Soil Microbial Function Research Articles

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.

Climate and edaphic factors drive soil enzyme activity dynamics and tolerance to Cd toxicity after rewetting of dry soil

The intense drying-rewetting cycle due to climate change can affect soil microbial community composition and function, resulting in long-term consequences for belowground carbon and nutrient dynamics. However, how climatic and edaphic factors influence the responses of enzymes to rewetting and their responses to additional perturbation (e.g., heavy metal pollution) after the drying-rewetting history are not well understood. In this study, we collected 18 surface soils from farmlands across various climate zones in China. We chose dehydrogenase (DHA) and alkaline phosphomonoesterase (ALP) as representative intracellular and extracellular enzymes, respectively, and investigated their tolerance to additional perturbation by adding metal ions (i.e., Cd2+) upon rewetting. In all soils, rewetting increased DHA activities but did not affect ALP activities compared to air-dried soils. Rewetting increased the tolerances of DHA and ALP to Cd stress, suggesting that the drying-rewetting history may reduce the susceptibility of soil enzymes to additional disturbance. The results demonstrate that differentiating enzymes based on their location in the soil will improve our ability to assess the stress response of microbial communities to drastic fluctuations in soil moisture, thereby better predicting the legacy of climate change on microbial function in soils contaminated with heavy metals.

Temporal Dynamics of Rare and Abundant Soil Bacterial Taxa from Different Fertilization Regimes Under Various Environmental Disturbances.

ABSTRACTGlobal climate change has emerged as a critical environmental problem. Different types of climate extremes drive soil microbial communities to alternative states, leading to a series of consequences for soil microbial ecosystems and related functions. An effective method is urgently needed for buffering microbial communities to tackle environmental disturbances. Here, we conducted a series of mesocosm experiments in which the organic (NOF) and chemical fertilizer (NCF) long-term-amended soil microbiotas were subjected to environmental disturbances that included drought, flooding, freeze-thaw cycles, and heat. We subsequently tracked the temporal dynamics of rare and abundant bacterial taxa in NOF and NCF treatment soils to assess the efficiencies of organic amendments in recovery of soil microbiome. Our results revealed that freeze-thaw cycles and drought treatments showed weaker effects on bacterial communities than flooding and heat. The turnover between rare and abundant taxa occurred in postdisturbance succession of flooding and heat treatments, indicating that new equilibria were tightly related to the rare taxa in both NCF and NOF treatment soils. The Bayesian fits of modeling for the microbiome recovery process revealed that the stability of abundant taxa in NOF was higher than that in NCF soil. In particular, the NOF treatment soil reduced the divergence from the initial bacterial community after weak perturbations occurred. Together, we demonstrated that long-term organic input is an effective strategy to enhance the thresholds for transition to alternative states via enhancing the stability of abundant bacterial species. These findings provide a basis for the sustainable development of agricultural ecosystems in response to changing climates.IMPORTANCE Different climate extremes are expected to be a major threat to crop production, and the soil microbiome has been known to play a crucial role in agricultural ecosystems. In recent years, we have known that organic amendments are an effective method for optimizing the composition and functioning of the soil microbial community and maintaining the health of the soil ecosystem. However, the effects of organic fertilization on buffering bacterial communities against environmental disturbances and the underlying mechanisms are still unclear. We conducted a series of mesocosm experiments and showed that organic fertilizers had additional capacities in promoting the soil microbiome to withstand climate change effects. Our study provides both mechanistic insights as well as a direct guide for the sustainable development of agricultural ecosystems in response to climate change.

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.

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.

Effects of micronutrient fertilization on soil carbon pools and microbial community functioning

Fertilization with macronutrients, e.g., nitrogen (N) and phosphorus (P), has wide-ranging and well-characterized effects on terrestrial ecosystem functions. In contrast, influences of other elements, e.g., sodium (Na), calcium (Ca), and potassium (K), hereafter, ‘micronutrients’, are poorly understood. To determine effects of macronutrients, micronutrients, and their interactions on soil carbon (C) cycling, we conducted a full factorial experiment where treatments consisted of fertilizing experimental plots with Na, Ca, and K (each manipulated individually) and macronutrients (N + P added together). Each year of the experiment we measured aboveground plant biomass and sampled soils to quantify mineralizable C pools and active microbial biomass. To further explore micronutrient effects on microbial-mediated soil C cycling, in the final year of the experiment we assessed microbial C cycle functions using a catabolic profiling technique and quantified multiple additional soil C pools: particulate (POM-C), mineral-associated (MAOM-C), and total (TC). Macronutrients (N + P) affected nearly all measured variables – when N + P was added, active microbial biomass increased, catabolic profiles were altered, and mineralizable C, POM-C, and TC pools all increased. Micronutrients also had effects on soil C cycling that were generally smaller than effects of macronutrients – Ca addition reduced mineralizable C pools relative to the other treatments and K addition increased POM-C and TC pools. Further, Ca + K addition altered microbial catabolic profiles, but only when N + P was also added. Our study reveals several influences of micronutrients on soil C cycling – specifically, that Ca and K may influence the size of soil C pools by influencing the C cycle functions of soil microbial communities.

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.

Effects of Different Vegetation Types on Soil Microbial Functional Genes and Enzyme Activities in Reclaimed Coal Mine

Long-term coal mining has seriously damaged soil structures and ecological environments. Reclaimed vegetation could effectively improve the ecological environment. There have been many studies on soil physical-chemical characteristics and microbial community structure, but there are few on soil functional microorganisms in mining areas. In this study, soil physical and chemical properties, soil enzyme activities, and the abundance of functional genes in carbon, nitrogen, phosphorus, and sulfur cycling were determined in five reclaimed lands of different vegetation types (Platycladus orientalis, Picea asperata, Pinus tabuliformis, Pinus sylvestris, and Sabina chinensis) in the Jinhuagong mining area, Datong City, Shanxi province. The results showed that the restoration types produced significant effects on soil physical and chemical properties, soil enzyme activities, and the abundance of 75 functional genes. The highest contents of total carbon, total nitrogen, and total sulfur were in the S. chinensis site. The activities of dehydrogenase and urease were the highest in P. asperata, and the lowest alkaline protease activity was in P. asperata. The alkaline protease activity was the highest in P. sylvestrist. The abundance of functional genes in the P. asperata forest was the highest, but the diversity index was significantly lower than that in other plots, which might be due to the fact that the total abundance of ureC, acsA, and mct in P. asperata accounted for more than 52%. Soil urease was significantly correlated with the abundance of six functional genes. The β diversity of the functional microbial community was significantly different among the different vegetation types, indicating that functional genes could better explain the effects of vegetation types on microbial function. The highest and lowest integrated fertility indexes were found in the P. sylvestris and P. orientalis plots, respectively. In conclusion, soil functional genes are sensitive indicators signifying the effects of different reclamation types on soil microorganisms, and P. asperata and P. sylvestris are more suitable for reclamation in this mining area.

Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes

Agroecosystem management practices, plant-microbe interactions, and climate are all factors that influence soil microbial community diversity and functionality. Herein, we assessed diversity of soil bacterial-archaeal assemblages and denitrification gene markers in a long-term tillage field experiment. We evaluated bulk and rhizosphere soils from two crop years (corn and soybean) of a three-year rotation of corn-soybean-small grain + cover crop. Soil samples were collected at three growth stages from corn and soybean plants and across three tillage practices that had been applied every year for 40 years. Tillage practices represented three levels of disturbance intensity ranging from low (no-till) to intermediate (chisel-disk) to high (moldboard plow) intensities. Bacterial assemblage diversity differed in soils having contrasting tillage histories and from bulk or rhizosphere soil (compartments), crop year, and growth stage. Compared to plowed and chisel-disked soils, no-till soils had lower abundances of denitrification genes, higher abundances of genes for dissimilatory nitrate reduction to ammonium (DNRA), and higher abundances of family-level taxa associated with archaeal nitrification and anammox. Soybean rhizospheres exerted stronger selection on bacterial-archaeal composition and diversity relative to corn rhizospheres. Abundances of N genes were grouped by factors related to weather, as well as management and soil compartment, which could impact activity related to denitrification and DNRA. Low intensity tillage may provide an option to reduce potential ‘hot spots’ or ‘hot moments’ for N losses in agricultural soils, although weather and crop type are also important factors that can influence how tillage affects microbial assemblages and microbial N use.

Responses of soil microbial biomass and carbon source utilization to simulated nitrogen deposition and drought in a Cunninghamia lanceolata plantation

Chinese fir (Cunninghamia lanceolata) plantation is a dominant forest type and carbon sink in the subtropical region in China. An experiment with simulated nitrogen deposition (addition of 40 kg N·hm-2·a-1) and drought (50% of precipitation exclusion, PE) was established in Chinese fir plantation in 2018. Soil samples (0-15 cm) were collected in summer (July 2020) and winter (January 2021). Soil microbial biomass, colony forming units (CFUs) and carbon source utilization were determined through phospholipid fatty acids (PLFAs), plate count, and Biolog methods, respectively. The results showed significant seasonal variations of PLFAs-related microbial biomass and composition. Soil bacterial and fungal CFUs tended to be decreased by nitrogen addition or precipitation exclusion treatment, and bacterial CFUs were more sensitive to the two treatments than fungal CFUs. Soil microbial function (i.e. carbon source utilization) was not affected by nitrogen addition, but significantly decreased by precipitation exclusion. There was a significant positive correlation between bacterial CFUs and microbial function, indicating the crucial roles of culturable bacteria in microbial carbon transformation. Our results highlight the critical effects of nitrogen deposition and 50% reduced precipitation on microbes in topsoil of fir plantation, with implications for unraveling soil microbial ecological function of subtropical forest ecosystem under global changes in future.

Deciphering the diversity, composition, function, and network complexity of the soil microbial community after repeated exposure to a fungicide boscalid

Boscalid is a novel, highly effective carboximide fungicide that has been substantially and irrationally applied in greenhouses. However, little is known about the residual characteristics of boscalid and its ecological effects in long-term polluted greenhouse soils. Therefore, actual boscalid pollution status in greenhouse soils was simulated by repeatedly introducing boscalid into the soil under laboratory conditions. The degradation characteristics of boscalid, and its effects on the diversity, composition, function, and co-occurrence patterns of the soil microbial community were systematically investigated. Boscalid degraded slowly, with its degradation half-lives ranging from 31.5 days to 180.1 days in the soil. Boscalid degradation was further delayed by repeated treatment and increasing its initial concentration. Boscalid significantly decreased soil microbial diversity, particularly at the recommended dosage. Amplicon sequencing analysis showed that boscalid altered the soil microbial community and further stimulated the phylum Proteobacteria and four potential boscalid-degrading bacterial genera, Sphingomonas, Starkeya, Citrobacter, and Castellaniella. Although the network analysis revealed that boscalid significantly reduced the microbial network complexity, it enhanced the vital roles of Proteobacteria by increasing its proportion and strengthening the relationships among the internal bacteria in the network. The soil microbial function in the boscalid treatment were simulated at the recommended dosage and two-fold recommended dosage but showed an inhibition-recovery-stimulation trend at the five-fold recommended dosage with an increase in treatment frequency. Moreover, the expression of nitrogen cycling functional genes, nifH, AOA amoA, AOB amoA, nirK, and nirS in all boscalid treatments displayed an inhibition-recovery-stimulation trend during the entire experimental period, and the effects were more pronounced at the five-fold recommended dosage. In conclusion, repeated boscalid treatments delayed degradation, reduced soil microbial diversity and network complexity, disturbed soil microbial community, and interfered with soil microbial function.

Effects of Biochar and Plant Growth-Promoting Rhizobacteria on Plant Performance and Soil Environmental Stability

(1) Background: Biochar and plant growth-promoting rhizobacteria (PGPR) are widely used as amendments to increase the availability of nutrients and the diversity of the bacterial community within soil. (2) Methods: In this study, we investigated the effects of biochar and PGPR amendments on plant performance, soil physicochemical property, and soil microbial diversity, as well as their relationship in a Eucalyptus (clone DH32−29) plantation in Guangxi, China. We determined the microbial AWCD, Simpson, Shannon, and McIntosh indices, and soil inorganic nitrogen (NH4+, NO3−), total phosphorus (TP), total potassium (TK), total nitrogen (TN), and plant growth and nutrient concentrations; (3) Results: Biochar-only had a significant impact on soil microbial community function, although the effects on plant performance were limited. PGPR plus biochar was found to significantly increase the diversity indices of soil microbes, as well as soil TK and TP. Besides, soil microbes displayed a preference for carbohydrates rather than other carbon sources. (4) Conclusion: Soil microbial functional diversity responded to changes in plant performance and, therefore, it could indicate soil ecological stability and ecosystem productivity. These findings may suggest that biochar and PGPR could potentially maintain ecological sustainability in the soil and improve plant performance through altering soil physicochemical properties in a eucalyptus plantation.

Land use intensification in a dry-hot valley reduced the constraints of water content on soil microbial diversity and multifunctionality but increased CO2 production

Conversion of abandoned land (mainly savanna) into cropland generally occurs in fragile ecosystems such as dry-hot valleys (DHVs) in southwest China, with the intent of increasing land productivity and conducting ecological restoration. However, the effects of conversion on soil microbial communities and carbon turnover of savanna ecosystems remain unclear, since savannas could be a vital but overlooked carbon sink. To illustrate the ecological consequences of land-use change (LUC) for savanna ecosystems, a 1-year field experiment was conducted in DHVs of southwest China. The soil properties, microbial respiration, and metagenomics from two different land-use types (grassland and mango plantation) were examined to reveal the effects of regional LUC on soil C turnover and microbial traits. Conversion from degraded grassland into cropland increased the contribution of soil microclimate to the microbial community composition, reduced the constraints of soil water content (SWC), and further decreased nutrient availability. LUC reshaped the composition and structure of soil bacterial communities. Specifically, soil dominant microbes that belonged to Actinobacteria and Proteobacteria were significantly enriched by conversion, while rare microbes that belonged to a wider range of phyla were generally depleted, leading to an overall decrease in community diversity. In addition, LUC-induced changes in soil characteristics and microbial communities further decreased soil multifunctionality as well as the carbon use efficiency of microbes. Intensified microbial respiration and a significant increase in the soil CO2 efflux were observed following LUC, which could drive changes in soil microbial community composition and functions (such as growth and regeneration). In summary, through simultaneously reducing constraints on SWC and decreasing nutrient availability, conversion from degraded grassland to cropland in a DHV decreased soil microbial diversity and multifunctionality, and increased microbial respiration and soil CO2 efflux. Our study provides new insights for understanding the role and mechanisms of LUC in soil carbon turnover in ecologically fragile areas such as DHVs.

Soil quality and r – K fungal communities in plantations after conversion from subtropical forest

Intensive clear-cutting of natural forests and conversion to monoculture plantations are ongoing worldwide, leading to the degradation of soil quality and microbial functions. Here, we compared soil quality index (SQI) and fungal communities in a natural forest (Forest) and four 5-year-old monoculture plantations, including Camellia oleifera (Oil), Amygdalus persica (Peach), Myrica rubra (Berry) and Cunninghamia lanceolate (Fir) in a subtropical region of China. After conversion, soil pH in the plantations rose up to 0.31, but organic carbon and total nitrogen contents, sucrase, acid protease, glutaminase, acid and alkaline phosphatase activities decreased by 83%, 59%, 40%, 64%, 66%, 94% and 59%, respectively. Correspondingly, the SQI dropped by 65%. High-throughput sequencing of the ITS1 region demonstrated an increase in α-diversity and a striking difference in β-diversity of fungi following conversion. Changes in the dominant fungal taxa following forest conversion to plantations were interpreted by r- and K-selection of life strategies. Conversion increased the fungal groups with r-strategies, such as Ascomycota and Zygomycota, but decreased the fungal groups with K-strategies, such as Basidiomycota. Genera affiliated to those phyla including Pseudophialophora, Rhytisma increased, but Russula decreased. Redundancy analysis and structural equation modeling indicated that the diversity and composition of fungal communities changed with soil degradation, which was mainly driven by increased pH and total phosphorus content, but decreased C/N ratio and C and N related enzymes activities. Overall, the conversion of forest to monoculture plantations decreased soil quality and the abundance of K-strategists, retarded the decomposition of persistent organic matter, but boosted the prevalence of r-strategists in a more diverse fungal community.

Artificial root exudates restore microbial functioning in a metal contaminated, barren, inactive soil

Restoring enzyme function in barren, brownfield soils using green strategies can improve microbial functioning and enable phytoremediation. It is known that adding simple, readily metabolized substrates secreted by growing plant roots (root exudates) or a laboratory prepared solution of root exudates (artificial root exudates) can stimulate soil microbial function. It is not known whether and how well this strategy works in a contaminated, low functioning soil from an industrial barren site because contaminants in the barren soil might inhibit microbial survival and functioning, or the microbial community might not be adapted to functionally benefit from root exudates. The objective of this study was to determine whether artificial root exudates stimulate microbial function in a barren soil. We collected soils from a barren brownfield (25R) site and an adjacent vegetated brownfield site (25F), with low and high enzyme activities, respectively. We subjected both soils to three treatments: switchgrass (native to the site), artificial root exudates, and a combination of switchgrass and artificial root exudates. We measured enzymatic activity, plant growth, soil moisture, organic matter content, and easily extractable glomalin content over 205 days. By day 157, artificial root exudates increased the phosphatase activity by 9-fold in previously vegetated brownfield soil and by 351-fold in barren brownfield soil. When exudates were added to the barren soil, the plant shoot mass was higher (52.2 ± 2.5 mg) than when they were not (35.4 ± 3.6 mg). In both soils, adding artificial root exudates significantly increased the percent moisture, organic matter, and glomalin content. Treating contaminated, barren soil with artificial root exudates resulted in increased soil microbial function and improved soil properties that might promote a hospitable habitat to support vegetation in such extreme environments.Summary: We added artificial root exudates to stimulate enzymatic function in two contaminated soils. Plant shoot mass, soil percent moisture, glomalin content, and organic matter content significantly increased due to the addition of artificial root exudates to the study soils. Microbially-mediated phosphatase activity was established in a barren, previously inactive, polluted soil.

Changes in microbial community composition drive the response of ecosystem multifunctionality to elevated ozone

Increasing tropospheric ozone poses a potential threat to both above- and belowground components of the terrestrial biosphere. Microorganisms are the main drivers of soil ecological processes, however, the link between soil microbial communities and ecological functions under elevated ozone remains poorly understood. In this study, we assessed the responses of three crop seedlings (i.e., soybean, maize, and wheat) growth and soil microbial communities to elevated ozone (40 ppb O3 above ambient air) in a pot experiment in the solardomes. Results showed that elevated ozone adversely affected ecosystem multifunctionality by reducing crop biomass, inhibiting soil extracellular enzyme activities, and altering nutrient availability. Elevated ozone increased bacterial and fungal co-occurrence network complexity, negatively correlated with ecosystem multifunctionality. Changes in the relative abundance of some specific bacteria and fungi were associated with multiple ecosystem functioning. In addition, elevated ozone significantly affected fungal community composition but not bacterial community composition and microbial alpha-diversity. Crop type played a key role in determining bacterial alpha-diversity and microbial community composition. In conclusion, our findings suggest that short-term elevated ozone could lead to a decrease in ecosystem multifunctionality associated with changes in the complexity of microbial networks in soils.

A field study of nano-FeS loaded lignin hydrogel application for Cd reduction, nutrient enhancement, and microbiological shift in a polluted paddy soil

Cadmium (Cd) pollution in paddy soil has caused serious harm to human health. Nano-ferrous sulfide@lignin hydrogel (FeS@LH) composites could be an ideal material for paddy soil Cd removal due to the excellent adsorption performance and mechanical strength. But the FeS@LH’s performance in a paddy field remains unclear. In this study, FeS@LH was applied to a Cd-contaminated paddy field when planting water spinach (Ipomoea aquatica Forssk). The results showed that FeS@LH effectively removed Cd from the soil (37.6 %) and water spinach (34.5 %) after 30 days. The concentrations of Pb, Zn, Cu, and other metals in soil and water spinach were co-reduced. When the FeS@LH dosage was 30 g·m−2, the effective functional distance was within 30 cm. FeS@LH application had a positive effect on soil nutrients. The soil nitrogen and organic matter contents increased by 16.1 % and 13.8 %, respectively. No significant effect on soil total phosphorus and potassium contents was presented. The survival rate of zebrafish in the acute toxicity test of FeS@LH was 98.9 %, indicating its biosafety. In addition, FeS@LH application decreased soil microbial community diversity probably due to the decreased pH. The microbial metabolism tended to enhance, suggesting a restoration of soil microbial community function after Cd removal.

Consequences of Grazing Cessation for Soil Environment and Vegetation in a Subalpine Grassland Ecosystem.

Areas covered by seminatural grasslands have been in constant decline for decades in Europe. This trend is particularly strong for mountain territories, where such traditional agricultural practices as cattle grazing are no longer economically feasible. This study was conducted in the subalpine pasture of Cinte Tesino (TN, Italy), where local farmers have applied the following different management strategies: shorter and longer grazing durations during the season and a complete abandonment for the last 15 years. We aimed to study how these different management strategies impact the functioning and diversity of vegetation and the chemical and biological characteristics of the soil. Species richness was higher in plots subjected to longer grazing with a prevalence of D. caespitosa in terms of biomass share. A decline in species richness in abandoned plots was accompanied by an increase in the share of other graminoids in collected biomass. A concomitant increase in leaf N concentration and light availability in grazed plots resulted in higher photosynthetic efficiency in some species, as revealed by the δ13C of plant tissues. Soils under grazing were characterised by a higher concentration of total and extractable N, almost doubled microbial biomass C and increased extracellular enzymes activity, evidencing nutrient cycling mobilization. While the microbial pool was characterised by lower mineralization rates, C was lost from the soil with 15 years of abandonment. The longer grazing season demonstrated to be the most beneficial, promoting species richness, C accumulation and better soil microbial functioning. A change in soil pH from strongly acidic to moderately acidic with longer grazing is likely one of the important factors adding to the success in the functioning of primary producers and decomposers in this site.

High-Throughput Sequencing Combined with Metabonomics to Analyze the Effect of Heavy Metal Contamination on Farmland Soil Microbial Community and Function

Heavy metal contamination affects microbial composition and diversity. The interaction between heavy metal contamination and soil microorganisms has been a hot topic in ecological research. Battery manufacturing has been going on for over six decades in Xinxiang City, resulting in severe soil heavy metal contamination due to battery wastewater runoff. Few studies have investigated the effect of heavy metal contamination due to long-term battery wastewater runoff on microbial diversity and metabolomics in Xinxiang City. In this study, we collected samples from three heavy metal contaminated sites in Xinxiang City and found that Cd and Pb exceeded the recommended thresholds by 34-66 fold and 1.5-2.32 fold, respectively. High-throughput sequencing showed that Bacillus, Arthrobacter, Sphingomonas, and Streptomyces were the dominant bacteria genera, while Olpidium, Plectosphaerella, and Gibellulopsis were the dominant fungi genera, indicating that heavy metal contaminated soil in Xinxiang City was rich in heavy metal tolerant bacteria and fungi due to the long-term heavy metal stress. Correlation analysis showed that total Cu, DTPA extract Cu, and water soluble Pb were significant factors in bacterial diversity, while total Cd, total Ni, total Pb, total Zn, DTPA extract Cu, and water soluble Pb were significant factors in fungal diversity. To better understand the effect of heavy metal contamination on the metabolism of soil microorganisms, we conducted non-targeted metabolomic profiling, which showed significant differences in metabolites across the samples. Pathway enrichment analysis showed that these differential metabolites were involved in pathways such as metabolism, environmental information processing, and genetic Information Processing, which may play a role in heavy metal stress mitigation and environmental adaptation.

Resilience of soil microbial metabolic functions to temporary E. coli invasion

Due to the globalization and increasing human activities, there is a significant increase in bacterial invasions to the soil ecosystems. Soil resident communities are vulnerable to bacterial invasion and suffered legacy effects after unsuccessful invasion. However, whether such changes in the soil ecosystems are permanent or temporary remains unclear. Here, we investigated the functional resilience of soil ecosystems to bacterial invasion and intensive managements. We used Escherichia coli O157:H7 (E. coli) as model strain examined the soil microbial metabolic functions, including enzyme activities, nitrogen and carbon use efficiency, community niche, and carbon metabolic potential, as well as soil physicochemical properties and microbial invader survival in 8 soil samples, 4 from natural hardwood forests and 4 from intensively managed Moso bamboo forests. The results showed that soil ecosystems were not resistant to E. coli invasion regardless of the intensity of management, which the finding was significantly reflected in the nutrient-acquiring activities or carbon utilization, or both. Besides, the invasion legacy effect (the effect after invader apoptosis) was positively related to E. coli survival time. However, most of the metabolic functions could recover almost to the initial state after 135 days of incubation, suggesting a strong recovery capacity of the soil ecosystems. These data indicate that E. coli invasion has a legacy effect on the functions of soil resident communities. However, soil ecosystems are highly resilient even under intensive human management.