Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil.

Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming-induced environmental changes is critical to evaluating their influences on soil biogeochemical cycles. In this study, a functional gene array (i.e., geochip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately, and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25% and 5%, while the community functional gene ß-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw-related soil and plant changes and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.

Phytoremediation of diphenylarsinic-acid-contaminated soil by Pteris vittata associated with Phyllobacterium myrsinacearum RC6b.

A pot experiment was conducted to explore the phytoremediation of a diphenylarsinic acid (DPAA)-spiked soil using Pteris vittata associated with exogenous Phyllobacterium myrsinacearum RC6b. Removal of DPAA from the soil, soil enzyme activities, and the functional diversity of the soil microbial community were evaluated. DPAA concentrations in soil treated with the fern or the bacterium were 35-47% lower than that in the control and were lowest in soil treated with P. vittata and P. myrsinacearum together. The presence of the bacterium added in the soil significantly increased the plant growth and DPAA accumulation. In addition, the activities of dehydrogenase and fluorescein diacetate hydrolysis and the average well-color development values increased by 41-91%, 37-78%, and 35-73%, respectively, in the treatments with P. vittata and/or P. myrsinacearum compared with the control, with the highest increase in the presence of P. vittata and P. myrsinacearum together. Both fern and bacterium alone greatly enhanced the removal of DPAA and the recovery of soil ecological function and these effects were further enhanced by P. vittata and P. myrsinacearum together. Our findings provide a new strategy for remediation of DPAA-contaminated soil by using a hyperaccumulator/microbial inoculant alternative to traditional physicochemical method or biological degradation.

Mixed planting of subtropical Chinese fir in South China improves microbial carbon source metabolism and functional diversity through the accumulation of nutrients from soil aggregates.

Introduction: Soil microbial functional traits are key indicators of soil microbial ecological traits; however, how mixing patterns of Chinese fir and broadleaved trees drive soil microbial functional trait variation at the aggregate scale and how soil microbial functional traits are linked to soil fertility factors have largely not been determined. Methods: In this study, soil from the 0-20 cm depths in three Chinese fir plantations was collected, and the soil samples were separated into >2 mm (large macro-aggregate), 0.25-2 mm (macro-aggregate) and <0.25 mm (micro-aggregate) by complying with an optimal moisture sieving procedure. The metabolic activities, functional diversity and different carbon sources utilization characteristics of the soil microorganisms were determined by the Biolog Eco microplate method. Results: In all Chinese fir plantations, micro-aggregates (<0.25 mm) consistently exhibited the highest levels of microbial metabolic activity, a more uniform carbon source utilisation capacity, and the highest microbial diversity. Micro-aggregates also showed elevated levels of soil organic carbon (OC), total nitrogen (TN), total phosphorus (TP), and higher ratios of C/N and C/P compared to large macro-aggregates and macro-aggregates, indicating that micro-aggregates contain more resources available to soil microorganisms. Soil OC, TN, and TP content were enhanced by integration with Michelia macclurei, suggesting that this combination promotes relatively favourable soil conditions for microbial growth and multiplication. This, in turn, promotes microbial metabolic activity. Furthermore, redundancy and correlation analyses showed that soil OC, TN, and TP were identified as principal determinants of soil microbial functional properties in Chinese fir plantations. Discussion: In summary, mixed cultivation and aggregate size influenced microbial functional properties via soil nutrient alterations. Consequently, adopting a mixed cultivation approach of Chinese fir and broadleaved trees is advocated in the subtropical regions of Guangxi. Employing a diversity of tree species, including M. macclurei, is recommended for optimal soil quality preservation.

Deep soil microbial carbon metabolic function is important but often neglected: a study on the Songnen Plain reed wetland, Northeast China.

Soil microbial carbon metabolism is critical in wetland soil carbon cycling, and is also a research hotspot at present. However, most studies focus on the surface soil layer in the wetlands and the microorganisms associated with this layer. In this study, 0-75 cm soil profiles were collected from five widely separated reed wetlands in the Songnen Plain, which has a large number of middle-high latitude inland saline-sodic wetlands. The Biolog-ECO method was used to determine the carbon metabolic activity and functional diversity of soil microorganisms. The results showed that soil carbon metabolic activity decreased with increasing soil depth. The carbon metabolic activity of soil microorganisms in the 60-75 cm layer was approximately 57.41%-74.60% of that in the 0-15 cm layer. The soil microbial Shannon index and utilization rate of amines decreased with an increase in soil depth, while the Evenness index and utilization rate of polymers tended to increase with soil depth. Dissolved organic carbon (DOC) is the most important factor affecting microbial carbon source utilization preference, because microorganisms mainly obtain the carbon source from DOC. The result of the correlation analysis showed that the soil microbial carbon metabolic activity, Shannon index, and Evenness index significantly correlated with soil total carbon (TC), microbial biomass carbon (MBC), DOC, total nitrogen (TN), ammonium nitrogen (NH4 +-N), nitrate nitrogen (NO3 --N) contents, and electrical conductivity (EC). This study emphasized the important role of microbial carbon metabolic function in deep soil.

Heavy metal effects on multitrophic level microbial communities and insights for ecological restoration of an abandoned electroplating factory site.

The response of soil microbes to heavy metal pollution provides a metric to evaluate the soil health and ecological risks associated with heavy metal contamination. However, a multitrophic level perspective of how soil microbial communities and their functions respond to long-term exposure of multiple heavy metals remains unclear. Herein, we examined variations in soil microbial (including protists and bacteria) diversity, functional guilds and interactions along a pronounced metal pollution gradient in a field surrounding an abandoned electroplating factory. Given the stressful soil environment resulting from extremely high heavy metal concentrations and low nutrients, beta diversity of protist increased, but that of bacteria decreased, at high versus low pollution sites. Additionally, the bacteria community showed low functional diversity and redundancy at the highly polluted sites. We further identified indicative genus and "generalists" in response to heavy metal pollution. Predatory protists in Cercozoa were the most sensitive protist taxa with respect to heavy metal pollution, whereas photosynthetic protists showed a tolerance for metal pollution and nutrient deficiency. The complexity of ecological networks increased, but the communication among the modules disappeared with increasing metal pollution levels. Subnetworks of tolerant bacteria displaying functional versatility (Blastococcus, Agromyces and Opitutus) and photosynthetic protists (microalgae) became more complex with increasing metal pollution levels, indicating their potential for use in bioremediation and restoration of abandoned industrial sites contaminated by heavy metals.

Coriander (Coriandrum sativum L.) in Combination with Organic Amendments and Arbuscular Mycorrhizal Inoculation: An Efficient Option for the Phytomanagement of Trace Elements-Polluted Soils.

The cultivation of coriander (Coriandrum sativum L.) destined for essential oils production was recently presented as an innovative and economically viable alternative for the phytomanagement of trace elements (TE)-polluted soils. However, Cd accumulation in shoots has proven to be an obstacle in the valorization of the distillation residues and the development of these phytotechnologies. The present study aimed to evaluate the effect of arbuscular mycorrhizal fungus (Funneliformis mosseae) inoculation and organic amendment application on the soil TE bioavailability and plant uptake, as well as on the soil quality and health improvement. The application of compost and sewage sludge improved the growth of coriander and Cd and Zn immobilization in soil, resulting in reduced Cd plant uptake. A synergistic effect of arbuscular mycorrhizal fungi (AMF) inoculation and organic amendments was observed in the decrease in the extractable soil Cd and Zn concentrations, but not in the Cd plant uptake. Despite a significant decrease in Cd accumulation in shoots, coriander retained its accumulative phenotype, with a metal bioconcentration factor close to 1. Furthermore, both the vegetation and the organic amendments improved the soil quality and health by increasing its microbial biomass, as estimated by phospholipid fatty acids, soil enzyme activities (dehydrogenase, phosphatase, ß-glucosidase, and cellubiosidase), and the bacterial metabolic function and diversity. The findings demonstrate the potential of C. sativum, particularly in combination with organic amendments and AMF inoculation, for the phytomanagement of TE-polluted soils and soil quality and health improvement.

Effect of controlled-release urea fertilizers for oilseed rape (Brassica napus L.) on soil carbon storage and CO2 emission.

Fertilizer-induced CO2 emission is a primary driver of global warming. The experiment was used to study whether controlled-release urea (CRU) application in winter oilseed rape can play a positive role in mitigating CO2 emission and promoting C utilization by soil microorganisms. Five fertilizer types consisted of N0 (0 g N plant-1), conventional CRU application (CRU100%), monotypic CRU at the 80% of conventional rate (CRU80%), co-application of CRU with uncoated urea (CRC), and organic fertilizer (CRO). Results showed that soil CO2 fluxes were significantly affected by N fertilizer types after the start of the stem growing (P < 0.05). CO2 emissions typically peaked during the seed filling period, with the highest emission of 1.99 µmol m-2 s-1 being registered for CRU100%. CRU100% had 25.00%, 30.60%, and 4.17% greater CO2 emissions than CRU80%, CRC, and CRO practices by harvest, respectively. Compared to the conventional CRU treatment, CRU80% led to a lower root volume and root mass ratio than CRU100%, which could partly contribute to the reduced CO2 emission. Conversely, CRU80% performed better in N agronomic efficiency than that of CRU100% treatment. Also, C source utilization by soil microbiomes as well as microbial diversity indices following CRU80% along with CRO applications was substantially higher than that under the conventional CRU supply. These observations suggest that opportunity exists to maintain N balance by N fertilization practices to mitigate CO2 emission from cropland. Further, a close and positive relationship between soil total nitrogen and CO2 emission also supports this. CRO-treated soils substantially elevated the contents of total carbon and readily oxidation carbon over CK. Moreover, the enzyme activity of ß-glucosidase in CRO soil was about twice as high as the CRU100%. Consequently, CRU amendments by decreasing CRU rate application and the incorporation of organic fertilizer into CRU have the potential for mitigating of CO2 emission and positive effect on the soil microbial functional diversity to improve nitrogen use efficiency of rapeseed.

Comparative effects of the recovery from sulfuric and nitric acid rain on the soil enzyme activities and metabolic functions of soil microbial communities.

Acid rain (AR) is a serious issue in China, particularly in the Yangtze River Delta region where the economy has undergone rapid development. Over the last few years, the composition of acid rain in the Yangtze River Delta region has gradually changed from sulfuric acid rain (SAR) to nitric acid rain (NAR) due to controls on SO2 emissions, but increased NOx emissions. These changes have made ecosystems more complex. For this study, we halted AR treatments in Quercus acutissima forest plots that had received simulated AR for one year and monitored them from the following February to November. We investigated their soil resident enzyme and microbial metabolic activities, as well as community functional diversity. The results revealed that AR treatments negatively affected both the soil microbial activity and soil microbial community functional diversity; however, both managed to recover over time, once the AR treatments were stopped. During the AR treatment and recovery periods, four main categories (carbohydrates, carboxylic acids, amino acids, and polymers) were dominantly utilized. The utilization of pyruvic acid, which was affected by the AR treatments, as well as d-mannitol and tween 80, accounted for changes in the peak values of the C substrate groups during the AR treatment recovery period. Finally, changes in the activities of soil enzymes recorded following AR recovery, were closely related to the utilization of six C substrate groups. Our results suggested that the recovery of soils following the cessation of NAR stress was more rapid than from SAR. Further, that short-term NAR could be easily treated during the transformation from SAR to NAR in the Yangtze River Delta region. These results might also enrich the basic data relating to post-AR treatments on the soil environment, while having significance toward guiding further studies on the recovery of ecosystems from AR.