1
|
Huang H, Xie C, Xia Z, Sun Z, Chen Y, Gou M, Tang Y, Cui H, Wu X. Multi-omics association study of hexadecane degradation in haloarchaeal strain Halogranum rubrum RO2-11. ENVIRONMENTAL RESEARCH 2024; 252:118751. [PMID: 38522738 DOI: 10.1016/j.envres.2024.118751] [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: 12/17/2023] [Revised: 03/01/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Haloarchaea with the capacity to degrade alkanes is promising to deal with petroleum pollution in hypersaline environments. However, only a limited number of haloarchaeal species are investigated, and their pathway and mechanism for alkane degradation remain unclear. In this study, Halogranum rubrum RO2-11, a haloarchaeal strain, verified the ability to degrade kerosene and hexadecane in 184 g/L NaCl, with 53% and 52% degradation rates after 9 and 4 days, respectively. Genome sequencing and gene annotation indicated that strain RO2-11 possesses a complete potential alkane-degrading pathway, of which alkane hydroxylases may include CYP450, AlmA, and LadA. Transcriptome and metabolome analyses revealed that the upregulation of related genes in TCA cycle, lysine biosynthesis, and acetylation may help improve hexadecane degradation. Additionally, an alternative degrading pathway of hexadecane based on dual-terminal β-oxidation may occur in strain RO2-11. It is likely to be the first report of alkane degradation by the genus Halogranum, which may be helpful for applications of oil-pollution bioremediation under high-salt conditions.
Collapse
Affiliation(s)
- HeLang Huang
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China; Chengdu Surveying Geotechnical Research Institute Co. Ltd. of MCC, Chengdu, 610023, China.
| | - CaiYun Xie
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - ZiYuan Xia
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - ZhaoYong Sun
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - YaTing Chen
- Institute for Disaster Management and Reconstruction, Sichuan University, Sichuan, 610207, China.
| | - Min Gou
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - YueQin Tang
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - HengLin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - XiaoLei Wu
- College of Engineering, Peking University, Beijing, 100871, China.
| |
Collapse
|
2
|
Valencia‐Agami SS, Cerqueda‐García D, Gamboa‐Muñoz AM, Aguirre‐Macedo ML, García‐Maldonado JQ. Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon-degrading microorganisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13264. [PMID: 38692840 PMCID: PMC11062854 DOI: 10.1111/1758-2229.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/06/2024] [Indexed: 05/03/2024]
Abstract
This study assessed the bacterioplankton community and its relationship with environmental variables, including total petroleum hydrocarbon (TPH) concentration, in the Yucatan shelf area of the Southern Gulf of Mexico. Beta diversity analyses based on 16S rRNA sequences indicated variations in the bacterioplankton community structure among sampling sites. PERMANOVA indicated that these variations could be mainly related to changes in depth (5 to 180 m), dissolved oxygen concentration (2.06 to 5.93 mg L-1), and chlorophyll-a concentration (0.184 to 7.65 mg m3). Moreover, SIMPER and one-way ANOVA analyses showed that the shifts in the relative abundances of Synechococcus and Prochlorococcus were related to changes in microbial community composition and chlorophyll-a values. Despite the low TPH content measured in the studied sites (0.01 to 0.86 μL L-1), putative hydrocarbon-degrading bacteria such as Alteromonas, Acinetobacter, Balneola, Erythrobacter, Oleibacter, Roseibacillus, and the MWH-UniP1 aquatic group were detected. The relatively high copy number of the alkB gene detected in the water column by qPCR and the enrichment of hydrocarbon-degrading bacteria obtained during lab crude oil tests exhibited the potential of bacterioplankton communities from the Yucatan shelf to respond to potential hydrocarbon impacts in this important area of the Gulf Mexico.
Collapse
Affiliation(s)
- Sonia S. Valencia‐Agami
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoMexico CityMexico
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del MarMeridaYucatánMexico
| | - Daniel Cerqueda‐García
- Clúster Científico y Tecnológico BioMimic®, Red de Manejo Biorracional de Plagas y VectoresInstituto de Ecología, AC–INECOLXalapaVeracruzMexico
| | - Abril M. Gamboa‐Muñoz
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del MarMeridaYucatánMexico
| | - M. Leopoldina Aguirre‐Macedo
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del MarMeridaYucatánMexico
| | - José Q. García‐Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del MarMeridaYucatánMexico
| |
Collapse
|
3
|
Vogel AL, Thompson KJ, Straub D, Musat F, Gutierrez T, Kleindienst S. Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations. FEMS Microbiol Ecol 2024; 100:fiae060. [PMID: 38614960 PMCID: PMC11099662 DOI: 10.1093/femsec/fiae060] [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: 09/06/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024] Open
Abstract
Polycyclic aromatic hydrocarbon (PAH) contamination in marine environments range from low-diffusive inputs to high loads. The influence of PAH concentration on the expression of functional genes [e.g. those encoding ring-hydroxylating dioxygenases (RHDs)] has been overlooked in PAH biodegradation studies. However, understanding marker-gene expression under different PAH loads can help to monitor and predict bioremediation efficiency. Here, we followed the expression (via RNA sequencing) of Cycloclasticus pugetii strain PS-1 in cell suspension experiments under different naphthalene (100 and 30 mg L-1) concentrations. We identified genes encoding previously uncharacterized RHD subunits, termed rhdPS1α and rhdPS1β, that were highly transcribed in response to naphthalene-degradation activity. Additionally, we identified six RHD subunit-encoding genes that responded to naphthalene exposure. By contrast, four RHD subunit genes were PAH-independently expressed and three other RHD subunit genes responded to naphthalene starvation. Cycloclasticus spp. could, therefore, use genetic redundancy in key PAH-degradation genes to react to varying PAH loads. This genetic redundancy may restrict the monitoring of environmental hydrocarbon-degradation activity using single-gene expression. For Cycloclasticus pugetii strain PS-1, however, the newly identified rhdPS1α and rhdPS1β genes might be potential target genes to monitor its environmental naphthalene-degradation activity.
Collapse
Affiliation(s)
- Anjela L Vogel
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Katharine J Thompson
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Daniel Straub
- Eberhard Karls University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Florin Musat
- Aarhus University, Department of Biology, Section for Microbiology, Ny Munkegade 116, Aarhus C 8000, Denmark
- Babeş-Bolyai University, Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Str. Republicii nr 44, Cluj-Napoca 400015, Romania
| | - Tony Gutierrez
- Heriot-Watt University, Institute of Mechanical Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Edinburgh EH14 4AS, UK
| | - Sara Kleindienst
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| |
Collapse
|
4
|
Cui Z, Li Y, Jing X, Luan X, Liu N, Liu J, Meng Y, Xu J, Valentine DL. Cycloalkane degradation by an uncultivated novel genus of Gammaproteobacteria derived from China's marginal seas. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133904. [PMID: 38422739 DOI: 10.1016/j.jhazmat.2024.133904] [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: 10/05/2023] [Revised: 01/30/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
The consumption of cycloalkanes is prevalent in low-temperature marine environments, likely influenced by psychrophilic microorganisms. Despite their significance, the primary active species responsible for marine cycloalkane degradation remain largely unidentified due to cultivation challenges. In this study, we provide compelling evidence indicating that the uncultured genus C1-B045 of Gammaproteobacteria is a pivotal participant in cycloalkane decomposition within China's marginal seas. Notably, the relative abundance of C1-B045 surged from 15.9% in the methylcyclohexane (MCH)-consuming starter culture to as high as 97.5% in MCH-utilizing extinction cultures following successive dilution-to-extinction and incubation cycles. We used stable isotope probing, Raman-activated gravity-driven encapsulation, and 16 S rRNA gene sequencing to link cycloalkane-metabolizing phenotype to genotype at the single-cell level. By annotating key enzymes (e.g., alkane monooxygenase, cyclohexanone monooxygenase, and 6-hexanolactone hydrolase) involved in MCH metabolism within C1-B045's representative metagenome-assembled genome, we developed a putative MCH degradation pathway.
Collapse
Affiliation(s)
- Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China.
| | - Yingchao Li
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Xiao Luan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100048, People's Republic of China
| | - Na Liu
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Jinyan Liu
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Yu Meng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
| |
Collapse
|
5
|
Dong X, Zhang T, Wu W, Peng Y, Liu X, Han Y, Chen X, Gao Z, Xia J, Shao Z, Greening C. A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps. SCIENCE ADVANCES 2024; 10:eadl2281. [PMID: 38669328 PMCID: PMC11051675 DOI: 10.1126/sciadv.adl2281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
In deep-sea cold seeps, microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds, differing from photosynthetically driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and 7 metabolomes derived from nine different cold seep areas to investigate their secondary metabolites. Cold seep microbiomes encode diverse and abundant biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling. The BGCs encode diverse antimicrobial compounds that potentially shape community dynamics and various metabolites predicted to influence biogeochemical cycling. BGCs from key players are widely distributed and highly expressed, with their abundance and expression levels varying with sediment depth. Sediment metabolomics reveals unique natural products, highlighting uncharted chemical potential and confirming BGC activity in these sediments. Overall, these results demonstrate that cold seep sediments serve as a reservoir of hidden natural products and sheds light on microbial adaptation in chemosynthetically driven ecosystems.
Collapse
Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Tianxueyu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310005, China
| | - Weichao Wu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiangwei Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Jinmei Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
6
|
Summers S, Bin-Hudari MS, Magill C, Henry T, Gutierrez T. Identification of the bacterial community that degrades phenanthrene sorbed to polystyrene nanoplastics using DNA-based stable isotope probing. Sci Rep 2024; 14:5229. [PMID: 38433255 PMCID: PMC10909871 DOI: 10.1038/s41598-024-55825-9] [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: 06/04/2023] [Accepted: 02/28/2024] [Indexed: 03/05/2024] Open
Abstract
In the Anthropocene, plastic pollution has become a new environmental biotope, the so-called plastisphere. In the oceans, nano- and micro-sized plastics are omnipresent and found in huge quantities throughout the water column and sediment, and their large surface area-to-volume ratio offers an excellent surface to which hydrophobic chemical pollutants (e.g. petrochemicals and POPs) can readily sorb to. Our understanding of the microbial communities that breakdown plastic-sorbed chemical pollutants, however, remains poor. Here, we investigated the formation of 500 nm and 1000 nm polystyrene (PS) agglomerations in natural seawater from a coastal environment, and we applied DNA-based stable isotope probing (DNA-SIP) with the 500 nm PS sorbed with isotopically-labelled phenanthrene to identify the bacterial members in the seawater community capable of degrading the hydrocarbon. Whilst we observed no significant impact of nanoplastic size on the microbial communities associated with agglomerates that formed in these experiments, these communities were, however, significantly different to those in the surrounding seawater. By DNA-SIP, we identified Arcobacteraceae, Brevundimonas, Comamonas, uncultured Comamonadaceae, Delftia, Sphingomonas and Staphylococcus, as well as the first member of the genera Acidiphilum and Pelomonas to degrade phenanthrene, and of the genera Aquabacterium, Paracoccus and Polymorphobacter to degrade a hydrocarbon. This work provides new information that feeds into our growing understanding on the fate of co-pollutants associated with nano- and microplastics in the ocean.
Collapse
Affiliation(s)
- Stephen Summers
- Institute of Mechanical, Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
- Singapore Centre for Environmental Life Sciences Engineering, Life Sciences Institute, National University of Singapore, Singapore, 119077, Singapore
- St John's Island National Marine Laboratory, National University of Singapore, Singapore, 098634, Singapore
| | - Mohammad Sufian Bin-Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Clayton Magill
- Institute for GeoEnergy Engineering, School of Energy, Geoscience, Infrastructure and Society, The Lyell Centre, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Theodore Henry
- School of Energy, Geoscience, Infrastructure and Society (EGIS), Heriot-Watt University, Edinburgh, EH14 4AS, UK
- Department of Forestry Wildlife and Fisheries, Centre for Environmental Biotechnology, The University of Tennessee, Knoxville, TN, 36849, USA
| | - Tony Gutierrez
- Institute of Mechanical, Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
| |
Collapse
|
7
|
Olivera C, Laura Tondo M, Girardi V, Sol Herrero M, Lucía Balaban C, Matías Salvatierra L. High-performance diesel biodegradation using biogas digestate as microbial inoculum in lab-scale solid supported bioreactors. CHEMOSPHERE 2024; 352:141384. [PMID: 38350516 DOI: 10.1016/j.chemosphere.2024.141384] [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: 06/28/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/15/2024]
Abstract
Industrial anaerobic digestion (AD) produces biogas and a digestate that is usually applied as a biofertilizer. However, the study and application of this by-product in terms of its rich microbial diversity and high metabolic activity have been barely investigated. In this work, the digestate regarded as an inoculum-without any further manipulation-was faced to a target hydrocarbon (i.e., diesel oil) to explore its biodegradation capability and potential application in bioaugmentation strategies. Lab-scale single batch bioreactors with solid support (i.e., sand or gravel) embedded with the inoculum and diesel were used to improve bioaccessibility and biofilm formation. In addition, different experimental conditions were assayed varying the initial diesel concentration, microbial load, type of solid support, inoculum aging time, and presence or absence of oxygen. Remaining diesel concentration, dehydrogenase activity and microbial community structure were periodically determined. Remarkably, this low-cost consortium was capable of a significant reduction (>90%) in the concentration of diesel, within 14 days and when the initial load was as high as 6950 mg/kg dry solid support. Furthermore, a 10-fold increment in dehydrogenase activity, alongside an increase in the abundance of hydrocarbon-degrading bacterial groups, and the enrichment of genes for alkane monooxygenase and aromatic ring-hydroxylating dioxygenases, encourage further study of this consortium for bioremediation purposes.
Collapse
Affiliation(s)
- Camila Olivera
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Laura Tondo
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Valentina Girardi
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Sol Herrero
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina
| | - Cecilia Lucía Balaban
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Lucas Matías Salvatierra
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada - INGEBIO-, Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, (S2002QEO), Rosario, (Santa Fe), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| |
Collapse
|
8
|
Li J, Luo C, Cai X, Dai Y, Zhang D, Zhang G. Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC). ENVIRONMENT INTERNATIONAL 2024; 185:108555. [PMID: 38458119 DOI: 10.1016/j.envint.2024.108555] [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: 12/14/2023] [Revised: 01/28/2024] [Accepted: 03/02/2024] [Indexed: 03/10/2024]
Abstract
High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from 13C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from 13C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.
Collapse
Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xixi Cai
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yeliang Dai
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Key Laboratory of Regional Environment and Eco-restoration, Ministry of Education, Shenyang University, Shenyang 110044, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| |
Collapse
|
9
|
Wang M, Chen X, Fang Y, Zheng X, Huang T, Nie Y, Wu XL. The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities. Cell Syst 2024; 15:63-74.e5. [PMID: 38237552 DOI: 10.1016/j.cels.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/17/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
In microbial systems, a metabolic pathway can be either completed by one autonomous population or distributed among a consortium performing metabolic division of labor (MDOL). MDOL facilitates the system's function by reducing the metabolic burden; however, it may hinder the function by reducing the exchange efficiency of metabolic intermediates among individuals. As a result, the function of a community is influenced by the trade-offs between the metabolic specialization and versatility of individuals. To experimentally test this hypothesis, we deconstructed the naphthalene degradation pathway into four steps and introduced them individually or combinatorically into different strains with varying levels of metabolic specialization. Using these strains, we engineered 1,456 synthetic consortia and found that 74 consortia exhibited higher degradation function than both the autonomous population and rigorous MDOL consortium. Quantitative modeling provides general strategies for identifying the most effective MDOL configuration. Our study provides critical insights into the engineering of high-performance microbial systems.
Collapse
Affiliation(s)
- Miaoxiao Wang
- College of Engineering, Peking University, Beijing 100871, China; Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland; Department of Environmental Microbiology, Eawag, Dübendorf 8600, Switzerland
| | - Xiaoli Chen
- College of Engineering, Peking University, Beijing 100871, China; Institute of Ocean Research, Peking University, Beijing 100871, China
| | - Yuan Fang
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Xin Zheng
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Ting Huang
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230000, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing 100871, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, China; Institute of Ocean Research, Peking University, Beijing 100871, China; Institute of Ecology, Peking University, Beijing 100871, China.
| |
Collapse
|
10
|
Martinez-Varela A, Casas G, Berrojalbiz N, Lundin D, Piña B, Dachs J, Vila-Costa M. Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:119988-119999. [PMID: 37934408 DOI: 10.1007/s11356-023-30650-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023]
Abstract
Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h-1. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.
Collapse
Affiliation(s)
- Alicia Martinez-Varela
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Gemma Casas
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Naiara Berrojalbiz
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, 35195, Kalmar, Sweden
| | - Benjamin Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, c/ Jordi Girona 18-26, 08034, Barcelona, Catalunya, Spain.
| |
Collapse
|
11
|
Li J, Zhang D, Luo C, Li B, Zhang G. In Situ Discrimination and Cultivation of Active Degraders in Soils by Genome-Directed Cultivation Assisted by SIP-Raman-Activated Cell Sorting. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17087-17098. [PMID: 37823365 DOI: 10.1021/acs.est.3c04247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The identification and in situ cultivation of functional yet uncultivable microorganisms are important to confirm inferences regarding their ecological functions. Here, we developed a new method that couples Raman-activated cell sorting (RACS), stable-isotope probing (SIP), and genome-directed cultivation (GDC)─namely, RACS-SIP-GDC─to identify, sort, and cultivate the active toluene degraders from a complex microbial community in petroleum-contaminated soil. Using SIP, we successfully identified the active toluene degrader Pigmentiphaga, the single cells of which were subsequently sorted and isolated by RACS. We further successfully assembled the genome of Pigmentiphaga based on the metagenomic sequencing of 13C-DNA and genomic sequencing of sorted cells, which was confirmed by gyrB gene comparison and average nucleotide identity determination. Additionally, the genotypes and phenotypes of this degrader were directly linked at the single-cell level, and its complete toluene metabolic pathways in petroleum-contaminated soil were reconstructed. Based on its unique metabolic properties uncovered by genome sequencing, we modified the traditional cultivation medium with antibiotics, amino acids, carbon sources, and growth factors (e.g., vitamins and metals), achieving the successful cultivation of RACS-sorted active degrader Pigmentiphaga sp. Our results implied that RACS-SIP-GDC is a state-of-the-art approach for the precise identification, targeted isolation, and cultivation of functional microbes from complex communities in natural habitats. RACS-SIP-GDC can be used to explore specific and targeted organic-pollution-degrading microorganisms at the single-cell level and provide new insights into their biodegradation mechanisms.
Collapse
Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, China
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bei Li
- State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 130033 Changchun, China
- HOOKE Instruments Ltd., 130033 Changchun, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| |
Collapse
|
12
|
Vázquez Rosas Landa M, De Anda V, Rohwer RR, Angelova A, Waldram G, Gutierrez T, Baker BJ. Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean. mSystems 2023; 8:e0061923. [PMID: 37702502 PMCID: PMC10654063 DOI: 10.1128/msystems.00619-23] [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: 06/15/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native microbial communities to oil spills is not well understood. Here, we explored the baseline hydrocarbon-degrading communities of a subarctic Atlantic region to uncover the metabolic potential of the bacteria that inhabit the surface and subsurface water. We conducted enrichments with a 13C-labeled hydrocarbon to capture the fraction of the community actively using the hydrocarbon. We then combined this approach with metagenomics to identify the metabolic potential of this hydrocarbon-degrading community. This revealed previously undescribed uncultured bacteria with unique metabolic mechanisms involved in aerobic hydrocarbon degradation, indicating that temperature may be pivotal in structuring hydrocarbon-degrading baseline communities. Our findings highlight gaps in our understanding of the metabolic complexity of hydrocarbon degradation by native marine microbial communities.
Collapse
Affiliation(s)
- Mirna Vázquez Rosas Landa
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
- Instituto de Ciencias del Mar y Limnologia Universidad Nacional Autónoma de Mexico, Unidad Académica de Ecologia y Biodiversidad Acuática, Mexico City, Mexico
| | - Valerie De Anda
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Robin R. Rohwer
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Angelina Angelova
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering (IMPEE), Heriot-Watt University, Edinburgh, United Kingdom
| | - Georgia Waldram
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering (IMPEE), Heriot-Watt University, Edinburgh, United Kingdom
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering (IMPEE), Heriot-Watt University, Edinburgh, United Kingdom
| | - Brett J. Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
13
|
Peña-Montenegro TD, Kleindienst S, Allen AE, Eren AM, McCrow JP, Sánchez-Calderón JD, Arnold J, Joye SB. Species-specific responses of marine bacteria to environmental perturbation. ISME COMMUNICATIONS 2023; 3:99. [PMID: 37736763 PMCID: PMC10516948 DOI: 10.1038/s43705-023-00310-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
Environmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.
Collapse
Affiliation(s)
- Tito D Peña-Montenegro
- Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, GA, 30602-3636, USA
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA, 30602-7229, USA
- Grupo de Investigación y Desarrollo en Ciencias, Tecnología e Innovación (BioGRID), Sociedad de Doctores e Investigadores de Colombia (SoPhIC), Bogotá, Colombia
| | - Sara Kleindienst
- Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, GA, 30602-3636, USA
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Bandtäle 2, 70569, Stuttgart, Germany
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, University of Oldenburg, Oldenburg, 26129, Germany
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - John P McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Juan D Sánchez-Calderón
- Grupo de Investigación en Gestión Ecológica y Agroindustrial (GEA), Programa de Microbiología, Facultad de Ciencias Exactas y Naturales, Universidad Libre, Seccional Barranquilla, Barranquilla, Colombia
| | - Jonathan Arnold
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA, 30602-7229, USA
- Department of Genetics, University of Georgia, 120 Green St., Athens, GA, 30602-7223, USA
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, GA, 30602-3636, USA.
| |
Collapse
|
14
|
Tang L, Bao Z, Zhao X, Wang X, Gao Y, Lu C, Ling W. Variations of different PAH fractions and bacterial communities during the biological self-purification in the soil vertical profile. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131903. [PMID: 37352779 DOI: 10.1016/j.jhazmat.2023.131903] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/29/2023] [Accepted: 06/18/2023] [Indexed: 06/25/2023]
Abstract
Wild PAH-contaminated sites struggle to provide continuous and stable monitoring, resulting in the potential risks of contaminated soil utilization could not be evaluated effectively. This work provided a 9-months laboratory simulation which was close to the natural ecological process. These results believed that PAH-degrading bacteria (PDB) preferred to degrade organic extracted PAH (PAH_OS) and fresh bound-PAH (79.36-99.97%). The formation and migration efficiency of PAH binding with HA humic acid (HA) (PAH_HA) was lower than that of PAH binding with fulvic acid (FA) and humin (HM) (PAH_FA and PAH_HM), leading to PAH_HA had more persistent retention and influenced bacterial communities in shallow soils. Besides, phylum Proteobacteria gradually dominated the bacterial community and decreased 12.05-20.48% diversity at all depths during the biological self-purification process. Although the effect of this process enhanced the abundance of 28 genes 16 s rRNA and three PAH-degrading genes (PDGs) by 5.91-2047.34 times (phe, nahAc and nidA), the top 30 genera maintained their ecological characteristics. This study provided insights into the important influencing factor and mechanism of the biological self-purification processes and discerned the linkages between bacterial communities and environmental variables in the vertical profile, which is important to the isolation and application of PDB and ecological risk assessment.
Collapse
Affiliation(s)
- Lei Tang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongkang Bao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuqiang Zhao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinbo Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Lu
- National Agricultural Experiment Station for Agricultural Environment, Luhe, Ministry of Agriculture, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
15
|
Durand M, Touchette D, Chen YJ, Magnuson E, Wasserscheid J, Greer CW, Whyte LG, Altshuler I. Effects of marine diesel on microbial diversity and activity in high Arctic beach sediments. MARINE POLLUTION BULLETIN 2023; 194:115226. [PMID: 37442053 DOI: 10.1016/j.marpolbul.2023.115226] [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: 03/22/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023]
Abstract
Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.
Collapse
Affiliation(s)
- Margaux Durand
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada; Energy, Mining and Environment Research Centre, National Research Council Canada (NRC), Montreal, Quebec, Canada; Université Paris-Saclay, INRAE, AgroParisTech, Paris-Saclay Applied Economics, 91120 Palaiseau, France
| | - David Touchette
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada; River Ecosystems Laboratory, ALPOLE, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ya-Jou Chen
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada
| | - Elisse Magnuson
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada
| | - Jessica Wasserscheid
- Energy, Mining and Environment Research Centre, National Research Council Canada (NRC), Montreal, Quebec, Canada
| | - Charles W Greer
- Energy, Mining and Environment Research Centre, National Research Council Canada (NRC), Montreal, Quebec, Canada
| | - Lyle G Whyte
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada
| | - Ianina Altshuler
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada; Energy, Mining and Environment Research Centre, National Research Council Canada (NRC), Montreal, Quebec, Canada; MACE Laboratory, ALPOLE, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| |
Collapse
|
16
|
Chen X, Cai R, Zhuo X, Chen Q, He C, Sun J, Zhang Y, Zheng Q, Shi Q, Jiao N. Niche differentiation of microbial community shapes vertical distribution of recalcitrant dissolved organic matter in deep-sea sediments. ENVIRONMENT INTERNATIONAL 2023; 178:108080. [PMID: 37429058 DOI: 10.1016/j.envint.2023.108080] [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] [Received: 03/12/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023]
Abstract
Sedimentary organic matter provides carbon substrates and energy sources for microorganisms, which drive benthic biogeochemical processes and in turn modify the quantity and quality of dissolved organic matter (DOM). However, the molecular composition and distribution of DOM and its interactions with microbes in deep-sea sediments remain poorly understood. Here, molecular composition of DOM and its relationship with microbes were analyzed in samples collected from two sediment cores (∼40 cm below the sea floor), at depths of 1157 and 2253 m from the South China Sea. Results show that niche differentiation was observed on a fine scale in different sediment layers, with Proteobacteria and Nitrososphaeria dominating the shallow sediments (0-6 cm) and Chloroflexi and Bathyarchaeia prevailing in deeper sediments (6-40 cm), indicating correspondence of microbial community composition with both geographical isolation and the availability of organic matter. An intimate link between the DOM composition and microbial community further indicates that, microbial mineralization of fresh organic matter in the shallow layer potentially resulted in the accumulation of recalcitrant DOM (RDOM), while relatively low abundance of RDOM was linked to anaerobic microbial utilization in deeper sediment layers. In addition, higher RDOM abundance in the overlying water, as compared to that in the surface sediment, suggests that sediment might be a source of deep-sea RDOM. These results emphasize the close relation between the distribution of sediment DOM and different microbial community, laying a foundation for understanding the complex dynamics of RDOM in deep-sea sediment and water column.
Collapse
Affiliation(s)
- Xiaoxia Chen
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Ruanhong Cai
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China.
| | - Xiaocun Zhuo
- State Key Laboratory of Heavy Oil Processing, Research Centre for Geomicrobial Resources and Application, China University of Petroleum, Beijing 102249, China
| | - Quanrui Chen
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, Research Centre for Geomicrobial Resources and Application, China University of Petroleum, Beijing 102249, China
| | - Jia Sun
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Qiang Zheng
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, Research Centre for Geomicrobial Resources and Application, China University of Petroleum, Beijing 102249, China
| | - Nianzhi Jiao
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China; Carbon Neutral Innovation Research Center, Xiamen University, Xiamen 361005, China.
| |
Collapse
|
17
|
Villela H, Modolon F, Schultz J, Delgadillo-Ordoñez N, Carvalho S, Soriano AU, Peixoto RS. Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host. Sci Rep 2023; 13:12273. [PMID: 37507453 PMCID: PMC10382565 DOI: 10.1038/s41598-023-38512-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.
Collapse
Affiliation(s)
- Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Flúvio Modolon
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Júnia Schultz
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | | | - Raquel Silva Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| |
Collapse
|
18
|
Tang L, Zhao X, Chen X, Jiang Y, Gudda F, Wang Y, Ling W. Distribution of bound-PAH residues and their correlations with the bacterial community at different depths of soil from an abandoned chemical plant site. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131328. [PMID: 37043862 DOI: 10.1016/j.jhazmat.2023.131328] [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: 02/15/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
The situ pollutant residue and microbial characteristics in contaminated environments are crucial for ecological restoration and soil utilization. This work reported the variation of polycyclic aromatic hydrocarbon (PAH) residues and the bacterial community at different depths in an aged-abandoned site. These results unveiled that over 90% of low molecular weight (LMW) and medium molecular weight (MMW), 52.84-76.88% of high molecular weight (HMW) bound-PAH (BP) residues were sequestrated in humin (HM). The stresses of PAH and soil depth enhanced the frequency of bacteria associations, especially positive associations. We enriched and cultured PAH degradation bacteria (PDB) from the sampling site mainly consisting of Pseudomonas and Acinetobacter, which were originally 0.39-0.52% abundant in the sampling site. The abundances of PDB and PAH-degradation genes (PDGs) were higher at shallower depths and increased with high PAH concentration. Simultaneously, Pearson correlation analysis and experimental verification found that the process of PAH binding with SOM limited the further increase of PDB and PDGs in PAH-contaminated sites. These findings may illustrate possible ecological risks of contaminated soils and provide guidance for the isolation and application of PDB.
Collapse
Affiliation(s)
- Lei Tang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuqiang Zhao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuwen Chen
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yi Jiang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fredrick Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunhao Wang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
19
|
Li Y, Cui Z, Luan X, Bian X, Li G, Hao T, Liu J, Feng K, Song Y. Degradation potential and pathways of methylcyclohexane by bacteria derived from Antarctic surface water. CHEMOSPHERE 2023; 329:138647. [PMID: 37037356 DOI: 10.1016/j.chemosphere.2023.138647] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
Cycloalkanes pose a tremendous environmental risk due to their high concentration in petroleum hydrocarbons and hazardous effects to organisms. Numerous studies have documented the biodegradation of acyclic alkanes and aromatic hydrocarbons. However, insufficient attention has been paid to studies on the microbial degradation of cycloalkanes, which might be closely linked to psychrophilic microbes derived from low-temperature habitats. Here we show that endemic methylcyclohexane (MCH, an abundant cycloalkane species in oil) consumers proliferated in seawater samples derived from the Antarctic surface water (AASW). The MCH-consuming bacterial communities derived from AASW exhibited a distinct species composition compared with their counterparts derived from other cold-water habitats. We also probed Colwellia and Roseovarius as the key active players in cycloalkane degradation by dilution-to-extinction-based incubation with MCH as sole source of carbon and energy. Furthermore, we propose two nearly complete MCH degradation pathways, lactone formation and aromatization, concurrently in the high-quality metagenome-assembled genomes of key MCH consumer Roseovarius. Overall, we revealed that these Antarctic microbes might have strong interactions that enhance the decomposition of more refractory hydrocarbons through complementary degradation pathways.
Collapse
Affiliation(s)
- Yingchao Li
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, 266061, People's Republic of China
| | - Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, 266061, People's Republic of China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.
| | - Xiao Luan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, 100048, People's Republic of China
| | - Xinqi Bian
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, 266061, People's Republic of China
| | - Guoqing Li
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, 266061, People's Republic of China
| | - Tong Hao
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, People's Republic of China
| | - Jinyan Liu
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, 266061, People's Republic of China
| | - Ke Feng
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, 266061, People's Republic of China
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China.
| |
Collapse
|
20
|
Vogel AL, Thompson KJ, Straub D, App CB, Gutierrez T, Löffler FE, Kleindienst S. Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation. Front Microbiol 2023; 14:1185619. [PMID: 37455737 PMCID: PMC10338962 DOI: 10.3389/fmicb.2023.1185619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 07/18/2023] Open
Abstract
Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. Cycloclasticus spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including rhd3α, rhd2α, and pahE. However, it remains unknown if the expression of these genes can serve as an indicator for active PAH degradation. Here, we determined transcript-to-gene (TtG) ratios with (reverse transcription) qPCR in cultures of Cycloclasticus pugetii strain PS-1 grown with naphthalene, phenanthrene, a mixture of these PAHs, or alternate substrates (i.e., no PAHs). Mean TtG ratios of 1.99 × 10-2, 1.80 × 10-3, and 3.20 × 10-3 for rhd3α, rhd2α, and pahE, respectively, were measured in the presence or absence of PAHs. The TtG values suggested that marker-gene expression is independent of PAH degradation. Measurement of TtG ratios in Arctic seawater microcosms amended with water-accommodated crude oil fractions, and incubated under in situ temperature conditions (i.e., 1.5°C), only detected Cycloclasticus spp. rhd2α genes and transcripts (mean TtG ratio of 4.15 × 10-1). The other marker genes-rhd3α and pahE-were not detected, suggesting that not all Cycloclasticus spp. carry these genes and a broader yet-to-be-identified repertoire of PAH-degradation genes exists. The results indicate that the expression of PAH marker genes may not correlate with PAH-degradation activity, and transcription data should be interpreted cautiously.
Collapse
Affiliation(s)
- Anjela L. Vogel
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
| | - Katharine J. Thompson
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
| | - Daniel Straub
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Constantin B. App
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
| | - Frank E. Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Sara Kleindienst
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
| |
Collapse
|
21
|
Sherry A, Dell’Agnese BM, Scott J. Biohybrids: Textile fibres provide scaffolds and highways for microbial translocation. Front Bioeng Biotechnol 2023; 11:1188965. [PMID: 37383521 PMCID: PMC10293675 DOI: 10.3389/fbioe.2023.1188965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction: Living materials (biohybrids, textile-microbial hybrids, hybrid living materials) have gained much attention in recent years with enormous potential for applications in biomedical science, the built environment, construction and architecture, drug delivery and as environmental biosensors. Living materials contain matrices which incorporate microorganisms or biomolecules as the bioactive components. A cross-disciplinary approach, operating at the intersection of creative practice and scientific research, incorporated textile technology and microbiology to demonstrate textile fibres providing microbial scaffolds and highways during this study. Methods: The study evolved from previous research which showed bacteria utilising the water layer surrounding fungal mycelium for motility, termed the 'fungal highway', which led to the investigation of the directional dispersal of microbes across a range of fibre types (natural and synthetic). The application of the study centred around the potential for biohybrids to be used as a biotechnology to improve oil bioremediation through seeding of hydrocarbon-degrading microbes into polluted environments via fungal or fibre highways, therefore treatments in the presence of crude oil were tested. Furthermore, from a design perspective, textiles have huge potential to act as a conduit for water and nutrients, essential to sustain microorganisms within living materials. Using the moisture absorption properties of natural fibres, the research explored how to engineer variable liquid absorption rates using cellulosics and wool to produce shape-changing knitted fabrics suitable for adaptation to oil spill capture. Results: At a cellular scale, confocal microscopy provided evidence to show that bacteria were able to utilise a water layer surrounding the fibres, supporting the hypothesis that fibres can aid bacterial translocation through their use as 'fibre highways'. A motile bacterial culture, Pseudomonas putida, was shown to translocate around a liquid layer surrounding polyester, nylon, and linen fibres, yet no evidence of translocation was apparent on silk or wool fibres, suggesting microbes elicit different responses to specific fibre types. Findings showed that translocation activity around highways did not diminish in the presence of crude oil, known to contain an abundance of toxic compounds, in comparison to oil-free controls. A design series demonstrated the growth of fungal mycelium (Pleurotus ostreatus) through knitted structures, highlighting the ability for natural fabrics to provide a scaffold to support microbial communities whilst retaining the ability to undergo environmentally responsive shape-change. A final prototype, Ebb&Flow, demonstrated the potential to scale up the responsive capacities of the material system using locally produced UK wool. The prototype conceptualised both the uptake of a hydrocarbon pollutant by fibres, and the translocation of microbes along fibre highways. Discussion: The research works towards facilitating the translation of fundamental science and design into biotechnological solutions that can be used in real world applications.
Collapse
Affiliation(s)
- Angela Sherry
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Bruna Martins Dell’Agnese
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Jane Scott
- Hub for Biotechnology in the Built Environment, School of Architecture Planning and Landscape, Newcastle University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
22
|
Vogel AL, Thompson KJ, Kleindienst S, Zarfl C. Dosage concentration and pulsing frequency affect the degradation efficiency in simulated bacterial polycyclic aromatic hydrocarbon-degrading cultures. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:59813-59825. [PMID: 37016250 PMCID: PMC10163121 DOI: 10.1007/s11356-023-26546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/15/2023] [Indexed: 05/08/2023]
Abstract
A major source of anthropogenic polycyclic aromatic hydrocarbon (PAH) inputs into marine environments are diffuse emissions which result in low PAH concentrations in the ocean water, posing a potential threat for the affected ecosystems. However, the remediation of low-dosage PAH contaminations through microbial processes remains largely unknown. Here, we developed a process-based numerical model to simulate batch cultures receiving repeated low-dosage naphthalene pulses compared to the conventionally used one-time high-dosage. Pulsing frequency as well as dosage concentration had a large impact on the degradation efficiency. After 10 days, 99.7%, 97.2%, 86.6%, or 83.5% of the 145 mg L-1 naphthalene was degraded when given as a one-time high-dosage or in 2, 5, or 10 repeated low-concentration dosages equally spaced throughout the experiment, respectively. If the simulation was altered, giving the system that received 10 pulses time to recover to 99.7%, pulsing patterns affected the degradation of naphthalene. When pulsing 10 days at once per day, naphthalene accumulated following each pulse and if the degradation was allowed to continue until the recovered state was reached, the incubation time was prolonged to 17 days with a generation time of 3.81 days. If a full recovery was conditional before the next pulse was added, the scenario elongated to 55 days and generation time increased to 14.15 days. This indicates that dissolution kinetics dominate biodegradation kinetics, and the biomass concentration of PAH-degrading bacteria alone is not a sufficient indicator for quantifying active biodegradation. Applying those findings to the environment, a one-time input of a high dosage is potentially degraded faster than repeated low-dosage PAH pollution and repeated low-dosage input could lead to PAH accumulation in vulnerable pristine environments. Further research on the overlooked field of chronic low-dosage PAH contamination is necessary.
Collapse
Affiliation(s)
- Anjela L Vogel
- Department of Geosciences, Eberhard Karls University of Tübingen, Schnarrenbergstr. 94-96, 72076, Tübingen, Germany.
| | - Katharine J Thompson
- Department of Geosciences, Eberhard Karls University of Tübingen, Schnarrenbergstr. 94-96, 72076, Tübingen, Germany
| | - Sara Kleindienst
- Department of Geosciences, Eberhard Karls University of Tübingen, Schnarrenbergstr. 94-96, 72076, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
| | - Christiane Zarfl
- Department of Geosciences, Eberhard Karls University of Tübingen, Schnarrenbergstr. 94-96, 72076, Tübingen, Germany
| |
Collapse
|
23
|
Wu J, Cui Z, Su Y, Yu Y, Yue B, Hu J, Qu J, Tian D, Zhan X, Li J, Cai Y. Biomimetic cellulose-nanocrystalline-based composite membrane with high flux for efficient purification of oil-in-water emulsions. JOURNAL OF HAZARDOUS MATERIALS 2023; 446:130729. [PMID: 36621295 DOI: 10.1016/j.jhazmat.2023.130729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/11/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
The massive discharge of oily wastewater and oil spills are causing serious pollution to water resources. It is urgent to require clean and efficient method of purifying oily emulsions. Although the separation membranes with selective wettability have been widely used in the efficient purification of oil/water emulsions. It is still very challenging to develop functional films that are environmentally friendly, fouling resistant, inexpensive, easy to prepare, easy to scale, and highly efficient. Cellulose nanocrystalline-based composite membranes (CCM) were prepared by surface-initiated atom transfer radical polymerization (SATRP) and vacuum self-assembly. The prepared CCM is superhydrophilic and superoleophobic underwater due to the hydrophilic nature of the modified cellulose-nanocrystalline and the micro-nano surface structure. The CCM shows high separation efficiency (> 99.9 %), high flux (16,692 L-1·m-2·h-1·bar-1) for surfactant-stabilized oil-in-water emulsions, good cycle stability and anti-fouling performance. This biomass-derived membrane is green, cheap, easy to manufacture, scalable, super-wettability, and durability, it promises to be an alternative to separation membranes in today's market.
Collapse
Affiliation(s)
- Jianfei Wu
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Ziwei Cui
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Yuxuan Su
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Yang Yu
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Bo Yue
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jundie Hu
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Jiafu Qu
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Dan Tian
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Xianxu Zhan
- Dehua Tubaobao New Decoration Material Co., Ltd., Huzhou 313200, PR China.
| | - Jianzhang Li
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, PR China; Key Laboratory of Wood Material Science and Application (Beijing Forestry University), Ministry of Education, Beijing 100083, PR China.
| | - Yahui Cai
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, PR China; Dehua Tubaobao New Decoration Material Co., Ltd., Huzhou 313200, PR China.
| |
Collapse
|
24
|
Succession Patterns of Microbial Composition and Activity following the Diesel Spill in an Urban River. Microorganisms 2023; 11:microorganisms11030698. [PMID: 36985271 PMCID: PMC10058704 DOI: 10.3390/microorganisms11030698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Diesel spills in freshwater systems have adverse impacts on the water quality and the shore wetland. Microbial degradation is the major and ultimate natural mechanism that can clean the diesel from the environment. However, which, and how fast, diesel-degrading microorganisms could degrade spilled diesel has not been well-documented in river water. Using a combination of 14C-/3H--based radiotracer assays, analytical chemistry, MiSeq sequencing, and simulation-based microcosm incubation approaches, we demonstrated succession patterns of microbial diesel-degrading activities, and bacterial and fungal community compositions. The biodegradation activities of alkanes and polycyclic aromatic hydrocarbons (PAHs) were induced within 24 h after diesel addition, and reached their maximum after incubation for 7 days. Potential diesel-degrading bacteria Perlucidibaca, Acinetobacter, Pseudomonas, Acidovorax, and Aquabacterium dominated the community initially (day 3 and day 7), but later community structure (day 21) was dominated by bacteria Ralstonia and Planctomyces. The key early fungi responders were Aspergillus, Mortierella, and Phaeoacremonium by day 7, whereas Bullera and Basidiobolus dominated the fungal community at day 21. These results directly characterize the rapid response of microbial community to diesel spills, and suggest that the progression of diesel microbial degradation is performed by the cooperative system of the versatile obligate diesel-degrading and some general heterotrophic microorganisms in river diesel spills.
Collapse
|
25
|
Gofstein TR, Leigh MB. Metatranscriptomic shifts suggest shared biodegradation pathways for Corexit 9500 components and crude oil in Arctic seawater. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:51-59. [PMID: 36177554 PMCID: PMC10103760 DOI: 10.1111/1758-2229.13127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 09/12/2022] [Indexed: 05/20/2023]
Abstract
While the genes and pathways responsible for petroleum biodegradation in marine environments have received substantial attention, considerably less is known about those active in the biodegradation of the commonly applied chemical dispersant Corexit 9500. Yet, their fate in the Arctic marine environment is an increasingly important unknown. To elucidate the genes and pathways active in the biodegradation of oil and dispersants, we performed metatranscriptomic sequencing on microbial communities in Arctic seawater exposed to oil, Corexit, or both for 0, 5, and 30 days in a mesocosm incubation experiment. While oil and Corexit stimulated significantly different metatranscriptomic profiles overall, both enriched a suite of fatty acid degradation gene transcripts. Based on the gene transcripts observed and the chemical structures of Corexit 9500 surfactant components, we propose a hypothetical pathway for Corexit surfactant biodegradation in which surfactant ester groups are transformed into fatty acids that are then funnelled into the β-oxidation fatty acid degradation pathway. Several microbial taxa within Oceanospirillales, Pseudomonadales, and Alteromonadales were associated with either oil-only or Corexit-only exposure, potentially implicating them in the degradation of these mixtures. Metabolic gene transcripts were associated with diverse gammaproteobacterial lineages, with many genera exhibiting functional redundancy. These findings offer new insight into the potential genes, pathways, and microbial consortia involved in the biodegradation of Corexit 9500 in the Arctic marine environment.
Collapse
Affiliation(s)
- Taylor R. Gofstein
- Institute of Arctic BiologyUniversity of Alaska FairbanksFairbanksAlaskaUSA
- Department of Chemistry & BiochemistryUniversity of Alaska FairbanksFairbanksAlaskaUSA
| | - Mary Beth Leigh
- Institute of Arctic BiologyUniversity of Alaska FairbanksFairbanksAlaskaUSA
- Department of Biology and WildlifeUniversity of Alaska FairbanksFairbanksAlaskaUSA
| |
Collapse
|
26
|
Otur Ç, Okay S, Kurt-Kızıldoğan A. Whole genome analysis of Flavobacterium aziz-sancarii sp. nov., isolated from Ardley Island (Antarctica), revealed a rich resistome and bioremediation potential. CHEMOSPHERE 2023; 313:137511. [PMID: 36509185 DOI: 10.1016/j.chemosphere.2022.137511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Despite being one of the most isolated regions in the world, Antarctica is at risk of increased contamination with potentially toxic elements and other toxic chemicals through anthropogenic interventions. In this study, a psychrotolerant bacterium was isolated using the lake water collected from Ardley Island (Antarctica), which can grow at temperatures between 4 and 30 °C and pH values between 6.0 and 9.0. The isolate, named AC, had protease, amylase, and lipase activities with no NaCl tolerance and could degrade 1-5% diesel fuel. Multilocus sequence analysis (MLSA) using 16S rRNA, gyrB, tuf, and rpoD genes resulted in 92.91-98.6% sequence similarities between the isolate AC and other Flavobacterium spp. Whole genome analysis indicated that the genome length of Flavobacterium sp. AC is 5.8 Mbp with a GC content of 34.04% and 1274 genes predicted. The strain AC branched independently from other Flavobacterium spp. in the phylogenetic and phylogenomic trees and ranked a new species named Flavobacterium aziz-sancarii. Genome mining identified several cold-inducible genes, including stress-associated genes such as cold-shock proteins, chaperones, carotenoid biosynthetic genes, or oxidative-stress response genes. In addition, virulence, gliding motility, and biofilm-related genes were determined. Its genome contains 35 and 88 open-reading frames related to potentially toxic element and antibiotic resistance, respectively. F. aziz-sancarii showed a remarkable tolerance of Cr and Ni, with minimal inhibitory concentration values of 2.88 and 2.81 mM, respectively. Pb, Cu, and Zn exposure resulted in moderate toxicity (2.14-2.41 mM), while Cd showed the highest inhibitory effect in bacterial growth (0.74 mM). Antibiotic susceptibility testing indicated multidrug-resistant phenotype in correlation to in silico prediction of antibiotic resistance genes. Overall, our results contribute to biodiversity of Antarctica and provide new insights into resistome profile of Antarctic microorganisms. Additionally, the diesel degradation feature of F. aziz-sancarii offers potential use for the bioremediation of hydrocarbon-contaminated polar ecosystems.
Collapse
Affiliation(s)
- Çiğdem Otur
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55139, Samsun, Turkey
| | - Sezer Okay
- Department of Vaccine Technology, Vaccine Institute, Hacettepe University, 06230, Ankara, Turkey
| | - Aslıhan Kurt-Kızıldoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55139, Samsun, Turkey.
| |
Collapse
|
27
|
Iriarte J, Dachs J, Casas G, Martínez-Varela A, Berrojalbiz N, Vila-Costa M. Snow-Dependent Biogeochemical Cycling of Polycyclic Aromatic Hydrocarbons at Coastal Antarctica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1625-1636. [PMID: 36655903 PMCID: PMC9893724 DOI: 10.1021/acs.est.2c05583] [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: 08/02/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 05/28/2023]
Abstract
The temporal trend of polycyclic aromatic hydrocarbons (PAHs) in coastal waters with highly dynamic sources and sinks is largely unknown, especially for polar regions. Here, we show the concurrent measurements of 73 individual PAHs and environmental data, including the composition of the bacterial community, during three austral summers at coastal Livingston (2015 and 2018) and Deception (2017) islands (Antarctica). The Livingston 2015 campaign was characterized by a larger snow melting input of PAHs and nutrients. The assessment of PAH diagnostic ratios, such as parent to alkyl-PAHs or LMW to HMW PAHs, showed that there was a larger biodegradation during the Livingston 2015 campaign than in the Deception 2017 and Livingston 2018 campaigns. The biogeochemical cycling, including microbial degradation, was thus yearly dependent on snow-derived inputs of matter, including PAHs, consistent with the microbial community significantly different between the different campaigns. The bivariate correlations between bacterial taxa and PAH concentrations showed that a decrease in PAH concentrations was concurrent with the higher abundance of some bacterial taxa, specifically the order Pseudomonadales in the class Gammaproteobacteria, known facultative hydrocarbonoclastic bacteria previously reported in degradation studies of oil spills. The work shows the potential for elucidation of biogeochemical processes by intensive field-derived time series, even in the harsh and highly variable Antarctic environment.
Collapse
|
28
|
Xia L, Chen F, Chao J, Zhang D, Tian Y, Zhang D. Femtosecond laser engineered eggshell membrane for durable oil/water separation under harsh conditions. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.121242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
29
|
Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor. Cell Rep 2022; 40:111410. [PMID: 36170826 DOI: 10.1016/j.celrep.2022.111410] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/10/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within a linear pathway, a phenomenon termed metabolic division of labor (MDOL). However, little is known about how such metabolic behaviors shape microbial communities. Here, we derive a theoretical framework to define the assembly of a community that degrades an organic compound through MDOL. The framework indicates that to ensure community stability, the strains performing the initial steps should hold a growth advantage (m) over the "private benefit" (n) of the strain performing the last step. The steady-state frequency of the last strain is then determined by the quotient of n and m. Our experiments show that the framework accurately predicts the assembly of our synthetic consortia that degrade naphthalene through MDOL. Our results provide insights for designing and managing stable microbial systems for metabolic pathway optimization.
Collapse
|
30
|
Sah D, Rai JPN, Ghosh A, Chakraborty M. A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils. 3 Biotech 2022; 12:218. [PMID: 35965658 PMCID: PMC9365905 DOI: 10.1007/s13205-022-03277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/21/2022] [Indexed: 11/01/2022] Open
Abstract
The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.
Collapse
Affiliation(s)
- Diksha Sah
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - J. P. N. Rai
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Ankita Ghosh
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Moumita Chakraborty
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| |
Collapse
|
31
|
Vila-Costa M, Lundin D, Casamayor EO, Meijer SN, Fernández P, Dachs J. Microbial metabolic routes in metagenome assembled genomes are mirrored by the mass balance of polycyclic aromatic hydrocarbons in a high altitude lake. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119592. [PMID: 35688389 DOI: 10.1016/j.envpol.2022.119592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/20/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Semivolatile organic pollutants have potential for long range atmospheric transport and can thus reach pristine remote lakes by atmospheric deposition. Polycyclic aromatic hydrocarbons (PAHs) are among the most abundant and toxic semivolatile pollutants affecting lakes, however, the main factors controlling their fate are still poorly known. Here we show two contrasting lines of evidence for the importance of microbial degradation on the environmental fate of PAHs in a high altitude deep lake. The first evidence is given by an assessment of the metagenomes from surface and deep waters from Lake Redon (Pyrenees Mountains), which shows the occurrence of the initial ring hydroxylating dioxygenases as well as other PAH degrading genes from the complete metabolic route of PAH degradation. The second line of evidence is by the application of an environmental fate model for PAHs to Lake Redon under two contrasting scenarios considering the inclusion or not of degradation. When degradation is included in the model, PAH concentrations in the sediment are predicted within a factor of two of those measured in Lake Redon. Finally, the extent of the degradation sink is quantified and compared to other cycling PAH fluxes in the lake.
Collapse
Affiliation(s)
- Maria Vila-Costa
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain.
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Sweden
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes, CEAB-CSIC, Blanes, Catalunya, Spain
| | - Sandra N Meijer
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Pilar Fernández
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| |
Collapse
|
32
|
Zhu Z, Merlin F, Yang M, Lee K, Chen B, Liu B, Cao Y, Song X, Ye X, Li QK, Greer CW, Boufadel MC, Isaacman L, Zhang B. Recent advances in chemical and biological degradation of spilled oil: A review of dispersants application in the marine environment. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129260. [PMID: 35739779 DOI: 10.1016/j.jhazmat.2022.129260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Growing concerns over the risk of accidental releases of oil into the marine environment have emphasized our need to improve both oil spill preparedness and response strategies. Among the available spill response options, dispersants offer the advantages of breaking oil slicks into small oil droplets and promoting their dilution, dissolution, and biodegradation within the water column. Thus dispersants can reduce the probability of oil slicks at sea from reaching coastal regions and reduce their direct impact on mammals, sea birds and shoreline ecosystems. To facilitate marine oil spill response operations, especially addressing spill incidents in remote/Arctic offshore regions, an in-depth understanding of the transportation, fate and effects of naturally/chemically dispersed oil is of great importance. This review provides a synthesis of recent research results studies related to the application of dispersants at the surface and in the deep sea, the fate and transportation of naturally and chemically dispersed oil, and dispersant application in the Arctic and ice-covered waters. Future perspectives have been provided to identify the research gaps and help industries and spill response organizations develop science-based guidelines and protocols for the application of dispersants application.
Collapse
Affiliation(s)
- Zhiwen Zhu
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | | | - Min Yang
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON K1A 0E6, Canada
| | - Bing Chen
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Bo Liu
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Yiqi Cao
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Xing Song
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Xudong Ye
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada
| | - Qingqi K Li
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC H4P 2R2, Canada
| | - Michel C Boufadel
- Center for Natural Resources, Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Lisa Isaacman
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON K1A 0E6, Canada
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada.
| |
Collapse
|
33
|
Alami NH, Hamzah A, Tangahu BV, Warmadewanti I, Bachtiar Krishna Putra A, Purnomo AS, Danilyan E, Putri HM, Aqila CN, Dewi AAN, Pratiwi A, Putri SK, Luqman A. Microbiome profile of soil and rhizosphere plants growing in traditional oil mining land in Wonocolo, Bojonegoro, Indonesia. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2022; 25:697-705. [PMID: 35867913 DOI: 10.1080/15226514.2022.2103094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Traditional oil mining poses negative effects on the environment through pollution with crude oil. One of the traditional mining sites in Wonocolo, Bojonegoro, Indonesia was reported to contaminate the surrounding area with a high level of crude oil. Therefore, this study aims to examine the microbiome profiles of contaminated soil and the rhizosphere of naturalized plants growing at the sites. It was conducted in Wonocolo, Bojonegoro to obtain an insight into the possible remediation efforts of using indigenous hydrocarbon-degrading bacteria and naturalized plants as in situ remediation agents. The results showed that the soil located close to the oil well-contained a high level of crude oil at 24.8%, and exhibited a distinct microbiome profile compared to those located further which had lower crude oil contamination of 14.15, 10.89, and 4.9%. Soil with the highest level of crude oil contamination had a comparatively higher relative abundance of assA, an anaerobic alkene-degrading gene. Meanwhile, the rhizosphere of the two naturalized plants, Muntingia calabura, and Pennisetum purpureum, exhibited indifferent microbiome profiles compared to the soil. They were found to contain less abundant hydrocarbon-degrading genes, such as C230, PAH-RHD-GP, nahAc, assA, and alkB suggesting that these naturalized plants might not be a suitable tool for in-situ remediation.
Collapse
Affiliation(s)
- Nur Hidayatul Alami
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Afan Hamzah
- Industrial Chemical Engineering Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Bieby Voijant Tangahu
- Environmental Engineering Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Idaa Warmadewanti
- Environmental Engineering Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | | | - Adi Setyo Purnomo
- Chemistry Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Edo Danilyan
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Hellen Melati Putri
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Citra Nesa Aqila
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Aulia An Nisaa Dewi
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Ayudia Pratiwi
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | | | - Arif Luqman
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| |
Collapse
|
34
|
Saeed M, Ilyas N, Jayachandran K, Shabir S, Akhtar N, Shahzad A, Sayyed RZ, Bano A. Advances in Biochar and PGPR engineering system for hydrocarbon degradation: A promising strategy for environmental remediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119282. [PMID: 35413406 DOI: 10.1016/j.envpol.2022.119282] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/24/2022] [Accepted: 04/06/2022] [Indexed: 05/22/2023]
Abstract
In soil, polycyclic aromatic hydrocarbons (PAHs) have resulted in severe environmental deterioration, compromised soil characteristics, and negatively affect all life forms, including humans. Developing appropriate and effective clean-up technology is crucial in solving the contamination issues. The traditional methods to treat PHAs contaminated soil are less effective and not ecofriendly. Bioremediation, based on bioaugmentation and biostimulation approaches, is a promising strategy for remediating contaminated soil. The use of plant growth-promoting rhizobacteria (PGPR) as a bioaugmentation tool is an effective technique for treating hydrocarbon contaminated soil. Plant growth-promoting rhizobacteria (PGPR) are group of rhizospheric bacteria that colonize the roots of plants. Biochar is a carbon-rich residue, which acts as a source of nutrients, and is also a bio-stimulating candidate to enhance the activities of oil-degrading bacteria. The application of biochar as a nutrient source to bioremediate oil-contaminated soil is a promising approach for reducing PHA contamination. Biochar induces polyaromatic hydrocarbons (PAHs) immobilization and removes the contaminants by various methods such as ion exchange electrostatic attractions and volatilization. In comparison, PGPR produce multiple types of biosurfactants to enhance the adsorption of hydrocarbons and mineralize the hydrocarbons with the conversion to less toxic substances. During the last few decades, the use of PGPR and biochar in the bioremediation of hydrocarbons-contaminated soil has gained greater importance. Therefore, developing and applying a PGPR-biochar-based remediating system can help manage hazardous PAH contaminated soil. The goal of this review paper is to (i) provide an overview of the PGPR mechanism for degradation of hydrocarbons and (ii) discuss the contaminants absorbent by biochar and its characteristics (iii) critically discuss the combined effect of PGPR and biochar for degradation of hydrocarbons by decreasing their mobility and bioavailability. The present review focuses on techniques of bioaugmentation and biostimulation based on use of PGPR and biochar in remediating the oil-contaminated soil.
Collapse
Affiliation(s)
- Maimona Saeed
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, Pakistan; Department of Botany, Government College Women University, Sialkot, Pakistan
| | - Noshin Ilyas
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, Pakistan.
| | | | - Sumera Shabir
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Nosheen Akhtar
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Asim Shahzad
- Department of Botany, Mohi-ud-Din Islamic University, Nerian Sharif AJ&K, Pakistan
| | - R Z Sayyed
- Department of Microbiology, P.S.G.V.P. Mandal's, Arts, Science, and Commerce College, Shahada, 425409, India
| | - Asghari Bano
- Department of Biosciences University of Wah, Quaid Avenue, Wah Cantt, Pakistan
| |
Collapse
|
35
|
Martinez-Varela A, Casas G, Berrojalbiz N, Piña B, Dachs J, Vila-Costa M. Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica. Front Microbiol 2022; 13:907265. [PMID: 35910648 PMCID: PMC9329070 DOI: 10.3389/fmicb.2022.907265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
As much as 400 Tg of carbon from airborne semivolatile aromatic hydrocarbons is deposited to the oceans every year, the largest identified source of anthropogenic organic carbon to the ocean. Microbial degradation is a key sink of these pollutants in surface waters, but has received little attention in polar environments. We have challenged Antarctic microbial communities from the sea-surface microlayer (SML) and the subsurface layer (SSL) with polycyclic aromatic hydrocarbons (PAHs) at environmentally relevant concentrations. PAH degradation rates and the microbial responses at both taxonomical and functional levels were assessed. Evidence for faster removal rates was observed in the SML, with rates 2.6-fold higher than in the SSL. In the SML, the highest removal rates were observed for the more hydrophobic and particle-bound PAHs. After 24 h of PAHs exposure, particle-associated bacteria in the SML showed the highest number of significant changes in their composition. These included significant enrichments of several hydrocarbonoclastic bacteria, especially the fast-growing genera Pseudoalteromonas, which increased their relative abundances by eightfold. Simultaneous metatranscriptomic analysis showed that the free-living fraction of SML was the most active fraction, especially for members of the order Alteromonadales, which includes Pseudoalteromonas. Their key role in PAHs biodegradation in polar environments should be elucidated in further studies. This study highlights the relevant role of bacterial populations inhabiting the sea-surface microlayer, especially the particle-associated habitat, as relevant bioreactors for the removal of aromatic hydrocarbons in the oceans.
Collapse
Affiliation(s)
| | | | | | | | | | - Maria Vila-Costa
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Spain
| |
Collapse
|
36
|
A Review on Biotechnological Approaches Applied for Marine Hydrocarbon Spills Remediation. Microorganisms 2022; 10:microorganisms10071289. [PMID: 35889007 PMCID: PMC9324126 DOI: 10.3390/microorganisms10071289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 12/04/2022] Open
Abstract
The increasing demand for petroleum products generates needs for innovative and reliable methods for cleaning up crude oil spills. Annually, several oil spills occur around the world, which brings numerous ecological and environmental disasters on the surface of deep seawaters like oceans. Biological and physico-chemical remediation technologies can be efficient in terms of spill cleanup and microorganisms—mainly bacteria—are the main ones responsible for petroleum hydrocarbons (PHCs) degradation such as crude oil. Currently, biodegradation is considered as one of the most sustainable and efficient techniques for the removal of PHCs. However, environmental factors associated with the functioning and performance of microorganisms involved in hydrocarbon-degradation have remained relatively unclear. This has limited our understanding on how to select and inoculate microorganisms within technologies of cleaning and to optimize physico-chemical remediation and degradation methods. This review article presents the latest discoveries in bioremediation techniques such as biostimulation, bioaugmentation, and biosurfactants as well as immobilization strategies for increasing the efficiency. Besides, environmental affecting factors and microbial strains engaged in bioremediation and biodegradation of PHCs in marines are discussed.
Collapse
|
37
|
Wang M, Chen X, Tang Y, Nie Y, Wu X. Substrate availability and toxicity shape the structure of microbial communities engaged in metabolic division of labor. MLIFE 2022; 1:131-145. [PMID: 38817679 PMCID: PMC10989799 DOI: 10.1002/mlf2.12025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/05/2022] [Accepted: 05/08/2022] [Indexed: 06/01/2024]
Abstract
Metabolic division of labor (MDOL) represents a widespread natural phenomenon, whereby a complex metabolic pathway is shared between different strains within a community in a mutually beneficial manner. However, little is known about how the composition of such a microbial community is regulated. We hypothesized that when degradation of an organic compound is carried out via MDOL, the concentration and toxicity of the substrate modulate the benefit allocation between the two microbial populations, thus affecting the structure of this community. We tested this hypothesis by combining modeling with experiments using a synthetic consortium. Our modeling analysis suggests that the proportion of the population executing the first metabolic step can be simply estimated by Monod-like formulas governed by substrate concentration and toxicity. Our model and the proposed formula were able to quantitatively predict the structure of our synthetic consortium. Further analysis demonstrates that our rule is also applicable in estimating community structures in spatially structured environments. Together, our work clearly demonstrates that the structure of MDOL communities can be quantitatively predicted using available information on environmental factors, thus providing novel insights into how to manage artificial microbial systems for the wide application of the bioindustry.
Collapse
Affiliation(s)
- Miaoxiao Wang
- Department of Energy & Resources Engineering, College of EngineeringPeking UniversityBeijingChina
- Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyEawagDübendorfSwitzerland
- Department of Environmental Science and Engineering, College of Architecture and EnvironmentSichuan UniversityChengduChina
| | - Xiaoli Chen
- Department of Energy & Resources Engineering, College of EngineeringPeking UniversityBeijingChina
- Institute of Ocean ResearchPeking UniversityBeijingChina
| | - Yue‐Qin Tang
- Department of Environmental Science and Engineering, College of Architecture and EnvironmentSichuan UniversityChengduChina
| | - Yong Nie
- Department of Energy & Resources Engineering, College of EngineeringPeking UniversityBeijingChina
| | - Xiao‐Lei Wu
- Department of Energy & Resources Engineering, College of EngineeringPeking UniversityBeijingChina
- Institute of Ocean ResearchPeking UniversityBeijingChina
- Institute of EcologyPeking UniversityBeijingChina
| |
Collapse
|
38
|
Mahor D, Cong Z, Weissenborn MJ, Hollmann F, Zhang W. Valorization of Small Alkanes by Biocatalytic Oxyfunctionalization. CHEMSUSCHEM 2022; 15:e202101116. [PMID: 34288540 DOI: 10.1002/cssc.202101116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/18/2021] [Indexed: 06/13/2023]
Abstract
The oxidation of alkanes into valuable chemical products is a vital reaction in organic synthesis. This reaction, however, is challenging, owing to the inertness of C-H bonds. Transition metal catalysts for C-H functionalization are frequently explored. Despite chemical alternatives, nature has also evolved powerful oxidative enzymes (e. g., methane monooxygenases, cytochrome P450 oxygenases, peroxygenases) that are capable of transforming C-H bonds under very mild conditions, with only the use of molecular oxygen or hydrogen peroxide as electron acceptors. Although progress in alkane oxidation has been reviewed extensively, little attention has been paid to small alkane oxidation. The latter holds great potential for the manufacture of chemicals. This Minireview provides a concise overview of the most relevant enzyme classes capable of small alkanes (C<6 ) oxyfunctionalization, describes the essentials of the catalytic mechanisms, and critically outlines the current state-of-the-art in preparative applications.
Collapse
Affiliation(s)
- Durga Mahor
- National Innovation Center for Synthetic Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- Indian Institute of Science Education and Research Berhampur, Odisha, 760010, India
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, Shandong, 266101, P. R. China
| | - Martin J Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Saale), Germany
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Wuyuan Zhang
- National Innovation Center for Synthetic Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| |
Collapse
|
39
|
Zhong C, Nesbø CL, von Gunten K, Zhang Y, Shao X, Jin R, Konhauser KO, Goss GG, Martin JW, He Y, Qian PY, Lanoil BD, Alessi DS. Complex impacts of hydraulic fracturing return fluids on soil microbial community respiration, structure, and functional potentials. Environ Microbiol 2022; 24:4108-4123. [PMID: 35416402 DOI: 10.1111/1462-2920.16009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
The consequences of soils exposed to hydraulic fracturing (HF) return fluid, often collectively termed flowback and produced water (FPW), are poorly understood, even though soils are a common receptor of FPW spills. Here, we investigate the impacts on soil microbiota exposed to FPW collected from the Montney Formation of western Canada. We measured soil respiration, microbial community structure, and functional potentials under FPW exposure across a range of concentrations, exposure time, and soil types (luvisol and chernozem). We find that soil type governs microbial community response upon FPW exposure. Within each soil, FPW exposure led to reduced biotic soil respiration, and shifted microbial community structure and functional potentials. We detect substantially higher species richness and more unique functional genes in FPW-exposed soils than in FPW-unexposed soils, with metagenome-assembled genomes (e.g., Marinobacter persicus) from luvisol soil exposed to concentrated FPW being most similar to genomes from HF/FPW sites. Our data demonstrate the complex impacts of microbial communities following FPW exposure, and highlight the site-specific effects in evaluation of spills and agricultural reuse of FPW on the normal soil functions. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Cheng Zhong
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada.,Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangzhou, China
| | - Camilla L Nesbø
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Konstantin von Gunten
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Yifeng Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xiaoqing Shao
- Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, M1C 1A4, Canada
| | - Rong Jin
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Greg G Goss
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Jonathan W Martin
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yuhe He
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangzhou, China
| | - Brian D Lanoil
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| |
Collapse
|
40
|
Li J, Zhang D, Li B, Luo C, Zhang G. Identifying the Active Phenanthrene Degraders and Characterizing Their Metabolic Activities at the Single-Cell Level by the Combination of Magnetic-Nanoparticle-Mediated Isolation, Stable-Isotope Probing, and Raman-Activated Cell Sorting (MMI-SIP-RACS). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2289-2299. [PMID: 35061946 DOI: 10.1021/acs.est.1c04952] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Magnetic-nanoparticle-mediated isolation coupled with stable-isotope probing (MMI-SIP) is a cultivation-independent higher-resolution approach for isolating active degraders in their natural habitats. However, it addresses the community level and cannot directly link the microbial identities, phenotypes, and in situ functions of the active degraders at the single-cell level within complex microbial communities. Here, we used 13C-labeled phenanthrene as the target and developed a new method coupling MMI-SIP and Raman-activated cell sorting (RACS), namely, MMI-SIP-RACS, to identify the active phenanthrene-degrading bacterial cells from polycyclic aromatic hydrocarbon (PAH)-contaminated wastewater. MMI-SIP-RACS significantly enriched the active phenanthrene degraders and successfully isolated the representative single cells. Amplicon sequencing analysis by SIP, 13C shift of the single cell in Raman spectra, and the 16S rRNA gene from single cell sequencing via RACS confirmed that Novosphingobium was the active phenanthrene degrader. Additionally, MMI-SIP-RACS reconstructed the phenanthrene metabolic pathway and genes of Novosphingobium, including two novel genes encoding phenanthrene dioxygenase and naphthalene dioxygenase. Our findings suggested that MMI-SIP-RACS is a powerful method to efficiently and precisely isolate active PAH degraders from complex microbial communities and directly link their identities to functions at the single-cell level.
Collapse
Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Bei Li
- The State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 130033 Changchun, China
- HOOKE Instruments Ltd., 130033 Changchun, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| |
Collapse
|
41
|
Govindarajan A, Crum M, Adolacion J, Kiaghadi A, Acuña-Gonzalez E, Rifai HS, Willson RC. Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey. MARINE POLLUTION BULLETIN 2022; 175:113359. [PMID: 35124375 DOI: 10.1016/j.marpolbul.2022.113359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/26/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.
Collapse
Affiliation(s)
| | - Mary Crum
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Jay Adolacion
- School of Engineering and Science, Tecnológico de Monterrey, Monterrey, Mexico
| | - Amin Kiaghadi
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA
| | - Edgar Acuña-Gonzalez
- School of Medicine and Health Sciences, Tecnológico de Monterrey, Monterrey, Mexico
| | - Hanadi S Rifai
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA.
| | - Richard C Willson
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| |
Collapse
|
42
|
Khot V, Zorz J, Gittins DA, Chakraborty A, Bell E, Bautista MA, Paquette AJ, Hawley AK, Novotnik B, Hubert CRJ, Strous M, Bhatnagar S. CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. Front Microbiol 2022; 12:764058. [PMID: 35069469 PMCID: PMC8767102 DOI: 10.3389/fmicb.2021.764058] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/08/2021] [Indexed: 02/04/2023] Open
Abstract
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.
Collapse
Affiliation(s)
- Varada Khot
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jackie Zorz
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Daniel A Gittins
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Anirban Chakraborty
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Emma Bell
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - María A Bautista
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Alexandre J Paquette
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K Hawley
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Breda Novotnik
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Casey R J Hubert
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marc Strous
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Srijak Bhatnagar
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
43
|
Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill. Appl Environ Microbiol 2022; 88:e0215121. [PMID: 35020455 DOI: 10.1128/aem.02151-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.
Collapse
|
44
|
Shapiro TN, Lobakova ES, Dolnikova GA, Ivanova EA, Sandzhieva DA, Burova AA, Dzhabrailova KS, Dedov AG. Community of Hydrocarbon-Oxidizing Bacteria in Petroleum Products on the Example of TS-1 Jet Fuel and AI-95 Gasoline. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821090076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
45
|
Chemical Diversity and Antimicrobial Potential of Cultivable Fungi from Deep-Sea Sediments of the Gulf of Mexico. Molecules 2021; 26:molecules26237328. [PMID: 34885908 PMCID: PMC8659086 DOI: 10.3390/molecules26237328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 11/17/2022] Open
Abstract
A collection of 29 cultivable fungal strains isolated from deep-sea sediments of the Gulf of Mexico were cultivated under the “one strain, many compounds” approach to explore their chemical diversity and antimicrobial potential. From the 87 extracts tested, over 50% showed antimicrobial activity, and the most active ones were those from cultures grown at 4 °C in darkness for 60 days (resembling deep-sea temperature). PCA analysis of the LC-MS data of all the extracts confirmed that culture temperature is the primary factor in the variation of the 4462 metabolite features, accounting for 21.3% of the variation. The bioactivity-guided and conventional chemical studies of selected fungal strains allowed the identification of several active and specialized metabolites. Finally, metabolomics analysis by GNPS molecular networking and manual dereplication revealed the biosynthetic potential of these species to produce interesting chemistry. This work uncovers the chemical and biological study of marine-derived fungal strains from deep-sea sediments of the Gulf of Mexico.
Collapse
|
46
|
Calm and Frenzy: marine obligate hydrocarbonoclastic bacteria sustain ocean wellness. Curr Opin Biotechnol 2021; 73:337-345. [PMID: 34768202 DOI: 10.1016/j.copbio.2021.09.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/03/2022]
Abstract
According to current estimates, the annual volume of crude oil entering the ocean due to both anthropogenic activities and naturally occurring seepages reaches approximately 8.3 million metric tons. Huge discharges from accidents have caused large-scale environmental disasters with extensive damage to the marine ecosystem. The natural clean-up of petroleum spills in marine environments is carried out primarily by naturally occurring obligate hydrocarbonoclastic bacteria (OHCB). The natural hosts of OHCB include a range of marine primary producers, unicellular photosynthetic eukaryotes and cyanobacteria, which have been documented as both, suppliers of hydrocarbon-like compounds that fuel the 'cryptic' hydrocarbon cycle and as a source of isolation of new OHCB. A very new body of evidence suggests that OHCB are not only the active early stage colonizers of plastics and hence the important component of the ocean's 'plastisphere' but also encode an array of enzymes experimentally proven to act on petrochemical and bio-based polymers.
Collapse
|
47
|
Achberger AM, Doyle SM, Mills MI, Holmes CP, Quigg A, Sylvan JB. Bacteria-Oil Microaggregates Are an Important Mechanism for Hydrocarbon Degradation in the Marine Water Column. mSystems 2021; 6:e0110521. [PMID: 34609162 PMCID: PMC8547462 DOI: 10.1128/msystems.01105-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023] Open
Abstract
Following oil spills in aquatic environments, oil-associated flocculants observed within contaminated waters ultimately lead to the sedimentation of oil as marine oil snow (MOS). To better understand the role of aggregates in hydrocarbon degradation and transport, we experimentally produced a MOS sedimentation event using Gulf of Mexico coastal waters amended with oil or oil plus dispersant. In addition to the formation of MOS, smaller micrometer-scale (10- to 150-μm) microbial aggregates were observed. Visual inspection of these microaggregates revealed that they were most abundant in the oil-amended treatments and frequently associated with oil droplets, linking their formation to the presence of oil. The peak abundance of the microaggregates coincided with the maximum rates of biological hydrocarbon oxidation estimated by the mineralization of 14C-labeled hexadecane and naphthalene. To elucidate the potential of microaggregates to serve as hot spots for hydrocarbon degradation, we characterized the free-living and aggregate-associated microbial assemblages using 16S rRNA gene sequencing. The microaggregate population was found to be bacterially dominated and enriched with putative hydrocarbon-degrading taxa. Direct observation of some of these taxa using catalyzed reporter deposition fluorescence in situ hybridization confirmed their greater abundance within microaggregates relative to the surrounding seawater. Metagenomic sequencing of these bacteria-oil microaggregates (BOMAs) further supported their community's capacity to utilize a wide variety of hydrocarbon compounds. Taken together, these data highlight that BOMAs are inherent features in the biological response to oil spills and likely important hot spots for hydrocarbon oxidation in the ocean. IMPORTANCE Vast quantities of oil-associated marine snow (MOS) formed in the water column as part of the natural biological response to the Deepwater Horizon drilling accident. Despite the scale of the event, uncertainty remains about the mechanisms controlling MOS formation and its impact on the environment. In addition to MOS, we observed micrometer-scale (10- to 150-μm) aggregates whose abundance coincided with maximum rates of hydrocarbon degradation and whose composition was dominated by hydrocarbon-degrading bacteria with the genetic potential to metabolize a range of these compounds. This targeted study examining the role of these bacteria-oil microaggregates in hydrocarbon degradation reveals details of this fundamental component of the biological response to oil spills, and with it, alterations to biogeochemical cycling in the ocean.
Collapse
Affiliation(s)
- Amanda M. Achberger
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Shawn M. Doyle
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Makeda I. Mills
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Charles P. Holmes
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Antonietta Quigg
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
- Department of Marine Biology, Texas A&M University-Galveston, Galveston, Texas, USA
| | - Jason B. Sylvan
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| |
Collapse
|
48
|
Cai X, Li J, Guan F, Luo X, Yuan Y. Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil. Environ Microbiol 2021; 23:7093-7104. [PMID: 34674400 DOI: 10.1111/1462-2920.15814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 10/05/2021] [Indexed: 01/17/2023]
Abstract
Exploring the metabolic characteristics of indigenous PAH degraders is critical to understanding the PAH bioremediation mechanism in the natural environment. While stable-isotopic probing (SIP) is a viable method to identify functional microorganisms in complex environments, the metabolic characteristics of uncultured degraders are still elusive. Here, we investigated the naphthalene (NAP) biodegradation of petroleum polluted soils by combining SIP, amplicon sequencing and metagenome binning. Based on the SIP and amplicon sequencing results, an uncultured Gammaproteobacterium sp. was identified as the key NAP degrader. Additionally, the assembled genome of this uncultured degrader was successfully obtained from the 13 C-DNA metagenomes by matching its 16S rRNA gene with the SIP identified OTU sequence. Meanwhile, a number of NAP degrading genes encoding naphthalene/PAH dioxygenases were identified in this genome, further confirming the direct involvement of this indigenous degrader in the NAP degradation. The degrader contained genes related to the metabolisms of several carbon sources, energy substances and vitamins, illuminating potential reasons for why microorganisms cannot be cultivated and finally realize their cultivation. Our findings provide novel information on the mechanisms of in situ PAH biodegradation and add to our current knowledge on the cultivation of non-culturable microorganisms by combining both SIP and metagenome binning.
Collapse
Affiliation(s)
- Xixi Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.,CAS Center for Excellence in Deep Earth Science, Guangzhou, 510640, China
| | - Fengyi Guan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Xiaoshan Luo
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| |
Collapse
|
49
|
Murphy SMC, Bautista MA, Cramm MA, Hubert CRJ. Diesel and Crude Oil Biodegradation by Cold-Adapted Microbial Communities in the Labrador Sea. Appl Environ Microbiol 2021; 87:e0080021. [PMID: 34378990 PMCID: PMC8478444 DOI: 10.1128/aem.00800-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/24/2021] [Indexed: 11/20/2022] Open
Abstract
Oil spills in the subarctic marine environment off the coast of Labrador, Canada, are increasingly likely due to potential oil production and increases in ship traffic in the region. To understand the microbiome response and how nutrient biostimulation promotes biodegradation of oil spills in this cold marine setting, marine sediment microcosms amended with diesel or crude oil were incubated at in situ temperature (4°C) for several weeks. Sequencing of 16S rRNA genes following these spill simulations revealed decreased microbial diversity and enrichment of putative hydrocarbonoclastic bacteria that differed depending on the petroleum product. Metagenomic sequencing revealed that the genus Paraperlucidibaca harbors previously unrecognized capabilities for alkane biodegradation, which were also observed in Cycloclasticus. Genomic and amplicon sequencing together suggest that Oleispira and Thalassolituus degraded alkanes from diesel, while Zhongshania and the novel PGZG01 lineage contributed to crude oil alkane biodegradation. Greater losses in PAHs from crude oil than from diesel were consistent with Marinobacter, Pseudomonas_D, and Amphritea genomes exhibiting aromatic hydrocarbon biodegradation potential. Biostimulation with nitrogen and phosphorus (4.67 mM NH4Cl and 1.47 mM KH2PO4) was effective at enhancing n-alkane and PAH degradation following low-concentration (0.1% [vol/vol]) diesel and crude oil amendments, while at higher concentrations (1% [vol/vol]) only n-alkanes in diesel were consumed, suggesting toxicity induced by compounds in unrefined crude oil. Biostimulation allowed for a more rapid shift in the microbial community in response to petroleum amendments, more than doubling the rates of CO2 increase during the first few weeks of incubation. IMPORTANCE Increases in transportation of diesel and crude oil in the Labrador Sea will pose a significant threat to remote benthic and shoreline environments, where coastal communities and wildlife are particularly vulnerable to oil spill contaminants. Whereas marine microbiology has not been incorporated into environmental assessments in the Labrador Sea, there is a growing demand for microbial biodiversity evaluations given the pronounced impact of climate change in this region. Benthic microbial communities are important to consider given that a fraction of spilled oil typically sinks such that its biodegradation occurs at the seafloor, where novel taxa with previously unrecognized potential to degrade hydrocarbons were discovered in this work. Understanding how cold-adapted microbiomes catalyze hydrocarbon degradation at low in situ temperature is crucial in the Labrador Sea, which remains relatively cold throughout the year.
Collapse
Affiliation(s)
- Sean M. C. Murphy
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - María A. Bautista
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Margaret A. Cramm
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
50
|
Kayani MUR, Huang W, Feng R, Chen L. Genome-resolved metagenomics using environmental and clinical samples. Brief Bioinform 2021; 22:bbab030. [PMID: 33758906 PMCID: PMC8425419 DOI: 10.1093/bib/bbab030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/29/2020] [Accepted: 01/20/2021] [Indexed: 12/25/2022] Open
Abstract
Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.
Collapse
Affiliation(s)
- Masood ur Rehman Kayani
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| | - Wanqiu Huang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 200,000, China
| | - Ru Feng
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| | - Lei Chen
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| |
Collapse
|