Nitrification, denitrification, and related functional genes under elevated CO2 : A meta-analysis in terrestrial ecosystems

Impact of elevated CO2 on microbial communities and functions in riparian sediments: Role of pollution levels in modulating effects

The impact of elevated CO2 levels on microorganisms is a focal point in studying the environmental effects of global climate change. A growing number of studies have demonstrated the importance of the direct effects of elevated CO2 on microorganisms, which are confounded by indirect effects that are not easily identified. Riparian zones have become key factor in identifying the environmental effects of global climate change because of their special location. However, the direct effects of elevated CO2 levels on microbial activity and function in riparian zone sediments remain unclear. In this study, three riparian sediments with different pollution risk levels of heavy metals and nutrients were selected to explore the direct response of microbial communities and functions to elevated CO2 excluding plants. The results showed that the short-term effects of elevated CO2 did not change the diversity of the bacterial and fungal communities, but altered the composition of their communities. Additionally, differences were observed in the responses of microbial functions to elevated CO2 levels among the three regions. Elevated CO2 promoted the activities of nitrification and denitrification enzymes and led to significant increases in N2O release in the three sediments, with the greatest increase of 76.09 % observed in the Yuyangshan Bay (YYS). Microbial carbon metabolism was promoted by elevated CO2 in YYS but was significantly inhibited by elevated CO2 in Gonghu Bay and Meiliang Bay. Moreover, TOC, TN, and Pb contents were identified as key factors contributing to the different microbial responses to elevated CO2 in sediments with different heavy metal and nutrient pollution. In conclusion, this study provides in-depth insights into the responses of bacteria and fungi in polluted riparian sediments to elevated CO2, which helps elucidate the complex interactions between microbial activity and environmental stressors.

Nitrogen and phosphorus additions alter soil N transformations in a Metasequoia glyptostroboides plantation

Introduction

Nitrogen (N) and phosphorus (P) enrichment due to anthropogenic activities can significantly affect soil N transformations in forest ecosystems. However, the effects of N and P additions on nitrification and denitrification processes in Metasequoia glyptostroboides plantations, and economically important forest type in China, remain poorly understood.

Methods

This study investigated the responses of soil nitrification and denitrification rates, as well as the abundances of nitrifiers and denitrifiers, to different levels of N and P additions in a 6-year nutrient addition experiment in a M. glyptostroboides plantation.

Results

Stepwise multiple regression analysis was used to identify the main predictors of nitrification and denitrification rates. The results showed that moderate N addition (N2 treatment, 2.4 mol·m-2) stimulated nitrification rates and abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB), while excessive N and P additions inhibited denitrification rates and reduced the abundance of nirS-type denitrifiers. AOB abundance was the main predictor of nitrification rates under N additions, whereas microbial biomass carbon and nirS gene abundance were the key factors controlling denitrification rates. Under P additions, tree growth parameters (diameter at breast height and crown base height) and AOB abundance were the primary predictors of nitrification and denitrification rates.

Discussion

Our study reveals complex interactions among nutrient inputs, plant growth, soil properties, and microbial communities in regulating soil N transformations in plantation forests. This study also offers valuable insights for formulating effective nutrient management strategies to enhance the growth and health of M. glyptostroboides plantations under scenarios of increasing elevated nutrient deposition.

Land use modified impacts of global change factors on soil microbial structure and function: A global hierarchical meta-analysis

Nitrogen cycling in terrestrial ecosystems is critical for biodiversity, vegetation productivity and biogeochemical cycling. However, little is known about the response of functional nitrogen cycle genes to global change factors in soils under different land uses. Here, we conducted a multiple hierarchical mixed effects meta-analyses of global change factors (GCFs) including warming (W+), mean altered precipitation (MAP+/-), elevated carbon dioxide concentrations (eCO2), and nitrogen addition (N+), using 2706 observations extracted from 200 peer-reviewed publications. The results showed that GCFs had significant and different effects on soil microbial communities under different types of land use. Under different land use types, such as Wetland, Tundra, Grassland, Forest, Desert and Agriculture, the richness and diversity of soil microbial communities will change accordingly due to differences in vegetation cover, soil management practices and environmental conditions. Notably, soil bacterial diversity is positively correlated with richness, but soil fungal diversity is negatively correlated with richness, when differences are driven by GCFs. For functional genes involved in nitrification, eCO2 in agricultural soils and the interaction of N+ with other GCFs in grassland soils stimulate an increase in the abundance of the AOA-amoA gene. In agricultural soil, MAP+ increases the abundance of nifH. W+ in agricultural soils and N+ in grassland soils decreased the abundance of nifH. The abundance of the genes nirS and nirK, involved in denitrification, was mainly negatively affected by W+ and positively affected by eCO2 in agricultural soil, but negatively affected by N+ in grassland soil. This meta-analysis was important for subsequent research related to global climate change. Considering data limitations, it is recommended to conduct multiple long-term integrated observational experiments to establish a scientific basis for addressing global changes in this context.

Greenhouse gas emissions in the Indian agriculture sector and mitigation by best management practices and smart farming technologies-a review

The growing demand for agricultural products, driven by the Green Revolution, has led to a significant increase in food production. However, the demand is surpassing production, making food security a major concern, especially under climatic variation. The Indian agriculture sector is highly vulnerable to extreme rainfall, drought, pests, and diseases in the present climate change scenario. Nonetheless, the key agriculture sub-sectors such as livestock, rice cultivation, and biomass burning also significantly contribute to greenhouse gas (GHG) emissions, a driver of global climate change. Agriculture activities alone account for 10-12% of global GHG emissions. India is an agrarian economy and a hub for global food production, which is met by intensive agricultural inputs leading to the deterioration of natural resources. It further contributes to 14% of the country's total GHG emissions. Identifying the drivers and best mitigation strategies in the sector is thus crucial for rigorous GHG mitigation. Therefore, this review aims to identify and expound the key drivers of GHG emissions in Indian agriculture and present the best strategies available in the existing literature. This will help the scientific community, policymakers, and stakeholders to evaluate the current agricultural practices and uphold the best approach available. We also discussed the socio-economic, and environmental implications to understand the impacts that may arise from intensive agriculture. Finally, we examined the current national climate policies, areas for further research, and policy amendments to help bridge the knowledge gap among researchers, policymakers, and the public in the national interest toward GHG reduction goals.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

Warming-Induced Stimulation of Soil N2O Emissions Counteracted by Elevated CO2 from Nine-Year Agroecosystem Temperature and Free Air Carbon Dioxide Enrichment

Globally, agricultural soils account for approximately one-third of anthropogenic emissions of the potent greenhouse gas and stratospheric ozone-depleting substance nitrous oxide (N2O). Emissions of N2O from agricultural soils are affected by a number of global change factors, such as elevated air temperatures and elevated atmospheric carbon dioxide (CO2). Yet, a mechanistic understanding of how these climatic factors affect N2O emissions in agricultural soils remains largely unresolved. Here, we investigate the soil N2O emission pathway using a 15N tracing approach in a nine-year field experiment using a combined temperature and free air carbon dioxide enrichment (T-FACE). We show that the effect of CO2 enrichment completely counteracts warming-induced stimulation of both nitrification- and denitrification-derived N2O emissions. The elevated CO2 induced decrease in pH and labile organic nitrogen (N) masked the stimulation of organic carbon and N by warming. Unexpectedly, both elevated CO2 and warming had little effect on the abundances of the nitrifying and denitrifying genes. Overall, our study confirms the importance of multifactorial experiments to understand N2O emission pathways from agricultural soils under climate change. This better understanding is a prerequisite for more accurate models and the development of effective options to combat climate change.

Elevated CO2 and nitrogen addition enhance the symbiosis and functions of rhizosphere microorganisms under cadmium exposure

Soil microbes are fundamental to ecosystem health and productivity. How soil microbial communities are influenced by elevated atmospheric carbon dioxide (eCO2) concentration and nitrogen (N) deposition under heavy metal pollution remains uncertain, despite global exposure of terrestrial ecosystems to eCO2, high N deposition and heavy metal stress. Here, we conducted a four year's open-top chamber experiment to assess the effects of soil cadmium (Cd) treatment (10 kg hm-2 year-1) alone and combined treatments of Cd with eCO2 concentration (700 ppm) and/or N addition (100 kg hm-2 year-1) on tree growth and rhizosphere microbial community. Relative to Cd treatment alone, eCO2 concentration in Cd contaminated soil increased the complexity of microbial networks, including the number links, average degree and positive/negative ratios. The combined effect of eCO2 and N addition in Cd contaminated soil not only increased the complexity of microbial networks, but also enhanced the abundance of microbial urealysis related UreC and nitrifying related amoA1 and amoA2, and the richness of arbuscular mycorrhiza fungi (AMF), thereby improving the symbiotic functions between microorganisms and plants. Results from correlation analysis and structural equation model (SEM) further demonstrated that eCO2 concentration and N addition acted on functions and networks differently. Elevated CO2 positively regulated microbial networks and functions through phosphorus (P) and Cd concentration in roots, while N addition affected microbial functions through soil available N and soil organic carbon (SOC) concentration and microbial network through soil Cd concentration. Overall, our findings highlight that eCO2 concentration and N addition make microbial communities towards ecosystem health that may mitigate Cd stress, and provide new insights into the microbiology supporting phytoremediation for Cd contaminated sites in current and future global change scenarios.

Spatial distribution characteristics of denitrification functional genes and the environmental drivers in Liaohe estuary wetland

Genes nirS, nirK, and nosZ are specific for the denitrification process, which is associated with greenhouse gas N2O emission. The abundances and diversities of community containing these three genes are usually used as a common index to reflect the denitrification process, and they would be affected by differences in environmental factors caused by changes from warm to cold conditions. The quantification of denitrification in natural wetlands is complex, and straightforward identification of spatial distribution and drivers affecting the process is still developing. In this study, the bacterial communities, gene diversities, and relative abundances involved in denitrification were investigated in Liaohe Estuary Wetland. We analyzed the relative abundances, diversities, and communities of bacteria containing the three genes at warm and cold conditions using Illumina MiSeq sequencing and detected the potential environmental factors influencing their distribution by using a random forest algorithm. There are great differences in the community composition of the bacteria containing genes nirS, nirK, and nosZ. All the abundant taxa of nirS and nirK communities belonged to phylum Proteobacteria. Compared with the community composition of bacteria containing nirS and nirK, the community of bacteria containing nosZ is more diverse, and the subdivision taxa of phylum Euryarchaeota was also abundant in the community containing nosZ. The distribution characteristics of the relative abundance of nirS and nirK showed obvious differences both at warm and cold climate conditions. The oxidation-reduction potential, nitrite nitrogen, and salinity were detected as potential variables that might explain the diversity of nirS. The total nitrogen and nitrite nitrogen were the important variables for predicting the relative abundance of nirS at warm climate condition, while oxidation-reduction potential and pH contributed to the diversity of nirS at cold condition. The bulk density of sediment was detected as a potential variable affecting the relative abundance of nirK at warm and cold conditions, and diversity of nirK at warm condition, while nitrite nitrogen was detected as an important environmental factor for predicting the diversity of nirK at cold condition. Overall, our results show that the key environmental factors, which affect the relative abundance, diversity, and community of bacteria containing the functional denitrification genes, are not exactly the same, and the diversities of nirS, nirK, and nosZ have a higher environmental sensitivity than their relative abundances.

Biochar alters the persistence of PAHs in soils by affecting soil physicochemical properties and microbial diversity: A meta-analysis

Polycyclic aromatic hydrocarbons (PAHs) pollution in soil is a pervasive environmental issue worldwide. Although biochar has the potential to immobilize PAHs in soils, there remains a study gap in the use of systematic analyses to assess the effectiveness of biochar for PAH removal and the factors that affect biochar. Hence, a meta-analysis utilizing 56 published studies was aimed to assess the impact of biochar on the PAH content, soil physicochemical properties, and microbial diversity in PAH-contaminated soils and to elucidate what factors impact the capability of biochar to alter PAH persistence. With biochar application, soil Ctot PAH concentrations were significantly reduced (15.4%), while the levels of Cfree PAHs and Cbioacc PAHs were reduced by 55.6% and 46.5%, respectively. Additionally, biochar improved the physicochemical properties of PAH-contaminated soil and increased the diversity of microorganisms. Particularly, the relative abundance of PAH degraders increased significantly (43.7%), which indicated that PAH biodegradation was significantly enhanced. Soil physicochemical properties and biochar production conditions are indispensable for the study of the PAH persistence. The overall findings revealed that the pyrolysis of woody biochar at 300-500 °C was beneficial for reducing the PAH persistence in acidic, coarse, or fine and high soil organic matter content (>20 g/kg) soils.