Functional structures of soil microbial community relate to contrasting N2O emission patterns from a highly acidified forest

Microbiome of High-Rank Coal Reservoirs in the High-Production Areas of the Southern Qinshui Basin

To study the distribution features of microorganisms in distinct hydrological areas of the southern Qinshui Basin, C-N-S microorganisms were studied using 16S RNA sequencing, metagenome sequencing and geochemical technologies, showing the high sensitivity of microorganisms to the hydrodynamic dynamics of coal. The hydrodynamic intensity of the #3 coal gradually decreased from the runoff areas to the stagnant areas. The stagnant zones have higher reservoir pressure, methane content, δ¹³C_DIC and TDS and lower SO₄^2-, Fe³⁺ and NO₃^- concentrations than the runoff areas. C-N-S-cycling microorganisms, including those engaged in methanogenesis, nitrate respiration, fermentation, nitrate reduction, dark oxidation of sulfur compounds, sulfate respiration, iron respiration, chlorate reduction, aromatic compound degradation, denitrification, ammonification and nitrogen fixation, were more abundant in the stagnant areas. The relative abundance of C-N-S functional genes, including genes related to C metabolism (e.g., mcr, mer, mtr, fwd and mtd), N metabolism (e.g., nifDKH, nirK, narGHI, nosZ, amoB, norC and napAB) and sulfur metabolism (e.g., dsrAB and PAPSS), increased in the stagnant zones, indicating that there was active microbiological C-N-S cycling in the stagnant areas. The degradation and fermentation of terrestrial plant organic carbon and coal seam organic matter could provide substrates for methanogens, while nitrogen fixation and nitrification can provide nitrogen for methanogens, which are all favorable factors for stronger methanogenesis in stagnant areas. The coal in the study area is currently in the secondary biogenic gas generation stage because of the rising of the strata, which recharges atmospheric precipitation. The random forest model shows that the abundance of C-N-S microorganisms and genes could be used to distinguish different hydrological zones in coal reservoirs. Since stagnant zones are usually high-gas-bearing zones and high-production areas of CBM exploration, these microbiological indicators can be used as effective parameters to identify high-production-potential zones. In addition, nitrate respiration and sulfate respiration microorganisms consumed NO₃^- and SO₄^2-, causing a decrease in the content of these two ions in the stagnant areas.

N Addition Overwhelmed the Effects of P Addition on the Soil C, N, and P Cycling Genes in Alpine Meadow of the Qinghai-Tibetan Plateau

Although human activities have greatly increased nitrogen (N) and phosphorus (P) inputs to the alpine grassland ecosystems, how soil microbial functional genes involved in nutrient cycling respond to N and P input remains unknown. Based on a fertilization experiment established in an alpine meadow of the Qinghai-Tibetan Plateau, we investigated the response of the abundance of soil carbon (C), N, and P cycling genes to N and P addition and evaluated soil and plant factors related to the observed effects. Our results indicated that the abundance of C, N, and P cycling genes were hardly affected by N addition, while P addition significantly increased most of them, suggesting that the availability of P plays a more important role for soil microorganisms than N in this alpine meadow ecosystem. Meanwhile, when N and P were added together, the abundance of C, N, and P cycling genes did not change significantly, indicating that the promoting effects of P addition on microbial functional genes abundances were overwhelmed by N addition. The Mantel analysis and the variation partitioning analysis revealed the major role of shoot P concentration in regulating the abundance of C, N, and P cycling genes. These results suggest that soil P availability and plant traits are key in governing C, N, and P cycling genes at the functional gene level in the alpine grassland ecosystem.

Metagenomic analysis of microbial community structure and function in a improved biofilter with odorous gases

Biofilters have been broadly applied to degrade the odorous gases from industrial emissions. A industrial scale biofilter was set up to treat the odorous gases. To explore biofilter potentials, the microbial community structure and function must be well defined. Using of improved biofilter, the differences in microbial community structures and functions in biofilters before and after treatment were investigated by metagenomic analysis. Odorous gases have the potential to alter the microbial community structure in the sludge of biofilter. A total of 90,016 genes assigned into various functional metabolic pathways were identified. In the improved biofilter, the dominant phyla were Proteobacteria, Planctomycetes, and Chloroflexi, and the dominant genera were Thioalkalivibrio, Thauera, and Pseudomonas. Several xenobiotic biodegradation-related pathways showed significant changes during the treatment process. Compared with the original biofilter, Thermotogae and Crenarchaeota phyla were significantly enriched in the improved biofilter, suggesting their important role in nitrogen-fixing. Furthermore, several nitrogen metabolic pathway-related genes, such as nirA and nifA, and sulfur metabolic pathway-related genes, such as fccB and phsA, were considered to be efficient genes that were involved in removing odorous gases. Our findings can be used for improving the efficiency of biofilter and helping the industrial enterprises to reduce the emission of waste gases.

Employing gene chip technology for monitoring and assessing soil heavy metal pollution

Soil heavy metals pollution can cause many serious environment problems because of involving a very complex pollution process for soil health. Therefore, it is very important to explore methods that can effectively evaluate heavy metal pollution. Researchers were actively looking for new ideas and new methods for evaluating and predicting levels of soil heavy metal pollution. The study on microbial communities is one of the effective methods using gene chip technology. Gene chip technology, as a high-throughput metagenomics analysis technique, has been widely used for studying the structure and function of complex microbial communities in different polluted environments from different pollutants, including the soil polluted by heavy metals. However, there is still a lack of a systematic summarization for the polluted soil by heavy metals. This paper systematically analyzed soil heavy metals pollution via reviewing previous studies on applying gene chip technology, including single species, tolerance mechanisms, enrichment mechanisms, anticipation and evaluation of soil remediation, and multi-directional analysis. The latest gene chip technologies and corresponding application cases for discovering critical species and functional genes via analyzing microbial communities and evaluating heavy metal pollution of soil were also introduced in this paper. This article can provide scientific guidance for researchers actively investigating the soil polluted by heavy metals.

Nitrous oxide fluxes from long-term limed soils following P and glucose addition: Nonlinear response to liming rates and interaction from added P

Liming of acidic soils to regulate pH for crop growth may decrease emissions of nitrous oxide (N₂O) due to direct effects of pH on the synthesis of N₂O reductases by denitrifying bacteria. However, liming also changes general pH-dependent soil properties, including availability of phosphorus (P), with a feedback on N₂O fluxes that remains largely unknown. Here we used a mesocosm approach to study the combined role of liming and P in regulating N₂O fluxes from denitrification in an arable coarse sandy soil where N₂O emissions under field condition coincided with rainfall events and irrigation, which facilitated anoxia. Soils from three long-term liming treatments (0, 4, and 12 Mg ha^-1) with resulting pH(CaCl₂) of 3.6, 4.7 and 6.3 were incubated at original bulk density first at 60% water filled pore space (WFPS) and successively at 75% WFPS with added nitrate, inorganic P (0 and 10 μg P g^-1 soil) and glucose as labile carbon. N₂O fluxes were measured during 28 days and were supplemented with measurements of CO₂ fluxes, microbial biomass, potential denitrification, and acid phosphatase activity. The results showed a nonlinear response of N₂O fluxes to liming rates, with highest fluxes at the intermediate liming level (4 Mg ha^-1). Furthermore, inorganic P stimulated N₂O fluxes only at the intermediate liming level. Assays of potential denitrification indicated that the N₂O/(N₂O + N₂) product ratio decreased consistently with increasing liming rates, but total N₂O fluxes responded nonlinearly likely due to combined effects on N₂O/(N₂O + N₂) product ratios and total denitrification rates. The results suggest that liming and P addition interact on microbial properties and N₂O emissions from acidic arable soils and may not follow linear trends. This makes it uncertain to predict and model the resulting net effect, which may depend on the actual pH range and P availability from the unlimed to the limed treatments.

Distribution Characteristics of C-N-S Microorganism Genes in Different Hydraulic Zones of High-Rank Coal Reservoirs in Southern Qinshui Basin

Microbial decomposition of carbon and biogenic methane in coal is one of the most important issues in CBM exploration. Using metagenomic technologies, the microbial C-N-S functional genes in different hydraulic zones of high-rank coal reservoirs were systematically studied, demonstrating the high sensitivity of this ecosystem to hydrodynamic conditions. The results show that the hydrodynamic strength of coal reservoir #3 in the Shizhuangnan block gradually weakened from east to west, forming a transitional feature from a runoff area to a stagnant area. Compared with runoff areas, stagnant areas have higher reservoir pressure, gas content, and ion concentrations. The relative abundance of genes associated with C, N, and S cycling increased from the runoff area to the stagnant area, including cellulose-degrading genes (e.g., cellulose 1,4-beta-cellobiosidase), methane metabolism genes (e.g., mcr, fwd, mtd, mer, and mtr), N-cycling genes (e.g., nifDKH, amoB, narGHI, napAB, nirK, norC, and nosZ), and S-cycling genes (e.g., dsrAB, sir, cysN, sat, aprAB, and PAPSS). This indicates that the stagnant zone had a more active microbial C-N-S cycle. The machine learning model shows that these significantly different genes could be used as effective indices to distinguish runoff and stagnant areas. Carbon and hydrogen isotopes indicate that methane in the study area was thermally generated. Methanogens compete with anaerobic heterotrophic bacteria to metabolize limited substrates, resulting in a low abundance of methanogens. In addition, the existence of methane-oxidizing bacteria suggests that biogenic methane was consumed by methanotrophic bacteria, which is the main reason why biogenic methane in the study area was not effectively preserved. In addition, weakened hydrodynamic conditions increased genes involved in nutrient cycling, including organic matter decomposition, methanogenesis, denitrification, and sulfate reduction, which contributed to the increase in CO₂ and consumption of sulfate and nitrate from runoff areas to stagnant areas.

Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe

High amounts of deposited nitrogen (N) dramatically influence the stability and functions of alpine ecosystems by changing soil microbial community functions, but the mechanism is still unclear. To investigate the impacts of increased N deposition on microbial community functions, a 2-year multilevel N addition (0, 10, 20, 40, 80 and 160 kg N ha^-1 year^-1) field experiment was set up in an alpine steppe on the Tibetan Plateau. Soil microbial functional genes (GeoChip 4.6), together with soil enzyme activity, soil organic compounds and environmental variables, were used to explore the response of microbial community functions to N additions. The results showed that the N addition rate of 40 kg N ha^-1 year^-1 was the critical value for soil microbial functional genes in this alpine steppe. A small amount of added N (≤40 kg N ha^-1 year^-1) had no significant effects on the abundance of microbial functional genes, while high amounts of added N (>40 kg N ha^-1 year^-1) significantly increased the abundance of soil organic carbon degradation genes. Additionally, the abundance of microbial functional genes associated with NH₄⁺, including ammonification, N fixation and assimilatory nitrate reduction pathways, was significantly increased under high N additions. Further, high N additions also increased soil organic phosphorus utilization, which was indicated by the increase in the abundance of phytase genes and alkaline phosphatase activity. Plant richness, soil NO₂^-/NH₄⁺ and WSOC/WSON were significantly correlated with the abundance of microbial functional genes, which drove the changes in microbial community functions under N additions. These findings help us to predict that increased N deposition in the future may alter soil microbial functional structure, which will lead to changes in microbially-mediated biogeochemical dynamics in alpine steppes on the Tibetan Plateau and will have extraordinary impacts on microbial C, N and P cycles.