Microbial taxonomic and functional attributes consistently predict soil CO2 emissions across contrasting croplands

Impacts of plant root traits and microbial functional attributes on soil respiration components in the desert-oasis ecotone

Dividing soil respiration (Rs) into autotrophic respiration (Ra) and heterotrophic respiration (Rh) represents a pivotal step in deciphering how Rs responds to environmental perturbations. Nevertheless, in arid ecosystems beset by environmental stress, the partitioning of Rs and the underlying mechanisms through which microbial and root traits govern the distinct components remain poorly understood. This study was strategically designed to investigate Rs and its components (Ra and Rh), soil properties, and root traits within the desert-oasis ecotone (encompassing the river bank, transitional zone, and desert margin) of northwest China. Employing metagenomics, we quantitatively characterized microbial taxonomic attributes (i.e., taxonomic composition) and functional attributes (specifically, functional genes implicated in microbial carbon metabolism). Field measurements during the growing season of 2019 unveiled a pronounced decline in soil respiration rates along the environmental gradient from the river bank to the desert margin. The mean soil respiration rate was recorded as 1.82 ± 0.41 μmol m-2 s-1 at the river bank, 0.49 ± 0.15 μmol m-2 s-1 in the transitional zone, and a meager 0.45 ± 0.12 μmol m-2 s-1 in the desert margin. Concomitantly, the Ra and Rh components exhibited a similar trend throughout the study period, with Rh emerging as the dominant driver of Rs. Utilizing random forest modeling, we unearthed significant associations between microbial taxonomic and functional features and Rs components. Notably, both Ra and Rh displayed robust positive correlations with the abundance of phosphatidylinositol glycan A, a key player in microbial carbon metabolism. Partial least squares path modeling further elucidated that soil properties and microbial functions exerted direct and positive influences on both Ra and Rh, whereas taxonomic features failed to register a significant impact. When considering the combined effects of biotic and abiotic factors, microbial functional attributes emerged as the linchpin in dictating Rs composition. Collectively, these findings suggest that a trait-based approach holds great promise in more effectively revealing the response mechanisms of Rs composition to environmental changes, thereby offering novel vistas for future investigations into carbon cycling in terrestrial soils.

Effects of stand age and soil microbial communities on soil respiration throughout the growth cycle of poplar plantations in northeastern China

Introduction

Many studies have identified stand age and soil microbial communities as key factors influencing soil respiration (Rs). However, the effects of stand age on Rs and soil microbial communities throughout the growth cycle of poplar (Populus euramevicana cv.'I-214') plantations remain unclear.

Methods

In this study, we adopted a spatial approach instead of a temporal one to investigate Rs and soil microbial communities in poplar plantations of 15 different ages (1-15  years old).

Results

The results showed that Rs exhibited clear seasonal dynamics, with the highest rates observed in the first year of stand age (1-year-old). As stand age increased, Rs showed a significant decreasing trend. We further identified r-selected microbial communities (copiotrophic species) as key biological factors influencing the decline in Rs with increasing stand age. Other abiotic factors, such as soil temperature (ST), pH, soil organic carbon (SOC), nitrate nitrogen (NO3 --N), and the C/N ratio of plant litter (Litter C/N), were also significantly correlated with Rs. Increased stand age promoted fungal community diversity but suppressed bacterial community diversity. Bacterial and fungal communities differed significantly in abundance, composition, and function, with the Litter C/N ratio being a key variable affected by microbial community changes.

Conclusion

This study provides crucial empirical evidence on how stand age affects Rs, highlighting the connection between microbial community assemblages, their trophic strategies, and Rs over the growth cycle of poplar plantations.

The responses of CO2 emission to nitrogen application and earthworm addition in the soybean cropland

The effects of nitrogen application or earthworms on soil respiration in the Huang-Huai-Hai Plain of China have received increasing attention. However, the response of soil carbon dioxide (CO2) emission to nitrogen application and earthworm addition is still unclear. A field experiment with nitrogen application frequency and earthworm addition was conducted in the Huang-Huai-Hai Plain. Results showed nitrogen application frequency had a significant effect on soil respiration, but neither earthworms nor their interaction with nitrogen application frequency were significant. Low-frequency nitrogen application (NL) significantly increased soil respiration by 25%, while high-frequency nitrogen application (NH), earthworm addition (E), earthworm and high-frequency nitrogen application (E*NH), and earthworm and low-frequency nitrogen application (E*NL) also increased soil respiration by 21%, 21%, 12%, and 11%, respectively. The main reason for the rise in soil respiration was alterations in the bacterial richness and keystone taxa (Myxococcales). The NH resulted in higher soil nitrogen levels compared to NL, but NL had the highest bacterial richness. The abundance of Corynebacteriales and Gammaproteobacteria were positively connected with the CO2 emissions, while Myxococcales, Thermoleophilia, and Verrucomicrobia were negatively correlated. Our findings indicate the ecological importance of bacterial communities in regulating the carbon cycle in the Huang-Huai-Hai Plain.

Time-dependent effects of microplastics on soil bacteriome

Microplastic threats to biodiversity, health and ecological safety are adding to concern worldwide, but the real impacts on the functioning of organisms and ecosystems are obscure owing to their inert characteristics. Here we investigated the long-lasting ecological effects of six prevalent microplastic types: polyethylene (PE), polypropylene (PP), polyamide (PA), polystyrene (PS), polyethylene terephthalate (PET), and polyvinyl chloride (PVC) on soil bacteria at a 2 % (w/w) level. Due to the inertia and lack of available nitrogen of these microplastics, their effects on bacteriome tended to converge after one year and were strongly different from their short-term effects. The soil volumes around microplastics were very specific, in which the microplastic-adapted bacteria (e.g., some genera in Actinobacteria) were enriched but the phyla Bacteroidetes and Gemmatimonadetes declined, resulting in higher microbial nitrogen requirements and reduced organic carbon mineralization. The reshaped bacteriome was specialized in the genetic potential of xenobiotic and lipid metabolism as well as related oxidation, esterification, and hydrolysis processes, but excessive oxidative damage resulted in severe weakness in community genetic information processing. According to model predictions, microplastic effects are indirectly derived from nutrients and oxidative stress, and the effects on bacterial functions are stronger than on structure, posing a heavy risk to soil ecosystems.

Impact of selenium on rhizosphere microbiome of a hyperaccumulation plant Cardamine violifolia

Cardamine violifolia is the only selenium hyperaccumulation plant found in China. It has been developed as a source of medicinal and edible products that we can consume as selenium supplements. Many planting approaches have been developed to increase the selenium content of C. violifolia for nutrient biofortification. However, the contribution of rhizosphere microbes of C. violifolia to selenium enrichment has not been investigated. In this study, four types of selenium, i.e., selenate, selenite, nanoparticles selenium from Bacillus subtilis (B. subtilis-Se), and organic selenium from yeast (yeast-Se), were added to the soil that C. violifolia was grown in, respectively. Selenate led to the greatest accumulation of selenium in C. violifolia, followed by selenite, B. subtilis-Se, and yeast-Se. Except for yeast-Se, the concentration of selenium in C. violifolia positively correlated with the amount of selenium added to the soil. Furthermore, the different types of exogenous selenium exhibited distinct effects on the rhizosphere microbiome of C. violifolia. Alpha and beta diversity analyses demonstrated that rhizosphere microbiome was more obviously affected by selenium from B. subtilis and yeast than from selenate and selenite. Different microbial species were enriched in the rhizosphere of C. violifolia under various exogenous selenium treatments. B. subtilis-Se application enhanced the abundance of Leucobacter, Sporosarcina, Patulibacter, and Denitrobacter, and yeast-Se application enriched the abundance of Singulishaera, Lactobacillus, Bdellovibrio, and Bosea. Bosea and the taxon belonging to the order Solirubrobacterales were enriched in the samples with selenate and selenite addition, respectively, and the abundances of these were linearly related to the concentrations of selenate and selenite applied in the rhizosphere of C. violifolia. In summary, this study revealed the response of the rhizosphere microbiome of C. violifolia to exogenous selenium. Our findings are useful for developing suitable selenium fertilizers to increase the selenium hyperaccumulation level of this plant.

Root Functional Trait and Soil Microbial Coordination: Implications for Soil Respiration in Riparian Agroecosystems

Predicting respiration from roots and soil microbes is important in agricultural landscapes where net flux of carbon from the soil to the atmosphere is of large concern. Yet, in riparian agroecosystems that buffer aquatic environments from agricultural fields, little is known on the differential contribution of CO₂ sources nor the systematic patterns in root and microbial communities that relate to these emissions. We deployed a field-based root exclusion experiment to measure heterotrophic and autotrophic-rhizospheric respiration across riparian buffer types in an agricultural landscape in southern Ontario, Canada. We paired bi-weekly measurements of in-field CO₂ flux with analysis of soil properties and fine root functional traits. We quantified soil microbial community structure using qPCR to estimate bacterial and fungal abundance and characterized microbial diversity using high-throughput sequencing. Mean daytime total soil respiration rates in the growing season were 186.1 ± 26.7, 188.7 ± 23.0, 278.6 ± 30.0, and 503.4 ± 31.3 mg CO₂-C m^-2 h^-1 in remnant coniferous and mixed forest, and rehabilitated forest and grass buffers, respectively. Contributions of autotrophic-rhizospheric respiration to total soil CO₂ fluxes ranged widely between 14 and 63% across the buffers. Covariation in root traits aligned roots of higher specific root length and nitrogen content with higher specific root respiration rates, while microbial abundance in rhizosphere soil coorindated with roots that were thicker in diameter and higher in carbon to nitrogen ratio. Variation in autotrophic-rhizospheric respiration on a soil area basis was explained by soil temperature, fine root length density, and covariation in root traits. Heterotrophic respiration was strongly explained by soil moisture, temperature, and soil carbon, while multiple factor analysis revealed a positive correlation with soil microbial diversity. This is a first in-field study to quantify root and soil respiration in relation to trade-offs in root trait expression and to determine interactions between root traits and soil microbial community structure to predict soil respiration.

Effect of Organic and Conventional Systems Used to Grow Pecan Trees on Diversity of Soil Microbiota

Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) orchards located in Coahuila, Mexico. The analyzed variables were pH, N, P, K, soil organic matter, organic matter quality, soil organic carbon, C/N ratio, carbon fractions, microbial biomass carbon, easily extractable Glomalin, colony-forming units, CO2 emissions, and the enzyme activity. The DNA of soil bacteria was extracted, amplified (V3-V4 16S rRNA), and sequenced using Illumina. To compare variables between agronomic managements, t tests were used. Sequences were analyzed in QIIME (Quantitative Insights Into Microbial Ecology). A canonical correspondence analysis (CCA) was used to observe associations between the ten most abundant phyla and soil variables in both types of agronomic managements. In Org management, variables related to the capture of recalcitrant carbon compounds were significant, and there was a greater diversity of bacterial communities capable of promoting organic carbon sequestration. In Conv management, variables related to the increase in carbon mineralization, as well as the enzymatic activity related to the metabolism of labile compounds, were significant. The CCA suggested a separation between phyla associated with some variables. Agronomic management impacted soil chemical and biological parameters related to carbon dynamics, including bacterial communities associated with carbon sequestration. Further research is still necessary to understand the plasticity of some bacterial communities, as well as the soil–plant dynamics.