Soil Microbial Function Research Articles

Soil fungal community is more sensitive than bacterial community to modified materials application in saline-alkali land of Hetao Plain.

Soil salinization has become a major challenge that severely threatens crop growth and influences the productivity of agriculture. It is urgent to develop effective management measures to improve saline-alkali soil. Thus, in this study, soil properties, microbial communities, and function under desulfurization gypsum (DE), soil amendment (SA), farm manure (FA), and co-application of desulfurization gypsum, soil amendment, and farm manure (TA) in a field experiment were examined by high-throughput sequencing. The results showed that the application of modified materials is an effective approach in improving saline-alkali soil, especially TA treatment significantly increased the content of available phosphorus (AP), available potassium (AK), soil organic matter (SOM), and alkaline hydrolysis nitrogen (AHN) and decreased pH, bulk density (BD), and electrical conductivity (EC). The application of modified materials resulted in notable enhancement in fungal diversity and altered the composition and structure of the fungal community. Conversely, the effect on the bacterial community was comparatively minor, with changes limited to the structure of the community. Regarding the fungal community composition, Ascomycota, Mortierellomycota, and Basidiomycota emerged as the dominant phyla across all treatments. At each taxonomic level, the community composition exhibited significant variations in response to different modified materials, resulting in divergent soil quality. The TA treatment led to a decrease in Mortierellomycota and an increase in Ascomycota, potentially enhancing the ability to decompose organic matter and facilitate soil nutrient cycling. Additionally, the sensitivity of fungal biomarkers to modified materials surpassed that of the bacterial community. The impact of modified materials on soil microbial communities primarily stemmed from alterations in soil EC, AP, AK, and SOM. FUNGuild analysis indicated that the saprotroph trophic mode group was the dominant component, and the application of modified materials notably increased the symbiotroph group. PICRUSt analysis revealed that metabolism was the most prevalent functional module observed at pathway level 1. Overall, the application of modified materials led to a decrease in soil EC and an increase in nutrient levels, resulting in more significant alterations in the soil fungal community, but it did not dramatically change the soil bacterial community. Our study provides new insights into the application of modified materials in increasing soil nutrients and altering soil microbial communities and functions and provides a better approach for improving saline-alkali soil of Hetao Plain.

Effects of increasing drip irrigation at different maize growth stages on soil microorganisms.

To investigate the effects of different drip irrigation periods on soil microbial communities and functions. Increasing drip irrigation amount at the seedling (S), jointing (J), bell (B), tasseling (T) and grain filling (G) stages of maize were studied using no increase in irrigation amount as control (CK). Principal component analysis was conducted to comprehensively evaluate soil microbial quality following the different drip irrigation treatments. In addition, the characteristics of the community structure and the potential functional composition of soil bacteria and fungi were comparatively analyzed by combining amplicon sequencing and functional prediction methods. The results indicated that MBNT15 was the most important genus for the classification of soil bacterial samples, Saitozyma was the most important genus for the classification of soil fungal samples, and fungi were more important than bacteria for the classification of soil microbial samples. Compared with fungal communities, bacterial communities exhibited high levels of functional diversity. The proportion of metabolism was the highest in the prediction of bacterial primary functions, and carbohydrate metabolism and amino acid metabolism were important functions in the prediction of bacterial secondary functions. BugBase phenotype prediction results showed that soil bacteria under B treatment had a higher number of aerobic bacteria and greater resistance to disease and stress. The J treatment had the highest number of bacteria with biofilm forms, and the J, S, and G treatments contained more potentially pathogenic bacteria but fewer stress-tolerant bacteria compared with the CK treatment. The number of Saprotroph was the largest and the number of Symbiotroph was the least. The relative abundances of Saprotroph, Pathotroph and Symbiotroph were 68.60%~74.33%, 15.76%~20.60% and 9.16%~11.13%, respectively. The findings provide a reference for conserving water resources, improving maize yield, and predicting soil microbial metabolic potential and function by reflecting the richness of the soil microbial community structure in maize fields.

Illegal dumping of oil and gas wastewater alters arid soil microbial communities.

The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.

Moderate increase of precipitation stimulates CO2 production by regulating soil organic carbon in a saltmarsh.

Saltmarsh is widely recognized as a blue carbon ecosystem with great carbon storage potential. Yet soil respiration with a major contributor of atmospheric CO2 can offset its carbon sink function. Up to date, mechanisms ruling CO2 emissions from saltmarsh soil remain unclear. In particular, the effect of precipitation on soil CO2 emissions is unclear in coastal wetlands, due the lack of outdoor data in real situations. We conducted a 7-year field manipulation experiment in a saltmarsh in the Yellow River Delta, China. Soil respiration in five treatments (-60%, -40%, +0%, +40%, and + 60% of precipitation) was measured in the field. Topsoils from the last 3 years (2019-2021) were analyzed for CO2 production potential by microcosm experiments. Furthermore, quality and quantity of soil organic carbon and microbial function were tested. Results show that only the moderate precipitation rise of +40% induced a 66.2% increase of CO2 production potential for the microcosm experiments, whereas other data showed a weak impact. Consistently, soil respiration was also found to be strongest at +40%. The CO2 production potential is positively correlated with soil organic carbon, including carbon quantity and quality. But microbial diversity did not show any positive response to precipitation sizes. r-/K-strategy seemed to be a plausible explanation for biological factors. Overall, our finding reveal that a moderate precipitation increase, not decrease or a robust increase, in a saltmarsh is likely to improve soil organic carbon quality and quantity, and bacterial oligotroph:copiotroph ratio, ultimately leading to an enhanced CO2 production.

Comparison of cover crop termination methods for small-scale organic vegetable production: effect on soil fertility and health

Termination methods and the timing of the termination of the cover crops are critical factors determining the efficacy of cover crops in improving soil fertility and quality. We hypothesized that different termination methods will produce varying quantities of organic residue which will affect microbial diversity and thereby nutrient cycling and availability. The objective of this study was to compare termination methods (roller-crimper, flail mowing, rotary mowing, sickle bar mowing, and occultation using black tarps) for fall-grown cover crop combination (hairy vetch-cereal rye) under organic vegetable production. Field experiments were carried out in three consecutive years (2018–2021) and soil samples were collected from 0 to 15 cm and processed for analysis. Soil organic matter content, nutrients, health parameters, enzymes, and microbial diversity were measured. Flail mowing significantly enhanced the potentially mineralizable nitrogen, available phosphorus, and active carbon. Total Phospholipid Fatty Acid (PLFA) analysis showed a 24% increase for flail mowed, 17% for rotary mowed, and 15% for sickle bar mowed termination methods. There was a significant increase in active carbon content which ranged from 38.9% (rotary mowed), 25.4% (sickle bar mowed), 23.5% (flail mowed), 16.4% for crimper rolled method, and with 2.8% (occultation) respectively. Individual termination methods had varying effects on select enzyme activities. Results indicated that integrating cover crops has the potential to modify soil microbial community structure and increase soil enzyme activities. In this study, flail mowing appeared to be a good method for managing cover crops of choice in terms of soil microbial functionality and fertility.

Influence of Grass Mulching and Organic Fertilizer Addition on Soil Microbial Community Composition and Function in a ‘Dongzao’ Jujube (Ziziphus jujuba Mill. ‘Dongzao’) Orchard

Influence of Grass Mulching and Organic Fertilizer Addition on Soil Microbial Community Composition and Function in a ‘Dongzao’ Jujube (Ziziphus jujuba Mill. ‘Dongzao’) Orchard

Inhibition of high sulfur on functional microorganisms and genes in slightly contaminated soil by cadmium and chromium

It is generally accepted that sulfur can passivate the bioavailability of heavy metals in soil, but it is not clear whether high sulfur in cadmium (Cd) and chromium (Cr) contaminated soil has negative effect on soil microbial community and ecological function. In this study, total sulfur (TS) inhibited the Chao 1, Shannon, Phylogenetic diversity (Pd) of bacterial and Pd of fungi in slightly contaminated soil by Cd and Cr around pyrite. TS, total potassium, pH, total chromium, total cadmium, total nitrogen, soil organic matter were the predominant factors for soil microbial community; the contribution of TS in shaping bacterial and fungal communities ranked at first and fifth, respectively. Compared with the low sulfur group, the abundance of sulfur sensitive microorganisms Gemmatimonas, Pseudolabrys, MND1, and Schizothecium were decreased by 68.79–97.22% (p < 0.01) at high sulfur one; the carbon fixation, nitrogen cycling, phosphorus cycling and resistance genes abundance were significantly lower (p < 0.01) at the latter. Such variations were strongly and closely correlated to the suppression of energy metabolism (M00009, M00011, M00086) and carbon fixation (M00173, M00376) functional module genes abundance in the high sulfur group. Collectively, high sulfur significantly suppressed the abundances of functional microorganisms and functional genes in slightly contaminated soil with Cd and Cr, possibly through inhibition of energy metabolism and carbon fixation of functional microorganisms. This study provided new insights into the environmental behavior of sulfur in slightly contaminated soil with Cd and Cr.

Changes in soil microbial functions involved in the carbon cycle response to conventional and biodegradable microplastics

Biodegradable mulch film has become an encouraging alternative to conventional petroleum–based plastic, but it is likely to generate more microplastics (MPs) than conventional films with lower resistance and thus profoundly affects the soil environment. However, the effects of biodegradable (BMPs) and conventional polyethylene MPs (PE–MPs) on soil microbial carbon (C) cycle remain unclear. Here, metagenomic sequencing was used to investigate microbial functional and relative taxonomic traits in response to PE–MP and BMP addition (5 % w/w) via a soil microcosm experiment. The results showed that the presence of BMPs, rather than PE–MPs, significantly changed soil microbial C cycling patterns at the functional and taxonomic levels. In soils, BMP addition significantly increased the abundances of genes regulating aerobic respiration, C decomposition (intracellular), C fixation, fermentation and CO oxidation pathways compared to those in the control and PE–MP added soils. Specifically, BMPs promoted soil starch and PHA (liable C) degradation, acetate and ethanol fermentation, Calvin–Benson–Bassham (CBB) cycle and 3–hydroxypropionate/4–hydroxybutyrate (3HP/4HB) associated with C fixation. Most of these C cycling pathways were further strengthened in the microplastisphere of BMPs. Furthermore, MPs selectively enriched specific taxa on their surface and subsequently increased their abundance in soils; Bradyrhizobium, Ramlibacter and Variovorax (enriched by BMPs) positively regulated labile C degradation, and Amycolatopsis and Nocardia (enriched by PE–MPs) promoted recalcitrant C degradation. Moreover, Pseudonocardia and Variovorax that were enriched by BMPs improved C dissimilation and assimilation by regulating fermentation and C fixation processes, respectively. Taken together, these results improve the understanding of the influence of conventional and biodegradable MPs on soil C cycling pathways and related microbial communities, highlighting that the presence of BMPs rather than PE–MPs accelerates soil C turnover.

Analyzing soil enzymes to assess soil quality parameters in long-term copper accumulation through a machine learning approach

Soil contamination by agrochemicals is a big concern for soil health and ecosystem functioning. This is especially true for non-degradable substances like heavy metals (HM) that, because of their long-term use, are reaching significant values today due to soil accumulation. Among agrochemicals, copper (Cu) has been important in fighting fungal diseases on perennial crops for centuries.Laboratory experiments can be useful to understand the highest potential toxic effect of Cu but need to reflect what happens with long-term application in a dynamic and living agroecosystem. This study uses multivariate data analysis and machine learning to investigate long-term Cu accumulation on soil quality parameters, especially soil extracellular enzymatic activities. We collected soil samples from 21 apple orchards in South Tyrol, Italy. The orchards had different concentrations of Cu. We took 315 samples in total and analyzed them for various soil properties. We also measured the concentrations of elements in apple leaves and the activities of soil extracellular enzymes. We depicted the effect of Cu on several enzymatic activities, shedding light on the effect of Cu on the soil microbial communities functionality. Our results show that Cu concentrations in the study area affect only phosphatase activity, showing effects above 60 mg kg−1 of available Cu. Protease activity was positively correlated with Cu, while soil organic matter and management mainly influenced the carbon (C) cycle enzymes. Phosphatase decrease could be of concern for the potential disruption of the Phosphorus (P) cycle in the soil and plays a role in plant nutrition, as seen by P concentration in apple trees' leaves.We demonstrated how machine learning can help interpret complex and multivariate environmental data and overcome some downsides of traditional statistical models.

Effects of Organic Fertilizer of Kitchen Waste on Soil Microbial Activity and Function

Changes in soil microbial activity and ecological function can be used to assess the level of soil fertility and the stability of ecosystems. To assess the fertility and safety of organic fertilizer of kitchen waste (OFK), soils containing 0% (CK), 1%, 3%, and 5% OFK were cultured, and the physical, chemical, and microbial properties of the soils were measured dynamically with routine agrochemical analysis measures and amplicon sequencing. The results showed that compared with those in CK, the contents of organic matter, available phosphorus, available potassium, NH4+-N, and NO3--N in soils with OFK increased by 23.80%-35.13%, 13.29%-29.72%, 16.91%-39.37%, 164.7%-340.2%, and 28.56%-32.71%, respectively. The activities of hydrolases related to the cycle of carbon, nitrogen, and phosphorus (α-glucosidase, leucine aminopeptidase, acid phosphatase, etc.) were also significantly higher than those of the CK treatment. OFK stimulated the growth of soil microorganisms and increased the carbon content of the microbial biomass. The amplicon sequencing analysis found that the microbial community structures of different treatments were significantly different at both the class and genus levels. In addition, it was found that the abundance of beneficial microbes in the soils with OFK increased, whereas pathogenic microbes decreased. RDA results confirmed that soil properties (including soil pH, organic matter, available nutrients, and microbial biomass) had a significant impact on microbial community structure. The results of investing bacterial community based on PICRUSt and FAPROTAX revealed that the function of the soil bacterial community was similar in the four treatments, but OFK supply significantly improved the microbial carbon utilization and metabolic ability. Moreover, by using the FUNGuild software, we found that the application of OFK increased the proportion of saprotroph-symbiotroph and symbiotroph and stimulated the growth of ectomycorrhizal fungi-undefined saprophytic fungi but inhibited plant and animal pathogenic fungi in soil. These results implied that OFK could promote the establishment of symbiotic relationships and inhibit the growth of pathogenic fungi. In summary, OFK could improve soil fertility and hydrolase activity, stimulate the growth of beneficial microorganisms, and defend against pathogens, indicating a promising use as safe and efficient organic fertilizer.

Overgrazing on unmanaged grassland interfered with the restoration of adjacent grazing-banned grassland by affecting soil properties and microbial community.

A "grazing ban" policy has been implemented in some pastoral areas in China to fence degraded grasslands for restoration. However, fencing increased grazing pressures in unmanaged grasslands. Based on the mechanism of negative edge effect, we investigated whether overgrazing on unmanaged grassland interfered with the restoration of adjacent grazing-banned grassland by affecting soil properties and microbial community using a sample in Hulun Buir of Inner Mongolia, in order to optimize the "grazing ban" policy. Plant and soil were sampled in areas 30 m away from the fence in unmanaged grassland (UM) and in areas 30 m (adjacent to UM) and 30-60 m (not adjacent to UM) away from the fence in the grazing-banned grassland (F-30 m and F-60 m). The species richness and diversity of plant communities and the ASV number of fungal communities significantly decreased in F-30 m and UM, and the Simpson index of the bacterial community significantly decreased in F-30 m compared with F-60 m. The abundance of fungi involved in soil organic matter decomposition significantly decreased and the abundance of stress-resistant bacteria significantly increased, while the abundance of bacteria involved in litter decomposition significantly decreased in UM and F-30 m compared with F-60 m. The simplification of plant communities decreased in soil water and total organic carbon contents can explain the variations of soil microbial communities in both UM and F-30 m compared with F-60 m. The results of PLS-PM show that changes in plant community and soil microbial function guilds in UM may affect those in F-30 m by changing soil water and total organic carbon contents. These results indicate that overgrazing on unmanaged grassland interfered with the restoration of adjacent grazing-banned grassland by affecting soil properties and microbial community. The grazing-banned grasslands should be adjusted periodically in order to avoid negative edge effects.

Photo-oxidation of Micro- and Nanoplastics: Physical, Chemical, and Biological Effects in Environments.

Micro- and nanoplastics (MNPs) are attracting increasing attention due to their persistence and potential ecological risks. This review critically summarizes the effects of photo-oxidation on the physical, chemical, and biological behaviors of MNPs in aquatic and terrestrial environments. The core of this paper explores how photo-oxidation-induced surface property changes in MNPs affect their adsorption toward contaminants, the stability and mobility of MNPs in water and porous media, as well as the transport of pollutants such as organic pollutants (OPs) and heavy metals (HMs). It then reviews the photochemical processes of MNPs with coexisting constituents, highlighting critical factors affecting the photo-oxidation of MNPs, and the contribution of MNPs to the phototransformation of other contaminants. The distinct biological effects and mechanism of aged MNPs are pointed out, in terms of the toxicity to aquatic organisms, biofilm formation, planktonic microbial growth, and soil and sediment microbial community and function. Furthermore, the research gaps and perspectives are put forward, regarding the underlying interaction mechanisms of MNPs with coexisting natural constituents and pollutants under photo-oxidation conditions, the combined effects of photo-oxidation and natural constituents on the fate of MNPs, and the microbiological effect of photoaged MNPs, especially the biotransformation of pollutants.

Oligotrophic microbes are recruited to resist multiple global change factors in agricultural subsoils

An increasing number of anthropogenic pressures can have negative effects on biodiversity and ecosystem functioning. However, our understanding of how soil microbial communities and functions in response to multiple global change factors (GCFs) is still incomplete, particularly in less frequently disturbed subsoils. In this study, we examined the impact of different levels of GCFs (0–9) on soil functions and bacterial communities in both topsoils (0–20 cm) and subsoils (20–40 cm) of an agricultural ecosystem, and characterized the intrinsic factors influencing community resistance based on microbial life history strategy. Our experimental results showed a decline in soil multifunctionality, bacterial diversity, and community resistance as the number of GCFs increased, with a more drastic reduction in community resistance of subsoils. Specifically, we observed a significantly positive relationship between the oligotroph/copiotroph ratio and community resistance in subsoils, which was also verified by the negative correlation between 16S rRNA operon (rrn) copy number and community resistance. Structural equation modeling further revealed the direct effects of community resistance in promoting the ecosystem functioning, regardless of top- and subsoils. Therefore, these results suggested that subsoils may recruit more oligotrophic microbes to enhance their originally weaker community resistance under multiple GCFs, which was essential for maintaining sustainable agroecological functions and services. Overall, our study represents a significant advance in linking microbial life history strategy to the resistance of belowground microbial community and functionality.

Selective logging impacts on soil microbial communities and functioning in Bornean tropical forest.

Rainforests provide vital ecosystem services that are underpinned by plant-soil interactions. The forests of Borneo are globally important reservoirs of biodiversity and carbon, but a significant proportion of the forest that remains after large-scale agricultural conversion has been extensively modified due to timber harvest. We have limited understanding of how selective logging affects ecosystem functions including biogeochemical cycles driven by soil microbes. In this study, we sampled soil from logging gaps and co-located intact lowland dipterocarp rainforest in Borneo. We characterised soil bacterial and fungal communities and physicochemical properties and determined soil functioning in terms of enzyme activity, nutrient supply rates, and microbial heterotrophic respiration. Soil microbial biomass, alpha diversity, and most soil properties and functions were resistant to logging. However, we found logging significantly shifted soil bacterial and fungal community composition, reduced the abundance of ectomycorrhizal fungi, increased the abundance of arbuscular mycorrhizal fungi, and reduced soil inorganic phosphorous concentration and nitrate supply rate, suggesting some downregulation of nutrient cycling. Within gaps, canopy openness was negatively related to ectomycorrhizal abundance and phosphomonoesterase activity and positively related to ammonium supply rate, suggesting control on soil phosphorus and nitrogen cycles via functional shifts in fungal communities. We found some evidence for reduced soil heterotrophic respiration with greater logging disturbance. Overall, our results demonstrate that while many soil microbial community attributes, soil properties, and functions may be resistant to selective logging, logging can significantly impact the composition and abundance of key soil microbial groups linked to the regulation of vital nutrient and carbon cycles in tropical forests.

Interactive Effect of Residue Quality and Agroecologies Modulate Soil C‐ and N‐Cycling Enzyme Activities, Microbial Gene Abundance, and Metabolic Quotient

Understanding interactive effect of agroecology explained by rainfall, temperature, elevation, and biochemical composition of residues on soil microbial abundance and functions is crucial for unraveling soil ecological processes. This study aimed to investigate how agroecology and residue quality influence enzymatic activities, gene abundance, and metabolic quotient (qCO2). A field experiment was conducted using Leucaena leucocephala (LL) (high‐quality residue) and Acacia decurrens (AD) (low‐quality residue) in soils of highland and midland agroecologies. These residues differed in decomposability, characterized by a ratio of (lignin + polyphenol)/N of 5.0 for high‐quality residue versus 21.0 for low‐quality residue. Two experimental setups were employed: soil with litter mixture in polyvinyl chloride (PVC) tubes and residues buried in the surface soil using litterbags. Soil samples were collected after 30, 120, and 270 days of incubation and analyzed for biochemical properties, enzyme activities, and the abundance of nitrifying and total archaea and bacteria. Soil respiration was also measured at different intervals in the field. qCO2 was calculated using microbial biomass (MBC) and daily respiration (DCO2). Linear mixed model (P &lt; 0.05) revealed that combined factors of agroecologies and residue qualities affected enzymatic activities, microbial abundance, soil properties, and qCO2. Agroecological differences exerted a greater influence than residue qualities. Positive and negative significant correlations (P &lt; 0.05, r = 0.27 to 0.67) were found between different C and N pools as well as enzymatic activities. Positive correlations (P &lt; 0.05) were observed between the abundance of total bacteria, total archaea, and ammonia‐oxidizing bacteria versus leucine‐aminopeptidases. qCO2 was influenced more by β‐xylosidase, leucine‐aminopeptidases, and thermolysin‐like neutral metalloproteases (TLP) than by β‐D‐glucosidase and β‐D‐cellobiohydrolase. Leucine‐aminopeptidases and TLP were identified as rate‐limiting factors for protein and peptide decomposition, while β‐xylosidase controlled hemicellulose degradation. In summary, this study provides insights into the intricate relationships between agroecology, residue quality, enzymatic activities, and microbial communities, shedding light on key processes governing soil ecological functions.

Land management of formerly subtropical Atlantic Forest reduces soil carbon stocks and alters microbial community structure and function

Soil carbon (C) sequestration has been proposed as one means to mitigate the effects of climate change and to guarantee food safety. However, forest conversion to managed land uses can deplete soil C stocks and affect soil microbial communities, potentially impacting a wide range of ecosystem services. Our objective was to investigate the effect of forest conversion to intensive land uses on soil C dynamics and soil microbial community structure and function in the subtropical portion of the Atlantic Forest biome. We evaluated four land uses - forest fragment, grassland, and agriculture with five or fifty years of cultivation. We analyzed soil C pools, edaphic variables, and soil bacterial/archaeal (16S) and fungal (ITS) communities. Forest conversion to managed land uses reduced soil C stocks and altered soil microbial community structure, with implications for soil C dynamics. Bacterial/archaeal and fungal community composition were strongly correlated with pH, base saturation, and calcium (Ca) and magnesium (Mg) content. However, soil C pools were not associated with potential extracellular enzyme activity or microbial diversity. Finally, the fungal species Mortierella minutissima ASV_1 and several bacterial groups were positively correlated with soil C stocks, potentially representing indicators of soil C storage. Our study indicates that land use change affects the interplay between soil microbial communities and soil C pools, with consequences to soil C storage. Our findings may support the development of soil C enhancement programs within the Atlantic Forest biome.

Soil microbial activity profiles associated with organic compost fertilizers in an urban garden

AbstractBiological soil health is recognized as an important component of sustainable agriculture due to microbial biomineralization of nutrients. However, soil health can be difficult to assess consistently across urban agricultural systems due to diverse land use histories, soil heterogeneity, and lack of mechanistic links to agricultural management practices (e.g., recycled compost addition) and crop outcomes. In this study, we characterized soil microbial activity profiles in an urban agriculture system in Minnesota, USA, including microbial abundance, soil respiration, extracellular enzyme activity, and crop yield. Garden plots were fertilized with recycled organic compost (either manure or municipal) at high or low rates (ranging from 2.6 to 39 tons ha−1) targeted to crop N and P demands. Control plots received inorganic fertilizer or no fertilizer. We found that a high application rate of manure compost supported 6–10x higher basal respiration than municipal compost or inorganic fertilizer. Enzyme activity data demonstrated that soil microbial communities exhibited unique profiles of biochemical function that varied among fertilizers of different compositions. Microbial biochemical function predicted 50% of the variability in bell pepper (Capsicum annuum) yield, while soil microbial community size alone was a poor predictor of yield. Yield was highest in plots fertilized with municipal compost, outperforming inorganic fertilizer by threefold. High‐yield plots exhibited higher ratios of N to P enzyme activity compared to those with lower yield. Our findings demonstrate that “more is better” may not necessarily be true regarding soil microorganisms in biological soil health, and that measures of soil microbial biochemical function may be more important.

Analysis of rhizosphere soil microbial diversity and its functions between Dahongpao mother tree and cutting Dahongpao.

Dahongpao mother tree (Camellia sinensis (L.) O. Ktze) is a representative of Wuyi rock tea. Whether there is a difference in rhizosphere soil microbial diversity and function between asexually propagated cuttings of Dahongpao (PD) and the parent Dahongpao mother tree (MD) has not been reported. In this study, high throughput sequencing technology was used to analyze rhizosphere soil microbial diversity, functions and their relationship with soil available nutrients and enzyme activities in MD and PD. The results showed that available nitrogen, phosphorus and potassium contents and urease, protease, acid phosphatase and sucrase activities of rhizosphere soils in MD were significantly higher than those in PD. Both bacterial and fungal diversity were higher in rhizosphere soils in MD than in PD, and secondly, the bacterial community structure was less stable while the fungal community structure was more stable in PD compared to MD. There were significant differences between MD and PD tea tree rhizosphere soils in 6 genera of characteristic bacteria and 4 genera of characteristic fungi. The results of function and interaction effect analysis showed that the rhizosphere soil available nutrient content and enzyme activities in MD were significantly higher than those in PD, and their contributions mainly originated from Pirellula and Acidisphaera of characteristic bacteria and Alatospora of characteristic fungi. Secondly, MD maybe had a stronger ability to inhibit soil pathogens than PD, with the main contribution coming from Scopulariopsis and Tolypocladium of characteristic fungi. Overall, compared with PD, soil texture in MD was relatively better, and its soil nutrient cycling-related enzyme activities were stronger, which was more favorable to soil nutrient cycling and increased the available nutrient content of the soil, which in turn promoted the growth of tea trees. This study provides an important reference for the planting and management of tea tree cuttings and microbial regulation of tea tree growth.

Soil microbial community structure, function and network along a mangrove forest restoration chronosequence

Mangrove forests have high ecological, social and economic values, but due to environmental changes and human activities, natural mangrove forests have experienced serious degradations and reductions in distribution area worldwide. In the coastal zones of southern China, an introduced mangrove species, Sonneratia apetala, has been extensively used for mangrove restoration because of its rapid growth and strong environmental adaptability. However, little is known about how soil microorganisms vary with the restoration stages of the afforested mangrove forests. Here, we examined the changes in soil physicochemical properties and microbial biomass, community structure and function, and network in three afforested S. apetala forests with restoration time of 7, 12, and 18 years and compared them with a bare flat and a 60-year-old natural Kandelia obovata forest in a mangrove nature reserve. Our results showed that the contents of soil salinity, organic carbon, total nitrogen, ammonium nitrogen, and microbial biomass increased, while soil pH and bacterial alpha diversity decreased with afforestation age. Soil microbial community structure was significantly affected by soil salinity, organic carbon, pH, total nitrogen, ammonium nitrogen, available phosphorus, and available kalium, and susceptibility to environmental factors was more pronounced in bacterial than fungal community structure. The relative abundances of aerobic chemoheterotrophy were significantly higher in 12- and 18-year-old S. apetala than in K. obovata forest, while that of sulfate-reducing bacteria showed a decreasing trend with afforestation age. The abundance of dung saprotroph was significantly higher in 12- and 18-year-old S. apetala forests than in the natural forest. With the increasing afforestation age, the modularity of microbial networks increased, while stability and robustness decreased. Our results suggest that planting S. apetala contributes to improving soil fertility and microbial biomass but may make soil microbial networks more vulnerable.

Divergent rhizosphere and non-rhizosphere soil microbial structure and function in long-term warmed steppe due to altered root exudation.

While there is an extensive body of research on the influence of climate warming on total soil microbial communities, our understanding of how rhizosphere and non-rhizosphere soil microorganisms respond to warming remains limited. To address this knowledge gap, we investigated the impact of 4 years of soil warming on the diversity and composition of microbial communities in the rhizosphere and non-rhizosphere soil of a temperate steppe, focusing on changes in root exudation rates and exudate compositions. We used open top chambers to simulate warming conditions, resulting in an average soil temperature increase of 1.1°C over a span of 4 years. Our results showed that, in the non-rhizosphere soil, warming had no significant impact on dissolved organic carbon concentrations, compositions, or the abundance of soil microbial functional genes related to carbon and nitrogen cycling. Moreover, soil microbial diversity and community composition remained largely unaffected, although warming resulted in increased complexity of soil bacteria and fungi in the non-rhizosphere soil. In contrast, warming resulted in a substantial decrease in root exudate carbon (by 19%) and nitrogen (by 12%) concentrations and induced changes in root exudate compositions, primarily characterized by a reduction in the abundance in alcohols, coenzymes and vitamins, and phenylpropanoids and polyketides. These changes in root exudation rates and exudate compositions resulted in significant shifts in rhizosphere soil microbial diversity and community composition, ultimately leading to a reduction in the complexity of rhizosphere bacterial and fungal community networks. Altered root exudation and rhizosphere microbial community composition therefore decreased the expression of functional genes related to soil carbon and nitrogen cycling. Interestingly, we found that changes in soil carbon-related genes were primarily driven by the fungal communities and their responses to warming, both in the rhizosphere and non-rhizosphere soil. The study of soil microbial structure and function in rhizosphere and non-rhizosphere soil provides an ideal setting for understanding mechanisms for governing rhizosphere and non-rhizosphere soil carbon and nitrogen cycles. Our results highlight the distinctly varied responses of soil microorganisms in the rhizosphere and non-rhizosphere soil to climate warming. This suggests the need for models to address these processes individually, enabling more accurate predictions of the impacts of climate change on terrestrial carbon cycling.