Integration of physiology, genomics and microbiomics analyses reveal the biodegradation mechanism of petroleum hydrocarbons by Medicago sativa L. and growth-promoting bacterium Rhodococcus erythropolis KB1.

Despite the effectiveness of microbial-phytoremediation for remediating total petroleum hydrocarbons (TPH)-contaminated soil, the underlying mechanisms remain elusive. This study investigated the whole-genome and biological activity of Rhodococcus erythropolis KB1, revealing its plant growth promotion (PGP), TPH degradation, and stress resistance capabilities. Phytoremediation (using alfalfa) and plant-microbial remediation (using alfalfa and KB1) were employed to degrade TPH. The highest TPH degradation rate, reaching 95%, was observed with plant-microbial remediation. This is attributed to KB1's ability to promote alfalfa growth, induce the release of signaling molecules to activate plant antioxidant enzymes, actively recruit TPH-degrading bacteria (e.g., Sphingomonas, Pseudomonas, C1-B045), and increase soil nitrogen and phosphorus levels, thereby accelerating TPH degradation by both plants and microorganisms. This study demonstrates that R. erythropolis KB1 holds great potential for enhancing the remediation of TPH-contaminated soil through its multifaceted mechanisms, particularly in plant-microbial remediation strategies, providing valuable theoretical support for the application of this technology.

A nationwide study of heavy metal(loid)s in agricultural soils and the soil-grown black morel Morchella sextelata in China.

The accumulation of heavy metal(loid)s (HMs) in soil-grown mushrooms poses potential health risks. Morchella sextelata (black morel) is a typical soil-grown mushroom with a rapidly expanding cultivation area. This study investigated the distribution of arsenic, cadmium, chromium, copper, mercury, nickel, lead, and zinc in 213 pairs of soil and morel samples collected from 29 provincial administrative regions in China, together with the nutritional contents in the morel samples. The HM contents in the arable soils used to cultivate morels were 2.4-33.1 times higher than those in desert soils, while the HM contents in arable-soil morels were 2.9-155.9 times higher than desert morels. The HM contents of morels and their cultivation soils were significantly correlated (0.465 ≤ R ≤ 0.778, P < 0.001). Furthermore, the enrichment factors of most HMs were higher in arable soils than in desert soils (P < 0.05), except Hg. A considerable proportion of the arable soils produced morels with HMs exceeding the risk control standards (RCSs) for food and the health-risk thresholds of dietary intake. In comparison, HMs in morels from desert soils were far below the RCSs and health-risk thresholds. In addition, desert morels contained higher contents of crude proteins, total polysaccharides, and free amino acids (P < 0.001). These findings indicate that growing morels in desert soils is a way of green production that provides mushroom products with improved safety and nutrition.

Degradation of petroleum hydrocarbon contaminants by Rhodococcus erythropolis KB1 synergistic with alfalfa (Medicago sativa L.).

Petroleum hydrocarbons are a stubborn pollutant that is difficult to degrade globally, and plant-microbial degradation is the main way to solve this type of pollutant. In this study, the physiological and ecological responses of alfalfa to petroleum hydrocarbons in different concentrations of petroleum hydrocarbon-contaminated soil with KB1 (Rhodococcus erythropolis) were analyzed and determined by laboratory potting techniques. The growth of alfalfa (CK) and alfalfa with KB1 (JZ) in different concentrations of petroleum hydrocarbons contaminated soil was compared and analyzed. The results of the CK group showed that petroleum hydrocarbons could significantly affect the activity of alfalfa antioxidant enzyme system, inhibit the development of alfalfa roots and the normal growth of plants, especially in the high-concentration group. KB1 strain had the ability to produce IAA, form biofilm, fix nitrogen, produce betaine and ACC deaminase, and the addition of KB1 could improve the growth traits of alfalfa in the soil contaminated with different concentrations of petroleum hydrocarbons, the content of soluble sugars in roots, and the stress resistance and antioxidant enzyme activities of alfalfa. In addition, the degradation kinetics of the strain showed that the degradation rate of petroleum could reach 75.2% after soaking with KB1. Furthermore, KB1 can efficiently degrade petroleum hydrocarbons in advance and significantly alleviate the damage of high concentration of petroleum hydrocarbons to plant roots. The results showed that KB1 strains and alfalfa plants could effectively enhance the degradation of petroleum hydrocarbons, which provided new ideas for improving bioremediation strategies.

Networks of mineral-associated organic matter fractions in forest ecosystems.

Mineral-associated organic matter (MAOM), the largest soil carbon pool, is formed through a series of organo-mineral interaction mechanisms. However, different organo-mineral fractions relevant to specific stabilization mechanisms and their response to environmental variables are poorly understood, which hinders accurate prediction of MAOM preservation under climate change. We applied sequential chemical extraction to separate MAOM into different organo-mineral fractions. To assess of response of different organo-mineral fractions to climate change, alpine forest soils with high environmental sensitivity along a controlled environmental gradient were selected. Residual OM and weakly adsorbed OM were the primary organo-mineral fractions, accounting for approximately 45.1-67.7 % and 16.4-30.6 %, respectively, of the total organic carbon (TOC). Climate exerted considerable indirect effects on the preservation of organo-mineral fractions through weathering and edaphic and biotic variables. Moreover, organo-mineral fractions were closely associated with metal cations (mainly Fe3+/Al3+) and secondary minerals, forming complex networks. Water-soluble OM (WSOM), weakly adsorbed OM and Fe/Al oxyhydroxides-stabilized OM were tightly linked, occupying the central position of the networks, and were closely related to soil pH, moisture and prokaryotic composition, indicating that edaphic and biotic factors might play important roles in maintaining the network structure and topology. In addition, Fe/Al-OM complexes, oxyhydroxides-stabilized OM and residual OM in the network were greatly impacted by climate and weathering factors, including precipitation, temperature and the plagioclase index of alteration (PIA). The complex network among organo-mineral fractions sheds light on MAOM dynamic stabilization for better predicting MAOM preservation under climate change.

pH: A core node of interaction networks among soil organo-mineral fractions.

Mineral-associated organic matter (MAOM) is the largest soil organic carbon (OC) pool with the longest turnover. MAOM is expected to have relatively little sensitivity to climate change due to mineral protection, but its persistence involves several organo-mineral fractions. The uncertainty in the response of specific organo-mineral fractions to climate change hampers the reliability of predictions of MAOM preservation in the future. Here, we applied a sequential chemical fractionation method integrated with network analysis to investigate MAOM stabilization mechanisms across five alpine ecosystems: alpine desert, alpine steppe, alpine meadow, alpine wetland, and alpine forest. Hierarchical cluster analysis revealed grouping of seven extractable OM fractions in MAOM into three OM clusters: a cluster with weak bondings consisting of water-soluble OM (WSOM) and weakly adsorbed fractions (2.1-21.3% of total OC); a cluster with metal-bound complexes comprising Ca-OM complexes and Fe/Al-OM complexes (3.8-12.2% of total OC); and a cluster with strong bonding composed of Al oxyhydroxides, carbonates and Fe oxyhydroxides (12.2-33.5% of total OC). The relative percentages of OM from soils of the five ecosystems in the three clusters exhibited distinct pH dependence patterns. With the increase in pH, the cluster with weak bondings decreased, and that with strong bondings increased, while the one with metal-bound complexes showed a maximum at weakly acidic pH. Organo-mineral fractions and metal cations in MAOM constructed a complex network with pH as the central node. Results suggest that precipitation does not only alter vegetation type and microbial biomass but also regulate soil pH, which is balanced by specific metal cations, thus resulting in particular pH preference of specific OM clusters. These findings demonstrate that soil pH plays a central role in unveiling MAOM dynamics and can serve as a good predictor of soil organo-mineral fractions across alpine ecosystems.

Multistage Hydrocarbon Generation of Saline Lacustrine Source Rocks in Hydrous Pyrolysis: Insights from Clay Mineral-Organic Matter Interactions.

The organic matter (OM) in shale is closely associated with clay minerals, and its maturation is usually accompanied by the diagenesis of these minerals, especially smectite illitization. However, the effect of mineral transformation and its accompanying change of mineral-OM interactions in shale on hydrocarbon generation is still unclear. To investigate this question, smectite-rich immature shale was selected to carry out hydrous pyrolysis. Organic geochemistry and mineralogy of pyrolysates at different temperatures show that the maturation of OM is accompanied by the transformation of bulk and clay minerals. Based on the change in hydrocarbon yield, Rock-Eval parameters, and mineral composition, hydrocarbon generation in this study is divided into three stages: 25-300, 300-400, and 400-500 °C, which are the result of the synergistic evolution of clay minerals and OM. Multistage hydrocarbon generation can be attributed to the mineral transformation-induced desorption of mineral-bound soluble OM (SOM), decarboxylation and hydrocracking of kerogen promoted by solid acids, and cross-linking and cracking reactions of free SOM and residual kerogen under high temperatures. Although different from the classical hydrocarbon generation model of kerogen, this multistage hydrocarbon generation is consistent with the characteristics of the saline lacustrine source rocks in nature. The mineral transformation-induced desorption of SOM is a new pathway for petroleum formation, which can well explain the formation of low-mature oils in nature. In addition, the release of mineral-bound and kerogen-bound biomarkers results in two reversals of isomerization ratios. Considering mineral transformation and mineral-OM interactions can help us better understand and refine the hydrocarbon generation theory of OM.

Soil texture and microorganisms dominantly determine the subsoil carbonate content in the permafrost-affected area of the Tibetan Plateau.

Under climate warming conditions, storage and conversion of soil inorganic carbon (SIC) play an important role in regulating soil carbon (C) dynamics and atmospheric CO2 content in arid and semi-arid areas. Carbonate formation in alkaline soil can fix a large amount of C in the form of inorganic C, resulting in soil C sink and potentially slowing global warming trends. Therefore, understanding the driving factors affecting carbonate mineral formation can help better predict future climate change. Till date, most studies have focused on abiotic drivers (climate and soil), whereas a few examined the effects of biotic drivers on carbonate formation and SIC stock. In this study, SIC, calcite content, and soil microbial communities were analyzed in three soil layers (0-5 cm, 20-30 cm, and 50-60 cm) on the Beiluhe Basin of Tibetan Plateau. Results revealed that in arid and semi-arid areas, SIC and soil calcite content did not exhibit significant differences among the three soil layers; however, the main factors affecting the calcite content in different soil layers are different. In the topsoil (0-5 cm), the most important predictor of calcite content was soil water content. In the subsoil layers 20-30 cm and 50-60 cm, the ratio of bacterial biomass to fungal biomass (B/F) and soil silt content, respectively, had larger contributions to the variation of calcite content than the other factors. Plagioclase provided a site for microbial colonization, whereas Ca2+ contributed in bacteria-mediated calcite formation. This study aims to highlight the importance of soil microorganisms in managing soil calcite content and reveals preliminary results on bacteria-mediated conversion of organic to inorganic C.

Soil texture influences soil bacterial biomass in the permafrost-affected alpine desert of the Tibetan plateau.

Under warm climate conditions, permafrost thawing results in the substantial release of carbon (C) into the atmosphere and potentially triggers strong positive feedback to global warming. Soil microorganisms play an important role in decomposing organic C in permafrost, thus potentially regulating the ecosystem C balance in permafrost-affected regions. Soil microbial community and biomass are mainly affected by soil organic carbon (SOC) content and soil texture. Most studies have focused on acidic permafrost soil (pH < 7), whereas few examined alkaline permafrost-affected soil (pH > 7). In this study, we analyzed soil microbial communities and biomass in the alpine desert and steppe on the Tibetan plateau, where the soil pH values were approximately 8.7 ± 0.2 and 8.5 ± 0.1, respectively. Our results revealed that microbial biomass was significantly associated with mean grain size (MGS) and SOC content in alkaline permafrost-affected soils (p < 0.05). In particular, bacterial and fungal biomasses were affected by SOC content in the alpine steppe, whereas bacterial and fungal biomasses were mainly affected by MGS and SOC content, respectively, in the alpine desert. Combined with the results of the structural equation model, those findings suggest that SOC content affects soil texture under high pH-value (pH 8-9) and that soil microbial biomass is indirectly affected. Soils in the alpine steppe and desert are dominated by plagioclase, which provides colonization sites for bacterial communities. This study aimed to highlight the importance of soil texture in managing soil microbial biomass and demonstrate the differential impacts of soil texture on fungal and bacterial communities in alkaline permafrost-affected regions.

Distribution characteristics, source identification, and risk assessment of heavy metals in surface sediments of the salt lakes in the Ordos Plateau, China.

Salt lakes considerably affect the regional climate, environment, and ecology of semiarid regions characterized by low rainfall and high evaporation. However, under the stresses of global change and human disturbance, anthropogenic pollution is the primary factor threatening the lake's ecological environment. Surface sediment samples collected from four salt lakes in the Ordos Plateau were used to investigate the salinity, concentration, pollution status, potential sources of heavy metals, and influencing factors. The surface sediments of Beida Pond and Gouchi Pond were weakly alkaline (pH < 9) due to the presence of Na2SO4, whereas those of Chaigannaoer and Hongjiannao were strongly alkaline (pH > 9) due to the presence of Na2CO3. The concentration range of Cr, Ni, Cu, Zn, As, Cd, and Pb in the sediment samples collected from the salt lakes in the Ordos Plateau followed the order of Cr > Zn > Ni > Pb > Cu > As > Cd. The Cr concentration values were higher in Chagannaoer and Hongjiannao; however, the Ni, Cu, and Zn values were higher in Beida Pond and Gouchi Pond. The geoaccumulation index (Igeo) and enrichment factor (EF) consistently indicated that Cr posed the greatest potential ecological risk and that Ni, Cu, and Zn pollution was more severe in Beida Pond and Gouchi Pond than in Chagannaoer or Hongjiannao. However, the ecological risk index and potential ecological risk value indicated that these heavy metals posed low risks to the environment. The risk assessment code (RAC) revealed that Pb and Cr exhibited no mobility and had low potential bioavailability risk. Meanwhile, Zn, Ni, and As were categorized as medium risk. Cu had the highest mobility and was categorized as high risk. Principal component analysis for the four salt lakes revealed that the source of Ni, Cu, Zn, and Cd might be associated with water-soluble elements associated with aqueous migration, while the source of Cr, Pb, and As might be the lithospheric minerals carried by dust storms. Pearson's correlation analysis indicated that clay minerals were the primary adsorbers of Ni, Cu, Zn, and Cd. Moreover, pH was identified as the main environmental factor controlling the distribution of heavy metals in the salt lakes.

A dataset representing the impact of aromatic nuclei on the carbon isotope of gases.

This work presents a dataset which provides information on the influence of aromatic nuclei on the carbon isotope of gases. Gases analyzed herein were obtained by pyrolysis of model compounds and kerogens. The carbon isotope of gases from paraffin cracking with and without the addition of aromatic nuclei is summarized. We also obtained carbon isotope data for the gases from different type of kerogens, which indicate the role of aromatic nuclei in the formation of natural gases from kerogen cracking. Further interpretation and discussion of these data can be found in the related research article entitled "The methylation of aromatic nuclei - I: Implications for the geochemical evolution of gas" [1].

Increased precipitation accelerates soil organic matter turnover associated with microbial community composition in topsoil of alpine grassland on the eastern Tibetan Plateau.

Large quantities of carbon are stored in alpine grassland of the Tibetan Plateau, which is extremely sensitive to climate change. However, it remains unclear whether soil organic matter (SOM) in different layers responds to climate change analogously, and whether microbial communities play vital roles in SOM turnover of topsoil. In this study we measured and collected SOM turnover by the 14C method in alpine grassland to test climatic effects on SOM turnover in soil profiles. Edaphic properties and microbial communities in the northwestern Qinghai Lake were investigated to explore microbial influence on SOM turnover. SOM turnover in surface soil (0-10 cm) was more sensitive to precipitation than that in subsurface layers (10-40 cm). Precipitation also imposed stronger effects on the composition of microbial communities in the surface layer than that in deeper soil. At the 5-10 cm depth, the SOM turnover rate was positively associated with the bacteria/fungi biomass ratio and the relative abundance of Acidobacteria, both of which are related to precipitation. Partial correlation analysis suggested that increased precipitation could accelerate the SOM turnover rate in topsoil by structuring soil microbial communities. Conversely, carbon stored in deep soil would be barely affected by climate change. Our results provide valuable insights into the dynamics and storage of SOM in alpine grasslands under future climate scenarios.

Aliphatic and polycyclic aromatic hydrocarbons (PAHs) in soils of the northwest Qinling Mountains: Patterns, potential risk and an appraisal of the PAH ratios to infer their source.

Surface soils from the tourist areas of the northwest Qinling Mountains were analyzed to determine the concentrations, probable sources and potential risks of hydrocarbons. Concentrations of aliphatic and aromatic hydrocarbons ranged from 4.18 to 3240 ng g-1 and 0.0462 to 101 ng g-1 dry weight, respectively. The extent of soil contamination by hydrocarbons was generally typified by unpolluted to slightly polluted levels. The incremental lifetime cancer risks (ILCRs) for exposure to soil-borne PAHs indicated complete safety for tourists. Early diagenesis of natural products, bacteria activities and petroleum were the three main sources of aliphatic hydrocarbons, while the transport of air pollutants from pyrolytic processes was the main origin of PAHs. Because the photochemical reaction of PAHs in the atmosphere would produce lower ratios for Ant/(Ant + Phe), BaA/(BaA + Chr) and IcdP/(IcdP + BghiP), but a higher ratio for Fla/(Fla + Pyr), the source classification highly depended on the diagnostic ratios chosen. The plot of ΣCOM/Σ13PAH vs. ΣLMW/ΣHMWPAH provide additional information to distinguish the origins of PAHs, and it showed a cluster of pyrogenic sources except for sample JFS-8. Four sources were resolved by principal component analysis: (1) a low temperature pyrogenic process related to the use of fossil fuel and biomass, such as charcoal, straw and wood, which contributes 63.1% of the measured PAHs; (2) the potential contribution of diagenetic processes, contributing 18.4%; (3) traffic emissions, contributing 9.27%; and (4) bioconversion/bacterial action, contributing 5.82%. Additionally, there was a good exponential relationship (r2 = 0.969) between the natural n-alkanes ratio (NAR) and carbon preference index for C23-C35 (CPI23-35) for all samples, which is of great use for the determination of the origins of aliphatic hydrocarbon.