1
|
Qurbani K, Hamzah H. Intimate communication between Comamonas aquatica and Fusarium solani in remediation of heavy metal-polluted environments. Arch Microbiol 2020; 202:1397-1406. [DOI: 10.1007/s00203-020-01853-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/26/2020] [Accepted: 03/01/2020] [Indexed: 12/28/2022]
|
2
|
Chen YL, Lee CC, Lin YL, Yin KM, Ho CL, Liu T. Obtaining long 16S rDNA sequences using multiple primers and its application on dioxin-containing samples. BMC Bioinformatics 2015; 16 Suppl 18:S13. [PMID: 26681335 PMCID: PMC4682383 DOI: 10.1186/1471-2105-16-s18-s13] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Next-generation sequencing (NGS) technology has transformed metagenomics because the high-throughput data allow an in-depth exploration of a complex microbial community. However, accurate species identification with NGS data is challenging because NGS sequences are relatively short. Assembling 16S rDNA segments into longer sequences has been proposed for improving species identification. Current approaches, however, either suffer from amplification bias due to one single primer or insufficient 16S rDNA reads in whole genome sequencing data. Results Multiple primers were used to amplify different 16S rDNA segments for 454 sequencing, followed by 454 read classification and assembly. This permitted targeted sequencing while reducing primer bias. For test samples containing four known bacteria, accurate and near full-length 16S rDNAs of three known bacteria were obtained. For real soil and sediment samples containing dioxins in various concentrations, 16S rDNA sequences were lengthened by 50% for about half of the non-rare microbes, and 16S rDNAs of several microbes reached more than 1000 bp. In addition, reduced primer bias using multiple primers was illustrated. Conclusions A new experimental and computational pipeline for obtaining long 16S rDNA sequences was proposed. The capability of the pipeline was validated on test samples and illustrated on real samples. For dioxin-containing samples, the pipeline revealed several microbes suitable for future studies of dioxin chemistry.
Collapse
|
3
|
Zhang Y, Ge S, Jiang M, Jiang Z, Wang Z, Ma B. Combined bioremediation of atrazine-contaminated soil by Pennisetum and Arthrobacter sp. strain DNS10. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:6234-6238. [PMID: 24352545 DOI: 10.1007/s11356-013-2410-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/26/2013] [Indexed: 06/03/2023]
Abstract
Strain DNS10 was isolated from the black soil collected from the northeast of China which had been cultivated with atrazine as the sole nitrogen source. Pennisetum is a common plant in Heilongjiang Province of China. The main objective of this paper was to evaluate the efficiency of plant-microbe joint interactions (Arthrobacter sp. DNS10 + Pennisetum) in atrazine degradation compared with single-strain and single-plant effects. Plant-microbe joint interactions degraded 98.10 % of the atrazine, while single strain and single plant only degraded 87.38 and 66.71 % after a 30-day experimental period, respectively. The results indicated that plant-microbe joint interactions had a better degradation effect. Meanwhile, we found that plant-microbe joint interactions showed a higher microbial diversity. The results of microbial diversity illustrated that the positive effects of cropping could improve soil microbial growth and activity. In addition, we planted atrazine-sensitive plants (soybean) in the soil after repair. The results showed that soybean growth in soil previously treated with the plant-microbe joint interactions treatment was better compared with other treatments after 20 days of growth. This was further proved that the soil is more conducive for crop cultivation. Hence, plant-microbe joint interactions are considered to be a potential tool in the remediation of atrazine-contaminated soil.
Collapse
Affiliation(s)
- Ying Zhang
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, People's Republic of China,
| | | | | | | | | | | |
Collapse
|
4
|
Peng A, Liu J, Gao Y, Chen Z. Distribution of endophytic bacteria in Alopecurus aequalis Sobol and Oxalis corniculata L. from soils contaminated by polycyclic aromatic hydrocarbons. PLoS One 2013; 8:e83054. [PMID: 24358247 PMCID: PMC3866203 DOI: 10.1371/journal.pone.0083054] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 10/25/2013] [Indexed: 11/22/2022] Open
Abstract
The distributions of endophytic bacteria in Alopecurus aequalis Sobol and Oxalis corniculata L. grown in soils contaminated with different levels of polycyclic aromatic hydrocarbons (PAHs) were investigated with polymerase chain reaction followed by denaturing gradient gel electrophoresis technology (PCR-DGGE) and cultivation methods. Twelve types of PAHs, at concentrations varying from 0.16 to 180 mg·kg−1, were observed in the roots and shoots of the two plants. The total PAH concentrations in Alopecurus aequalis Sobol obtained from three different PAH-contaminated stations were 184, 197, and 304 mg·kg−1, and the total PAH concentrations in Oxalis corniculata L. were 251, 346, and 600 mg·kg−1, respectively. The PCR-DGGE results showed that the endophytic bacterial communities in the roots and shoots of the two plants were quite different, although most bacteria belonged to Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. A total of 68 endophytic bacterial strains were isolated from different tissues of the two plants and classified into three phyla: Firmicutes, Proteobacteria and Bacteroidetes. In both plants, Bacillus spp. and Pseudomonas spp. were the dominant cultivable populations. With an increase in the PAH pollution level, the diversity and distribution of endophytic bacteria in the two plants changed correspondingly, and the number of cultivable endophytic bacterial strains decreased rapidly. Testing of the isolated endophytic bacteria for tolerance to each type of PAH showed that most isolates could grow well on Luria-Bertani media in the presence of different PAHs, and some isolates were able to grow rapidly on a mineral salt medium with a single PAH as the sole carbon and energy source, indicating that these strains may have the potential to degrade PAHs in plants. This research provides the first insight into the characteristics of endophytic bacterial populations under different PAH pollution levels and provides a species resource for the isolation of PAH-degrading endophytic bacteria.
Collapse
Affiliation(s)
- Anping Peng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
- * E-mail: (JL); (YG)
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
- * E-mail: (JL); (YG)
| | - Zeyou Chen
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| |
Collapse
|
5
|
Weiss M, Kesberg AI, Labutti KM, Pitluck S, Bruce D, Hauser L, Copeland A, Woyke T, Lowry S, Lucas S, Land M, Goodwin L, Kjelleberg S, Cook AM, Buhmann M, Thomas T, Schleheck D. Permanent draft genome sequence of Comamonas testosteroni KF-1. Stand Genomic Sci 2013; 8:239-54. [PMID: 23991256 PMCID: PMC3746432 DOI: 10.4056/sigs.3847890] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Comamonas testosteroni KF-1 is a model organism for the elucidation of the novel biochemical degradation pathways for xenobiotic 4-sulfophenylcarboxylates (SPC) formed during biodegradation of synthetic 4-sulfophenylalkane surfactants (linear alkylbenzenesulfonates, LAS) by bacterial communities. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,026,527 bp long chromosome (one sequencing gap) exhibits an average G+C content of 61.79% and is predicted to encode 5,492 protein-coding genes and 114 RNA genes.
Collapse
Affiliation(s)
- Michael Weiss
- Department of Biological Sciences, University of Konstanz, Germany ; Konstanz Research School Chemical Biology, University of Konstanz, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Wang Y, Oyaizu H. Enhanced remediation of dioxins-spiked soil by a plant-microbe system using a dibenzofuran-degrading Comamonas sp. and Trifolium repens L. CHEMOSPHERE 2011; 85:1109-14. [PMID: 21839489 DOI: 10.1016/j.chemosphere.2011.07.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 05/18/2023]
Abstract
In this study, rhizoremediation technology was applied to dioxins-spiked soil. A dibenzofuran-degrading bacterium Comamonas sp. strain KD7, reported in the previous paper, was used in combination with white clover (Trifolium repens L.). First, the effect of strain KD7 on clover seed germination and root elongation was examined in the presence of dioxins compounds. As a result, the white clover seeds inoculated with strain KD7 exhibited a higher germination efficiency and increased root elongation compared with uninoculated white clover. Next, the recovery efficiency of two extraction methods were considered for analyzing the dioxin concentration in soil samples, then, the potential of the plant-microbe combination was evaluated for the remediation of dioxins-spiked soil. After 12 week of growth, significant reductions in the soil were confirmed for most compounds. Our results demonstrated that clover can function as a carrier in order to increase the dioxin-degrading activity of strain KD7. The association of clover and strain KD7 is considered to be a potential tool in the remediation of dioxin-contaminated soil.
Collapse
Affiliation(s)
- Yanxu Wang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | | |
Collapse
|
7
|
Wang Y, Oyaizu H. Evaluation of the phytoremediation potential of four plant species for dibenzofuran-contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2009; 168:760-4. [PMID: 19321258 DOI: 10.1016/j.jhazmat.2009.02.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 12/17/2008] [Accepted: 02/16/2009] [Indexed: 05/18/2023]
Abstract
In this experiment, three grasses, bermuda grass (Cynodon dactylon), bent grass (Agrostis palustris Huds.), lawn grass (Zoysia japonica), and a shallow-rooted legume, white clover (Trifolium repens L.) were planted into uncontaminated soil and dibenzofuran (DBF)-contaminated soil. The germination rates of all plants were investigated using contaminated soils to evaluate their sensitivities to DBF. During 2 months of growth, the root biomass and heterotrophic microbial numbers were measured in order to evaluate the potential of remediation. Furthermore, the number of DBF-degrading bacteria was counted to evaluate plants that enhance the microbial DBF degradation potential in contaminated soil. The DBF-removal performance of four plant species was also compared. Regardless of the contamination of DBF, white clover had not only the highest root biomass, but also the highest DBF-degrading bacterial numbers compared to those of the other three grasses. Moreover, white clover-planted contaminated soil exhibited the highest rate of DBF removal among all tested plants. These results suggest that microbial populations capable of degrading DBF were selectively increased by the addition of DBF in the rhizosphere, and also indicate that the presence of plants significantly enhances the reduction of DBF in soils. Based upon these results, white clover was selected for the further investigation of the phytoremediation of dioxin-contaminated soil.
Collapse
Affiliation(s)
- Yanxu Wang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | | |
Collapse
|
8
|
Kimura N, Kamagata Y. Impact of dibenzofuran/dibenzo-p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations. Appl Microbiol Biotechnol 2009; 84:365-73. [PMID: 19513710 DOI: 10.1007/s00253-009-2046-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 05/11/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022]
Abstract
The impact of dibenzofuran (DF) and dibenzo-p-dioxin (DD) on the changes in bacterial community structure and the transition of catabolic genes were studied using forest soil. The bacterial community structure of soil suspensions amended with 1 microg/g of either DF or DD was analyzed by 16S rRNA and functional gene sequencing. To analyze the functional genes in the communities, we targeted a gene sequence that functions as the binding site of Rieske iron sulfur center common to ring-hydroxylating dioxygenases (RHDs) for monocyclic, bicyclic, and tricyclic aromatic compounds. The gene fragments were polymerase chain reaction-amplified from DNAs extracted from soil suspensions spiked with either DF or DD, cloned, and sequenced (70 clones). Bacterial community analysis based on 16S rRNA genes revealed that specific 16S rRNA gene sequences, in particular, phylotypes within alpha-Proteobacteria, increased in the soil suspension amended with DF or DD. RHD gene-based functional community analysis showed that, in addition to two groups of RHD genes that were also detected in unamended soil suspensions, another two groups of RHD genes, each of which is specific to DF- and DD-amended soil, respectively, emerged to a great extent. The DD-specific genotype is phylogenetically distant from any known RHDs. These results strongly suggest that soil microbial community potentially harbors a wide array of organisms having diverse RHDs including those previously unknown, and that they could quickly respond to an impact of contamination of hazardous chemicals by changing the microbial community and gene diversity.
Collapse
Affiliation(s)
- Nobutada Kimura
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
| | | |
Collapse
|
9
|
Miyauchi K, Sukda P, Nishida T, Ito E, Matsumoto Y, Masai E, Fukuda M. Isolation of dibenzofuran-degrading bacterium, Nocardioides sp. DF412, and characterization of its dibenzofuran degradation genes. J Biosci Bioeng 2008; 105:628-35. [DOI: 10.1263/jbb.105.628] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Accepted: 03/05/2008] [Indexed: 11/17/2022]
|
10
|
Iida T, Nakamura K, Izumi A, Mukouzaka Y, Kudo T. Isolation and characterization of a gene cluster for dibenzofuran degradation in a new dibenzofuran-utilizing bacterium, Paenibacillus sp. strain YK5. Arch Microbiol 2005; 184:305-15. [PMID: 16284749 DOI: 10.1007/s00203-005-0045-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Revised: 08/15/2005] [Accepted: 09/19/2005] [Indexed: 10/25/2022]
Abstract
Spore-forming bacterial strains capable of utilizing dibenzofuran (DF) as a sole source of carbon and energy were isolated. Characteristics of the isolates justified their classification into the genus Paenibacillus, and their closest relative was P. naphthalenovorans. Degenerate primers for aromatic hydrocarbon dioxygenase alpha subunit (AhDOa) genes and genomic DNA of the strain YK5 were used for gene isolation. The nucleotide sequences of clones of the PCR products revealed that the strain YK5 carries at least five different AhDOa genes. Northern hybridization analysis showed that one of the AhDOa genes was transcribed under DF-containing culture conditions. A gene cluster encoding the AhDOa was isolated. The genes predicted to encode extradiol dioxygenase (dbfB) and hydrolase (dbfC) were found to be an upstream of genes encoding the alpha and beta subunit of the AhDO (dbfA1 and dbfA2, respectively); the latter two gene products showed 60 and 53% identity to the amino acid sequences of DbfA1 and DbfA2 of Terrabacter sp. DBF63, respectively. Two Paenibacillus validus JCM 9077 strains transformed with the dbf gene clusters acquired the ability to convert DF to 2,2',3-trihydroxybiphenyl (THBP) and salicylic acid (SAL). These results suggest that the enzymes encoded by the gene cluster isolated in this study are involved in DF metabolism in YK5.
Collapse
Affiliation(s)
- Toshiya Iida
- Environmental Molecular Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan.
| | | | | | | | | |
Collapse
|