Soil Microbial Abundance Research Articles

Soil sample sizes for DNA extraction substantially affect the examination of microbial diversity and co-occurrence patterns but not abundance

As the cornerstone of most soil microbial diversity and abundance research, soil DNA extraction is inherently influenced by soil sample sizes, yet the effects remain far from fully understood. In this study, soils were collected from desert, meadow, forest, and cropland ecosystems to examine the effects of soil sample sizes (i.e., 0.01, 0.025, 0.25, 0.50, and 1.00 g) on prokaryotic and fungal community analysis. Soil microbial abundance and diversity were analyzed through real-time PCR and NovaSeq high-throughput sequencing, respectively. We found that soil sample sizes for DNA extraction generally did not affect microbial abundance determination. In contrast, microbial richness, community composition, and co-occurrence patterns varied with different soil sample sizes. The microbial richness and co-occurrence frequency obtained from 0.01 to 0.025 g of soils were lower than those determined based on 0.25–1.00 g of soils in most ecosystems. Microbial community composition was also affected by the soil sample sizes when they were 0.50 g or less. In particular, small soil sample sizes for DNA extraction (i.e., ≤ 0.025 g) revealed dramatic variations in microbial community profiles among soil microhabitats. Collectively, in most ecosystems, at least 0.25 g of soils should be used to determine the overall diversity of microbes. As for the soils with low microbial cellular density, DNA should be extracted from 0.50 g or even more soils. Thus, the analysis of soil microbial diversity and co-occurrence patterns rather than abundance are substantially affected by the soil sample sizes for DNA extraction, and the choice of optimum soil sample sizes depends on soil types and research purposes.

Soil Microbial Response to Cover Crop Termination Methods under Two Water Levels

Cover crops (CC) promote soil health, but the termination method can condition the benefits for soil microorganisms. In a greenhouse experiment, we evaluated the legacy effects of four common CC termination methods on mycorrhization, soil microbial abundance, structure, and activity, as well as other soil properties, and its interaction with water levels (well-watered and water deficit). Mowing and residue incorporation (INC), glyphosate (GLY), roller crimper (ROL) and glyphosate + roller crimper (RGL) were evaluated, together with no CC, at two sampling dates of a subsequent maize. The water level modulated the soil microbial response to CC termination methods, especially in the glyphosate methods. Legacy effects on soil microbial attributes were notable and evolved differently from maize, from pre-emergence to ~3 months later. At final sampling, INC showed the best microbial response at both water levels, enhancing most microbial attributes. ROL was the second most beneficial method, especially in well-watered soil, promoting fungi but nullifying the CC positive effect on bacteria. Regardless of water level, GLY and RGL showed a similar microbial response. In well-watered soil, GLY and RGL had a negative effect on the total fungi, which separated the RGL response from the ROL. Overall, the time since CC termination and water level modulated the soil microbial response to the termination methods. Further research is needed to investigate CC termination impacts under different environmental conditions, in order to better understand the processes involved and provide farm-level recommendations.

Effects of Warming on Microbial Community Characteristics in the Soil Surface Layer of Niaodao Wetland in the Qinghai Lake Basin

Lakeshore wetlands are important terrestrial ecosystems worldwide, and the lakeshore wetlands of the Tibetan Plateau are sensitive to climate change. Therefore, in the context of global warming, studying the effects of temperature rise on surface soil microbial communities is essential for wetland biodiversity conservation. In this study, we used metagenomic sequencing to examine changes in the structure of surface soil microbial communities and their metabolic pathways in the Niaodao lakeshore wetland (NLW) in Qinghai Lake at 1.2 °C warming. Under natural control and warming conditions, Proteobacteria and Actinobacteria were the most dominant bacterial phyla, and Ascomycota and Basidiomycota were the predominant fungal phyla. Soil pH, electrical conductivity, and temperature affected the relative abundances of the dominant soil microbes. Effect size estimation in a linear discriminant analysis revealed 11 differential pathways between warming and natural conditions. Warming considerably enhanced the peptidoglycan biosynthetic pathways but inhibited the ATP-binding cassette transporter pathway. Warming treatment affected α-diversity indices, with an increase in the Shannon, Chao1, and richness indices and a decrease in the Simpson index compared with the index changes for the natural control conditions. Analysis of similarities showed significant differences between warming and control samples. Overall, temperature rise altered surface soil microbial community structure and increased surface soil microbial diversity and abundance in NLW.

Soil microbial abundance was more affected by soil depth than the altitude in peatlands.

Soil microbial abundance is a key factor to predict soil organic carbon dynamics in peatlands. However, little is known about the effects of altitude and soil depth and their interaction on soil microbial abundance in peatlands. In this study, we measured the microbial abundance and soil physicochemical properties at different soil depths (0-30 cm) in peatlands along an altitudinal gradient (from 200 to 1,500 m) on Changbai Mountain, China. The effect of soil depth on soil microbial abundance was stronger than the altitude. The total microbial abundance and different microbial groups showed the same trend along the soil depth and altitudinal gradients, respectively. Microbial abundance in soil layer of 5-10 cm was the highest and then decreased with soil depth; microbial abundance at the altitude of 500-800 m was the highest. Abiotic and biotic factors together drove the change in microbial abundance. Physical variables (soil water content and pH) and microbial co-occurrence network had negative effects on microbial abundance, and nutrient variables (total nitrogen and total phosphorus) had positive effects on microbial abundance. Our results demonstrated that soil depth had more effects on peatland microbial abundance than altitude. Soil environmental change with peat depth may lead to the microorganisms receiving more disturbances in future climate change.

Linking nitrogen- and straw-sensitive indicator species and their co-occurrences to priming effect in agricultural soil exposed to long-term nitrogen fertilization

The increasing input of nitrogen (N) fertilizers has a considerable impact on agricultural soil carbon (C) cycling due to its influence on soil microbial abundance and assemblages. However, the microbial mechanism underlying the response of straw-induced priming effect to long-term N application remains an open question. Here, using soils with three N fertilization levels (0, 300, and 570 kg N ha−1 y−1) from a long-term experimental site, we established a 40-day microcosm experiment to investigate the priming effect of straw addition on SOM mineralization and the associated microbial activity and community composition. We found that long-term N application significantly inhibited soil respiration while increasing straw-induced priming effect. The soil microbial biomass (including bacterial and fungal abundance) decreased with increasing N levels, accompanied by decreased bacterial α-diversity and altered β-diversity. In addition, the N fertilization level significantly influenced bacterial and fungal indicator species that were sensitive to straw addition (siOTUs) and long-term N fertilization (niOTUs), as well as their co-occurrence patterns. In the first three days of straw decomposition, long-term N fertilization decreased the oligotroph-to-copiotroph ratio of bacterial siOTUs. In contrast, long-term N fertilization increased this ratio on days 20 and 40, along with facilitated microbial investment in extracellular enzymes and microbial N demand. This caused a stronger “N mining” process and consequently enhanced the priming effect in soil exposed to long-term N fertilization at the later stage of incubation. Linking indicator species analysis with priming effect, these results advance our understanding of the complex C cycling in agricultural soils undergoing long-term nitrogen management.

Modified biochar/humic substance/fertiliser compound soil conditioner for highly efficient improvement of soil fertility and heavy metals remediation in acidic soils

Fertile and uncontaminated soil with appropriate pH is crucial in terms of the agricultural sustainable development. Herein, a compound soil conditioner containing chitosan modified straw biochar (CBC), kitchen waste compost product-derived humic substance (HS), NPK compound fertiliser (NPK-CF) was prepared to simultaneously adjust acidic soil pH, improve fertility, and immobilize heavy metal. The results exhibited that the best Pb and NH4+ adsorption performance was obtained in CBC with chitosan:biochar of 1:5. Then, the acid soil pH was improved from 5.03 to 6.66 in the presence of CBC/HS (5:5) with 3% addition weight (the mass ratio of conditioner to soil). Meanwhile, compared with the control, the contents of organic matter, available nitrogen, and available phosphorus significantly increased by 52.4%, 92.6%, and 136.3%, respectively. Moreover, Pb was highly efficient immobilised by CBC, and the concentration of Pb in the soil was decreased by 55.2%. The optimal growth trend of ryegrass was obtained in the presence of 3% addition weight (the mass ratio of conditioner to soil) CBC/HS (CBC:HS = 5:5) combined with 60% of the recommended NPK-CF application weight, which was mainly contributed by the improvement of the soil microbial abundance and community structure diversity. The addition of CBC/HS could effectively reduce the addition of NPK-CF and contribute to simultaneous controlling nitrogen loss, releasing phosphorus, immobilising Pb, adjusting pH, improving soil quality and controlling nonpoint pollution.

Effects of Intercropping Pandanus amaryllifolius on Soil Properties and Microbial Community Composition in Areca Catechu Plantations

The areca nut (Areca catechu L.) and pandan (Pandanus amaryllifolius Roxb.) intercropping cultivation system has been widely practiced to improve economic benefits and achieve the development of sustainable agriculture in Hainan Province, China. However, there is a lack of research on the relationships among soil properties, soil enzyme activities, and microbes in this cultivation system. Therefore, a random block field experiment of pandan intercropped with areca nut was established to investigate the effects of environmental factors on the diversity and functions of soil microbial communities in Lingshui county, Hainan Province. The diversity and composition of soil microbial communities under different cropping modes were compared using Illumina sequencing of 16S rRNA (bacteria) and ITS-1 rRNA (fungi) genes, and FAPROTAX and FUNGuild were used to analyze and predict the bacteria and fungi community functions, respectively. Correlation analysis and redundancy analysis were used to explore the responses of soil microbial communities to soil environmental factors. The results showed that the bacterial community was more sensitive to the areca nut and pandan intercropping system than the fungal community. The functional predictions of fungal microbial communities by FAPROTAX and FUNGuild indicated that chemoheterotrophy, aerobic chemoheterotrophy, and soil saprotroph were the most dominant functional communities. The intercropping of pandan in the areca nut plantation significantly enhanced the soil bacterial Ace and Chao indices by reducing the soil organic carbon (SOC) and total phosphorus (TP) content. In the intercropping system, urease (UE) and acid phosphatase were the key factors regulating the soil microbial community abundance. The dominant bacterial and fungal phyla, such as Firmicutes, Methylomirabilota, Proteobacteria, Actinobacteria, Chloroflexi, Verrucomicrobia, and Ascomycota significantly responded to the change in planting modes. Soil properties, such as UE, total nitrogen, and SOC had a significant stimulating effect on Proteobacteria, Chloroflexi, and Ascomycota. In summary, soil bacteria responded more significantly to the change in cropping modes than soil fungi and better reflected the changes in soil environmental factors, suggesting that intercropping with pandan positively affects soil microbial homeostasis in the long-term areca nut plantation.

Effects of Straw Returning on Soil Chemical Properties and Microbial Community Diversity under the Rice-Crayfish Integrated System

This study presents an investigation of soil chemical properties and microbial community diversity by Biolog ECO analysis in a seven-year field experiment using winter flooded fallow + no straw returning (W), winter flooded fallow + straw returning (WS), and winter flooded fallow + straw returning + crayfish farming (WSC) at soil depths of 0–10 cm and 10–20 cm. Compared with the WS treatment, the WSC treatment had significantly higher total organic carbon (TOC) content in the 0–10 cm layer as well as greater available nitrogen (AN) and total nitrogen (TN) contents and acid phosphatase and sucrase activities in the 10–20 cm layer, while the pH value, total reducing substances, and Fe2+ content in the 0–20 cm layer were considerably lower. The WSC treatment improved the microbial species abundance in the 10–20 cm layer and the utilization rate of carbon sources in the 0–20 cm layer compared with the WS treatment. The soil microbial species abundance, microbial community diversity, and utilization rate of carbon sources in all of the layers examined were significantly higher in the WSC treatment than in the W treatment. The results indicate that straw returning under the rice-crayfish integrated system improves the contents of TOC, TN, and AN, decreases reducing substances properties, increases acid phosphatase and sucrase activities, and improves microbial community functional diversity, thereby contributing to the improvement of soil quality and the long-term sustainable development of the rice-crayfish integrated system.

Agricultural soil physico-chemical parameters and microbial abundance and diversity under long-run farming practices: A greenhouse study

The growth of agriculture led to indiscriminate use of synthetic pesticides or fertilizers and unsustainable crop management farming practices which can aggravate harmful impacts on the microbial population and physical and chemical characteristics of soil ecosystem. Based on this fact, the present study was planned to evaluate the effect of long run farming practices on different soil physico-chemical parameters and soil microbial abundance and diversity within different soil depth (0–20 cm and 20–40 cm) at Quzhou Experimental Station of China Agricultural University, Hebei, China during October and December, 2016. The effect of farming practices on soil microbial abundance and diversity was studied by phospho-lipid fatty acid (PLFA) and DNA high-throughput sequencing methods. The findings revealed that soil is neutral to slightly alkaline in nature with highest water content under organic farming (ORF) at 0–20 cm and least under conventional farming at 20–40 cm depth. It was found that the ORF significantly increased the contents of total organic carbon (TOC), total carbon (TC), ammonium nitrogen, available nitrogen (AN), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) followed by low input and conventional farming modes in both October and December soil samples. The correlation analysis showed significantly (atp≤ 0.05 and 0.01) strong positive relationship within different physical and chemical properties of the soil under study. ANOVA and MANOVA analysis indicated significant effect of interaction between soil depth and farming modes on soil parameters. PCA analysis showed the most significant correlation between most of the bacterial types (G + bacteria, G− bacteria, actinomycetes) and soil AP, total available nitrogen, TOC and soil WC. Pearson correlation analysis revealed a significant correlation between microbial phylum groups (Proteobacteria, Bacteroidetes, andLatescibacteria) and microbial class group (Alphaproteobacteria, Sphingobacteriia, Flavobacteriia) with most of the soil physicochemical properties.

Long‐term Camellia oleifera cultivation influences the assembly process of soil bacteria in different soil aggregate particles

AbstractUnderstanding the mechanisms that govern microbial community assembly across a soil–plant continuum is crucial for predicting the responses of ecosystems to environmental changes. However, the impact of the health status of plants on microbial assemblies across these continuums remains poorly understood. In this study, we investigated the stochastic and deterministic processes associated with different aggregate particles and Camellia oleifera growth stages (sapling, maturity, and degeneration periods). The composition of bacterial communities in C. oleifera soil was significantly affected by cultivation length and aggregate size, and cultivation length plays a more important role in the regulation of bacterial composition. The assembly processes of the bacterial community were dominated by deterministic processes in soil aggregates at different growth stages. Soil structurality determined soil α‐diversity and β‐diversity to a greater extent than soil nutrient content. This study provides a comprehensive understanding of the evolutionary mechanisms of soil bacterial community in different soil aggregates and C. oleifera plantation lengths and highlights the significance of soil physical properties to mediate soil microbial community composition and abundance.

Impacts of Co-application of Chemical Fertilizer Reduction and Organic Material Amendment on Fluvo-aquic Soil Microbial N-cycling Functional Gene Abundances and N-converting Genetic Potentials in Northern China

The emerging environment-associated issues due to the overuse of inorganic fertilizers in agricultural production are of global concern despite the benefit of high yields. Eco-friendly organic materials with the capability to fertilize soil are encouraged to partially replace mineral fertilizer. The N cycle conducted by soil microorganisms is the most important biogeochemical process, dictating the N bioavailability in farmland ecosystems; however, little is known about how organic material amendment affects soil microbial N cycling under chemical fertilizer reduction. Hence, a fixed field trial with five fertilization practices was implemented to experimentally alter microorganisms essential for the soil N cycle, including conventional chemical fertilization (NPK), reduced chemical fertilization (NPKR), reduced chemical fertilization plus straw (NPKRS), reduced chemical fertilization plus organic fertilizer (NPKRO), and reduced chemical fertilization plus organic fertilizer and straw (NPKROS). The microbial N-cycling gene abundances and associated N-converting genetic potentials were evaluated using real-time quantitative PCR. In comparison to conventional chemical fertilization (NPK), organic addition significantly increased the amounts of heterotrophic microbes involved in organic N decomposition, N fixation, and N reduction; however, it reduced autotrophic microbes performing ammonia oxidization. Consequently, the overall proportion of heterotrophic microbes was remarkably enhanced, and the autotrophic proportion was correspondingly lowered. The fertilization practice shift significantly improved N fixation and gaseous N emission potentials, whereas it suppressed NO3- leaching potential. A significant discrepancy among five fertilization treatments was observed based on functional gene abundances (PERMANOVA, P=0.002),as revealed by distance-based redundancy analysis (db-RDA), with NH4+ as the dominant factor. Organic fertilizer addition was beneficial for heterotrophic N functional microorganisms, with simultaneous input of straw augmenting such an effect. Pearson's correlation analysis revealed that N storage and gaseous N emission potentials were both substantially negatively correlated with NH4+; NO3- leaching potential was notably negatively associated with SOC and TN but significantly related to NH4+. In conclusion, chemical fertilizer reduction combined with organic material amendments, a main fertilization recommendation, may enhance soil N storage, diminish N loss by leaching, and mitigate the environmental risk of N2O emission. This deserves attention considering that healthy and sustainable agricultural soil environment can be cultivated from the view of microbial N-cycling.

Current Challenges and Pitfalls in Soil Metagenomics.

Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.

Soil Microbial Communities Associated with Three Arctic Plants in Different Local Environments in Ny-Ålesund, Svalbard.

Understanding soil microbial community structure in the Arctic is essential for predicting the impact of climate change on interactions between organisms living in polar environments. The hypothesis of the present study was that soil microbial communities and soil chemical characteristics would vary depending on their associated plant species and local environments in Arctic mature soils. We analyzed soil bacterial communities and soil chemical characteristics from soil without vegetation (bare soil) and rhizosphere soil of three Arctic plants (Cassiope tetragona [L.] D. Don, Dryas octopetala L. and Silene acaulis [L.] Jacq.) in different local environments (coal-mined site and seashore-adjacent site). We did not observe any clear differences in microbial community structure in samples belonging to different plant rhizospheres; however, samples from different environmental sites had distinct microbial community structure. The samples from coal-mined site had a relatively higher abundance of Bacteroidetes and Firmicutes. On the other hand, Acidobacteria was more prevalent in seashore-adjacent samples. The relative abundance of Proteobacteria and Acidobacteria decreased toward higher soil pH, whereas that of Bacteroidetes and Firmicutes was positively correlated with soil pH. Our results suggest that soil bacterial community dissimilarity can be driven by spatial heterogeneity in deglaciated mature soil. Furthermore, these results indicate that soil microbial composition and relative abundance are more affected by soil pH, an abiotic factor, than plant species, a biotic factor.

Meta-analysis of the impacts of phosphorus addition on soil microbes

Soil microbes play a crucial role in myriad ecological processes in terrestrial ecosystem. With increasing nitrogen (N) loading, phosphorus (P) may become more limiting for soil microbes and these processes. However, it remains unclear to what extent P addition impacts soil microbial communities and respiration at global scale, especially under different N loadings. Therefore, we used a global meta-analysis to examine the effects of phosphorus addition on soil microbes based on 2293 paired observations from 129 studies in the world. Overall, P addition increased significantly total as well as fungal, bacterial, and actinomycete (ACT) phospholipid fatty acids (PLFAs), together with Gram+ bacteria (G+) and Gram- bacteria (G-) abundance regardless of N input or not. The increments were more pronounced under higher P addition rate or places with higher mean annual temperature or mean annual precipitation. Moreover, the fungi: bacteria ratio significantly decreased along elevational gradients. Furthermore, higher P addition frequency tended to have significantly more ACT PLFAs, as well as higher G+:G-, but significantly lower fungi: bacteria ratio (F:B). However, the responses of P addition on bacterial PLFAs and F:B were larger in forest than grassland, and cropland and varied with P fertilizer forms. In addition, the responses of soil organic carbon (SOC) contents was positively correlated with those of microbial biomass carbon (MBC) and bacterial PLFAs, and all these three parameters, in addition to fungal PLFAs, correlated positively with the response of soil respiration (Rs). Our results suggest that phosphorus addition had globally positive effects on soil microbes with different N loadings, and the positive effects of soil microbial abundance tended to promote heterotrophic respiration (Rh) and Rs. These results deepen our understanding of soil microbial community structure and function dynamics under increasing P deposition. They also provide extensive evidences and bases for parameterization of soil carbon cycling models incorporating microbial responses under global climate change.

Responses of soil heterotrophic respiration and microbial biomass to organic and conventional production systems

The effects of organic and conventional production systems on crop productivity have been greatly explored, but their effects on soil microbial processes were often neglected. A comparative field study of organic and conventional production systems was conducted at the Tennessee State University research farm to determine soil heterotrophic respiration and microbial biomass carbon. Leafy green vegetables were grown in a conventional production system in an open field, and they were grown in an organic production system, using three different row covers (agribon cloth, insect net, and plastic), and in an open field. Soil samples (0-15cm) were collected from the two production systems. Soil heterotrophic respiration rate (RH), microbial biomass carbon (MBC), and biomass-specific heterotrophic respiration rate (the inverse is used as a proxy for microbial carbon use efficiency) were quantified. The results showed that the conventional production system significantly increased RH relative to the organic system. Organic production system, however, significantly enhanced MBC and reduced biomass-specific respiration rate indicating an increase in carbon use efficiency. Although MBC remained unchanged among the row covers, insect net increased RH and biomass-specific heterotrophic respiration rate. Our results suggest that the organic production system not only promoted soil microbial abundance but also limited soil heterotrophic respiration to the atmosphere governed by the elevated carbon use efficiency.

Short-term application of chicken manure under different nitrogen rates alters structure and co-occurrence pattern but not diversity of soil microbial community in wheat field.

Manure application is an effective way to improve the utilization efficiency of organic resources and alleviate the adverse effects of long-term application of chemical fertilizers. However, the impact of applying manure under different nitrogen rates on soil microbial community in wheat field remains unclear. Treatments with and without chicken manure application under three nitrogen rates (N 135, 180 and 225 kg⋅hm–2) were set in wheat field. Soil organic carbon, available nutrients, and abundance, diversity, structure and co-occurrence pattern of soil microbial community at wheat maturity were investigated. Compared with no manure application, chicken manure application increased the soil organic carbon and available phosphorus, while the effects on soil mineral nitrogen and available potassium varied with different nitrogen rates. Chicken manure application significantly increased soil bacterial abundance under the nitrogen fertilization of 135 and 225 kg⋅hm–2, increased soil fungal abundance under the nitrogen fertilization of 135 kg⋅hm–2, but decreased soil fungal abundance under the nitrogen fertilization of 180 and 225 kg⋅hm–2 (P < 0.05). There was no significant difference in alpha diversity indices of soil microbial communities between treatments with and without chicken manure application under different nitrogen rates (P > 0.05). Chicken manure application and its interaction with nitrogen rate significantly changed soil bacterial and fungal community structures (P < 0.05). There were significantly different taxa of soil microbial communities between treatments with and without chicken manure application. Chicken manure application reduced the ecological network complexity of soil bacterial community and increased that of soil fungal community. In summary, the responses of soil available nutrients and microbial abundance to applying chicken manure varied with different nitrogen rates. One growing season application of chicken manure was sufficient to alter the soil microbial community structure, composition and co-occurrence pattern, whereas not significantly affected soil microbial community diversity.

Cover crop composition drives changes in the abundance and diversity of nitrifiers and denitrifiers in citrus orchards with critical effects on N2O emissions

• Cover crop C and N effects linked to N-cycling community abundance and diversity. • Lower soil N 2 O fluxes with legume + non-legume cover crops vs non-legumes. • Cover crop mixture had significant effects on nirK and nosZ I community diversity. • nirK and nosZ I community composition attributed to soil properties and CC mixtures. • amoA AOA, nirK, and nosZ I species potential indicators of CC N 2 O changes. Tree crops contribute to global agriculture production, but they are usually cultivated in soils with low nutrient availability. Cover crops (CCs) have been reported as a sustainable management strategy to improve soil nutrient availability for vegetable systems, but less is known about their influence on soil nutrient cycling, greenhouse gas emissions (GHG), and the soil microbiome in tree crops. We examined the effect of replacing the traditional weedy row middles of a commercial Florida citrus orchard with two different mixtures of CCs (legumes and non-legumes, LG + NL; and non-legumes only, NL) compared to a grower standard control (GSC) over a period of two years. Both CC mixtures significantly increased soil carbon (C) availability, microbial abundance, and soil respiration in the row middles compared to the GSC. Significant increases in soil nitrogen (N) concentrations and abundance of genes associated with N-fixation and nitrification were observed in soils treated with LG + NL. Planting LG + NL significantly increased the abundance of nosZ -type denitrifiers compared to NL and the GSC treatments, and significantly reduced nitrous oxide (N 2 O) emissions. The use of both CC mixtures reduced bacterial diversity and affected the composition of nirK and nosZ I communities. The composition of nosZ I communities differed between CC mixtures, possibly due to changes in soil moisture and carbon. Specific amoA ammonia-oxidizing archaea, nirK, and nosZ I species were identified as potential indicators for changes in N 2 O emissions after planting CCs. Our results show that CCs can be a good strategy to improve soil nutrient cycling in the row middles of tree crops and that CC composition drives changes in the abundance and diversity of N-cycling communities which ultimately impact GHG emissions.

Soil depth and agricultural irrigation activities drive variation in microbial abundance and nitrogen cycling

Understanding the vertical diversity and abundance of soil microorganisms in shifting environments is crucial for the improvement of crop yield, tackling climate change and optimizing biogeochemical cycles in the Earth’s critical zone. In this study, a comprehensive survey of soil microbial communities was conducted in fields in an irrigated area and an abandoned area in western China. In total, 40 soil cores (600 cm deep) were taken from land under irrigation–fertilization management (IL; 34 cores) and abandoned land (AL; six cores) from July 2013 to April 2018. Spatiotemporal variation in the abundance of soil bacteria, fungi and nitrogen (N)-cycling microbes was evaluated. Soil depth was found to drive soil microbial abundance, but not diversity, throughout the vertical soil profile. The results suggest that in winter, the abundances were mainly driven by environmental variables (depth and temperature), but in summer, by depth, temperature and nutrient status. Depth had strong direct effects, and indirect impacts via temperature and TN, on microbial abundance in summer. The sequence counts for some prokaryotic taxa presented clear, mid-profile peaks in the vertical soil profiles. These distributions may be partially explained by soil texture. Consequently, the environmental filtering associated with depth controls local microbial abundance along resource gradients in the soil profile. Other factors, including temperature, moisture, pH and nutrients, were secondary regulators of microbial abundance. Further, irrigated agriculture land use could accelerate N cycling, increase nitrate leaching, and N2O and N2 production. Such findings, which enhance our understanding of how soil microbial communities respond to environmental changes and N-cycling pathways in the deeper soil profile, could improve field nitrogen management.

Effects of planting quinoa on soil properties and microbiome in saline soil

AbstractQuinoa is widely cultivated for its nutritional value and its high tolerance to environmental problems. Our study was conducted at two planting densities (LD, 10 plants/m2; HD, 65 plants/m2) on ameliorated coastal mudflats in Jiangsu Province, China. The microbial composition in soil was determined by high‐throughput sequencing technology, and root metabolites were determined by a liquid chromatograph‐mass spectrometer (LC–MS). The results showed soil salinity and organic matter were higher at the HD than LD treatment and compared with the non‐rhizosphere (bulk) soil, the salinity of the rhizosphere soil was higher. Quinoa grown at HD was taller, with thicker stalks and lower yields per plant, but higher yield per unit area. Amplicon sequencing showed that Proteobacteria, Bacteroidota and Acidobacteria accounted for the absolute majority. Regarding the rhizosphere soil, the Shannon index was higher in the HD than LD, and Proteobacteria and Bacteroidota were more abundant in the HD treatment. Fifty‐one differential metabolites were identified by metabolomic assays, belonging to 14 annotated metabolic pathways. S‐adenosylmethionine was the most abundant and up‐regulated metabolite (fold change &gt;1.67), and was more abundant in the roots from the LD than in HD treatment. Docosahexaenoic acid was more abundant in the HD than LD treatment, and was a down‐regulated metabolite. In conclusion, planting density was an important factor affecting quinoa yield; compared with unplanted soil, planting quinoa at low density increased the content of the important metabolite S‐adenosylmethionine in the root system of quinoa, and high‐density cultivation of quinoa increased soil salinity and microbial abundance and diversity.

Bacterial Diversity and Potential Functions in Response to Long-Term Nitrogen Fertilizer on the Semiarid Loess Plateau.

Bacterial diversity and its functions are essential to soil health. N fertilization changes bacterial communities and interferes with the soil biogeochemical N cycle. In this study, bacterial community and soil physicochemical properties were studied in 2018 after applying N fertilizers (0, 52.5, 105, 157.5, and 210 kg N ha−1) for a long (2003–2018) and a short (2003–2004) duration in a wheat field on the Loess Plateau of China. Soil bacteria were determined using 16S rRNA Illumina-MiSeq®, and the prediction function was analyzed through PICRUSt. The study showed that N fertilizer significantly changed the diversity and abundance of bacterial communities. The phyla Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi were most abundant, accounting for 74–80% of the bacterial community abundance. The optimum rates of N fertilizer application (N105) maintain soil health by promoting soil microbial diversity and abundance. The bacterial population abundance was higher after short-term N application than after N application for a long duration and lowest with the high N-fertilizer treatment (N210). High N enrichment led to more heterotrophic N-fixing microorganisms (Alphaproteobacteria), in which metabolism and genetic information processing dominated, while cellular processes, genetic information processing, metabolism, and organismal systems were the main functional categories under low N. The phyla Gemmatimonadetes, Actinobacteria, Bacteroidetes, and Chloroflexi were the key bacteria in the co-occurrence network. The genus Saccharimonadales of the superphylum Patescibacteria has a more significant impact under low N treatment. Long-term N fertilization affected the soil pH, NO3-N, and other physicochemical properties, and soil NO3-N was the highest indicator, contributing 81% of the bacterial community function under different N fertilizer treatments.