1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Brzeszcz J, Steliga T, Ryszka P, Kaszycki P, Kapusta P. Bacteria degrading both n-alkanes and aromatic hydrocarbons are prevalent in soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:5668-5683. [PMID: 38127231 PMCID: PMC10799122 DOI: 10.1007/s11356-023-31405-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
This study was undertaken to determine the distribution of soil bacteria capable of utilizing both n-alkanes and aromatic hydrocarbons. These microorganisms have not been comprehensively investigated so far. Ten contaminated (4046-43,861 mg of total petroleum hydrocarbons (TPH) kg-1 of dry weight of soil) and five unpolluted (320-2754 mg TPH kg-1 of dry weight of soil) soil samples from temperate, arid, and Alpine soils were subjected to isolation of degraders with extended preferences and shotgun metagenomic sequencing (selected samples). The applied approach allowed to reveal that (a) these bacteria can be isolated from pristine and polluted soils, and (b) the distribution of alkane monooxygenase (alkB) and aromatic ring hydroxylating dioxygenases (ARHDs) encoding genes is not associated with the contamination presence. Some alkB and ARHD genes shared the same taxonomic affiliation; they were most often linked with the Rhodococcus, Pseudomonas, and Mycolicibacterium genera. Moreover, these taxa together with the Paeniglutamicibacter genus constituted the most numerous groups among 132 culturable strains growing in the presence of both n-alkanes and aromatic hydrocarbons. All those results indicate (a) the prevalence of the hydrocarbon degraders with extended preferences and (b) the potential of uncontaminated soil as a source of hydrocarbon degraders applied for bioremediation purposes.
Collapse
Affiliation(s)
- Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute - National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland.
| | - Teresa Steliga
- Department of Production Technology of Reservoir Fluids, Oil and Gas Institute - National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland
| | - Przemysław Ryszka
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University in Kraków, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Paweł Kaszycki
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, Al. Mickiewicza 21, 31-425, Kraków, Poland
| | - Piotr Kapusta
- Department of Microbiology, Oil and Gas Institute - National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland
| |
Collapse
|
3
|
Salter C, Westrick JA, Chaganti SR, Birbeck JA, Peraino NJ, Weisener CG. Elucidating microbial mechanisms of microcystin-LR degradation in Lake Erie beach sand through metabolomics and metatranscriptomics. WATER RESEARCH 2023; 247:120816. [PMID: 37952399 DOI: 10.1016/j.watres.2023.120816] [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: 07/10/2023] [Revised: 09/11/2023] [Accepted: 10/29/2023] [Indexed: 11/14/2023]
Abstract
As one of five Laurentian Great Lakes, Lake Erie ranks among the top freshwater drinking sources and ecosystems globally. Historical and current agriculture mismanagement and climate change sustains the environmental landscape for late summer cyanobacterial harmful algal blooms, and consequently, cyanotoxins such as microcystin (MC). Microcystin microbial degradation is a promising mitigation strategy, however the mechanisms controlling the breakdown of MCs in Lake Erie are not well understood. Pelee Island, Ontario, Canada is located in the western basin of Lake Erie and the bacterial community in the sand has demonstrated the capacity of metabolizing the toxin. Through a multi-omic approach, the metabolic, functional and taxonomical signatures of the Pelee Island microbial community during MC-LR degradation was investigated over a 48-hour period to comprehensively study the degradation mechanism. Cleavage of bonds surrounding nitrogen atoms and the upregulation of nitrogen deamination (dadA, alanine dehydrogenase, leucine dehydrogenase) and assimilation genes (glnA, gltB) suggests a targeted isolation of nitrogen by the microbial community for energy production. Methylotrophic pathways RuMP and H4MPT control assimilation and dissimilation of carbon, respectively and differential abundance of Methylophilales indicates an interconnected role through electron exchange of denitrification and methylotrophic pathways. The detected metabolites did not resolve a clear breakdown pathway, but rather the diversity of products in combination with taxonomic and functional results supports that a variety of strategies are applied, such as epoxidation, hydroxylation, and aromatic degradation. Annual repeated exposure to the toxin may have allowed the community to adaptatively establish a novel pathway through functional plasticity and horizontal gene transfer. The culmination of these results reveals the complexity of the Pelee Island sand community and supports a dynamic and cooperative metabolism between microbial species to achieve MC degradation.
Collapse
Affiliation(s)
- Chelsea Salter
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada.
| | - Judy A Westrick
- Lumigen Instrument Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, School for Environment and Sustainability, University of Michigan, 440 Church Street, Ann Arbor, MI 48109, United States
| | - Johnna A Birbeck
- Lumigen Instrument Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Nicholas J Peraino
- Lumigen Instrument Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
| |
Collapse
|
4
|
Juárez K, Reza L, Bretón-Deval L, Morales-Guzmán D, Trejo-Hernández MR, García-Guevara F, Lara P. Microaerobic degradation of crude oil and long chain alkanes by a new Rhodococcus strain from Gulf of Mexico. World J Microbiol Biotechnol 2023; 39:264. [PMID: 37515608 PMCID: PMC10386958 DOI: 10.1007/s11274-023-03703-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/12/2023] [Indexed: 07/31/2023]
Abstract
Bacterial degradation of crude oil is a promising strategy for reducing the concentration of hydrocarbons in contaminated environments. In the first part of this study, we report the enrichment of two bacterial consortia from deep sediments of the Gulf of Mexico with crude oil as the sole carbon and energy source. We conducted a comparative analysis of the bacterial community in the original sediment, assessing its diversity, and compared it to the enrichment observed after exposure to crude oil in defined cultures. The consortium exhibiting the highest hydrocarbon degradation was predominantly enriched with Rhodococcus (75%). Bacterial community analysis revealed the presence of other hydrocarbonoclastic members in both consortia. In the second part, we report the isolation of the strain Rhodococcus sp. GOMB7 with crude oil as a unique carbon source under microaerobic conditions and its characterization. This strain demonstrated the ability to degrade long-chain alkanes, including eicosane, tetracosane, and octacosane. We named this new strain Rhodococcus qingshengii GOMB7. Genome analysis revealed the presence of several genes related to aromatic compound degradation, such as benA, benB, benC, catA, catB, and catC; and five alkB genes related to alkane degradation. Although members of the genus Rhodococcus are well known for their great metabolic versatility, including the aerobic degradation of recalcitrant organic compounds such as petroleum hydrocarbons, this is the first report of a novel strain of Rhodococcus capable of degrading long-chain alkanes under microaerobic conditions. The potential of R. qingshengii GOMB7 for applications in bioreactors or controlled systems with low oxygen levels offers an energy-efficient approach for treating crude oil-contaminated water and sediments.
Collapse
Affiliation(s)
- Katy Juárez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México.
| | - Lizeth Reza
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México
| | - Luz Bretón-Deval
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México
- Consejo Nacional de Ciencia y Tecnología, Avenida Insurgentes Sur 1582, Crédito Constructor, Ciudad de México, México
| | - Daniel Morales-Guzmán
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001. Col. Chamilpa., Cuernavaca, Morelos, 62209, México
| | - María R Trejo-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001. Col. Chamilpa., Cuernavaca, Morelos, 62209, México
| | - Fernando García-Guevara
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - Paloma Lara
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001. Col. Chamilpa., Cuernavaca, Morelos, 62210, México.
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62210, México.
| |
Collapse
|
5
|
Fenibo EO, Selvarajan R, Abia ALK, Matambo T. Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162951. [PMID: 36948313 DOI: 10.1016/j.scitotenv.2023.162951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
Collapse
Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Akebe Luther King Abia
- Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Tonderayi Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa.
| |
Collapse
|
6
|
Táncsics A, Banerjee S, Soares A, Bedics A, Kriszt B. Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: Rhodoferax─A Hitherto Unknown Player Emerges from the Microbial Dark Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2846-2855. [PMID: 36752053 DOI: 10.1021/acs.est.2c09283] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Among monoaromatic hydrocarbons, xylenes, especially the ortho and para isomers, are the least biodegradable compounds in oxygen-limited subsurface environments. Although much knowledge has been gained regarding the anaerobic degradation of xylene isomers in the past 2 decades, the diversity of those bacteria which are able to degrade them under microaerobic conditions is still unknown. To overcome this limitation, aerobic and microaerobic xylene-degrading enrichment cultures were established using groundwater taken from a xylene-contaminated site, and the associated bacterial communities were investigated using a polyphasic approach. Our results show that the xylene-degrading bacterial communities were distinctly different between aerobic and microaerobic enrichment conditions. Although members of the genus Pseudomonas were the most dominant in both types of enrichments, the Rhodoferax and Azovibrio lineages were only abundant under microaerobic conditions, while Sphingobium entirely replaced them under aerobic conditions. Analysis of a metagenome-assembled genome of a Rhodoferax-related bacterium revealed aromatic hydrocarbon-degrading ability by identifying two catechol 2,3-dioxygenases in the genome. Moreover, phylogenetic analysis indicated that both enzymes belonged to a newly defined subfamily of type I.2 extradiol dioxygenases (EDOs). Aerobic and microaerobic xylene-degradation experiments were conducted on strains Sphingobium sp. AS12 and Pseudomonas sp. MAP12, isolated from the aerobic and microaerobic enrichments, respectively. The obtained results, together with the whole-genome sequence data of the strains, confirmed the observation that members of the genus Sphingobium are excellent aromatic hydrocarbon degraders but effective only under clear aerobic conditions. Overall, it was concluded that the observed differences between the bacterial communities of aerobic and microaerobic xylene-degrading enrichments were driven primarily by (i) the method of aromatic ring activation (monooxygenation vs dioxygenation), (ii) the type of EDO enzymes, and (iii) the ability of degraders to respire utilizing nitrate.
Collapse
Affiliation(s)
- András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. u. 1., 2100 Gödöllö, Hungary
| | - Sinchan Banerjee
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. u. 1., 2100 Gödöllö, Hungary
| | - André Soares
- Group for Aquatic Microbial Ecology, Institute for Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Anna Bedics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. u. 1., 2100 Gödöllö, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. u. 1., 2100 Gödöllö, Hungary
| |
Collapse
|
7
|
Zhao Y, Wei HM, Yuan JL, Xu L, Sun JQ. A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains. Front Microbiol 2023; 14:1177951. [PMID: 37138596 PMCID: PMC10149724 DOI: 10.3389/fmicb.2023.1177951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.
Collapse
Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Hua-Mei Wei
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jia-Li Yuan
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- *Correspondence: Ji-Quan Sun,
| |
Collapse
|
8
|
Liu Y, Sun Y, Yu J, Xia X, Ding A, Zhang D. Impacts of groundwater level fluctuation on soil microbial community, alkane degradation efficiency and alkane-degrading gene diversity in the critical zone: Evidence from an accelerated water table fluctuation simulation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:83060-83070. [PMID: 35759097 DOI: 10.1007/s11356-022-21246-2] [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: 11/18/2021] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Petroleum hydrocarbons are hazardous to ecosystems and human health, commonly containing n-alkanes and polycyclic aromatic hydrocarbons. Previous researches have studied alkane degraders and degrading genes under aerobic or anaerobic conditions, but seldom discussed them in the intermittent saturation zone which is a connective area between the vadose zone and the groundwater aquifer with periodic alteration of oxygen and moisture. The present study investigated the difference in alkane degradation efficiency, bacterial community, and alkane degrading gene diversity in aerobic, anaerobic, and aerobic-anaerobic fluctuated treatments. All biotic treatments achieved over 90% of n-alkane removal after 120 days of incubation. The removal efficiencies of n-alkanes with a carbon chain length from 16 to 25 were much higher in anaerobic scenarios than those in aerobic scenarios, explained by different dominant microbes between aerobic and anaerobic conditions. The highest removal efficiency was found in fluctuation treatments, indicating an accelerated n-alkane biodegradation under aerobic-anaerobic alternation. In addition, the copy numbers of the 16S rRNA gene and two alkB genes (alkB-P and alkB-R) declined dramatically when switched from aerobic to anaerobic scenarios and oppositely from anaerobic to aerobic conditions. This suggested that water level fluctuation could notably change the presence of aerobic alkane degrading genes. Our results suggested that alkane degradation efficiency, soil microbial community, and alkane-degrading genes were all driven by water level fluctuation in the intermittent saturation zone, helping better understand the effects of seasonal water table fluctuation on the biodegradation of petroleum hydrocarbons in the subsurface environment.
Collapse
Affiliation(s)
- Yueqiao Liu
- Experiment and Practice Innovation Education Center, Beijing Normal University at Zhuhai, Zhuhai, 519087, China
| | - Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jingshan Yu
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xuefeng Xia
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, China.
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun, 130021, China.
| |
Collapse
|
9
|
Ganesan M, Mani R, Sai S, Kasivelu G, Awasthi MK, Rajagopal R, Wan Azelee NI, Selvi PK, Chang SW, Ravindran B. Bioremediation by oil degrading marine bacteria: An overview of supplements and pathways in key processes. CHEMOSPHERE 2022; 303:134956. [PMID: 35588873 DOI: 10.1016/j.chemosphere.2022.134956] [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: 03/18/2022] [Revised: 05/01/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Oil spillage is one of the most common pollutants which brings greater economic loss and damage to the environment. The intensity and amount of the damage may vary depending on factors such as the type of oil, the location of the spill, and the climatic parameters in the area. As for any pollution management, the guidelines are Reduce, Re-use, Recover and Disposal. Amongst the other remediation processes, Bioremediation is amongst the most significant environmentally friendly and cost-effective approaches for marine biological restoration because it allows complex petroleum hydrocarbons in spilt oil to decompose completely into harmless compounds. Mainly, the necessity and essence of bioremediation were talked about. This review discussed the bacteria identified which are capable of degrading various oil related pollutants and their components. Also, it covered the various media components used for screening and growing the oil degrading bacteria and the pathways that are associated with oil degradation. This article also reviewed the recent research carried out related to the oil degrading bacteria.
Collapse
Affiliation(s)
- Mirunalini Ganesan
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Ravi Mani
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Sakthinarenderan Sai
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Govindaraju Kasivelu
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi, 712100, PR China.
| | - Rajinikanth Rajagopal
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Nur Izyan Wan Azelee
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, 81310, Johor, Malaysia
| | - P K Selvi
- Central Pollution Control Board, Nisarga Bhawan, Shivanagar, Bengaluru, India
| | - Soon Woong Chang
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea
| | - Balasubramani Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea; Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai 602 105, Tamil Nadu, India.
| |
Collapse
|
10
|
Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions. Antonie Van Leeuwenhoek 2022; 115:1113-1128. [PMID: 35841500 PMCID: PMC9363352 DOI: 10.1007/s10482-022-01759-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022]
Abstract
In the present study, the bacterial community structure of enrichment cultures degrading benzene under microaerobic conditions was investigated through culturing and 16S rRNA gene Illumina amplicon sequencing. Enrichments were dominated by members of the genus Rhodoferax followed by Pseudomonas and Acidovorax. Additionally, a pale amber-coloured, motile, Gram-stain-negative bacterium, designated B7T was isolated from the microaerobic benzene-degrading enrichment cultures and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene and whole genome-based phylogenetic analyses revealed that strain B7T formed a lineage within the family Comamonadaceae, clustered as a member of the genus Ideonella and most closely related to Ideonella dechloratans CCUG 30977T. The sole respiratory quinone is ubiquinone-8. The major fatty acids are C16:0 and summed feature 3 (C16:1ω7c/iso-C15:0 2-OH). The DNA G + C content of the type strain is 68.8 mol%. The orthologous average nucleotide identity (OrthoANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain B7T and closest relatives were below the threshold values for species demarcation. The genome of strain B7T, which is approximately 4.5 Mb, contains a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including a I.2.C-type catechol 2,3-dioxygenase (C23O) gene. As predicted by the genome, the type strain is involved in aromatic hydrocarbon-degradation: benzene, toluene and ethylbenzene are degraded aerobically and also microaerobically as sole source of carbon and energy. Based on phenotypic characteristics and phylogenetic analysis, strain B7T is a member of the genus Ideonella and represents a novel species for which the name Ideonella benzenivorans sp. nov. is proposed. The type strain of the species is strain B7T (= LMG 32,345T = NCAIM B.02664T).
Collapse
|
11
|
Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease. Clin Microbiol Rev 2022; 35:e0014021. [PMID: 35658516 DOI: 10.1128/cmr.00140-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm3 and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.
Collapse
|
12
|
Nnabuife OO, Ogbonna JC, Anyanwu C, Ike AC, Eze CN, Enemuor SC. Mixed bacterial consortium can hamper the efficient degradation of crude oil hydrocarbons. Arch Microbiol 2022; 204:306. [PMID: 35532873 DOI: 10.1007/s00203-022-02915-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 11/24/2022]
Abstract
Crude oil degradation efficiency can be improved because of co-metabolism that exists when bacterial consortium is applied. However, because of possible vulnerability to environmental conditions and/or antagonistic interactions among members of the consortium, the degradation efficiency can be hampered. In this laboratory-based study, the biodegradation potentials of pure bacterial isolates namely Pseudomonas aeruginosa strain W15 (MW320658), Providencia vermicola strain W8 (MW320661) and Serratia marcescens strain W13 (MW320662) earlier isolated from crude oil-contaminated site and their consortium were evaluated using 3% crude oil-supplemented Bushnell Haas media. The efficiency was evaluated based on the viable cell count, biosurfactant analyses, percentage hydrocarbon degradation using gravimetric analysis and gas chromatography-mass spectrophotometry (GC-MS) analysis. There was decline in the population of W13 and predominance of W15 in the consortium as the incubation period progressed. Accelerated biodegradation of the crude oil hydrocarbons through co-metabolism was not achieved with the consortium; neither was there any improved resilience nor resistance to environmental changes of strain W13. The GC-MS analyses showed that the highest degradation was produced by W15 (48.23%) compared to W8 (46.04%), W13 (45.24%) and the Consortium (28.51%). The biodegradation of the crude oil hydrocarbons by W15, W8, W13 axenic cultures and their consortium treatments demonstrated that the bacterial constituent in a consortium can influence the synergistic effect that improves bioremediation. Future research that focuses on evaluating possible improvement in bioremediation through maintenance of diversity by continuous bioaugmentation using vulnerable but efficient degraders in a consortium is necessary to further understand the application of consortia for bioremediation improvement.
Collapse
Affiliation(s)
- Obianuju Obiajulu Nnabuife
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria.
| | - James Chukwuma Ogbonna
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chukwudi Anyanwu
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Anthony Chibuogwu Ike
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chibuzor Nwadibe Eze
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Simeon Chukwuemeka Enemuor
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| |
Collapse
|
13
|
Buzmakov SA, Ivshina IB, Egorova DO, Khotyanovskaya YV, Andreev DN, Nazarov AV, Dziuba EA, Shestakov IE, Kuyukina MS, Elkin AA. Ecological criteria for assessing the content of petroleum hydrocarbons in the main soils of coniferous-deciduous forests and forest steppe. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:5099-5118. [PMID: 34117609 DOI: 10.1007/s10653-021-00998-9] [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: 12/29/2020] [Accepted: 06/02/2021] [Indexed: 06/12/2023]
Abstract
The effect of pollution of Albicluvisols/Retisols, Calcaric Leptosols, Luvic Phaeozems, Greyzamic Phaeozems and Folic Fluvisols with oil (Solovatovsky oil field, Perm region) added in amounts of 1, 2, 3 and 5 g oil/kg of soil on the organisms was studied in a model laboratory experiment. Oil addition showed phytotoxic effects on root length in Triticum aestivum L., Lepidium sativum L., Picea obovata Ledeb. and Pinus sylvestris L. in all soils. However, oil contamination of Calcaric Leptosols and Greyzamic Phaeozems led to growth stimulation in Picea obovata seedlings. A remarkable shift in the diversity and number of colony-forming units of heterotrophic and oil-oxidizing bacteria was detected in all soil types. The maximum decrease in biodiversity (45%) was noted for heterotrophic bacteria in Luvic Phaeozems. Aqueous extracts from all oil-contaminated soils had a toxic effect on Chlorella vulgaris Beijer, causing an increase in biomass by more than 30%, but did not show acute toxicity on Daphnia magna Straus. Oil addition in the range of 1-3 g oil/kg soil posed no environmental risk to human health. However, oil addition at 5 g oil/kg of soil led to an increase in the level of carcinogenic risk to children to the threshold values of acceptable risk and ranged from 0.95 × 10-4 for Greyzamic Phaeozems and Folic Fluvisols to 1.098 × 10-4 for Luvic Phaeozems. Our results suggest that the reaction of test organisms to oil pollution depends on the soil type, and their complex application makes it possible to identify the most sensitive factor and assess the dangerous level of pollution.
Collapse
Affiliation(s)
- S A Buzmakov
- Department of Biogeocenology and Nature Protection, Perm State University, 15, Bukireva st, Perm, Russia, 614990
| | - I B Ivshina
- Microbiology and Immunology Department, Perm State University, 15, Bukireva st, Perm, Russia, 614990
- Laboratory of Alkanotrophic Microorganisms, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Ural Branch, Russian Academy of Sciences, Perm, Russia, 614081
| | - D O Egorova
- Department of Biogeocenology and Nature Protection, Perm State University, 15, Bukireva st, Perm, Russia, 614990.
- Laboratory of Molecular Microbiology and Biotechnology, Perm Federal Research Center, Ural Branch, Russian Academy of Sciences, Perm, Russia, 614081.
| | - Y V Khotyanovskaya
- Department of Biogeocenology and Nature Protection, Perm State University, 15, Bukireva st, Perm, Russia, 614990
| | - D N Andreev
- Department of Biogeocenology and Nature Protection, Perm State University, 15, Bukireva st, Perm, Russia, 614990
| | - A V Nazarov
- Laboratory of Molecular Microbiology and Biotechnology, Perm Federal Research Center, Ural Branch, Russian Academy of Sciences, Perm, Russia, 614081
| | - E A Dziuba
- Department of Biogeocenology and Nature Protection, Perm State University, 15, Bukireva st, Perm, Russia, 614990
| | - I E Shestakov
- Department of Biogeocenology and Nature Protection, Perm State University, 15, Bukireva st, Perm, Russia, 614990
| | - M S Kuyukina
- Microbiology and Immunology Department, Perm State University, 15, Bukireva st, Perm, Russia, 614990
- Laboratory of Alkanotrophic Microorganisms, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Ural Branch, Russian Academy of Sciences, Perm, Russia, 614081
| | - A A Elkin
- Microbiology and Immunology Department, Perm State University, 15, Bukireva st, Perm, Russia, 614990
- Laboratory of Alkanotrophic Microorganisms, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Ural Branch, Russian Academy of Sciences, Perm, Russia, 614081
| |
Collapse
|
14
|
Singh NK, Choudhary S. Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:58819-58836. [PMID: 33410029 DOI: 10.1007/s11356-020-11705-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO3- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.
Collapse
Affiliation(s)
- Nishi Kumari Singh
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India
| | - Sangeeta Choudhary
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India.
| |
Collapse
|
15
|
Ni G, Shi G, Hu C, Wang X, Nie M, Cai M, Cheng Q, Zhao X. Selenium improved the combined remediation efficiency of Pseudomonas aeruginosa and ryegrass on cadmium-nonylphenol co-contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117552. [PMID: 34175519 DOI: 10.1016/j.envpol.2021.117552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 06/13/2023]
Abstract
Most chemical plant wastewater contains both organic and inorganic pollutants, which are easy to diffuse along with surface runoff. The combined pollution of nonylphenol (NP) and cadmium (Cd) in soil is a serious problem that has not attracted enough attention. Based on the effects of selenium (Se) and Pseudomonas aeruginosa (P. aeruginosa) on plant and soil microbial communities, we speculated that the application of Se and P. aeruginosa in soil could improve the phytoremediation efficiency of ryegrass on contaminated soil. In this study, pot experiments with Cd and NP co-contaminated soil were conducted, and the results showed that application of P. aeruinosa alone could improve the removal rates of NP and Cd by ryegrass, and the supplementary of Se further enhanced the effect of micro-phyto remediation, with the highest removal rates of NP and Cd were 79.6% and 49.4%, respectively. The application of P. aeruginosa plus Se reduced the adsorption of Cd and NP through C-O and Si-O-Fe of the soil, changed the enzyme activity, and also affected the changing trend of the microbial community in soil. Pseudomonas, Sphingomonadales, Nitrospira, and other beneficial bacteria were enriched after a 60-day period with P. aeruginosa and Se treatment, thus promoting the removal of NP and Cd. In light of the above results, we suggest that P. aeruginosa application can efficiently facilitate the phytoremediation of ryegrass on Cd-NP co-contaminated soil, and Se supplementation in soil showed the synergistic effect on the remediation.
Collapse
Affiliation(s)
- Gang Ni
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Huazhong Agricultural University, Wuhan, 430070, China; Research Center of Trace Elements, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangyu Shi
- College of Environment Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Chengxiao Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Huazhong Agricultural University, Wuhan, 430070, China; Research Center of Trace Elements, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Min Nie
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Huazhong Agricultural University, Wuhan, 430070, China; Research Center of Trace Elements, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Miaomiao Cai
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Huazhong Agricultural University, Wuhan, 430070, China; Research Center of Trace Elements, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Cheng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Huazhong Agricultural University, Wuhan, 430070, China; Research Center of Trace Elements, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaohu Zhao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Huazhong Agricultural University, Wuhan, 430070, China; Research Center of Trace Elements, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
16
|
Figueroa-Gonzalez PA, Bornemann TLV, Adam PS, Plewka J, Révész F, von Hagen CA, Táncsics A, Probst AJ. Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities. Front Microbiol 2020; 11:587782. [PMID: 33424787 PMCID: PMC7786006 DOI: 10.3389/fmicb.2020.587782] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/03/2020] [Indexed: 01/05/2023] Open
Abstract
Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.
Collapse
Affiliation(s)
- Perla Abigail Figueroa-Gonzalez
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Till L V Bornemann
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Panagiotis S Adam
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Julia Plewka
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Fruzsina Révész
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllõ, Hungary.,Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllõ, Hungary
| | - Christian A von Hagen
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllõ, Hungary.,Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllõ, Hungary
| | - Alexander J Probst
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
17
|
Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K. New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. Front Microbiol 2020; 11:590049. [PMID: 33304336 PMCID: PMC7701123 DOI: 10.3389/fmicb.2020.590049] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
Collapse
Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | | | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| |
Collapse
|
18
|
Cerqueda-García D, Améndola-Pimenta M, Zamora-Briseño JA, González-Penagos CE, Árcega-Cabrera F, Ceja-Moreno V, Rodríguez-Canul R. Effects of chronic exposure to water accommodated fraction (WAF) of light crude oil on gut microbiota composition of the lined sole (Achirus lineatus). MARINE ENVIRONMENTAL RESEARCH 2020; 161:105116. [PMID: 32861142 DOI: 10.1016/j.marenvres.2020.105116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
Exposure of marine fish to hydrocarbon compounds from crude oil can cause physiological and ecological alterations that can result in several cytotoxic, genotoxic, and teratogenic damages. One consequence of this exposure is the dysbiosis of the gut microbiota, where the normal bacterial composition is modified. Herein, we assessed the effect of the exposure to water accommodated fraction (WAF) of a light crude oil into the gut microbiota of a native species, the lined sole Achirus lineatus, a benthonic fish widely distributed in the Gulf of Mexico (GoM). We performed a chronic bioassay using two WAF concentrations (5 and 10% v/v), collecting lined sole entire gastrointestinal tracts for microbiota analyses at two timepoints, 14 and 28 days. Changes in the gut microbiota composition were determined by high throughput amplicon sequencing of the gene 16S rRNA. Diversity analyses showed that WAF exposure produced similar changes in the microbiota composition at both concentrations. Metagenomic functional prediction showed that these alterations could result in a shift in the gut redox status, towards a more anoxygenic environment. Enrichment of bacteria capable of use hydrocarbon as carbon source seems to be fast regardless time of exposure or WAF concentrations. Our results suggest that chronic WAF exposure can cause a dysbiosis in this benthic native species from the GoM.
Collapse
Affiliation(s)
- Daniel Cerqueda-García
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN)-Unidad Mérida, Carretera Antigua a Progreso Km. 6, 97310, Mérida, Yucatán, Mexico
| | - Monica Améndola-Pimenta
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN)-Unidad Mérida, Carretera Antigua a Progreso Km. 6, 97310, Mérida, Yucatán, Mexico.
| | - Jesús Alejandro Zamora-Briseño
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN)-Unidad Mérida, Carretera Antigua a Progreso Km. 6, 97310, Mérida, Yucatán, Mexico
| | - Carlos Eduardo González-Penagos
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN)-Unidad Mérida, Carretera Antigua a Progreso Km. 6, 97310, Mérida, Yucatán, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México. Puerto de Abrigo S/N, Sisal Yucatán, 97356, Mexico
| | - Víctor Ceja-Moreno
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México. Puerto de Abrigo S/N, Sisal Yucatán, 97356, Mexico
| | - Rossanna Rodríguez-Canul
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN)-Unidad Mérida, Carretera Antigua a Progreso Km. 6, 97310, Mérida, Yucatán, Mexico.
| |
Collapse
|
19
|
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]
|
20
|
Révész F, Farkas M, Kriszt B, Szoboszlay S, Benedek T, Táncsics A. Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:31130-31142. [PMID: 32474783 PMCID: PMC7392937 DOI: 10.1007/s11356-020-09277-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/12/2020] [Indexed: 04/12/2023]
Abstract
The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.
Collapse
Affiliation(s)
- Fruzsina Révész
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - Milán Farkas
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - Balázs Kriszt
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - Sándor Szoboszlay
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - Tibor Benedek
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary.
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary.
| |
Collapse
|
21
|
Mitra M, Nguyen KMAK, Box TW, Gilpin JS, Hamby SR, Berry TL, Duckett EH. Isolation and characterization of a novel bacterial strain from a Tris-Acetate-Phosphate agar medium plate of the green micro-alga Chlamydomonas reinhardtii that can utilize common environmental pollutants as a carbon source. F1000Res 2020; 9:656. [PMID: 32855811 PMCID: PMC7425125 DOI: 10.12688/f1000research.24680.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/19/2020] [Indexed: 12/28/2022] Open
Abstract
Background:Chlamydomonas reinhardtii, a green micro-alga can be grown at the lab heterotrophically or photo-heterotrophically in Tris-Phosphate-Acetate (TAP) medium which contains acetate as the sole carbon source. When grown in TAP medium,
Chlamydomonas can utilize the exogenous acetate in the medium for gluconeogenesis using the glyoxylate cycle, which is also present in many bacteria and higher plants. A novel bacterial strain, LMJ, was isolated from a contaminated TAP medium plate of
Chlamydomonas. We present our work on the isolation and physiological and biochemical characterizations of LMJ. Methods: Several microbiological tests were conducted to characterize LMJ, including its sensitivity to four antibiotics. We amplified and sequenced partially the 16S rRNA gene of LMJ. We tested if LMJ can utilize cyclic alkanes, aromatic hydrocarbons, poly-hydroxyalkanoates, and fresh and combusted car motor oil as the sole carbon source on Tris-Phosphate (TP) agar medium plates for growth. Results: LMJ is a gram-negative rod, oxidase-positive, mesophilic, non-enteric, pigmented, salt-sensitive bacterium. LMJ can ferment glucose, is starch hydrolysis-negative, and is very sensitive to penicillin and chloramphenicol. Preliminary spectrophotometric analyses indicate LMJ produces pyomelanin. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of LMJ showed that it matched to that of an uncultured bacterium clone LIB091_C05_1243. The nearest genus relative of LMJ is an
Acidovorax sp. strain. LMJ was able to use alkane hydrocarbons, fresh and combusted car motor oil, poly-hydroxybutyrate, phenanthrene, naphthalene, benzoic acid and phenyl acetate as the sole carbon source for growth on TP-agar medium plates. Conclusions: LMJ has 99.14% sequence identity with the
Acidovorax sp. strain A16OP12 whose genome has not been sequenced yet. LMJ’s ability to use chemicals that are common environmental pollutants makes it a promising candidate for further investigation for its use in bioremediation and, provides us with an incentive to sequence its genome.
Collapse
Affiliation(s)
- Mautusi Mitra
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Kevin Manoap-Anh-Khoa Nguyen
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA.,Department of Mechanical Engineering, Kennesaw State University, Marietta, Georgia, 30060, USA
| | - Taylor Wayland Box
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Jesse Scott Gilpin
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Seth Ryan Hamby
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Taylor Lynne Berry
- Carrollton High School, Carrollton, Georgia, 30117, USA.,Department of Chemistry and Biochemistry, University of North Georgia, Dahlonega, Georgia, 30597, USA
| | - Erin Harper Duckett
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
| |
Collapse
|
22
|
Trudgeon B, Dieser M, Balasubramanian N, Messmer M, Foreman CM. Low-Temperature Biosurfactants from Polar Microbes. Microorganisms 2020; 8:E1183. [PMID: 32756528 PMCID: PMC7466143 DOI: 10.3390/microorganisms8081183] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 11/17/2022] Open
Abstract
Surfactants, both synthetic and natural, are used in a wide range of industrial applications, including the degradation of petroleum hydrocarbons. Organisms from extreme environments are well-adapted to the harsh conditions and represent an exciting avenue of discovery of naturally occurring biosurfactants, yet microorganisms from cold environments have been largely overlooked for their biotechnological potential as biosurfactant producers. In this study, four cold-adapted bacterial isolates from Antarctica are investigated for their ability to produce biosurfactants. Here we report on the physical properties and chemical structure of biosurfactants from the genera Janthinobacterium, Psychrobacter, and Serratia. These organisms were able to grow on diesel, motor oil, and crude oil at 4 °C. Putative identification showed the presence of sophorolipids and rhamnolipids. Emulsion index test (E24) activity ranged from 36.4-66.7%. Oil displacement tests were comparable to 0.1-1.0% sodium dodecyl sulfate (SDS) solutions. Data presented herein are the first report of organisms of the genus Janthinobacterium to produce biosurfactants and their metabolic capabilities to degrade diverse petroleum hydrocarbons. The organisms' ability to produce biosurfactants and grow on different hydrocarbons as their sole carbon and energy source at low temperatures (4 °C) makes them suitable candidates for the exploration of hydrocarbon bioremediation in low-temperature environments.
Collapse
Affiliation(s)
- Benjamin Trudgeon
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA; (B.T.); (M.M.); (C.M.F.)
- Department of Civil & Environmental Engineering, Montana State University, Bozeman, MT 59715, USA
| | - Markus Dieser
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA; (B.T.); (M.M.); (C.M.F.)
- Department of Chemical & Biological Engineering, Montana State University, Bozeman, MT 59715, USA
| | | | - Mitch Messmer
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA; (B.T.); (M.M.); (C.M.F.)
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA;
| | - Christine M. Foreman
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA; (B.T.); (M.M.); (C.M.F.)
- Department of Chemical & Biological Engineering, Montana State University, Bozeman, MT 59715, USA
| |
Collapse
|
23
|
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).
Collapse
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
| |
Collapse
|
24
|
Microbial Degradation of Hydrocarbons-Basic Principles for Bioremediation: A Review. Molecules 2020; 25:molecules25040856. [PMID: 32075198 PMCID: PMC7070569 DOI: 10.3390/molecules25040856] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/01/2022] Open
Abstract
Crude oil-derived hydrocarbons constitute the largest group of environmental pollutants worldwide. The number of reports concerning their toxicity and emphasizing the ultimate need to remove them from marine and soil environments confirms the unceasing interest of scientists in this field. Among the various techniques used for clean-up actions, bioremediation seems to be the most acceptable and economically justified. Analysis of recent reports regarding unsuccessful bioremediation attempts indicates that there is a need to highlight the fundamental aspects of hydrocarbon microbiology in a clear and concise manner. Therefore, in this review, we would like to elucidate some crucial, but often overlooked, factors. First, the formation of crude oil and abundance of naturally occurring hydrocarbons is presented and compared with bacterial ability to not only survive but also to utilize such compounds as an attractive energy source. Then, the significance of nutrient limitation on biomass growth is underlined on the example of a specially designed experiment and discussed in context of bioremediation efficiency. Next, the formation of aerobic and anaerobic conditions, as well as the role of surfactants for maintaining appropriate C:N:P ratio during initial stages of biodegradation is explained. Finally, a summary of recent scientific reports focused on the removal of hydrocarbon contaminants using bioaugmentation, biostimulation and introduction of surfactants, as well as biosurfactants, is presented. This review was designed to be a comprehensive source of knowledge regarding the unique aspects of hydrocarbon microbiology that may be useful for planning future biodegradation experiments. In addition, it is a starting point for wider debate regarding the limitations and possible improvements of currently employed bioremediation strategies.
Collapse
|