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Charalampous G, Fragkou E, Kalogerakis N, Antoniou E, Gontikaki E. Diversity links to functionality: Unraveling the impact of pressure disruption and culture medium on crude oil-enriched microbial communities from the deep Eastern Mediterranean Sea. MARINE POLLUTION BULLETIN 2024; 202:116275. [PMID: 38564821 DOI: 10.1016/j.marpolbul.2024.116275] [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: 10/31/2023] [Revised: 01/19/2024] [Accepted: 03/17/2024] [Indexed: 04/04/2024]
Abstract
Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS.
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Affiliation(s)
- Georgia Charalampous
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
| | - Efsevia Fragkou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Nicolas Kalogerakis
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Eleftheria Antoniou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; School of Mineral Resources Engineering, Technical University of Crete, Chania, Greece
| | - Evangelia Gontikaki
- Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
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Tedesco P, Balzano S, Coppola D, Esposito FP, de Pascale D, Denaro R. Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth. MARINE POLLUTION BULLETIN 2024; 200:116157. [PMID: 38364643 DOI: 10.1016/j.marpolbul.2024.116157] [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: 12/22/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024]
Abstract
The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.
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Affiliation(s)
- Pietro Tedesco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Sergio Balzano
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Daniela Coppola
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Fortunato Palma Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Donatella de Pascale
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy; Institute of Biochemistry and Cellular Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Renata Denaro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti Rome, Italy.
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Liu Y, Chen S, Xie Z, Zhang L, Wang J, Fang J. Influence of Extremely High Pressure and Oxygen on Hydrocarbon-Enriched Microbial Communities in Sediments from the Challenger Deep, Mariana Trench. Microorganisms 2023; 11:microorganisms11030630. [PMID: 36985204 PMCID: PMC10052102 DOI: 10.3390/microorganisms11030630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Recent studies reported that highly abundant alkane content exists in the ~11,000 m sediment of the Mariana Trench, and a few key alkane-degrading bacteria were identified in the Mariana Trench. At present, most of the studies on microbes for degrading hydrocarbons were performed mainly at atmospheric pressure (0.1 MPa) and room temperature; little is known about which microbes could be enriched with the addition of n-alkanes under in-situ environmental pressure and temperature conditions in the hadal zone. In this study, we conducted microbial enrichments of sediment from the Mariana Trench with short-chain (SCAs, C7–C17) or long-chain (LCAs, C18–C36) n-alkanes and incubated them at 0.1 MPa/100 MPa and 4 °C under aerobic or anaerobic conditions for 150 days. Microbial diversity analysis showed that a higher microbial diversity was observed at 100 MPa than at 0.1 MPa, irrespective of whether SCAs or LCAs were added. Non-metric multidimensional scaling (nMDS) and hierarchical cluster analysis revealed that different microbial clusters were formed according to hydrostatic pressure and oxygen. Significantly different microbial communities were formed according to pressure or oxygen (p < 0.05). For example, Gammaproteobacteria (Thalassolituus) were the most abundant anaerobic n-alkanes-enriched microbes at 0.1 MPa, whereas the microbial communities shifted to dominance by Gammaproteobacteria (Idiomarina, Halomonas, and Methylophaga) and Bacteroidetes (Arenibacter) at 100 MPa. Compared to the anaerobic treatments, Actinobacteria (Microbacterium) and Alphaproteobacteria (Sulfitobacter and Phenylobacterium) were the most abundant groups with the addition of hydrocarbon under aerobic conditions at 100 MPa. Our results revealed that unique n-alkane-enriched microorganisms were present in the deepest sediment of the Mariana Trench, which may imply that extremely high hydrostatic pressure (100 MPa) and oxygen dramatically affected the processes of microbial-mediated alkane utilization.
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Affiliation(s)
- Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518000, China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Li Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
- Correspondence: (J.W.); (J.F.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
- Correspondence: (J.W.); (J.F.)
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Barbato M, Palma E, Marzocchi U, Cruz Viggi C, Rossetti S, Aulenta F, Scoma A. Snorkels enhance alkanes respiration at ambient and increased hydrostatic pressure (10 MPa) by either supporting the TCA cycle or limiting alternative routes for acetyl-CoA metabolism. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115244. [PMID: 35598451 DOI: 10.1016/j.jenvman.2022.115244] [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: 01/31/2022] [Revised: 04/27/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
The impact of piezosensitive microorganisms is generally underestimated in the ecology of underwater environments exposed to increasing hydrostatic pressure (HP), including the biodegradation of crude oil components. Yet, no isolated pressure-loving (piezophile) microorganism grows optimally on hydrocarbons, and no isolated piezophile at all has a HP optimum <10 MPa (e.g. 1000 m below sea water level). Piezosensitive heterotrophs are thus largely accountable for oil clean up < 10 MPa, however, they are affected by such a mild HP increase in ways which are not completely clear. In a first study, the application of a bioelectrochemical system (called "oil-spill snorkel") enhanced the alkane oxidation capacity in sediments collected at surface water but tested up to 10 MPa. Here, the fingerprint left on transcript abundance was studied to explore which metabolic routes are 1) supported by snorkels application and 2) negatively impacted by HP increase. Transcript abundance was comparable for beta-oxidation across all treatments (also at a taxonomical level), while the metabolism of acetyl-CoA was highly impacted: at either 0.1 or 10 MPa, snorkels supported acetyl-CoA oxidation within the TCA cycle, while in negative controls using non-conductive rods several alternative routes for acetyl-CoA were stimulated (including those leading to internal carbon reserves e.g. 2,3 butanediol and dihydroxyacetone). In general, increased HP had opposite effects as compared to snorkels, thus indicating that snorkels could enhance hydrocarbons oxidation by alleviating in part the stressing effects imposed by increased HP on the anaerobic, respiratory electron transport chain. 16S rRNA gene analysis of sediments and biofilms on snorkels suggest a crosstalk between oil-degrading, sulfate-reducing microorganisms and sulfur oxidizers. In fact, no sulfur was deposited on snorkels, however, iron, aluminum and phosphorous were found to preferentially deposit on snorkels at 10 MPa. This data indicates that a passive BES such as the oil-spill snorkel can mitigate the stress imposed by increased HP on piezosensitive microorganisms (up to 10 MPa) without being subjected to passivation. An improved setup applying these principles can further support this deep-sea bioremediation strategy.
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Affiliation(s)
- Marta Barbato
- Engineered Microbial Systems (EMS) Lab, Industrial Biotechnology Section, Department of Biological and Chemical Engineering (BCE), Aarhus University, Aarhus, Denmark; Microbiology Section, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Enza Palma
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy
| | - Ugo Marzocchi
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark; Center for Water Technology WATEC, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy.
| | - Alberto Scoma
- Engineered Microbial Systems (EMS) Lab, Industrial Biotechnology Section, Department of Biological and Chemical Engineering (BCE), Aarhus University, Aarhus, Denmark; Microbiology Section, Department of Biology, Aarhus University, Aarhus, Denmark.
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Wu Y, Liu X, Dong Q, Xiao M, Li B, Topalović O, Tao Q, Tang X, Huang R, Chen G, Li H, Chen Y, Feng Y, Wang C. Remediation of petroleum hydrocarbons-contaminated soil: Analysis based on Chinese patents. CHEMOSPHERE 2022; 297:134173. [PMID: 35276108 DOI: 10.1016/j.chemosphere.2022.134173] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Increasing soil petroleum hydrocarbons (PHs) pollution have caused world-wide concerns. The removal of PHs from soils mainly involves physical, chemical, biological processes and their combinations. To date, most reviews in this field based on research articles, but limited papers focused on the integration of remediation technologies from the perspective of patents. In this study, 20-years Chinese patents related to the remediation of soil PHs were comprehensively analyzed. It showed an increasing number of patent applications and the patents' quantity were positively correlated with Chinese GDP over the years, suggesting the more the economy developed the more environmental problems and corresponding solutions emerged. In addition, chemical technologies were mostly used in a combination to achieve faster and better effects, while the physical technologies were often used alone due to high costs. In all PHs remediation techniques, bacteria-based bioremediation was the most used from 2000 to 2019. Bacillus spp. and Pseudomonas spp. were the most used bacteria for PHs treatment because these taxa were widely harboring functions such as biosurfactant production and hydrocarbon degradation. The future research on joint technologies combining microbial and physicochemical ones for better remediation effect and application are highly encouraged.
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Affiliation(s)
- Yingjie Wu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xipeng Liu
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747, AG Groningen, the Netherlands
| | - Qin Dong
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Meijuan Xiao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Olivera Topalović
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoyan Tang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Rong Huang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yulan Chen
- Liangshan Branch of Sichuan Provincial Tobacco Company, Xichang, 615000, China
| | - Ying Feng
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China.
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From Surface Water to the Deep Sea: A Review on Factors Affecting the Biodegradation of Spilled Oil in Marine Environment. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the past century, the demand for petroleum products has increased rapidly, leading to higher oil extraction, processing and transportation, which result in numerous oil spills in coastal-marine environments. As the spilled oil can negatively affect the coastal-marine ecosystems, its transport and fates captured a significant interest of the scientific community and regulatory agencies. Typically, the environment has natural mechanisms (e.g., photooxidation, biodegradation, evaporation) to weather/degrade and remove the spilled oil from the environment. Among various oil weathering mechanisms, biodegradation by naturally occurring bacterial populations removes a majority of spilled oil, thus the focus on bioremediation has increased significantly. Helping in the marginal recognition of this promising technique for oil-spill degradation, this paper reviews recently published articles that will help broaden the understanding of the factors affecting biodegradation of spilled oil in coastal-marine environments. The goal of this review is to examine the effects of various environmental variables that contribute to oil degradation in the coastal-marine environments, as well as the factors that influence these processes. Physico-chemical parameters such as temperature, oxygen level, pressure, shoreline energy, salinity, and pH are taken into account. In general, increase in temperature, exposure to sunlight (photooxidation), dissolved oxygen (DO), nutrients (nitrogen, phosphorous and potassium), shoreline energy (physical advection—waves) and diverse hydrocarbon-degrading microorganisms consortium were found to increase spilled oil degradation in marine environments. In contrast, higher initial oil concentration and seawater pressure can lower oil degradation rates. There is limited information on the influences of seawater pH and salinity on oil degradation, thus warranting additional research. This comprehensive review can be used as a guide for bioremediation modeling and mitigating future oil spill pollution in the marine environment by utilizing the bacteria adapted to certain conditions.
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Mapelli F, Barbato M, Chouaia B, Riva V, Daffonchio D, Borin S. Bacterial community structure and diversity along the halocline of Tyro deep-sea hypersaline anoxic basin. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01667-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Tyro is a deep hypersaline anoxic basin (DHAB) located at the seafloor of the Eastern Mediterranean sea. Tyro hosts a stratified eukaryotic microbiome moving from seawater to the brine, but no reports are available on its prokaryotic community. We provide the first snapshot of the bacterial community structure in Tyro brine, seawater-brine interface, and the overlaying deep seawater.
Methods
In this study, we combined the use of molecular analyses, i.e., DNA fingerprinting and 16S rRNA pyrosequencing for the description of the bacterial community structure and taxonomy. PiCRUST2 was used to infer information on the prokaryotes functional diversity. A culture-dependent approach was applied to enrich bacteria of interest for marine biotechnology.
Results
Bacterial communities sharply clustered moving from the seawater to the Tyro brine, in agreement with the abrupt increase of salinity values. Moreover, specific taxonomic groups inhabited the seawater-brine interface compared to the overlaying seawater and their identification revealed converging taxonomy with other DHABs in the Eastern Mediterranean sea. Functional traits inferred from the prokaryote taxonomy in the upper interface and the overlaying seawater indicated metabolic pathways for the synthesis of osmoprotectants, likely involved in bacterial adaptation to the steep increasing salinity. Metabolic traits related to methane and methylated compounds and to hydrocarbon degradation were also revealed in the upper interface of Tyro. The overall capability of the Tyro microbiome for hydrocarbon metabolism was confirmed by the isolation of hydrocarbonoclastic bacteria in the sediments.
Conclusions
Our results suggest that Tyro seawater-brine interface hosts a specific microbiome adapted to the polyextreme condition typical of DHABs with potential metabolic features that could be further explored for the characterization of the metabolic network connecting the brine with the deep seawater through the chemocline. Moreover, Tyro could be a reservoir of culturable microbes endowed with functionalities of interest for biotechnological applications like hydrocarbon bioremediation.
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Kong W, Zhao C, Gao X, Wang L, Tian Q, Liu Y, Xue S, Han Z, Chen F, Wang S. Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18126365. [PMID: 34208299 PMCID: PMC8296198 DOI: 10.3390/ijerph18126365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022]
Abstract
Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C18–C36), but not short- and medium-chain n-alkanes (C8–C16). The degradation rate of C20 was 91.25%, followed by C18, C22, C24, C32, and C36 with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C20 or CH3COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C20 compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C20, C24, and C32, and almA induction extent by C24 and C32 was higher than that with C20. Furthermore, ladA2 expression was only induced by C32, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment.
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Affiliation(s)
- Weina Kong
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Cheng Zhao
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Xingwang Gao
- Hulangmao Oil Production Area in No.3 Oil Production Plant of Changqing Oilfield Company, Yan’an 717500, China;
| | - Liping Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Qianqian Tian
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Yu Liu
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Shuwen Xue
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Zhuang Han
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China;
| | - Fulin Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
- Correspondence: (F.C.); (S.W.)
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
- Correspondence: (F.C.); (S.W.)
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9
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Ganesh Kumar A, Manisha D, Sujitha K, Magesh Peter D, Kirubagaran R, Dharani G. Genome sequence analysis of deep sea Aspergillus sydowii BOBA1 and effect of high pressure on biodegradation of spent engine oil. Sci Rep 2021; 11:9347. [PMID: 33931710 PMCID: PMC8087790 DOI: 10.1038/s41598-021-88525-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
A deep-sea fungus Aspergillus sydowii BOBA1 isolated from marine sediment at a depth of 3000 m was capable of degrading spent engine (SE) oil. The response of immobilized fungi towards degradation at elevated pressure was studied in customized high pressure reactors without any deviation in simulating in situ deep-sea conditions. The growth rate of A. sydowii BOBA1 in 0.1 MPa was significantly different from the growth at 10 MPa pressure. The degradation percentage reached 71.2 and 82.5% at atmospheric and high pressure conditions, respectively, within a retention period of 21 days. The complete genome sequence of BOBA1 consists of 38,795,664 bp in size, comprises 2582 scaffolds with predicted total coding genes of 18,932. A total of 16,247 genes were assigned with known functions and many families found to have a potential role in PAHs and xenobiotic compound metabolism. Functional genes controlling the pathways of hydrocarbon and xenobiotics compound degrading enzymes such as dioxygenase, decarboxylase, hydrolase, reductase and peroxidase were identified. The spectroscopic and genomic analysis revealed the presence of combined catechol, gentisate and phthalic acid degradation pathway. These results of degradation and genomic studies evidenced that this deep-sea fungus could be employed to develop an eco-friendly mycoremediation technology to combat the oil polluted marine environment. This study expands our knowledge on piezophilic fungi and offer insight into possibilities about the fate of SE oil in deep-sea.
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Affiliation(s)
- A. Ganesh Kumar
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - D. Manisha
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - K. Sujitha
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - D. Magesh Peter
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - R. Kirubagaran
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - G. Dharani
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
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10
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Enhanced Hydrocarbons Biodegradation at Deep-Sea Hydrostatic Pressure with Microbial Electrochemical Snorkels. Catalysts 2021. [DOI: 10.3390/catal11020263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In anaerobic sediments, microbial degradation of petroleum hydrocarbons is limited by the rapid depletion of electron acceptors (e.g., ferric oxide, sulfate) and accumulation of toxic metabolites (e.g., sulfide, following sulfate reduction). Deep-sea sediments are increasingly impacted by oil contamination, and the elevated hydrostatic pressure (HP) they are subjected to represents an additional limitation for microbial metabolism. While the use of electrodes to support electrobioremediation in oil-contaminated sediments has been described, there is no evidence on their applicability for deep-sea sediments. Here, we tested a passive bioelectrochemical system named ”oil-spill snorkel” with two crude oils carrying different alkane contents (4 vs. 15%), at increased or ambient HP (10 vs. 0.1 MPa). Snorkels enhanced alkanes biodegradation at both 10 and 0.1 MPa within only seven weeks, as compared to nonconductive glass controls. Microprofiles in anaerobic, contaminated sediments indicated that snorkels kept sulfide concentration to low titers. Bulk-sediment analysis confirmed that sulfide oxidation by snorkels largely regenerated sulfate. Hence, the sole application of snorkels could eliminate a toxicity factor and replenish a spent electron acceptor at increased HP. Both aspects are crucial for petroleum decontamination of the deep sea, a remote environment featured by low metabolic activity.
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Barbato M, Scoma A. Mild hydrostatic-pressure (15 MPa) affects the assembly, but not the growth, of oil-degrading coastal microbial communities tested under limiting conditions (5°C, no added nutrients). FEMS Microbiol Ecol 2020; 96:5894919. [PMID: 32816016 DOI: 10.1093/femsec/fiaa160] [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: 05/18/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023] Open
Abstract
Hydrostatic pressures (HP) <30-40 MPa are often considered mild, and their impact on petroleum biodegradation seldom considered. However, the frequent use of nutrient-rich media in lab-scale high-pressure reactors may exaggerate HP importance by resulting in a strong growth stimulation as compared to oligotrophic marine environments. Here, we tested coastal seawater microbial communities, presumably enriched in pressure-sensitive microorganisms. Limiting environmental conditions for growth were applied (i.e. low temperature [5°C], no added nutrients) and HP tested at 0.1 and 15 MPa, using crude oils from three different reservoirs. The cell number was not affected by HP contrary to the microbial community composition (based on 16S rRNA gene and 16S rRNA sequences). The most predominant genera were Zhongshania, Pseudomonas and Colwellia. The enrichment of Zhongshania was crude-oil dependent and comparable at 0.1 and 15 MPa, thus showing a piezotolerant phenotype under the present conditions; Pseudomonas' was crude-oil dependent at 0.1 MPa but unclear at 15 MPa. Colwellia was selectively enriched in the absence of crude oil and suppressed at 15 MPa. HP shaped the assemblage of oil-degrading communities even at mild levels (i.e. 15 MPa), and should thus be considered as a fundamental factor to assess oil bioremediation along the water column.
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Affiliation(s)
- Marta Barbato
- Department of Biology, Aarhus University, Ny munkegade 116, 8000, Aarhus C, Denmark.,Biological and Chemical Engineering Section (BCE), Department of Engineering, Aarhus University, Hangøvej 2, 8200, Aarhus N, Denmark
| | - Alberto Scoma
- Department of Biology, Aarhus University, Ny munkegade 116, 8000, Aarhus C, Denmark.,Biological and Chemical Engineering Section (BCE), Department of Engineering, Aarhus University, Hangøvej 2, 8200, Aarhus N, Denmark
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12
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Van Landuyt J, Cimmino L, Dumolin C, Chatzigiannidou I, Taveirne F, Mattelin V, Zhang Y, Vandamme P, Scoma A, Williamson A, Boon N. Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders. FEMS Microbiol Ecol 2020; 96:5841521. [PMID: 32436568 DOI: 10.1093/femsec/fiaa097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/20/2020] [Indexed: 11/12/2022] Open
Abstract
Deep-sea environments can become contaminated with petroleum hydrocarbons. The effects of hydrostatic pressure (HP) in the deep sea on microbial oil degradation are poorly understood. Here, we performed long-term enrichments (100 days) from a natural cold seep while providing optimal conditions to sustain high hydrocarbon degradation rates. Through enrichments performed at increased HP and ambient pressure (AP) and by using control enrichments with marine broth, we demonstrated that both pressure and carbon source can have a big impact on the community structure. In contrast to previous studies, hydrocarbonoclastic operational taxonomic units (OTUs) remained dominant at both AP and increased HP, suggesting piezotolerance of these OTUs over the tested pressure range. Twenty-three isolates were obtained after isolation and dereplication. After recultivation at increased HP, an Alcanivorax sp. showed promising piezotolerance in axenic culture. Furthermore, preliminary co-cultivation tests indicated synergistic growth between some isolates, which shows promise for future synthetic community construction. Overall, more insights into the effect of increased HP on oil-degrading communities were obtained as well as several interesting isolates, e.g. a piezotolerant hydrocarbonoclastic bacterium for future deep-sea bioaugmentation investigation.
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Affiliation(s)
- Josefien Van Landuyt
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, ENAC-IIE, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Charles Dumolin
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ioanna Chatzigiannidou
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Felix Taveirne
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Valérie Mattelin
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, 800 Dongchuan Rd, 200240 Shanghai, China
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Alberto Scoma
- Engineered Microbial Systems (EMS) Laboratory, Section of Biological and Chemical Engineering (BCE), Department of Engineering, Aarhus University, Hangøvej 2, 8200 Aarhus, Denmark
| | - Adam Williamson
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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13
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Pinto ÉSM, Dorn M, Feltes BC. The tale of a versatile enzyme: Alpha-amylase evolution, structure, and potential biotechnological applications for the bioremediation of n-alkanes. CHEMOSPHERE 2020; 250:126202. [PMID: 32092569 DOI: 10.1016/j.chemosphere.2020.126202] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/10/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
As the primary source of a wide range of industrial products, the study of petroleum-derived compounds is of pivotal importance. However, the process of oil extraction and refinement is among the most environmentally hazardous practices, impacting almost all levels of the ecological chain. So far, the most appropriate strategy to overcome such an issue is through bioremediation, which revolves around the employment of different microorganisms to degrade hazardous compounds, generating less environmental impact and lower monetary costs. In this sense, a myriad of organisms and enzymes are considered possible candidates for the bioremediation process. Amidst the potential candidates is α-amylase, an evolutionary conserved starch-degrading enzyme. Notably, α-amylase was not only seen to degrade n-alkanes, a subclass of alkanes considered the most abundant petroleum-derived compounds but also low-density polyethylene, a dangerous pollutant produced from petroleum. Thus, due to its high conservation in both eukaryotic and prokaryotic lineages, in addition to the capability to degrade different types of hazardous compounds, the study of α-amylase becomes a rising interest. Nevertheless, there are no studies that review all biotechnological applications of α-amylase for bioremediation. In this work, we critically review the potential biotechnological applications of α-amylase, focusing on the biodegradation of petroleum-derived compounds. Evolutionary aspects are discussed, as well for all structural information and all features that could impact on the employment of this protein in the biotechnological industry, such as pH, temperature, and medium conditions. New perspectives and critical assessments are conducted regarding the application of α-amylase in the bioremediation of n-alkanes.
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Affiliation(s)
- Éderson Sales Moreira Pinto
- Laboratory of Structural Bioinformatics and Computational Biology, Center for Biotechnology, Federal University of Rio Grande do Sul, Brazil
| | - Márcio Dorn
- Laboratory of Structural Bioinformatics and Computational Biology, Institute of Informatics, Federal University of Rio Grande do Sul, Brazil; Laboratory of Structural Bioinformatics and Computational Biology, Center for Biotechnology, Federal University of Rio Grande do Sul, Brazil
| | - Bruno César Feltes
- Laboratory of Structural Bioinformatics and Computational Biology, Institute of Informatics, Federal University of Rio Grande do Sul, Brazil.
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14
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Hackbusch S, Noirungsee N, Viamonte J, Sun X, Bubenheim P, Kostka JE, Müller R, Liese A. Influence of pressure and dispersant on oil biodegradation by a newly isolated Rhodococcus strain from deep-sea sediments of the gulf of Mexico. MARINE POLLUTION BULLETIN 2020; 150:110683. [PMID: 31753565 DOI: 10.1016/j.marpolbul.2019.110683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
A new Rhodococcus strain, capable of degrading crude oil, was isolated from the Gulf of Mexico deep-sea sediment and was investigated for its biodegradation characteristics under atmospheric as well as under deep-sea pressure (1500 m = 15 MPa). Additionally, the effect of dispersant (Corexit EC9500A) addition was studied. Rhodococcus sp. PC20 was shown to degrade 60.5 ± 10.7% of the saturated and aromatic fraction of crude oil at atmospheric pressure and 74.2 ± 9.1% at deep-sea level pressure within 96 h. Degradation rates, especially for monoaromatic hydrocarbons, were significantly higher at elevated pressure compared to atmospheric pressure. This study found a growth inhibiting effect at a dispersant to oil ratio of 1:100 and higher. This effect of the dispersant was enhanced when elevated pressure was applied.
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Affiliation(s)
- Steffen Hackbusch
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Nuttapol Noirungsee
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Juan Viamonte
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Xiaoxu Sun
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Paul Bubenheim
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Joel E Kostka
- Georgia Institute of Technology School of Biology and Earth & Atmospheric Sciences, Atlanta, GA, USA.
| | - Rudolf Müller
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology (TUHH), Hamburg, Germany.
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15
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Pavlova ON, Adamovich SN, Novikova AS, Gorshkov AG, Izosimova ON, Ushakov IA, Oborina EN, Mirskova AN, Zemskaya TI. Protatranes, effective growth biostimulants of hydrocarbon-oxidizing bacteria from Lake Baikal, Russia. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2019; 24:e00371. [PMID: 31516851 PMCID: PMC6732725 DOI: 10.1016/j.btre.2019.e00371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/02/2019] [Accepted: 08/09/2019] [Indexed: 11/30/2022]
Abstract
Under natural conditions, biodegradation processes proceed slowly, especially in regions with low temperature. To activate vital processes in hydrocarbon-oxidizing microorganisms at low temperatures, biologically active compounds can be employed as growth stimulants. A low-temperature (10 °C) study has shown that tris-(2 hydroxyethyl) ammonium arylchalcogenylacetates, "protatranes" exert an effect on the growth of hydrocarbon-oxidizing strains of Rhodococcus erythropolis and Pseudomonas fluorescens, isolated from natural oil seepage on Lake Baikal. It has been found that "protatranes", at microconcentrations, increase the growth rate of R. erythropolis bacteria by 2-16 times. It has been established that compounds slightly effect the growth of P. fluorescens. The positive effect of "protatranes" compounds on the growth rate of hydrocarbon-oxidizing microorganisms at low positive temperatures can be used for the development of environmentally benign methods for the restoration of natural objects after their contamination with oil.
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Affiliation(s)
- Olga N. Pavlova
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, 3, Ulan-Batorskaya, 664033, Irkutsk, Russia
- Irkutsk Scientific Center of the Siberian Branch, Russian Academy of Sciences, 134, Lermontov st., 664033, Irkutsk, Russia
| | - Sergey N. Adamovich
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1, Favorsky st., 664033, Irkutsk, Russia
- Irkutsk Scientific Center of the Siberian Branch, Russian Academy of Sciences, 134, Lermontov st., 664033, Irkutsk, Russia
| | - Angelina S. Novikova
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, 3, Ulan-Batorskaya, 664033, Irkutsk, Russia
| | - Alexander G. Gorshkov
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, 3, Ulan-Batorskaya, 664033, Irkutsk, Russia
| | - Oksana N. Izosimova
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, 3, Ulan-Batorskaya, 664033, Irkutsk, Russia
| | - Igor A. Ushakov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1, Favorsky st., 664033, Irkutsk, Russia
| | - Elizaveta N. Oborina
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1, Favorsky st., 664033, Irkutsk, Russia
| | - Anna N. Mirskova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1, Favorsky st., 664033, Irkutsk, Russia
| | - Tamara I. Zemskaya
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, 3, Ulan-Batorskaya, 664033, Irkutsk, Russia
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16
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Potts LD, Perez Calderon LJ, Gontikaki E, Keith L, Gubry-Rangin C, Anderson JA, Witte U. Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates. FEMS Microbiol Ecol 2019; 94:5047303. [PMID: 29982504 PMCID: PMC6166136 DOI: 10.1093/femsec/fiy127] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022] Open
Abstract
Oil reserves in deep-sea sediments are currently subject to intense exploration, with associated risks of oil spills. Previous research suggests that microbial communities from deep-sea sediment (>1000m) can degrade hydrocarbons (HCs), but have a lower degradation ability than shallow (<200m) communities, probably due to in situ temperature. This study aimed to assess the effect of marine origin on microbial HC degradation potential while separating the influence of temperature, and to characterise associated HC-degrading bacterial communities. Microbial communities from 135 and 1000 m deep sediments were selectively enriched on crude oil at in situ temperatures and both consortia were subsequently incubated for 42 days at 20°C with two HC mixtures: diesel fuel or model oil. Significant HC biodegradation occurred rapidly in the presence of both consortia, especially of low molecular weight HCs and was concomitant with microbial community changes. Further, oil degradation was higher with the shallow consortium than with the deep one. Dominant HC-degrading bacteria differed based on both spatial origin of the consortia and supplemented HC types. This study provides evidence for influence of sediment spatial origin and HC composition on the selection and activity of marine HC-degrading bacterial communities and is relevant for future bioremediationdevelopments.
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Affiliation(s)
- Lloyd D Potts
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom.,Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Luis J Perez Calderon
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom.,Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Evangelia Gontikaki
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - Lehanne Keith
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - James A Anderson
- Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Ursula Witte
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
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Periodic and Spatial Spreading of Alkanes and Alcanivorax Bacteria in Deep Waters of the Mariana Trench. Appl Environ Microbiol 2019; 85:AEM.02089-18. [PMID: 30446553 PMCID: PMC6344633 DOI: 10.1128/aem.02089-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/04/2018] [Indexed: 12/20/2022] Open
Abstract
In the oligotrophic environment of the Mariana Trench, alkanes as carbohydrates are important for the ecosystem, but their spatial and periodic spreading in deep waters has never been reported. Alkane-degrading bacteria such as Alcanivorax spp. are biological signals of the alkane distribution. In the present study, Alcanivorax was abundant in some waters, at depths of up to 6,000 m, in the Mariana Trench. Genomic, transcriptomic, and chemical analyses provide evidence for the presence and activities of Alcanivorax jadensis in deep sea zones. The periodic spreading of alkanes, probably from the subductive plates, might have fundamentally modified the local microbial communities, as well as perhaps the deep sea microenvironment. In subduction zones, serpentinization and biological processes may release alkanes to the deep waters, which would probably result in the rapid spread of Alcanivorax. However, the timing and area of the alkane distribution and associated enrichment of alkane-degrading microbes in the dark world of the deep ocean have not been explored. In this study, we report the richness (up to 17.8%) of alkane-degrading bacteria, represented by Alcanivorax jadensis, in deep water samples obtained at 3,000 to 6,000 m in the Mariana Trench in two cruises. The relative abundance of A. jadensis correlated with copy numbers of functional almA and alkB genes, which are involved in alkane degradation. In these water samples, we detected a high flux of alkanes, which probably resulted in the prevalence of A. jadensis in the deep waters. Contigs of A. jadensis were binned from the metagenomes for examination of alkane degradation pathways and deep sea-specific pathways, which revealed a lack of nitrate and nitrite dissimilatory reduction in our A. jadensis strains. Comparing the results for the two cruises conducted close to each other, we suggest periodic release of alkanes that may spread widely but periodically in the trench. Distribution of alkane-degrading bacteria in the world’s oceans suggests the periodic and remarkable contributions of Alcanivorax to the deep sea organic carbon and nitrogen sources. IMPORTANCE In the oligotrophic environment of the Mariana Trench, alkanes as carbohydrates are important for the ecosystem, but their spatial and periodic spreading in deep waters has never been reported. Alkane-degrading bacteria such as Alcanivorax spp. are biological signals of the alkane distribution. In the present study, Alcanivorax was abundant in some waters, at depths of up to 6,000 m, in the Mariana Trench. Genomic, transcriptomic, and chemical analyses provide evidence for the presence and activities of Alcanivorax jadensis in deep sea zones. The periodic spreading of alkanes, probably from the subductive plates, might have fundamentally modified the local microbial communities, as well as perhaps the deep sea microenvironment.
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18
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Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities. ISME JOURNAL 2018; 13:1004-1018. [PMID: 30542078 DOI: 10.1038/s41396-018-0324-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/12/2018] [Accepted: 11/17/2018] [Indexed: 12/30/2022]
Abstract
Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure. In long-term enrichments, increased HP selectively inhibited obligate hydrocarbon-degraders and downregulated the expression of beta-oxidation-related proteins (i.e., the main hydrocarbon-degradation pathway) resulting in low cell growth and CO2 production. Short-term experiments with HP-adapted synthetic communities confirmed this data, revealing a HP-dependent accumulation of citrate and dihydroxyacetone. Citrate accumulation suggests rates of aerobic oxidation of fatty acids in the TCA cycle were reduced. Dihydroxyacetone is connected to citrate through glycerol metabolism and glycolysis, both upregulated with increased HP. High degradation rates by obligate hydrocarbon-degraders may thus be unfavourable at increased HP, explaining their selective suppression. Through lab-scale cultivation, the present study is the first to highlight a link between impaired cell metabolism and microbial community assembly in hydrocarbon degradation at high HP. Overall, this data indicate that hydrocarbons fate differs substantially in surface waters as compared to deep-sea environments, with in situ low temperature and limited nutrients availability expected to further prolong hydrocarbons persistence at deep sea.
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19
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Gontikaki E, Potts L, Anderson J, Witte U. Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel). J Appl Microbiol 2018; 125:1040-1053. [PMID: 29928773 PMCID: PMC6849767 DOI: 10.1111/jam.14030] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/16/2018] [Accepted: 06/18/2018] [Indexed: 02/04/2023]
Abstract
AIMS The aim of this study was the baseline description of oil-degrading sediment bacteria along a depth transect in the Faroe-Shetland Channel (FSC) and the identification of biomarker taxa for the detection of oil contamination in FSC sediments. METHODS AND RESULTS Oil-degrading sediment bacteria from 135, 500 and 1000 m were enriched in cultures with crude oil as the sole carbon source (at 12, 5 and 0°C respectively). The enriched communities were studied using culture-dependent and culture-independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. Bacterial isolates included well-known oil-degrading taxa and several that are reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at genus level particularly between the shallow and the deep, cold-water stations. Alcanivorax constituted 64% of clones at FSC135 but was absent at deeper stations. Pseudoalteromonas and Oleispira dominated the bacterial community at 500 and 1000 m. CONCLUSIONS The genus Oleispira emerged as a major player in the early stages of crude oil degradation in deep-sea sediments of the FSC particularly at subzero temperatures. This finding is offering a direction for future research into biomonitoring tools for the detection of low levels of crude oil contamination in the deep FSC, and possibly high latitude cold waters in general. SIGNIFICANCE AND IMPACT OF THE STUDY Oil and gas exploration in the FSC occurs at depths >1000 m but baseline environmental data necessary for the assessment of ecosystem recovery to prespill conditions in the event of an oil spill are lacking. This study will contribute to our ability to assess the impact of oil release in the FSC and guide the direction of bioremediation strategies tailored to the area.
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Affiliation(s)
- E. Gontikaki
- School of Biological SciencesUniversity of AberdeenAberdeenUK
| | - L.D. Potts
- School of Biological SciencesUniversity of AberdeenAberdeenUK
| | - J.A. Anderson
- Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of EngineeringUniversity of AberdeenAberdeenUK
| | - U. Witte
- School of Biological SciencesUniversity of AberdeenAberdeenUK
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20
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Nguyen UT, Lincoln SA, Valladares Juárez AG, Schedler M, Macalady JL, Müller R, Freeman KH. The influence of pressure on crude oil biodegradation in shallow and deep Gulf of Mexico sediments. PLoS One 2018; 13:e0199784. [PMID: 29969471 PMCID: PMC6029805 DOI: 10.1371/journal.pone.0199784] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/13/2018] [Indexed: 11/19/2022] Open
Abstract
A significant portion of oil released during the Deepwater Horizon disaster reached the Gulf of Mexico (GOM) seafloor. Predicting the long-term fate of this oil is hindered by a lack of data about the combined influences of pressure, temperature, and sediment composition on microbial hydrocarbon remineralization in deep-sea sediments. To investigate crude oil biodegradation by native GOM microbial communities, we incubated core-top sediments from 13 GOM sites at water depths from 60–1500 m with crude oil under simulated aerobic seafloor conditions. Biodegradation occurred in all samples and followed a predictable compound class sequence dictated by molecular weight and structure. 45 to ~100% of total n-alkane and 3 to 60% of total polycyclic aromatic hydrocarbons (PAH) were depleted. In reactors incubated at 4°C and at pressures of 6–15 MPa, the depletion in total n-alkane was inversely correlated to pressure (R2 ~ 0.85), equivalent to a 4% decrease in total n-alkane depletion for every 1 MPa increase. Our results indicated a modest inhibitory effect of pressure on biodegradation over our experimental range. However, the expansion of oil exploration to deeper waters (e.g., 5000 m) opens the risk of spills at conditions at which pressure might have a more pronounced effect.
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Affiliation(s)
- Uyen T. Nguyen
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| | - Sara A. Lincoln
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | | | - Martina Schedler
- Institute of Technical Biocatalysis, Hamburg University of Technology, Hamburg, Germany
| | - Jennifer L. Macalady
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Rudolf Müller
- Institute of Technical Biocatalysis, Hamburg University of Technology, Hamburg, Germany
| | - Katherine H. Freeman
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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21
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Marietou A, Chastain R, Beulig F, Scoma A, Hazen TC, Bartlett DH. The Effect of Hydrostatic Pressure on Enrichments of Hydrocarbon Degrading Microbes From the Gulf of Mexico Following the Deepwater Horizon Oil Spill. Front Microbiol 2018; 9:808. [PMID: 29755436 PMCID: PMC5932198 DOI: 10.3389/fmicb.2018.00808] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/10/2018] [Indexed: 01/13/2023] Open
Abstract
The Deepwater Horizon oil spill was one of the largest and deepest oil spills recorded. The wellhead was located at approximately 1500 m below the sea where low temperature and high pressure are key environmental characteristics. Using cells collected 4 months following the Deepwater Horizon oil spill at the Gulf of Mexico, we set up Macondo crude oil enrichments at wellhead temperature and different pressures to determine the effect of increasing depth/pressure to the in situ microbial community and their ability to degrade oil. We observed oil degradation under all pressure conditions tested [0.1, 15, and 30 megapascals (MPa)], although oil degradation profiles, cell numbers, and hydrocarbon degradation gene abundances indicated greatest activity at atmospheric pressure. Under all incubations the growth of psychrophilic bacteria was promoted. Bacteria closely related to Oleispira antarctica RB-8 dominated the communities at all pressures. At 30 MPa we observed a shift toward Photobacterium, a genus that includes piezophiles. Alphaproteobacterial members of the Sulfitobacter, previously associated with oil-degradation, were also highly abundant at 0.1 MPa. Our results suggest that pressure acts synergistically with low temperature to slow microbial growth and thus oil degradation in deep-sea environments.
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Affiliation(s)
- Angeliki Marietou
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.,Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Roger Chastain
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Felix Beulig
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Alberto Scoma
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Douglas H Bartlett
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
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22
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Zhang S, Hu Z, Wang H. A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill. Front Microbiol 2018; 9:520. [PMID: 29628913 PMCID: PMC5876298 DOI: 10.3389/fmicb.2018.00520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 03/08/2018] [Indexed: 12/19/2022] Open
Abstract
The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico in 2010 resulted in serious damage to local marine and coastal environments. In addition to the physical removal and chemical dispersion of spilled oil, biodegradation by indigenous microorganisms was regarded as the most effective way for cleaning up residual oil. Different microbiological methods were applied to investigate the changes and responses of bacterial communities after the DWH oil spills. By summarizing and analyzing these microbiological methods, giving recommendations and proposing some methods that have not been used, this review aims to provide constructive guidelines for microbiological studies after environmental disasters, especially those involving organic pollutants.
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Affiliation(s)
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou, China
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23
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Branchu P, Canette A, Medina Fernandez S, Mounier J, Meylheuc T, Briandet R, Grimaud R, Naïtali M. Impact of temperature on Marinobacter hydrocarbonoclasticus SP17 morphology and biofilm structure during growth on alkanes. MICROBIOLOGY-SGM 2017; 163:669-677. [PMID: 28535844 DOI: 10.1099/mic.0.000466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alkanes are widespread pollutants found in soil, freshwater and marine environments. Marinobacter hydrocarbonoclasticus (Mh) strain SP17 is a marine bacterium able to use many hydrophobic organic compounds, including alkanes, through the production of biofilms that allow their poor solubility to be overcome. This study pointed out that temperature is an environmental factor that strongly affects the biofilm formation and morphology of Mh on the model alkanes, hexadecane and paraffin. We showed that Mh biofilm formation and accumulation of intracytoplasmic inclusions are higher on solid alkanes (hexadecane at 10 °C and paraffin at 10 °C and 30 °C) than on liquid alkane (hexadecane at 30 °C) or soluble substrate (lactate at both temperatures). We also found that Mh produces more extracellular polymeric substances at 30 °C than at 10 °C on alkanes and none on lactate. We observed that bacterial length is significantly higher at 10 °C than at 30 °C on lactate and hexadecane. On paraffin, at 30 °C, the cell morphology is markedly altered by large rounded or irregularly shaped cytoplasmic inclusions. Altogether, the results showed that Mh is able to adapt and use alkanes as a carbon source, even at low temperature.
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Affiliation(s)
- Priscilla Branchu
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,Present address: IRSD, Université de Toulouse, INSERM, INRA, ENVT, Toulouse, France
| | - Alexis Canette
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Sara Medina Fernandez
- CNRS/Univ Pau & Pays Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, UMR5254, 64000, Pau, France
| | - Julie Mounier
- CNRS/Univ Pau & Pays Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, UMR5254, 64000, Pau, France
| | - Thierry Meylheuc
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Régis Grimaud
- CNRS/Univ Pau & Pays Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, UMR5254, 64000, Pau, France
| | - Murielle Naïtali
- Micalis Institute, AgroParisTech, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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24
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Scoma A, Yakimov MM, Daffonchio D, Boon N. Self-healing capacity of deep-sea ecosystems affected by petroleum hydrocarbons: Understanding microbial oil degradation at hydrocarbon seeps is key to sustainable bioremediation protocols. EMBO Rep 2017; 18:868-872. [PMID: 28515083 DOI: 10.15252/embr.201744090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Alberto Scoma
- Center for Microbial Ecology and Technology (CMET), Ghent University (UGent), Gent, Belgium.,Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Michail M Yakimov
- Institute for Coastal Marine Environment (IAMC), National Council of Research (CNR), Messina, Italy.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University (UGent), Gent, Belgium
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25
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Mapelli F, Scoma A, Michoud G, Aulenta F, Boon N, Borin S, Kalogerakis N, Daffonchio D. Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms. Trends Biotechnol 2017; 35:860-870. [PMID: 28511936 DOI: 10.1016/j.tibtech.2017.04.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/09/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022]
Abstract
The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.
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Affiliation(s)
- Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy
| | - Alberto Scoma
- Center for Microbial Ecology and Technology (CMET), University of Gent, B 9000 Gent, Belgium
| | - Grégoire Michoud
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, 23955-6900 Thuwal, Saudi Arabia
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00015 Monterotondo, Italy
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), University of Gent, B 9000 Gent, Belgium
| | - Sara Borin
- Department of Food Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy
| | - Nicolas Kalogerakis
- School of Environmental Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, 23955-6900 Thuwal, Saudi Arabia.
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26
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Gkorezis P, Daghio M, Franzetti A, Van Hamme JD, Sillen W, Vangronsveld J. The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective. Front Microbiol 2016; 7:1836. [PMID: 27917161 PMCID: PMC5116465 DOI: 10.3389/fmicb.2016.01836] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022] Open
Abstract
Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.
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Affiliation(s)
- Panagiotis Gkorezis
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Matteo Daghio
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
- Department of Biological Sciences, Thompson Rivers University, KamloopsBC, Canada
| | - Andrea Franzetti
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
| | | | - Wouter Sillen
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
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