Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil

Tree phylogeny predicts more than litter chemical components in explaining enzyme activities in forest leaf litter decomposition

Litter decomposition is an important process in ecosystem and despite recent research elucidating the significant influence of plant phylogeny on plant-associated microbial communities, it remains uncertain whether a parallel correlation exists between plant phylogeny and the community of decomposers residing in forest litter. In this study, we conducted a controlled litterbag experiment using leaf litter from ten distinct tree species in a central subtropical forest ecosystem in a region characterized by subtropical humid monsoon climate in China. The litterbags were placed in situ using a random experimental design and were collected after 12 months of incubation. Then, the litter chemical properties, microbial community composition and activities of enzyme related to the decomposition of organic carbon (C) and nitrogen (N) were assessed. Across all ten tree species, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were identified as the predominant bacterial classes, while the primary fungal classes were Dothideomycetes, Sordariomycetes and Eurotiomycetes. Mantel test revealed significant correlations between litter chemical component and microbial communities, as well as enzyme activities linked to N and C metabolism. However, after controlling for plant phylogenetic distance in partial Mantel test, the relationships between litter chemical component and microbial community structure and enzyme activities were not significant. Random forest and structural equation modeling indicated that plant phylogenetic distance exerted a more substantial influence than litter chemical components on microbial communities and enzyme activities associated with the decomposition of leaf litter. In summary, plant phylogenic divergence was found to be a more influential predictor of enzyme activity variations than microbial communities and litter traits, which were commonly considered reliable indicators of litter decomposition and ecosystem function, thereby highlighting the previously underestimated significance of plant phylogeny in shaping litter microbial communities and enzyme activities associated with degradation processes in forest litter.

Stimulation of primed carbon under climate change corresponds with phosphorus mineralization in the rhizosphere of soybean

Elevated CO2 and temperature likely alter photosynthetic carbon inputs to soils, which may stimulate soil microbial activity to accelerate the decomposition of soil organic carbon (SOC), liberating more phosphorus (P) into the soil solution. However, this hypothesis on the association of SOC decomposition and P transformation in the plant rhizosphere requires robust soil biochemical evidence, which is critical to nutrient management for the mitigation of soil quality against climate change. This study investigated the microbial functional genes relevant to P mineralization together with priming processes of SOC in the rhizosphere of soybean grown under climate change. Soybean plants were grown under elevated CO2 (eCO2, 700 ppm) combined with warming (+ 2 °C above ambient temperature) in open-top chambers. Photosynthetic carbon flow in the plant-soil continuum was traced with 13CO2 labeling. The eCO2 plus warming treatment increased the primed carbon (C) by 43 % but decreased the NaHCO3-extratable organic P by 33 %. Furthermore, NaHCO3-Po was negatively correlated with phosphatase activity and microbial biomass C. Elevated CO2 increased the abundances of C degradation genes, such as abfA and ManB, and P mineralization genes, such as gcd, phoC and phnK. The results suggested that increased photosynthetic carbon inputs to the rhizosphere of plants under eCO2 plus warming stimulated the microbial population and metabolic functions of both SOC and organic P mineralization. There is a positive relationship between the rhizosphere priming effect and P mineralization. The response of microorganisms to plant-C flow is decisive for coupled C and P cycles, which are likely accelerated under climate change.

Chicken manure application alters microbial community structure and the distribution of antibiotic-resistance genes in rhizosphere soil of Cinnamomum camphora forests

The distribution of antibiotic-resistance genes (ARGs) in environmental soil is greatly affected by livestock and poultry manure fertilization, the application of manure will lead to antibiotic residues and ARGs pollution, and increase the risk of environmental pollution and human health. Cinnamomum camphora is an economically significant tree species in Fujian Province, China. Here, through high-throughput sequencing analysis, significant differences in the composition of the bacterial community and ARGs were observed between fertilized and unfertilized rhizosphere soil. The application of chicken manure organic fertilizer significantly increased the relative abundance and alpha diversity of the bacterial community and ARGs. The content of organic matter, soluble organic nitrogen, available phosphorus, nitrate reductase, hydroxylamine reductase, urease, acid protease, β-glucosidase, oxytetracycline, and tetracycline in the soil of C. camphora forests have significant effects on bacterial community and ARGs. Significant correlations between environmental factors, bacterial communities, and ARGs were observed in the rhizosphere soil of C. camphora forests according to Mantel tests. Overall, the findings of this study revealed that chicken manure organic fertilizer application has a significant effect on the bacterial community and ARGs in the rhizosphere soil of C. camphora forests, and several environmental factors that affect the bacterial community and ARGs were identified.

Impact of long-term resource conservation techniques on biogeochemical characteristics and biological soil quality indicators in a rice green-gram farming system

Nutrient management in resource conservation practices influence the structural and functional microbial diversities and thereby affect biological processes and biochemical properties in soil. We studied the long-term effects of resource conservation technologies on functional microbial diversity and their interactions with soil biochemical properties and enzymatic activities in tropical rice-green gram cropping system. The experiment includes seven treatments viz., conventional practice (CC), brown manuring (BM), green manuring (GM), wet direct drum sowing, zero tillage, green manuring-customized leaf colour chart based-N application (GM-CLCC-N) and biochar (BC) application. The result of the present study revealed that microbial biomass nitrogen (N), carbon (C) and phosphorus (P) in GM practice were increased by 23.3, 37.7 and 35.1%, respectively than CC. GM, BM and GM-CLCC-N treatments provide higher yields than conventional practice. The average well color development value, Shannon index and McIntosh index were significantly higher by 26.6%, 86.9% and 29.2% in GM as compared to control treatment. So, from this study we can conclude that resource conservation practices like GM, GM-CLCC N and BM in combination with chemical fertilizers provide easily decomposable carbon source to support the microbial growth. Moreover, dominance of microbial activity in biomass amended treatments (GM, GM-CLCC N and BM) indicated that these treatments could supply good amount of labile C sources on real time basis for microbial growth that may protect the stable C fraction in soil, hence could support higher yield and soil organic carbon build-up in long run under rice-green gram soil.

Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes

The microbiome function responses to land use change are important for the long-term prediction and management of soil ecological functions under human influence. However, it has remains uncertain how the biogeographic patterns of soil functional composition change when transitioning from natural steppe soils (NS) to agricultural soils (AS). We collected soil samples from adjacent pairs of AS and NS across 900 km of Mollisol areas in northeast China, and the soil functional composition was characterized using shotgun sequencing. AS had higher functional alpha-diversity indices with respect to KO trait richness and a higher Shannon index than NS. The distance-decay slopes of functional gene composition were steeper in AS than in NS along both spatial and environmental gradients. Land-use conversion from steppe to farmland diversified functional gene profiles both locally and spatially; it increased the abundances of functional genes related to labile carbon, but decreased those related to recalcitrant substrate mobilization (e.g., lignin), P cycling, and S cycling. The composition of gene functional traits was strongly driven by stochastic processes, while the degree of stochasticity was higher in NS than in AS, as revealed by the neutral community model and normalized stochasticity ratio analysis. Alpha-diversity of core functional genes was strongly related to multi-nutrient cycling in AS, suggesting a key relationship to soil fertility. The results of this study challenge the paradigm that the conversion of natural to agricultural habitat will homogenize soil properties and biology while reducing local and regional gene functional diversity.

Responses of soil microbial communities and enzyme activities under nitrogen addition in fluvo-aquic and black soil of North China

This research investigates the impact of long-term nitrogen (N) addition on fluvo-aquic and black soils in north China, with a focus on soil microbial communities and enzyme activities. In each site, there were three N fertilization treatments, i.e., control, moderate-N, and high-N. Phospholipid Fatty Acid Analysis was employed to analyze the microbial community composition, and enzyme activities related to N, carbon (C), and phosphorus (P) cycling were assessed. The results showed that increasing N fertilization levels led to higher soil organic carbon (SOC) and total N (TN) concentrations, indicating enhanced nutrient availability. N fertilization reduced soil pH across both soils, with a more pronounced acidification effect observed in the black soil. Across both soils, N addition increased maize yield, but the higher crop yield was attained in moderate-N rate compared with high-N rate. Microbial community composition analysis revealed that N fertilization induced shifts in the relative abundances of specific microbial groups. The black soil exhibited pronounced shifts in the microbial groups compared to the fluvo-aquic soil, i.e., decreased fungal abundance and fungi: bacteria ratio in response to N input. In addition, the application of N fertilizer led to an elevated ratio of gram-positive to gram-negative (GP:GN) bacteria, but this effect was observed only in black soil. N fertilization had an impact on the enzyme activities related to C, N, and P cycling in both soil types, but black soil showed more pronounced changes in enzyme activities. Permutational multivariate analysis of variance indicated that soil types rather than N fertilization mediated the response of the soil microbial community and enzyme activities. Partial least square path modeling demonstrated that soil pH was the only key driver impacting soil microbial groups and enzyme activities in both soils. In conclusion, our findings highlighted that N fertilization exerted more pronounced impacts on soil biochemical properties, microbial community composition, and enzyme activities in black soil furthermore, moderate N rate resulted in higher crop productivity over high N rate.

Dynamic Responses of Rhizosphere Microorganisms to Biogas Slurry Combined with Chemical Fertilizer Application during the Whole Life Cycle of Rice Growth

Biogas slurry combined with chemical fertilizer (BCF) is widely used as a fertilizer in paddy fields and rhizosphere microorganisms are key players in plant growth and reproduction. However, the dynamic responses of rhizosphere microorganisms of field-grown rice to BCF application still remain largely unknown. In this study, a field experiment was conducted in two proximate paddy fields in Chongming Island to study the impacts of BCF on the changes in rhizosphere microorganisms during the whole rice growth, including seedling, tillering, booting, and grain-filling stages, with solely chemical fertilizer (CF) treatment as control. The results showed BCF could increase the N-, P-, and C- levels in paddy water as well as the rhizosphere microbial abundance and diversity compared with control. In particular, the phosphate-solubilizing- and cellulose-decomposing-bacteria (e.g., Bacillus) and fungi (e.g., Mortierella) were more abundant in the rhizosphere of BCF than those of CF. Moreover, these microbes increased markedly at the booting and grain-filling stages in BCF, which could promote rice to obtain available nutrients (P and C). It was noted that denitrifying-like bacteria (e.g., Steroidobacteraceae) decreased and dissimilatory nitrate reduction to ammonia-related bacteria (e.g., Geobacter, Anaeromyxobacter, and Ignavibacterium) increased at the booting and filling stages, which could promote N-availability. TP in paddy water of BCF was most correlated to the bacteria, while COD was the most critical regulator for the fungi. Furthermore, correlation network analysis showed nutrient-cycling-related microorganisms were more closely interconnected in BCF than those in CF. These findings showed the application of biogas slurry plus chemical fertilizer could regulate rhizosphere microorganisms towards a beneficial fertilizer use for rice growth.

Impact of Two Phosphorus Fertilizer Formulations on Wheat Physiology, Rhizosphere, and Rhizoplane Microbiota

Phosphorus (P) is the second most important macronutrient for crop growth and a limiting factor in food production. Choosing the right P fertilizer formulation is important for crop production systems because P is not mobile in soils, and placing phosphate fertilizers is a major management decision. In addition, root microorganisms play an important role in helping phosphorus fertilization management by regulating soil properties and fertility through different pathways. Our study evaluated the impact of two phosphorous formulations (polyphosphates and orthophosphates) on physiological traits of wheat related to yield (photosynthetic parameters, biomass, and root morphology) and its associated microbiota. A greenhouse experiment was conducted using agricultural soil deficient in P (1.49%). Phenotyping technologies were used at the tillering, stem elongation, heading, flowering, and grain-filling stages. The evaluation of wheat physiological traits revealed highly significant differences between treated and untreated plants but not between phosphorous fertilizers. High-throughput sequencing technologies were applied to analyse the wheat rhizosphere and rhizoplane microbiota at the tillering and the grain-filling growth stages. The alpha- and beta-diversity analyses of bacterial and fungal microbiota revealed differences between fertilized and non-fertilized wheat, rhizosphere, and rhizoplane, and the tillering and grain-filling growth stages. Our study provides new information on the composition of the wheat microbiota in the rhizosphere and rhizoplane during growth stages (Z39 and Z69) under polyphosphate and orthophosphate fertilization. Hence, a deeper understanding of this interaction could provide better insights into managing microbial communities to promote beneficial plant-microbiome interactions for P uptake.

Microbial necromass under global change and implications for soil organic matter

Microbial necromass is an important source and component of soil organic matter (SOM), especially within the most stable pools. Global change factors such as anthropogenic nitrogen (N), phosphorus (P), and potassium (K) inputs, climate warming, elevated atmospheric carbon dioxide (eCO₂ ), and periodic precipitation reduction (drought) strongly affect soil microorganisms and consequently, influence microbial necromass formation. The impacts of these global change factors on microbial necromass are poorly understood despite their critical role in the cycling and sequestration of soil carbon (C) and nutrients. Here, we conducted a meta-analysis to reveal general patterns of the effects of nutrient addition, warming, eCO₂ , and drought on amino sugars (biomarkers of microbial necromass) in soils under croplands, forests, and grasslands. Nitrogen addition combined with P and K increased the content of fungal (+21%), bacterial (+22%), and total amino sugars (+9%), consequently leading to increased SOM formation. Nitrogen addition alone increased solely bacterial necromass (+10%) because the decrease of N limitation stimulated bacterial more than fungal growth. Warming increased bacterial necromass, because bacteria have competitive advantages at high temperatures compared to fungi. Other global change factors (P and NP addition, eCO₂ , and drought) had minor effects on microbial necromass because of: (i) compensation of the impacts by opposite processes, and (ii) the short duration of experiments compared to the slow microbial necromass turnover. Future studies should focus on: (i) the stronger response of bacterial necromass to N addition and warming compared to that of fungi, and (ii) the increased microbial necromass contribution to SOM accumulation and stability under NPK fertilization, and thereby for negative feedback to climate warming.

Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability

BACKGROUND

For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability.

RESULTS

We found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass.

CONCLUSIONS

Our results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification. Video Abstract.

Dynamic Monitoring of Nutrition Inputs and Fertility Evaluation during a Decade in the Main Peach-Producing Areas of Shandong Province, China

The main peach-producing area in Shandong is an important peach fruit-producing area in China. Understanding the nutritional properties of the soil in peach orchards helps us to understand the evolution of soil properties and adjust management methods in a timely manner. This study focuses on 52 peach orchards in the main peach-producing area in Shandong as the research object. The spatiotemporal changes in soil traits and their influential factors were studied in depth, and the changes in soil fertility were effectively evaluated. The results showed that the input of nitrogen, phosphorus and potassium from organic fertilizer in 2021 was significantly higher than that in 2011, while the input of fertilizer in 2011 was significantly higher than that in 2021. Compared with traditional parks, both organic fertilizer inputs and chemical fertilizer inputs in demonstration parks showed a significant downwards trend. There was no significant change in pH values between 2011 and 2021. In 2021, the soil organic matter (SOM) contents of the 0-20 cm and 20-40 cm layers were 24.17 g·kg^-1 and 23.38 g·kg^-1, respectively, an increase of 29.3% and 78.47% over the values measured in 2011. Compared with 2011, the content of soil alkaloid nitrogen (AN) decreased significantly in 2021, and the contents of available phosphorus (AP) and available potassium (AK) in the soil increased significantly. According to the calculation results of the comprehensive fertility index (IFI) value, we found that in 2021, compared with 2011, the quality of soil fertility improved, most of which was at the medium and high levels. The research results show that the fertilizer-saving and synergistic approach in peach orchards in China significantly improved the soil nutrition. In the future, research on suitable comprehensive technologies should be strengthened in the management of peach orchards.

Alleviation of Cd-polluted paddy soils through Si fertilizer application and its effects on the soil microbial community

In this study, the effects of slag-based Si fertilizers on Cd-polluted paddy soils, soil microbial diversity, and functional properties were evaluated through a long-term field experiment conducted in a double-rice cropping system in southern China. The results showed that soil pH significantly increased from 5.15 to 6.13 after seven years of Si fertilization. Cd accumulation in both the soil and rice plants were significantly decreased for all the Si fertilizers treatments. Treatments using Si fertilizer in powder form exhibited the best alleviation effects, where soil available Cd decreased from 0.50 mg kg^-1 to 0.43 mg kg^-1, and Cd accumulation in rice roots, straw, and grains decreased by 32.2 %, 57.2 %, and 45.5 %, respectively, than that in the control. Following Si application, the soil microbial richness and Shannon diversity increased from 6731 to 7549 and 7.12 to 7.28, respectively. Proteobacteria, Nitrospirae, and Gemmatimonadetes, were significantly enriched in the Si-treated samples, whereas Verrucomicrobia, Chlamydiia, Ktedonobacteria and Candidatus_Saccharibacteria exhibited opposite patterns. Bioinformatics analysis using phylogenetic investigation of communities by reconstruction of unobserved states tools revealed that the varied microbial community induced functional adaption of soil microorganisms involved in metabolism, genetic information processing, cellular processes, and environmental information processing. The soil pH, NH₄-N, and available Cd and Si contents were the key factors that best explained the variations in bacterial community composition among different treatments. Slag-based Si fertilizers are effective for Cd detoxication and can benefit the growth of rice plants throng the regulation of soil microorganisms.

Amino Acids in the Root Exudates of Agave lechuguilla Torr. Favor the Recruitment and Enzymatic Activity of Nutrient-Improvement Rhizobacteria

Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked. Thus, we investigated how the variations of amino acids in the rhizosphere at different growth stages of A. lechuguilla affect the rhizobacterial community composition, its functions, and activity of the beneficial bacteria. In this regard, it was found that arginine and tyrosine were related to the composition of the rhizobacterial community associated to A. lechuguilla, where the most abundant genera were from the phylum Proteobacteria and Bacteroidetes. Moreover, Firmicutes was largely represented by Bacillus in the phosphorus-mineralizing bacteria community, which may indicate its great distribution and versatility in the harsh environments of the Chihuahuan Desert. In contrast, we found a high proportion of Unknown taxa of nitrogen-fixing bacteria, reflecting the enormous diversity in the rhizosphere of these types of plants that remains to be explored. This work also reports the influence of micronutrients and the amino acids methionine and arginine over the increased activity of the nitrogen-fixing and phosphorus-mineralizing bacteria in the rhizosphere of lechuguillas. In addition, the results highlight the multiple beneficial functions present in the microbiome that could help the host to tolerate arid conditions and improve nutrient availability.

Biochar fertilization effects on soil bacterial community and soil phosphorus forms depends on the application rate

Biochar plays a key role in soil phosphorus (P) forms and distribution by affecting soil biochemical characteristics with relevant effects on the microbial community. In this study, we aimed to study the role of biochar in the variation of microbial community and P forms, and the relationships between soil properties, microbial community, and P forms. Here, we conducted a five-year field experiment NPK minerally fertilized with different application rates of biochar; control (B0, 0 kg ha^-1 yr^-1), low rate (B1500, 1500 kg ha^-1 yr^-1), medium rate (B3000, 3000 kg ha^-1 yr^-1), high rate (B6000, 6000 kg ha^-1 yr^-1). Our study showed that the highest increases in bacterial diversity and abundances coincided with increases in P forms typically retained in bacterial cells (β-glucosidase, adenosine monophosphate-AMP, choline phosphate, and glucose-6 phosphate) and occurred at medium application rates. At low application rates, N₂-fixing and P solubilizing and mineralizing bacteria (Sphingomonas, Haliangium, and Bradyrhizobium) increased. P forms retained in bacterial cells decreased at the highest application rates while the most stable forms such as DNA and inositol hexaphosphate (IHP), steadily increased. Stereoisomers of IHP derived from soil microbes (scyllo-IHP and D-chiro-IHP) accounted for the total IHP increases at high application rates. pH and available P and K and total P were highest at high biochar application rates whereas the proportion of organic P was reduced. The most relevant genus in such soils was Gemmatimonas, a polyphosphate accumulating and pyrogenic material degrading bacterium. Therefore, it appears that applying biochar at higher rates reduced the abundance of plant growth promoting bacteria while enhancing the abundance of P accumulating and pyrogenic degrading types.

Long-term organic fertilizer additions elevate soil extracellular enzyme activities and tobacco quality in a tobacco-maize rotation

Organic fertilizer is effective in improving soil quality, and promoting crop growth. Combined organic and inorganic fertilization has been proved as a more favorable way to tobacco yield and quality. However, the mechanisms underlying tobacco yield and quality under combinations of different organic and inorganic fertilizer remain unclear. We conducted a 12-year tobacco (Nicotiana tabacum L.)-maize crop rotation field experiment in Yanhe experimental station, China to examine the yields and qualities of tobacco, soil nutrients, and extracellular enzyme activities associated with carbon, nitrogen, and phosphorus cycles in response to different fertilization treatments. Five fertilization treatments (no fertilization; 75 kg N fertilizer ha^-1; 450 kg oil cake ha^-1 + 75 kg N fertilizer ha^-1; 15,000 kg pig dung ha^-1 + 60 kg N fertilizer ha^-1; 3,000 kg straw ha^-1 + 75 kg N fertilizer ha^-1) were applied to tobacco while maize was fertilized with inorganic compound fertilizers. After 12 years of tobacco-maize rotation, the results showed that organic fertilizer additions elevate tobacco yield and quality, and the soil extracellular enzymes activities. Gram-negative bacteria, actinomycetes, and total soil microbial biomass were increased by organic fertilizer additions, both plant-based (oil cake and straw) and animal-based (pig dung) organics. The levels of soil organic matter, total organic carbon, total phosphorus and available phosphorus are higher in pig dung addition treatment than oil cake and straw additions. By variance analysis with respect to fertilization treatments, organic sources differentially affected the activities of diverse soil enzymes. The redundancy analysis gave that yield and quality of tobacco leaves (upper, middle, and lower leaves) positively related to soil extracellular enzyme activities. Based on analysis of yield and quality of tobacco leaves with extracellular enzyme activities and soil nutrients, it is suggested animal-based organic fertilizer, thus pig dung, should be used in combining with chemical fertilizers to improve the quality of tobacco and soil nutrients.

Long-term fertilization altered microbial community structure in an aeolian sandy soil in northeast China

Soil microorganisms play crucial roles in nutrient cycling and determining soil quality and fertility; thus, they are important for agricultural production. However, the impacts of long-term fertilization on soil microbial community remain ambiguous due to inconsistent results from different studies. The objective of this study was to characterize changes in bacterial and fungal diversity and community structures after 12 years of different fertilization in aeolian sandy soil by analyzing 16S rRNA and ITS rRNA gene sequences and the soil properties to discover the driving factors. Eight different fertilizer treatments have been set up since 2009: no fertilizer (CK), chemical N fertilizer (N), chemical N and P fertilizer (NP), chemical N, P and K fertilizer (NPK), pig manure only (M), pig manure plus chemical N fertilizer (MN), pig manure plus chemical N and P fertilizer (MNP), pig manure plus chemical N, P, and K fertilizer (MNPK). The results indicated that the long-term application of chemical fertilizer reduced soil pH, whereas the addition of pig manure alleviated a decrease in soil pH value. Chemical fertilizer plus pig manure significantly improved soil available nutrients and soil organic carbon. Long-term MNPK fertilization resulted in changes in bacterial diversity due to effects on specific bacterial species; by contrast, all fertilization treatments resulted in changes in fungal diversity due to changes in soil properties. Principal component analysis indicated that fertilization had a significant effect on soil microbial community structure, and the effect of chemical fertilizer combined with pig manure was greater than that of chemical fertilizer alone. Soil available phosphorus, total phosphorus, and pH were the most important factors that influenced bacterial taxa, whereas soil pH, total phosphorus, organic carbon, ammonium nitrogen and nitrate nitrogen were the most important factors influencing fungal taxa after 12 years of fertilization in aeolian sandy soil.

Overfertilization reduces tomato yield under long-term continuous cropping system via regulation of soil microbial community composition

Long-term monoculture cropping and overfertilization degrade soil fertility, which reduces crop growth and promotes the development of soil-borne diseases. However, it remains unclear what the temporal effects of the above factors are on the tomato yield and microbial community structure. Thus, a greenhouse experiment with different amounts of fertilization [2,196 kg ha⁻¹ (control) and 6,588 kg ha⁻¹ (overfertilization) of inorganic fertilizers (NPK)] was carried out with the soils used previously for 1, 2, and 12 years under monoculture of tomato. A 12-year overfertilization decreased soil pH by 1.37 units. Soil electrical conductivity (EC) and concentrations of soil nutrients are enhanced with the increase in tomato cropping duration. Higher content of soil nutrients was found under overfertilization compared to the control in the 12-year soil. Overfertilization decreased the activity of β-1,4-glucosidase (BG) and oxidase compared to the control in the 12-year soil. Bacterial diversity and richness decreased by 6 and 31%, respectively, under overfertilization in 12-year soil compared to the control. The relative abundance of Gemmatimonas and Gp6 in 12-year soil under overfertilization was 17 and 78%, respectively, lower than in control soil. Soil pH and total carbon (TC) were the major factors explaining changes in microbial composition. A 38% decrease in yield was caused by overfertilization in 12-year soil compared to the control. Microbial community composition was the main factor that moderated tomato yield. In addition, fertilization rather than cropping duration had a greater impact on tomato yield. Therefore, our results suggest that long-term overfertilization influenced soil pH, soil TC, and soil microbial community composition to regulate tomato yield.

Understanding Responses of Soil Microbiome to the Nitrogen and Phosphorus Addition in Metasequoia glyptostroboides Plantations of Different Ages

Nitrogen (N) and phosphorus (P) have significant effects on soil microbial community diversity, composition, and function. Also, trees of different life stages have different fertilization requirements. In this study, we designed three N additions and three P levels (5 years of experimental treatment) at two Metasequoia glyptostroboides plantations of different ages (young, 6 years old; middle mature, 24 years old) to understand how different addition levels of N and P affect the soil microbiome. Here, the N fertilization of M. glyptostroboides plantation land (5 years of experimental treatment) significantly enriched microbes (e.g., Lysobacter, Luteimonas, and Rhodanobacter) involved in nitrification, denitrification, and P-starvation response regulation, which might further lead to the decreasing in alpha diversity (especially in 6YMP soil). The P addition could impact the genes involved in inorganic P-solubilization and organic P-mineralization by increasing soil AP and TP. Moreover, the functional differences in the soil microbiomes were identified between the 6YMP and 24YMP soil. This study provides valuable information that improves our understanding on the effects of N and P input on the belowground soil microbial community and functional characteristics in plantations of different stand ages.

Effect of biochar and hydrochar from cow manure and reed straw on lettuce growth in an acidified soil

Soil acidification has become a major environmental and economic concern worldwide. Char materials (e.g biochar, hydrochar) have attracted considerable attention as soil amendments to restore degraded soil. However, the comparative study of biochar and hydrochar on plant growth in acidified soil is limited. In this study, a microcosmic experiment was used to compare the effect of biochar and hydrochar from cow manure (CBC, CHC) and reed straw (RBC, RHC) on the growth of lettuce in the acidified soil. CBC and RHC significantly increased and decreased the biomass of lettuce by 18.7% and 32.5% in the acidified soil, respectively. The increase of the lettuce growth by CBC primarily attributed to the enhancement of soil properties (SOM and pH) and soil nutrient content (Olsen-P, K, Ca, Mg, Zn, Fe and Mn). Moreover, CBC enhanced the microbial activity and complexity and increased the abundance of beneficial genera like Gemmatimonas, Ramlibacter and Haliangium, which improved soil health and might indirectly benefited the lettuce growth. Our findings highlighted the priority of char materials feedstock and preparation technology for remediating the acidified soil.

Effects of Nitrogen Addition on Plant Properties and Microbiomes Under High Phosphorus Addition Level in the Alpine Steppe

Nitrogen (N) addition can increase the vegetative growth, improve the plant production, and restore the degraded terrestrial ecosystems. But, it simultaneously aggravates the soil phosphorus (P) limitation for plant growth, thus affecting its positive effects on ecosystems. However, how plants and soil microorganisms will change under conditions of high P content in soil is still unknown. In this study, we explored the effects of three levels of N addition (0, 7.5, and 15 g.N.m^-2.year^-1) on plants and microorganisms at the high P addition level (13.09 g.P.m^-2.year^-1) in the alpine steppe. We found that the soil microbial community composition had no significant difference between different N addition levels, and the soil AN and AP had a significant effect on the phospholipid fatty acid (PLFA) composition. The abundance of the core PLFAs (i.e., 16:1ω7c, 16:0, a17:1, i17:0, 18:1ω9c, and 18:1ω7c) also remained unchanged after N addition, and microbes at individual, population, and community levels were all correlated with SOM, AK, AN, and pH. Conversely, plant biomass and nutrient content showed linear trends with increasing N addition, especially the dominant functional groups. Specifically, the biomass and plant tissue N content of Gramineae, and the total N content of aboveground biomass were all improved by N addition. They were correlated with soil ammonium and AP. The structural equation modeling (SEM) demonstrated that N addition had a direct negative effect on soil microbial biomass, but an indirect positive effect on aboveground biomass via soil ammonium. These findings clarify the importance of N-amendment in regulating plants and microorganisms under high P conditions and provide a better understanding of the N-added effects in the alpine steppe.

Integrated microbiology and metabolomics analysis reveal responses of soil microorganisms and metabolic functions to phosphorus fertilizer on semiarid farm

Localized fertilization of phosphorus has potential benefits in achieving higher crop productivity and nutrient use efficiency, but the underlying biological mechanisms of interactions between soil microorganisms and related metabolic cycle remain largely to be recognized. Here, we combined microbiology with non-target metabolomics to explore how P fertilizer levels and fertilization patterns affect wheat soil microbial communities and metabolic functions based on high-throughput sequencing and UPLC-MS/MS platforms. The results showed P fertilizer decreased the diversity of bacterial 16S rRNA genes and fungal ITS genes, and it did significantly change both soil bacterial and fungal overall community structures and compositions. The P levels and patterns also interfered with complexity of soil bacterial and fungal symbiosis networks. Moreover, metabolomics analysis showed that P fertilizer significantly changed soil metabolite spectrum, and the differential metabolites were significantly enriched to 7 main metabolic pathways, such as arginine and proline metabolism, biosynthesis of plant hormones, amino acids, plant secondary metabolites, and alkaloids derived from ornithine. Additionally, microbes also were closely related to the accumulation of metabolites through correlation analysis. Our results indicated that localized appropriate phosphorus fertilizer plays an important role in regulating soil microbial metabolism, and their interactions in soil providing valuable information for understanding how the changed phosphorus management practices affect the complex biological processes and the adaption capacity of plants to environments.

Phosphorus Shapes Soil Microbial Community Composition and Network Properties During Grassland Expansion Into Shrubs in Tibetan Dry Valleys

Alpine ecosystem stability and biodiversity of the Tibetan plateau are facing threat from dry valley vegetation uplift expansion, a process which is highly connected to variations in the soil microbial community and soil nutrients. However, the variation of microbial community properties and their relationship to soil nutrients have scarcely been explored in Tibetan dry valleys, which is a gap that hampers understanding the dry valley ecosystem's response to vegetation change. In this study, we sampled grasslands (G), a grass-shrub transition area (T), and shrublands (S) along an uplift expansion gradient and investigated the link between microbial community properties and soil nutrients. The results showed that shrub degradation by grass expansion in Tibetan dry valley was accompanied by increasing relative phosphorus (P) limitation, which was the main driver for bacterial and fungal composition variation as it offered highest total effect on PC1 (0.38 and 0.63, respectively). Total phosphorus (TP) was in the center module of bacterial and fungal network under shrub soil and even acted as key nodes in fungal networks. During the replacement by grass, TP was gradually marginalized from both bacterial and fungal center network module and finally disappeared in networks, with ammonia and nitrate gradually appearing in the bacterial network. However, TC and total nitrogen (TN) were always present in the center modules of both fungal and bacterial network. These support that a TP variation-induced compositional and network functional shift in the microbial community was a potential reason for vegetation uplift expansion in Tibetan dry valley. This study highlighted the effect of TP on microbial community properties during dry valley vegetation uplift expansion and offered basic information on Tibetan alpine dry valley ecosystem's response to climate change.

Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes

Enhancing soil phosphate solubilization is a promising strategy for agricultural sustainability, while little is known about the mechanisms of how microorganisms cope with differing phosphorus availability. Using a combination of genome-resolved metagenomics and amplicon sequencing, we investigated the microbial mechanisms involved in phosphorus cycling under three agricultural treatments in a wheat-maize rotation system and two natural reforestation treatments. Available soil phosphorus was the key factor shaping bacterial and fungal community composition and function across our agricultural and reforestation sites. Membrane-bound quinoprotein glucose dehydrogenase (PQQGDH) and exopolyphosphatases (PPX) governed microbial phosphate solubilization in agroecosystems. In contrast, genes encoding glycerol-3-phosphate transporters (ugpB, ugpC, and ugpQ) displayed a significantly greater abundance in the reforestation soils. The gcd gene encoding PQQGDH was found to be the best determinant for bioavailable soil phosphorus. Metagenome-assembled genomes (MAGs) affiliated with Cyclobacteriaceae and Vicinamibacterales were obtained from agricultural soils. Their MAGs harbored not only gcd but also the pit gene encoding low-affinity phosphate transporters. MAGs obtained from reforestation soils were affiliated with Microtrichales and Burkholderiales. These contain ugp genes but no gcd, and thereby are indicative of a phosphate transporter strategy. Our study demonstrates that knowledge of distinct microbial phosphorus acquisition strategies between agricultural and reforestation soils could help in linking microbial processes with phosphorus cycling.

IMPORTANCE The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity. In this study, we combined functional metagenomics and amplicon sequencing to analyze microbial phosphorus cycling processes in natural reforestation and agricultural soils. We found that the phosphorus acquisition strategies significantly differed between these two ecosystems. A microbial phosphorus solubilization strategy dominated in the agricultural soils, while a microbial phosphate transporter strategy was observed in the reforestation soils. We further identified microbial taxa that contributed to enhanced phosphate solubilization in the agroecosystem. These microbes are predicted to be beneficial for the increase in phosphate bioavailability through agricultural practices.

Phosphorus-arsenic interaction in the 'soil-plant-microbe' system and its influence on arsenic pollution

Elevated arsenic (As) in soil is of public concern due to the carcinogenicity. Phosphorus (P) strongly influences the adsorption, absorption, transport, and transformation of As in the soil and in organisms due to the similarity of the chemical properties of P and As. In soil, P, particularly inorganic P, can release soil-retained As (mostly arsenate) by competing for adsorption sites. In plant and microbial systems, P usually reduces As (mainly arsenate) uptake and affects As biotransformation by competing for As transporters. The intensity and pattern of PAs interaction are highly dependent on the forms of As and P, and strongly influenced by various biotic and abiotic factors. An understanding of the PAs interaction in 'soil-plant-microbe' systems is of great value to prevent soil As from entering the human food chain. Here, we review PAs interactions and the main influential factors in soil, plant, and microbial subsystems and their effects on the As release, absorption, transformation, and transport in the 'soil-plant-microbe' system. We also analyze the application potential of P fertilization as a control for As pollution and suggest the research directions that need to be followed in the future.

Long-term effects of combination of organic and inorganic fertilizer on soil properties and microorganisms in a Quaternary Red Clay

Quaternary Red Clay (QRC) is the most common planting soil with low soil fertility and low crop yields in Southeast China, with low soil fertility and low crop yields. Many factors can impact the fertility and utilization efficiency of QRC. Here, we conducted a long-term fertilization experiment from 1984 to 2013. Five fertilization measures were carried out, including non-fertilization group; chemical Fertilizer group; 70% chemical and 30% organic fertilizer group; 50% chemical and 50% organic fertilizer group; 30% chemical and 70% organic fertilizer group. Soil organic matter (OM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), soil microbial biomass carbon (SMBC) and nitrogen (SMBN), and soil enzymes activity were measured to evaluate the changes of soil. In addition, soil microorganisms were determined by high-throughput sequencing technology, and the dominant microbes were screened. The higher the proportion of organic fertilizer was, the higher the soil OM content was. The OM content of the non-fertilization group was the lowest. Similarly, SMBC and SMBN showed a consistent trend with OM content. Illumina sequence results showed that the application of organic fertilizer reduced the relative abundance of Chloroflexi, Acidobacteria and Nitrospirae, but increased Proteobacteria and Actinobacteria. The relative abundance of Acremonium and Mortierella were also greatly increased by different fertilization strategies. However, when high proportion of organic fertilizer was applied, the abundance of Acremonium and Mortierella decreased. Long-term balanced inorganic fertilization (NPK, 60%N:20%P:20%K) can effectively improve the quality and fertility of QRC. The effect of different fertilization strategies on fungi was greater than that on bacteria. The change of soil microorganism also proved the validity of inorganic fertilizer application.

Soil Rehabilitation Promotes Resilient Microbiome with Enriched Keystone Taxa than Agricultural Infestation in Barren Soils on the Loess Plateau

Drylands provide crucial ecosystem and economic services across the globe. In barren drylands, keystone taxa drive microbial structure and functioning in soil environments. In the current study, the Chinese Loess plateau’s agricultural (AL) and twenty-year-old rehabilitated lands (RL) provided a unique opportunity to investigate land-use-mediated effects on barren soil keystone bacterial and fungal taxa. Therefore, soils from eighteen sites were collected for metagenomic sequencing of bacteria specific 16S rRNA and fungi specific ITS2 regions, respectively, and to conduct molecular ecological networks and construct microbial OTU-based correlation matrices. In RL soils we found a more complex bacterial network represented by a higher number of nodes and links, with a link percentage of 77%, and a lower number of nodes and links for OTU-based fungal networks compared to the AL soils. A higher number of keystone taxa was observed in the RL (66) than in the AL (49) soils, and microbial network connectivity was positively influenced by soil total nitrogen and microbial biomass carbon contents. Our results indicate that plant restoration and the reduced human interventions in RL soils could guide the development of a better-connected microbial network and ensure sufficient nutrient circulation in barren soils on the Loess plateau.

Balanced fertilization over four decades has sustained soil microbial communities and improved soil fertility and rice productivity in red paddy soil

The influence of long-term fertilization on soil microbial communities is critical for revealing the association between belowground microbial flora and aboveground crop productivity-a relationship of great importance to food security, environmental protection, and ecosystem functions. Here, we examined shifts in soil chemical properties, microbial communities, and the nutrient uptake and yield of rice subjected to different chemical and organic fertilization treatments over a 40-year period in red paddy soil. Ten different treatments were used: a control without fertilizer, and applications of nitrogen (N), phosphorus (P), potassium (K), NP, NK, PK, NPK, double NPK, or NPK plus manure. Compared with the effects of withholding one or two nutrients (N, P, or K), the balanced application of chemical NPK and organic fertilizers markedly improved soil nutrient status and rice yield. This improvement of soil fertility and rice yield was not associated with bacterial, archaeal, or fungal alpha diversities. The bacterial abundance and community structure and archaeal abundance effectively explained the variation in rice yield, whereas those of fungi did not. The community structure of bacteria and archaea, but not that of fungi, was correlated with soil properties. Among various soil properties, P was the key factor influencing rice yield and soil microbial communities because of the extremely low content of soil available P. Seven keystones at the operational taxonomic unit level were identified: four archaea (belonging to Thermoplasmata, Methanosaeta, Bathyarchaeia, and Nitrososphaeraceae) and three bacteria (in Desulfobacteraceae and Acidobacteriales). These keystones, which were mainly related to soil C and N transformation and pH, may work cooperatively to influence rice yield by regulating soil fertility. Our results collectively suggest that four decades of balanced fertilization has sustained the bacterial and archaeal abundances, bacterial community structure, and keystones, which potentially contribute to soil fertility and rice yield in red paddy soil.

Responses of Root Endophytes to Phosphorus Availability in Peach Rootstocks With Contrasting Phosphorus-Use Efficiencies

Phosphorus (P) is an important macronutrient for all lives, but it is also a finite resource. Therefore, it is important to understand how to increase the P availability and plant uptake. The endophytes can help host plants to improve P uptake and will be apparently affected by plant genotypes. To investigate the mechanism of root endophytes in promoting P uptake of peach rootstocks, we analyzed the variations of the root endophytic fungal and bacterial communities of peach rootstocks with different P efficiencies under high or low level of P addition. Results showed that Proteobacteria was the dominant bacterial phylum in the roots of all rootstocks under the two levels of P addition. At low P level, the abundance of Actinoplanes in phosphorus-inefficiency root system was apparently higher than that at high P level. Actinoplanes produced important secondary metabolites, improving the stress resistance of plants. Under high P condition, the abundance of Ferrovibrio was higher in Qing Zhou Mi Tao than in Du Shi. Fe oxides considerably reduced the availability of applied P, which partially explained why the P utilization in Qing Zhou Mi Tao is inefficient. Further, Ascomycota was the dominant fungal phylum in the roots of all rootstocks under different levels of P addition. The fungi community of roots varied in different rootstocks at each P level, but was similar for the same rootstock at different P levels, which indicated that genotype had a greater effect than P addition on the fungal community of peach rootstocks.

Comparative Effect of Fertilization Practices on Soil Microbial Diversity and Activity: An Overview

Continuously increasing human population demands increased food production, which needs greater fertilizer's input in agricultural lands to enhance crop yield. In this respect, different fertilization practices gained acceptance among farmers. We reviewed effect of three main fertilization practices (Conventional-, Organic-, and Bio-fertilization) on soil microbial diversity, activity, and community composition. Studies reported that over application of inorganic fertilizers decline soil pH, change soil osmolarity, cause soil degradation, disturb taxonomic diversity and metabolism of soil microbes and cause accumulation of extra nutrients into the soil such as phosphorous (P) accumulation. On the contrary, organic fertilizers increase organic carbon (OC) input in the soil, which strongly encourage growth of heterotrophic microbes. Organic fertilizer vermicompost application provides readily available nutrients to both plants as well as microbes and encourage overall microbial number in the soil. Most recently, role of beneficial bacteria in long-term sustainable agriculture attracted attention of scientists towards their use as biofertilizer in the soil. Studies documented favorable effect of biofertilization on microbial Shannon, Chao and ACE diversity indices in the soil. It is concluded from intensive review of literature that all the three fertilization practices have their own way to benefit the soil with nutrients, but biofertilization provides long-term sustainability to crop lands. When it is used in integration with organic fertilizers, it makes the soil best for microbial growth and activity and increase microbial diversity, providing nutrients to soil for a longer time, thus improving crop productivity.

Response of Root-Associated Bacterial Communities to Different Degrees of Soft Rot Damage in Amorphophallus konjac Under a Robinia pseudoacacia Plantation

Bacterial soft rot is a destructive disease that restricts the development of the konjac (Amorphophallus konjac K. Koch ex N.E.Br) industry. The objective of this study was to investigate how soft rot disease affects bacterial communities associated with the roots of konjac plants growing under a pure Robinia pseudoacacia plantation. Three sampling sites affected by different degrees of soft rot damage were selected based on the disease incidence [0%, non-diseased (ND); 4.2%, moderately diseased (MD); and 18.6%, highly diseased (HD)]. The variation in soil and root bacterial diversity and community composition among the sampling sites was determined by Illumina HiSeq sequencing of the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. The results showed that the contents of soil organic matter and available nutrients (N, P, and K) increased with increasing damage degree, whereas higher damage degree resulted in lower soil pH and enzymatic activity (sucrase, urease, catalase, and polyphenol oxidase). The composition of root-associated bacterial communities differed among the three sampling sites. Proteobacteria was the most dominant bacterial phylum in all soil and root samples. Pseudomonas, Bacillus, Rhizobium, and Streptomyces were the most abundant in all samples from the ND sites, whereas Pectobacterium carotovorum and Serratia were predominant in the samples from the MD and HD sites. The abundance and alpha diversity of root-associated bacteria were significantly higher (p < 0.05) in the ND sites than in the diseased sites. The results suggested pronounced differences in the abundance, alpha diversity, and community composition of bacteria associated with the roots of konjac plants affected by different degrees of soft rot damage. Such differences in bacterial community structure were related to dynamic changes in soil variables, especially soil available potassium content, sucrase activity, and urease activity. Analysis of the dominant root-associated bacterial taxa offers an approach to predict the damage degree due to soft rot in konjac and provides evidence for the prevention of this soil-borne disease via microecological regulation.

Changes in Soil Microbial Activity, Bacterial Community Composition and Function in a Long-Term Continuous Soybean Cropping System After Corn Insertion and Fertilization

Corn-soybean rotation and fertilization are common practices improving soil fertility and crop yield. Their effects on bacterial community have been extensively studied, yet, few comprehensive studies about the microbial activity, bacterial community and functional groups in a long-term continuous soybean cropping system after corn insertion and fertilization. The effects of corn insertions (Sm: no corn insertion, CS: 3 cycles of corn-soybean rotations and CCS: 2 cycles of corn-corn-soybean rotations) with two fertilization regimes (No fertilization and NPK) on bacterial community and microbial activity were investigated in a long-term field experiment. The bacterial communities among treatments were evaluated using high-throughput sequencing then bacterial functions were predicted based on the FaProTax database. Soil respiration and extracellular enzyme activities were used to assess soil microbial activity. Soil bacterial community structure was significantly altered by corn insertions (p < 0.01) and fertilization (p < 0.01), whereas bacterial functional structure was only affected by corn insertion (p < 0.01). The activities of four enzymes (invertase, β-glucosidase, β-xylosidase, and β-D-1,4-cellobiohydrolase) involved in soil C cycling were enhanced by NPK fertilizer, and were also enhanced by corn insertions except for the invertase and β-xylosidase under NPK fertilization. NPK fertilizer significantly improved soil microbial activity except for soil metabolic quotient (qCO₂) and the microbial quotient under corn insertions. Corn insertions also significantly improved soil microbial activity except for the ratio of soil induced respiration (SIR) to basal respiration (BR) under fertilization and the qCO₂ was decreased by corn insertions. These activity parameters were highly correlated with the soil functional capability of aromatic compound degradation, which was the main predictors of bacterial functional structure. In general, the combination of soil microbial activity, bacterial community and corresponding functional analysis provided comprehensive insights into compositional and functional adaptations to corn insertions and fertilization.

Influence of the neonicotinoid insecticide thiamethoxam on soil bacterial community composition and metabolic function

Understanding of neonicotinoid insecticides toxicity on non-target organisms, such as bees, has indirectly promoted their soil treatment use. However, their effect on soil ecosystems haven't fully understood. Here, based on 16S rRNA high-throughput sequencing and metagenomics, the effects of neonicotinoid insecticide thiamethoxam on bacterial communities and metabolic functions in two types of soils were studied. Thiamethoxam treatment significantly affected soil bacterial abundance, reduced microbial diversity, and changed the bacterial community structure in the short term, and the structure soon returned to a stable state. Soil type and time were important factors affecting bacterial community structure. Some plant growth-promoting rhizosphere bacteria (PGPR) including Actinobacteria were found, and their populations were reduced, while pollutant-degrading bacteria including Firmicutes were also found, and their populations were increased. Based on metagenomics analysis, thiamethoxam treatment insignificantly promoted or inhibited multiple metabolic processes, but gene abundance of some key processes significantly changed. Subtypes of 18 biodegradation genes (BDGs) and 5 pesticide degradation genes (PDGs) were identified. Thiamethoxam treatment significantly increased the abundance of BDGs and PDGs, including cytochrome P450. Potential hosts of P450 degradation genes, including the genus Rhodococcus, were discovered. Conclusions of this study will promote safety evaluation and degradation-related research on neonicotinoid insecticides in soil.

Long-Term Fertilization Shapes the Putative Electrotrophic Microbial Community in Paddy Soils Revealed by Microbial Electrosynthesis Systems

Electrotrophs play an important role in biogeochemical cycles, but the effects of long-term fertilization on electrotrophic communities in paddy soils remain unclear. Here, we explored the responses of electrotrophic communities in paddy soil-based microcosms to different long-term fertilization practices using microbial electrosynthesis systems (MESs), high-throughput quantitative PCR, and 16s rRNA gene-based Illumina sequencing techniques. Compared to the case in the unfertilized soil (CK), applications of only manure (M); only chemical nitrogen, phosphorous, and potassium fertilizers (NPK); and M plus NPK (MNPK) clearly changed the electrotrophic bacterial community structure. The Streptomyces genus of the Actinobacteria phylum was the dominant electrotroph in the CK, M, and MNPK soils. The latter two soils also favored Truepera of Deinococcus-Thermus or Arenimonas and Thioalkalispira of Proteobacteria. Furthermore, Pseudomonas of Proteobacteria and Bacillus of Firmicutes were major electrotrophs in the NPK soil. These electrotrophs consumed biocathodic currents coupled with nitrate reduction and recovered 18-38% of electrons via dissimilatory nitrate reduction to ammonium (DNRA). The increased abundances of the nrfA gene for DNRA induced by electrical potential further supported that the electrotrophs enhanced DNRA for all soils. These expand our knowledge about the diversity of electrotrophs and their roles in N cycle in paddy soils and highlight the importance of fertilization in shaping electrotrophic communities.

Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment

Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing environments. Here, we used multitrophic ecological networks to investigate the importance of soil biodiversity, in particular, the biodiversity of key-stone taxa in controlling soil functioning and wheat production in a 35-year field fertilization experiment. We found strong and positive associations between soil functional genes, crop production and the biodiversity of key-stone phylotypes; soils supporting a larger number of key-stone nematode, bacteria and fungi phylotypes yielded the highest wheat production. These key-stone phylotypes were also positively associated with plant growth (phototrophic bacteria, nitrogen fixers) and multiple functional genes related to nutrient cycling. The retrieved information on the genomes clustered with key-stone bacterial phylotypes indicated that the key-stone taxa had higher gene copies of oxidoreductases (participating most biogeochemical cycles of ecosystems and linking to microbial energetics) and 71 essential functional genes associated with carbon, nitrogen, phosphorus, and sulfur cycling. Altogether, our work highlights the fundamental role of the biodiversity of key-stone phylotypes in maintaining soil functioning and crop production after several decades of fertilization, and provides a list of key-stone phylotypes linking to crop production and soil nutrient cycling, which could give science-based guidance for sustainable food production.

Keystone Microbiomes Revealed by 14 Years of Field Restoration of the Degraded Agricultural Soil Under Distinct Vegetation Scenarios

Agricultural intensification accelerates the degradation of cropland, and restoration has been managed by changing its vegetation. However, the keystone microbiome that drives the decomposition of plant-associated organic matter in the restoration is poorly understood. In this study, we established a 14-year field restoration experiment on a degraded cropland with four treatments: (1) bare land soil without biomass input (BL), (2) maize cropland (CL) without fertilization and biomass input, (3) natural grassland (GL), and (4) alfalfa cropland (AL) with biomass left in the fields. The activity of total soil microbiome was assessed by community-level physiological profiling (CLPP) with Biolog EcoPlates analysis, and keystone microbiome was identified as phylotypes showing statistically significant increase in the restored soils (GL and AL) relative to the degraded BL soil. The results showed that GL and AL treatments improved soil fertility as indicated by significant increase in soil organic carbon, total nitrogen, and available phosphorus when compared to BL treatment. The significant difference was not observed between CL and BL treatments except for pH and available phosphorus, indicating that the input and microbial decomposition of plant-associated organic matter were the key for restoration of soil fertility. Similar results were obtained for soil microbial activities of carbon utilization efficiency via CLPP analysis, and real-time quantitative polymerase chain reaction of 16S rRNA genes further revealed significantly higher abundance of total soil microbial community in GL and AL soils than in BL and CL. High-throughput sequencing of total 16S rRNA genes revealed the Bacteroidetes as the only keystone taxa at phylum level, and 106 and 120 genera were keystone phylotypes. Compared with BL and CL, the genera that increase significantly in GL and AL are called keystone genera of ecological restoration. The dominant keystone genera included Reyranella, Mesorhizobium, Devosia, Haliangium, Nocardioides, and Pseudonocardia. Significantly higher abundance of Bacillus genus in BL soil implied it might serve as an indicator of agricultural land degradation. Statistical analysis showed that soil organic carbon and pH were significantly correlated with the input of plant-associated organic matters and dynamic changes of keystone taxa. These results suggest that the vegetation of natural grass (GL) and alfalfa plant (AL) and subsequent decomposition of plant-associated materials could serve as effective strategies for restoration of the degraded cropland by stimulating the keystone microbiomes and improving their physiological metabolisms of carbon utilization efficiency.

Short term effects of biochar with different particle sizes on phosphorous availability and microbial communities

Despite the increasing interest for biochar as a soil amendment, a knowledge gap remains on different particle size of biochar on soil phosphorous (P) availability and its impacts on microbial community. We hypothesized that biochar particle size and incubation temperature can significantly influence soil P availability and microbial community in subtropical acidic soil. A laboratory incubation study was established to investigate the effects of soil pH, available P and soil microbial responses to biochar addition having varying particle sizes using paddy soil and red soil under different incubation temperatures (15 °C & 25 °C). Biochar produced via pyrolysis of spent mushroom substrate feedstock was sieved into three particle sizes ((≤0.5 mm (fine), 0.5-1.0 mm (medium) and 1.0-2.0 mm (large)). The results exhibited that the fine particle biochar resulted in significantly higher release of P, soil pH, available P and bacterial species richness while simultaneously reducing the activities of phosphatase enzyme in both soils. Apprehending the impact of biochar particle size and incubation temperature, principal coordinate analysis (PCoA) predicted that soil microbial communities with fine particle biochar and high incubation temperature (25 °C) clustered separately. Redundancy analysis depicted that fine particle biochar had a direct association with available P and soil pH while high incubation temperature depicted a strong affinity for microbial communities. Hence, it is suggested that fine particle biochar and high incubation temperature may provide better habitat for microorganisms compared to the other particle sizes which may be due to improved soil pH and available P. However, a long term study of different biochar particles application in subtropical acidic soil needs to be pursued further for a more comprehensive understanding on this issue.

Drought is a stronger driver of soil respiration and microbial communities than nitrogen or phosphorus addition in two Mediterranean tree species

The drivers of global change, such as increasing drought and nutrient deposition, are affecting soils and their microbial communities in many different habitats, but how these factors interact remains unclear. Quercus ilex and Pinus sylvestris are two important tree species in Mediterranean montane areas that respond differently to drought, which may be associated with the soils in which they grow. We measured soil respiration and physiologically profiled microbial communities to test the impact of drought and subsequent recovery on soil function and diversity for these two species. We also tested whether the addition of nitrogen and phosphorus modified these effects. Drought was the stronger driver of changes to the soil communities, decreasing diversity (Shannon index), and evenness for both species and decreasing soil respiration for Q. ilex when N was added. Soil respiration for P. sylvestris during the drought period was positively affected by N addition but was not affected by water stress. P addition during the drought period did not affect soil respiration for either tree species but did interact with soil-water content to affect community evenness for P. sylvestris. The two species also differed following the recovery from drought. Soil respiration for Q. ilex recovered fully after the drought treatment ended but decreased for P. sylvestris, whereas the soil community was more resilient for P. sylvestris than Q. ilex. Nutrient addition did not affect respiration or community composition or diversity during the recovery period. Soil respiration was generally weakly positively correlated with soil diversity. We demonstrate that short-term water stress and nutrient addition can have variable effects on the soil communities associated with different tree species and that the compositions of the communities can become uncoupled from soil respiration. Overall, we show that drought may be a stronger driver of changes to soil communities than nitrogen or phosphorus deposition.

High starter phosphorus fertilization facilitates soil phosphorus turnover by promoting microbial functional interaction in an arable soil

Microbial phosphorus (P) turnover is critical in C utilization efficiency in agroecosystems. It is therefore necessary to understand the P mobilization processes occurring during P fertilization in order to ensure both crop yield and environmental quality. Here, we established a controlled pot experiment containing soil amended with three different levels of starter P fertilizer and collected soil samples after 30, 60, and 90 days of incubation. Quantitative microbial element cycling (QMEC) smart chip technology and 16S rRNA gene sequencing were used to investigate functional gene structures involved in carbon, nitrogen and P cycling and the bacterial community composition of the collected samples. Although P fertilization did not significantly affect the structure of the soil microbial community, some rare microbiota were changed in particular phosphorus-solubilizing bacteria were enriched at the high P fertilization level, suggesting that the rare taxa make an important contribution to P turnover. P fertilization also altered the functional gene structure, and high P concentrations enhanced the functional gene diversity and abundance. Partial redundancy analysis further revealed that changes in rare taxa and functional genes of soil microorganisms drive the alteration of soil P pools. These findings extend our understanding of the microbial mechanisms of P turnover.

A four-year phytoremediation trial to decontaminate soil polluted by wood preservatives: phytoextraction of arsenic, chromium, copper, dioxins and furans

Widely used as wood preservatives for the last century, Pentachlorophenol (PCP) and chromated copper arsenate (CCA) have been shown to leach from treated surfaces and contaminate soil of wood storage sites. We performed a four-year field phytoremediation trial in southern Quebec (Canada) on a site contaminated with PCP and CCA with the following objectives: (1) assess the potential of willow, fescue, alfalfa and Indian mustard to tolerate and translocate CCA and PCP residues in their aerial tissues, (2) investigate the possibility of phytoextraction of dioxins and furans, and (3) test the effect of nitrogen fertilizer on phytoremediation performance. We showed that while nitrogen fertilization increased the chlorophyll content of plants, it did not result in a significantly greater plant biomass. We also showed that plants grown in the presence of PCP/CCA residues were able to translocate and concentrate trace elements in their aerial tissues, but also dioxins and furans (PCDD/F). This suggests that plants grown on sites polluted by PCP might contain dioxins and furans and should be treated as contaminated by these toxic chemicals. Finally, the reduction of soil contaminants at the end of the trial suggests that phytoremediation is a promising approach for decontaminating such sites.

Successive mineral nitrogen or phosphorus fertilization alone significantly altered bacterial community rather than bacterial biomass in plantation soil

Bacteria play determining roles in forest soil environment and contribute to essential functions in the cycling of nitrogen (N) and phosphorus (P). Understanding the effects of different fertilizer applications, especially successive fertilization, on soil properties and bacterial community could reveal the impacts of fertilization on forest soil ecology and shed light on the nutrient cycling in forest system. This study aimed to evaluate the impacts of successive mineral N (NH₄NO₃) and P (NaH₂PO₄) fertilization at different rates, alone or together, on soil bacterial biomass and communities at 0-5, 5-10, and 10-20 cm. Compared with the control, N fertilization decreased soil pH, but P alone or with N fertilization had negligibly negative impacts on soil pH. Different mineral fertilizer applications, alone or together, showed no significant effects on soil organic matter contents, relative to the control treatment. Bacterial biomass remained stable to different fertilizations but decreased with sampling depths. Sole N or P fertilization, rather than combined fertilizations, significantly changed soil bacterial community structures. Our results demonstrated that mineral N or P fertilization alone significantly affected bacterial community structures rather than biomass in the plantation soils. KEY POINTS: • Impacts of successive mineral fertilization on soil bacteria were determined. • Mineral fertilization showed negligible impacts on bacterial biomass. • N additions stimulated Chloroflexi relative abundances. • Mineral N or P fertilization significantly altered bacterial community structure.

High-yield grass Pennisetum sinese Roxb plantation and organic manure alter bacterial and fungal communities structure in an ecological agriculture farm

Pennisetum sinese Roxb (P. sinese) is an efficient and economic energy crop for its high productivity, and has been well studied in its application in phytoremediation and fodder production. However, little is known about how P. sinese plantation and fermented manures of P. sinese-feed livestock affect the composition of soil bacterial and fungal communities. In this study, 16S rRNA/ITS1 gene-based Illumina Miseq sequencing was employed to compare the bacterial and fungal community structure among soils that had been subjected to uncultivated control (CK), 2-year P. sinese plantation (P), and P. sinese plantation combined with the use of organic manures (P-OM) in a "P. sinese-breeding industry" ecological agriculture farm. The results found microbial communities were altered by P. sinese plantation and fertilization. The P. sinese plantation resulted in increased Actinobacteria and Planctomycetes abundance. Comparatively, significant increased abundance of Chloroflexi, Firmicutes, Nitrospirae, and Euryarchaeota, and genes related with nitrogen and carbon metabolic pathways based on PICRUSt prediction was observed in P-OM soil. Fungal compositions suggested a markedly increased abundance of Ascomycota in P soil. Potential organic matter decomposers Candida, Thermoascus, and Aspergillus were enriched in P soil, indicating the enhanced role of fungi in litter decomposition. Redundancy analysis suggested that soil properties (NH₄⁺-N, total nitrogen, organic matter content, and soil water content) significantly correlated with the changes of microbial compositions (P < 0.05). These results highlight the divergence of microbial communities occurs during P. sinese-based plantation, implying functional diversification of soil ecosystem in P. sinese fields.

Anthropogenic global shifts in biospheric N and P concentrations and ratios and their impacts on biodiversity, ecosystem productivity, food security, and human health

The availability of carbon (C) from high levels of atmospheric carbon dioxide (CO2 ) and anthropogenic release of nitrogen (N) is increasing, but these increases are not paralleled by increases in levels of phosphorus (P). The current unstoppable changes in the stoichiometries of C and N relative to P have no historical precedent. We describe changes in P and N fluxes over the last five decades that have led to asymmetrical increases in P and N inputs to the biosphere. We identified widespread and rapid changes in N:P ratios in air, soil, water, and organisms and important consequences to the structure, function, and biodiversity of ecosystems. A mass-balance approach found that the combined limited availability of P and N was likely to reduce C storage by natural ecosystems during the remainder of the 21st Century, and projected crop yields of the Millennium Ecosystem Assessment indicated an increase in nutrient deficiency in developing regions if access to P fertilizer is limited. Imbalances of the N:P ratio would likely negatively affect human health, food security, and global economic and geopolitical stability, with feedbacks and synergistic effects on drivers of global environmental change, such as increasing levels of CO2 , climatic warming, and increasing pollution. We summarize potential solutions for avoiding the negative impacts of global imbalances of N:P ratios on the environment, biodiversity, climate change, food security, and human health.

DNA Stable-Isotope Probing Delineates Carbon Flows from Rice Residues into Soil Microbial Communities Depending on Fertilization

Decomposition of crop residues in soil is mediated by microorganisms whose activities vary with fertilization. The complexity of active microorganisms and their interactions utilizing residues is impossible to disentangle without isotope applications. Thus, 13C-labeled rice residues were employed, and DNA stable-isotope probing (DNA-SIP) combined with high-throughput sequencing was applied to identify microbes active in assimilating residue carbon (C). Manure addition strongly modified microbial community compositions involved in the C flow from rice residues. Relative abundances of the bacterial genus Lysobacter and fungal genus Syncephalis were increased, but abundances of the bacterial genus Streptomyces and fungal genus Trichoderma were decreased in soils receiving mineral fertilizers plus manure (NPKM) compared to levels in soils receiving only mineral fertilizers (NPK). Microbes involved in the flow of residue C formed a more complex network in NPKM than in NPK soils because of the necessity to decompose more diverse organic compounds. The fungal species (Jugulospora rotula and Emericellopsis terricola in NPK and NPKM soils, respectively) were identified as keystone species in the network and may significantly contribute to residue C decomposition. Most of the fungal genera in NPKM soils, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded faster to residue addition than those in NPK soils. This is connected with the changes in the composition of the rice residue during degradation and with fungal adaptation (abundance and activity) to continuous manure input. Our findings provide fundamental information about the roles of key microbial groups in residue decomposition and offer important cues on manipulating the soil microbiome for residue utilization and C sequestration in soil.IMPORTANCE Identifying and understanding the active microbial communities and interactions involved in plant residue utilization are key questions to elucidate the transformation of soil organic matter (SOM) in agricultural ecosystems. Microbial community composition responds strongly to management, but little is known about specific microbial groups involved in plant residue utilization and, consequently, microbial functions under different methods of fertilization. We combined DNA stable-isotope (13C) probing and high-throughput sequencing to identify active fungal and bacterial groups degrading residues in soils after 3 years of mineral fertilization with and without manure. Manuring changed the active microbial composition and complexified microbial interactions involved in residue C flow. Most fungal genera, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded to residue addition faster in soils that historically had received manure. We generated a valuable library of microorganisms involved in plant residue utilization for future targeted research to exploit specific functions of microbial groups in organic matter utilization and C sequestration.

Alteration of soil nitrifiers and denitrifiers and their driving factors during intensive management of Moso bamboo (Phyllostachys pubescens)

Long-term intensive management, such as inorganic fertilization and soil tillage, have been reported to decrease soil organic carbon content (SOC) and diversity of soil bacterial communities, as well as increase N₂O emissions in moso bamboo forests. However, the response of the N-cycling soil microbial community to intensive management remains unclear. To address this, we examined the effects of intensive moso bamboo management on nitrifying and denitrifying microorganisms. Soils receiving non-management (NM) and 10, 15, 20, and 25 years of intensive management (IM10, IM15, IM20, IM25) were characterized using quantitative real-time PCR (qPCR) and high-through sequencing methods. Our results showed that abundances of ammonia monooxygenase (amoA) from ammonia-oxidizing archaea (AOA) significantly increased (P < 0.05) and were greatest in IM15 (8.37 × 10⁷ copies/g dry soils) and IM25 (5.42 × 10⁷ copies/g dry soils) in top- and subsoils, respectively, while nitrous oxide reductase (nosZ) abundance significantly decreased by 59.1% (topsoil) and 36.4% (subsoil) in IM20 (P < 0.05). GroupI.1a-associated affiliating to AOA, and Bradyrhizobium affiliating to nosZ, were keys groups for nitrifiers and denitrifiers, respectively, and showed the greatest variations in response to long-term intensive management. Abundances of ammonia-oxidizing bacteria (AOB) and the nitrite reductase gene nirS were less affected, as were the dominant Nitrosospira species belonging to the AOB community. Except the AOB amoA abundance, soil nitrogen was found to be the main factor influencing the abundance, diversity, and composition of nitrifying genes, while denitrifying genes were mainly affected by SOC and available potassium, indicating that different factors control populations of nitrifiers and denitrifiers. Collectively, our study revealed that groupings of nitrifying and denitrifying microorganisms responded differently to intensive management. This information is of potential value towards identifying strategies to minimize nitrogen loss in moso bamboo plantations.

Rhizoplane Bacteria and Plant Species Co-determine Phosphorus-Mediated Microbial Legacy Effect

Much effort has been directed toward increasing the availability of soil residual phosphorus (P). However, little information is available for the P fertilization-induced biotic P legacy and its mediation of plant P uptake. We collected microbial inocula from a monoculture maize field site with a 10-year P-fertilization history. A greenhouse experiment was conducted to investigate whether bacterial communities, as a result of different P-fertilization history (nil P, 33 and/or 131 kg P kg ha-1 yr-1), affected the growth of a conspecific (maize) or heterospecific (clover) plant, at two levels of current P application (5 and 30 mg P kg-1 soil; P5 and P30). Deep amplicon sequencing (16S rRNA) was used to determine the maize and clover root-associated bacterial microbiome in different rhizocompartments (rhizoplane, rhizosphere, bulk soil). For both maize and clover, rhizocompartment and host identity were the dominant factors shaping bacterial assemblages, followed by P supply level and the inoculum effect was smallest. Bacterial operational taxonomic unit (OTU) numbers decreased from bulk soil to rhizoplane, whilst specific OTUs were enriched from bulk soil to rhizoplane. A clear hierarchical habitat filtering of bacterial communities was observed in the rhizoplane of the two plant species. The functional prediction of dominant bacterial taxa in the rhizoplane differed between clover and maize, and clover microbiota were more closely associated with P metabolism and maize with carbon cycling. More connected and complex interactions were observed in the clover rhizoplane compared to maize. The microbial legacy effect caused by long-term P fertilization is overridden by host identity and rhizocompartment. Our results highlight the importance of crop diversification in improving P efficiency. The fine-tuning of rhizosphere microbiome in host metabolism indicates that the functions of microbial communities should be integrated into P management to increase P use efficiency and sustainable food production.

Bacteria with Different Assemblages in the Soil Profile Drive the Diverse Nutrient Cycles in the Sugarcane Straw Retention Ecosystem

Straw retention, an alternative to artificial fertilization, commonly mitigates soil degradation and positively affects soil fertility. In this study, we investigated the succession of soil bacteria during two sugarcane straw retention treatments (control (CK) and sugarcane straw retention (SR)) and at four depths (0–10, 10–20, 20–30, and 30–40 cm) in fallow soil in a sugarcane cropping system. Using an Illumina MiSeq (16S rRNA) and soil enzyme activity, we explored the SR influence on soil bacterial communities and enzyme activities and its inclusive impact on soil fertility, with an emphasis on topsoil (0–10 cm) and subsoil (10–40 cm). Our results show that SR effectively improved soil fertility indicators (C, N, and P), including enzyme activities (C and N cycling), throughout the soil profile: these soil parameters greatly improved in the topsoil compared to the control. Sugarcane straw retention and soil depth (0–10 cm vs. 10–40 cm) were associated with little variation in bacterial species richness and alpha diversity throughout the soil profile. Subsoil and topsoil bacterial communities differed in composition. Compared to the CK treatment, SR enriched the topsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, and Nitrospirae, while the subsoil was depleted in Nitrospirae and Acidobacteria. Similarly, SR enriched the subsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes, while the topsoil was depleted in Acidobacteria, Gemmatimonadetes, and Planctomycetes compared to the CK. At the genus level, SR enriched the topsoil with Gp1, Gp2, Gp5, Gp7, Gemmatimonas, Kofleria, Sphingomonas, and Gaiella, which decompose lignocellulose and contribute to nutrient cycling. In summary, SR not only improved soil physicochemical properties and enzyme activities but also enriched bacterial taxa involved in lignocellulosic decomposition and nutrient cycling (C and N) throughout the soil profile. However, these effects were stronger in topsoil than in subsoil, suggesting that SR enhanced fertility more in topsoil than in subsoil in fallow land.

Microbial Community Structures and Important Associations Between Soil Nutrients and the Responses of Specific Taxa to Rice-Frog Cultivation

Rice-frog cultivation is a traditional farming system in China and has been reintroduced as an agricultural practice in China in recent years. The microbial community in paddy rhizospheric soils has attracted much attention because many microorganisms participate in functional processes in soils. In this study, Illumina MiSeq sequencing-based techniques were used to investigate soil microbial communities and functional gene patterns across samples obtained by conventional rice cultivation (CR) and rice-frog cultivation (RF). The results showed that RF significantly affected the microbial community composition and richness, which indicated that the rhizospheric microorganisms responded to the introduction of tiger frogs into the paddy fields. Operational taxonomic units (OTUs) from Sandaracinaceae, Anaerolineaceae, Candidatus Nitrososphaera, Candidatus Nitrosotalea, Candidatus Nitrosoarchaeum and some unclassified OTUs from Euryarchaeota and Agaricomycetes were significantly enriched by RF. The abiotic parameters soil organic carbon (SOC), nitrate nitrogen (NO3 --N), and available phosphorus (AP) changed under RF treatment and played essential roles in establishing the soil bacterial, archaeal, and fungal compositions. Correlations between environmental factors and microbial communities were described using network analysis. SOC was strongly correlated with Anaerolineaceae, Methanosaeta, and Scutellinia. NO3 --N showed strong positive correlations with Opitutus, Geobacter, and Methanosaeta. NH4 ++-N was strongly positively associated with Sideroxydans, and TN was strongly positively correlated with Candidatus Nitrotoga. Compared to conventional CR, RF greatly enriched specific microbial taxa. These taxa may be involved in the decomposition of complex organic matter and the transformation of soil nutrients, thus promoting plant growth by improving nutrient cycling. The unique patterns of microbial taxonomic and functional composition in soil profiles suggested functional redundancy in these paddy soils. RF could significantly affect the bacterial, archaeal, and fungal communities though changing SOC and AP levels.

Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests

Subtropical broadleaved forests play a crucial role in supporting terrestrial ecosystem functions, but little is known about their belowground soil fungal communities despite that they have central functions in C, N, and P cycles. This study investigated the structures and identified the drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests, using high-throughput sequencing and FUNGuild for fungal identification and assignment to the trophic guild. Fungal richness was much higher in the deciduous than in the evergreen forest. Both forests were dominated by Ascomycota and Basidiomycota phyla, but saprophytic fungi were more abundant in the deciduous forest and ectomycorrhizal fungi predominated in the evergreen forest. Fungal communities had strong links to plant and soil properties. Specifically, plant diversity and litter biomass were the main aboveground drivers of fungal diversity and composition in the deciduous forest, while host effects were prominent in the evergreen forest. The belowground factors, i.e., soil pH, water content, and nutrients especially available P, were identified as the primary drivers of soil fungal communities in the broadleaved forests. Co-occurrence network analysis revealed assembly of fungal composition in broadleaved forest soils was non-random. The smaller modularity of the network in the deciduous forest reflects lower resistance to environment changes. Concluding, these results showed that plant community attributes, soil properties, and potential interactions among fungal functional guilds operate jointly on the divergence of soil fungal community assembly in the two broadleaved forest types.

Divergent responses of bacterial activity, structure, and co-occurrence patterns to long-term unbalanced fertilization without nitrogen, phosphorus, or potassium in a cultivated vertisol

Unbalanced fertilization lacking nitrogen (N), phosphorus (P), or potassium (K) is a worldwide phenomenon; however, whether they affect bacterial community composition and intraspecific interactions in a similar pattern and how they affect bacterial activity are not systematically compared. Soils under different kinds of unbalanced fertilization in a 21-year field experiment were collected to investigate the variation in dehydrogenase activity (DHA), bacterial community diversity, structure, composition, and possible interactions. Compared to the balanced fertilization of NPK, the DHA from unbalanced fertilization of NP, PK, and NK was 8.70, 11.59, and 14.17% lower, respectively, and from the unfertilized treatment (Nil) was 13.41% lower; however, the Shannon index from NP, PK, and Nil was 4.48-7.21% higher and from NK was 3.95% lower. Based on principal coordinate analyses (PCoA), bacterial community structure was separated by N application or not along PCo1 and was further separated by P application or not along PCo2, indicating a more influence by N deficiency. Moreover, the structure was mainly determined by soil pH, soil organic carbon (SOC), and total phosphorus (TP). The network complexity using co-occurrence analysis followed the order NP > NPK > PK > NK > Nil, indicating a more influence by P deficiency on intraspecific interactions. Structural equation modeling (SEM) revealed that the reduced DHA in NP was mainly regulated by the decreased SOC and increased Shannon index, in PK by the decreased SOC and increased Shannon index and pH, and in NK by the decreased SOC and TP and increased PCo2. The significantly lower abundance of Bacteroidetes and Chitinophagaceae in NK may also contribute to the reduced DHA. Our results imply that N deficiency had the greatest impact on bacterial community structure and composition, P deficiency had the greatest impact on network construction and bacterial activity, and K deficiency has minimal effect. Our results also suggest that main factors regulating the variation in soil functions may vary among different nutrient deficiencies.