Plant Growth-Promoting Rhizobacteria as Tools to Improve the Growth of Kohlrabi (Brassica oleracea var. gongylodes) Plants in an Aquaponics System.

The use of nitrogen as a fertilizer can be highly risky when used excessively, and it is therefore necessary to find novel techniques to reduce its use. Aquaponics reduces the use of synthetic fertilizers and water, and the leaching of nitrate into the environment. One way to avoid problems due to a reduction in nitrogen availability could be the use of plant growth promoting rhizobacteria (PGPR). This study examines the effect of PGPR on kohlrabi plants grown with a traditional nutrient solution (100S), in combination with "fish water" (50F/50D), or with a supplement of synthetic fertilizers (50F/50D + S). Two formulations were used: T1 (Azospirillum brasilense and Pantoea dispersa) and T2 (Azotobacter salinestris). Irrigation with 50F/50D caused a reduction in several of the measured parameters. The combined application of 50F/50D with T1 attenuated the negative effects. T2 did not present significant effects on the parameters measured. The results obtained with 50F/50D + S hardly showed differences with the 100S. Thus, by irrigating with 50F/50D + S, we were able to maintain the yields while reducing fertilizer use and water. The combined use of T1 and 50F/50D was also positive; however, it would be necessary to continue adjusting the amount of nitrate supplied to maintain production.

Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils.

Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.

Phosphorus extractors in soil under no-tillage system with 19 years of swine manure applications.

The objective of this study was to evaluate the availability of phosphorus (P) in a soil under no-tillage system after successive applications of liquid swine manure (LSM) doses in soil samples collected at different depths and to select the most appropriate chemical extractors. It was used soil with LSM applications for 19 years, using doses of 0, 25, 50, 75 and 100 m3 ha-1 and mineral fertilization (350 kg ha-1 in formulation 02-20-18), evaluated at the following depths: 0-10, 10-20 and 20-40 cm. The extractors used were Mehlich-1, Mehlich-3, Prem, Olsen, Bray-1 and Resin. Successive fertilizations with LSM, especially with 100 m3 ha-1, increase the availability of P, especially in the 0-10 cm layer, as well adding P in the deeper layers evaluated (20-40 cm). The organic P content in relation to the total P ranged from 16 to 19 %. Bray-1, Olsen and Resin extractors are more efficient in extracting P in soil under no-tillage cultivation after successive fertilizations with liquid swine manure.

Deciphering the biotic and abiotic drivers of coalescence asymmetry between soil and manure microbiomes.

Manure application improves soil fertility, yet its implications on the success of invasion of manure-borne microorganisms in the soil are poorly understood. Here, we assessed the importance of abiotic and biotic factors in modulating the extent to which manure-borne fungal and bacterial communities can invade resident soil microbial communities. For this purpose, we applied varying frequencies of two different amounts of manure to nine soils differing in physico-chemical properties, as well as in land-use history, over 180 days and monitored changes in bacterial and fungal communities. Variance partitioning revealed differential contributions of abiotic and biotic factors to invasion success, which together accounted for up to 82 % of the variance explained. We showed that the effects of interactions between biotic and abiotic factors increased with coalescence frequency and manure amount for the bacterial and fungal communities, respectively. Both abiotic and biotic factors were important for modulating coalescence asymmetry for the bacterial community, whereas abiotic factors had a greater effect on the fungal community. These results provide new insights into the drivers of coalescence events between manure and resident soil microbial communities. Moreover, our findings highlight the roles of the mixing ratio and frequency of coalescence events in modulating the survival of manure-borne microorganisms.

Seeds Act as Vectors for Antibiotic Resistance Gene Dissemination in a Soil-Plant Continuum.

Though the evidence for antibiotic resistance spread via plant microbiome is mounting, studies regarding antibiotic resistome in the plant seed, a reproductive organ and important food resource, are still in their infancy. This study investigated the effects of long-term organic fertilization on seed bacterial endophytes, resistome, and their intergenerational transfer in the microcosm. A total of 99 antibiotic resistance genes (ARGs) and 26 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR. The amount of organic fertilizer applied was positively correlated to the number and relative abundance of seed-associated ARGs and MGEs. Moreover, the transmission of ARGs from the rhizosphere to the seed was mainly mediated by the shared bacteria and MGEs. Notably, the rhizosphere of progeny seedlings derived from seeds harboring abundant ARGs was found to have a higher relative abundance of ARGs. Using structural equation models, we further revealed that seed resistome and MGEs were key factors affecting the ARGs in the progeny rhizosphere, implying the seed was a potential resistome reservoir for rhizosphere soil. This study highlights the overlooked role of seed endophytes in the dissemination of resistome in the soil-plant continuum, and more attention should be paid to plant seeds as vectors of ARGs within the "One-Health" framework.

Migration from inorganic to organic fertilization for a more sustainable oil palm agro-industry.

The rapid growth in oil palm production has raised environmental concerns due to the massive discharge of liquid and solid waste. To address this issue, waste generated need to be optimized by composting and converting the waste into organic fertilizer. The practice of pure inorganic fertilization must also be discontinued due to the rising cost of imported fertilizers and their detrimental effect on the soil. Furthermore, several studies have established that recycling self-produced organic waste as fertilizer is an excellent method to achieve sustainability. Therefore, this study investigates a significant response to organic fertilization treatment. The bioorganic empty fruit bunch (EFB) compost was tested on Podzols soil (Typic Placorthods) in the nursery and in the young mature stage of the palm that was treated from the beginning of planting. The results showed that organic fertilization using low and high concentrations of fresh and composted EFB had a more significant effect on seedling growth. A high dose of composted EFB positively affected the N and K content of the leaf. Composted EFB had added value, especially in improving soil chemical properties and assimilation of N nutrients by oil palm seedlings, especially Podzols (Typic Placorthods). Pure inorganic fertilization on Podzols (Typic Placorthods) could not have been more practical due to inadequate nutrient uptake. Composted EFB had a positive effect superior that of the fresh EFB on the chemical composition of the soil, such as improving the saturation rate of the cation exchange capacity and the exchangeable K and Mg. Fresh EFB was good, but composted EFB was better for maintaining yield and less attractivity to Oryctes, which is essential in replanting.

Meta-Analysis of Organic Fertilization Effects on Soil Bacterial Diversity and Community Composition in Agroecosystems.

Application of organic fertilizers or their combination with chemical fertilizers is a feasible practice for improving soil fertility and reducing soil degradation in agroecosystems, and these regulations are mainly mediated though soil microbial communities. Despite bacteria ranking among the most abundant and diverse groups of soil microorganisms, the effects of long-term organic fertilization (OF) and chemical-organic fertilization (COF) on soil bacterial diversity and community composition remain unclear. In this study, we conducted a meta-analysis and demonstrated that OF had no significant effect on bacterial alpha diversity. Application of chemical fertilizer and crop residue significantly decreased bacterial Richness index. Both OF and COF significantly altered bacterial community structure, with these changes being predominately attributed to shifts in soil pH. For bacterial phyla, both OF and COF significantly increased the relative abundance of Proteobacteria and Bacteroidetes, suggesting that OF and COF may cause the enrichment of copiotrophic taxa. In addition, COF significantly increased the relative abundance of Gammaproteobacteria but decreased the relative abundance of Acidobacteria. Overall, our results suggest that organic and chemical-organic fertilization can effectively maintain bacterial diversity and enhance soil fertility in agroecosystems, and the alteration of soil bacterial community structure is closely intertwined with soil pH.

Agronomic performance and remote sensing assessment of organic and mineral fertilization in rice fields.

Introduction: Rice heavily relies on nitrogen fertilizers, posing environmental, resource, and geopolitical challenges. This study explores sustainable alternatives like animal manure and remote sensing for resource-efficient rice cultivation. It aims to assess the long-term impact of organic fertilization and remote sensing monitoring on agronomic traits, yield, and nutrition. Methods: A six-year experiment in rice fields evaluated fertilization strategies, including pig slurry (PS) and chicken manure (CM) with mineral fertilizers (MIN), MIN-only, and zero-fertilization. Traits, yield, spectral responses, and nutrient content were measured. Sentinel-2 remote sensing tracked crop development. Results: Cost-effective organic fertilizers (PS and CM) caused a 13% and 15% yield reduction but still doubled zero-fertilization yield. PS reduced nitrogen leaching. Heavy metals in rice grains were present at safe amounts. Organic-fertilized crops showed nitrogen deficiency at the late vegetative stages, affecting yield. Sentinel-2 detected nutrient deficiencies through NDVI. Discussion: Organic fertilizers, especially PS, reduce nitrogen loss, benefiting the environment. However, they come with yield trade-offs and nutrient management challenges that can be managed and balanced with reduced additional mineral applications. Sentinel-2 remote sensing helps manage nutrient deficiencies. In summary, this research favors cost-effective organic fertilizers with improved nutrient management for sustainable rice production.

Cannabis Hunger Games: nutrient stress induction in flowering stage - impact of organic and mineral fertilizer levels on biomass, cannabidiol (CBD) yield and nutrient use efficiency.

Indoor medicinal cannabis cultivation systems enable year-round cultivation and better control of growing factors, however, such systems are energy and resource intensive. Nutrient deprivation during flowering can trigger nutrient translocation and modulate the production of cannabinoids, which might increase agronomic nutrient use efficiency, and thus, a more sustainable use of fertilizers. This experiment compares two fertilizer types (mineral and organic) applied in three dilutions (80, 160 and 240 mg N L-1) to evaluate the effect of nutrient deprivation during flowering on biomass, Cannabidiol (CBD) yield and nutrient use efficiency of N, P and K. This is the first study showing the potential to reduce fertilizer input while maintaining CBD yield of medicinal cannabis. Under nutrient stress, inflorescence yield was significantly lower at the final harvest, however, this was compensated by a higher CBD concentration, resulting in 95% of CBD yield using one-third less fertilizer. The higher nutrient use efficiency of N, P, and K in nutrient-deprived plants was achieved by a larger mobilization and translocation of nutrients increasing the utilization efficiency of acquired nutrients. The agronomic nutrient use efficiency of CBD yield - for N and K - increased 34% for the organic fertilizers and 72% for the mineral fertilizers comparing the dilution with one-third less nutrients (160) with the highest nutrient concentration (240). Differences in CBD yield between fertilizer types occurred only at the final harvest indicating limitations in nutrient uptake due to nutrient forms in the organic fertilizer. Our results showed a lower acquisition and utilization efficiency for the organic fertilizer, proposing the necessity to improve either the timing of bio-availability of organic fertilizers or the use of soil amendments.

Flooding drives the temporal turnover of antibiotic resistance gene in manure-amended soil-water continuum.

Rice paddy soil is a hotspot of antibiotic resistance genes (ARGs) due to the application of organic fertilizers. However, the temporal dynamics of ARGs in rice paddy soil and its flooded water during the growing season remain underexplored. In this study, a microcosm experiment was conducted to explore the ARG profiles in a long term (130 days) flooded two-phase manure-amended soil-water system. By using high-throughput quantitative PCR array, a total of 23-98 and 34-85 ARGs were detected in the soil and overlying water, respectively. Regression analysis exhibited significant negative correlations between ARG profile similarities and flooding duration, indicating that flooding significantly altered the resistome (P < 0.001). This finding was validated by the increased ARG abundance in the soil and the overlying water, for example, after 130 days flooding, the abundance of ARGs in CK soil was increased from 0.03 to 1.20 copies per 16S rRNA. The PCoA analysis further suggested pig manure application resulted in distinct ARG profiles in the soil-water continuum compared with those of the non-amended control (Adonis, P < 0.05). The Venn diagram showed that all ARGs detected in the pig manure were present in the treated soil. Twelve ARGs (e.g., sul1) were shared among the pig manure, manure-amended soil, and overlying water, indicating that certain manure- or soil-borne ARGs were readily dispersed from the soil to the overlying water. Moreover, the enhanced relationships between the ARGs and mobile genetic elements in pig manure applied soil-water continuum indicate that the application of organic matter could accelerate the emergence and dissemination of ARGs. These findings suggested that flooding represents a crucial pathway for dispersal of ARGs from the soil to the overlying water. Identification of highly mobile ARGs in the soil-water continuum is essential for assessing their potential risk to human health and promoting the development of sustainable agricultural practices to mitigate their spread.

Organic fertilization integrated with water management to remediate As and Cd contamination in a paddy soil.

Soil heavy metal pollution is the main risk for sustainable agriculture, especially the combination of As and Cd pollution in paddy fields which may lead to the superimposed accumulation in rice. There is an urgent need for environmental-friendly and cost-effective strategies to remediate the contamination of As and Cd in soils. In this work, a pot culture experiment was conducted in a As and Cd polluted paddy soil to explore the effects of organic fertilization (OF) and two water managements (continuous flooding, CF; intermittent irrigation, II) on the fractionation of As and Cd in soil, and the uptake of As and Cd by rice. The results showed that OF integrated with intermittent irrigation performed best in reducing the contents of As and Cd in rice grains by 58.9 % and 69.3 %, respectively, under compound pollution. The significant conversion of available As and Cd to stable species (specifically adsorbed and Fe-Mn/Al oxide bound) under OF + II were supported by the changes in an array of soil attributes such as pH, Eh, soluble Fe and dissolved organic carbon (DOC). Intermittent irrigation was more conducive to the accumulation of As outside the roots, and Fe-plaque prevented As uptake by roots and the translocation to shoots. While more accumulation of Fe-plaque along with Cd on root surface induced by continuous flooding is helpful for depressed assimilation of Cd by rice. Considering the combined contamination of As and Cd polluted in paddy soils, a management approach was proposed based on intermittent irrigation and application of organic fertilizer at the rate of 0.1 % (∼ 2.3 t/ha) in two phases (two weeks before planting or drainage). Organic fertilization will hold great promise in restoring polluted soils and maintaining soil health via suppressing the lability of heavy metals and providing nutrients.

Sewage sludge application stimulated soil N2O emissions with a low heavy metal pollution risk in Eucalyptus plantations.

Sewage sludge (SS) has been extensively used as an alternative fertilizer in forest plantations, which are beneficial in supplying timbers and mitigating climate change. However, whether the extra nitrogen (N) applied by SS would enhance the soil nitrous oxide (N2O) emission, an important greenhouse gas, in forest plantations have not been well understood. The objective of this study is to evaluate the ecological effects of SS application on soils, by investigating the soil N2O emission and the toxicity of the potentially toxic elements (PTEs) in soil. A field fertilization experiment was conducted in Eucalyptus plantations with four fertilization rates (0 kg m-2, 1.5 kg m-2, 3.0 kg m-2, and 4.5 kg m-2). The soil N2O emissions were monitored at a soil depth of 0-10 cm using static chamber method, soil chemical properties, and PTEs were determined at soil depths of 0-10 cm, 10-20 cm, and 20-40 cm. The average soil N2O emission rate was 8.1 µg N2O-N h-1 m-2 in plots without SS application (control). The application of SS significantly increased the soil N2O emissions by 7-10 times as to control. The increased N2O emissions were positively related to the soil total phosphorus and nitrogen and negatively correlated with copper and zinc, which increased with the SS application. However, the potential ecological risk index (Ei) and the comprehensive potential ecological risk index (RI) of PTEs were lower than 40 and 150 respectively, which indicating a low toxicity of PTEs to soil health. After seven months of SS application, the priming effects of SS on soil N2O emissions gradually diminished. These findings suggest that the application of SS may increase N2O emissions at the initial stages of application (<7 months) and may have a low PTEs pollution risk, even at a high SS addition rate (4.5 kg m-2).

N-Source Determines Barley Productivity, Nutrient Accumulation, and Grain Quality in Cyprus Rainfed Agricultural Systems.

The Eastern Mediterranean and Middle East (EMME) region is already experiencing the negative effects of increased temperatures and the increase in prolonged drought periods. The use of organic fertilization could be a valuable tool to meet the main challenges of climate change and maintain the productivity, quality, and sustainability of rainfed agricultural ecosystems. In the current study, we compare the effect of manure, compost, and chemical fertilization (NH4NO3) on barley grain and straw yield in a field study for three consecutive growing seasons. The hypothesis that the barley productivity, nutrient accumulation, and grain quality remain similar among the different nutrient management strategies was tested. The results showed that both growing season and type of nutrient source significantly affected barley grain and straw yield (F6,96 = 13.57, p < 0.01). The lowest productivity was noticed in the non-fertilized plots while chemical and organic fertilization exhibited similar grain yield, ranging from 2 to 3.4 t/ha throughout the growing seasons. For straw, the use of compost had no effect on the yield in any of the growing seasons examined. The use of manure and compost had a significant effect on grain macro- and micronutrient content but this was highly related to growing season. Principal component analysis (PCA) clearly demonstrated the discrimination of the different type of fertilization on barley performance during the course of the study, while the application of compost was highly associated with an increase in micronutrients in grain samples. Furthermore, structural equational modeling (SEM) showed that both chemical and organic fertilization had a direct positive effect on macro- (r = 0.44, p < 0.01) and micronutrient (r = 0.88, p < 0.01) content of barley grain and a positive indirect effect on barley productivity through N accumulation in grain (ß = 0.15, p = 0.007). The current study showed that barley grain and straw yield was similar between manure and NH4NO3 treatments, while compost exhibited a residual positive effect causing an increase in grain yield during the growing season. The results highlight that N fertilization under rainfed conditions is beneficial to barley productivity through its indirect effects on N accumulation in grain and straw, while it improves grain quality through the increased accumulation of micronutrients.

Changes in bacterial diversity, co-occurrence pattern, and potential pathogens following digestate fertilization: Extending pathogen management to field for anaerobic digestion of livestock manure.

Digestate can spread pathogens into agroecosystem, posing serious threats to public health. However, the effect of digestate fertilization on digestate- or soil-borne pathogens has not been fully explored. Herein, two settings of microcosm experiment were performed with arable soil and digestate collected at two sites (Beilangzhong or Shunyi) to dissect the succession of the total and potential pathogenic bacterial communities following digestate fertilization. Each experimental setting consisted of three treatments, including digestate aerobically incubated in sterilized soil, and soil amended with sterilized or non-sterilized digestate. Digestate-borne potential pathogenic bacteria were enriched after the aerobic incubation, with Streptococcus sobrinus in the Beilangzhong setting, and Escherichia coli and Enterococcus faecium in the Shunyi setting. Potential soil-borne pathogenic bacteria, such as Acinetobacter lowffii and Pseudomonas fluorescens, were stimulated by the sterilized digestate in the Shunyi setting. Interestingly, S. sobrinus, E. coli, and Ent. faecium did not increase when digestate was amended into the non-sterilized soil, suggesting that soil microorganisms can inhibit the resurgence of these digestate-borne pathogens. A large-scale survey further revealed that organic fertilization exerted a site-dependent effect on different species of potential pathogen, but it did not enrich the total relative abundance of potential pathogenic bacteria in soils. Collectively, these results highlight that pathogen management of anaerobic digestion of livestock manure needs to be extended from anaerobic reactor to field.

Long-term application of organic compost is the primary contributor to microplastic pollution of soils in a wheat-maize rotation.

Microplastics (MPs) are posing new threats to soil ecosystems. Organic fertilizers are considered as an emerging contributor to MPs accumulation in agricultural soils. However, few studies have focused on the MPs fate in soils under long-term organic fertilizer application. Based on an 11-year field test with wheat-maize cropping rotation, this study investigated the characteristics of MPs in pig manure and cow manure composts, and examined the impact of long-term compost application on soil MPs accumulation, surface morphology, and distribution. The MPs contents in pig manure and cow manure composts were 3547 and 4520 items kg-1, respectively. Microplastics abundances in soils under long-term use of these two composts were 144 to 287 and 140 to 316 items kg-1, respectively, which increased significantly with increasing compost application amount and was substantially higher than that in soils without compost. Accumulated soil MPs sourced from long-term compost application were 1.73 × 108 to 7.22 × 108 items ha-1, accounting for 43.0 %-75.9 % of the total, and the contribution value doubled as the compost application rate doubled. The proportion of MPs <1 mm in composts (31.0 %) was lower when compared with that in compost-amended soils (43.8 %), and size and abundance reduced with increasing soil depth. Microplastics shapes and polymer types in composts and compost-amended soils were similar and mostly included fragments of polyethylene and polypropylene and fibers of polyethylene terephthalate. Microplastics in compost-amended soils showed complicated weathered surface morphologies, and soil mineral colloids were attached. These results demonstrate that compost-derived MPs in soils can be gradually weathered and degraded into smaller particles under long-term compost application. These findings provide key insights into the pollution level of soil MPs with organic fertilizer application and serve as a scientific basis for developing MPs mitigation measures in agricultural soils.

Organic fertilization enhances the resistance and resilience of soil microbial communities under extreme drought.

INTRODUCTION: The soil bacterial microbiome plays a crucial role in ecosystem functioning. The composition and functioning of the microbiome are tightly controlled by the physicochemical surrounding. Therefore, the microbiome is responsive to management, such as fertilization, and to climate change, such as extreme drought. It remains a challenge to retain microbiome functioning under drought. OBJECTIVES: This work aims to reveal if fertilization with organic fertilizer, can enhance resistance and resilience of bacterial communities and their function in extreme drought and subsequent rewetting compared with conventional fertilizers. METHODS: In soil mesocosms, we induced a long-term drought for 80 days with subsequent rewetting for 170 days to follow bacterial community dynamics in organic (NOF) and chemical (NCF) fertilization regimes. RESULTS: Our results showed that bacterial diversity was higher with NOF than with NCF during drought. In particular, the ecological resilience and recovery of bacterial communities under NOF were higher than in NCF. We found these bacterial community features to enhance pathogen-inhibiting functions in NOF compared to NCF during late recovery. The other soil ecology functional analyses revealed that bacterial biomass recovered in the early stage after rewetting, while soil respiration increased continuously following prolonged time after rewetting. CONCLUSION: Together, our study indicates that organic fertilization can enhance the stability of the soil microbiome and ensures that specific bacterial-driven ecosystem functions recover after rewetting. This may provide the basis for more sustainable agricultural practices to counterbalance negative climate change-induced effects on soil functioning.

Soiltesting formula fertilization with organic fertilizer addition for target yield cannot stand long due to stem lodging of rice.

Introduction: Soil testing formula fertilization using organic fertilizer (STFFOF)could increase grain yields and protect the ecological environment but the potential risks of STFFOF remains unclear. Methods: In order to assess the risk on rice stem lodging, a STFFOF field experiment is conducted continuously for 11 years. Results: After 11 years of continuous STFFOF treatment, the stem lodging rate of rice substantially increases by 81.1%*, which completely overweigh its increase in yield. Further research found that STFFOF greatly decreases the concentration of Ca, SiO2, K, Mg, and non-structural carbohydrates in basal internodes, dramatically increases that of N, P, and weight per ear, but slightly affects the structural carbohydrates. The strong correlations imply the increasement in weight per ear, N, and P concentrations, and the significant decrease in starch in the basal internodes might directly increase the brittleness of stem internodes and further cause severe stem lodging and yield loss of rice. Discussion: Results suggest that the potential risks of rice production including stem lodging must be considered when adopting the excessive exploration mode of productivity technology of paddy fields.

Watermelon responds to organic fertilizer by enhancing root-associated acid phosphatase activity to improve organic phosphorus utilization.

Organic fertilizer is commonly used to increase crop yields and improve soil quality. However, it is unclear whether crops adapt to organic fertilizer by regulating metabolic pathways that are involved in nutrient utilization. In this study, we focused on the organic phosphorus (Po) in organic fertilizer and, using watermelon, investigated changes in gene expression and metabolic pathways in response to organic fertilizer and the combination of chemical fertilizer and organic fertilizer (chemical fertilizer 70% and organic fertilizer 30%, based on phosphorus supply). Purple acid phosphatase (PAP) gene expression was upregulated in leaves and roots of watermelon grown in organic fertilizer alone and in the combination of chemical/organic fertilizer, resulting in enhanced phosphatase activity in roots. When the ratio of chemical to organic fertilizer was 85/15, root-associated acid phosphatase (APase) activity increased over chemical fertilizer alone. This formulation also resulted in increased inorganic phosphate (Pi) concentration in roots and leaves, and the upregulation of the secretory APase genes ClaPAP10/12/15/26, and ClaPAP18 in roots. In conclusion, watermelon responds to organic fertilizer by upregulating expression of secretory ClaPAP genes, subsequently enhancing root-associated APase activity further improving the hydrolysis of phosphomonoesters, and ultimately facilitating Po utilization by roots. The mechanisms of P utilization by roots comprise the enhancement of APase and phytase activity, absorption of small Po molecules, uptake of Pi, and the increase of lateral root number when organic fertilizer is applied to the plants. These findings help to establish the mechanisms by which plants respond to organic fertilizer by regulating metabolic pathways at the transcriptional level.

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

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

Effects of organic fertilization on functional microbial communities associated with greenhouse gas emissions in paddy soils.

Soil microbial communities play a key role in the biochemical processes and nutrient cycles of the soil ecosystem and their byproducts, including greenhouse gases (GHGs). Organic fertilization influences bacterial soil biodiversity and is an essential emission source of GHGs in paddy soil ecosystems. However, the impact of organic fertilization on the functional microorganisms associated with the GHGs methane and nitrous oxide remains unknown. We conducted paddy soil field experiments under three different treatments (no fertilization, base fertilization, and organic fertilization) to investigate the contribution of organic fertilization to soil nutrients and the functional microorganisms associated with GHG emissions. We found that organic fertilization effectively increased the soil organic matter (P < 0.001), soil organic carbon (P < 0.001), and total nitrogen (P < 0.05) as well as the richness (operational taxonomic units and abundance-based coverage estimators) of the methanogenic communities. Correlation analyses showed that methanogenic communities that were present in abundance were more vulnerable to perturbations in soil properties compared to nitrifying bacterial communities. Partial least squares path model analyses elucidated that organic fertilization directly affected both methanogenic communities and nitrifying bacterial communities (P < 0.05), thereby accelerating methane emissions. Strong co-occurrence networks were observed within the soil-dominant phyla Acidobacteria, Bacteroidetes, and Proteobacteria. Our findings highlight the impact of organic fertilization on soil nutrients and functional microorganisms and guide mitigating GHG emissions from paddy soil agroecosystems.