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Wang T, Zhou Y, Li J, Qin S. Molecular insights into nitrogen constraint for niche partitioning and physiological adaptation of coastal Synechococcus assemblages. ENVIRONMENTAL RESEARCH 2023; 239:117383. [PMID: 37832763 DOI: 10.1016/j.envres.2023.117383] [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: 08/14/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 10/15/2023]
Abstract
Coastal nitrogen input has substantially increased due to human activity. However, much remains unknown about the nitrogen-driven patterns and the underlying genetic basis of coastal picoplankton. To investigate the response and mechanisms of picoplankton induced by nitrogen variation, we conducted in-situ investigations using high-throughput sequencing in the Bohai Sea and performed laboratory nitrogen simulation experiments accompanied by physiological, genomic, and transcriptomic analyses, with Synechococcus as a representative. The results of in-situ investigation revealed that Synechococcus clades I, III, WPC1, and VI of subcluster 5.1 (S5.1) are prevalent in strait areas characterized by robust water exchange with the North Yellow Sea, while clades II, VIII, and IX of S5.1, as well as subcluster 5.2 (S5.2) and subcluster 5.3 (S5.3) are more abundant in central and bay areas experiencing elevated nitrate and nitrite loads. The laboratory experiments further confirmed that inorganic nitrogen is a crucial determinant of diversity and niche partitioning of Synechococcus lineages. Besides, the raising inorganic nitrogen concentration within the current in-situ range (0.1-10 μmol L-1) enhances photosynthesis and carbon fixation of Synechococcus, however further escalation of inorganic nitrogen (100 μmol L-1) may hinder these processes instead. The phenomenon could be associated with the differential expression of genes in metabolic pathways regulating nitrogen metabolism, photosynthetic system II, and photosynthesis-antenna proteins in response to nitrogen concentration and type variation. These findings expand our understanding of the impact of macronutrient variation resulting from human activities on marine picoplankton and biogeochemical cycles.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yuting Zhou
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Jialin Li
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
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2
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Márquez-Villa JM, Rodríguez-Sierra JC, Amtanus Chequer N, Cob-Calan NN, García-Maldonado JQ, Cadena S, Hernández-Núñez E. Phenanthrene Degradation by Photosynthetic Bacterial Consortium Dominated by Fischerella sp. Life (Basel) 2023; 13:life13051108. [PMID: 37240753 DOI: 10.3390/life13051108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Microbial degradation of aromatic hydrocarbons is an emerging technology, and it is well recognized for its economic methods, efficiency, and safety; however, its exploration is still scarce and greater emphasis on cyanobacteria-bacterial mutualistic interactions is needed. We evaluated and characterized the phenanthrene biodegradation capacity of consortium dominated by Fischerella sp. under holoxenic conditions with aerobic heterotrophic bacteria and their molecular identification through 16S rRNA Illumina sequencing. Results indicated that our microbial consortium can degrade up to 92% of phenanthrene in five days. Bioinformatic analyses revealed that consortium was dominated by Fischerella sp., however different members of Nostocaceae and Weeksellaceae, as well as several other bacteria, such as Chryseobacterium, and Porphyrobacter, were found to be putatively involved in the biological degradation of phenanthrene. This work contributes to a better understanding of biodegradation of phenanthrene by cyanobacteria and identify the microbial diversity related.
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Affiliation(s)
| | | | - Nayem Amtanus Chequer
- Department of Marine Resources, Centro de Investigación y de Estudios Avanzados del IPN, Merida 97310, Yucatan, Mexico
| | - Nubia Noemí Cob-Calan
- Instituto Tecnológico Superior de Calkiní en el Estado de Campeche, Calkiní 24900, Campeche, Mexico
| | | | - Santiago Cadena
- Department of Marine Resources, Centro de Investigación y de Estudios Avanzados del IPN, Merida 97310, Yucatan, Mexico
| | - Emanuel Hernández-Núñez
- Department of Marine Resources, Centro de Investigación y de Estudios Avanzados del IPN, Merida 97310, Yucatan, Mexico
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3
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Yang R, Zhou S, Zhang L, Qin C. Pronounced temporal changes in soil microbial community and nitrogen transformation caused by benzalkonium chloride. J Environ Sci (China) 2023; 126:827-835. [PMID: 36503808 PMCID: PMC9553405 DOI: 10.1016/j.jes.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 05/16/2023]
Abstract
As one typical cationic disinfectant, quaternary ammonium compounds (QACs) were approved for surface disinfection in the coronavirus disease 2019 pandemic and then unintentionally or intentionally released into the surrounding environment. Concerningly, it is still unclear how the soil microbial community succession happens and the nitrogen (N) cycling processes alter when exposed to QACs. In this study, one common QAC (benzalkonium chloride (BAC) was selected as the target contaminant, and its effects on the temporal changes in soil microbial community structure and nitrogen transformation processes were determined by qPCR and 16S rRNA sequencing-based methods. The results showed that the aerobic microbial degradation of BAC in the two different soils followed first-order kinetics with a half-life (4.92 vs. 17.33 days) highly dependent on the properties of the soil. BAC activated the abundance of N fixation gene (nifH) and nitrification genes (AOA and AOB) in the soil and inhibited that of denitrification gene (narG). BAC exposure resulted in the decrease of the alpha diversity of soil microbial community and the enrichment of Crenarchaeota and Proteobacteria. This study demonstrates that BAC degradation is accompanied by changes in soil microbial community structure and N transformation capacity.
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Affiliation(s)
- Rui Yang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Shaohong Zhou
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Lilan Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Cunli Qin
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
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4
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Liu A, Wang W, Chen X, Zheng X, Fu W, Wang G, Ji J, Guan C. Phytoremediation of DEHP and heavy metals co-contaminated soil by rice assisted with a PGPR consortium: Insights into the regulation of ion homeostasis, improvement of photosynthesis and enrichment of beneficial bacteria in rhizosphere soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120303. [PMID: 36181940 DOI: 10.1016/j.envpol.2022.120303] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/20/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
The coexistence of di (2-ethylhexyl) phthalate (DEHP), Cd, and Zn poses a serious challenge to soil ecosystems. This study aimed to evaluate the phytoremediation potential of rice assisted with a plant growth promoting rhizobacteria (PGPR) consortium for the remediation of DEHP, Cd, and Zn co-contaminated soil. The consortium consisted of four bacterial strains, all of which exhibited Cd-Zn resistance and DEHP degradability. The results showed that the rice assisted by the bacterial consortium dissipated 86.1% DEHP while removing 76.0% Cd2+ and 92.2% Zn2+ from soil within 30 d. The presence of the PGPR consortium promoted plant growth and improved soil enzymatic activity, which may have helped enhance the removal of DEHP and heavy metals from the soil. Moreover, the application of the consortium modified the bacterial community and increased the relative abundance of bacteria related to DEHP degradation (Sphingomonas, Xanthobacteraceae), heavy metal immobilization (Massilia), and soil nutrient cycling (Nitrospira, Vicinamibacterales), which promoted plant growth and the removal of DEHP and heavy metals from soil. Notably, the DEHP and heavy metal contents in rice decreased substantially during the phytoremediation process. Therefore, the PGPR consortium could be beneficial for enhancing the removal of DEHP and heavy metals from the soil, without inducing the accumulation of these pollutants in rice. In general, this study confirmed that the combined use of rice and the PGPR consortium could remedy DEHP and heavy metal co-contaminated soil economically and ecologically without simultaneously posing risks for rice consumption.
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Affiliation(s)
- Anran Liu
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Wenjing Wang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Xiancao Chen
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Xiaoyan Zheng
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Wenting Fu
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Gang Wang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Jing Ji
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - Chunfeng Guan
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
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5
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Jiang X, Mao Z, Zhong L, Yu J, Tang Y. Strategy to Promote the Biodegradation of Phenanthrene in Contaminated Soil by a Novel Bacterial Consortium in Slurry Bioreactors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095515. [PMID: 35564911 PMCID: PMC9101024 DOI: 10.3390/ijerph19095515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/12/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are typical high-risk, persistent organic pollutants. Biological slurry reactors are widely used for enhanced bioremediation. In this experiment, a highly efficient phenanthrene-degrading bacteria group was obtained through screening and domestication, and the community was named MZJ_21. After the addition of MZJ_21 to the aerobic slurry bioreactor, with the optimum conditions of the temperature, stirring speed, and aeration rate of 30 °C, 120 rpm, and 1 L/min, respectively, the phenanthrene degradation ratio reached 95.41% within 48 h. The exploration of the degradation of phenanthrene by MZJ_21 indicated that most MZJ_21 communities adsorbed on the soil particle, mainly because MZI_21 could secrete extracellular polymers, which could stably adhere MZJ_21 on the solid phase. At the same time, the distribution ratio of phenanthrene in the solid phase is increased, so that the efficient phenanthrene degradation reaction takes place in the solid phase.
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Affiliation(s)
| | - Zhen Mao
- Correspondence: ; Tel.: +86-151-6218-2112
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Semenova EM, Grouzdev DS, Sokolova DS, Tourova TP, Poltaraus AB, Potekhina NV, Shishina PN, Bolshakova MA, Avtukh AN, Ianutsevich EA, Tereshina VM, Nazina TN. Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae. Microorganisms 2022; 10:microorganisms10020378. [PMID: 35208832 PMCID: PMC8878594 DOI: 10.3390/microorganisms10020378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
The goal of the present work was to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. The composition of the anaerobic oil-degrading methanogenic enrichment obtained from an oil reservoir was determined by 16S rRNA-based survey, and the facultatively anaerobic chemoorganotrophic bacterial strain HO-Ch2T was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2T grew optimally at 28 °C, pH 8.0, and 1–2% (w/v) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2T had 98.8% similarity with the sequence of Actinotalea ferrariae CF5-4T. The genomic DNA G + C content of strain HO-Ch2T was 73.4%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the genome of strain HO-Ch2T and Actinotalea genomes were 79.8–82.0% and 20.5–22.2%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic, and chemotaxonomic characterization, we propose strain HO-Ch2T (= VKM Ac-2850T = KCTC 49656T) as the type strain of a new species within the genus Actinotalea, with the name Actinotalea subterranea sp. nov. Based on the phylogenomic analysis of 187 genomes of Actinobacteria we propose the taxonomic revision of the genera Actinotalea and Pseudactinotalea and of the family Actinotaleaceae. We also propose the reclassification of Cellulomonas carbonis as Actinotalea carbonis comb. nov., Cellulomonas bogoriensis as Actinotalea bogoriensis comb. nov., Actinotalea caeni as Pseudactinotalea caeni comb. nov., and the transfer of the genus Pseudactinotalea to the family Ruaniaceae of the order Ruaniales.
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Affiliation(s)
- Ekaterina M. Semenova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | | | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | - Tatiyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | | | - Polina N. Shishina
- Geological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; (P.N.S.); (M.A.B.)
| | - Maria A. Bolshakova
- Geological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; (P.N.S.); (M.A.B.)
| | - Alexander N. Avtukh
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia;
| | - Elena A. Ianutsevich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | - Vera M. Tereshina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
| | - Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (D.S.S.); (T.P.T.); (E.A.I.); (V.M.T.)
- Correspondence: ; Tel.: +7-499-135-0341
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7
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Mahto KU, Kumari S, Das S. Unraveling the complex regulatory networks in biofilm formation in bacteria and relevance of biofilms in environmental remediation. Crit Rev Biochem Mol Biol 2021; 57:305-332. [PMID: 34937434 DOI: 10.1080/10409238.2021.2015747] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biofilms are assemblages of bacteria embedded within a matrix of extracellular polymeric substances (EPS) attached to a substratum. The process of biofilm formation is a complex phenomenon regulated by the intracellular and intercellular signaling systems. Various secondary messenger molecules such as cyclic dimeric guanosine 3',5'-monophosphate (c-di-GMP), cyclic adenosine 3',5'-monophosphate (cAMP), and cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) are involved in complex signaling networks to regulate biofilm development in several bacteria. Moreover, the cell to cell communication system known as Quorum Sensing (QS) also regulates biofilm formation via diverse mechanisms in various bacterial species. Bacteria often switch to the biofilm lifestyle in the presence of toxic pollutants to improve their survivability. Bacteria within a biofilm possess several advantages with regard to the degradation of harmful pollutants, such as increased protection within the biofilm to resist the toxic pollutants, synthesis of extracellular polymeric substances (EPS) that helps in the sequestration of pollutants, elevated catabolic gene expression within the biofilm microenvironment, higher cell density possessing a large pool of genetic resources, adhesion ability to a wide range of substrata, and metabolic heterogeneity. Therefore, a comprehensive account of the various factors regulating biofilm development would provide valuable insights to modulate biofilm formation for improved bioremediation practices. This review summarizes the complex regulatory networks that influence biofilm development in bacteria, with a major focus on the applications of bacterial biofilms for environmental restoration.
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Affiliation(s)
- Kumari Uma Mahto
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology, Odisha, India
| | - Swetambari Kumari
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology, Odisha, India
| | - Surajit Das
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology, Odisha, India
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8
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D’Ugo E, Bruno M, Mukherjee A, Chattopadhyay D, Giuseppetti R, De Pace R, Magurano F. Characterization of microbial response to petroleum hydrocarbon contamination in a lacustrine ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:26187-26196. [PMID: 33871774 PMCID: PMC8154760 DOI: 10.1007/s11356-021-13885-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Microbiomes of freshwater basins intended for human use remain poorly studied, with very little known about the microbial response to in situ oil spills. Lake Pertusillo is an artificial freshwater reservoir in Basilicata, Italy, and serves as the primary source of drinking water for more than one and a half million people in the region. Notably, it is located in close proximity to one of the largest oil extraction plants in Europe. The lake suffered a major oil spill in 2017, where approximately 400 tons of crude oil spilled into the lake; importantly, the pollution event provided a rare opportunity to study how the lacustrine microbiome responds to petroleum hydrocarbon contamination. Water samples were collected from Lake Pertusillo 10 months prior to and 3 months after the accident. The presence of hydrocarbons was verified and the taxonomic and functional aspects of the lake microbiome were assessed. The analysis revealed specialized successional patterns of lake microbial communities that were potentially capable of degrading complex, recalcitrant hydrocarbons, including aromatic, chloroaromatic, nitroaromatic, and sulfur containing aromatic hydrocarbons. Our findings indicated that changes in the freshwater microbial community were associated with the oil pollution event, where microbial patterns identified in the lacustrine microbiome 3 months after the oil spill were representative of its hydrocarbonoclastic potential and may serve as effective proxies for lacustrine oil pollution.
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Affiliation(s)
- Emilio D’Ugo
- Department of Infection Diseases, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Milena Bruno
- Core Facilities, National Institute of Health, Rome, Italy
| | - Arghya Mukherjee
- Center for Genetic Engineering and the Department of Biotechnology, University of Calcutta, Calcutta, India
| | - Dhrubajyoti Chattopadhyay
- Center for Genetic Engineering and the Department of Biotechnology, University of Calcutta, Calcutta, India
| | - Roberto Giuseppetti
- Department of Infection Diseases, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Rita De Pace
- Department of Foggia, Experimental Zooprophylactic Institute of Puglia and Basilicata Regions, Foggia, Italy
| | - Fabio Magurano
- Department of Infection Diseases, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
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9
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Development of nitrate stimulated hydrocarbon degrading microbial consortia from refinery sludge as potent bioaugmenting agent for enhanced bioremediation of petroleum contaminated waste. World J Microbiol Biotechnol 2020; 36:156. [DOI: 10.1007/s11274-020-02925-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022]
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10
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Benedek T, Szentgyörgyi F, Szabó I, Farkas M, Duran R, Kriszt B, Táncsics A. Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm. Appl Microbiol Biotechnol 2020; 104:6023-6043. [PMID: 32415320 PMCID: PMC7306034 DOI: 10.1007/s00253-020-10668-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022]
Abstract
In this study, we aimed at determining the impact of naphthalene and different oxygen levels on a biofilm bacterial community originated from a petroleum hydrocarbon-contaminated groundwater. By using cultivation-dependent and cultivation-independent approaches, the enrichment, identification, and isolation of aerobic and oxygen-limited naphthalene degraders was possible. Results indicated that, regardless of the oxygenation conditions, Pseudomonas spp. became the most dominant in the naphthalene-amended selective enrichment cultures. Under low-oxygen conditions, P. veronii/P. extremaustralis lineage affiliating bacteria, and under full aerobic conditions P. laurentiana-related isolates were most probably capable of naphthalene biodegradation. A molecular biological tool has been developed for the detection of naphthalene 1,2-dioxygenase-related 2Fe-2S reductase genes of Gram-negative bacteria. The newly developed COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP-PCR) technique may be used in the monitoring of the natural attenuation capacity of PAH-contaminated sites. A bacterial strain collection with prolific biofilm-producing and effective naphthalene-degrading organisms was established. The obtained strain collection may be applicable in the future for the development of biofilm-based bioremediation systems for the elimination of PAHs from groundwater (e.g., biofilm-based biobarriers).
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Affiliation(s)
- Tibor Benedek
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary.
| | - Flóra Szentgyörgyi
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - István Szabó
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Milán Farkas
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, Pau, France
| | - Balázs Kriszt
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - András Táncsics
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
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11
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Fei Y, Huang S, Zhang H, Tong Y, Wen D, Xia X, Wang H, Luo Y, Barceló D. Response of soil enzyme activities and bacterial communities to the accumulation of microplastics in an acid cropped soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 707:135634. [PMID: 31761364 DOI: 10.1016/j.scitotenv.2019.135634] [Citation(s) in RCA: 271] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 05/07/2023]
Abstract
The ecological stress of microplastics (MPs) contamination in agroecosystems raise worldwide concerns. However very few studies concentrated on the effects of MPs exposure on soil microbial community. The alterations of enzymatic activities and bacterial communities were assayed by spiking 1% and 5% (w/w) of polyethylene (PE) and polyvinyl chloride (PVC) MPs in an acid soil. The results showed that both PE and PVC addition inhibited fluorescein diacetate hydrolase activity and stimulated urease and acid phosphatase activities, and declined the richness and diversity of the bacterial communities. More severe effects were observed in the PE treated soils compared to the PVC treated soils generally. The relative abundances of families Burkholderiaceae increased significantly (p < .05) after MPs addition, suggesting the bacteria associated with nitrogen fixation stimulated by the MPs input. Meanwhile, significant (p < .05) decline of Sphingomonadaceae and Xanthobacteraceae after addition of 5% PVC and 1% PE MPs, respectively implied that MPs might inhibit the biodegradation of xenobiotics in the soil. Mover, the PICRUSt analysis demonstrated that membrane transporter was a sensitive prediction functional gene of microplastics exposure in the soil. Future studies could be focused on the role of MPs on the regulation of nitrogen cycling and organic compounds degradation in soils.
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Affiliation(s)
- Yufan Fei
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Shunyin Huang
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Haibo Zhang
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
| | - Yazhi Tong
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Dishi Wen
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Xiaoyu Xia
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Han Wang
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Yongming Luo
- Nanjing Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Damià Barceló
- Water and Soil Quality Research Group, Institute of Environmental Assessment and Water Research (IDAEA), Barcelona, Spain
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12
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Chalupa J, Pocik O, Halecky M, Kozliak E. Thermophilic waste air treatment of an airborne ethyl acetate/toluene mixture in a bubble column reactor: Stability towards temperature changes. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:120744. [PMID: 31812476 DOI: 10.1016/j.jhazmat.2019.120744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 05/04/2019] [Accepted: 06/05/2019] [Indexed: 06/10/2023]
Abstract
Thermophilic waste air treatment in a lab-scale bubble column reactor (BCR) was used to remove an ethyl acetate/toluene mixture under both mesophilic and thermophilic conditions, at 30-50 °C. Additional tests, e.g., toluene mass transfer measurement and monitoring of microbial population development, explained the observed bioreactor response to the conducted loading tests and temperature changes. The maximum overall elimination capacity at thermophilic conditions (50 °C) was 136.9 g·m-3 h-1, however hysteresis in elimination capacity was observed in response to ascending/descending temperature and inlet concentration changes. Representatives of genera Cupriavidus, Variovorax and order Rhodospirillales were found to be predominant in the degrading microbial population, depending on the operating temperature. Thermobacillus and Blastocatella were abundant at high (50 °C) and low (30 °C) temperatures, respectively. The observed gradual shift in microbial population caused a small yet significant gradual change in developing a preference for toluene at the expense of ethyl acetate, which explains the observed hysteresis. Yet, the whole bioreactor removal efficiency remained similar at the same temperature, thus demonstrating the advantages of using thermophiles in bioreactors with temperature variation, such as robustness and flexibility.
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Affiliation(s)
- Jan Chalupa
- University of Chemistry and Technology, Prague, Department of Biotechnology, Technicka 5, 166 28, Prague, Czech Republic
| | - Ondrej Pocik
- University of Chemistry and Technology, Prague, Department of Biotechnology, Technicka 5, 166 28, Prague, Czech Republic
| | - Martin Halecky
- University of Chemistry and Technology, Prague, Department of Biotechnology, Technicka 5, 166 28, Prague, Czech Republic.
| | - Evguenii Kozliak
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota, USA
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13
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Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures. Arch Microbiol 2019; 202:329-342. [PMID: 31664492 PMCID: PMC7012980 DOI: 10.1007/s00203-019-01749-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/02/2019] [Accepted: 10/10/2019] [Indexed: 02/03/2023]
Abstract
The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with high an abundance of Betaproteobacteriales (36.5%), followed by Alphaproteobacteria (8.7%), Actinobacteria (5.6%), and Candidatus Saccharibacteria (4.5%). The most abundant alkane monooxygenase (alkB) genotypes in this enrichment could be linked to members of the genus Rhodococcus and to a novel Gammaproteobacterium, for which we generated a high-quality draft genome using genome-resolved metagenomics of the enrichment culture. Contrarily, in the microaerobic enrichment, Gammaproteobacteria (99%) overwhelmingly dominated the microbial community with a high abundance of the genera Acinetobacter (66.3%), Pseudomonas (11%) and Acidovorax (11%). Under microaerobic conditions, the vast majority of alkB gene sequences could be linked to Pseudomonas veronii. Consequently, results shed light on the fact that the excellent aliphatic hydrocarbon degrading Rhodococcus species favour clear aerobic conditions, while oxygen-limited conditions can facilitate the high abundance of Acinetobacter species in aliphatic hydrocarbon-contaminated subsurface environments.
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14
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Marín P, Martirani‐Von Abercron SM, Urbina L, Pacheco‐Sánchez D, Castañeda‐Cataña MA, Retegi A, Eceiza A, Marqués S. Bacterial nanocellulose production from naphthalene. Microb Biotechnol 2019; 12:662-676. [PMID: 31087504 PMCID: PMC6559018 DOI: 10.1111/1751-7915.13399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 11/29/2022] Open
Abstract
Polycyclic aromatic compounds (PAHs) are toxic compounds that are released in the environment as a consequence of industrial activities. The restoration of PAH-polluted sites considers the use of bacteria capable of degrading aromatic compounds to carbon dioxide and water. Here we characterize a new Xanthobacteraceae strain, Starkeya sp. strain N1B, previously isolated during enrichment under microaerophilic conditions, which is capable of using naphthalene crystals as the sole carbon source. The strain produced a structured biofilm when grown on naphthalene crystals, which had the shape of a half-sphere organized over the crystal. Scanning electron microscopy (SEM) and GC-MS analysis indicated that the biofilm was essentially made of cellulose, composed of several micron-long nanofibrils of 60 nm diameter. A cellulosic biofilm was also formed when the cells grew with glucose as the carbon source. Fourier transformed infrared spectroscopy (FTIR) confirmed that the polymer was type I cellulose in both cases, although the crystallinity of the material greatly depended on the carbon source used for growth. Using genome mining and mutant analysis, we identified the genetic complements required for the transformation of naphthalene into cellulose, which seemed to have been successively acquired through horizontal gene transfer. The capacity to develop the biofilm around the crystal was found to be dispensable for growth when naphthalene was used as the carbon source, suggesting that the function of this structure is more intricate than initially thought. This is the first example of the use of toxic aromatic hydrocarbons as the carbon source for bacterial cellulose production. Application of this capacity would allow the remediation of a PAH into such a value-added polymer with multiple biotechnological usages.
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Affiliation(s)
- Patricia Marín
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Sophie Marie Martirani‐Von Abercron
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Leire Urbina
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Daniel Pacheco‐Sánchez
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Mayra Alejandra Castañeda‐Cataña
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Aloña Retegi
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Arantxa Eceiza
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Silvia Marqués
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
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15
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Lemmel F, Maunoury-Danger F, Fanesi A, Leyval C, Cébron A. Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient. MICROBIAL ECOLOGY 2019; 77:993-1013. [PMID: 30467715 DOI: 10.1007/s00248-018-1297-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/16/2018] [Indexed: 05/20/2023]
Abstract
The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.
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Affiliation(s)
- Florian Lemmel
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | | | - Andrea Fanesi
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | - Corinne Leyval
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France.
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Benedek T, Szentgyörgyi F, Szabó I, Kriszt B, Révész F, Radó J, Maróti G, Táncsics A. Aerobic and oxygen-limited enrichment of BTEX-degrading biofilm bacteria: dominance of Malikia versus Acidovorax species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:32178-32195. [PMID: 30220065 DOI: 10.1007/s11356-018-3096-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/28/2018] [Indexed: 05/14/2023]
Abstract
Due to their high resistance against environmental challenges, bacterial biofilms are ubiquitous and are frequently associated with undesired phenomena in environmental industry (e. g. biofouling). However, because of the high phylogenetic and functional diversity, bacterial biofilms are important sources of biotechnologically relevant microorganisms, e.g. those showing bioremediation potential. In our previous work, the high phylogenetic and metabolic diversity of a clogging biofilm, developed in a simple aromatic hydrocarbon (BTEX)-contaminated groundwater well was uncovered. The determination of relationships between different groups of biofilm bacteria and certain metabolic traits has been omitted so far. Therefore, by setting up new biofilm-based enrichment microcosms, the research goal of the present study was to identify the aerobic/hypoxic BTEX-degrading and/or prolific biofilm-forming bacteria. The initial bacterial community composition as well as temporal dynamics due to the selective enrichment has been determined. The obtained results indicated that the concentration of dissolved oxygen may be a strong selective force on the evolution and final structure of microbial communities, developed in hydrocarbon-contaminated environments. Accordingly, members of the genus Malikia proved to be the most dominant community members of the aerobic BTEX-degrading enrichments. Acidovorax spp. dominated the oxygen-limited/hypoxic setup. During the study, a strain collection of 23 different bacterial species was obtained. Non-pathogenic members of this strain collection, with outstanding biodegradation (e.g. Pseudomonas, Variovorax isolates) and biofilm-forming potential (e.g. Rhizobium), may potentially be applied in the development of biofilm-based semipermeable reactive biobarriers.
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Affiliation(s)
- Tibor Benedek
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary.
| | - Flóra Szentgyörgyi
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - István Szabó
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Fruzsina Révész
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Júlia Radó
- Department of Environmental Safety and Ecotoxicology, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, Hungary
- Faculty of Agricultural and Economics Studies, Tessedik Campus, Szent István University, Szabadság u. 1-3, Szarvas, H-5530, Hungary
| | - András Táncsics
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
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17
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Netzer R, Henry IA, Ribicic D, Wibberg D, Brönner U, Brakstad OG. Petroleum hydrocarbon and microbial community structure successions in marine oil-related aggregates associated with diatoms relevant for Arctic conditions. MARINE POLLUTION BULLETIN 2018; 135:759-768. [PMID: 30301095 DOI: 10.1016/j.marpolbul.2018.07.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
Oil-related aggregates (ORAs) may contribute to the fate of oil spilled offshore. However, our understanding about the impact of diatoms and associated bacteria involved in the formation of ORAs and the fate of oil compounds in these aggregates is still limited. We investigated these processes in microcosm experiments with defined oil dispersions in seawater at 5 °C, employing the Arctic diatom Fragilariopsis cylindrus and its associated bacterial assemblage to promote ORA formation. Accumulation of oil compounds, as well as biodegradation of naphthalenes in ORAs and corresponding water phases, was enhanced in the presence of diatoms. Interestingly, the genus Nonlabens was predominating the bacterial communities in diatom-supplemented microcosms, while this genus was not abundant in other samples. This work elucidates the relevance of diatom biomass for the formation of ORAs, microbial community structures and biodegradation processes in chemically dispersed oil at low temperatures relevant for Arctic conditions.
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Affiliation(s)
- Roman Netzer
- SINTEF Ocean, Brattørkaia 17C, 7010 Trondheim, Norway.
| | | | - Deni Ribicic
- SINTEF Ocean, Brattørkaia 17C, 7010 Trondheim, Norway
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Ute Brönner
- SINTEF Ocean, Brattørkaia 17C, 7010 Trondheim, Norway
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18
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Wilhelm RC, Hanson BT, Chandra S, Madsen E. Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater. Environ Microbiol 2018; 20:3543-3559. [PMID: 30051558 DOI: 10.1111/1462-2920.14309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022]
Abstract
Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from 13 C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.
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Affiliation(s)
- Roland C Wilhelm
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Buck T Hanson
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Subhash Chandra
- Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Eugene Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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19
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Martirani-Von Abercron SM, Marín P, Solsona-Ferraz M, Castañeda-Cataña MA, Marqués S. Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity. Microb Biotechnol 2017; 10:1781-1796. [PMID: 28840968 PMCID: PMC5658598 DOI: 10.1111/1751-7915.12842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 11/27/2022] Open
Abstract
Toxic polycyclic aromatic hydrocarbons (PAHs) are frequently released into the environment from anthropogenic sources. PAH remediation strategies focus on biological processes mediated by bacteria. The availability of oxygen in polluted environments is often limited or absent, and only bacteria able to thrive in these conditions can be considered for bioremediation strategies. To identify bacterial strains able to degrade PAHs under oxygen‐limiting conditions, we set up enrichment cultures from samples of an oil‐polluted aquifer, using either anoxic or microaerophilic condition and with PAHs as the sole carbon source. Despite the presence of a significant community of nitrate‐reducing bacteria, the initial community, which was dominated by Betaproteobacteria, was incapable of PAH degradation under strict anoxic conditions, although a clear shift in the structure of the community towards an increase in the Alphaproteobacteria (Sphingomonadaceae), Actinobacteria and an uncultured group of Acidobacteria was observed in the enrichments. In contrast, growth under microaerophilic conditions with naphthalene as the carbon source evidenced the development of a biofilm structure around the naphthalene crystal. The enrichment process selected two co‐dominant groups which finally reached 97% of the bacterial communities: Variovorax spp. (54%, Betaproteobacteria) and Starkeya spp. (43%, Xanthobacteraceae). The two dominant populations were able to grow with naphthalene, although only Starkeya was able to reproduce the biofilm structure around the naphthalene crystal. The pathway for naphthalene degradation was identified, which included as essential steps dioxygenases with high affinity for oxygen, showing 99% identity with Xanthobacter polyaromaticivorans dbd cluster for PAH degradation. Our results suggest that the biofilm formation capacity of Starkeya provided a structure to allocate its cells at an appropriate distance from the toxic carbon source.
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Affiliation(s)
| | - Patricia Marín
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Marta Solsona-Ferraz
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Mayra-Alejandra Castañeda-Cataña
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Silvia Marqués
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
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