Deep mining decreases the microbial taxonomic and functional diversity of subsurface oil reservoirs

Soil microbial community, dissolved organic matter and nutrient cycling interactions change along an elevation gradient in subtropical China

To identify possible dominating processes involved in soil microbial community assembly, dissolved organic matter (DOM) and multi-nutrient cycling (MNC) interactions and contribute to understanding of climate change effects on these important cycles, we investigated the interaction of soil chemistry, DOM components and microbial communities in five vegetation zones - ranging from evergreen broad-leaved forest to alpine meadow - along an elevation gradient of 290-1960 m in the Wuyi Mountains, Fujian Province, China. Soil DOM composition and microbial community assembly were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and Illumina MiSeq high-throughput sequencing, respectively. Sloan's neutral model and the modified stochasticity ratio were used to infer community assembly processes. Key microbial drivers of the soil MNC index were identified from partial least squares path models. Our results showed that soil DOM composition is closely related to the vegetation types along an elevation gradient, the structure and composition of the microbial community, and soil nutrient status. Overall, values of the double bond equivalent (DBE), modified aromaticity index (AImod) increased, and H/C ratio and molecular lability boundary (MLBL) percentage decreased with elevation. Lignins/CRAM-like structures compounds dominated soil DOM in each vegetation type and its relative abundance decreased with elevation. Aliphatic/protein and lipids components also decreased, but the relative abundance of aromatic structures and tannin increased with elevation. The alpha diversity index of soil bacteria gradually decreased with elevation, with deterministic processes dominating the microbial community assembly in the highest elevation zone. Bacterial communities were conducive to the decomposition of labile degradable DOM compounds (H/C ≥ 1.5) at low elevation. In the cooler and wetter conditions at higher-elevation sites the relative abundance of potentially resistant soil DOM components (H/C < 1.5) gradually increased. Microbial community diversity and composition were important predictors of potential soil nutrient cycling. Although higher elevation sites have higher nutrient cycling potential, soil DOM was assessed to be a more stable carbon store, with apparent lower lability and bioavailability than at lower elevation sites. Overall, this study increases understanding of the potential linkage between soil microbial community, multiple nutrient cycling and DOM fate in subtropical mountain ecosystems that can help predict the effect of climate change on soil carbon sequestration and thus inform ecosystem management.

N/S element transformation modulating lithospheric microbial communities by single-species manipulation

BACKGROUND

The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation.

RESULTS

Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil.

CONCLUSIONS

The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.

Urine metabolomics analysis of sleep quality in deep-underground miners: A pilot study

Background

In previous questionnaire surveys of miners, sleep disorders were found among underground workers. The influence of the special deep-underground environment and its potential mechanism are still unclear. Therefore, this study intends to utilize LC-MS metabolomics to study the potential differences between different environments and different sleep qualities.

Methods

Twenty-seven miners working at 645-1,500 m deep wells were investigated in this study, and 12 local ground volunteers were recruited as the control group. The Pittsburgh Sleep Quality Index (PSQI) was used to examine and evaluate the sleep status of the subjects in the past month, and valuable basic information about the participants was collected. PSQI scores were obtained according to specific calculation rules, and the corresponding sleep grouping and subsequent analysis were carried out. Through liquid chromatography-mass spectrometry (LC-MS) non-targeted metabolomics analysis, differences in metabolism were found by bioinformatics analysis in different environments.

Results

Between the deep-underground and ground (DUvsG) group, 316 differential metabolites were identified and 125 differential metabolites were identified in the good sleep quality vs. poor sleep quality (GSQvsPSQ) group. The metabolic pathways of Phenylalanine, tyrosine and tryptophan biosynthesis (p = 0.0102) and D-Glutamine and D-glutamate metabolism (p = 0.0241) were significantly enriched in DUvsG. For GSQvsPSQ group, Butanoate metabolism was statistically significant (p = 0.0276). L-Phenylalanine, L-Tyrosine and L-Glutamine were highly expressed in the deep-underground group. Acetoacetic acid was poorly expressed, and 2-hydroxyglutaric acid was highly expressed in good sleep quality.

Conclusions

The influence of the underground environment on the human body is more likely to induce specific amino acid metabolism processes, and regulate the sleep-wake state by promoting the production of excitatory neurotransmitters. The difference in sleep quality may be related to the enhancement of glycolytic metabolism, the increase in excitatory neurotransmitters and the activation of proinflammation. L-phenylalanine, L-tyrosine and L-glutamine, Acetoacetic acid and 2-hydroxyglutaric acid may be potential biomarkers correspondingly.

Effect of remediation reagents on bacterial composition and ecological function in black-odorous water sediments

Black-odorous urban water bodies and sediments pose a serious environmental problem. In this study, we conducted microcosm batch experiments to investigate the effect of remediation reagents (magnesium hydroxide and calcium nitrate) on native bacterial communities and their ecological functions in the black-odorous sediment of urban water. The dominant phyla (Proteobacteria, Actinobacteria, Chloroflexi, and Planctomycetes) and classes (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, Actinobacteria, Anaerolineae, and Planctomycetia) were determined under calcium nitrate and magnesium hydroxide treatments. Functional groups related to aerobic metabolism, including aerobic chemoheterotrophy, dark sulfide oxidation, and correlated dominant genera (Thiobacillus, Lysobacter, Gp16, and Gaiella) became more abundant under calcium nitrate treatment, whereas functional genes potentially involved in dissimilatory sulfate reduction became less abundant. The relative abundance of chloroplasts, fermentation, and correlated genera (Desulfomonile and unclassified Cyanobacteria) decreased under magnesium hydroxide treatment. Overall, these results indicated that calcium nitrate addition improved hypoxia-related reducing conditions in the sediment and promoted aerobic chemoheterotrophy.