Analysis of bacterial diversity in two oil blocks from two low-permeability reservoirs with high salinities

Horizontal and Vertical Comparison of Microbial Community Structures in a Low Permeability Reservoir at the Local Scale

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.

Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential

The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis.

Bacterial and Archaeal Community Distribution in Oilfield Water Re-injection Facilities and the Influences from Microorganisms in Injected Water

Water flooding is widely employed for oil production worldwide. However, there has never been a systematic investigation of the microbial communities occurring in oilfield water re-injection facilities. Here, we investigated the distribution of bacterial and archaeal communities in water re-injection facilities of an oilfield, and illustrated the combined influences of environmental variation and the microorganisms in injected water on the microbial communities. Bacterial communities from the surface injection facilities were dominated by aerobic or facultative anaerobic Betaproteobacteria, Alphaproteobacteria, and Flavobacteria, whereas Clostridia, Deltaproteobacteria, Anaerolineae, and Synergistia predominated in downhole of the injection wells, and Gammaproteobacteria, Betaproteobacteria, and Epsilonproteobacteria predominated in the production wells. Methanosaeta, Methanobacterium, and Methanolinea were dominant archaea in the injection facilities, while Methanosaeta, Methanomethylovorans, and Methanoculleus predominated in the production wells. This study also demonstrated that the microorganisms in injected water could be easily transferred from injection station to wellheads and downhole of injection wells, and environmental variation and diffusion-limited microbial transfer resulted from formation filtration were the main factors determining microbial community assembly in oil-bearing strata. The results provide novel information on the bacterial and archaeal communities and the underlying mechanisms occurring in oilfield water re-injection facilities, and benefit the development of effective microbiologically enhanced oil recovery and microbiologically prevented reservoir souring programs.

Biosurfactant production by Bacillus subtilis SL and its potential for enhanced oil recovery in low permeability reservoirs

Microbial enhanced oil recovery (MEOR) technology is an environmental-friendly EOR method that utilizes the microorganisms and their metabolites to recover the crude oil from reservoirs. This study aims to research the potential application of strain SL in low permeability reservoirs. Strain SL is identified as Bacillus subtilis by molecular methods. Based on the mass spectrometry, the biosurfactant produced by strain SL is characterized as lipopeptide, and the molecular weight of surfactin is 1044, 1058, 1072, 1084 Da. Strain SL produces 1320 mg/L of biosurfactant with sucrose as the sole carbon source after 72 h. With the production of biosurfactant, the surface tension of cell-free broth considerably decreases to 25.65 ± 0.64 mN/m and the interfacial tension against crude oil reaches 0.95 ± 0.22 mN/m. The biosurfactant exhibits excellent emulsification with crude oil, kerosene, octane and hexadecane. In addition, the biosurfactant possesses splendid surface activity at pH 5.0–12.0 and NaCl concentration of 10.0% (w/v), even at high temperature of 120 °C. The fermentation solution of strain SL is applied in core flooding experiments under reservoir conditions and obtains additional 5.66% of crude oil. Hence, the presented strain has tremendous potential for enhancing the oil recovery from low-permeability reservoirs.

Alleviation of Salt Stress via Habitat-Adapted Symbiosis

Halotolerant plant-growth-promoting rhizobacteria (PGPR) could not only promote plant growth, but also help in counteracting the detrimental effects of salt stress. In the present study, a total of 76 bacteria were isolated from the rhizosphere, non-rhizospheric soil and endophytes of the halophyte Salsola tetrandra, collected from natural saline soils in Algeria. Phylogenetic analysis based on the 16S rDNA sequence of Gram-negative bacteria (n = 51) identified, showed seventeen representative isolates grouped into four genera (Pseudomonas, Acinetobacter, Enterobacter, and Providencia). These bacterial isolates that exhibited different PGPR traits were selected and tested for their ability to tolerate different abiotic stress (NaCl, PEG8000, and pH). The majority of isolates were drought tolerant (60% of PEG8000) and had an optimal growth at high pH values (pH 9 and 11) and some strains tolerated 2 M of NaCl. Strains identified as Enterobacter xiangfangensis BE1, Providencia rettgeri BR5 and Pseudomonas stutzeri MLR6 showed high capacity of adaptation on their PGP traits. The salt-tolerant isolates were finally chosen to promote growth and enhance salt tolerance, separately or combined, of Arabidopsis thaliana (Col-0) exposed or not to 0.1 M NaCl, by following fresh and root weight, primary root elongation and lateral root number. The best bacterial effect was recorded for the MLR6 strain in increasing shoot fresh weight and for BE1 in terms of root fresh weight in the absence of salt stress. At stressed conditions, all growth parameters declined. However, inoculation of Arabidopsis thaliana with the three bacterial strains (MLR6, BE1 and BR5), single or in co-culture, conferred an increase in the shoot weight, primary root length and lateral root number. The use of these strains separately or combined as biofertilizers seems to be a powerful tool in the development of sustainable agriculture in saline soils.

Culturable Bacterial Community on Leaves of Assam Tea (Camellia sinensis var. assamica) in Thailand and Human Probiotic Potential of Isolated Bacillus spp

Assam tea plants (Camellia sinensis var. assamica) or Miang are found in plantations and forests of Northern Thailand. Leaf fermentation has been performed for centuries, but little information is available about their associated microbial community. One hundred and fifty-seven bacterial isolates were isolated from 62 Assam tea leaf samples collected from 6 provinces of Northern Thailand and classified within the phyla of Firmicutes, Actinobacteria, and Proteobacteria. Phayao and Phrae provinces exhibited the highest and the lowest bacterial diversities, respectively. The bacterial community structural pattern demonstrated significant differences between the west and the east sides. Since some Bacillus spp. have been reported to be involved in fermented Miang, Bacillus spp. isolated in this study were chosen for further elucidation. Bacillus siamensis ML122-2 exhibited a growth inhibitory effect against Staphylococcus aureus ATCC 25923 and MRSA DMST 20625, and the highest survival ability in simulated gastric and intestinal fluids (32.3 and 99.7%, respectively), autoaggregation (93.2%), cell surface hydrophobicity (50.0%), and bacterial adherence with Vero cells (75.8% of the control Lactiplantibacillusplantarum FM03-1). This B. siamensis ML122-2 is a promising probiotic to be used in the food industry and seems to have potential antibacterial properties relevant for the treatment of antibiotic-resistant infections.

Densely Populated Water Droplets in Heavy-Oil Seeps

Most of the microbial degradation in oil reservoirs is believed to take place at the oil-water transition zone (OWTZ). However, a recent study indicates that there is microbial life enclosed in microliter-sized water droplets dispersed in heavy oil of Pitch Lake in Trinidad and Tobago. This life in oil suggests that microbial degradation of oil also takes place in water pockets in the oil-bearing rock of an oil leg independent of the OWTZ. However, it is unknown whether microbial life in water droplets dispersed in oil is a generic property of oil reservoirs rather than an exotic exception. Hence, we took samples from three heavy-oil seeps, Pitch Lake (Trinidad and Tobago), the La Brea Tar Pits (California, USA), and an oil seep on the McKittrick oil field (California, USA). All three tested oil seeps contained dispersed water droplets. Larger droplets between 1 and 10 μl revealed high cell densities of up to 10⁹ cells ml^-1 Testing for ATP content and LIVE/DEAD staining showed that these populations consist of active and viable microbial cells with an average of 60% membrane-intact cells and ATP concentrations comparable to those of other subsurface ecosystems. Microbial community analyses based on 16S rRNA gene amplicon sequencing revealed the presence of known anaerobic oil-degrading microorganisms. Surprisingly, the community analyses showed similarities between all three oil seeps, revealing common OTUs, although the sampling sites were thousands of kilometers apart. Our results indicate that small water inclusions are densely populated microhabitats in heavy oil and possibly a generic trait of degraded-oil reservoirs.IMPORTANCE Our results confirmed that small water droplets in oil are densely populated microhabitats containing active microbial communities. Since these microhabitats occurred in three tested oil seeps which are located thousands of kilometers away from each other, such populated water droplets might be a generic trait of biodegraded oil reservoirs and might be involved in the overall oil degradation process. Microbial degradation might thus also take place in water pockets in the oil-bearing oil legs of the reservoir rock rather than only at the oil-water transition zone.

Occurrence of antibiotic resistance genes in an oilfield's water re-injection systems

The recent widespread increase in antibiotic resistance has become a real threat to both human and environmental ecosystem health. In oil reservoirs, an extreme environment potentially influenced by human activity such as water flooding, the distribution and abundance of antibiotic resistance genes (ARGs) remains poorly understood. Herein, we investigated the distribution of ARGs at different positions in a water-flooding oilfield in China, and found that ARGs were observed in all parts of the investigated system. The surface regions of the water re-injection system were more vulnerable to ARG pollution, and the final ARG concentration was up to 2.2 × 10⁸ gene copies/L, and sulfonamide were the most abundant. However, ARG concentration decreased sharply in the samples from underground part of the re-injection system. The bacterial community composition was also varied with sampling position. The sample from production well, which was enriched in crude oil, contained more bacteria but the community richness was simpler. This study also indicated the wastewater-recycling process above ground, which proposed to reduce the discharge into environment directly, may pose a risk for ARGs spread.

Isolation and Characterization of Biosurfactant-Producing Bacteria From Oil Well Batteries With Antimicrobial Activities Against Food-Borne and Plant Pathogens

Microbial biosurfactants, produced by fungi, yeast, and bacteria, are surface-active compounds with emulsifying properties that have a number of known activities, including the solubilization of microbial biofilms. In an on-going survey to uncover new or enhanced antimicrobial metabolite-producing microbes from harsh environments, such as oil-rich niches, 123 bacterial strains were isolated from three oil batteries in the region of Chauvin, Alberta, and characterized by 16S rRNA gene sequencing. Based on their nucleotide sequences, the strains are associated with 3 phyla (Actinobacteria, Proteobacteria and Firmicutes), as well as 17 other discrete genera that shared high homology with known sequences, with the majority of these strains identified to the species level. The most prevalent strains associated with the three oil wells belonged to the Bacillus genus. Thirty-four of the 123 strains were identified as biosurfactant-producers, among which Bacillus methylotrophicus strain OB9 exhibited the highest biosurfactant activity based on multiple screening methods and a comparative analysis with the commercially available biosurfactant, Tween 20. B. methylotrophicus OB9 was selected for further antimicrobial analysis and addition of live cultures of B. methylotrophicus OB9 (or partially purified biosurfactant fractions thereof) were highly effective on biofilm disruption in agar diffusion assays against several Gram-negative food-borne bacteria and plant pathogens. Upon co-culturing with B. methylotrophicus OB9, the number of either Salmonella enterica subsp. enterica Newport SL1 or Xanthomonas campestris B07.007 cells significantly decreased after 6 h and were not retrieved from co-cultures following 12 h exposure. These results also translated to studies on plants, where bacterized tomato seedlings with OB9 significantly protected the tomato leaves from Salmonella enterica Newport SL1 contamination, as evidenced by a 40% reduction of log10 CFU of Salmonella/mg leaf tissue compared to non-bacterized tomato leaves. When B. methylotrophicus 0B9 was used for bacterized lettuce, the growth of X. campestris B07.007, the causal agent of bacterial leaf spot of lettuce, was completely inhibited. While limited, these studies are noteworthy as they demonstrate the inhibition spectrum of B. methylotrophicus 0B9 against both human and plant pathogens; thereby making this bacterium attractive for agricultural and food safety applications in a climate where microbial-biofilm persistence is an increasing problem.

Analysis of Bacterial Diversity in Different Heavy Oil Wells of a Reservoir in South Oman with Alkaline pH

The identification of potential hydrocarbon utilizing bacteria is an essential requirement in microbial enhanced oil recovery (MEOR). Molecular approaches like proteomic and genomic characterization of the isolates are replacing the traditional method of identification with systemic classification. Genotypic profiling of the isolates includes fingerprint or pattern-based technique and sequence-based technique. Understanding community structure and dynamics is essential for studying diversity profiles and is challenging in the case of microbial analysis. The present study aims to understand the bacterial community composition from different heavy oil contaminated soil samples collected from geographically related oil well areas in Oman and to identify spore-forming hydrocarbon utilizing cultivable bacteria. V4 region of 16S rDNA gene was the target for Ion PGM™. A total of 825081 raw sequences were obtained from Ion torrent from all the 10 soil samples. The species richness and evenness were found to be moderate in all the samples with four main phyla, Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, the most abundant being Firmicutes. Bacillus sp. ubiquitously dominated in all samples followed by Paenibacillus, which was followed by Brevibacillus, Planococcus, and Flavobacterium. Principal Coordinate Analysis (PCoA) and UPGMA dendrogram clustered the 10 soil samples into four main groups. Weighted UniFrac significance test determined that there was significant difference in the communities present in soil samples examined. It can be concluded that the microbial community was different in all the 10 soil samples with Bacillus and Paenibacillus sp. as predominating genus. The 16S rDNA sequencing of cultivable spore-forming bacteria identified the hydrocarbon utilizing bacteria as Bacillus and Paenibacillus sp. and the nucleotide sequences were submitted to NCBI GenBank under accession numbers KP119097-KP119115. Bacillus and Paenibacillus sp., which were relatively abundant in the oil fields, can be recommended to be chosen as candidates for hydrocarbon utilization study.

Application of an in-situ soil sampler for assessing subsurface biogeochemical dynamics in a diesel-contaminated coastal site during soil flushing operations

Subsurface biogeochemistry and contaminant dynamics during the remediation of diesel-contamination by in-situ soil flushing were investigated at a site located in a coastal region. An in-situ sampler containing diesel-contaminated soils separated into two size fractions (<0.063- and <2-mm) was utilized in two monitoring wells: DH1 (located close to the injection and extraction wells for in-situ soil flushing) and DH2 (located beyond sheet piles placed to block the transport of leaked diesel). Total petroleum hydrocarbon (TPH) concentrations and biogeochemical properties were monitored both in soil and groundwater for six months. A shift occurred in the groundwater type from Ca-HCO₃ to Na-Cl due to seawater intrusion during intense pumping, while the concentrations of Ni, Cu, Co, V, Cr, and Se increased substantially following surfactant (TWEEN 80) injection. The in-situ sampler with fine particles was more sensitive to variations in conditions during the remedial soil flushing process. In both wells, soil TPH concentrations in the <0.063-mm fraction were much higher than those in the <2-mm fraction. Increases in soil TPH in DH1 were consistent with the expected outcomes following well pumping and surfactant injection used to enhance TPH extraction. However, the number of diesel-degrading microorganisms decreased after surfactant injection. 16S-rRNA gene-based analysis also showed that the community composition and diversity depended on both particle size and diesel contamination. The multidisciplinary approach to the contaminated site assessments showed that soil flushing with surfactant enhanced diesel extraction, but negatively impacted in-situ diesel biodegradation as well as groundwater quality. The results also suggest that the in-situ sampler can be an effective monitoring tool for subsurface biogeochemistry as well as contaminant dynamics.

Biostimulation of indigenous microorganisms for bioremediation of oily hypersaline microcosms from the Arabian Gulf Kuwaiti coasts

Hypersaline soil and water samples were collected in summer and winter from the "sabkha" area at the Kuwaiti shore of the Arabian Gulf. Physicochemical parameters were analyzed, and found suitable for microbial oil-removal. Summer- and winter-microcosms were treated with individual cation (K⁺, Ca²⁺, Mg²⁺, Fe³⁺) salts, and with animal blood and commercial yeast, as cost-effective vitamin sources. Those microcosms were exposed to the open environment for six winter and six summer months, and analyzed for their hydrocarbonoclastic microorganisms at time zero and in two month intervals. The hydrocarbonoclastic microbial communities in the microcosms consisted of halophilic bacteria and haloarchaea. The constituent bacterial species varied according to the season. Three species, Dietzia kunjamensis, Marinobacter lacisalsi and Halomonas oxialensis consistently occurred both in summer- and winter-samples, but the remaining species were different. On the other hand, the haloarchaeal communities in summer and winter were quite similar, and consisted mainly of Haloferax spp and Halobacterium spp. Treating the microcosms with cations and with vitamin-containing natural products enhanced microbial numbers and oil-removal. The effectiveness of the cations in oil-removal was in the order; Fe³⁺ (94%) > Ca²⁺ (89%) > Mg²⁺ (85%) > K⁺ (82%). Thus, oily microcosms amended with trivalent and divalent cations lost most of the oil, and those amended with commercial yeast and with animal blood, as vitamin sources, lost 78% and 72% oil, respectively.

Compositions and Abundances of Sulfate-Reducing and Sulfur-Oxidizing Microorganisms in Water-Flooded Petroleum Reservoirs with Different Temperatures in China

Sulfate-reducing bacteria (SRB) have been studied extensively in the petroleum industry due to their role in corrosion, but very little is known about sulfur-oxidizing bacteria (SOB), which drive the oxidization of sulfur-compounds produced by the activity of SRB in petroleum reservoirs. Here, we surveyed the community structure, diversity and abundance of SRB and SOB simultaneously based on 16S rRNA, dsrB and soxB gene sequencing, and quantitative PCR analyses, respectively in petroleum reservoirs with different physicochemical properties. Similar to SRB, SOB were found widely inhabiting the analyzed reservoirs with high diversity and different structures. The dominant SRB belonged to the classes Deltaproteobacteria and Clostridia, and included the Desulfotignum, Desulfotomaculum, Desulfovibrio, Desulfobulbus, and Desulfomicrobium genera. The most frequently detected potential SOB were Sulfurimonas, Thiobacillus, Thioclava, Thiohalomonas and Dechloromonas, and belonged to Betaproteobacteria, Alphaproteobacteria, and Epsilonproteobacteria. Among them, Desulfovibrio, Desulfomicrobium, Thioclava, and Sulfurimonas were highly abundant in the low-temperature reservoirs, while Desulfotomaculum, Desulfotignum, Thiobacillus, and Dechloromonas were more often present in high-temperature reservoirs. The relative abundances of SRB and SOB varied and were present at higher proportions in the relatively high-temperature reservoirs. Canonical correspondence analysis also revealed that the SRB and SOB communities in reservoirs displayed high niche specificity and were closely related to reservoir temperature, pH of the formation brine, and sulfate concentration. In conclusion, this study extends our knowledge about the distribution of SRB and SOB communities in petroleum reservoirs.

Bacterias hidrocarburoclásticas del género Pseudomonas en la rizosfera de Samanea saman (Jacq.) Merr

El objetivo de esta investigación incluye el aislamiento, caracterización e identificación de las especies de Pseudomonas existentes en la rizosfera de una leguminosa presente (colonizadora o sobreviviente) en un suelo de sabana contaminado por un derrame de petróleo con el fin de explicar el apoyo al crecimiento de esta leguminosa a través de la reducción de la toxicidad del crudo derramado (efectos hidrocarburoclásticos) El sitio se encuentra a la  entrada del pueblo de Amana del Tamarindo, estado Monagas, Venezuela (9° 38' 52" N, 63° 7' 20'' E, 46 msnm). Se muestreó un área de 50 m2.  Según las descripciones, claves y comparación con las exsiccatae del herbario UOJ, la leguminosa colectada fue identificada como Samanea saman (Jacq.) Merr., la cual pertenece a la Familia Fabaceae. Los resultados de la caracterización bioquímica y la producción de los pigmentos piocianina y fluoresceína permitieron identificar diez aislados como P. fluorescens, 5 como P. putida y 5 como P. aeruginosa. Se recomienda la revegetación con S. saman del área contaminada.