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Romantschuk M, Lahti-Leikas K, Kontro M, Galitskaya P, Talvenmäki H, Simpanen S, Allen JA, Sinkkonen A. Bioremediation of contaminated soil and groundwater by in situ biostimulation. Front Microbiol 2023; 14:1258148. [PMID: 38029190 PMCID: PMC10658714 DOI: 10.3389/fmicb.2023.1258148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
Bioremediation by in situ biostimulation is an attractive alternative to excavation of contaminated soil. Many in situ remediation methods have been tested with some success; however, due to highly variable results in realistic field conditions, they have not been implemented as widely as they might deserve. To ensure success, methods should be validated under site-analogous conditions before full scale use, which requires expertise and local knowledge by the implementers. The focus here is on indigenous microbial degraders and evaluation of their performance. Identifying and removing biodegradation bottlenecks for degradation of organic pollutants is essential. Limiting factors commonly include: lack of oxygen or alternative electron acceptors, low temperature, and lack of essential nutrients. Additional factors: the bioavailability of the contaminating compound, pH, distribution of the contaminant, and soil structure and moisture, and in some cases, lack of degradation potential which may be amended with bioaugmentation. Methods to remove these bottlenecks are discussed. Implementers should also be prepared to combine methods or use them in sequence. Chemical/physical means may be used to enhance biostimulation. The review also suggests tools for assessing sustainability, life cycle assessment, and risk assessment. To help entrepreneurs, decision makers, and methods developers in the future, we suggest founding a database for otherwise seldom reported unsuccessful interventions, as well as the potential for artificial intelligence (AI) to assist in site evaluation and decision-making.
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Affiliation(s)
- Martin Romantschuk
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Katariina Lahti-Leikas
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Merja Kontro
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | | | - Harri Talvenmäki
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Suvi Simpanen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - John A. Allen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Aki Sinkkonen
- Natural Resources Institute Finland (Luke), Horticulture Technologies, Turku, Finland
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Suleiman MK, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential. PLoS One 2019; 14:e0220679. [PMID: 31877136 PMCID: PMC6932743 DOI: 10.1371/journal.pone.0220679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 11/19/2019] [Indexed: 12/31/2022] Open
Abstract
Kuwait is a semi-arid region with soils that are relatively nitrogen-poor. Thus, biological nitrogen fixation is an important natural process in which N2-fixing bacteria (diazotrophs) convert atmospheric nitrogen into plant-usable forms such as ammonium and nitrate. Currently, there is limited information on free-living and root-associated nitrogen-fixing bacteria and their potential to fix nitrogen and aid natural plant communities in the Kuwait desert. In this study, free living N2-fixing diazotrophs were enriched and isolated from the rhizosphere soil associated with three native keystone plant species; Rhanterium epapposum, Farsetia aegyptia, and Haloxylon salicornicum. Root-associated bacteria were isolated from the root nodules of Vachellia pachyceras. The result showed that the strains were clustered in five groups represented by class: γ-proteobacteria, and α-proteobacteria; phyla: Actinobacteria being the most dominant, followed by phyla: Firmicutes, and class: β-proteobacteria. This study initially identified 50 nitrogen-fixers by16S rRNA gene sequencing, of which 78% were confirmed to be nitrogen-fixers using the acetylene reduction assay. Among the nitrogen fixers identified, the genus Rhizobium was predominant in the rhizosphere soil of R. epapposum and H. salicornicum, whereas Pseudomonas was predominant in the rhizosphere soil of F. aegyptia, The species Agrobacterium tumefaciens was mainly found to be dominant among the root nodules of V. pachyceras and followed by Cellulomonas, Bacillus, and Pseudomonas genera as root-associated bacteria. The variety of diazotrophs revealed in this study, signifying the enormous importance of free-living and root-associated bacteria in extreme conditions and suggesting potential ecological importance of diazotrophs in arid ecosystem. To our knowledge, this study is the first to use culture-based isolation, molecular identification, and evaluation of N2-fixing ability to detail diazotroph diversity in Kuwaiti desert soils.
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Affiliation(s)
- M. K. Suleiman
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - A. M. Quoreshi
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
- * E-mail:
| | - N. R. Bhat
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - A. J. Manuvel
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - M. T. Sivadasan
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
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Yang J, Liu T, Liu H, Zhai L, Wang M, Du Y, Chen Y, Yang C, Xiao H, Wang H. Dimethylolurea as a Novel Slow-Release Nitrogen Source for Nitrogen Leaching Mitigation and Crop Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7616-7625. [PMID: 31251044 DOI: 10.1021/acs.jafc.9b01432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rapid hydrolysis of urea results in further fertilization frequency and excessive nitrogen (N) input. A modified urea, dimethylolurea (DMU), was synthesized in this study. The structure of the sample was characterized by Fourier transform infrared and nuclear magnetic resonance analysis, manifesting the formation of DMU. N release investigation confirmed that DMU enabling provided a gradual N supply. The N leaching experiment indicated that increasing the applied DMU significantly reduced the NH4+-N, NO3--N, and total N leaching, compared with urea application alone. The application effect on maize and wheat was evaluated. The results revealed that singly applied DMU with 100% or 80% N input, irrespective of the amount, promoted crop yield and agronomic characteristic and N use efficiency (NUE) of maize and wheat, beyond urea with two split applications at the recommended rate. Thus, the potential availability of DMU was proven; this could be widely used in agricultural fields as a slow-release fertilizer.
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Affiliation(s)
- Jinhui Yang
- School of Materials Science and Engineering , Shijiazhuang Tiedao University , Shijiazhuang , Hebei Province 050043 , China
| | - Tai Liu
- School of Materials Science and Engineering , Shijiazhuang Tiedao University , Shijiazhuang , Hebei Province 050043 , China
- Key Laboratory of Non-point Source Pollution Control, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Hongbin Liu
- Key Laboratory of Non-point Source Pollution Control, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Limei Zhai
- Key Laboratory of Non-point Source Pollution Control, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Man Wang
- School of Materials Science and Engineering , Shijiazhuang Tiedao University , Shijiazhuang , Hebei Province 050043 , China
| | - Yonggang Du
- School of Materials Science and Engineering , Shijiazhuang Tiedao University , Shijiazhuang , Hebei Province 050043 , China
| | - Yanxue Chen
- School of Materials Science and Engineering , Shijiazhuang Tiedao University , Shijiazhuang , Hebei Province 050043 , China
| | - Cheng Yang
- School of Materials Science and Engineering , Shijiazhuang Tiedao University , Shijiazhuang , Hebei Province 050043 , China
| | - Huining Xiao
- Department of Chemical Engineering , University of New Brunswick , Fredericton , NB E3B 5A3 Canada
| | - Hongyuan Wang
- Key Laboratory of Non-point Source Pollution Control, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
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Tang WJ, Zhang LS, Fang Y, Zhou Y, Ye BC. Biodegradation of phthalate esters by newly isolated Rhizobium
sp. LMB-1 and its biochemical pathway of di-n
-butyl phthalate. J Appl Microbiol 2016; 121:177-86. [DOI: 10.1111/jam.13123] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 02/23/2016] [Accepted: 03/04/2016] [Indexed: 11/29/2022]
Affiliation(s)
- W.-J. Tang
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
| | - L.-S. Zhang
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
| | - Y. Fang
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
| | - Y. Zhou
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
| | - B.-C. Ye
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
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Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil. Appl Microbiol Biotechnol 2016; 100:6815-6826. [DOI: 10.1007/s00253-016-7502-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 12/16/2022]
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Nicotine Dehydrogenase Complexed with 6-Hydroxypseudooxynicotine Oxidase Involved in the Hybrid Nicotine-Degrading Pathway in Agrobacterium tumefaciens S33. Appl Environ Microbiol 2016; 82:1745-1755. [PMID: 26729714 DOI: 10.1128/aem.03909-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 12/29/2015] [Indexed: 01/04/2023] Open
Abstract
Nicotine, a major toxic alkaloid in tobacco wastes, is degraded by bacteria, mainly via pyridine and pyrrolidine pathways. Previously, we discovered a new hybrid of the pyridine and pyrrolidine pathways in Agrobacterium tumefaciens S33 and characterized its key enzyme 6-hydroxy-3-succinoylpyridine (HSP) hydroxylase. Here, we purified the nicotine dehydrogenase initializing the nicotine degradation from the strain and found that it forms a complex with a novel 6-hydroxypseudooxynicotine oxidase. The purified complex is composed of three different subunits encoded by ndhAB and pno, where ndhA and ndhB overlap by 4 bp and are ∼26 kb away from pno. As predicted from the gene sequences and from chemical analyses, NdhA (82.4 kDa) and NdhB (17.1 kDa) harbor a molybdopterin cofactor and two [2Fe-2S] clusters, respectively, whereas Pno (73.3 kDa) harbors an flavin mononucleotide and a [4Fe-4S] cluster. Mutants with disrupted ndhA or ndhB genes did not grow on nicotine but grew well on 6-hydroxynicotine and HSP, whereas the pno mutant did not grow on nicotine or 6-hydroxynicotine but grew well on HSP, indicating that NdhA and NdhB are responsible for initialization of nicotine oxidation. We successfully expressed pno in Escherichia coli and found that the recombinant Pno presented 2,6-dichlorophenolindophenol reduction activity when it was coupled with 6-hydroxynicotine oxidation. The determination of reaction products catalyzed by the purified enzymes or mutants indicated that NdhAB catalyzed nicotine oxidation to 6-hydroxynicotine, whereas Pno oxidized 6-hydroxypseudooxynicotine to 6-hydroxy-3-succinoylsemialdehyde pyridine. These results provide new insights into this novel hybrid pathway of nicotine degradation in A. tumefaciens S33.
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Draft Genome Sequence of a Phthalate Ester-Degrading Bacterium, Rhizobium sp. LMB-1, Isolated from Cultured Soil. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00392-15. [PMID: 25953182 PMCID: PMC4424298 DOI: 10.1128/genomea.00392-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rhizobium sp. LMB-1, newly isolated from greenhouse soil, can effectively degrade phthalate. Here, we present a 5.2-Mb assembly of this Rhizobium sp. genome for the first time. It may provide abundant molecular information for the transformation of phthalates.
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Ikeda S, Suzuki K, Kawahara M, Noshiro M, Takahashi N. An assessment of urea-formaldehyde fertilizer on the diversity of bacterial communities in onion and sugar beet. Microbes Environ 2014; 29:231-4. [PMID: 24882062 PMCID: PMC4103532 DOI: 10.1264/jsme2.me13157] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The impact of a urea-formaldehyde (UF) fertilizer on bacterial diversity in onion bulbs and main roots of sugar beet were examined using a 16S rRNA gene clone library. The UF fertilizer markedly increased bacterial diversity in both plants. The results of principal coordinates analysis (PCoA) revealed that nearly 30% of the variance observed in bacterial diversity in both the onion and sugar beet was attributed to the fertilization conditions and also that the community structures in both plants shifted unidirectionally in response to the UF fertilizer.
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Affiliation(s)
- Seishi Ikeda
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
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