Soil carbon sequestration - An interplay between soil microbial community and soil organic matter dynamics

Body size: A hidden trait of the organisms that influences the distribution of antibiotic resistance genes in soil

Body size is a key life-history trait of organisms, which has important ecological functions. However, the relationship between soil antibiotic resistance gene (ARG) distribution and organisms' body size has not been systematically reported so far. Herein, the impact of organic fertilizer on the soil ARGs and organisms (bacteria, fungi, and nematode) at the aggregate level was analyzed. The results showed that the smaller the soil aggregate size, the greater the abundance of ARGs, and the larger the body size of bacteria and nematodes. Further analysis revealed significant positive correlations of ARG abundance with the body sizes of bacteria, fungi, and nematodes, respectively. Additionally, the structural equation model demonstrated that changes in soil fertility mainly regulate the ARG abundance by affecting bacterial body size. The random forest model revealed that total phosphorus was the primary soil fertility factor influencing the body size of organisms. Therefore, these findings proposed that excessive application of phosphate fertilizers could increase the risk of soil ARG transmission by increasing the body size of soil organisms. This study highlights the significance of organisms' body size in determining the distribution of soil ARGs and proposes a new disadvantage of excessive fertilization from the perspective of ARGs.

UHPM dominance in driving the formation of petroleum-contaminated soil aggregate, the bacterial communities succession, and phytoremediation

This study focused on the effects of urea humate-based porous materials (UHPM) on soil aggregates, plant physiological characteristics, and microbial diversity to explore the effects of UHPM on the phytoremediation of petroleum-contaminated soil. The compositions of soil aggregates, ryegrass (Lolium perenne) biomass, plant petroleum enrichment capacity, and bacterial communities in soils with and without UHPM were investigated. The results showed that UHPM significantly increased soil aggregate content by 0.25 mm-5 mm, resulting in higher fertilizer holding capacity, erosion resistance capacity, and plant biomass and microbial number than the soil without UHPM mixed. In addition, UHPM decreased the absorption of petroleum by plants in the soil while increasing the abundance of degrading bacteria and petroleum-degrading-related genes in the soil, thereby promoting the removal of hard-to-degrade petroleum components. RDA showed that, compared with the unimproved soil, each soil indicator was positively correlated with a high abundance of degrading bacteria in the improved soil and was significant. UHPM can be regarded as a petroleum-contaminated soil remediation agent that combines slow nutrient release with soil improvement effects.

Interplay of soil characteristics and arbuscular mycorrhizal fungi diversity in alpine wetland restoration and carbon stabilization

Alpine wetlands are critical ecosystems for global carbon (C) cycling and climate change mitigation. Ecological restoration projects for alpine grazing wetlands are urgently needed, especially due to their critical role as carbon (C) sinks. However, the fate of the C pool in alpine wetlands after restoration from grazing remains unclear. In this study, soil samples from both grazed and restored wetlands in Zoige (near Hongyuan County, Sichuan Province, China) were collected to analyze soil organic carbon (SOC) fractions, arbuscular mycorrhizal fungi (AMF), soil properties, and plant biomass. Moreover, the Tea Bag Index (TBI) was applied to assess the initial decomposition rate (k) and stabilization factor (S), providing a novel perspective on SOC dynamics. The results of this research revealed that the mineral-associated organic carbon (MAOC) was 1.40 times higher in restored sites compared to grazed sites, although no significant difference in particulate organic carbon (POC) was detected between the two site types. Furthermore, the increased MAOC after restoration exhibited a significant positive correlation with various parameters including S, C and N content, aboveground biomass, WSOC, AMF diversity, and NH4+. This indicates that restoration significantly increases plant primary production, litter turnover, soil characteristics, and AMF diversity, thereby enhancing the C stabilization capacity of alpine wetland soils.

Application of Artificial Intelligence and Sensor Fusion for Soil Organic Matter Prediction

Soil organic matter (SOM) is one of the best indicators to assess soil health and understand soil productivity and fertility. Therefore, measuring SOM content is a fundamental practice in soil science and agricultural research. The traditional approach (oven-dry) of measuring SOM is a costly, arduous, and time-consuming process. However, the integration of cutting-edge technology can significantly aid in the prediction of SOM, presenting a promising alternative to traditional methods. In this study, we tested the hypothesis that an accurate estimate of SOM might be obtained by combining the ground-based sensor-captured soil parameters and soil analysis data along with drone images of the farm. The data are gathered using three different methods: ground-based sensors detect soil parameters such as temperature, pH, humidity, nitrogen, phosphorous, and potassium of the soil; aerial photos taken by UAVs display the vegetative index (NDVI); and the Haney test of soil analysis reports measured in a lab from collected samples. Our datasets combined the soil parameters collected using ground-based sensors, soil analysis reports, and NDVI content of farms to perform the data analysis to predict SOM using different machine learning algorithms. We incorporated regression and ANOVA for analyzing the dataset and explored seven different machine learning algorithms, such as linear regression, Ridge regression, Lasso regression, random forest regression, Elastic Net regression, support vector machine, and Stochastic Gradient Descent regression to predict the soil organic matter content using other parameters as predictors.

Life at the borderlands: microbiomes of interfaces critical to One Health

Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.

Drivers and human impacts on topsoil bacterial and fungal community biogeography across Australia

Soil microbial diversity mediates a wide range of key processes and ecosystem services influencing planetary health. Our knowledge of microbial biogeography patterns, spatial drivers and human impacts at the continental scale remains limited. Here, we reveal the drivers of bacterial and fungal community distribution in Australian topsoils using 1384 soil samples from diverse bioregions. Our findings highlight that climate factors, particularly precipitation and temperature, along with soil properties, are the primary drivers of topsoil microbial biogeography. Using random forest machine-learning models, we generated high-resolution maps of soil bacteria and fungi across continental Australia. The maps revealed microbial hotspots, for example, the eastern coast, southeastern coast, and west coast were dominated by Proteobacteria and Acidobacteria. Fungal distribution is strongly influenced by precipitation, with Ascomycota dominating the central region. This study also demonstrated the impact of human modification on the underground microbial community at the continental scale, which significantly increased the relative abundance of Proteobacteria and Ascomycota, but decreased Chloroflexi and Basidiomycota. The variations in microbial phyla could be attributed to distinct responses to altered environmental factors after human modifications. This study provides insights into the biogeography of soil microbiota, valuable for regional soil biodiversity assessments and monitoring microbial responses to global changes.

Ecological and human health hazards of soil heavy metals after wildfire: A case study of Liangshan Yi autonomous prefecture, China

Soil samples were collected in at different depths from the conflagration area in Liangshan Yi Autonomous Region, China, to investigate the distribution characteristics and ecological and human health risks of heavy metals after a wildfire. The samples collected comprise wildfire ash (WA) above the soil surface, ash soil (AS) 0-5 cm, and plain soil (PS) 5-15 cm below the soil surface. Additionally, reference soil (RS) was collected from a nearby unburned area at the same latitude as the conflagration area. The results showed that the concentrations of zinc (Zn), copper (Cu), lead (Pb), and cadmium (Cd) in the WA and AS were significantly higher than in reference soil (RS) (p < 0.05). Concentrations of Pb in the PS were 2.52 times higher than that in RS (17.9 mg kg-1) (p < 0.05). The AS and WA had the highest Index of potential ecological risks (RI > 600). In addition, The Cd in AS and WA contributed the most to the highest Improved nemerow index (INI) and RI with a contribution of more than 80%. The concentration of heavy metals was used to establish non-carcinogenic effects and cancer risks in humans via three exposure pathways: accident ingestion of soil, dermal contact with soil, and inhalation of soil particles. Hazard index (HI) values of each sample were all less than 1, indicating the non-carcinogenic risk was within the acceptable range and would not adversely affect the local population's health. The Cancer risk (CR) values of Cr, As, Cd, and Ni were all below 1 × 10-6, indicating that heavy metal pollution from this wildfire did not pose a cancer risk to residents.

Changes in soil organic carbon stocks and its physical fractions along an elevation in a subtropical mountain forest

Soil microorganisms are the drivers of soil organic carbon (SOC) mineralization, and the activities of these microorganisms are considered to play a key role in SOC dynamics. However, studies of the relationship between soil microbial carbon metabolism and SOC stocks are rare, especially in different physical fractions (e.g., particulate organic carbon (POC) fraction and mineral-associated organic carbon (MAOC) fraction). In this study, we investigated the changing patterns of SOC stocks, POC stocks, MAOC stocks and microbial carbon metabolism (e.g., microbial growth, carbon use efficiency and biomass turnover time) at 0-20 cm along an elevational gradient in a subtropical mountain forest ecosystem. Our results showed that SOC and POC stocks increased but MAOC stocks remained stable along the elevational gradient. Soil microbial growth increased while microbial turnover time decreased with elevation. Using structural equation modeling, we found that heightened microbial growth is associated with elevated POC stocks. Moreover, MAOC stocks positively correlate with microbial growth but show negative associations with both POC stocks and soil pH. Overall, the increase in SOC stocks along the elevational gradient is primarily driven by changes in POC stocks rather than MAOC stocks. These findings underscore the importance of considering diverse soil carbon fractions and microbial activities in predicting SOC responses to elevation, offering insights into potential climate change feedbacks.

Applying sludge hydrolysate as a carbon source for biological denitrification after composition optimization via red soil filtration

Sludge hydrolysate, the byproduct generated during sludge hydrothermal treatment (HT), is a potential carbon source for biological denitrification. However, the refractory organic matters and the nutrient substances are unfavorable to the nitrogen removal. In this study, effects of HT conditions on the hydrolysate properties, and the hydrolysate compositions optimization via red soil (RS) filtration were investigated. At HT temperature of 160-220 °C and reaction time of 1-4 h, the highest dissolution rate of organics from sludge to hydrolysate achieved 70.1 %, while the acetic acid dominated volatile fatty acids (VFAs) was no more than 5.0 % of the total organic matter content. The NH4+-N and dissolved organic nitrogen (DON) were the main nitrogen species in hydrolysate. When the hydrolysate was filtered by RS, the high molecular weight organic matters, DON, NH4+ and PO43- were effectively retained by RS, while VFAs and polysaccharide favorable for denitrification were kept in the filtrate. When providing same COD as the carbon source, the filtrate group (Fi-Group) introduced lower concentrations of TN and humic substances but higher content of VFAs. This resulted in TN removal rate (57.0 %) and denitrification efficiency (93.6 %) in Fi-Group higher than those in hydrolysate group (Hy-Group), 39.4 % and 83.7 %, respectively. It is noticeable that both Hy- and Fi- Groups up-regulated most of denitrification functional genes, and increased the richness and diversity of denitrifying bacteria. Also, more denitrifying bacteria genera appeared, and their relative abundance increased significantly from 3.31 % in Control to 21.15 % in Hy- Group and 31.31 % in Fi-Group. This indicates that the filtrate is a more suitable carbon source for denitrification than hydrolysate. Moreover, the pH rose from 4.6 ± 0.14 to 6.5 ± 0.05, and the organic carbon, TN, TP and cation exchange capacity (CEC) of RS increased as well after being filtered, implying that the trapped compounds may have the potential to improve soil quality. This study provides a new insight for hydrolysate application according to its composition characteristics, and helps make the most use of wasted sludge.

Microalgae biomass as a conditioner and regulator of soil quality and fertility

Characteristics of an acid soil cultivated with Urochloa brizantha cv. Marandu were evaluated in relation to two types of fertilization: a conventional one, chemical based on nitrogen and potassium, and a biofertilizer, based on microalgae biomass. The results were compared among three treatments, control, conventional, and biological fertilization, with seven replications each. The study evaluated microalgae community, total carbon and nitrogen contents, mineral nitrogen, and enzymatic activity. Chlorella vulgaris showed the highest organism density, which can be explained by its rapid growth and high resistance. The highest species diversity was detected in the control 1,380,938 org cm-3 and biological 1,841,250 org cm-3 treatments, with the latter showing a higher density of cyanobacteria, especially Pseudanabaena limnetica with 394,554 org cm-3. The soil treated with chemical fertilization showed higher nitrate (9.14 mg NKg-1 NO3--N) and potassium (52.32 mg dm-3) contents. The highest levels of sulfur (21.73 mg dm-3) and iron (96.46 mgdm-3) were detected in the biological treatment. The chemical treatment showed higher activity of the enzymes acid phosphatase, acetylglucosaminidase, and sulfatase, while α-glucosidase and leucine aminopeptidase stood out in the biological treatment. Soil properties were not significantly affected by the treatments. The use of microalgae biomass derived from wastewater treatment from milking parlors was evaluated and presented as a promising biofertilizer for agriculture, following the line of recovering nutrient-rich wastes. In this sense, although many challenges need to be overcome, the results suggest that microalgal-based fertilizers could lead to low-impact agriculture.

Soil microbial responses to simulated climate change across polar ecosystems

The polar regions are among the most biologically constrained in the world, characterized by cold temperatures and reduced liquid water. These limitations make them among the most climate-sensitive regions on Earth. Despite the overwhelming constraints from low temperatures and resource availability, many polar ecosystems, including polar deserts and tundras across the Arctic and Antarctic host uniquely diverse microbial communities. Polar regions have warmed more rapidly than the global average, with continued warming predicted for the future, which will reduce constraints on soil microbial activity. This could alter polar carbon (C) cycles, increasing CO2 emissions into the atmosphere. The objective of this study was to determine how increased temperature and moisture availability impacts microbial respiration in polar regions, by focusing on a diversity of ecosystem types (polar desert vs. tundra) that are geographically distant across Antarctica and the Arctic. We found that polar desert soil microbes were co-limited by temperature and moisture, though C and nitrogen (N) mineralization were only stimulated at the coldest and driest of the two polar deserts. Only bacterial biomass was impacted at the less harsh of the polar deserts, suggesting microbial activity is limited by factors other than temperature and moisture. Of the tundra sites, only the Antarctic tundra was climate-sensitive, where increased temperature decreased C and N mineralization while water availability stimulated it. The greater availability of soil resources and vegetative biomass at the Arctic tundra site might lead to its lack of climate-sensitivity. Notably, while C and N dynamics were climate-sensitive at some of our polar sites, P availability was not impacted at any of them. Our results demonstrate that soil microbial processes in some polar ecosystems are more sensitive to changes in temperature and moisture than others, with implications for soil C and N storage that are not uniformly predictable across polar regions.

Grazing management for soil carbon in Australia: A review

The livestock industry accounts for a considerable proportion of agricultural greenhouse gas emissions, and in response, the Australian red meat industry has committed to an aspirational target of net-zero emissions by 2030. Increasing soil carbon storage in grazing lands has been identified as one method to help achieve this, while also potentially improving production and provision of other ecosystem services. This review examined the effects of grazing management on soil carbon and factors that drive soil carbon sequestration in Australia. A systematic literature search and meta-analysis was used to compare effects of stocking intensity (stocking rate or utilisation) and stocking method (i.e, continuous, rotational or seasonal grazing systems) on soil organic carbon, pasture herbage mass, plant growth and ground cover. Impacts on below ground biomass, soil nitrogen and soil structure are also discussed. Overall, no significant impact of stocking intensity or method on soil carbon sequestration in Australia was found, although lower stocking intensity and incorporating periods of rest into grazing systems (rotational grazing) had positive effects on herbage mass and ground cover compared with higher stocking intensity or continuous grazing. Minimal impact of grazing management on pasture growth rate and below-ground biomass has been reported in Australia. However, these factors improved with grazing intensity or rotational grazing in some circumstances. While there is a lack of evidence in Australia that grazing management directly increases soil carbon, this meta-analysis indicated that grazing management practices have potential to benefit the drivers of soil carbon sequestration by increasing above and below-ground plant production, maintaining a higher residual biomass, and promoting productive perennial pasture species. Specific recommendations for future research and management are provided in the paper.

Soil microbiome engineering for sustainability in a changing environment

Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.

Artificial Soil-Like Material Enhances CO2 Bio-Valorization into Chemicals in Gas Fermentation

Gas fermentation offers a carbon-neutral route for producing industrial feedstocks using autotrophic microbes to convert carbon dioxide (CO2) in waste gases, such as industrial emissions and biogas, into valuable chemicals or biofuels. However, slow microbial metabolism owing to low gaseous solubility causes significant challenges in gas fermentation. Although chemical or genetic manipulations have been explored to improve gas fermentation, they are either nonsustainable or complex. Herein, an artificial soil-like material (SLM) inspired by natural soil was fabricated to improve the growth and metabolism ofCupriavidus necatorfor enhanced poly-β-hydroxybutyrate (PHB) biosynthesis from CO2 and hydrogen (H2). Porous SLM comprises low-cost nanoclay, boehmite, and starch and serves as a biocarrier to facilitate the colonization of bacteria and delivery of CO2 to bacteria. With 3.0 g/L SLM addition, the solubility of CO2 in water increased by ∼4 times and biomass and PHB production boosted by 29 and 102%, respectively, in the 24 h culture. In addition, a positive modulation was observed in the metabolism of PHB biosynthesis. PHB biosynthesis-associated gene expression was found to be enhanced in response to the SLM addition. The concentrations of intermediates in the metabolic pathway of PHB biosynthesis, such as pyruvate and acetyl-CoA, as well as reducing energy (ATP and NADPH) significantly increased with SLM addition. SLM also demonstrated the merits of easy fabrication, high stability, recyclability, and plasticity, thereby indicating its considerable potential for large-scale application in gas fermentation.

Co-application of chitooligosaccharides and arbuscular mycorrhiza fungi reduced greenhouse gas fluxes in saline soil by improving the rhizosphere microecology of soybean

Soil salinization can affect the ecological environment of soil and alter greenhouse gas (GHG) emissions. Chitooligosaccharides and Arbuscular mycorrhizal fungi (AMF) reduced the GHG fluxes of salinized soil, and this reduction was attributed to an alteration in the rhizosphere microecology, including changes in the activities of β-glucosidase, acid phosphatase, N-acetyl-β-D-glucosidase, and Leucine aminopeptidase. Additionally, certain bacteria species such as paracoccus, ensifer, microvirga, and paracyclodium were highly correlated with GHG emissions. Another interesting finding is that foliar spraying of chitooligosaccharides could transport to the soybean root system, and improve soybean tolerance to salt stress. This is achieved by enhancing the activities of antioxidant enzymes, and the changes in amino acid metabolism, lipid metabolism, and membrane transport. Importantly, the Co-application of chitooligosaccharides and Arbuscular mycorrhiza fungi was found to have a greater effect compared to their application alone.

Synergistic effects of earthworms and cow manure under reduced chemical fertilization modified microbial community structure to mitigate continuous cropping effects on Chinese flowering cabbage

The substitution of chemical fertilizers with organic fertilizers is a viable strategy to enhance crop yield and soil quality. In this study, the aim was to investigate the changes in soil microorganisms, soil chemical properties, and growth of Chinese flowering cabbage under different fertilization treatments involving earthworms and cow manure. Compared with the control (100% chemical fertilizer), CE (30% reduction in chemical fertilizer + earthworms) and CFE (30% reduction in chemical fertilizer + cow dung + earthworms) treatments at soil pH 8.14 and 8.07, respectively, and CFC (30% reduction in chemical fertilizer + cow manure) and CFE treatments increased soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), and available potassium (AK) contents. Earthworms and cow manure promoted the abundance of Bacillus and reduced that of the pathogens Plectosphaerella and Gibberella. The mantle test revealed that pH was not correlated with the microbial community. Random forest analysis verified that AN, SOM, and TN were important factors that jointly influenced bacterial and fungal diversity. Overall, the synergistic effect of earthworms and cow manure increased soil fertility and microbial diversity, thereby promoting the growth and development of Chinese flowering cabbage. This study enhanced the understanding of how bioregulation affects the growth and soil quality of Chinese flowering cabbage, and thus provided a guidance for the optimization of fertilization strategies to maximize the yield and quality of Chinese flowering cabbage while reducing environmental risks.

Integrating microbial community properties, biomass and necromass to predict cropland soil organic carbon

Manipulating microorganisms to increase soil organic carbon (SOC) in croplands remains a challenge. Soil microbes are important drivers of SOC sequestration, especially via their necromass accumulation. However, microbial parameters are rarely used to predict cropland SOC stocks, possibly due to uncertainties regarding the relationships between microbial carbon pools, community properties and SOC. Herein we evaluated the microbial community properties (diversity and network complexity), microbial carbon pools (biomass and necromass carbon) and SOC in 468 cropland soils across northeast China. We found that not only microbial necromass carbon but also microbial community properties (diversity and network complexity) and biomass carbon were correlated with SOC. Microbial biomass carbon and diversity played more important role in predicting SOC for maize, while microbial network complexity was more important for rice. Models to predict SOC performed better when the microbial community and microbial carbon pools were included simultaneously. Taken together our results suggest that microbial carbon pools and community properties influence SOC accumulation in croplands, and management practices that improve these microbial parameters may increase cropland SOC levels.

Temporal and spatial changes in rhizosphere bacterial diversity of mountain Rhododendron mucronulatum

To better conserve the ecology of the wild Rhododendron mucronulatum range, we studied the rhizosphere microenvironment of R. mucronulatum in Beijing's Yunmeng Mountain National Forest Park. R. mucronulatum rhizosphere soil physicochemical properties and enzyme activities changed significantly with temporal and elevational gradients. The correlations between soil water content (SWC), electrical conductivity (EC), organic matter content (OM), total nitrogen content (TN), catalase activity (CAT), sucrose-converting enzyme activity (INV), and urease activity (URE) were significant and positive in the flowering and deciduous periods. The alpha diversity of the rhizosphere bacterial community was significantly higher in the flowering period than in the deciduous period, and the effect of elevation was insignificant. The diversity of the R. mucronulatum rhizosphere bacterial community changed significantly with the change in the growing period. A network analysis of the correlations revealed stronger linkages between the rhizosphere bacterial communities in the deciduous period than in the flowering period. Rhizomicrobium was the dominant genus in both periods, but its relative abundance decreased in the deciduous period. Changes in the relative abundance of Rhizomicrobium may be the main factor influencing the changes in the R. mucronulatum rhizosphere bacterial community. Moreover, the R. mucronulatum rhizosphere bacterial community and soil characteristics were significantly correlated. Additionally, the influence of soil physicochemical properties on the rhizosphere bacterial community was larger than that of enzyme activity on the bacterial community. We mainly analyzed the change patterns in the rhizosphere soil properties and rhizosphere bacterial diversity of R. mucronulatum during temporal and spatial variation, laying the foundation for further understanding of the ecology of wild R. mucronulatum.

Date Palm Waste Compost Application Increases Soil Microbial Community Diversity in a Cropping Barley (Hordeum vulgare L.) Field

Application of date palm waste compost is quite beneficial in improving soil properties and crop growth. However, the effect of its application on soil microbial communities is less understood. High-throughput sequencing and quantitative real-time PCR (qPCR) were used to evaluate the effect of compost application on the soil microbial composition in a barley field during the tillering, booting and ripening stages. The results showed that compost treatment had the highest bacterial and fungal abundance, and its application significantly altered the richness (Chao1 index) and α-diversity (Shannon index) of fungal and bacterial communities. The dominant bacterial phyla found in the samples were Proteobacteria and Actinobacteria while the dominant fungal orders were Ascomycota and Mortierellomycota. Interestingly, compost enriched the relative abundance of beneficial microorganisms such as Chaetomium, Actinobacteriota, Talaromyces and Mortierella and reduced those of harmful microorganisms such as Alternaria, Aspergillus and Neocosmospora. Functional prediction based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that amplicon sequence variant (ASV) sequences related to energy metabolism, amino acid metabolism and carbohydrate metabolism were associated with compost-treated soil. Based on Fungi Functional Guild (FUNGuild), identified fungi community metabolic functions such as wood saprotroph, pathotroph, symbiotroph and endophyte were associated with compost-treated soil. Overall, compost addition could be considered as a sustainable practice for establishing a healthy soil microbiome and subsequently improving the soil quality and barley crop production.

The relationships between heavy metals and bacterial communities in a coal gangue site

Coal is the main source of energy for China's economic development, but coal gangue dumps are a major source of heavy metal pollution. Bacterial communities have a major effect on the bioremediation of heavy metals in coal gangue dumps. The effects of different concentrations of heavy metals on the composition of bacterial communities in coal gangue sites remain unclear. Soil bacterial communities from four gangue sites that vary in natural heavy metal concentrations were investigated using high-throughput sequencing in this study. Correlations among bacterial communities, heavy metal concentrations, physicochemical properties of the soil, and the composition of dissolved organic matter of soil in coal gangue dumps were also analyzed. Our results indicated that Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota were the bacterial taxa most resistant to heavy metal stress at gangue sites. Heavy metal contamination may be the main cause of changes in bacterial communities. Heavy metal pollution can foster mutually beneficial symbioses between microbial species. Microbial-derived organic matter was the main source of soil organic matter in unvegetated mining areas, and this could affect the toxicity and transport of heavy metals in soil. Polar functional groups such as hydroxyl and ester groups (A_226-400) play an important role in the reaction of cadmium (Cd) and lead (Pb), and organic matter with low molecular weight (S_R) tends to bind more to mercury (Hg). In addition to heavy metals, the content of nitrogen (N), phosphorus (P), and total organic carbon (TOC) also affected the composition of the bacterial communities; TOC had the strongest effect, followed by N, SOM, and P. Our findings have implications for the microbial remediation of heavy metal-contaminated soils in coal gangue sites and sustainable development.

CNN_FunBar: Advanced Learning Technique for Fungi ITS Region Classification

Fungal species identification from metagenomic data is a highly challenging task. Internal Transcribed Spacer (ITS) region is a potential DNA marker for fungi taxonomy prediction. Computational approaches, especially deep learning algorithms, are highly efficient for better pattern recognition and classification of large datasets compared to in silico techniques such as BLAST and machine learning methods. Here in this study, we present CNN_FunBar, a convolutional neural network-based approach for the classification of fungi ITS sequences from UNITE+INSDC reference datasets. Effects of convolution kernel size, filter numbers, k-mer size, degree of diversity and category-wise frequency of ITS sequences on classification performances of CNN models have been assessed at all taxonomic levels (species, genus, family, order, class and phylum). It is observed that CNN models can produce >93% average accuracy for classifying ITS sequences from balanced datasets with 500 sequences per category and 6-mer frequency features at all levels. The comparative study has revealed that CNN_FunBar can outperform machine learning-based algorithms (SVM, KNN, Naïve-Bayes and Random Forest) as well as existing fungal taxonomy prediction software (funbarRF, Mothur, RDP Classifier and SINTAX). The present study will be helpful for fungal taxonomy classification using large metagenomic datasets.

Environmental pseudotargeted metabolomics: A high throughput and wide coverage method for metabolic profiling of 1000-year paddy soil chronosequences

Pseudotargeted metabolomics is achieved by introducing an algorithm designed to choose ions for selected ion monitoring from identified metabolites. This method integrates the advantages of both untargeted and targeted metabolomics. In this study, environmental pseudotargeted metabolomics was established to analyze the soil metabolites, based on microwave assisted derivatization followed by gas chromatography-mass spectrometry analysis. The method development included the optimization of extraction factors and derivatization conditions, evaluation of silylation reagent types and matrix-dependent behaviors. Under the optimal conditions, the microwave oximation and silylation were completed in 5 min and 9 min. A total of 184 metabolites from 26 chemical classifications were identified in soil matrices. The method validation demonstrated excellent performance in terms of linearity (correlation coefficient > 0.99), repeatability (relative standard deviation (RSD) < 20 %), reproducibility (RSD < 25 %), stability (relative difference < 10 % within 18 h), and sensitivity (16-110 times higher signal-to-noise ratio). This developed method was applied to characterize the metabolite compositions and metabolic profiling in a 1000-year paddy soil chronosequence. The relative abundance of trehalose was highest in 6-(40.3 %), 60-(55.8 %), 300-(67.7 %)and 1000-(61.7 %)years paddy soil, respectively, but long-chain fatty acids were most abundant in marine sediment (57.4 %). Forty-two characteristic metabolites were considered as primarily responsible for discriminating and characterizing the paddy soil chronosequences development and seven major metabolic pathways were altered. In addition, GC-MS metabolite profile presented better discriminating power in paddy soil ecosystem changes than phospholipid fatty acids (PLFAs). Overall, environmental pseudotargeted metabolomics can provide a high throughout and wide coverage approach for performing metabolic profiling in the soil research.

Metagenomic insights into the characteristics of soil microbial communities in the decomposing biomass of Moso bamboo forests under different management practices

Introduction

Considering the rapid growth and high biomass productivity, Moso bamboo (Phyllostachys edulis) has high carbon (C) sequestration potential, and different management practices can strongly modify its C pools. Soil microorganisms play an important role in C turnover through dead plant and microbial biomass degradation. To date, little is known about how different management practices affect microbial carbohydrate-active enzymes (CAZymes) and their responses to dead biomass degradation.

Methods

Based on metagenomics analysis, this study analyzed CAZymes in three comparable stands from each Moso bamboo plantation: undisturbed (M0), extensively managed (M1), and intensively managed (M2).

Results

The results showed that the number of CAZymes encoding plant-derived component degradation was higher than that encoding microbe-derived component degradation. Compared with the M0, the CAZyme families encoding plant-derived cellulose were significantly (p < 0.05) high in M2 and significantly (p < 0.05) low in M1. For microbe-derived components, the abundance of CAZymes involved in the bacterial-derived peptidoglycan was higher than that in fungal-derived components (chitin and glucans). Furthermore, M2 significantly increased the fungal-derived chitin and bacterial-derived peptidoglycan compared to M0, whereas M1 significantly decreased the fungal-derived glucans and significantly increased the bacterial-derived peptidoglycan. Four bacterial phyla (Acidobacteria, Actinobacteria, Proteobacteria, and Chloroflexi) mainly contributed to the degradation of C sources from the plant and microbial biomass. Redundancy analysis (RDA) and mantel test suggested the abundance of CAZyme encoding genes for plant and microbial biomass degradation are significantly correlated with soil pH, total P, and available K. Least Squares Path Modeling (PLS-PM) showed that management practices indirectly affect the CAZyme encoding genes associated with plant and microbial biomass degradation by regulating the soil pH and nutrients (total N and P), respectively.

Discussion

Our study established that M2 and M1 impact dead biomass decomposition and C turnover, contributing to decreased C accumulation and establishing that the bacterial community plays the main role in C turnover in bamboo plantations.

Extraradical Mycorrhizal Hyphae Promote Soil Carbon Sequestration through Difficultly Extractable Glomalin-Related Soil Protein in Response to Soil Water Stress

Soil water stress (WS) affects the decomposition of soil organic carbon (SOC) and carbon (C) emissions. Glomalin, released by arbuscular mycorrhizal fungi into soil that has been defined as glomalin-related soil protein (GRSP), is an important pool of SOC, with hydrophobic characteristics. We hypothesized that mycorrhizal fungi have a positive effect on SOC pools under soil WS for C sequestration in GRSP secreted by extraradical mycorrhizal hyphae. A microsystem was used to establish a root chamber (co-existence of roots and extraradical mycorrhizal hyphae) and a hyphal chamber (the presence of extraradical mycorrhizal hyphae) to study changes in plant growth, leaf water potential, soil aggregate stability, SOC, GRSP, C concentrations in GRSP (C_GRSP), and the contribution of C_GRSP to SOC after inoculating Rhizophagus intraradices with trifoliate orange (Poncirus trifoliata) in the root chamber under adequate water (AW) and WS. Inoculation with R. intraradices alleviated negative effects on leaf water potential and plant growth after 7 weeks of WS. Soil WS decreased SOC and mean weight diameter (MWD), while AMF inoculation led to an increase in SOC and MWD in both chambers, with the most prominent increase in the hyphal chamber under WS. The C concentration in easily extractable GRSP (EE-GRSP) and difficultly extractable GRSP (DE-GRSP) was 7.32 - 12.57 and 24.90 - 32.60 mg C/g GRSP, respectively. WS reduced C_GRSP, while AMF mitigated the reduction. Extraradical mycorrhizal hyphae increased GRSP production and C_GRSP, along with a more prominent increase in DE-GRSP under WS than under AW. Extraradical mycorrhizal hyphae increased the contribution of C_DE-GRSP to SOC only under WS. C_EE-GRSP and C_DE-GRSP were significantly positively correlated with SOC and MWD. It is concluded that extraradical mycorrhizal hyphae prominently promoted C sequestration of recalcitrant DE-GRSP under soil WS, thus contributing more organic C accumulation and preservation in aggregates and soil C pool.

Long-Read Sequencing Analysis Revealed the Impact of Forest Conversion on Soil Fungal Diversity in Limu Mountain, Hainan

Soil fungi are essential to soil microorganisms that play an important role in the ecosystem's soil carbon cycle and mineral nutrient transformation. Understanding the structural characteristics and diversity of soil fungal communities helps understand the health of forest ecosystems. The transition from tropical rainforest to artificial forest greatly impacts the composition and diversity of fungal communities. Hainan Limushan tropical rainforest National Park has a large area of artificial forests. Ecologists have conducted in-depth studies on the succession of animals and plants to regenerate tropical rainforests. There are few reports on the diversity of soil fungi and its influencing factors in the succession of tropical rainforests in Limu Mountain. In this study, 44 soil samples from five different stands were collected in the tropical rainforest of Limushan, Hainan. High-throughput sequencing of rDNA in its region was used to analyze fungal communities and study their α and β diversity. Analysis of variance and multiple regression models was used to analyze soil variables and fungal functional groups to determine the effects of interaction between fungi and environmental factors. A total of 273,996 reads and 1290 operational taxonomic units (OTUs) were obtained, belonging to 418 species, 325 genera, 159 families, eight phyla, 30 classes, and 73 orders. The results showed that the composition of soil fungal communities in the five stands was similar, with ascomycetes accounting for 70.5% and basidiomycetes accounting for 14.7%. α and β diversity analysis showed that soil fungi in Limushan tropical rainforest had high abundance and diversity. Multiple regression analysis between soil variables and functional groups showed that organic matter, TN, TP, TK, and AK were excellent predictors for soil fungi. TP was the strongest predictor in all functional groups except soil saprotroph. Organic matter and total nitrogen were the strongest predictors of soil rot. The transformation from tropical rainforest to artificial forest in Limushan did not change the soil fungal community structure, but the richness and diversity of soil fungi changed. The forest transformation did not lead to decreased soil fungal abundance and diversity. Different vegetation types and soil properties affect the diversity of soil fungal communities. We found that Caribbean pine plantations can improve soil fungal diversity, while long-term Eucalyptus spp. plantations may reduce soil fungal diversity.

Dolit S, K. Khamis A, Abd-Aziz N, R. Azman N, A. Asli U. Regenerating Soil Microbiome: Balancing Microbial CO2 Sequestration and Emission

Soil microbiome plays a significant role in soil’s ecosystem for soils to be physically and biologically healthy. Soil health is fundamental for plant growth and crops productivity. In the introduction part, the roles and dynamics of the microbial community in soils, primarily in the cycle of soil organic carbon and CO2 release and absorption, are deliberated. Next, the impact of crop management practices and climate change on the soil carbon balance are described, as well as other issues related to soil degradation, such as unbalanced nutrient recycling and mineral weathering. In response to these issues, various approaches to soil regeneration have been developed in order to foster an efficient and active soil microbiome, thereby balancing the CO2 cycle and carbon sequestration in the soil ecosystem.

Model Test Study on the Enhancement of Ecological Self-Repairing Ability of Surface Slope Soil by New Polymer Composites

Plant-based ecological protection is one of the effective methods to improve the stability of slope soils. However, plants need a stable growth environment and water supply. Although it has been demonstrated that polymer materials can effectively enhance the stability and water retention of soils, their improvement mechanism and long-term effects are yet to be clear. In this paper, we use a new polymer composite material (ADNB), an optimized compound of nano-aqueous binder (NAB) and super absorption resin (SAR), to conduct outdoor model tests to study the effects of different ADNB ratios on soil compactness, biochemical properties, and plant growth at longer time scales, and to explore its action law and mechanism of enhancing the ecological self-repairing ability of surface slope soil. The results show that ADNB can effectively improve the soil structure, increase the compactness of the soil, increase the organic matter content, microbial population and available nutrient content in the soil, thus promoting plant growth. The adsorption and agglomeration effect of the NAB in ADNB on soil particles and its degradation in natural environment can be observed by SEM. In summary, ADNB can not only effectively enhance the ecological self-repairing ability of surface slope soil, but also has good environmental friendliness and can be completely degraded under natural conditions without additional adverse effects on soil and environment.

Soil carbon sequestration, greenhouse gas emissions, and water pollution under different tillage practices

Tillage is a common agricultural practice and a critical component of agricultural systems that is frequently employed worldwide in croplands to reduce climatic and soil restrictions while also sustaining various ecosystem services. Tillage can affect a variety of soil-mediated processes, e.g., soil carbon sequestration (SCS) or depletion, greenhouse gas (GHG) (CO₂, CH_4, and N₂O) emission, and water pollution. Several tillage practices are in vogue globally, and they exhibit varied impacts on these processes. Hence, there is a dire need to synthesize, collate and comprehensively present these interlinked phenomena to facilitate future researches. This study deals with the co-benefits and trade-offs produced by several tillage practices on SCS and related soil properties, GHG emissions, and water quality. We hypothesized that improved tillage practices could enable agriculture to contribute to SCS and mitigate GHG emissions and leaching of nutrients and pesticides. Based on our current understanding, we conclude that sustainable soil moisture level and soil temperature management is crucial under different tillage practices to offset leaching loss of soil stored nutrients/pesticides, GHG emissions and ensuring SCS. For instance, higher carbon dioxide (CO₂) and nitrous oxide (N₂O) emissions from conventional tillage (CT) and no-tillage (NT) could be attributed to the fluctuations in soil moisture and temperature regimes. In addition, NT may enhance nitrate (NO₃^-) leaching over CT because of improved soil structure, infiltration capacity, and greater water flux, however, suggesting that the eutrophication potential of NT is high. Our study indicates that the evaluation of the eutrophication potential of different tillage practices is still overlooked. Our study suggests that improving tillage practices in terms of mitigation of N₂O emission and preventing NO₃^- pollution may be sustainable if nitrification inhibitors are applied.