Alter Soil Microbial Community Research Articles

The effects of plant density and nitrogen fertilization on maize yield and soil microbial communities in the black soil region of Northeast China

To obtain high maize yield (Zea mays L.), nitrogen (N) fertilizer is widely used across the world and has greatly altered soil microbial communities and influenced soil health. Increasing plant density is an effective strategy for increasing maize yield, while variations in soil microbial communities in response to plant density under high N levels have not been well-studied. In Northeast China, maize was grown at low (LD, 67,500 plants ha−1) and high (HD, 90,000 plants ha−1) densities, combined with three N application rates of 0, 200, and 400 kg N ha−1yr−1(N0, N200 and N400). Based on a six-year field experiment, key soil microbial characteristics and physicochemical properties of top soils (0–20 cm), as well as yield and vegetative parameters were examined. Compared with that of LD, the maize grain yield of HD increased 10.8 % across N application rates from 2012 to 2017 (P < 0.05), while no significant differences between N200 and N400 were observed. HD significantly increased microbial biomass carbon (MBC), microbial biomass N (MBN), and bacterial and fungal diversity at N400 (P < 0.05). Dominant bacterial phyla across all samples were Proteobacteria, Acidobacteria, Actinobacteria and Thaumarchaeota, and fungal phyla were Ascomycota, Basidiomycota and Zygomycota. Species composition of HD shared more similarity between N200 and N400 than that of LD. HD significantly increased the abundance of Nitrososphaera and reduced the abundance of Pseudomonas and Sphingobium. From LD to HD, ammonia-oxidizing archaea (AOA) gene abundance increased while nirK gene abundance decreased at all N application rates, and ammonia oxidizing bacteria (AOB) and nirS gene abundances decreased at N0 and N400 but increased at N200 (P < 0.05). Shoot biomass and N uptake were positively correlated with MBC and MBN but negatively correlated with microbial community diversity. HD directly increased root biomass and N uptake, then reduced soil N contents (NH4+-N, NO3–-N, and TN) and thus positively regulated soil microbial communities. Relative differences of diversity indexes and functional gene abundances between N application rates of HD were significantly lower than those of LD. Overall, our findings indicate that higher plant density of maize could mitigate the adverse effects of N fertilizer overuse on soil microbial communities, thus reconciling maize productivity and black soil health in Northeast China.

The controlled-release nitrogen fertilizer driving the symbiosis of microbial communities to improve wheat productivity and soil fertility

Controlled-release nitrogen (CRN) fertilizers gradually release N in synchronization with root nutrient absorption, increasing wheat productivity and soil fertility. The role of the soil microbial community in wheat productivity and soil fertility, on the other hand, is unknown. Amplicon sequencing and a co-occurrence network were used in this study to investigate the role of microbial symbiosis in controlling wheat productivity and soil fertility in a 12-year (2008–2019) calcareous soil field experiment. Furthermore, the effects of various fertilization models were compared. The soil microbial community was divided into three closely coexisting symbiotic modules (Modules #1, 2, and 3). Module #1 and #2 were dominated by bacteria, while Module #3e was dominated by fungi. Modules #1 and #3 had higher network transmissibility (closeness centrality) and stability (degree) than Module #2, and they had a significant positive correlation with wheat productivity and soil fertility. Then, using random forests analysis, we examined the relationship between the module microorganism and wheat productivity and soil fertility. Module #1 microorganisms contributed more to wheat productivity and soil fertility than Module #3 microorganisms, and the microorganisms with significant relationships had a more complex composition (P < 0.05), primarily composed of Actinobacteria, Chloroflexi, Gemmatimonadetes, and Proteobacteria. Module #3, on the other hand, was primarily composed of Ascomycota. Finally, according to the structural equation model, CRN fertilizers could significantly improve wheat productivity and soil fertility when compared to soluble N (SN) fertilizers by increasing the diversity of the symbiotic module. In conclusion, our study discovered that Modules #1 and 3 are closely related to wheat productivity and soil fertility. The composition of module microorganisms, as well as the role of CRN fertilizer in symbiotic modules, were also investigated. • Controlled-release nitrogen (CRN) fertilizer improved wheat productivity and soil fertility. • Long-term CRN fertilization altered soil microbial community structure. • Key symbiotic module significantly affected wheat productivity and soil fertility. • CRN increased the diversity of the key symbiotic module.

Conversion of grassland to abandoned land and afforested land alters soil bacterial and fungal communities on the Loess Plateau

On China's Loess Plateau (CLP), shifts in land use are particularly influential in altering soil microbial communities. While one might expect shifts between grassland, forest and arable land to affect soil microbial communities, the specific ensuing responses of bacterial and fungal diversity and composition on the CLP are poorly understood. Soil microbial diversity and composition among the CLP's native grasslands, afforested lands, and ‘abandoned’ arable lands (fallow roughly 10 years in 2020) were determined using high-throughput sequencing of 16S rRNA and ITS genes. A comparison of land use types showed the abandonment of arable land and grassland afforestation to have had a negligible impact on soil bacterial α-diversity but to result in significantly lower soil fungal diversity. Grassland afforestation also increased fungal richness. Both bacterial and fungal β-diversity differed significantly among the land uses. Conversion of grassland to abandoned land significantly altered the relative phylum-level abundance of bacteria (except that of the Acidobacteria), but not that of fungal phyla. Grassland afforestation only influenced the abundance of bacteria and fungi of lower relative abundance (<10 % except Proteobacteria). The quantity of above- and below-ground biomass and soil properties explained most of the variation in soil microbial communities. Having important ecological implications, these findings can inform land management decisions in the study area and similar ecologically-fragile regions.

Cotton stubble return and subsoiling alter soil microbial community, carbon and nitrogen in coastal saline cotton fields

Long-term cotton stubble return and subsoiling improve root growth and soil properties and alter microbial colonization in the rhizosphere. However, it is unknown if cotton stubble return and subsoiling would change the soil microbial biomass carbon (MBC) and nitrogen (MBN) sequestration by changing the microbial community in coastal saline soil. We used an experiment to quantify the effects of stubble management (removal or return), tillage (non-subsoiling or subsoiling), and soil compartments (non-rhizosphere or rhizosphere) on the bacterial and fungal communities after 9-year treatments. Soil compartments were the main factor affecting the soil bacterial community. The abundance of Bacillus, Pseudomonas, and Sphingomonas in the rhizosphere soil increased by 63.64%, 20.40%, and 109.24%, respectively, compared to the non-rhizosphere soil. Moreover, Bacillus was increased by both stubble return and subsoiling. The Chao1, Simpson, and Shannon indices in alpha diversity of the bacterial community were increased by rhizosphere soil, stubble return, and subsoiling. The MBC and MBN in the rhizosphere soil was 22.4% and 13.2% higher than in the non-rhizosphere soil. Stubble management was the main factor affecting the fungal community composition. Stubble return significantly increased some fungal abundance, e.g., Cephalotrichum and Fusarium, by 243.11% and 95.24% than stubble removal. The abundance of Cephalotrichum, Fusarium, and Alternaria in the rhizosphere soil was significantly higher than that in the non-rhizosphere soil. The Chao1, Simpson, and Shannon indices of the fungal community were only significantly increased by stubble return. Compared with cotton stubble removal, stubble return increased MBC and MBN by 31.8% and 23.0%, respectively. The effects of the plant growth promoting rhizobacteria (PGPR) (Bacillus and Pseudomonas) on rhizosphere microbial community and MBC and MBN were higher than those of pathogenic fungi (Fusarium and Alternaria) from Structural Equation Models (SEM). Our results suggest that long-term cotton stubble return and subsoiling could play a role in improving soil microbial community and C and N and enhance the sustainability of coastal saline soil.

Aboveground herbivory can promote exotic plant invasion through intra- and interspecific aboveground-belowground interactions.

Aboveground herbivores and soil biota profoundly affect plant invasions. However, how they interactively affect plant invasions through plant-soil feedbacks (PSFs) remains unclear. To explore how herbivory by the introduced beetle Agasicles hygrophila affects Alternanthera philoxeroides invasions in China, we integrated multiyear field surveys and a 2-yr PSF experiment, in which we examined how herbivory affects PSFs on the performance of native and invasive plants and the introduced beetles. Despite increased herbivory from A.hygrophila, A.philoxeroides dominance over co-occurring congeneric native Alternanthera sessilis remained constant from 2014 to 2019. While occurring at lower abundances, A.sessilis experienced similar herbivore damage, suggesting apparent competitive effects. Our experiments revealed that herbivory on A.philoxeroides altered soil microbial communities, prolonged its negative PSF on A.sessilis, and decreased A.hygrophila larvae performance on the next-generation invasive plants. Consequently, A.hygrophila larvae performed better on leaves of natives than those of invasives when grown in soils conditioned by invasive plants defoliated by the introduced beetles. Our findings suggest that aboveground herbivory might promote rather than suppress A.philoxeroides invasion by enhancing its soil-mediated self-reinforcement, providing a novel mechanistic understanding of plant invasions. These findings highlight the need to incorporate an aboveground-belowground perspective during the assessment of potential biocontrol agents.

Biochar and nitrogen fertilizer promote rice yield by altering soil enzyme activity and microbial community structure

AbstractBiochar can significantly change soil properties and improve soil quality. However, the effects of long‐term combined application of biochar (B) and nitrogen (N) fertilizer on relationships between soil enzyme activity, microbial community structure, and crop yield are still obscure. We characterized these relationships in a long‐term (8 years) field experiment with rice, two biochar rates of 0 and 13.5 t ha−1 year−1 (B0 and B) and two N fertilizer rates of 0 and 300 kg N ha−1 year−1 (N0 and N). The repeated, long‐term combined applications of biochar and N fertilizer significantly increased microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but biochar decreased the abundance of total bacteria, fungi, actinomycetes, and gram‐positive and gram‐negative bacteria as well as the amount of total phospholipid fatty acids. The activity of leucine aminopeptidase (LAP) decreased significantly in the biochar‐amended and N fertilized treatment, but the LAP activity either remained unchanged or increased with biochar amendment at N0. The relative abundance of bacterial phylum Chloroflexi was increased in the combined biochar and N fertilizer treatment. The changes in soil organic matter and the activity of α‐1,4‐xylosidase were the major properties influencing soil bacterial community composition, whereas the structure of fungal community was governed by MBC, MBN, and LAP activities. In addition, long‐term biochar and N fertilizer applied together significantly increased rice yield (more than biochar and nitrogen fertilizer applied alone). Yield was significantly positively correlated with LAP activity, but significantly negatively correlated with the relative abundance of Chloroflexi. In conclusion, long‐term biochar and nitrogen fertilizer applications increased rice yield, which was associated with altered soil microbial community and enhanced activity of some enzymes.

Aridity differentially alters the stability of soil bacterial and fungal networks in coastal and inland areas of Australia.

Despite the importance of soil bacterial and fungal communities for ecosystem services and human welfare, how their ecological networks respond to climatic aridity have yet been evaluated. Here, we collected soil samples from 47 sites across 2500 km in coastal and inland areas of eastern Australia with contrasting status of aridity. We found that the diversity of both bacteria and fungi significantly differed between inland and coastal soils. Despite the significant differences in soil nutrient availability and stoichiometry between the inland and coastal regions, aridity was the most important predictor of bacterial and fungal community compositions. Aridity has altered the potential microbial migration rates and further impacted the microbial assembly processes by increasing the importance of stochasticity in bacterial and fungal communities. More importantly, ecological network analysis indicated that aridity enhanced the complexity and stability of the bacterial network but reduced that of the fungal network, possibly due to the contrasting impacts of aridity on the community-level habitat niche breadth and overlaps. Our work paves the way towards a more comprehensive understanding of how climate changes will alter soil microbial communities, which is integral to predicting their long-term consequences for ecosystem sustainability and resilience to future disturbances.

Intensity and duration of exposure determine prokaryotic community response to salinization in freshwater wetland soils

The salinization of coastal freshwater wetlands may impact the biogeochemical cycling of critical nutrients by altering soil microbial community structure and function. Nitrate (NO3–) reduction pathways appear particularly sensitive, though the interactive effects of salinization intensity and duration of exposure remain unclear. To address this knowledge gap, we performed a transplant experiment that exposed soil from a freshwater (≤0.1 ppt) wetland to oligohaline (1 ppt) and mesohaline (14 ppt) conditions for two years. In transplanted soils, we found physicochemical changes characteristic of salinization events, including elevated porewater concentrations of ammonium and sulfate and decreased soil organic matter and redox potential. Amplicon sequencing (16S rRNA) revealed that mesohaline levels of salinization caused rapid community restructuring; distinct transition communities were evident by the first sampling event (5 months) and persisted for ∼2 years (19–22 months). In contrast, freshwater communities transplanted to oligohaline conditions were highly resistant to restructuring, and it took nearly 2 years of salinization for differences to manifest. For both transplants, community shifts included changes in the distribution and abundance of taxa capable of NO3– reduction, including several groups also known for sulfur redox metabolism. Nitrate (15NO3-) reduction assays were performed to determine how rates were affected. Dissimilatory nitrate reduction to ammonium (DNRA) increased for all sampling events, but only under mesohaline conditions, whereas denitrification responses depended more on the duration of exposure than salinity level. These findings may be useful for determining when and how the ability of wetlands to remove nitrogen will be impacted by sea-level rise. Further, these results suggest that efforts to synthesize and generalize prior research regarding salinization effects on wetland microbial community structure and function must explicitly consider both salinity intensity and exposure length.

Recovery of soil microbial diversity and functions along a tropical montane forest disturbance gradient

Logging and forest conversion are occurring at alarming rates in tropical forests. These disturbances alter soil microbial community structure and functions. While direct links between changes in soil properties, such as pH and microbial community structure are well established, the indirect effects of logging and forest conversion on soil microbial community structure and functions are poorly understood. We used a space-for-time substitution to investigate the changes in soil microbial diversity and functions across a forest recovery gradient in the tropical montane forests of northern Borneo. We used surface (top 5 cm) soil to assess soil physicochemical and microbial (next-generation DNA sequencing) properties, and standardized litterbags (Tea Bag Index) to assess litter decomposition and stabilization. Our results show that bacterial and fungal diversity increases with recovery time and reaches pre-disturbance levels between 60- and 80-years post-disturbance. Litter decomposition rate constants increased linearly with increasing bacterial and fungal diversity. Litter stabilization also increased linearly with fungal diversity, but was highest at intermediate levels of bacterial diversity. Our results provide insights on the effects of forest logging and conversion on soils and highlight the tight coupling between soil microbial diversity and soil functions in tropical montane forests.

Nitrogen Fertilization Increases Soil Microbial Biomass and Alters Microbial Composition Especially Under Low Soil Water Availability.

Soil microbial biomass and composition are affected by resource supply and water availability. However, the response of soil microbial communities to nitrogen fertilization under different water availability conditions is unclear. Therefore, this study conducted a 6-year pot experiment comprising five watering regimes (40%, 50%, 60%, 80%, and 100% of field capacity (FC)) and three nitrogen fertilization levels (NH4NO3 solution; 0 [N0], 20 [N1], and 40 [N2] g N m-2year-1) to investigate soil microbial biomass, composition, and properties. The results indicated that soil microbial biomass and composition were more strongly affected by nitrogen fertilization compared with water regime. Nitrogen fertilization increased soil microbial biomass and altered soil microbial community composition, especially under low soil water availability. Soil microbial biomass was positively linearly associated with soil water regimes under N0, whereas it responded polynomially to soil water regimes under N1 and N2. The maximal soil microbial biomass was observed at FC80 for N1 and FC60 for N2. Furthermore, the biomass of soil microbial groups with high nitrogen and carbon acquisition ability as well as the enzyme activities of carbon and nitrogen cycling (β-1,4-glucosidase and β-1,4-N-acetyl-glucosaminidase, respectively) were stimulated by nitrogen fertilization. Soil microbial biomass was affected directly by nitrogen fertilization and indirectly by nitrogen and water regimes, via altering soil pH, dissolved inorganic nitrogen (NH4+-N and NO3--N) concentration, and soil organic carbon concentration. This study provides new insights into the effect of interaction between soil nitrogen and water availabilities on soil microbial biomass, composition, and its underlying mechanism.

Compost amendment maintains soil structure and carbon storage by increasing available carbon and microbial biomass in agricultural soil – A six-year field study

Soil organic amendments in agricultural production can benefit crop production and a wide range of soil properties, including soil aggregation. Soil aggregate formation is largely driven by microbial activities, and can in-turn influence microbial communities by generating distinct microbial habitats, as well as associated impacts on water and nutrient dynamics. We investigated the long-term effects of two fertilizer management strategies (poultry manure compost vs. mineral fertilizer) and biochar amendment (0 vs. 10 t ha−1 walnut shell biochar, 900 °C pyrolysis temperature, by-product of gasification) on soil aggregation, soil organic C, and microbial community dynamics in water-stable aggregate fractions in corn-tomato rotations. Using wet-sieving, soils (0–15 cm) were divided into four size fractions: large macroaggregates (2000–8000 μm), small macroaggregates (250–2000 μm), microaggregates (53–250 μm) and silt and clay (<53 μm) for calculation of mean weight diameter in both 2014 and 2018. The total C and microbial community composition and abundance within each fraction were evaluated in 2018. Across all treatments, six years of continuous compost application maintained soil aggregate stability and C storage by increasing soil microbial biomass and associated dissolved organic C. Bacterial and fungal populations under compost treatments were significantly higher than under mineral fertilizer treatments based on 16S rRNA gene copy number and internal transcribed spacer (ITS) abundance, which likely contributed to the formation and maintenance of macroaggregates in compost treatments. Interestingly, continuous application of manure compost may increase microbial available C sources by increasing the abundance of bacteria with the potential to degrade aromatic C as predicted from 16S sequences. Soil under the mineral fertilizer treatment showed decreases in the proportion of large macroaggregates, bulk soil C, and aggregate-associated C storage compared to the compost treatment. The application of highly recalcitrant walnut shell biochar had limited long-term impacts on soil aggregation and C dynamics, likely due to its lack of microbially-available C and limited interaction with the soil environment. Our results indicate that continuous compost inputs maintained soil structure and associated physical stabilization of SOM by enlarging soil microbial available C pool, higher soil microbial biomass, and increasing aggregate formation. The soil aggregate structure, in-turn, generated diverse habitats and altered soil microbial communities. Compost inputs, in addition to or in partial replacement of mineral fertilizer inputs, can provide valuable microbial-driven ecosystem services, such as carbon storage and soil structure, while still providing fertility for crop growth.

Effect of fumigants and non-fumigants on nematode and weed control, crop yield, and soil microbial diversity and predicted functionality in a strawberry production system

Fumigants are commonly used to control soil-borne pathogens of high-value crops, but they may also impact non-target soil microorganisms. Increasing interest in the use of sustainable management practices to control plant- and root-parasitic nematodes has resulted in the formulation of non-fumigant nematicides (chemicals or bionematicides) which are considered environmentally friendly alternatives to fumigants. However, the impact of these new products compared to standard fumigants on soil-borne pathogens, plant production, and the diversity and composition of non-target microbial communities in all crops remains unclear. To begin to address this knowledge gap, we examined the effect of fumigants commonly used in Florida (United States) strawberry production and newly formulated non-fumigant nematicides on nematode and weed control, plant growth, crop yield, and bacterial and fungal community diversity and predicted functionality. We found the standard fumigants increased crop yields and reduced weed pressure more than non-fumigants. Both fumigants and non-fumigants were an efficient management strategy to control sting nematodes. Treatments also impacted the abundance of specific beneficial and antagonistic taxa. Both fumigants and non-fumigants reduced soil bacterial and fungal diversity, an effect that remained for six months, thus suggesting a potential residual impact of these products on soil microorganisms. However, only fumigants altered soil microbial community composition and reduced network complexity, inducing a decrease or even a loss of some predicted bacterial and fungal functions, particularly during the first weeks after fumigation. Nevertheless, soil collected at the end of the season showed significant levels of root-knot nematode suppression in a growth chamber experiment, irrespective of the previous treatment. By linking the effect of fumigants and non-fumigants on soil-borne pests, plant and production, and the soil microbiome, this study increases our knowledge regarding the environmental impact of these products.

Effects of rape/common vetch intercropping on biomass, soil characteristics, and microbial community diversity

Legume–brassica intercropping is widely used to increase productivity in modern, sustainable agricultural systems. However, few studies have assessed the linkages between soil properties and soil microorganisms. Soil microorganisms play a key role in soil nutrient turnover and plant community composition. To elucidate the responses of soil microbial community diversity and structure to intercropping, we conducted a 2-year experiment based on common vetch (CV) monoculture, rape (R) monoculture, and common vetch–rape intercropping (IRCV) with phosphorus (P) addition in alkaline soil. The microbial communities of bacteria and fungi in the rhizosphere soil were examined based on high-throughput sequencing targeting the 16S rRNA and ITS genes, respectively. In addition, we analyzed changes in soil properties and enzyme activities. Intercropping significantly increased dry matter (up to 98.86% and 81.48%, respectively dry matter is the aboveground biomass.) compared with common vetch monoculture. Intercropping decreased soil bulk density and pH and enhanced soil available phosphorus (AP) by 14.54–34.38%, 7.25–22.67%, soil organic matter (SOM) by 15.57–22.85, 6.82–15.57%, soil sucrase (Suc.) by 13.69–16.10%, 35.57–40.24% compared to monoculture common vetch and rape, respectively. However, bacterial alpha diversity was higher under rape monoculture than IRCV. In addition, the dominant soil bacterial phyla Proteobacteria (1.25–3.60%), Gemmatimonadetes (7.88–15.16%), Bacteroidetes (9.39–11.76%), and Rokubacteria (0.49–5.69%) were present at greater abundance with IRCV relative to those with CV and R, but phyla Chloroflexi was significantly decreased by 11.56–12.94% with IRCV compared with the other two treatments. The redundant analysis showed that SOM and AP were positively correlated with the dominant bacterial and fungal flora. Common vetch–rape intercropping resulted in increased biomass and altered soil microbial community composition as well as soil properties. Our results showed that intercropping systems positively improve soil microbial activity; this strategy could help in the cultivation of multiple crops and improve soil properties through sustainable production.

Combined apatite, biochar, and organic fertilizer application for heavy metal co-contaminated soil remediation reduces heavy metal transport and alters soil microbial community structure

Soil amendments are used extensively to remediate soils contaminated with heavy metals. However, the effects of soil amendments on heavy metal bioavailability, plant yield, and bacterial community structure in tropical farmland soils remain largely unknown. In the present study, seaweed organic fertilizer (S), apatite (A), biochar (B), and seaweed organic fertilizer-apatite-biochar mixtures (SAB) were applied at different rates to assess their influence on cadmium (Cd), lead (Pb), and chromium (Cr) bioavailability in contaminated farmland soils, using different component ratios and doses in maize field plots, and maize yield. Effects on soil bacterial community structure were also evaluated based on high-throughput sequencing. Following addition of 2 % S + A + B combined amendment at a ratio of 1:0.5:1.5 (2%S1A0.5B1.5), soil pH and electrical conductivity (EC) were elevated, and bioavailable Cd, Pb, and Cr concentrations were reduced in potted soils, leading to higher heavy metal immobilization. Under field conditions, soil pH, EC, organic matter, ammonium‑nitrogen, available phosphorus, available potassium, and crop productivity were all increased considerably, whereas soil Cd and Cr bioavailability were lower in the combined amendment treatments than in the control treatments. Particularly, application of a 2.49 t·ha−1 combined amendment (0.83 t·ha−1 S + 0.41 t·ha−1A + 1.25 t·ha−1B,1:0.5:1.5) decreased Cd, Pb, and Cr concentrations in maize grain by 68.9 %, 68.9 %, and 65.7 %, respectively. Species abundance and evenness in bacterial communities increased in field soils subjected to combined amendments, with shifts in community structure and function mostly driven by changes in soil pH, organic matter content, and nutrient availability. Overall, the results suggest that 1.5%S1A0.5B1.5 is the optimal treatment for remediating heavy metal co-contaminated soil, and thereby, improving maize yield and quality. Combined organic and inorganic amendments achieve high remediation efficiency, mainly by improving chemical properties, reducing heavy metal bioavailability, and altering bacterial community structure and function in heavy metal contaminated farmland soils.

Unraveling consequences of the co-exposure of polyethylene microplastics and acid rain on plant-microbe-soil system

Emerging microplastics (MPs) pollution and continuing acid rain (AR) co-exist in terrestrial ecosystems, and are considered as threats to ecosystems health. However, few data are available on MPs-AR interactions in plant-microbe-soil systems. Here, a microcosm experiment was manipulated to elucidate the co-exposure of polyethylene MPs (PE MPs; 1%, 5% and 10%) and AR (pH 4.0) on soil-lettuce system, in which the properties of soil and lettuce, and their links were explored. We found that 10% PE MPs increased soil CO2 emission and its temperature sensitivity (Q10) in combination with AR, while 1% PE MPs reduced soil CO2 emission irrespective of AR. PE MPs addition did not influence lettuce production (total biomass) though its photosynthesis was affected. PE MPs exerted negative impact on soil water availability. PE MPs treatments increased NH4+-N content of soil without AR, and dissolved organic carbon content of soil sprayed with AR. 10% PE MPs combined with AR reduced soil microbial biomass, while soil microbial community diversity was not affected by PE MPs or AR. Interestingly, 10% PE MPs addition altered soil microbial community structure, and promoted the complexity and connectivity of soil microbial networks. 5% and 10% PE MPs addition decreased soil urease activity under AR, but this was not the case without AR. These findings highlight the critical role of AR in regulating PE MPs impacts on plant-microbe-soil ecosystems, and the necessity to incorporate other environmental factors when evaluating the actual impacts or risks of MPs pollution in terrestrial ecosystems.

Wheat cover crop alters soil microbial community and increases cucumber yield under different potassium regimes

Cover crops can promote the subsequent plant growth and improve soil potassium (K) fertility. However, whether and how wheat cover crop benefits cucumber growth and yield under different K regimes and their functional roles are still unclear. In this study, a two-year greenhouse experiment from spring 2017 to autumn 2018 was conducted to evaluate the effects of wheat cover crop on cucumber plant growth, nutrition and yield. Moreover, a litterbag experiment was carried out in the greenhouse in spring 2018 to investigate the nutrient dynamics during decomposition of wheat shoot and root residues under the two K regimes. Soil bacterial and fungal communities during residues decomposition were analyzed by high-throughput amplicon sequencing, and the abundances of total bacterial, fungal, Bacillus and Pseudomonas spp. communities were also estimated by quantitative PCR. The responses of cucumber growth to changes in the soil microbial communities induced by wheat cover crop were assessed by plant-soil feedback experiment. Wheat cover crop increased cucumber yield except for in spring 2017 and plant growth and K concentration at 70 d in spring 2018, and reduced K application did not weaken the beneficial effects of wheat on cucumber growth and yield. Decomposition rate and nutrient release of wheat shoot residue differed from root residue, but no differences in shoot or root residue decomposition rate and nutrient release between the two K regimes. Wheat shoot and root residues differently changed the abundances, compositions and diversities of soil bacterial and fungal communities. Wheat shoot residue increased total bacteria, Bacillus and Pseudomonas spp. community abundances compared with root residue irrespective of K regimes, and Bacillus spp. community abundance was higher in shoot residue with reduced K application than that with normal K application from 220 to 240 d. Wheat shoot residue decreased the Shannon and inverse Simpson diversities of soil bacterial and fungal communities compared with root residue from 200 to 240 d. Moreover, there was significant difference in these diversities of soil fungal community of root residue between the two K regimes except for 240 d. In addition, wheat cover crop caused more stable co-occurrence network with more positive and negative total links and wheat shoot residue had higher these links than root residue, while reduced K application decreased these links of both shoot and root residues. Feedback effects of changes in soil microbial communities induced by wheat cover crop on cucumber growth were positive, and such effect was stronger in shoot residue than in root residue irrespective of K regimes. Overall, wheat cover crop can alter soil microbial communities and enhance cucumber productivity through positive plant-soil feedbacks mediated by soil biota, and reduced K application did not weaken such beneficial effects.

Canopy and Understory Nitrogen Addition Alters Organic Soil Bacterial Communities but Not Fungal Communities in a Temperate Forest.

Atmospheric nitrogen (N) deposition is known to alter soil microbial communities, but how canopy and understory N addition affects soil bacterial and fungal communities in different soil layers remains poorly understood. Conducting a 6-year canopy and understory N addition experiment in a temperate forest, we showed that soil bacterial and fungal communities in the organic layer exhibited different responses to N addition. The main effect of N addition decreased soil bacterial diversity and altered bacterial community composition in the organic layer, but not changed fungal diversity and community composition in all layers. Soil pH was the main factor that regulated the responses of soil bacterial diversity and community composition to N addition, whereas soil fungal diversity and community composition were mainly controlled by soil moisture and nutrient availability. In addition, compared with canopy N addition, the understory N addition had stronger effects on soil bacterial Shannon diversity and community composition but had a weaker effect on soil bacteria richness in the organic soil layer. Our study demonstrates that the bacterial communities in the organic soil layer were more sensitive than the fungal communities to canopy and understory N addition, and the conventional method of understory N addition might have skewed the effects of natural atmospheric N deposition on soil bacterial communities. This further emphasizes the importance of considering canopy processes in future N addition studies and simultaneously evaluating soil bacterial and fungal communities in response to global environmental changes.

The positive role of root decomposition on the bioremediation of organic pollutants contaminated soil: A case study using PCB-9 as a model compound

Root decomposition keeps occurring widely in soils, particularly after plant harvest and death, and drives critical microbial ecological functions. However, its role in the destiny of soil organic pollutants and underlying mechanisms remain unclear. In this study, DNA stable isotope probing (DNA-SIP) was combined with metabolomics to investigate the mechanisms of soil polychlorinated biphenyls (PCBs) degradation in the root decomposition process by identifying the active PCBs degraders in situ and corresponding metabolites. The 2,5-dichlorobiphenyl (PCB-9) degradation was improved by 7.4% in the root decomposition treatment relative to the rhizosphere treatment, and the degradation was faster in both treatments than the control after 6-week cultivation. Both root decomposition and rhizosphere treatments altered soil microbial community, changing the active PCB-9 degraders to different extents. The root decomposition treatment had the highest “average phylogenetic distance index” (ADI) value, indicating a competition reduction effect of root decomposition on microbial survival, and the lowest corrected average phylogenetic distance index (ADIC) value, suggesting a preference toward aerobic PCBs degraders during root decomposition. Metabolites associated with the root decomposition process critically affected both the whole microbial community and active PCB-9 degraders. Compounds related to carbohydrate and lipid metabolisms were enriched during the root decomposition process and might be important to the active PCB-9-degrading community assembly. Our results confirmed that root decomposition improved the biodegradation of organic pollutants in soil and reminded us of its importance in soil quality.

Acetaminophen Levels Found in Recycled Wastewater Alter Soil Microbial Community Structure and Functional Diversity

The practice of using recycled wastewater (RWW) has been successfully adopted to address the growing demand for clean water. However, chemicals of emerging concern (CECs) including pharmaceutical products remain in the RWW even after additional cleaning. When RWW is used to irrigate crops or landscapes, these chemicals can enter these and adjacent environments. Unfortunately, the overall composition and concentrations of CECs found in different RWW sources vary, and even the same source can vary over time. Therefore, we selected one compound that is found frequently and in high concentrations in many RWW sources, acetaminophen (APAP), to use for our study. Using greenhouse grown eggplants treated with APAP concentrations within the ranges found in RWW effluents, we investigated the short-term impacts of APAP on the soil bacterial population under agricultural settings. Using Illumina sequencing-based approaches, we showed that APAP has the potential to cause shifts in the microbial community most likely by positively selecting for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The Biolog plates indicated that the metabolism of amines, amino acids, carbohydrates, carboxylic acids, and polymers was significantly higher in the presence of APAP. Abundance of microorganisms of importance to plant health and productivity was altered by APAP. Our results indicate that the soil microbial community and functions could be altered by APAP at concentrations found in RWW. Our findings contribute to the knowledge base needed to guide policies regulating RWW reuse in agriculture and also highlight the need to further investigate the effects of CECs found in RWW on soil microbiomes.

Microbial Community-Level Physiological Profiles and Genetic Prokaryotic Structure of Burned Soils Under Mediterranean Sclerophyll Forests in Central Chile.

Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou’s evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3– was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.