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Yun Y, Lv T, Gui Z, Su T, Cao W, Tian X, Chen Y, Wang S, Jia Z, Li G, Ma T. Composition and metabolic flexibility of hydrocarbon-degrading consortia in oil reservoirs. BIORESOURCE TECHNOLOGY 2024; 409:131244. [PMID: 39127363 DOI: 10.1016/j.biortech.2024.131244] [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: 05/21/2024] [Revised: 08/06/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Hydrocarbon-degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining 13C-DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme.
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Affiliation(s)
- Yuan Yun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Tianhua Lv
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Ziyu Gui
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Tianqi Su
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Weiwei Cao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China
| | - Xuefeng Tian
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Yu Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Shaojing Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, PR China.
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, PR China.
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Zhou Y, Wang Y, Yao S, Zhao X, Kong Q, Cui L, Zhang H. Driving mechanisms for the adaptation and degradation of petroleum hydrocarbons by native microbiota from seas prone to oil spills. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135060. [PMID: 38943887 DOI: 10.1016/j.jhazmat.2024.135060] [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: 02/15/2024] [Revised: 06/15/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Offshore waters have a high incidence of oil pollution, which poses an elevated risk of ecological damage. The microbial community composition and metabolic mechanisms influenced by petroleum hydrocarbons vary across different marine regions. However, research on metabolic strategies for in-situ petroleum degradation and pollution adaptation remains in its nascent stages. This study combines metagenomic techniques with gas chromatography-mass spectrometry (GC-MS) analysis. The data show that the genera Pseudoalteromonas, Hellea, Lentisphaera, and Polaribacter exhibit significant oil-degradation capacity, and that the exertion of their degradation capacity is correlated with nutrient and oil pollution stimuli. Furthermore, tmoA, badA, phdF, nahAc, and fadA were found to be the key genes involved in the degradation of benzene, polycyclic aromatic hydrocarbons, and their intermediates. Key genes (INSR, SLC2A1, and ORC1) regulate microbial adaptation to oil-contaminated seawater, activating oil degradation processes. This process enhances the biological activity of microbial communities and accounts for the geographical variation in their compositional structure. Our results enrich the gene pool for oil pollution adaptation and degradation and provide an application basis for optimizing bioremediation intervention strategies.
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Affiliation(s)
- Yumiao Zhou
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shudi Yao
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Xinyu Zhao
- Laoshan Laboratory, Qingdao 266237, China
| | - Qiang Kong
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Lihua Cui
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Huanxin Zhang
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China.
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3
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An L, Liu X, Wang J, Xu J, Chen X, Liu X, Hu B, Nie Y, Wu XL. Global diversity and ecological functions of viruses inhabiting oil reservoirs. Nat Commun 2024; 15:6789. [PMID: 39117673 PMCID: PMC11310422 DOI: 10.1038/s41467-024-51101-6] [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: 10/27/2023] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Oil reservoirs, being one of the significant subsurface repositories of energy and carbon, host diverse microbial communities affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil reservoirs remain undetermined. Here, we assemble a catalogue encompassing viral and prokaryotic genomes sourced from oil reservoirs. The catalogue comprises 7229 prokaryotic genomes and 3,886 viral Operational Taxonomic Units (vOTUs) from 182 oil reservoir metagenomes. The results show that viruses are widely distributed in oil reservoirs, and 85% vOTUs in oil reservoir are detected in less than 10% of the samples, highlighting the heterogeneous nature of viral communities within oil reservoirs. Through combined microcosm enrichment experiments and bioinformatics analysis, we validate the ecological roles of viruses in regulating the community structure of sulfate reducing microorganisms, primarily through a virulent lifestyle. Taken together, this study uncovers a rich diversity of viruses and their ecological functions within oil reservoirs, offering a comprehensive understanding of the role of viral communities in the biogeochemical cycles of the deep biosphere.
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Affiliation(s)
- Liyun An
- College of architecture and environment, Sichuan University, Chengdu, 610065, China
| | - Xinwu Liu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jianwei Wang
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jinbo Xu
- School of Earth and Space Sciences, Peking University, Beijing, 100871, China
| | - Xiaoli Chen
- College of Engineering, Peking University, Beijing, 100871, China
- Institute of Ocean Research, Peking University, Beijing, 100871, China
| | - Xiaonan Liu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Bingxin Hu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China.
| | - Xiao-Lei Wu
- College of architecture and environment, Sichuan University, Chengdu, 610065, China.
- College of Engineering, Peking University, Beijing, 100871, China.
- School of Earth and Space Sciences, Peking University, Beijing, 100871, China.
- Institute of Ocean Research, Peking University, Beijing, 100871, China.
- Institute of Ecology, Peking University, Beijing, 100871, China.
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Cheng W, Tian W, Wang W, Lv T, Su T, Wu M, Yun Y, Ma T, Li G. Nutrient availability contributes to structural and functional diversity of microbiome in Xinjiang oilfield. Front Microbiol 2024; 15:1450226. [PMID: 39144231 PMCID: PMC11322141 DOI: 10.3389/fmicb.2024.1450226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/10/2024] [Indexed: 08/16/2024] Open
Abstract
Indigenous microbial enhanced oil recovery (IMEOR) is a promising alternative way to promote oil recovery. It activates oil recovery microorganisms in the reservoir by adding nutrients to the injected water, utilizing microbial growth and metabolism to enhance recovery. However, few studies have focused on the impact of injected nutrients on reservoir microbial community composition and potential functions. This limits the further strategic development of IMEOR. In this study, we investigated the effects of nutrition on the composition of the reservoir bacterial community and functions in the Qizhong block of Xinjiang Oilfield, China, by constructing a long core microbial flooding simulation device. The results showed that the microbial community structure of the reservoir changed from aerobic state to anaerobic state after nutrient injection. Reducing the nutrient concentration increased the diversity and network stability of the reservoir bacterial community. At the same time, the nitrogen metabolism function also showed the same change response. Overall, these results indicated that nutrition significantly affected the community structure and function of reservoir microorganisms. Injecting low concentrations of nutrients may be more beneficial to improve oil recovery. This study is of great significance for guiding IMEOR technology and saving costs at the field site.
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Affiliation(s)
- Wei Cheng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenzhuo Tian
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Weilong Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Tianhua Lv
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Tianqi Su
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mengmeng Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuan Yun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin, China
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin, China
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Dong D, Guo Z, Yang X, Dai Y. Comprehensive understanding of the aging and biodegradation of polystyrene-based plastics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123034. [PMID: 38016589 DOI: 10.1016/j.envpol.2023.123034] [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: 08/06/2023] [Revised: 10/27/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023]
Abstract
The extensive utilization and inadequate handling of plastics have resulted in severe environmental ramifications. In particular, plastics composed solely of a carbon-carbon (C-C) backbone exhibit limited degradation due to the absence of hydrolyzable functional groups. Plastics with enduring longevity in the natural environment are susceptible to environmental factors and their intrinsic properties, subsequently undergoing a series of aging processes that culminate in biodegradation. This article focuses on polystyrene (PS), which constitutes 20% of total plastic waste, as a case study. Initially, the application of PS in life and the impacts it poses are introduced. Following that, the key factors influencing the aging of PS are discussed, primarily encompassing its properties (e.g., surface characteristics, additives) and environmental factors (e.g., water matrices, biofilms). Lastly, an overview of microbial degradation of PS is provided, including potential microorganisms involved in PS degradation (bacteria, fungi, algae, and insects), four processes of microbial degradation (colonization, bio-fragmentation, assimilation, and mineralization), and potential mechanisms of microbial degradation. This study provides a comprehensive understanding of the multifaceted influences affecting the aging and biodegradation mechanisms of PS, thereby contributing valuable insights for the future management of plastic pollution.
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Affiliation(s)
- Dazhuang Dong
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Zhi Guo
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China.
| | - Xue Yang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Yaodan Dai
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
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6
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Zhi Z, Bian Z, Chen Y, Zhang X, Wu Y, Wu H. Horizontal and Vertical Comparison of Microbial Community Structures in a Low Permeability Reservoir at the Local Scale. Microorganisms 2023; 11:2862. [PMID: 38138006 PMCID: PMC10745628 DOI: 10.3390/microorganisms11122862] [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: 10/24/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Petroleum microorganisms play a crucial role in the application of microbial-enhanced oil recovery, and the community structures of petroleum microorganisms have been widely studied. Due to variations in reservoir geological conditions, reservoir microbial communities exhibit unique characteristics. However, previous studies have primarily focused on microbial community changes within a single well, a single block, and before and after water flooding, and thus, cross-horizon and cross-regional comparative studies of in situ microbial communities are lacking. In this study, the 16S rRNA full-length sequencing method was adopted to study bacterial communities in crude oil samples taken from two wells at the same depths (depths of 2425 m and 2412 m) but approximately 20 km apart in the Hujianshan oilfield, located in the Ordos Basin. At the same time, the results were combined with another layer of research data from another article (from a depth of 2140 m). The aim was to compare the differences in the microbial community structures between the oil wells on a horizontal scale and a vertical scale. The results revealed that there were minimal differences in the microbial community structures that were influenced by the horizontal distances within a small range (<20 km), while differences were observed at a larger spatial scale. However, the dominant bacteria (Proteobacteria and Bacteroidetes) in the different oilfields were similar. Vertical depth variations (>300 m) had significant impacts on the communities, and this was mainly controlled by temperature. The greater the depth, the higher formation temperature, leading to an increase in thermophilic and anaerobic bacteria within a community.
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Affiliation(s)
- Zena Zhi
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an 710069, China; (Z.Z.); (Z.B.)
| | - Ziwei Bian
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an 710069, China; (Z.Z.); (Z.B.)
| | - Yuan Chen
- College of Food Science and Technology, Northwest University, Xi’an 710069, China;
| | - Xiangchun Zhang
- College of Biology and Agriculture, Zunyi Normal University, Zunyi 563006, China;
| | - Yifei Wu
- College of Food Science and Technology, Northwest University, Xi’an 710069, China;
| | - Hanning Wu
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an 710069, China; (Z.Z.); (Z.B.)
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Wang J, Wang C, Hu M, Bian L, Qu L, Sun H, Wu X, Ren G. Bacterial co-occurrence patterns are more complex but less stable than archaea in enhanced oil recovery applied oil reservoirs. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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8
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pH and Nitrate Drive Bacterial Diversity in Oil Reservoirs at a Localized Geographic Scale. Microorganisms 2023; 11:microorganisms11010151. [PMID: 36677443 PMCID: PMC9865607 DOI: 10.3390/microorganisms11010151] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Oil reservoirs are one of the most important deep subsurface biospheres. They are inhabited by diverse microorganisms including bacteria and archaea with diverse metabolic activities. Although recent studies have investigated the microbial communities in oil reservoirs at large geographic scales, it is still not clear how the microbial communities assemble, as the variation in the environment may be confounded with geographic distance. In this work, the microbial communities in oil reservoirs from the same oil field were identified at a localized geographic scale. We found that although the injected water contained diverse exogenous microorganisms, this had little effect on the microbial composition of the produced water. The Neutral Community Model analysis showed that both bacterial and archaeal communities are dispersal limited even at a localized scale. Further analysis showed that both pH and nitrate concentrations drive the assembly of bacterial communities, of which nitrate negatively correlated with bacterial alpha diversity and pH differences positively correlated with the dissimilarity of bacterial communities. In contrast, the physiochemical parameters had little effect on archaeal communities at the localized scale. Our results suggest that the assembly of microbial communities in oil reservoirs is scale- and taxonomy-dependent. Our work provides a comprehensive analysis of microbial communities in oil reservoirs at a localized geographic scale, which improves the understanding of the assembly of the microbial communities in oil reservoirs.
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Bedoya K, Niño J, Acero J, Jaimes-Prada R, Cabarcas F, Alzate JF. Metagenomic Analysis of Biocide-Treated Neotropical Oil Reservoir Water Unveils Microdiversity of Thermophile Tepidiphilus. Front Microbiol 2021; 12:741555. [PMID: 34790180 PMCID: PMC8591294 DOI: 10.3389/fmicb.2021.741555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are capable of colonizing extreme environments like deep biosphere and oil reservoirs. The prokaryotes diversity in exploited oil reservoirs is composed of indigenous microbial communities and artificially introduced microbes. In the present work, high throughput sequencing techniques were applied to analyze the microbial community from the injected and produced water in a neotropical hyper-thermophile oil reservoir located in the Orinoquia region of Colombia, South America. Tepidiphilus is the dominant bacteria found in both injection and produced waters. The produced water has a higher microbial richness and exhibits a Tepidiphilus microdiversity. The reservoir injected water is recycled and treated with the biocides glutaraldehyde and tetrakis-hydroxymethyl-phosphonium sulfate (THPS) to reduce microbial load. This process reduces microbial richness and selects a single Tepidiphilus genome (T. sp. UDEAICP_D1) as the dominant isolate. Thermus and Hydrogenobacter were subdominants in both water systems. Phylogenomic analysis of the injection water dominant Tepidiphilus positioned it as an independent branch outside T. succinatimandens and T. thermophilus lineage. Comparative analysis of the Tepidiphilus genomes revealed several genes that might be related to the biocide-resistant phenotype and the tolerance to the stress conditions imposed inside the oil well, like RND efflux pumps and type II toxin-antitoxin systems. Comparing the abundance of Tepidiphilus protein-coding genes in both water systems shows that the biocide selected Tepidiphilus sp. UDEAICP_D1 genome has enriched genes annotated as ABC-2 type transporter, ABC transporter, Methionine biosynthesis protein MetW, Glycosyltransferases, and two-component system NarL.
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Affiliation(s)
- Katherine Bedoya
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia -UdeA, Medellín, Colombia
| | - Jhorman Niño
- Centro de Innovación y Tecnología ICP, Ecopetrol S.A, Gerencia de Operaciones, Bucaramanga, Colombia
| | - Julia Acero
- Centro de Innovación y Tecnología ICP, Ecopetrol S.A, Gerencia de Operaciones, Bucaramanga, Colombia
| | - Ronald Jaimes-Prada
- Centro de Innovación y Tecnología ICP, Ecopetrol S.A, Gerencia de Operaciones, Bucaramanga, Colombia
| | - Felipe Cabarcas
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia -UdeA, Medellín, Colombia.,Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia - UdeA, Medellín, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia -UdeA, Medellín, Colombia
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