome of strain B7T, which is approximately 4.5 Mb, contains a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including a I.2.C-type catechol 2,3-dioxygenase (C23O) gene. As predicted by the genome, the type strain is involved in aromatic hydrocarbon-degradation: benzene, toluene and ethylbenzene are degraded aerobically and also microaerobically as sole source of carbon and energy. Based on phenotypic characteristics and phylogenetic analysis, strain B7T is a member of the genus Ideonella and represents a novel species for which the name Ideonella benzenivorans sp. nov. is proposed. The type strain of the species is strain B7T (= LMG 32,345T = NCAIM B.02664T).
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Kim KH, Baek JH, Wenting R, Jeon CO. Rheinheimera maricola sp. nov., isolated from seawater of the Yellow Sea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005423] [Citation(s) in RCA: 4] [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-negative and facultative aerobic strain, designated as strain MA-13T, was isolated from seawater in the Yellow Sea Republic of Korea. Cells were oxidase- and catalase-positive and non-motile short rods. Growth of strain MA-13T was observed over a range of 10–37 °C (optimum, 30 °C), pH 6.0–11.0 (optimum, pH 7.0) and in the presence of 0–5.5 % (w/v) sodium chloride (optimum, 1.0–2.0 %). Strain MA-13T contained ubiquinone-8 as the respiratory quinone, phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and four unidentified lipids as major polar lipids and C16 : 0, C12 : 0 3-OH and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) as major cellular fatty acids. The G+C content of the genomic DNA was 48.3 mol%. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain MA-13T formed a distinct phyletic lineage in the genus
Rheinheimera
. Strain MA-13T was most closely related to
Rheinheimera lutimaris
YQF-2T,
Rheinheimera aquimaris
SW-353T,
Rheinheimera pacifica
KMM 1406T and
Rheinheimera baltica
DSM 14885T with 98.10, 98.08, 98.07 and 97.94 % 16S rRNA gene sequence similarities. Average nucleotide identity and DNA–DNA hybridization values between strain MA-13T and
R. aquimaris
KCTC 12840T,
R. pacifica
DSM 17616T and
R. baltica
DSM 14885T were 76.3, 78.6 and 76.9 % and 19.5, 21.3 and 20.5 %, respectively. Based on the phenotypic, chemotaxonomic and molecular features, strain MA-13T represents a novel species of the genus
Rheinheimera
, for which the name Rheinheimera maricola sp. nov. is proposed. The type strain is MA-13T (=KACC 22113T=JCM 34600T).
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Affiliation(s)
- Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ruan Wenting
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Arslan M, Müller JA, Gamal El-Din M. Aerobic naphthenic acid-degrading bacteria in petroleum-coke improve oil sands process water remediation in biofilters: DNA-stable isotope probing reveals methylotrophy in Schmutzdecke. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:151961. [PMID: 34843771 DOI: 10.1016/j.scitotenv.2021.151961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
There is an increasing interest in treatment of oil sands process water (OSPW) via biofiltration with petroleum coke (PC) as a substratum. In fixed bed biofilters (FBBs) with PC, the dominance of anaerobic digestion of dissolved organics results in poor removal of naphthenic acids (NAs) along with a high degree of methanogenesis. In this study, the operation of FBBs was modified to improve OSPW remediation by supporting the filtering bed with aerobic naphthenic acid-degrading bacteria treating aerated OSPW (FBBbioaugmentation). The results were compared with a biofilter operated under controlled conditions (FBBcontrol). To this end, a consortium of three aerobic NAs-degrading bacterial strains was immobilized on PC as a top layer (10 cm). These bacteria were pre-screened for growth on 15 different NAs surrogates as a sole carbon source, and for the presence of catabolic genes coding alkane hydroxylase (CYP153) and alkane monooxygenase (alkB) enzymes. The results illustrated that biofiltration in FBBbioaugmentation removed 32% of classical NAs in 15 days; while in the FBBcontrol, degradation was limited to 19%. The degradation of fluorophore (aromatic) compounds was also improved from 16% to 39% for single ring (OI), 22% to 29% for double ring (OII), and 15% to 23% for three rings (OIII) compounds. DNA-Stable Isotope Probing revealed that potential hydrocarbons degraders such as Pseudomonas (inoculated), Pseudoxanthomonas (indigenous) were present up to 9.0% in the 13C-labelled DNA fraction. Furthermore, a high abundance of methylotrophs was observed in the Schmutzdecke, with Methylobacillus comprising more than two-third of the total community. This study shows that bioaugmentation rapidly improved OSPW remediation. Aeration mostly contributed to methane consumption in the top layer, thus minimizing its release into the environment.
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Affiliation(s)
- Muhammad Arslan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Jochen A Müller
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada.
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Kim KH, Kristyanto S, Kim HM, Kim KR, Jeon CO. Nitratireductor rhodophyticola sp. nov., isolated from marine red algae. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, strictly aerobic bacteria, strains L1-7-SET and R6, isolated from marine red algae, were characterized. They shared 99.9 % 16S rRNA gene sequence similarity and a 100 % digital DNA–DNA hybridization (DDH) value, representing members of a single species. Cells of strains L1-7-SET and R6 were catalase- and oxidase-positive motile rods with a single polar flagellum. Strains L1-7-SET and R6 optimally grew at 30–35 °C, pH 7.0–8.0 and with 1.0–2.0 % (w/v) NaCl. Ubiquinone-10 was the sole isoprenoid quinone and C19 : 0 cyclo ω8c and summed feature 8 (comprising C18 : 1
ω7c and/or C18 : 1
ω6c) were detected as the major cellular fatty acids. The DNA G+C contents of strains L1-7-SET and R6 were both 61.62 mol%. The polar lipids of strain L1-7-SET consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and two unidentified polar lipids. Phylogenetic analyses based on 16S rRNA gene and 120 protein marker sequences revealed that strains L1-7-SET and R6 formed a phyletic lineage within the genus
Nitratireductor
and they were most closely related to
Nitratireductor aquibiodomus
NL21T and
Nitratireductor kimnyeongensis
KY 101T with both 98.8 % 16S rRNA gene sequence similarities. Digital DDH values between strain L1-7-SET and the type strains of
N. aquibiodomus
and
N. kimnyeongensis
were 60.3 and 29.5 %, respectively. The phenotypic, chemotaxonomic and molecular features support that strains L1-7-SET and R6 represents a novel species of the genus
Nitratireductor
, for which the name Nitratireductor rhodophyticola sp. nov. is proposed. The type strain is L1-7-SET (=KACC 19076T=KCTC 92231T=JCM 31802T).
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Affiliation(s)
- Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sylvia Kristyanto
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyung Min Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyeong Ryeol Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Kracmarova M, Uhlik O, Strejcek M, Szakova J, Cerny J, Balik J, Tlustos P, Kohout P, Demnerova K, Stiborova H. Soil microbial communities following 20 years of fertilization and crop rotation practices in the Czech Republic. ENVIRONMENTAL MICROBIOME 2022; 17:13. [PMID: 35346385 PMCID: PMC8962459 DOI: 10.1186/s40793-022-00406-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/08/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Although fertilization and crop rotation practices are commonly used worldwide in agriculture to maximize crop yields, their long-term effect on the structures of soil microorganisms is still poorly understood. This study investigated the long-term impact of fertilization and crop rotation on soil microbial diversity and the microbial community structure in four different locations with three soil types. Since 1996, manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and NPK (NPK; 330 kg N/ha) fertilizers were periodically applied to the soils classified as chernozem, luvisol and cambisol, which are among the most abundant or fertile soils used for agricultural purposes in the world. In these soils, potato (Solanum tuberosum L.), winter wheat (Triticum aestivum L.), and spring barley (Hordeum vulgare L.) were rotated every three years. RESULTS Soil chemistry, which was significantly associated with location, fertilization, crop rotation, and the interaction of fertilization and location, was the dominant driver of soil microbial communities, both prokaryotic and fungal. A direct effect of long-term crop rotation and fertilization on the structure of their communities was confirmed, although there was no evidence of their influence on microbial diversity. Fungal and bacterial communities responded differently to fertilization treatments; prokaryotic communities were only significantly different from the control soil (CF) in soils treated with MF and SF3x, while fungal communities differed across all treatments. Indicator genera were identified for different treatments. These taxa were either specific for their decomposition activities or fungal plant pathogens. Sequential rotation of the three crops restricted the growth of several of the indicator plant pathogens. CONCLUSIONS Long-term fertilization and crop rotation significantly altered microbial community structure in the soil. While fertilization affected soil microorganisms mainly through changes in nutrient profile, crop rotations lead to the attraction and repulsion of specific plant pathogens. Such changes in soil microbial communities need to be considered when planning soil management.
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Affiliation(s)
- Martina Kracmarova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Jirina Szakova
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jindrich Cerny
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jiri Balik
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Pavel Tlustos
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Videnska 1083, 142 20, Praha 4, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Vinicna 5, 128 44, Praha 2, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
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KIm KH, Seo YL, Baek JH, Jin HM, Jeon CO. Paenibacillus agri sp. nov., isolated from soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34435945 DOI: 10.1099/ijsem.0.004981] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strict aerobic bacterium, strain JW14T was isolated from soil in the Republic of Korea. Cells were Gram-stain-positive, non-endospore-forming and motile rods showing catalase-positive and oxidase-negative activities. Growth of strain JW14T was observed at 20-37 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.0) and in the presence of 0-2.0% NaCl (optimum, 0%). Strain JW14T contained menaquinone-7 as the sole isoprenoid quinone, anteiso-C15:0, C16:0 and iso-C16 : 0 as the major fatty acids (>10.0%), and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and an unidentified lipid as the major polar lipids. The cell-wall peptidoglycan of strain JW14T contained meso-diaminopimelic acid. The DNA G+C content of strain JW14T calculated from the whole genome sequence was 48.1 mol%. Strain JW14T was most closely related to Paenibacillus graminis DSM 15220T with 97.4% 16S rRNA gene sequence similarity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JW14T formed a distinct phyletic lineage from closely related type strains within the genus Paenibacillus. Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain JW14T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus agri sp. nov. is proposed. The type strain is JW14T (=KACC 21840T=JCM 34279T).
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Affiliation(s)
- Kyung Hyun KIm
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ye Lin Seo
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Mi Jin
- Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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11
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Vanhoutte I, De Tender C, Demeyere K, Abdallah MF, Ommeslag S, Vermeir P, Saeger SD, Debode J, Meyer E, Croubels S, Audenaert K, De Gelder L. Bacterial Enrichment Cultures Biotransform the Mycotoxin Deoxynivalenol into a Novel Metabolite Toxic to Plant and Porcine Cells. Toxins (Basel) 2021; 13:toxins13080552. [PMID: 34437423 PMCID: PMC8402469 DOI: 10.3390/toxins13080552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
The mycotoxin deoxynivalenol (DON), produced in wheat, barley and maize by Fusarium graminearum and Fusarium culmorum, is threatening the health of humans and animals. With its worldwide high incidence in food and feed, mitigation strategies are needed to detoxify DON, maintaining the nutritional value and palatability of decontaminated commodities. A promising technique is biological degradation, where microorganisms are used to biotransform mycotoxins into less toxic metabolites. In this study, bacterial enrichment cultures were screened for their DON detoxification potential, where DON and its potential derivatives were monitored. The residual phytotoxicity was determined through a bioassay using the aquatic plant Lemna minor L. Two bacterial enrichment cultures were found to biotransform DON into a still highly toxic metabolite for plants. Furthermore, a cytotoxic effect was observed on the cellular viability of intestinal porcine epithelial cells. Through liquid chromatography high-resolution mass spectrometry analysis, an unknown compound was detected, and tentatively characterized with a molecular weight of 30.0 Da (i.e., CH2O) higher than DON. Metabarcoding of the subsequently enriched bacterial communities revealed a shift towards the genera Sphingopyxis, Pseudoxanthomonas, Ochrobactrum and Pseudarthrobacter. This work describes the discovery of a novel bacterial DON-derived metabolite, toxic to plant and porcine cells.
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Affiliation(s)
- Ilse Vanhoutte
- Laboratory of Environmental Biotechnology, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; (C.D.T.); (S.O.); (J.D.)
- Computer Science and Statistics, Department of Applied Mathematics, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
| | - Kristel Demeyere
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (K.D.); (E.M.); (S.C.)
| | - Mohamed F. Abdallah
- Centre of Excellence in Mycotoxicology and Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.F.A.); (S.D.S.)
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; (C.D.T.); (S.O.); (J.D.)
| | - Pieter Vermeir
- Laboratory of Chemical Analysis (LCA), Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Sarah De Saeger
- Centre of Excellence in Mycotoxicology and Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.F.A.); (S.D.S.)
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; (C.D.T.); (S.O.); (J.D.)
| | - Evelyne Meyer
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (K.D.); (E.M.); (S.C.)
| | - Siska Croubels
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (K.D.); (E.M.); (S.C.)
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Leen De Gelder
- Laboratory of Environmental Biotechnology, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
- Correspondence: ; Tel.: +32-9-243-24-75
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12
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Shift of Dominant Species in Plant Community and Soil Chemical Properties Shape Soil Bacterial Community Characteristics and Putative Functions: A Case Study on Topographic Variation in a Mountain Pasture. Microorganisms 2021; 9:microorganisms9050961. [PMID: 33947019 PMCID: PMC8146586 DOI: 10.3390/microorganisms9050961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022] Open
Abstract
Reducing management intensity according to the topography of pastures can change the dominant plant species from sown forages to weeds. It is unclear how changes in species dominance in plant community drive spatial variation in soil bacterial community characteristics and functions in association with edaphic condition. Analysing separately the effects of both plant communities and soil chemical properties on bacterial community is crucial for understanding the biogeographic process at a small scale. In this paper, we investigated soil bacterial responses in five plant communities (two forage and three weed), where >65% of the coverage was by one or two species. The structure and composition of the bacterial communities in the different microbiome were analysed using sequencing and their characteristics were assessed using the Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Firmicutes and Planctomycetes responded only to one specific plant community, and each plant community harboured unique operational taxonomic units (OTUs) at the species level. There were a large percentage of uniquely absent OTUs for specific plant communities, suggesting that a negative effect is critical in the relationship between plants and bacteria. Bacterial diversity indices were influenced more by soil chemical properties than by plant communities. Some putative functions related to C and N recycling including nitrogen fixation were correlated with pH, electrical conductivity (EC) and nutrient levels, and this also implied that some biological functions, such as ureolysis and carbon metabolism, may decline when fertilisation intensity is reduced. Taken together, these results suggest that a shift of dominant species in plant community exerts individual effects on the bacterial community composition, which is different from the effect of soil chemical properties.
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Jung JY, Kang HK, Jin HM, Han SS, Kwon YC, Eun JJ, Kim SC, Seo MJ, Ryu BG, Chung EJ. Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed. Int J Syst Evol Microbiol 2021; 71. [PMID: 33502298 DOI: 10.1099/ijsem.0.004670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA-DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11T belonged to the genus Companilactobacillus. The 16S rRNA gene sequence of strain NFFJ11T exhibited high similarity to Companilactobacillus formosensis S215T (99.66 %), Companilactobacillus farciminis Rv4 naT (99.53 %), Companilactobacillus crustorum LMG 23699T (99.19 %), Companilactobacillus futsaii YM 0097T (99.06 %), Companilactobacillus zhachilii HBUAS52074T (98.86 %) and Companilactobacillus heilongiiangensis S4-3T (98.66 %). However, average nucleotide identity and in silico DNA-DNA hybridization values for these type strains were in the range of 79.90-92.93 % and 23.80-49.30 %, respectively, which offer evidence that strain NFFJ11T belongs to a novel species of the genus Companilactobacillus. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11T were C18 : 1 ω9c (43.3 %), C16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C19 : 1 ω7c, C19 : 1 ω6c and C19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11T represents a novel species belonging to the genus Companilactobacillus, for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11T (= KACC 21771T= JCM 34088T).
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Affiliation(s)
- Ji Young Jung
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Kyeong Kang
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hyun Mi Jin
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Sang-Soo Han
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Young Chul Kwon
- Nonghyup TMR agricultural Co., Ltd., 65, Ogwang 1-gil, Gongseong-myeon, Sangju-si, Gyeongsangbuk-do 37268, Republic of Korea
| | - Jong Jun Eun
- Nonghyup TMR agricultural Co., Ltd., 65, Ogwang 1-gil, Gongseong-myeon, Sangju-si, Gyeongsangbuk-do 37268, Republic of Korea
| | - Sang Cheol Kim
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Min Jeong Seo
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Byung-Gon Ryu
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Eu Jin Chung
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
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14
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BTEX biodegradation by Bacillus amyloliquefaciens subsp. plantarum W1 and its proposed BTEX biodegradation pathways. Sci Rep 2020; 10:17408. [PMID: 33060819 PMCID: PMC7562720 DOI: 10.1038/s41598-020-74570-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/10/2020] [Indexed: 12/04/2022] Open
Abstract
Benzene, toluene, ethylbenzene and (p-, m- and o-) xylene (BTEX) are classified as main pollutants by several environmental protection agencies. In this study, a non-pathogenic, Gram-positive rod-shape bacterium with an ability to degrade all six BTEX compounds, employed as an individual substrate or as a mixture, was isolated. The bacterial isolate was identified as Bacillus amyloliquefaciens subsp. plantarum strain W1. An overall BTEX biodegradation (as individual substrates) by strain W1 could be ranked as: toluene > benzene, ethylbenzene, p-xylene > m-xylene > o-xylene. When presented in a BTEX mixture, m-xylene and o-xylene biodegradation was slightly improved suggesting an induction effect by other BTEX components. BTEX biodegradation pathways of strain W1 were proposed based on analyses of its metabolic intermediates identified by LC–MS/MS. Detected activity of several putative monooxygenases and dioxygenases suggested the versatility of strain W1. Thus far, this is the first report of biodegradation pathways for all of the six BTEX compounds by a unique bacterium of the genus Bacillus. Moreover, B. amyloliquefaciens subsp. plantarum W1 could be a good candidate for an in situ bioremediation considering its Generally Recognized as Safe (GRAS) status and a possibility to serve as a plant growth-promoting rhizobacterium (PGPR).
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15
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Achromobacter aestuarii sp. nov., Isolated from an Estuary. Curr Microbiol 2020; 78:411-416. [PMID: 33033853 DOI: 10.1007/s00284-020-02231-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
A novel strain KS-M25T was isolated from estuary water in South Korea. Strain KS-M25T was Gram-staining-negative, strictly aerobic, motile rods-shaped bacterium and showed oxidase- and catalase-positive reactions. Growth of strain KS-M25T was observed at 10-25 °C (optimum, 20 °C), at pH 5.5-9.0 (optimum, pH 7.5), and with 0-6.0% (w/v) NaCl (optimum, 1%). Ubiquinone-8 was identified as the sole isoprenoid quinone and the major fatty acids were C16:0, cyclo-C17:0 and sum in feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c). The G+C content values based on genome sequences was 62.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KS-M25T formed a clear cluster within the genus Achromobacter. Strain KS-M25T was most closely related to Achromobacter anxifer LMG 26857T, Achromobacter dolens LMG 26840T, and Achromobacter xylosoxidans NBRC 15126T with 97.8%, 97.8%, and 97.7% 16S rRNA gene sequence similarities, respectively. Based on phenotypic, chemotaxonomic, and phylogenetic analysis, strain KS-M25T represents a novel species of the genes Achromobacter, for which the name Achromobacter aestuarii sp. nov. is proposed. The type strain is KS-M25T (= KACC 21219T = JCM 33329T).
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16
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Kumar M, Mahajan R, Saini HS. Evaluating metabolic potential of Thauera sp. M9 for the transformation of 4-chloroaniline (4-CA). BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Hocinat A, Boudemagh A, Ali-Khodja H, Medjemadj M. Aerobic degradation of BTEX compounds by Streptomyces species isolated from activated sludge and agricultural soils. Arch Microbiol 2020; 202:2481-2492. [PMID: 32617605 DOI: 10.1007/s00203-020-01970-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/28/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
In this study, we tested the ability of Streptomyces to use for their growth benzene, toluene, ethylbenzene, and o-, m-, p-xylenes as sole source of carbon and energy. These bacteria were isolated from agricultural soils and activated sludge samples from a wastewater treatment plant. The results show that Streptomyces are capable of degrading at least one of the BTEX compounds. Among them, 3 isolates from activated sludge called (U, F and V) and a single isolate (SA13) isolated from an agricultural soil, can use as the sole source of carbon and energy, all of these BTEX compounds at concentrations of 1500 mg/L. Based on the analysis of the 16S rRNA gene sequence, two active strains were identified as Streptomyces fimicarius, Streptomyces cavourensis, Streptomyces flavogriseus and Streptomyces pratensis. These strains can be excellent candidates for the bioremediation of the telluric and aquatic sites polluted by these xenobiotics.
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Affiliation(s)
- Amira Hocinat
- Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université Frères Mentouri-Constantine 1, 25017, Constantine, Algeria
| | - Allaoueddine Boudemagh
- Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université Frères Mentouri-Constantine 1, 25017, Constantine, Algeria
| | - Hocine Ali-Khodja
- Laboratoire de Pollution Et de Traitement Des Eaux, Faculté Des Sciences Exactes, Département de Chimie, Université Frères Mentouri-Constantine 1, Constantine, Algeria.
| | - Meissa Medjemadj
- Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université Frères Mentouri-Constantine 1, 25017, Constantine, Algeria
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18
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He YW, Cao XQ, Poplawsky AR. Chemical Structure, Biological Roles, Biosynthesis and Regulation of the Yellow Xanthomonadin Pigments in the Phytopathogenic Genus Xanthomonas. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:705-714. [PMID: 32027580 DOI: 10.1094/mpmi-11-19-0326-cr] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonadins are membrane-bound yellow pigments that are typically produced by phytopathogenic bacterial Xanthomonas spp., Xylella fastidiosa, and Pseudoxanthomonas spp. They are also produced by a diversity of environmental bacterial species. Considerable research has revealed that they are a unique group of halogenated, aryl-polyene, water-insoluble pigments. Xanthomonadins have been shown to play important roles in epiphytic survival and host-pathogen interactions in the phytopathogen Xanthomonas campestris pv. campestris, which is the causal agent of black rot in crucifers. Here, we review recent advances in the understanding of xanthomonadin chemical structures, physiological roles, biosynthetic pathways, regulatory mechanisms, and crosstalk with other signaling pathways. The aim of the present review is to provide clues for further in-depth research on xanthomonadins from Xanthomonas and other related bacterial species.
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Affiliation(s)
- Ya-Wen He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Qiang Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Alan R Poplawsky
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844, U.S.A
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19
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Jiang Y, Shang Y, Gong T, Hu Z, Yang K, Shao S. High concentration of Mn 2+ has multiple influences on aerobic granular sludge for aniline wastewater treatment. CHEMOSPHERE 2020; 240:124945. [PMID: 31726594 DOI: 10.1016/j.chemosphere.2019.124945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/08/2019] [Accepted: 09/22/2019] [Indexed: 06/10/2023]
Abstract
In this study, the effect of high concentration of Mn2+ on the aerobic granular sludge (AGS) systems for aniline wastewater treatment was systematically investigated in terms of AGS formation and pollutant removal efficiency. Two parallel sequencing batch reactors were operated to treat the aniline-rich wastewater with and without 20 mg L-1 of Mn2+. In the presence of Mn2+, the time to granulation was prolonged from 23 d to 30 d due to the toxicity of the high concentration of Mn2+. However, the mature granules with Mn2+ produced more protein and polysaccharides, and had a larger size (870 μm) than that without Mn2+ (740 μm). The extracellular polymeric substances of the granules in the two reactors had similar protein compositions, but some functional groups increased with Mn2+. The reactors showed high overall removal efficiency of chemical oxygen demand, NH4+-N, and total nitrogen with average concentrations below 40, 1.0, and 19 mg L-1, respectively, in the effluents. In one typical operating cycle, however, Mn2+ retarded nitrification and the degradation of aniline, while promoted denitrification. The microbial community analysis revealed that the growth of Terrisporobacter, Pseudomonas, and many other bacteria responsible for aniline degradation was inhibited by Mn2+, and so were the strains involved in nitrification. In contrast, Mn2+ facilitated the growth of denitrifying bacteria.
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Affiliation(s)
- Yu Jiang
- School of Civil Engineering, Wuhan University, Wuhan, 430072, China
| | - Yu Shang
- School of Civil Engineering, Wuhan University, Wuhan, 430072, China
| | - Tengjing Gong
- School of Civil Engineering, Wuhan University, Wuhan, 430072, China
| | - Zixin Hu
- School of Civil Engineering, Wuhan University, Wuhan, 430072, China
| | - Kai Yang
- School of Civil Engineering, Wuhan University, Wuhan, 430072, China
| | - Senlin Shao
- School of Civil Engineering, Wuhan University, Wuhan, 430072, China.
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Auti AM, Narwade NP, Deshpande NM, Dhotre DP. Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion. J Biosci 2019; 44:114. [PMID: 31719223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microbial community structure of crude petroleum oil (CP)- and refined petroleum oil (RP)-contaminated soil was investigated. The taxonomical and functional diversity of such soils can be a great source of information about microbial community and genes involved in petroleum hydrocarbon (PHC) degradation. In this study, microbial diversity of soils contaminated by RP from urban biome of Pune, India, and CP from agricultural biome of Gujarat, India, were assessed by 16S rRNA amplicon sequencing on Illumina MiSeq platform. Association between the soil microbial community and the physicochemical parameters were investigated for their potential role. In RP- and CP-contaminated soils, the microbiome analysis showed Proteobacteria as most dominant phylum followed by Actinobacteria. Interestingly, Firmicutes were most prevailing in a CP-contaminated sample while they were least prevailing in RP-contaminated soils. Soil moisture content, total organic carbon and organic nitrogen content influenced the taxa diversity in these soils. Species richness was more in RP as compared to CP soils. Further prediction of metagenome using PICRUSt revealed that the RP and CP soils contain microbial communities with excellent metabolic potential for PHC degradation. Microbial community contributing to genes essential for soil health improvement and plant growth promotion was also gauged. Our analysis showed promising results for future bioaugmentation assisted phytoremediation (BAP) strategies for treating such soils.
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Affiliation(s)
- Asim M Auti
- Department of Microbiology, MES Abasaheb Garware College, Pune, India
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21
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Hu Y, Li J, Li J, Zhang F, Wang J, Mo M, Liu Y. Biocontrol efficacy of Pseudoxanthomonas japonensis against Meloidogyne incognita and its nematostatic metabolites. FEMS Microbiol Lett 2019; 366:5266301. [PMID: 30596986 DOI: 10.1093/femsle/fny287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/14/2018] [Indexed: 11/14/2022] Open
Abstract
The rhizosphere bacterium ZKB-2 showed strong nematostatic activity against Meloidogyne incognita. Our study aimed to identify the nematostatic metabolites and evaluate the biocontrol efficiency in pot experiments. As the bacterial culture filtrate showed 100% nematostatic activity against M. incognita juveniles in 12 hr, we isolated and identified six compounds following activity guiding. 3-methoxycyclobutane-1, 2-dione showed 58.9% and 72.2% nematostatic activities against juveniles of M. incognita in 12 and 48 hr, with strong LC50 value at 447 μg mL-1. In pot experiments, treatments with the bacterial culture filtrate of strain ZKB-2 showed significant efficacy, especially at doses of 150 mL/pot, which were close to that of avermectin (positive control) at 0.01 g kg-1 soil. The most effective treatment inhibited 85.1% population of juveniles of M. incognita in the roots and 76.9% in the rhizosphere soil after 30 days. Furthermore, the promoting tomato growth also significantly increased in a dose-dependent manner. Our results revealed the potential of strain ZKB-2 to act as a biocontrol agent in the integrated management of root-knot nematodes on tomatoes.
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Affiliation(s)
- Yan Hu
- State Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, PR China
| | - Jing Li
- State Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, PR China
| | - Jiefang Li
- State Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, PR China
| | - Fei Zhang
- State Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, PR China
| | - Jinxing Wang
- State Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, PR China
| | - Minghe Mo
- State Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, PR China
| | - Yajun Liu
- State Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, PR China
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22
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Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion. J Biosci 2019. [DOI: 10.1007/s12038-019-9936-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Analysis of Microbial Community Dynamics during the Acclimatization Period of a Membrane Bioreactor Treating Table Olive Processing Wastewater. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9183647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Biological treatment of table olive processing wastewater (TOPW) may be problematic due to its high organic and polyphenolic compound content. Biomass acclimatization is a necessary, yet sensitive, stage for efficient TOPW biological treatment. Next-generation sequencing technologies can provide valuable insights into this critical process step. An aerobic membrane bioreactor (MBR) system, initially inoculated with municipal activated sludge, was acclimatized to treat TOPW. Operational stability and bioremediation efficiency were monitored for approx. three months, whereas microbial community dynamics and metabolic adaptation were assessed through metagenomic and metatranscriptomic analysis. A swift change was identified in both the prokaryotic and eukaryotic bio-community after introduction of TOPW in the MBR, and a new diverse bio-community was established. Thauera and Paracoccus spp. are dominant contributors to the metabolic activity of the stable bio-community, which resulted in over 90% and 85% removal efficiency of total organic carbon and total polyphenols, respectively. This is the first study assessing the microbial community dynamics in a well-defined MBR process treating TOPW, offering guidance in the start-up of large-scale applications.
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24
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Sphingobium terrigena sp. nov., isolated from gasoline-contaminated soil. Int J Syst Evol Microbiol 2019; 69:2459-2464. [DOI: 10.1099/ijsem.0.003514] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Lu C, Hong Y, Liu J, Gao Y, Ma Z, Yang B, Ling W, Waigi MG. A PAH-degrading bacterial community enriched with contaminated agricultural soil and its utility for microbial bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 251:773-782. [PMID: 31121542 DOI: 10.1016/j.envpol.2019.05.044] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/21/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
A bacterial community was enriched with polycyclic aromatic hydrocarbons (PAHs) polluted soil to better study PAH degradation by indigenous soil bacteria. The consortium degraded more than 52% of low molecular weight and 35% of high molecular weight (HMW) PAHs during 16 days in a soil leachate medium. 16S rRNA gene high-throughput sequencing and quantitative polymerase chain reaction analyses for alpha subunit genes of ring-hydroxylating-dioxygenase (RHDα) suggested that Proteobacteria and Actinobacteria at the phylum level, Pseudomonas, Methylobacillus, Nocardioides, Methylophilaceae, Achromobacter, Pseudoxanthomonas, and Caulobacter at the generic level were involved in PAH degradation and might have the ability to carry RHDα genes (nidA and nahAc). The community was selected and collected according to biomass and RHDα gene contents, and added back to the PAH-polluted soil. The 16 EPA priority PAHs decreased from 95.23 to 23.41 mg kg-1 over 35 days. Compared with soil without the introduction of this bacterial community, adding the community with RHDα genes significantly decreased soil PAH contents, particularly HMW PAHs. The metabolic rate of PAHs in soil was positively correlated with nidA and nahAc gene contents. These results indicate that adding an indigenous bacterial consortium containing RHDα genes to contaminated soil may be a feasible and environmentally friendly method to clean up PAHs in agricultural soil.
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Affiliation(s)
- Chao Lu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Hong
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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26
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Jeong SE, Kim KH, Lhee D, Yoon HS, Quan ZX, Lee EY, Jeon CO. Oceaniradius stylonematis gen. nov., sp. nov., isolated from a red alga, Stylonema cornu-cervi. Int J Syst Evol Microbiol 2019; 69:1967-1973. [DOI: 10.1099/ijsem.0.003413] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sang Eun Jeong
- 1Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- 1Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Duckhyun Lhee
- 2Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hwan Su Yoon
- 2Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Zhe-Xue Quan
- 3School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - En-Young Lee
- 4Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Che Ok Jeon
- 1Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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He Z, Mao R, Dong JE, Liang Z, Zhang H, Liu L. Remediation of deterioration in microbial structure in continuous Pinellia ternata cropping soil by crop rotation. Can J Microbiol 2019; 65:282-295. [DOI: 10.1139/cjm-2018-0409] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pinellia ternata is a traditional Chinese herb that suffers from continuous cropping (CC), which significantly decreases both yield and quality. The influence of CC on the microbiome in P. ternata rhizosphere and the effects of remediation on microbiota by rotational cropping (CR) were assessed by Illumina high-throughput sequencing technology. CC tends to decrease the α-diversities as a function of cultivation time, whereas CR tends to increase them. Differentially abundant analysis showed that microbial structure was important in maintaining the health status of P. ternata rhizosphere. Results suggested that CC soils were mainly enriched for Pseudomonas, Rhizobium, and Streptophyta operational taxonomic units (OTUs), while the CR soils were mainly enriched for Rhizobium, Pseudomonas, Flavobacterium, Sphingomonas, Rhizobacter, and Arthrobacter OTUs. On the basis of the community dissimilarities, we grouped all sample replicates into three post hoc clusters in which soils were defined as healthy, health-suppressed, and health-depressed soils. The three soil types represented different soil physicochemical properties. The activities of the microbiome features, including ammonia oxidizer, sulfate reducer, nitrite reducer, dehalogenation, xylan degrader, sulfide oxidizer, nitrogen fixation, atrazine metabolism, chitin degradation, degraded aromatic hydrocarbons, and chlorophenol degradation, were also considerably different among the three soils.
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Affiliation(s)
- Zhigui He
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- Institute of Food Science and Biological Engineering, Guilin Tourism University, Guilin 541006, P.R. China
| | - Renjun Mao
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
| | - Juan e Dong
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
| | - Zongsuo Liang
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Haihua Zhang
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Lin Liu
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
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28
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Jiang Y, Yang K, Shang Y, Zhang H, Wei L, Wang H. Response and recovery of aerobic granular sludge to pH shock for simultaneous removal of aniline and nitrogen. CHEMOSPHERE 2019; 221:366-374. [PMID: 30641378 DOI: 10.1016/j.chemosphere.2018.12.207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/22/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
Considering the pH fluctuation in industrial wastewater, the response and resilience to pH shock should be investigated during aerobic granular sludge (AGS) system operation. In this work, three AGS reactors, namely R1, R2, and R3 for simultaneous removal of aniline and nitrogen were exposed to neutral, acidic, and alkaline conditions, respectively. The removal efficiency of aniline and chemical oxygen demand with pH variation was over 99.9% and 91.0%, respectively after stable in the three reactors. The aniline removal rate modestly decreased in R2 and R3 after pH varied and denitrification was slightly improved in acidic environment with average removal efficiency of 61.2%. The mature AGS could maintain settleability in R1 and R2 with 30 min sludge volume index below 35 mL g-1 but was unstable under alkaline condition. Correspondingly, the secretion of extracellular polymeric substances especially protein decreased notably in R3. The bacterial groups varied with pH shock, but some could recover after adjustment to original pH value. Proteobacteria was the predominant phylum in the three reactors and Bacteroidetes was enriched in alkaline conditions. In addition, the main functional genera such as Achromobacter, Defluviimonas, Enterobacter, Pseudomonas, and Pseudoxanthomonas, were detected in the system and were found to be responsible for reduction of aniline and nitrogen.
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Affiliation(s)
- Yu Jiang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Kai Yang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Yu Shang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Huining Zhang
- School of Civil Engineering, Lanzhou University of Technology, Lanzhou 730000, China
| | - Li Wei
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hongyu Wang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China.
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29
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Bioremediation and metabolism of clothianidin by mixed bacterial consortia enriched from contaminated soils in Chinese greenhouse. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.12.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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30
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Fu L, Bai YN, Lu YZ, Ding J, Zhou D, Zeng RJ. Degradation of organic pollutants by anaerobic methane-oxidizing microorganisms using methyl orange as example. JOURNAL OF HAZARDOUS MATERIALS 2019; 364:264-271. [PMID: 30384235 DOI: 10.1016/j.jhazmat.2018.10.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic oxidation of methane (AOM) microorganisms widespread in nature and they are able to utilize methane as electron donor to reduce sulfate, nitrate, nitrite, and high valence metals. However, whether persistent organic contaminants can also be degraded remains unknown. In this study, the organic pollutant methyl orange (MO) was used to address this open question. The initial concentration of MO affected its degradation efficiency and higher concentration (>100 mg/L) caused considerable inhibition. A 13CH4 isotope experiment indicated that methane oxidation was involved in MO degradation, which produced N, N-dimethyl-p-phenylenediamine, and 4-aminobenzenesulfonic acid corresponded stoichiometrically. During the long-term experiment, the maximum degradation rate was 47.91 mg/(L·d). The percentage of Candidatus Methanoperedens and Pseudoxanthomonas significantly increased after 30-d of MO degradation under CH4 conditions; moreover, Candidatus Methanoperedens dominated (46.83%) the microbial community. Candidatus Methanoperedens, either alone or in combination with Pseudoxanthomonas, utilized methane as the sole carbon source to degrade MO via direct interspecies electron transfer or the syntrophy pathway. This study will add to our understanding of the functions and applications of AOM microorganisms.
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Affiliation(s)
- Liang Fu
- School of Environment, Northeast Normal University, Changchun 130117, China; CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Ya-Nan Bai
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yong-Ze Lu
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Jing Ding
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Dandan Zhou
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Raymond Jianxiong Zeng
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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31
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Lee Y, Lee Y, Jeon CO. Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil. Sci Rep 2019; 9:860. [PMID: 30696831 PMCID: PMC6351602 DOI: 10.1038/s41598-018-36165-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/16/2018] [Indexed: 11/09/2022] Open
Abstract
To isolate bacteria responsible for the biodegradation of naphthalene, BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene), and aliphatic hydrocarbons in petroleum-contaminated soil, three enrichment cultures were established using soil extract as the medium supplemented with naphthalene, BTEX, or n-hexadecane. Community analyses showed that Paraburkholderia species were predominant in naphthalene and BTEX, but relatively minor in n-hexadecane. Paraburkholderia aromaticivorans BN5 was able to degrade naphthalene and all BTEX compounds, but not n-hexadecane. The genome of strain BN5 harbors genes encoding 29 monooxygenases including two alkane 1-monooxygenases and 54 dioxygenases, indicating that strain BN5 has versatile metabolic capabilities, for diverse organic compounds: the ability of strain BN5 to degrade short chain aliphatic hydrocarbons was verified experimentally. The biodegradation pathways of naphthalene and BTEX compounds were bioinformatically predicted and verified experimentally through the analysis of their metabolic intermediates. Some genomic features including the encoding of the biodegradation genes on a plasmid and the low sequence homologies of biodegradation-related genes suggest that biodegradation potentials of strain BN5 may have been acquired via horizontal gene transfers and/or gene duplication, resulting in enhanced ecological fitness by enabling strain BN5 to degrade all compounds including naphthalene, BTEX, and short aliphatic hydrocarbons in contaminated soil.
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Affiliation(s)
- Yunho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Yunhee Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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32
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Feng T, Jeong SE, Lim JJ, Hyun S, Jeon CO. Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond. J Microbiol 2019; 57:232-237. [PMID: 30656589 DOI: 10.1007/s12275-019-8463-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 10/27/2022]
Abstract
A Gram-stain-negative, strictly aerobic bacterial strain, designated strain S27T, was isolated from soil near an artificial pond in South Korea. Cells were non-motile short rods showing oxidase- and catalase-positive activities. Growth of strain S27T was observed at 20-40°C (optimum, 30°C), pH 5.0-7.0 (optimum, pH 6.0), and 0-0.5% (w/v) NaCl (optimum, 0%). Ubiquinone-8 was detected as the sole respiratory quinone and the major fatty acids were C16:0, cyclo-C17:0, and cyclo-C19:0ω8c. The G + C content of the genomic DNA was 62.4 mol%. Phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid were detected as the major polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S27T formed a clearly distinct phyletic lineage from closely related Paraburkholderia species within the genus Paraburkholderia. Strain S27T was most closely related to Paraburkholderia rhynchosiae WSM3937T, Paraburkholderia ginsengiterrae DCY85T, Paraburkholderia fungorum NBRC 102489T, and Paraburkholderia graminis C4D1MT with 98.8%, 98.4%, 98.4%, and 97.7% 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness level between strain S27T and the type strain of P. rhynchosiae was 36.8 ± 2.6%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain S27T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia lacunae sp. nov. is proposed. The type strain is S27T (KACC 19714 T = JCM 32721T).
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Affiliation(s)
- Tingye Feng
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jin Ju Lim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Seogang Hyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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33
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Gauchotte-Lindsay C, Aspray TJ, Knapp M, Ijaz UZ. Systems biology approach to elucidation of contaminant biodegradation in complex samples – integration of high-resolution analytical and molecular tools. Faraday Discuss 2019; 218:481-504. [DOI: 10.1039/c9fd00020h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present here a data-driven systems biology framework for the rational design of biotechnological solutions for contaminated environments with the aim of understanding the interactions and mechanisms underpinning the role of microbial communities in the biodegradation of contaminated soils.
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Affiliation(s)
- Caroline Gauchotte-Lindsay
- Infrastructure and Environment Research Division
- School of Engineering
- University of Glasgow
- Glasgow G12 8QQ
- UK
| | - Thomas J. Aspray
- School of Energy, Geoscience, Infrastructure and Society
- Heriot-Watt University
- Edinburgh EH14 4AS
- UK
| | - Mara Knapp
- Department of Civil and Environmental Engineering
- University of Strathclyde
- Glasgow G1 1XQ
- UK
| | - Umer Z. Ijaz
- Infrastructure and Environment Research Division
- School of Engineering
- University of Glasgow
- Glasgow G12 8QQ
- UK
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34
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Cupriavidus lacunae sp. nov., isolated from pond-side soil. Antonie van Leeuwenhoek 2018; 112:543-551. [DOI: 10.1007/s10482-018-1187-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/10/2018] [Indexed: 11/25/2022]
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35
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Yu X, Lee K, Ma B, Asiedu E, Ulrich AC. Indigenous microorganisms residing in oil sands tailings biodegrade residual bitumen. CHEMOSPHERE 2018; 209:551-559. [PMID: 29945048 DOI: 10.1016/j.chemosphere.2018.06.126] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/22/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
The purpose of this study was to determine the capacity of indigenous microbes in tailings to degrade bitumen aerobically, and if acetate biostimulation further improved degradation. Fluid fine tailings, from Base Mine Lake (BML), were used as microbial inocula, and bitumen in the tailings served as a potential carbon source during the experiment. The tailings were capped with 0.22 μm-filtered BML surface water with or without BML bitumen and acetate addition and incubated for 100 days at 20 °C. CO2 production and petroleum hydrocarbon reductions (50-70% for the biostimulation treatment) in the tailings were observed. DNA was extracted directly from the tailings, and increased bacterial density was observed by qPCR targeting the rpoB gene in the biostimulated group. 16 S rRNA sequencing was used to determine microbial composition profiles in each treatment group. The microbial communities indigenous to the tailings shifted after the bitumen was added. Acidovorax, Rhodoferax, Pseudomonas and Pseudoxanthomonas spp. significantly increased compared to the original microbial community and demonstrated tolerance to bitumen-based toxicity. The first three genera showed more potential for biostimulation treatment with acetate and may be important bitumen/hydrocarbon-degraders in an oil sands end pit lake environment.
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Affiliation(s)
- Xiaoxuan Yu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
| | - Korris Lee
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
| | - Bin Ma
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
| | - Evelyn Asiedu
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, T6G 2B7, Canada.
| | - Ania C Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
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36
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Park YJ, Jeong SE, Jung HS, Park SY, Jeon CO. Nocardioides currus sp. nov., isolated from a mobile car air-conditioning system. Int J Syst Evol Microbiol 2018; 68:2977-2982. [DOI: 10.1099/ijsem.0.002933] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yu Jin Park
- 1Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sang Eun Jeong
- 1Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hye Su Jung
- 1Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - So Yoon Park
- 2Research & Development Division, Hyundai Motor Group, Gyeonggi 18280, Republic of Korea
| | - Che Ok Jeon
- 1Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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37
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O’Brien FJM, Dumont MG, Webb JS, Poppy GM. Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage ( Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory. Front Microbiol 2018; 9:1620. [PMID: 30083141 PMCID: PMC6064718 DOI: 10.3389/fmicb.2018.01620] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/28/2018] [Indexed: 11/16/2022] Open
Abstract
Rhizosphere microbial communities are known to be highly diverse and strongly dependent on various attributes of the host plant, such as species, nutritional status, and growth stage. High-throughput 16S rRNA gene amplicon sequencing has been used to characterize the rhizosphere bacterial community of many important crop species, but this is the first study to date to characterize the bacterial and archaeal community of Brassica oleracea var. capitata. The study also tested the response of the bacterial community to fertilizer type (organic or synthetic) and N dosage (high or low), in addition to plant age (9 or 12 weeks) and aphid (Myzus persicae) herbivory (present/absent). The impact of aboveground herbivory on belowground microbial communities has received little attention in the literature, and since the type (organic or mineral) and amount of fertilizer applications are known to affect M. percicae populations, these treatments were applied at agricultural rates to test for synergistic effects on the soil bacterial community. Fertilizer type and plant growth were found to result in significantly different rhizosphere bacterial communities, while there was no effect of aphid herbivory. Several operational taxonomic units were identified as varying significantly in abundance between the treatment groups and age cohorts. These included members of the S-oxidizing genus Thiobacillus, which was significantly more abundant in organically fertilized 12-week-old cabbages, and the N-fixing cyanobacteria Phormidium, which appeared to decline in synthetically fertilized soils relative to controls. These responses may be an effect of accumulating root-derived glucosinolates in the B. oleracea rhizosphere and increased N-availability, respectively.
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Affiliation(s)
- Flora J. M. O’Brien
- Biological Sciences, University of Southampton, Southampton, United Kingdom
- NIAB EMR, East Malling, United Kingdom
| | - Marc G. Dumont
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jeremy S. Webb
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Guy M. Poppy
- Biological Sciences, University of Southampton, Southampton, United Kingdom
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38
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Spatial Pattern of Bacterial Community Diversity Formed in Different Groundwater Field Corresponding to Electron Donors and Acceptors Distributions at a Petroleum-Contaminated Site. WATER 2018. [DOI: 10.3390/w10070842] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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39
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Brzeszcz J, Kaszycki P. Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility. Biodegradation 2018; 29:359-407. [PMID: 29948519 DOI: 10.1007/s10532-018-9837-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.
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Affiliation(s)
- Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland.
| | - Paweł Kaszycki
- Unit of Biochemistry, Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, al. 29 Listopada 54, 31-425, Kraków, Poland
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Feng T, Kim KH, Chun BH, Jeon CO. Amylibacter lutimaris sp. nov., isolated from sea-tidal flat sediment. Int J Syst Evol Microbiol 2018; 68:2088-2092. [DOI: 10.1099/ijsem.0.002805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tingye Feng
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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41
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Táncsics A, Szalay AR, Farkas M, Benedek T, Szoboszlay S, Szabó I, Lueders T. Stable isotope probing of hypoxic toluene degradation at the Siklós aquifer reveals prominent role of Rhodocyclaceae. FEMS Microbiol Ecol 2018; 94:4995907. [PMID: 29767715 PMCID: PMC5972620 DOI: 10.1093/femsec/fiy088] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 02/01/2023] Open
Abstract
The availability of oxygen is often a limiting factor for the degradation of aromatic hydrocarbons in subsurface environments. However, while both aerobic and anaerobic degraders have been intensively studied, degradation betwixt, under micro- or hypoxic conditions has rarely been addressed. It is speculated that in environments with limited, but sustained oxygen supply, such as in the vicinity of groundwater monitoring wells, hypoxic degradation may take place. A large diversity of subfamily I.2.C extradiol dioxygenase genes has been previously detected in a BTEX-contaminated aquifer in Hungary. Older literature suggests that such catabolic potentials could be associated to hypoxic degradation. Bacterial communities dominated by members of the Rhodocyclaceae were found, but the majority of the detected C23O genotypes could not be affiliated to any known bacterial degrader lineages. To address this, a stable isotope probing (SIP) incubation of site sediments with 13C7-toluene was performed under microoxic conditions. A combination of 16S rRNA gene amplicon sequencing and T-RFLP fingerprinting of C23O genes from SIP gradient fractions revealed the central role of degraders within the Rhodocyclaceae in hypoxic toluene degradation. The main assimilators of 13C were identified as members of the genera Quatrionicoccus and Zoogloea, and a yet uncultured group of the Rhodocyclaceae.
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Affiliation(s)
- András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - Anna Róza Szalay
- Institute of Groundwater Ecology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1., 85764 Neuherberg, Germany
| | - Milan Farkas
- Regional University Center of Excellence in Environmental Industry, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - Tibor Benedek
- Regional University Center of Excellence in Environmental Industry, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - Sándor Szoboszlay
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - István Szabó
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1., 2100 Gödöllő, Hungary
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1., 85764 Neuherberg, Germany
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Stringlis IA, Yu K, Feussner K, de Jonge R, Van Bentum S, Van Verk MC, Berendsen RL, Bakker PAHM, Feussner I, Pieterse CMJ. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc Natl Acad Sci U S A 2018; 115:E5213-E5222. [PMID: 29686086 DOI: 10.1094/pbiomes-11-18-0050-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Plant roots nurture a tremendous diversity of microbes via exudation of photosynthetically fixed carbon sources. In turn, probiotic members of the root microbiome promote plant growth and protect the host plant against pathogens and pests. In the Arabidopsis thaliana-Pseudomonas simiae WCS417 model system the root-specific transcription factor MYB72 and the MYB72-controlled β-glucosidase BGLU42 emerged as important regulators of beneficial rhizobacteria-induced systemic resistance (ISR) and iron-uptake responses. MYB72 regulates the biosynthesis of iron-mobilizing fluorescent phenolic compounds, after which BGLU42 activity is required for their excretion into the rhizosphere. Metabolite fingerprinting revealed the antimicrobial coumarin scopoletin as a dominant metabolite that is produced in the roots and excreted into the rhizosphere in a MYB72- and BGLU42-dependent manner. Shotgun-metagenome sequencing of root-associated microbiota of Col-0, myb72, and the scopoletin biosynthesis mutant f6'h1 showed that scopoletin selectively impacts the assembly of the microbial community in the rhizosphere. We show that scopoletin selectively inhibits the soil-borne fungal pathogens Fusarium oxysporum and Verticillium dahliae, while the growth-promoting and ISR-inducing rhizobacteria P. simiae WCS417 and Pseudomonas capeferrum WCS358 are highly tolerant of the antimicrobial effect of scopoletin. Collectively, our results demonstrate a role for coumarins in microbiome assembly and point to a scenario in which plants and probiotic rhizobacteria join forces to trigger MYB72/BGLU42-dependent scopolin production and scopoletin excretion, resulting in improved niche establishment for the microbial partner and growth and immunity benefits for the host plant.
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Affiliation(s)
- Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37077 Göttingen, Germany
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sietske Van Bentum
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Marcel C Van Verk
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37077 Göttingen, Germany
- Department of Plant Biochemistry, Göttingen Center for Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands;
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Kim KH, Cho GY, Chun BH, Weckx S, Moon JY, Yeo SH, Jeon CO. Acetobacter oryzifermentans sp. nov., isolated from Korean traditional vinegar and reclassification of the type strains of Acetobacter pasteurianus subsp. ascendens (Henneberg 1898) and Acetobacter pasteurianus subsp. paradoxus (Frateur 1950) as Acetobacter ascendens sp. nov., comb. nov. Syst Appl Microbiol 2018; 41:324-332. [PMID: 29655875 DOI: 10.1016/j.syapm.2018.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 02/07/2023]
Abstract
Twelve Acetobacter pasteurianus-related strains with publicly available genomes in GenBank shared high 16S rRNA gene sequence similarity (>99.59%), but average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values and multilocus sequence- and genome-based relatedness analyses suggested that they were divided into four different phylogenetic lineages. Relatedness analyses based on multilocus sequences, 1,194 core genes and whole-cell MALDI-TOF profiles supported that strains LMG 1590T and LMG 1591 (previously classified as the type strains of A. pasteurianus subsp. ascendens and paradoxus, respectively) and strain SLV-7T do not belong to A. pasteurianus. Strain SLV-7T, isolated from Korean traditional vinegar, shared low ANI (<91.0%) and in silico DDH (44.2%) values with all other Acetobacter type strains analyzed in this study, indicating that strain SLV-7T represents a new Acetobacter species. The phenotypic and chemotaxonomic analyses confirmed these results and therefore a new species named Acetobacter oryzifermentans sp. nov. is proposed with SLV-7T (=KACC 19301T=JCM 31096T) as the type strain. Strains LMG 1590T and LMG 1591 shared high ANI (99.4%) and in silico DDH (96.0%) values between them, but shared low ANI (<92.3%) and in silico DDH (<49.0%) values with other type strains analyzed in this study, indicating that strains LMG 1590T and LMG 1591 should be reclassified into a new single species that should be named Acetobacter ascendens sp. nov., comb. nov., with LMD 51.1T (=LMG 1590T=NCCB 51001T) as its type strain.
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Affiliation(s)
- Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ga Youn Cho
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Ji Young Moon
- Department of Agrofood Resources, National Institute of Agricultural Sciences, RDA, Wanju-gun 55365, Republic of Korea
| | - Soo-Hwan Yeo
- Department of Agrofood Resources, National Institute of Agricultural Sciences, RDA, Wanju-gun 55365, Republic of Korea.
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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Characterization of bacterial composition and diversity in a long-term petroleum contaminated soil and isolation of high-efficiency alkane-degrading strains using an improved medium. World J Microbiol Biotechnol 2018; 34:34. [DOI: 10.1007/s11274-018-2417-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/27/2018] [Indexed: 10/18/2022]
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Feng T, Jeong SE, Kim KH, Park HY, Jeon CO. Aestuariicoccus marinus gen. nov., sp. nov., isolated from sea-tidal flat sediment. Int J Syst Evol Microbiol 2018; 68:260-265. [DOI: 10.1099/ijsem.0.002494] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tingye Feng
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hye Yoon Park
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
- National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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46
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Feng T, Kim KH, Jeong SE, Kim W, Jeon CO. Aquicoccus porphyridii gen. nov., sp. nov., isolated from a small marine red alga, Porphyridium marinum. Int J Syst Evol Microbiol 2018; 68:283-288. [DOI: 10.1099/ijsem.0.002498] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tingye Feng
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University, College of Medicine, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Garbisu C, Garaiyurrebaso O, Epelde L, Grohmann E, Alkorta I. Plasmid-Mediated Bioaugmentation for the Bioremediation of Contaminated Soils. Front Microbiol 2017; 8:1966. [PMID: 29062312 PMCID: PMC5640721 DOI: 10.3389/fmicb.2017.01966] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 09/25/2017] [Indexed: 11/29/2022] Open
Abstract
Bioaugmentation, or the inoculation of microorganisms (e.g., bacteria harboring the required catabolic genes) into soil to enhance the rate of contaminant degradation, has great potential for the bioremediation of soils contaminated with organic compounds. Regrettably, cell bioaugmentation frequently turns into an unsuccessful initiative, owing to the rapid decrease of bacterial viability and abundance after inoculation, as well as the limited dispersal of the inoculated bacteria in the soil matrix. Genes that encode the degradation of organic compounds are often located on plasmids and, consequently, they can be spread by horizontal gene transfer into well-established, ecologically competitive, indigenous bacterial populations. Plasmid-mediated bioaugmentation aims to stimulate the spread of contaminant degradation genes among indigenous soil bacteria by the introduction of plasmids, located in donor cells, harboring such genes. But the acquisition of plasmids by recipient cells can affect the host’s fitness, a crucial aspect for the success of plasmid-mediated bioaugmentation. Besides, environmental factors (e.g., soil moisture, temperature, organic matter content) can play important roles for the transfer efficiency of catabolic plasmids, the expression of horizontally acquired genes and, finally, the contaminant degradation activity. For plasmid-mediated bioaugmentation to be reproducible, much more research is needed for a better selection of donor bacterial strains and accompanying plasmids, together with an in-depth understanding of indigenous soil bacterial populations and the environmental conditions that affect plasmid acquisition and the expression and functioning of the catabolic genes of interest.
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Affiliation(s)
- Carlos Garbisu
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, Neiker Tecnalia, Derio, Spain
| | - Olatz Garaiyurrebaso
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Lur Epelde
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, Neiker Tecnalia, Derio, Spain
| | | | - Itziar Alkorta
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, Neiker Tecnalia, Derio, Spain
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48
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Jeong SE, Kim KH, Baek K, Jeon CO. Parasphingopyxis algicola sp. nov., isolated from a marine red alga Asparagopsis taxiformis and emended description of the genus Parasphingopyxis Uchida et al. 2012. Int J Syst Evol Microbiol 2017; 67:3877-3881. [DOI: 10.1099/ijsem.0.002215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyunghwa Baek
- National Marine Biodiversity Institute of Korea, Seocheon, Chungchungnam-do 33662, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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49
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Lee Y, Jin HM, Jung HS, Jeon CO. Sphingobacterium humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:4632-4638. [PMID: 28945541 DOI: 10.1099/ijsem.0.002345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultatively aerobic bacterium, designated strain D1T, was isolated from soil in South Korea. Cells of strain D1T were non-motile rods with oxidase- and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30-37 °C), at pH 5.5-9.0 (optimum, pH 7.0-8.0) and in the presence of 0.0-5.0 % (w/v) NaCl (optimum, 0.0-1.0 %). The only respiratory quinone detected was menaquinone 7 (MK-7), and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) were identified as the major fatty acids. Phosphatidylethanolamine was the major polar lipid, and two unidentified glycophospholipids and four unidentified lipids were also detected as minor polar lipids. Sphingolipids, a typical chemotaxonomic feature of the genus Sphingobacterium, were detected. The G+C content of the genomic DNA was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D1T formed a phyletic lineage with Sphingobacterium hotanense XH4T within the genus Sphingobacterium. Strain D1T was most closely related to S. hotanense XH4T (98.1 % 16S rRNA gene sequence similarity) and Sphingobacterium cellulitidis R-53603T (97.2 %), and the DNA-DNA relatedness level between strain D1T and the type strain of S. cellulitidis was 43.1±0.7 %. Based on the phenotypic, chemotaxonomic and molecular features, strain D1T clearly represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium humi sp. nov. is proposed. The type strain is D1T (=KACC 18595T=JCM 31225T).
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Affiliation(s)
- Yunhee Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Mi Jin
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Su Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Yoshikawa M, Zhang M, Toyota K. Biodegradation of Volatile Organic Compounds and Their Effects on Biodegradability under Co-Existing Conditions. Microbes Environ 2017; 32:188-200. [PMID: 28904262 PMCID: PMC5606688 DOI: 10.1264/jsme2.me16188] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Volatile organic compounds (VOCs) are major pollutants that are found in contaminated sites, particularly in developed countries such as Japan. Various microorganisms that degrade individual VOCs have been reported, and genomic information related to their phylogenetic classification and VOC-degrading enzymes is available. However, the biodegradation of multiple VOCs remains a challenging issue. Practical sites, such as chemical factories, research facilities, and illegal dumping sites, are often contaminated with multiple VOCs. In order to investigate the potential of biodegrading multiple VOCs, we initially reviewed the biodegradation of individual VOCs. VOCs include chlorinated ethenes (tetrachloroethene, trichloroethene, dichloroethene, and vinyl chloride), BTEX (benzene, toluene, ethylbenzene, and xylene), and chlorinated methanes (carbon tetrachloride, chloroform, and dichloromethane). We also summarized essential information on the biodegradation of each kind of VOC under aerobic and anaerobic conditions, together with the microorganisms that are involved in VOC-degrading pathways. Interactions among multiple VOCs were then discussed based on concrete examples. Under conditions in which multiple VOCs co-exist, the biodegradation of a VOC may be constrained, enhanced, and/or unaffected by other compounds. Co-metabolism may enhance the degradation of other VOCs. In contrast, constraints are imposed by the toxicity of co-existing VOCs and their by-products, catabolite repression, or competition between VOC-degrading enzymes. This review provides fundamental, but systematic information for designing strategies for the bioremediation of multiple VOCs, as well as information on the role of key microorganisms that degrade VOCs.
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Affiliation(s)
- Miho Yoshikawa
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST).,Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology
| | - Ming Zhang
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Koki Toyota
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology
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