High coverage sequencing of DNA from microorganisms living in an oil reservoir 2.5 kilometres subsurface

Insights into the effects of anthropogenic activities on oil reservoir microbiome and metabolic potential

Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore, anthropogenic activities such as water flooding during oil production can affect microbial activities and community compositions in oil reservoirs through the injection of recycled produced water, often associated with biocides. However, it is still unclear to what extent the introduced chemicals and microbes influence the metabolic potential of the subsurface microbiome. Here we investigated an onshore oilfield in Germany (Field A) that undergoes secondary oil production along with biocide treatment to prevent souring and microbially induced corrosion (MIC). With the integrated approach of 16 S rRNA gene amplicon and shotgun metagenomic sequencing of water-oil samples from 4 production wells and 1 injection well, we found differences in microbial community structure and metabolic functions. In the injection water samples, amplicon sequence variants (ASVs) belonging to families such as Halanaerobiaceae, Ectothiorhodospiraceae, Hydrogenophilaceae, Halobacteroidaceae, Desulfohalobiaceae, and Methanosarcinaceae were dominant, while in the production water samples, ASVs of families such as Thermotogaceae, Nitrospiraceae, Petrotogaceae, Syntrophaceae, Methanobacteriaceae, and Thermoprotei were also dominant. The metagenomic analysis of the injection water sample revealed the presence of C1-metabolism, namely, genes involved in formaldehyde oxidation. Our analysis revealed that the microbial community structure of the production water samples diverged slightly from that of injection water samples. Additionally, a metabolic potential for oxidizing the applied biocide clearly occurred in the injection water samples indicating an adaptation and buildup of degradation capacity or resistance against the added biocide.

pH and Nitrate Drive Bacterial Diversity in Oil Reservoirs at a Localized Geographic Scale

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.

Groups of Geomicrobiological Indicators Are Spread across Gas-Hydrate and Non-Gas-Hydrate Areas in the Northern Part of the Sea of Japan

The bioindication of oil and gas fields is a field of geomicrobiology that is mainly devoted to the detection of hydrocarbon-oxidizing microbial indicator species or functional genes in total DNA. However, it appears promising to use the physiological properties of microorganisms detection deposit type of hydrocarbons, in particular their ability to oxidize hydrocarbons under aerobic and anaerobic conditions. In this study, the most promising approach in this area was the method used for assessing the anaerobic degradation of hydrocarbons. When comparing molecular genetics and cultured methods of bioindication, it can be concluded that molecular biomarkers of functional genes for the anaerobic destruction of hydrocarbons (masD) make it possible to separate areas with traditional and gas-hydrate types of deposits. Using cultured methods, we found that representatives of the Nocardiaceae family of the phylum Actinomycetota were tied to the areas where gas hydrates were found. The ability of aerobic and facultative anaerobic hydrocarbon-oxidizing microorganisms to anaerobically utilize hydrocarbons was determined with cultured methods. For the first time, this ability was revealed for the genera Stenotrophomonas, Psychrobacter, Micrococcus and Peribacillus. The wide distribution of this ability that we found in strains isolated from both study regions suggests its prominent role in the destruction of hydrocarbons in marine sediments.

Flow-based method for biofilm microbiota enrichment and exploration of metagenomes

Most bacteria live in biofilms in their natural habitat rather than the planktonic cell stage that dominates during traditional laboratory cultivation and enrichment schemes. The present study describes the establishment of a flow-based enrichment method based on multispecies biofilm communities for directing biofilm functionality using an environmental inoculum. By controlling flow conditions and physio-chemical properties, the set-up aims to simulate natural conditions ex situ for biofilm formation. The functionality of the method was demonstrated by enrichment of biofilm microbiomes using consortia from a warm compost pile and industrial waste materials as growth substrate, and further exploring the metagenomes by biotechnological tools. The 16S rRNA gene sequencing results revealed a difference in consortium composition and especially in genus abundance, in flow experiments compared to traditional liquid-shake experiments after enrichment, indicating good biofilm development and increased abundance of biofilm-forming taxa. The shotgun sequence mining demonstrated that different enzymes classes can be targeted by enriching biofilms on different substrates such as oat husk, pine saw dust, and lignin. The flow-based biofilm method is effective in reducing bacterial consortia complexity and in selecting biofilm-forming bacteria, and it is possible to enrich the biofilm community in various directions based on the choice of sample material, environmental conditions, and nutritional preferences, targeting enzymes or enzyme classes of industrial interest.

Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide

Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with a lower level of intervention were the most similar to the potential functional core, while the oil fields with a long history of water injection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical transformations in these ecosystems.

Microbial Involvement in Carbon Transformation via CH4 and CO2 in Saline Sedimentary Pool

Simple Summary

Methane and carbon dioxide are commonly found in the environment and are considered the most important greenhouse gases. Transformation of these gases is in large carried by microorganisms, which occur even in extreme environments. This study presents methane-related biological processes in saline sediments of the Miocene Wieliczka Formation, Poland. Biological activity (carbon dioxide and methane production or methane oxidation), confirmed by stable isotope indices, occurred in all of the studied Wieliczka rocks. CH₄-utilizing microbes constituted 0.7–3.6% while methanogens (represented by Methanobacterium) only 0.01–0.5% of taxa present in the Wieliczka Salt Mine rocks. Water activity was the key factor regulating microbial activity in saline subsurface sediments. Generally, CO₂ respiration was higher in anaerobic conditions while methanogenic and methanotrophic activities were dependent on the type of rock.

Abstract

Methane and carbon dioxide are one of the most important greenhouse gases and significant components of the carbon cycle. Biogeochemical methane transformation may occur even in the extreme conditions of deep subsurface ecosystems. This study presents methane-related biological processes in saline sediments of the Miocene Wieliczka Formation, Poland. Rock samples (W2, W3, and W4) differed in lithology (clayey salt with veins of fibrous salt and lenses of gypsum and anhydrite; siltstone and sandstone; siltstone with veins of fibrous salt and lenses of anhydrite) and the accompanying salt type (spiza salts or green salt). Microbial communities present in the Miocene strata were studied using activity measurements and high throughput sequencing. Biological activity (i.e., carbon dioxide and methane production or methane oxidation) occurred in all of the studied clayey salt and siltstone samples but mainly under water-saturated conditions. Microcosm studies performed at elevated moisture created more convenient conditions for the activity of both methanogenic and methanotrophic microorganisms than the intact sediments. This points to the fact that water activity is an important factor regulating microbial activity in saline subsurface sediments. Generally, respiration was higher in anaerobic conditions and ranged from 36 ± 2 (W2_200%t.w.c) to 48 ± 4 (W3_200%t.w.c) nmol CO₂ gdw⁻¹ day⁻¹. Methanogenic activity was the highest in siltstone and sandstone (W3, 0.025 ± 0.018 nmol CH₄ gdw⁻¹ day⁻¹), while aerobic methanotrophic activity was the highest in siltstone with salt and anhydrite (W4, 220 ± 66 nmol CH₄ gdw⁻¹ day⁻¹). The relative abundance of CH₄-utilizing microorganisms (Methylomicrobium, Methylomonas, Methylocystis) constituted 0.7–3.6% of all taxa. Methanogens were represented by Methanobacterium (0.01–0.5%). The methane-related microbes were accompanied by a significant number of unclassified microorganisms (3–64%) and those of the Bacillus genus (4.5–91%). The stable isotope composition of the CO₂ and CH₄ trapped in the sediments suggests that methane oxidation could have influenced δ¹³C_CH4, especially in W3 and W4.

Thermodynamically favorable reactions shape the archaeal community affecting bacterial community assembly in oil reservoirs

Microbial community assembly mechanisms are pivotal for understanding the ecological functions of microorganisms in biogeochemical cycling in Earth's ecosystems, yet rarely investigated in the context of deep terrestrial ecology. Here, the microbial communities in the production waters collected from water injection wells and oil production wells across eight oil reservoirs throughout northern China were determined and analyzed by proportional distribution analysis and null model analysis. A 'core' microbiota consisting of three bacterial genera, including Arcobacter, Pseudomonas and Acinetobacter, and eight archaeal genera, including Archaeoglobus, Methanobacterium, Methanothermobacter, unclassified Methanobacteriaceae, Methanomethylovorans, Methanoculleus, Methanosaeta and Methanolinea, was found to be present in all production water samples. Canonical correlation analysis reflected that the core archaea were significantly influenced by temperature and reservoir depth, while the core bacteria were affected by the combined impact of the core archaea and environmental factors. Thermodynamic calculations indicate that bioenergetic constraints are the driving force that governs the enrichment of two core archaeal guilds, aceticlastic methanogens versus hydrogenotrophic methanogens, in low- and high-temperature oil reservoirs, respectively. Collectively, our study indicates that microbial community structures in wells of oil reservoirs are structured by the thermodynamic window of opportunity, through which the core archaeal communities are accommodated directly followed by the deterministic recruiting of core bacterial genera, and then the stochastic selection of some other microbial members from local environments. Our study enhances the understanding of the microbial assembly mechanism in deep terrestrial habitats. Meanwhile, our findings will support the development of functional microbiota used for bioremediation and bioaugmentation in microbial enhanced oil recovery.

Sulfate reducing microorganisms in high temperature oil reservoirs

High temperature reservoirs offer a window into the microbial life of the deep biosphere. Sulfate reducing microorganisms have been recovered from high temperature oil reservoirs around the globe and characterized using culture-dependent and culture-independent approaches. The activities of sulfate reducers contribute to reservoir souring and hydrocarbon degradation among other attracting considerable interest from the oil industry for the last 100 years. The extremes of temperature and pressure shape the activities and distribution of sulfate reducing bacteria and archaea in high temperature reservoirs. This chapter will attempt to summarize the key findings on the diversity and activities of sulfate reducing microorganisms in high temperature reservoirs.

Responses to the Hydrostatic Pressure of Surface and Subsurface Strains of Pseudothermotoga elfii Revealing the Piezophilic Nature of the Strain Originating From an Oil-Producing Well

Microorganisms living in deep-oil reservoirs face extreme conditions of elevated temperature and hydrostatic pressure. Within these microbial communities, members of the order Thermotogales are predominant. Among them, the genus Pseudothermotoga is widespread in oilfield-produced waters. The growth and cell phenotypes under hydrostatic pressures ranging from 0.1 to 50 MPa of two strains from the same species originating from subsurface, Pseudothermotoga elfii DSM9442 isolated from a deep African oil-producing well, and surface, P. elfii subsp. lettingae isolated from a thermophilic sulfate-reducing bioreactor, environments are reported for the first time. The data support evidence for the piezophilic nature of P. elfii DSM9442, with an optimal hydrostatic pressure for growth of 20 MPa and an upper limit of 40 MPa, and the piezotolerance of P. elfii subsp. lettingae with growth occurring up to 20 MPa only. Under the experimental conditions, both strains produce mostly acetate and propionate as volatile fatty acids with slight variations with respect to the hydrostatic pressure for P. elfii DSM9442. The data show that the metabolism of P. elfii DSM9442 is optimized when grown at 20 MPa, in agreement with its piezophilic nature. Both Pseudothermotoga strains form chained cells when the hydrostatic pressure increases, especially P. elfii DSM9442 for which 44% of cells is chained when grown at 40 MPa. The viability of the chained cells increases with the increase in the hydrostatic pressure, indicating that chain formation is a protective mechanism for P. elfii DSM9442.

Methanogens Within a High Salinity Oil Reservoir From the Gulf of Mexico

Oil reservoirs contain microbial populations that are both autochthonously and allochthonously introduced by industrial development. These microbial populations are greatly influenced by external factors including, but not limited to, salinity and temperature. In this study, we used metagenomics to examine the microbial populations within five wells of the same hydrocarbon reservoir system in the Gulf of Mexico. These elevated salinity (149–181 ppt salinity, 4–5× salinity of seawater) reservoirs have limited taxonomic and functional microbial diversity dominated by methanogens, Halanaerobium and other Firmicutes lineages, and contained less abundant lineages such as Deltaproteobacteria. Metagenome assembled genomes (MAGs) were generated and analyzed from the various wells. Methanogen MAGs were closely related to Methanohalophilus euhalobius, a known methylotrophic methanogen from a high salinity oil environment. Based on metabolic reconstruction of genomes, the Halanaerobium perform glycine betaine fermentation, potentially produced by the methanogens. Industrial introduction of methanol to prevent methane hydrate formation to this environment is likely to be consumed by these methanogens. As such, this subsurface oil population may represent influences from industrial processes.

Characterization and efficient production of a thermostable, halostable and organic solvent-stable cellulase from an oil reservoir

The manufacture of biofuels from cellulose is regarded as one of practicable strategies to meet increasing energy demand and alleviate environmental issues. Cellulases, which play an important role in the production of second-generation biofuels, are expected to be highly thermostable, halostable and organic solvent-stable to adapt to the harsh conditions in practical application. Here we cloned and characterized a novel cellulase (MaCel) from Mahella australiensis 50-1 BON, an anaerobic thermophile isolated from an oil reservoir. MaCel exhibited excellent thermostability, halostability as well as organic solvent stability, and could be efficiently produced in a yield of 1.7 × 10⁶ U/L in 15 h with inexpensive culture medium. These results indicate that MaCel may be a suitable candidate for industrial applications, illustrating the potential benefits of enzymes from oil reservoir extremophiles in the manufacture of biofuels.

In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs

Microbial biodegradation of hydrocarbons in petroleum reservoirs has major consequences in the petroleum value and quality. The identification of microorganisms capable of in-situ degradation of hydrocarbons under the reservoir conditions is crucial to understand microbial roles in hydrocarbon transformation and the impact of oil exploration and production on energy resources. The aim of this study was to profile the metagenome of microbial communities in crude oils and associated formation water from two high temperature and relatively saline oil-production wells, where one has been subjected to water flooding (BA-2) and the other one is considered pristine (BA-1). The microbiome was studied in the fluids using shotgun metagenome sequencing. Distinct microbial compositions were revealed when comparing pristine and water flooded oil wells in contrast to the similar community structures observed between the aqueous and oil fluids from the same well (BA-2). The equal proportion of archaea and bacteria together with the greater anaerobic hydrocarbon degradation potential in the BA-1 pristine but degraded reservoir contrasted with the predominance of bacteria over archaea, aerobic pathways and lower frequency of anaerobic degradation genes in the BA-2 water flooded undegraded well. Our results suggest that Syntrophus, Syntrophomonas, candidatus Atribacteria and Synergistia, in association with mainly acetoclastic methanogenic archaea of the genus Methanothrix, were collectively responsible for the oil biodegradation observed in the pristine petroleum well BA-1. Conversely, the microbial composition of the water flooded oil well BA-2 was mainly dominated by the fast-growing and putatively aerobic opportunists Marinobacter and Marinobacterium. This presumable allochthonous community introduced a greater metabolic versatility, although oil biodegradation has not been detected hitherto perhaps due to in-reservoir unfavorable physicochemical conditions. These findings provide a better understanding of the petroleum reservoir microbiomes and their potential roles in biogeochemical processes occurring in environments with different geological and oil recovery histories.

Bacterial diversity and functional metagenomics expounding the diversity of xenobiotics, stress, defense and CRISPR gene ontology providing eco-efficiency to Himalayan Hot Springs

Sikkim is one of the bio-diverse states of India, which harbors diverse alkaline and sulfur rich hot springs in its vicinity. However, there is a dearth of data present in terms of microbial and its functional diversity as only a few hot springs have been studied in this area. Thus, in this regard, microbial and functional diversity of two hot springs by NGS, PLFA, and culture-independent approaches were carried out. PLFA and culture-dependent analysis was complementary as the Gram-positive bacteria were abundant in both the hot springs with the dominance of phylum Firmicutes with Geobacillus. Metagenomic analysis revealed the abundance of Proteobacteria, Actinobacteria, and Firmicutes in both hot springs. Functional metagenomics suggested that both Yumthang and Reshi hot spring possess a diverse set of genes analogous to stress such as genes allied to osmotic, heat shock, and acid stresses; defense analogies such as multidrug resistance efflux pump, multidrug transport system, and β-lactamase; and CRISPR analogues such as related to Cas1, Cas2, Cas3, cmr1-5 proteins, CT1972, and CT1133 gene families. The xenobiotic analogues were found against benzoate, nitrotolune, xylene, DDT, and chlorocyclohexane/chlorobenzene degradation. Thus, these defensive mechanisms against environmental and anthropogenic hiccups and hindrances provide the eco-efficiency to such thermal habitats. The higher enzymatic, degradation, defense, stress potential and the lower percentage identity (< 95%) of isolates encourage the further exploration and exploitation of these habitats for industrial and biotechnological purposes.

Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer

Hyperthermophilic methanogens are often H2 limited in hot subseafloor environments, and their survival may be due in part to physiological adaptations to low H2 conditions and interspecies H2 transfer. The hyperthermophilic methanogen Methanocaldococcus jannaschii was grown in monoculture at high (80 to 83 μM) and low (15 to 27 μM) aqueous H2 concentrations and in coculture with the hyperthermophilic H2 producer Thermococcus paralvinellae The purpose was to measure changes in growth and CH4 production kinetics, CH4 fractionation, and gene expression in M. jannaschii with changes in H2 flux. Growth and cell-specific CH4 production rates of M. jannaschii decreased with decreasing H2 availability and decreased further in coculture. However, cell yield (cells produced per mole of CH4 produced) increased 6-fold when M. jannaschii was grown in coculture rather than monoculture. Relative to high H2 concentrations, isotopic fractionation of CO2 to CH4 (εCO2-CH4) was 16‰ larger for cultures grown at low H2 concentrations and 45‰ and 56‰ larger for M. jannaschii growth in coculture on maltose and formate, respectively. Gene expression analyses showed H2-dependent methylene-tetrahydromethanopterin (H4MPT) dehydrogenase expression decreased and coenzyme F420-dependent methylene-H4MPT dehydrogenase expression increased with decreasing H2 availability and in coculture growth. In coculture, gene expression decreased for membrane-bound ATP synthase and hydrogenase. The results suggest that H2 availability significantly affects the CH4 and biomass production and CH4 fractionation by hyperthermophilic methanogens in their native habitats.IMPORTANCE Hyperthermophilic methanogens and H2-producing heterotrophs are collocated in high-temperature subseafloor environments, such as petroleum reservoirs, mid-ocean ridge flanks, and hydrothermal vents. Abiotic flux of H2 can be very low in these environments, and there is a gap in our knowledge about the origin of CH4 in these habitats. In the hyperthermophile Methanocaldococcus jannaschii, growth yields increased as H2 flux, growth rates, and CH4 production rates decreased. The same trend was observed increasingly with interspecies H2 transfer between M. jannaschii and the hyperthermophilic H2 producer Thermococcus paralvinellae With decreasing H2 availability, isotopic fractionation of carbon during methanogenesis increased, resulting in isotopically more negative CH4 with a concomitant decrease in H2-dependent methylene-tetrahydromethanopterin dehydrogenase gene expression and increase in F420-dependent methylene-tetrahydromethanopterin dehydrogenase gene expression. The significance of our research is in understanding the nature of hyperthermophilic interspecies H2 transfer and identifying biogeochemical and molecular markers for assessing the physiological state of methanogens and possible source of CH4 in natural environments.

Effect of inorganic nutrients on bacterial community composition in oil-bearing sandstones from the subsurface strata of an onshore oil reservoir and its potential use in Microbial Enhanced Oil Recovery

Microbial 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, we performed preliminary evaluation of the possibility of conducting MEOR at Mae Soon reservoir, an onshore reservoir in Northern Thailand. The reservoir’s physicochemical characteristics, including the characteristics of the wells, the oil-bearing sandstone cores, and the reservoir’s produced water, were determined. The microbiological characteristics of the oil wells in the reservoir were also investigated by submerging the reservoir’s sandstone core samples, obtained from 6 oil wells, in the reservoir’s produced water and in the produced water added with inorganic nutrients (KNO₃ and NaH₂PO₄). The uncultured bacteria in both treatments were determined, using tagged 16S rRNA gene amplicon with Ion Torrent Sequencing Analysis. The effects of inorganic nutrients and the reservoir’s parameters on the bacterial communities were analysed. A total number of 16,828 OTUs were taxonomically classified into 89 classes and 584 genera. In the controls (sandstone cores submerged in the produced water), the dominant bacterial populations were related to Deinococcus-Thermus, and Betaproteobacteria; while in the nutrient treated samples, there was a marked increase in the relative abundance of Gammaproteobacteria in three samples. Thermus, Acinetobacter, and Pseudomonas were the most abundant genera, and these are potential microorganisms for MEOR. Analysis of correlations between physiochemical properties of the reservoir and bacterial genera, using spearman’s correlation analysis, suggested that some of the reservoir’s properties, especially of the well and the rock, could influence some bacterial genera. To our knowledge, this is the first demonstration of the effect of inorganic nutrients on alteration of bacterial communities attached to reservoir’s rock, and how the bacterial, physical, and chemical properties of a reservoir were co-analysed to serve as a basis for designing a MEOR process.

Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry

Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, pH, alkalinity, Ca²⁺, Mg²⁺, Cl²⁺, and sulfur were main environmental variables influencing the microbial community composition and diversity. Also the piper diagram suggested that the water of both the hot springs are Ca-HCO^3- type and can be predicted as shallow fresh ground waters. This study has provided an insight into the ecological interaction of the diverse microbial communities and associated physicochemical parameters, which will help in determining the future studies on different biogeochemical pathways in these hot springs.

Distribution of Archaeal Communities along the Coast of the Gulf of Finland and Their Response to Oil Contamination

The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the archaeal core species network plausibly revealed resilience and the potential for oil degradation. Halobacteriaceae and putative cytochrome P450 pathways were significantly enriched in the oil-contaminated littoral sediment. The archaeal taxa formed highly interconnected and interactive networks, in which Halobacteriaceae, Thermococcus, and methanogens were the main components, implying a potential relevant trophic connection between hydrocarbon degradation, methanogenesis, sulfate reduction, and/or fermentative growth.

Novel archaeal thermostable cellulases from an oil reservoir metagenome

Microbial assemblages were sampled from an offshore deep sub-surface petroleum reservoir 2.5 km below the ocean floor off the coast of Norway, providing conditions of high temperature and pressure, to identify new thermostable enzymes. In this study, we used DNA sequences obtained directly from the sample metagenome and from a derived fosmid library to survey the functional diversity of this extreme habitat. The metagenomic fosmid library containing 11,520 clones was screened using function- and sequence-based methods to identify recombinant clones expressing carbohydrate-degrading enzymes. Open reading frames (ORFs) encoding carbohydrate-degrading enzymes were predicted by BLAST against the CAZy database, and many fosmid clones expressing carbohydrate-degrading activities were discovered by functional screening using Escherichia coli as a heterologous host. Each complete ORF predicted to encode a cellulase identified from sequence- or function-based screening was subcloned in an expression vector. Five subclones was found to have significant activity using a fluorescent cellulose model substrate, and three of these were observed to be highly thermostable. Based on phylogenetic analyses, the thermostable cellulases were derived from thermophilic Archaea and are distinct from known cellulases. Cellulase F1, obtained from function-based screening, contains two distinct cellulase modules, perhaps resulting from fusion of two archaeal cellulases and with a novel protein structure that may result in enhanced activity and thermostability. This enzyme was found to exhibit exocellulase function and to have a remarkably high activity compared to commercially available enzymes. Results from this study highlight the complementarity of hybrid approaches for enzyme discovery, combining sequence- and function-based screening.

Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C

Temperature is one of the defining parameters of an ecological niche. Most organisms thrive within a temperature range that rarely exceeds ~30 °C, but the deep subsurface bacterium Kosmotoga olearia can grow over a temperature range of 59 °C (20–79 °C). To identify genes correlated with this flexible phenotype, we compared transcriptomes of K. olearia cultures grown at its optimal 65 °C to those at 30, 40, and 77 °C. The temperature treatments affected expression of 573 of 2224 K. olearia genes. Notably, this transcriptional response elicits re-modeling of the cellular membrane and changes in metabolism, with increased expression of genes involved in energy and carbohydrate metabolism at high temperatures and up-regulation of amino acid metabolism at lower temperatures. At sub-optimal temperatures, many transcriptional changes were similar to those observed in mesophilic bacteria at physiologically low temperatures, including up-regulation of typical cold stress genes and ribosomal proteins. Comparative genomic analysis of additional Thermotogae genomes indicates that one of K. olearia’s strategies for low-temperature growth is increased copy number of some typical cold response genes through duplication and/or lateral acquisition. At 77 °C one-third of the up-regulated genes are of hypothetical function, indicating that many features of high-temperature growth are unknown.

Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes

Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.

Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly

Oil reservoirs exhibit extreme environmental conditions such as high salinity and high temperature. Insights into microbial community assemblages in oil reservoirs and their functional potentials are important for understanding biogeochemical cycles in the subterranean biosphere. In this study, we performed shotgun metagenomic sequencing of crude oil samples from two geographically distant oil reservoirs in China, and compared them with all the 948 available environmental metagenomes deposited in IMG database (until October 2013). Although the dominant bacteria and the proportion of hydrogenotrophic and acetoclastic methanogens were different among oil metagenomes, compared with the metagenomes from other environments, all the oil metagenomes contained higher abundances of genes involved in methanogenic hydrocarbon degradation and stress response systems. In addition, a "shape-sorting" manner was proposed for the assembly of microbial communities in oil reservoirs, with the oil reservoir acting as a function sorter to select microbes with special functions from its endemic pool of microorganisms. At the functional level, we found that environmental metagenomes were generally clustered according to their isolation environments but not their geographical locations, suggesting selective processes to be involved in the assembly of microbial communities based on functional gene composition.

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to be the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of the Acetothermia (OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylum Parcubacteria (OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, including Microgenomates (OP11), Atribacteria (OP9), candidate phyla TA06 and WS6, and Marinimicrobia (SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes.

The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. We show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes.

Bacteria in the injection water differently impacts the bacterial communities of production wells in high-temperature petroleum reservoirs

Water flooding is widely used for oil recovery. However, how the introduction of bacteria via water flooding affects the subsurface ecosystem remains unknown. In the present study, the distinct bacterial communities of an injection well and six adjacent production wells were revealed using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. All sequences of the variable region 3 of the 16S rRNA gene retrieved from pyrosequencing were divided into 543 operational taxonomic units (OTUs) based on 97% similarity. Approximately 13.5% of the total sequences could not be assigned to any recognized phylum. The Unifrac distance analysis showed significant differences in the bacterial community structures between the production well and injection water samples. However, highly similar bacterial structures were shown for samples obtained from the same oil-bearing strata. More than 69% of the OTUs detected in the injection water sample were absent or detected in low abundance in the production wells. However, the abundance of two OTUs reached as high as 17.5 and 26.9% in two samples of production water, although the OTUs greatly varied among all samples. Combined with the differentiated water flow rate measured through ion tracing, we speculated that the transportation of injected bacteria was impacted through the varied permeability from the injection well to each of the production wells. Whether the injected bacteria predominate the production well bacterial community might depend both on the permeability of the strata and the reservoir conditions.

Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs

The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or CO₂, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. The physiological groups reviewed here comprise iron-, manganese-, and nitrate-reducing microorganisms. In the context of recent findings also the potential of chlorate and perchlorate [jointly termed (per)chlorate] reduction in oil reservoirs will be discussed. Special attention is given to elevated temperatures that are predominant in the deep subsurface. Microbial reduction of (per)chlorate is a thermodynamically favorable redox process, also at high temperature. However, knowledge about (per)chlorate reduction at elevated temperatures is still scarce and restricted to members of the Firmicutes and the archaeon Archaeoglobus fulgidus. By analyzing the diversity and phylogenetic distribution of functional genes in (meta)genome databases and combining this knowledge with extrapolations to earlier-made physiological observations we speculate on the potential of (per)chlorate reduction in the subsurface and more precisely oil fields. In addition, the application of (per)chlorate for bioremediation, souring control, and microbial enhanced oil recovery are addressed.