Complete genome sequence of Cellulomonas sp. strain ATA003.

The Gram-positive, rod-shaped endophytic bacterium Cellulomonas sp. strain ATA003 was isolated from the endemic cactus Maihueniopsis domeykoensis seeds collected in the Coastal Atacama Desert, Chile. Here, we present a circular genome with a size of 4,084,881 bp and a GC content of 73.8% obtained by Nanopore sequencing.

Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis.

Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.

Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO2 terrestrial subsurface environments.

Introduction: Long-term stability of underground CO2 storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO2 makes the Eger Rift in the Czech Republic a natural analogue to underground CO2 storage. The Eger Rift is a seismically active region and H2 is produced abiotically during earthquakes, providing energy to indigenous microbial communities. Methods: To investigate the response of a microbial ecosystem to high levels of CO2 and H2, we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H2/CO2 headspace to simulate a seismically active period with elevated H2. Results and discussion: Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50-60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H2 and CO2, specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO2 driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO2 and H2-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO2 concentrations, similar to those found in CCS sites.

Genome Sequence of Arthrobacter sp. Strain ATA002, a Seed Endophytic Bacterium from the Atacama Desert.

The Gram-positive diazotrophic seed endophytic bacterium Arthrobacter sp. strain ATA002 was isolated from seeds of the endemic cactus Maihueniopsis domeykoensis collected in the Atacama Desert, Chile. Here, we present a circular genome sequence, obtained by Nanopore sequencing, with a size of 3,904,590 bp and a GC content of 65.9%.

Metagenome-Assembled Genome of a Putative Methanogenic Methanosarcina sp. Strain Enriched from Terrestrial High-CO2 Subsurface Sediments.

A metagenome-assembled genome (MAG), named Methanosarcina sp. strain ERenArc_MAG2, was obtained from a 3-month-old H2/CO2 atmosphere enrichment culture, originally inoculated with 60-m deep drill core sediment collected from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered draft genome revealed putative archaeal methanogenesis genes in the deep biosphere.

Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms.

Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes (MAGs) to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin (AppB). Our analyses resulted in the recovery of over 40 MAGs from 8 coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. The data presented herein provides novel insights into AppB coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.

Circular Metagenome-Assembled Genome of Methanobacterium sp. Strain ERen5, a Putative Methanogenic, H2-Utilizing Terrestrial Subsurface Archaeon.

A circular, single-contig Methanobacterium sp. metagenome-assembled genome (MAG) was recovered from high-CO2 enrichments inoculated with drill core material from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered MAG highlighted putative methanogenesis genes, providing valuable information on archaeal activity in the deep biosphere.

Draft Genome Sequence of Paenalcaligenes niemegkensis NGK35T, Isolated from Plastic-Polluted Soil of an Abandoned Landfill.

The Gram-negative bacterium Paenalcaligenes niemegkensis NGK35T was isolated from plastic debris in an abandoned landfill. It has the ability to grow on polyethylene and hexadecane as the sole carbon sources. Here, we report the corresponding draft genome, which contains 3.66 Mbp and is characterized by a G+C content of 52.1%.

Draft Genome Sequence of Nocardioides alcanivorans NGK65T, a Hexadecane-Degrading Bacterium.

The Gram-positive bacterium Nocardioides alcanivorans NGK65T was isolated from plastic-polluted soil and cultivated on medium with polyethylene as the single carbon source. Nanopore sequencing revealed the presence of candidate enzymes for the biodegradation of polyethylene. Here, we report the draft genome of this newly described member of the terrestrial plastisphere.

The Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing Microorganisms.

The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry. IMPORTANCE The Permian Basin is the largest producing oil and gas region in the United States and plays a critical role supplying national energy needs. Previous work in other basins has demonstrated that the geochemistry and microbiology of hydrocarbon regions can have a major impact on well infrastructure and production. Despite that, little work has been done to understand the complex dynamics present in the Permian Basin. This study characterizes and analyzes 10 unique wells and one groundwater sample in the Permian Basin using geochemical and microbial techniques. Across all wells we found a high number of classic and thiosulfate reducers, suggesting that hydrogen sulfide production may be especially prevalent in the Permian Basin. Additionally, our analysis revealed a biogeochemical signal impacted by the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. This information can be utilized by the oil and gas industry to improve oil recovery efforts and minimize commercial and environmental costs.

Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste.

Strain NGK65T, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65T hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0-1% NaCl and at pH 7.5-8.0. Glycerol, d-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate, sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C16:0 followed by iso-C17:0 and C18:1 ω9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65T belongs to the genus Nocardioides (phylum Actinobacteria), appearing most closely related to Nocardioides daejeonensis MJ31T (98.6%) and Nocardioides dubius KSL-104T (98.3%). The genomic DNA G+C content of strain NGK65T was 68.2%. Strain NGK65T and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9% as well as digital DNA-DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides. Based on phenotypic and molecular characterization, strain NGK65T can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65T (=DSM 113112T=NCCB 100846T).

Paenalcaligenes niemegkensis sp. nov., a novel species of the family Alcaligenaceae isolated from plastic waste.

Strain NGK35T is a motile, Gram-stain-negative, rod-shaped (1.0-2.1 µm long and 0.6-0.8 µm wide), aerobic bacterium that was isolated from plastic-polluted landfill soil. The strain grew at temperatures between 6 and 37 °C (optimum, 28 °C), in 0-10 % NaCl (optimum, 1 %) and at pH 6.0-9.5 (optimum, pH 7.5-8.5). It was positive for cytochrome c oxidase, catalase as well as H2S production, and hydrolysed casein and urea. It used a variety of different carbon sources including citrate, lactate and pyruvate. The predominant membrane fatty acids were C16 : 1 cis9 and C16 : 0, followed by C17 : 0 cyclo and C18 : 1 cis11. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, followed by diphosphatidyglycerol. The only quinone was ubiquinone Q-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK35T belongs to the genus Paenalcaligenes (family Alcaligenaceae), appearing most closely related to Paenalcaligenes hominis CCUG 53761AT (96.90 %) and Paenalcaligenes suwonensis ABC02-12T (96.94 %). The genomic DNA G+C content of strain NGK35T was 52.1 mol %. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Paenalcaligenes. Based on phenotypic and molecular characterization, strain NGK35T can clearly be differentiated from its phylogenetic neighbours establishing a novel species, for which the name Paenalcaligenes niemegkensis sp. nov. is proposed. The type strain is NGK35T (=DSM 113270T=NCCB 100854T).

Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert.

The existence of microbial activity hotspots in temperate regions of Earth is driven by soil heterogeneities, especially the temporal and spatial availability of nutrients. Here we investigate whether microbial activity hotspots also exist in lithic microhabitats in one of the most arid regions of the world, the Atacama Desert in Chile. While previous studies evaluated the total DNA fraction to elucidate the microbial communities, we here for the first time use a DNA separation approach on lithic microhabitats, together with metagenomics and other analysis methods (i.e., ATP, PLFA, and metabolite analysis) to specifically gain insights on the living and potentially active microbial community. Our results show that hypolith colonized rocks are microbial hotspots in the desert environment. In contrast, our data do not support such a conclusion for gypsum crust and salt rock environments, because only limited microbial activity could be observed. The hypolith community is dominated by phototrophs, mostly Cyanobacteria and Chloroflexi, at both study sites. The gypsum crusts are dominated by methylotrophs and heterotrophic phototrophs, mostly Chloroflexi, and the salt rocks (halite nodules) by phototrophic and halotolerant endoliths, mostly Cyanobacteria and Archaea. The major environmental constraints in the organic-poor arid and hyperarid Atacama Desert are water availability and UV irradiation, allowing phototrophs and other extremophiles to play a key role in desert ecology.

Microbial Signatures in Deep CO2-Saturated Miocene Sediments of the Active Hartousov Mofette System (NW Czech Republic).

The Hartousov mofette system is a natural CO2 degassing site in the central Cheb Basin (Eger Rift, Central Europe). In early 2016 a 108 m deep core was obtained from this system to investigate the impact of ascending mantle-derived CO2 on indigenous deep microbial communities and their surrounding life habitat. During drilling, a CO2 blow out occurred at a depth of 78.5 meter below surface (mbs) suggesting a CO2 reservoir associated with a deep low-permeable CO2-saturated saline aquifer at the transition from Early Miocene terrestrial to lacustrine sediments. Past microbial communities were investigated by hopanoids and glycerol dialkyl glycerol tetraethers (GDGTs) reflecting the environmental conditions during the time of deposition rather than showing a signal of the current deep biosphere. The composition and distribution of the deep microbial community potentially stimulated by the upward migration of CO2 starting during Mid Pleistocene time was investigated by intact polar lipids (IPLs), quantitative polymerase chain reaction (qPCR), and deoxyribonucleic acid (DNA) analysis. The deep biosphere is characterized by microorganisms that are linked to the distribution and migration of the ascending CO2-saturated groundwater and the availability of organic matter instead of being linked to single lithological units of the investigated rock profile. Our findings revealed high relative abundances of common soil and water bacteria, in particular the facultative, anaerobic and potential iron-oxidizing Acidovorax and other members of the family Comamonadaceae across the whole recovered core. The results also highlighted the frequent detection of the putative sulfate-oxidizing and CO2-fixating genus Sulfuricurvum at certain depths. A set of new IPLs are suggested to be indicative for microorganisms associated to CO2 accumulation in the mofette system.

Geochemistry and Microbiology Predict Environmental Niches With Conditions Favoring Potential Microbial Activity in the Bakken Shale.

The Bakken Shale and underlying Three Forks Formation is an important oil and gas reservoir in the United States. The hydrocarbon resources in this region are accessible using unconventional oil and gas extraction methods, including horizontal drilling and hydraulic fracturing. However, the geochemistry and microbiology of this region are not well understood, although they are known to have major implications for productivity and water management. In this study, we analyzed the produced water from 14 unconventional wells in the Bakken Shale using geochemical measurements, quantitative PCR (qPCR), and 16S rRNA gene sequencing with the overall goal of understanding the complex dynamics present in hydraulically fractured wells. Bakken Shale produced waters from this study exhibit high measurements of total dissolved solids (TDS). These conditions inhibit microbial growth, such that all samples had low microbial loads except for one sample (well 11), which had lower TDS concentrations and higher 16S rRNA gene copies. Our produced water samples had elevated chloride concentrations typical of other Bakken waters. However, they also contained a sulfate concentration trend that suggested higher occurrence of sulfate reduction, especially in wells 11 and 18. The unique geochemistry and microbial loads recorded for wells 11 and 18 suggest that the heterogeneous nature of the producing formation can provide environmental niches with conditions conducive for microbial growth. This was supported by strong correlations between the produced water microbial community and the associated geochemical parameters including sodium, chloride, and sulfate concentrations. The produced water microbial community was dominated by 19 bacterial families, all of which have previously been associated with hydrocarbon-reservoirs. These families include Halanaerobiaceae, Pseudomonadaceae, and Desulfohalobiaceae which are often associated with thiosulfate reduction, biofilm production, and sulfate reduction, respectively. Notably, well 11 was dominated by sulfate reducers. Our findings expand the current understanding of microbial life in the Bakken region and provide new insights into how the unique produced water conditions shape microbial communities. Finally, our analysis suggests that produced water chemistry is tightly linked with microbiota in the Bakken Shale and shows that additional research efforts that incorporate coupled microbial and geochemical datasets are necessary to understand this ecosystem.

Upregulation of peroxide scavenging enzymes and multidrug efflux proteins highlight an active sodium hypochlorite response in Pseudomonas fluorescens biofilms.

The oxidative biocide sodium hypochlorite is among the most commonly used antimicrobial agents in the control of surface-attached microbial communities (biofilms). Clarifying the genetic response of microorganisms in biofilms to hypochlorite may contribute to improved biofilm control strategies. Here, RNA-seq was used to investigate the differential gene expression response of industrially relevant Pseudomonas fluorescens biofilms to sub-lethal concentrations of sodium hypochlorite. Pseudomonas biofilms responded to hypochlorite exposure with increased transcription of genes encoding peroxide scavenging enzymes (e.g., alkyl hydroperoxide reductase (Ahp) and hydroperoxide resistance protein (Ohr)), oxidative stress repair enzymes (e.g., the periplasmic sulfoxide reductase YedYZ complex), and multidrug efflux (e.g., MexEF pumps). In addition, genes involved in amino acid synthesis and energy metabolism were down-regulated following hypochlorite exposure. This work improves the current understanding of genetic response mechanisms to biocides and contributes to the optimization of biocides and application strategies.

Glutaraldehyde inhibits biological treatment of organic additives in hydraulic fracturing produced water.

Water generated by hydraulic fracturing for the production of oil and gas, commonly termed 'produced water', may contain residual organic compounds from the fracturing process or the subsurface formation. Biological treatment is a potential technology to remove residual organic compounds in produced water. Biocides are often added to both fracturing fluids and produced water to limit undesirable microbiological activity, and glutaraldehyde is the most commonly used biocide in hydraulic fracturing. Residual biocides in produced water can limit biological treatment efficiency. We evaluated the effect of glutaraldehyde on the biodegradation of five of the most commonly reported organic compounds in hydraulic fracturing fluids in an engineered biofilm treatment. Our results demonstrated that glutaraldehyde delays biological organic compound removal by introducing a biodegradation lag phase. In addition, the effects of glutaraldehyde were more pronounced for more rapidly degraded compounds. Finally, the presence of glutaraldehyde did not decrease microbial abundance nor drive microbial community structure, suggesting that observed effects were due to altered microbial activity. These results highlight the necessity to consider co-contaminant interactions during treatment of complex waste streams where residual biocide may be present.

Insights into microbial community structure and function from a shallow, simulated CO2 -leakage aquifer demonstrate microbial selection and adaptation.

Geological carbon storage is likely to be a part of a comprehensive strategy to minimize the atmospheric release of carbon dioxide (CO2 ), raising concerns that injected CO2 will leak into overlying freshwater aquifers. CO2(aq) leakage may impact the dominant microbial community responsible for important ecosystem functions such as nutrient cycling, metal cycling and carbon conversion. Here, we examined the impact of an experimental in situ CO2 -leakage on a freshwater aquifer microbial community. High-throughput 16S rRNA gene sequencing demonstrated lower microbial diversity in freshwater wells with CO2 concentrations above 1.15 g l-1 . Metagenomic sequencing and population genome binning were used to evaluate the metabolic potential of microbial populations across four CO2 exposed samples and one control sample. Population genome binning resulted in the recovery and annotation of three metagenome assembled genomes (MAGs). Two of the MAGs, most closely related to Curvibacter and Sulfuricurvum, had the functional capacity for CO2 utilization via carbon fixation coupled to sulfur and iron oxidation. The third draft genome was an Archaea, most closely related to Methanoregula, characterized by the metabolic potential for methanogenesis. Together, these findings show that CO2 leakage in a freshwater aquifer poses a strong selection, driving both microbial community structure and metabolic function.

Microbial communities in Bakken region produced water.

The Bakken Shale has become one of the United States' most important oil and gas producing regions. This study examined the microbiology and geochemical characteristics of Bakken region produced water from 17 well sites sampled from the three-phase separator and produced water holding tank over a 6-month time frame. Produced water samples had high total dissolved solids (220 000-350 000 mg/L) and low dissolved organic carbon concentrations (41-132 mg/L). Microbial abundances varied between 101 and 104 16S rRNA gene copies/mL, approximately four orders of magnitude below those observed for produced waters from other hydraulic fracturing regions. The most abundant bacterial orders found in produced water samples were Bacillales, Halanaerobiales and Pseudomonadales, consistent with observations from other unconventional resource plays. Our observations suggest temporal community structuring, as produced waters sampled early in our sampling period were dominated by Halanaerobiales, and produced waters sampled at the remaining winter sampling time points were characterized by high relative abundances of Bacillales and Pseudomonadales. Data from this study extends the current available knowledge of the microbiology and chemistry associated with produced water from the Bakken region and provides insights into microbial community dynamics in hypersaline subsurface fluids.

Draft Genome Sequence of Pseudomonas sp. BDAL1 Reconstructed from a Bakken Shale Hydraulic Fracturing-Produced Water Storage Tank Metagenome.

We report the 5,425,832 bp draft genome of Pseudomonas sp. strain BDAL1, recovered from a Bakken shale hydraulic fracturing-produced water tank metagenome. Genome annotation revealed several key biofilm formation genes and osmotic stress response mechanisms necessary for survival in hydraulic fracturing-produced water.