1
|
Scheffer G, Hubert CRJ, Enning DR, Lahme S, Mand J, de Rezende JR. Metagenomic Investigation of a Low Diversity, High Salinity Offshore Oil Reservoir. Microorganisms 2021; 9:2266. [PMID: 34835392 PMCID: PMC8621343 DOI: 10.3390/microorganisms9112266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/22/2022] Open
Abstract
Oil reservoirs can represent extreme environments for microbial life due to low water availability, high salinity, high pressure and naturally occurring radionuclides. This study investigated the microbiome of saline formation water samples from a Gulf of Mexico oil reservoir. Metagenomic analysis and associated anaerobic enrichment cultures enabled investigations into metabolic potential for microbial activity and persistence in this environment given its high salinity (4.5%) and low nutrient availability. Preliminary 16S rRNA gene amplicon sequencing revealed very low microbial diversity. Accordingly, deep shotgun sequencing resulted in nine metagenome-assembled genomes (MAGs), including members of novel lineages QPJE01 (genus level) within the Halanaerobiaceae, and BM520 (family level) within the Bacteroidales. Genomes of the nine organisms included respiratory pathways such as nitrate reduction (in Arhodomonas, Flexistipes, Geotoga and Marinobacter MAGs) and thiosulfate reduction (in Arhodomonas, Flexistipes and Geotoga MAGs). Genomic evidence for adaptation to high salinity, withstanding radioactivity, and metal acquisition was also observed in different MAGs, possibly explaining their occurrence in this extreme habitat. Other metabolic features included the potential for quorum sensing and biofilm formation, and genes for forming endospores in some cases. Understanding the microbiomes of deep biosphere environments sheds light on the capabilities of uncultivated subsurface microorganisms and their potential roles in subsurface settings, including during oil recovery operations.
Collapse
Affiliation(s)
- Gabrielle Scheffer
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada;
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (S.L.); (J.R.d.R.)
| | - Dennis R. Enning
- Faculty of Life Sciences and Technology, Berlin University of Applied Sciences and Technology, D-13347 Berlin, Germany;
| | - Sven Lahme
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (S.L.); (J.R.d.R.)
- Exxon Mobil Upstream Research Company, Spring, TX 77389, USA;
| | - Jaspreet Mand
- Exxon Mobil Upstream Research Company, Spring, TX 77389, USA;
| | - Júlia R. de Rezende
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (S.L.); (J.R.d.R.)
- The Lyell Centre, Heriot-Watt University, Edinburgh EH14 4AS, UK
| |
Collapse
|
2
|
Amoozegar MA, Safarpour A, Noghabi KA, Bakhtiary T, Ventosa A. Halophiles and Their Vast Potential in Biofuel Production. Front Microbiol 2019; 10:1895. [PMID: 31507545 PMCID: PMC6714587 DOI: 10.3389/fmicb.2019.01895] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/31/2019] [Indexed: 11/13/2022] Open
Abstract
Global warming and the limitations of using fossil fuels are a main concern of all societies, and thus, the development of alternative fuel sources is crucial to improving the current global energy situation. Biofuels are known as the best alternatives of unrenewable fuels and justify increasing extensive research to develop new and less expensive methods for their production. The most frequent biofuels are bioethanol, biobutanol, biodiesel, and biogas. The production of these biofuels is the result of microbial activity on organic substrates like sugars, starch, oil crops, non-food biomasses, and agricultural and animal wastes. Several industrial production processes are carried out in the presence of high concentrations of NaCl and therefore, researchers have focused on halophiles for biofuel production. In this review, we focus on the role of halophilic microorganisms and their current utilization in the production of all types of biofuels. Also, the outstanding potential of them and their hydrolytic enzymes in the hydrolysis of different kind of biomasses and the production of biofuels are discussed.
Collapse
Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Atefeh Safarpour
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Kambiz Akbari Noghabi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Tala Bakhtiary
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| |
Collapse
|
3
|
Sulfate reduction by a haloalkaliphilic bench-scale sulfate-reducing bioreactor and its bacterial communities at different depths. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
4
|
Daly RA, Roux S, Borton MA, Morgan DM, Johnston MD, Booker AE, Hoyt DW, Meulia T, Wolfe RA, Hanson AJ, Mouser PJ, Moore JD, Wunch K, Sullivan MB, Wrighton KC, Wilkins MJ. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat Microbiol 2018; 4:352-361. [DOI: 10.1038/s41564-018-0312-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/30/2018] [Indexed: 12/20/2022]
|
5
|
Peng X, Pan X, Wang X, Li D, Huang P, Qiu G, Shan K, Chu X. Accelerated removal of high concentration p-chloronitrobenzene using bioelectrocatalysis process and its microbial communities analysis. BIORESOURCE TECHNOLOGY 2018; 249:844-850. [PMID: 29136940 DOI: 10.1016/j.biortech.2017.10.068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/09/2017] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
p-Chloronitrobenzene (p-CNB) is a persistent refractory and toxic pollutant with a concentration up to 200 mg/L in industrial wastewater. Here, a super-fast removal rate was found at 0.2-0.8 V of external voltage over a p-CNB concentration of 40-120 mg/L when a bioelectrochemical technology is used comparing to the natural biodegradation and electrochemical methods. The reduction kinetics (k) was fitted well according to pseudo-first order model with respect to the different initial concentration, indicating a 1.12-fold decrease from 1.80 to 0.85 h-1 within the experimental range. Meanwhile, the highest k was provided at 0.5 V with the characteristic of energy saving. It was revealed that the functional bacterial (Propionimicrobium, Desulfovibrio, Halanaerobium, Desulfobacterales) was selectively enriched under electro-stimulation, which possibly processed Cl-substituted nitro-aromatics reduction. The possible degradation pathway was also proposed. This work provides the beneficial choice on the rapid treatment of high-concentration p-CNB wastewater.
Collapse
Affiliation(s)
- Xinhong Peng
- Institute of Seawater Desalination and Multipurpose Utilization, State Oceanic Administration (SOA), Nankai District, Tianjin 300192, China; MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
| | - Xianhui Pan
- Institute of Seawater Desalination and Multipurpose Utilization, State Oceanic Administration (SOA), Nankai District, Tianjin 300192, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Dongyang Li
- Institute of Seawater Desalination and Multipurpose Utilization, State Oceanic Administration (SOA), Nankai District, Tianjin 300192, China
| | - Pengfei Huang
- Institute of Seawater Desalination and Multipurpose Utilization, State Oceanic Administration (SOA), Nankai District, Tianjin 300192, China
| | - Guanhua Qiu
- Institute of Seawater Desalination and Multipurpose Utilization, State Oceanic Administration (SOA), Nankai District, Tianjin 300192, China
| | - Ke Shan
- Institute of Seawater Desalination and Multipurpose Utilization, State Oceanic Administration (SOA), Nankai District, Tianjin 300192, China
| | - Xizhang Chu
- Institute of Seawater Desalination and Multipurpose Utilization, State Oceanic Administration (SOA), Nankai District, Tianjin 300192, China
| |
Collapse
|
6
|
Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells. Appl Environ Microbiol 2017; 83:AEM.02659-16. [PMID: 28159795 DOI: 10.1128/aem.02659-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/28/2017] [Indexed: 11/20/2022] Open
Abstract
Microbial activity in the produced water from hydraulically fractured oil and gas wells may potentially interfere with hydrocarbon production and cause damage to the well and surface infrastructure via corrosion, sulfide release, and fouling. In this study, we surveyed the microbial abundance and community structure of produced water sampled from 42 Marcellus Shale wells in southwestern Pennsylvania (well age ranged from 150 to 1,846 days) to better understand the microbial diversity of produced water. We sequenced the V4 region of the 16S rRNA gene to assess taxonomy and utilized quantitative PCR (qPCR) to evaluate the microbial abundance across all 42 produced water samples. Bacteria of the order Halanaerobiales were found to be the most abundant organisms in the majority of the produced water samples, emphasizing their previously suggested role in hydraulic fracturing-related microbial activity. Statistical analyses identified correlations between well age and biocide formulation and the microbial community, in particular, the relative abundance of Halanaerobiales We further investigated the role of members of the order Halanaerobiales in produced water by reconstructing and annotating a Halanaerobium draft genome (named MDAL1), using shotgun metagenomic sequencing and metagenomic binning. The recovered draft genome was found to be closely related to the species H. congolense, an oil field isolate, and Halanaerobium sp. strain T82-1, also recovered from hydraulic fracturing produced water. Reconstruction of metabolic pathways revealed Halanaerobium sp. strain MDAL1 to have the potential for acid production, thiosulfate reduction, and biofilm formation, suggesting it to have the ability to contribute to corrosion, souring, and biofouling events in the hydraulic fracturing infrastructure.IMPORTANCE There are an estimated 15,000 unconventional gas wells in the Marcellus Shale region, each generating up to 8,000 liters of hypersaline produced water per day throughout its lifetime (K. Gregory, R. Vidic, and D. Dzombak, Elements 7:181-186, 2011, https://doi.org/10.2113/gselements.7.3.181; J. Arthur, B. Bohm, and M. Layne, Gulf Coast Assoc Geol Soc Trans 59:49-59, 2009; https://www.marcellusgas.org/index.php). Microbial activity in produced waters could lead to issues with corrosion, fouling, and souring, potentially interfering with hydraulic fracturing operations. Previous studies have found microorganisms contributing to corrosion, fouling, and souring to be abundant across produced water samples from hydraulically fractured wells; however, these findings were based on a limited number of samples and well sites. In this study, we investigated the microbial community structure in produced water samples from 42 unconventional Marcellus Shale wells, confirming the dominance of the genus Halanaerobium in produced water and its metabolic potential for acid and sulfide production and biofilm formation.
Collapse
|
7
|
Daly RA, Borton MA, Wilkins MJ, Hoyt DW, Kountz DJ, Wolfe RA, Welch SA, Marcus DN, Trexler RV, MacRae JD, Krzycki JA, Cole DR, Mouser PJ, Wrighton KC. Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales. Nat Microbiol 2016; 1:16146. [PMID: 27595198 DOI: 10.1038/nmicrobiol.2016.146] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/15/2016] [Indexed: 01/22/2023]
Abstract
Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.
Collapse
Affiliation(s)
- Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Mikayla A Borton
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Michael J Wilkins
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA.,School of Earth Sciences, The Ohio State University, Columbus, Ohio 43214, USA
| | - David W Hoyt
- EMSL, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Duncan J Kountz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Richard A Wolfe
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Susan A Welch
- School of Earth Sciences, The Ohio State University, Columbus, Ohio 43214, USA
| | - Daniel N Marcus
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - Ryan V Trexler
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, Ohio 43214, USA
| | - Jean D MacRae
- Department of Civil and Environmental Engineering, University of Maine, Orono, Maine 04469, USA
| | - Joseph A Krzycki
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| | - David R Cole
- School of Earth Sciences, The Ohio State University, Columbus, Ohio 43214, USA
| | - Paula J Mouser
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, Ohio 43214, USA
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43214, USA
| |
Collapse
|
8
|
Zhou J, Zhou X, Li Y, Xing J. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing. JOURNAL OF HAZARDOUS MATERIALS 2015; 295:176-184. [PMID: 25897699 DOI: 10.1016/j.jhazmat.2015.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/17/2015] [Accepted: 04/04/2015] [Indexed: 06/04/2023]
Abstract
Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities.
Collapse
Affiliation(s)
- Jiemin Zhou
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xuemei Zhou
- 101 Institute, Ministry of Civil Affairs, Beijing 100070, PR China
| | - Yuguang Li
- 101 Institute, Ministry of Civil Affairs, Beijing 100070, PR China
| | - Jianmin Xing
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190, PR China.
| |
Collapse
|
9
|
Genome Sequence of Bacillus cereus Strain A1, an Efficient Starch-Utilizing Producer of Hydrogen. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00494-14. [PMID: 24874679 PMCID: PMC4038884 DOI: 10.1128/genomea.00494-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacillus cereus strain A1 is a newly isolated hydrogen producer capable of utilizing bioresources and biowaste, such as starch and starch wastewater. Here, we present a 5.67-Mb assembly of the genome sequence of strain A1, which may provide insights into the molecular mechanism of hydrogen production from bioresources and biowaste.
Collapse
|