scholarly journals Metagenomic Investigation of a Low Diversity, High Salinity Offshore Oil Reservoir

2021 ◽  
Vol 9 (11) ◽  
pp. 2266
Author(s):  
Gabrielle Scheffer ◽  
Casey R. J. Hubert ◽  
Dennis R. Enning ◽  
Sven Lahme ◽  
Jaspreet Mand ◽  
...  
Keyword(s):  
Oil Recovery ◽  
High Salinity ◽  
Extreme Environments ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Oil Reservoir ◽  
Deep Biosphere ◽  
Metabolic Potential ◽  
Microbial Life ◽  
Saline Formation

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.

scholarly journals 16S rRNA Gene Amplicon Sequencing Data of the Iron Quadrangle Ferruginous Caves (Brazil) Shows the Importance of Conserving This Singular and Threatened Geosystem

Diversity ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 494
Author(s):  
Camila G. C. Lemes ◽  
Morghana M. Villa ◽  
Érica B. Felestrino ◽  
Luiza O. Perucci ◽  
Renata A. B. Assis ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Metabolic Potential ◽  
Microbial Life ◽  
Iron Quadrangle ◽  
Abundance And Diversity

The Iron Quadrangle (IQ) is one of the main iron ore producing regions of the world. The exploitation of its reserves jeopardizes the high biological endemism associated with this region. This work aimed to understand the diversity and bacterial potential associated with IQ caves. Floor and ceiling samples of seven ferruginous caves and one quartzite cave were collected, and their microbial relative abundance and diversity were established by 16S rRNA gene amplicon sequencing data. The results showed that ferruginous caves present higher microbial abundance and greater microbial diversity compared to the quartzite cave. Many species belonging to genera found in these caves, such as Pseudonocardia and Streptacidiphilus, are known to produce biomolecules of biotechnological interest as macrolides and polyketides. Moreover, comparative analysis of microbial diversity and metabolic potential in a biofilm in pendant microfeature revealed that the microbiota associated with this structure is more similar to the floor rather than ceiling samples, with the presence of genera that may participate in the genesis of these cavities, for instance, Ferrovum, Geobacter, and Sideroxydans. These results provide the first glimpse of the microbial life in these environments and emphasize the need of conservation programs for these areas, which are under intense anthropogenic exploration.

scholarly journals Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

2021 ◽  
Vol 12 ◽  
Author(s):  
Charles S. Cockell ◽  
Bettina Schaefer ◽  
Cornelia Wuchter ◽  
Marco J. L. Coolen ◽  
Kliti Grice ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Granitic Rocks ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Deep Subsurface ◽  
Cell Biomass ◽  
Colonization Potential ◽  
The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

scholarly journals Bacterial community shift in nutrient-treated oil-bearing sandstones from the subsurface strata of an onshore oil reservoir and its potential use in Microbial Enhanced Oil Recovery

2018 ◽  
Author(s):  
Thanachai Phetcharat ◽  
Pinan Dawkrajai ◽  
Thararat Chitov ◽  
Pisanu Wongpornchai ◽  
Schradh Saenton ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Enhanced Oil Recovery ◽  
Oil Recovery ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Microbial Enhanced Oil Recovery ◽  
Nutrient Treatment ◽  
Chemical Structures

AbstractMicrobial Enhanced Oil Recovery (MEOR) is a promising strategy to improve recovery of residual oil in reservoirs, which can be performed by promoting specific indigenous microorganisms. In this study, bacterial communities and the effects of elemental nutrient treatment of oil-bearing sandstone cores originated from six oil wells of an onshore reservoir was determined by tagged 16S rRNA gene amplicon sequencing, using Ion Torrent Metagenomic Sequencing Analysis. A total number of sequences were taxonomically classified into 43 phyla, 320 families, and 584 genera, with the dominant bacterial populations being related to Deinococcus-Thermus, and Betaproteobacteria. The nutrient treatment resulted in markedly increase in the relative abundance of Gammaproteobacteria. Thermus, Acinetobacter, and Pseudomonas were the most abundant genera. To our knowledge, this is the first report on the effect of elemental nutrients on alteration of bacteria communities attached to the oil-bearing rock. It provides comprehensive data on bacterial, physical, and chemical structures within a reservoir and demonstrates how these parameters can be co-analyzed to serve as a basis for designing a MEOR process. It also provides a model of how a bacterial community in reservoirs’ strata can be altered by nutrient treatment to enhance the efficiency of MEOR applications.

scholarly journals Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
César Ruiz ◽  
Marcela Villegas-Plazas ◽  
Olivier P Thomas ◽  
Howard Junca ◽  
Thierry Pérez
Keyword(s):  
Extreme Environments ◽  
Amplicon Sequencing ◽  
Sponge Species ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
16S Amplicon Sequencing ◽  
Ecological Success ◽  
Specific Community ◽  
First Time ◽  
The 16S Rrna Gene

ABSTRACT The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

scholarly journals Effect of Salinity on the Gut Microbiome of Pike Fry (Esox lucius)

2020 ◽  
Vol 10 (7) ◽  
pp. 2506
Author(s):  
Tomasz Dulski ◽  
Roman Kujawa ◽  
Martyna Godzieba ◽  
Slawomir Ciesielski
Keyword(s):  
Gut Microbiome ◽  
High Salinity ◽  
Fish Farming ◽  
Amplicon Sequencing ◽  
Good Alternative ◽  
Control Group ◽  
Rrna Gene ◽  
Microbiological Analysis ◽  
Early Life Stages ◽  
The Impact

The increasing popularity of pike in angling and fish farming has created a need to increase pike production. However, intensive pike farming is subject to limitations due to diseases and pathogens. Sodium chloride (NaCl) could be a good alternative to chemotherapeutics, especially for protecting the fish against pathogens and parasites at early life stages. However, the impact of high salinity on the symbiotic bacteria inhabiting freshwater fish is still unclear. Therefore, our objective was to analyze the gut microbiome to find possible changes caused by salinity. In this study, the influence of 3‰ and 7‰ salinity on pike fry was investigated. High-throughput 16S rRNA gene amplicon sequencing was used to profile the gut microbiome of the fish. It was found that salinity had a statistically significant influence on pike fry mortality. Mortality was highest in the 7‰ salinity group and lowest in the 3‰ group. Microbiological analysis indicated that Proteobacteria and Actinobacteria predominated in the pike gut microbiome in all examined groups, followed by lower percentages of Bacteroidetes and Firmicutes. There were no statistically significant differences in the percent abundance of bacterial taxa between the control group and groups with a higher salinity. Our results suggest that salinity influences the gut microbiome structure in pike fry, and that 3‰ salinity may be a good solution for culturing pike at this stage in their development.

Genomic insights into the ecological role and evolution of a novel Thermoplasmata order, “ Candidatus Sysuiplasmatales”

2021 ◽  
Author(s):  
Yang Yuan ◽  
Jun Liu ◽  
Tao-Tao Yang ◽  
Shao-Ming Gao ◽  
Bin Liao ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Extreme Environments ◽  
Metabolic Reconstruction ◽  
Rrna Gene ◽  
Ancestral State ◽  
Metabolic Potential ◽  
Facultatively Anaerobic ◽  
Acid Generation ◽  
A Genome ◽  
Evolutionary Paths

Recent omics studies have provided invaluable insights into the metabolic potential, adaptation and evolution of novel archaeal lineages from a variety of extreme environments. We have utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order (“ Candidatus Sysuiplasmatales”) within Thermoplasmata from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene based analyses revealed a narrow habitat range for these uncultured archaea limiting to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain Archaea which typically show obligately anaerobic metabolisms. Notably, “ Ca. Sysuiplasmatales” could conserve energy through degradation of fatty acids, amino acid metabolism and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike its closely related Methanomassiliicoccales and “ Ca. Gimiplasmatales”, “ Ca. Sysuiplasmatales” lack the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that “ Ca. Sysuiplasmatales” and its closely related Methanomassiliicoccales, “ Ca. Gimiplasmatales”, and the SG8-5 and the RBG-16-68-12 orders originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type H 4 F Wood–Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. Importance A wide array of archaea populate Earth’s extreme environments thereby they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited considering the uncultured majority of archaeal diversity. For instance, most order-level lineages except Thermoplasmatales, Aciduliprofundales and Methanomassiliicoccales within Thermoplasmata do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, namely “ Ca . Sysuiplasmatales”, within Thermoplasmata in the extremely acidic mine environments. “ Ca . Sysuiplasmatales” are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between “ Ca . Sysuiplasmatales” and its closely related Thermoplasmata lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.

scholarly journals Sasso Pisano Geothermal Field Environment Harbours Diverse Ktedonobacteria Representatives and Illustrates Habitat-Specific Adaptations

2021 ◽  
Vol 9 (7) ◽  
pp. 1402
Author(s):  
Sania Arif ◽  
Corinna Willenberg ◽  
Annika Dreyer ◽  
Heiko Nacke ◽  
Michael Hoppert
Keyword(s):  
Hot Springs ◽  
Hot Spring ◽  
Amplicon Sequencing ◽  
Heavy Metal Resistance ◽  
18S Rrna Gene ◽  
Metal Resistance ◽  
Geothermal Field ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Eukaryotic Diversity

The hydrothermal steam environment of Sasso Pisano (Italy) was selected to investigate the associated microbial community and its metabolic potential. In this context, 16S and 18S rRNA gene partial sequences of thermophilic prokaryotes and eukaryotes inhabiting hot springs and fumaroles as well as mesophilic microbes colonising soil and water were analysed by high-throughput amplicon sequencing. The eukaryotic and prokaryotic communities from hot environments clearly differ from reference microbial communities of colder soil sites, though Ktedonobacteria showed high abundances in various hot spring samples and a few soil samples. This indicates that the hydrothermal steam environments of Sasso Pisano represent not only a vast reservoir of thermophilic but also mesophilic members of this Chloroflexi class. Metabolic functional profiling revealed that the hot spring microbiome exhibits a higher capability to utilise methane and aromatic compounds and is more diverse in its sulphur and nitrogen metabolism than the mesophilic soil microbial consortium. In addition, heavy metal resistance-conferring genes were significantly more abundant in the hot spring microbiome. The eukaryotic diversity at a fumarole indicated high abundances of primary producers (unicellular red algae: Cyanidiales), consumers (Arthropoda: Collembola sp.), and endoparasite Apicomplexa (Gregarina sp.), which helps to hypothesise a simplified food web at this hot and extremely nutrient-deprived acidic environment.

scholarly journals Genomics and Simulated Laboratory Studies Reveal Thermococcus sp. 101C5 as A Novel Hyperthermophilic Archaeon Possessing Specialized Metabolic Arsenal for Enhanced Oil Recovery from High-Temperature Oil Reservoirs (101 °C)

2021 ◽  
Author(s):  
Neelam G. Kapse ◽  
Vasundhara Paliwal ◽  
Sumit Singh Dagar ◽  
Dolly Pal Rana ◽  
Prashant K Dhakephalkar
Keyword(s):  
High Temperature ◽  
Enhanced Oil Recovery ◽  
Oil Recovery ◽  
Genome Analysis ◽  
Oil Reservoirs ◽  
Laboratory Evaluation ◽  
Oil Reservoir ◽  
Uptake System ◽  
Residual Oil ◽  
Metabolic Potential

Abstract Laboratory evaluation of hyperthermophiles with the potential for Enhanced Oil Recovery (EOR) is often hampered by the difficulties in replicating the in situ growth conditions in the lab. In the present investigation, genome analysis was used to gain insights into the metabolic potential of a hyperthermophile to mobilize the residual oil from depleting high-temperature oil reservoir. Here, we report the 1.9 Mb draft genome sequence of hyperthermophilic anaerobic archaeon, Thermococcus sp. 101C5 with a GC content of 44%, isolated from a high temperature oil reservoir of Gujarat, India. 101C5 possessed the genetic arsenal required for adaptation to harsh oil reservoir conditions, such as various heat shock proteins for thermo-adaptation, Trk potassium uptake system proteins for osmo-adaptation, and superoxide reductases against oxidative stress. MEOR potential of the strain was established by the presence of genes encoding enzymes involved in desired metabolite production like hydrogen, acetate, exopolysaccharide, bio-emulsifier, etc., which was further experimentally confirmed and validated. Also, the presence of crude oil degradative genes highlighted the ability of the strain to mobilize heavy residual oil, which was confirmed under simulated conditions in sand-pack studies. The obtained results demonstrated additional oil recoveries of 42.1% and 56.5% at 96°C and 101°C, respectively, by strain 101C5, illustrating its potential for application in high-temperature oil reservoirs. To our best knowledge, this is the first report of genome analysis of any microbe assessed for its suitability for MEOR from the high-temperature oil reservoir.

scholarly journals Exploring Microbial Biosignatures in Mn-Deposits of Deep Biosphere: A Preliminary Cross-Disciplinary Approach to Investigate Geomicrobiological Interactions in a Cave in Central Italy

2021 ◽  
Vol 9 ◽  
Author(s):  
Ilaria Vaccarelli ◽  
Federica Matteucci ◽  
Marika Pellegrini ◽  
Fabio Bellatreccia ◽  
Maddalena Del Gallo
Keyword(s):  
Manganese Oxides ◽  
Central Italy ◽  
Extreme Environments ◽  
Chemical Characterization ◽  
Biotic Interactions ◽  
Deep Biosphere ◽  
Microbial Life ◽  
Culture Independent ◽  
Manganese Mineralization

The terrestrial subsurface offers privileged sites both to search for microbial life and to observe still mostly unknown characteristic lithologies. In particular, caves represent natural laboratories to investigate unique minerogenetic processes and biotic interactions, connected to these phenomena. Manganese mineralization in cave environments provides a window to understand the complex Mn cycle and the development of microbial communities in special conditions, such as low constant temperature, absence of light and, in particular, low-energy environments. In the current study, we isolated and characterized Mn-samples taken from the cave “Grotta Grande dei Cervi,” L’Aquila, Central Italy, and we used a multidisciplinary approach to characterize them, with the purpose of understanding the biogeochemical processes in extreme environments. A chemical characterization of the samples was done by EDS; further investigations are underway with other multidisciplinary methodologies to understand whether the Mn laminae are related to biological processes. SEM investigations revealed microbial imprints, showing cell-like structures and suggesting that the cell-like shapes occur within internal laminae. A culture-independent approach was used to assess the possibility that biotic factors may be involved in the production of these mineralizations and to investigate the nature of the microbial community in these materials. A molecular approach was the first step to investigate the role of microorganisms in forming manganese oxides associated with water bearing rocks. DNA from the black deposits was extracted and sequence analyses of specimens were performed. Our data support the hypothesis that microorganisms may contribute to the mineralizations of manganese in this environment, providing new encouraging insight into the role of microorganisms in the Mn cycle and the processes of energy acquisition in unfavorable conditions, with relevant implications for astrobiology.

Novel Enhanced Oil Recovery Method Using Co2+xFe2+1-xFe3+2O4 as Magnetic Nanoparticles Activated by Electromagnetic Waves

2013 ◽  
Vol 26 ◽  
pp. 111-116 ◽  
Author(s):  
Hasan Soleimani ◽  
Noorhana Yahya ◽  
Noor Rasyada Ahmad Latiff ◽  
Hasnah Mohd Zaid ◽  
Birol Demiral ◽  
...  
Keyword(s):  
Magnetic Nanoparticles ◽  
Enhanced Oil Recovery ◽  
Oil Recovery ◽  
Electromagnetic Waves ◽  
High Salinity ◽  
Harsh Environment ◽  
Oil Reservoir ◽  
Core Flooding ◽  
Recovery Method ◽  
High Pressure And Temperature

Research on the application of nanoparticles, specifically magnetic nanoparticles in enhanced oil recovery has been increasing in recent years due to their potential to increase the oil production despite having to interact with reservoirs of high salinity, high pressure and temperature and un-natural pH. Unlike other conventional EOR agents e.g. surfactants and polymers, a harsh environment will cause degradation and failure to operate. Magnetic nanoparticles which are activated by a magnetic field are anticipated to have the ability to travel far into the oil reservoir and assist in the displacement of the trapped oil. In this work, ferromagnetic Co2+xFe2+1-xFe3+2O4 nanoparticles were synthesized and characterized for their morphological, structural and magnetic properties. At a composition x = 0.75, this nanomaterial shows its best magnetisation parameters i.e. highest value of saturation magnetization, remanence and coercivity of 65.23 emu/g, 12.18 emu/g and 239.10 Oe, respectively. Subsequently, a dispersion of 0.01 wt% Co2+0.75Fe2+0.25Fe3+2O4 nanoparticles in distilled water was used for core flooding test to validate its feasibility in enhanced oil recovery. In a core flooding test, the effect of electromagnetic waves irradiation to activate the magnetization of Co2+0.75Fe2+0.25Fe3+2O4 nanofluid was also investigated by irradiating a 78 MHz square wave to the porous medium while nanofluid injection was taking place. In conclusion, an almost 20% increment in the recovery of oil was obtained with the application of electromagnetic waves in 2 pore volumes injection of a Co2+0.75Fe2+0.25Fe3+2O4 nanofluid.

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