Mitigation of nitrous oxide emissions from acidic soils by Bacillus amyloliquefaciens, a plant growth-promoting bacterium

The microbial-driven nitrogen cycle and its relevance for plant nutrition

Nitrogen (N) is a vital nutrient and an essential component of biological macromolecules such as nucleic acids and proteins. Microorganisms are major drivers of N-cycling processes in all ecosystems, including the soil and plant environment. The availability of N is a major growth-limiting factor for plants and it is significantly affected by the plant microbiome. Plants and microorganisms form complex interaction networks resulting in molecular signaling, nutrient exchange, and other distinct metabolic responses. In these networks, microbial partners influence growth and N use efficiency of plants either positively or negatively. Harnessing the beneficial effects of specific players within crop microbiomes is a promising strategy to counteract the emerging threats to human and planetary health due to the overuse of industrial N fertilizers. However, in addition to N-providing activities (e.g. the well-known symbiosis of legumes and Rhizobium spp.), other plant-microorganism interactions must be considered to obtain a complete picture of how microbial-driven N transformations might affect plant nutrition. For this, we review recent insights into the tight interplay between plants and N-cycling microorganisms, focusing on microbial N-transformation processes representing N sources and sinks that ultimately shape plant N acquisition.

Bio-manure substitution declines soil N2O and NO emissions and improves nitrogen use efficiency and vegetable quality index

Substituting mineral fertilizer with manure or a combination of organic amendments plus beneficial soil microorganisms (bio-manure) in agriculture is a standard practice to mitigate N2O and NO emissions while enhancing crop performance and nitrogen use efficiency (NUE). Here, we conducted a greenhouse trial for three consecutive vegetable growth seasons for Spinach, Coriander herb, and Baby bok choy to reveal the response of N2O and NO emissions, NUE, and vegetable quality index (VQI) to fertilization strategies. Strategies included solely chemical nitrogen fertilizer (CN), 20 (M1N4) and 50% (M1N1) substitution with manure, 20 (BM1N4) and 50% (BM1N1) substitution with bio-manure, and no fertilization as a control and were organized in a completely randomized design (n = 3). Manure decreased N2O emissions by 24-45% and bio-manure by 44-53% compared to CN. Manure reduced NO emissions by 28-41% and bio-manure by 55-63%. Bio-manure increased NUE by 0.04-31% and yields by 0.05-61% while improving VQI, attributed to yield growth and reduced vegetable NO3- contents. Improvement of root growth was the main factor that explained the rise of NUE; NUE declined with the increase of N2O emissions, showing the loss of vegetable performance under conditions when denitrification processes prevailed. Under the BM1N1, the highest VQI and the lowest yield-scaled N-oxide emissions were observed, suggesting that substitution with bio-manure can improve vegetable quality and mitigate N-oxide emissions. These findings indicate that substituting 50% of mineral fertilizer with bio-manure can effectively improve NUE and VQI and mitigate N-oxides in intensive vegetable production.

Inoculation with Stutzerimonas stutzeri strains decreases N₂O emissions from vegetable soil by altering microbial community composition and diversity

Inoculation with plant growth-promoting rhizobacteria (PGPR) strains has promoted plant growth and decreased nitrous oxide (N₂O) emissions from agricultural soils simultaneously. However, limited PGPR strains can mitigate N₂O emissions from agricultural soils, and the microbial ecological mechanisms underlying N₂O mitigation after inoculation are poorly understood. In greenhouse pot experiments, the effects of inoculation with Stutzerimonas stutzeri NRCB010 and NRCB025 on tomato growth and N₂O emissions were investigated in two vegetable agricultural soils with contrasting textures. Inoculation with NRCB010 and NRCB025 significantly promoted tomato growth in both soils. Moreover, inoculation with NRCB010 decreased the N₂O emissions from the fine- and coarse-textured soils by 38.7% and 52.2%, respectively, and inoculation with NRCB025 decreased the N₂O emissions from the coarse-textured soil by 76.6%. Inoculation with NRCB010 and NRCB025 decreased N₂O emissions mainly by altering soil microbial community composition and the abundance of nitrogen-cycle functional genes. The N₂O-mitigating effect might be partially explained by a decrease in the (amoA + amoB)/(nosZI + nosZII) and (nirS + nirK)/(nosZI + nosZII) ratios, respectively. Soil pH and organic matter were key variables that explain the variation in abundance of N-cycle functional genes and subsequent N₂O emission. Moreover, the N₂O-mitigating effect varied depending on soil textures and individual strain after inoculation. This study provides insights into developing biofertilizers with plant growth-promoting and N₂O-mitigating effects.

IMPORTANCE

Plant growth-promoting rhizobacteria (PGPR) have been applied to mitigate nitrous oxide (N₂O) emissions from agricultural soils, but the microbial ecological mechanisms underlying N₂O mitigation are poorly understood. That is why only limited PGPR strains can mitigate N₂O emissions from agricultural soils. Therefore, it is of substantial significance to reveal soil ecological mechanisms of PGPR strains to achieve efficient and reliable N₂O-mitigating effect after inoculation. Inoculation with Stutzerimonas stutzeri strains decreased N₂O emissions from two soils with contrasting textures probably by altering soil microbial community composition and gene abundance involved in nitrification and denitrification. Our findings provide detailed insight into soil ecological mechanisms of PGPR strains to mitigate N₂O emissions from vegetable agricultural soils.

Differences in greenhouse gas emissions and microbial communities between underground and conventionally constructed wastewater treatment plants

Large quantities of greenhouse gases (GHGs) are emitted into the atmosphere during wastewater treatment. In this study, GHG and microbial samples were collected from four wastewater treatment plants (WWTPs), and their differences and relationships were assessed. The study showed that, compared with conventionally constructed WWTPs, well-established gas collection systems in underground WWTPs facilitate comprehensive collection and accurate accounting of GHGs. In aboveground WWTPs, capped anoxic ponds promote methane production releasing it at 2-8 times the rate of uncapped emissions, in contrast to nitrous oxide emissions. Moreover, a stable subsurface environment allows for smaller fluctuations in daily GHG emissions and higher microbial diversity and abundance. This study highlights differences in GHG emission fluxes and microbial communities in differently constructed WWTPs, which are useful for control and accurate accounting of GHG emissions.

Machine learning-based estimation and mitigation of nitric oxide emissions from Chinese vegetable fields

High fertilizer input and nitric oxide (NO) emissions characterize the intensive vegetable production system. However, the amount, geographic distribution, and effective mitigation strategies of NO emissions over Chinese vegetable fields remain largely uncertain. In this study, we developed a data-driven estimate of NO emissions and their spatial pattern in Chinese vegetable fields based on the Random Forest (RF) model. Additionally, we conducted a field experiment in a subtropical vegetable field to investigate the effect of climate-smart practices on NO emissions. The RF model results showed that soil NO emissions from Chinese vegetable fields were sensitive to nitrogen application amount, soil clay content, and pH. The total NO emission from Chinese vegetable fields in 2018 was estimated to be 75.9 Gg NO-N. The urgency to reduce NO emissions in vegetable fields was higher in northern than in southern China. Our meta-analysis and field experiment results suggested that biochar amendment and replacing chemical fertilizers with bio-organic fertilizers were win-win climate-smart management practices for mitigating NO emissions while improving vegetable production. Overall, our study provided new insights into NO emissions in vegetable soil ecosystems and can facilitate the development of regional NO emission inventories and effective mitigation strategies. These findings highlight the importance of adopting sustainable and climate-smart agricultural practices to reduce NO emissions and mitigate their adverse environmental impacts.

Biodegradable microplastics reduce the effectiveness of biofertilizers by altering rhizospheric microecological functions

The effectiveness of biofertilizers as a cost-effective crop yield enhancer can be compromised by residual soil pollutants. However, the impact of accumulated polyadipate/butylene terephthalate microplastics (PBAT-MPs) from biodegradable mulch films on biofertilizer application and the consequent growth of crop plants remains unclear. Here, the effects of different levels of PBAT-MPs in soil treated with Bacillus amyloliquefaciens biofertilizer were assessed in a four-week potted experiment. PBAT-MPs significantly decreased the growth-promoting effect of the biofertilizer on Brassica chinensis L., resulting in a notable reduction in both above- and belowground biomass (up to 52.91% and 57.53%, respectively), as well as nitrate and crude fiber contents (up to 12.18% and 13.64%, respectively). In the rhizosphere microenvironment, PBAT-MPs increased soil organic carbon by 2.63-fold and organic matter by 2.68-fold, while enhancing sucrase (from 67.55% to 108.89%) and cellulase (from 31.26% to 49.10%) activities. PBAT-MPs also altered the rhizospheric bacterial community composition/diversity, resulting in more complex microbial networks. With regard to microbial function, PBAT-MPs impacted carbon metabolic function by inhibiting the 3-hydroxypropionate/4-hydroxybutyrate fixation pathway and influencing chitin and lignin degradation processes. Overall, the rhizospheric microbial profiles (composition, function, and network interactions) were the main contributors to plant growth inhibition. This study provides a practical case and theoretical basis for rational use of biodegradable mulch films and indicates that the residue of biodegradable films needs pay attention.

Substitution of organic and bio-organic fertilizers for mineral fertilizers to suppress nitrous oxide emissions from intensive vegetable fields

To gain insight into the microbial mechanisms associated with the replacement of chemical fertilizers with organic or bio-organic fertilizers to mitigate soil nitrous oxide (N2O) emissions, we measured N2O emissions from greenhouse vegetable soils through field observations and pot experiments. Results showed that organic substitution suppressed N2O emissions by reducing soil mineral N content and stimulating the abundance of the nosZII gene. The trade-off effect of bio-organic substitution on N2O emissions may be due to the stimulated activity of the AOA-amoA gene, resulting in unfavorable conditions for N2O production and thus reduced N2O loss. We also linked the inhibitory effect of organic and bio-organic substitution on N2O emissions to the increased abundance of key species in bacterial co-occurrence networks represented by Patescibacteria as they were significantly and negatively correlated with N2O emissions. However, the mitigation effect of bio-organic substitution on N2O emissions was conteracted by an increase in Bacillus abundance due to the direct negative effect of Bacillus on the nosZII gene abundance. These findings suggest that conventional or bio-organic substitution is a promising strategy for alleviating the environmental costs of crop production.

Mitigation of N2O emission from granular organic fertilizer with alkali- and salt-resistant plant growth-promoting rhizobacteria

AIM

Organic fertilizer application significantly stimulates nitrous oxide (N2O) emissions from agricultural soils. Plant growth-promoting rhizobacteria (PGPR) strains are the core of bio-fertilizer or bio-organic fertilizer, while their beneficial effects are inhibited by environmental conditions, such as alkali and salt stress observed in organic manure or soil. This study aims to screen alkali- and salt-resistant PGPR that could mitigate N2O emission after applying strain-inoculated organic fertilizer.

METHODS AND RESULTS

Among the 29 candidate strains, 11 (7 Bacillus spp., 2 Achromobacter spp., 1 Paenibacillus sp., and 1 Pseudomonas sp.) significantly mitigated N2O emissions from the organic fertilizer after inoculation. Seven strains were alkali tolerant (pH 10) and five were salt tolerant (4% salinity) in pure culture. Seven strains were selected for further evaluation in two agricultural soils. Five of these seven strains could significantly decrease the cumulative N2O emissions from Anthrosol, while six could significantly decrease the cumulative N2O emissions from Cambisol after the inoculation into the granular organic fertilizer compared with the non-inoculated control.

CONCLUSIONS

Inoculating alkali- and salt-resistant PGPR into organic fertilizer can reduce N2O emissions from soils under microcosm conditions. Further studies are needed to investigate whether these strains will work under field conditions, under higher salinity, or at different soil pH.

Effects of magnesium-modified biochar on soil organic carbon mineralization in citrus orchard

In order to investigate the carbon sequestration potential of biochar on soil, citrus orchard soils with a forest age of 5 years was taken as the research object, citrus peel biochar (OBC) and magnesium-modified citrus peel biochar (OBC-mg) were selected as additive materials, and organic carbon mineralization experiments were carried out in citrus orchard soil. OBC and OBC-Mg were applied to citrus orchard soils at four application rates (0, 1, 2, and 4%), and incubated at a constant temperature for 100 days. Compared with CK, the cumulative mineralization of soil organic carbon decreased by 5.11% with 1% OBC and 2.14% with 1% OBC-Mg. The application of OBC and OBC-Mg significantly increased the content of soil organic carbon fraction, while the content of soil organic carbon fraction was higher in OBC-Mg treated soil than in OBC treated soil. Meanwhile, the cumulative mineralization of soil organic carbon was significantly and positively correlated with the activities of soil catalase, urease and sucrase. The enzyme activities increased with the cumulative mineralization of organic carbon, and the enzyme activities of the OBC-Mg treated soil were significantly higher than those of the OBC treated soil. The results indicated that the OBC-Mg treatment inhibited the organic carbon mineralization in citrus orchard soils and was more favorable to the increase of soil organic carbon fraction. The Mg-modified approach improved the carbon sequestration potential of biochar for citrus orchard soils and provided favorable support for the theory of soil carbon sink in orchards.

Bio-organic fertilizers improve Dendrocalamus farinosus growth by remolding the soil microbiome and metabolome

Organic and microbial fertilizers have potential advantages over inorganic fertilizers in improving soil fertility and crop yield without harmful side-effects. However, the effects of these bio-organic fertilizers on the soil microbiome and metabolome remain largely unknown, especially in the context of bamboo cultivation. In this study, we cultivated Dendrocalamus farinosus (D. farinosus) plants under five different fertilization conditions: organic fertilizer (OF), Bacillus amyloliquefaciens bio-fertilizer (Ba), Bacillus mucilaginosus Krassilnikov bio-fertilizer (BmK), organic fertilizer plus Bacillus amyloliquefaciens bio-fertilizer (OFBa), and organic fertilizer plus Bacillus mucilaginosus Krassilnikov bio-fertilizer (OFBmK). We conducted 16S rRNA sequencing and liquid chromatography/mass spectrometry (LC-MS) to evaluate the soil bacterial composition and soil metabolic activity in the different treatment groups. The results demonstrate that all the fertilization conditions altered the soil bacterial community composition. Moreover, the combination of organic and microbial fertilizers (i.e., in the OFBa and OFBmK groups) significantly affected the relative abundance of soil bacterial species; the largest number of dominant microbial communities were found in the OFBa group, which were strongly correlated with each other. Additionally, non-targeted metabolomics revealed that the levels of soil lipids and lipid-like molecules, and organic acids and their derivatives, were greatly altered under all treatment conditions. The levels of galactitol, guanine, and deoxycytidine were also markedly decreased in the OFBa and OFBmK groups. Moreover, we constructed a regulatory network to delineated the relationships between bamboo phenotype, soil enzymatic activity, soil differential metabolites, and dominant microbial. The network revealed that bio-organic fertilizers promoted bamboo growth by modifying the soil microbiome and metabolome. Accordingly, we concluded that the use of organic fertilizers, microbial fertilizers, or their combination regulated bacterial composition and soil metabolic processes. These findings provide new insights into how D. farinosus-bacterial interactions are affected by different fertilization regiments, which are directly applicable to the agricultural cultivation of bamboo.

Potential utilization of vitamin C industrial effluents in agriculture: Soil fertility and bacterial community composition

The potential of industrial effluents from vitamin C (VC) production was assessed for agricultural applications by monitoring plant growth, soil properties, and microbial community structure. The results demonstrated that two types of effluents-residue after evaporation (RAE) and concentrated bacterial solution after ultrafiltration (CBS)-had positive effects on the yield and VC content of pak choi. The highest yield and VC content were achieved with a combined RAE-CBS treatment (55.82 % and 265.01 % increase, respectively). The soil fertility was also enhanced by the application of RAE and CBS. Nitrate nitrogen and organic carbon contents in the soil were positively correlated with the RAE addition, while ammonium nitrogen and available phosphorus were positively correlated with the CBS addition. The diversity of bulk and rhizosphere soil bacterial communities increased significantly after the addition of RAE-CBS. The abundance of Sphingomonas and Rhizobium significantly increased after the RAE-CBS treatment, which affected aromatic compound hydrolysis and nitrogen fixation positively. Changes in plant growth and soil fertility were closely related to the upregulation of functional gene expression related to C, N, and P cycling. RAE and CBS application exerted various positive synergistic effects on plant growth, soil fertility, and bacterial community structure. Consequently, the study results confirmed the potential of RAE and CBS application in agriculture. This study provides an innovative solution for utilizing VC industrial wastewater in agriculture in a resourceful and economically beneficial manner while alleviating the corresponding environmental burden.

Impact of Biochar and Bioorganic Fertilizer on Rhizosphere Bacteria in Saline-Alkali Soil

Biochar and bioorganic fertilizers (BOF) that are used in agriculture can, both directly and indirectly, impact rhizosphere soil microorganisms. However, changes to the halophyte rhizosphere bacterial community after applying biochar and BOF to saline−alkali soil have not been thoroughly described. This study has investigated the bacterial communities of halophytes in saline−alkali soil through the addition of different biochar and BOF formulas using Illumina-based sequencing of the 16S rRNA gene fragment. B_BOF (biochar and BOF combined application) had the best effect, either by promoting the plant growth or by improving the physical and chemical properties of the soil. The concentration of the rhizosphere bacterial communities correlated with the changes in soil organic matter (OM) and organic carbon (OC). Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria accounted for >80% of the total bacteria in each treatment. In addition, the abundance of Micromonospora was much higher in response to B_BOF than to the other treatments. BOF, with or without biochar, significantly influenced the bacterial community composition in the saline−alkali soil. The OC, OM, total nitrogen, and the available phosphorus had significant effects on the bacterial structure of this soil. The complex correlation of the bacterial communities between CK and B_BOF was higher compared to that between CK and FB or between CK and BOF. These findings suggested that the plant growth, the soil characteristics, and the diversity or community composition of the rhizosphere bacteria in saline−alkali soil were significantly influenced by B_BOF, followed by BOF, and then biochar; fine biochar had a stronger effect than medium or coarse biochar. This study provides an insight into the complex microbial compositions that emerge in response to biochar and BOF.

Micromanaging the nitrogen cycle in agroecosystems

While large inputs of synthetic nitrogen fertilizers enable our current rate of crop production and feed a growing global population, these fertilizers come at a heavy environmental cost. Driven by microbial processes, excess applied nitrogen is lost from agroecosystems as nitrate and nitrous oxide (N₂O) contaminating aquatic ecosystems and contributing to climate change. Interest in nitrogen-fixing microorganisms as an alternative to synthetic fertilizers is rapidly accelerating. Microbial inoculants offer the promise of a sustainable and affordable source of nitrogen, but the impact of inoculants on nitrogen dynamics at an ecosystem level is not fully understood. This review synthesizes recent studies on microbial inoculants as tools for nutrient management and considers the ramifications of inoculants for nitrogen transformations beyond fixation.

Functional keystone drive nitrogen conversion during different animal manures composting

In this study, nitrogen transformation of chicken manure (CM) and cattle dung (CD) during composting was analyzed and its related functional keystones were identified. The results showed that chicken manure showed more severe nitrogen conversion during composting. The main N conversion factors in cattle dung were nitrite nitrogen (NO₂^--N) and ammonium nitrogen (NH₄⁺-N), while the main N conversion factors in chicken manure were NH₄⁺-N and nitrate nitrogen (NO₃^--N). The nitrogen-transforming bacterial community in chicken manure was more diverse. Variations in functional keystone abundances in cattle dung tended to be confined to the cooling and maturation periods, whereas changes in chicken manure persisted throughout the composting process. Environmental factors affected the functional keystones of nitrogen transformation. This study may provide directions for regulating nitrogen conversion in animal manure composting.

Inoculation effect of Pseudomonas sp. TF716 on N2O emissions during rhizoremediation of diesel-contaminated soil

The demand for rhizoremediation technology that can minimize greenhouse gas emissions while effectively removing pollutants in order to mitigate climate change has increased. The inoculation effect of N₂O-reducing Pseudomonas sp. TF716 on N₂O emissions and on remediation performance during the rhizoremediation of diesel-contaminated soil planted with tall fescue (Festuca arundinacea) or maize (Zea mays) was investigated. Pseudomonas sp. TF716 was isolated from the rhizosphere soil of tall fescue. The maximum N₂O reduction rate of TF716 was 18.9 mmol N₂O g dry cells⁻¹ h⁻¹, which is superior to the rates for previously reported Pseudomonas spp. When Pseudomonas sp. TF716 was added to diesel-contaminated soil planted with tall fescue, the soil N₂O-reduction potential was 2.88 times higher than that of soil with no inoculation during the initial period (0–19 d), and 1.08–1.13 times higher thereafter. However, there was no enhancement in the N₂O-reduction potential for the soil planted with maize following inoculation with strain TF716. In addition, TF716 inoculation did not significantly affect diesel degradation during rhizoremediation, suggesting that the activity of those microorganisms involved in diesel degradation was unaffected by TF716 treatment. Analysis of the dynamics of the bacterial genera associated with N₂O reduction showed that Pseudomonas had the highest relative abundance during the rhizoremediation of diesel-contaminated soil planted with tall fescue and treated with strain TF716. Overall, these results suggest that N₂O emissions during the rhizoremediation of diesel-contaminated soil using tall fescue can be reduced with the addition of Pseudomonas sp. TF716.

Microbial diversity composition of apple tree roots and resistance of apple Valsa canker with different grafting rootstock types

Background

The composition and diversity of root microbial community are affected by plant genotypes and soil environment, which in turn affect plant growth and development. Grafting rootstock types of the apple tree can affect phenotypes in cultivation practice, but it is not clear whether grafting rootstock types can affect the composition and diversity of root microbial community and the resistance of apple tree to apple Valsa canker.

Methods

To explore root microbial differences and the correlation, 16S rRNA and ITS genes were sequenced using Novaseq technology.

Results

The results showed that the influence of grafting rootstock types on the composition of the root fungal community was greater than that of bacteria. And the bacterial community richness was higher in the healthy (OTUs: 1693) and dwarfing rootstock (OTUs: 1526) than in the disease (OTUs: 1181) and standard rootstock (OTUs: 1412), while the fungal community richness was the opposite. Moreover, the bacterial abundance of root zone, rhizosphere, and root endophytic microorganisms with the same grafting rootstock type exhibited a decreasing trend. Results of Nested PCR assay on soil and root tissue of Valsa mali showed that the content of V. mali in dwarfing rootstocks are lower than standard rootstocks. These results suggest that apple trees grafting with dwarfing rootstocks are more resistant to V. mali than standard rootstocks.

Conclusions

Under different grafting types, the effect on the composition of fungal community in apple tree root was greater than that of bacteria. The bacterial community in dwarfing rootstocks is more abundant and diverse, including more beneficial microorganisms. Therefore, dwarfing rootstock is more conducive to the resistance to apple Valsa canker from biological control.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02517-x.

The impact of pristine and modified rice straw biochar on the emission of greenhouse gases from a red acidic soil

With the growing awareness of environmental impacts of land degradation, pressure is mounting to improve the health and productivity of degrading soils, which could be achieved through the use of raw and modified biochar materials. The primary objective of the current study was to investigate the efficiency of pristine and Mg-modified rice-straw biochar (RBC and MRBC) for the reduction of greenhouse gases (GHG) emissions and improvement of soil properties. A 90 days' incubation experiment was conducted using treatments which included control (CK), two RBC dosages (1% and 2.5%), and two MRBC doses (1% and 2.5%). Soil physico-chemical and biological properties were monitored to assess the effects due to the treatments. Results showed that both biochars improved soil physicochemical properties as the rate of biochar increased. The higher rates of biochar (RBC_2.5 and MRBC_2.5) particularly increased enzymatic activities (Catalase, Invertase and Urease) in comparison to the control. Data obtained for phospholipid fatty acid (PLFA) concentration indicated an increase in the Gram-negative bacteria (G-), actinomycetes and total PLFA with the increased biochar rate, while Gram-positive bacteria (G+) showed no changes to either level of biochar. As regards fungi concentration, it decreased with the biochar addition, whereas arbuscular mycorrhizal fungi (AMF) showed non-significant changes. The release of CO₂, CH₄ and N₂O showed a decreasing trend over the time. CO₂ cumulative emission decreased for MRBC₁ (5%) and MRBC_2.5 (9%) over the pristine biochar treatments. The cumulative N₂O emission decreased by 15-32% for RBC₁ and RBC_2.5 and by 22-33% for MRBC₁ and MRBC_2.5 as compared to the control, whereas CH₄ emission showed non-significant changes. Overall, the present study provides for the first-time data that could facilitate the correct use of Mg-modified rice biochar as a soil additive for the mitigation of greenhouse gas emission and improvement of soil properties.

The Immediate Hotspot of Microbial Nitrogen Cycling in an Oil-Seed Rape (Brassica campestris L.) Soil System Is the Bulk Soil Rather Than the Rhizosphere after Biofertilization

Biofertilizers are substances that promote plant growth through the efficacy of living microorganisms. The functional microbes comprising biofertilizers are effective mediators in plant-soil systems in the regulation of nitrogen cycling, especially in nitrification repression. However, the deterministic or stochastic distribution of the functional hotspot where microbes are active immediately after biofertilization is rarely investigated. Here, pot experiments with oil-seed rape (Brassica campestris L.) were conducted with various chemical and biological fertilizers in order to reveal the distribution of the hotspot after each fertilization. A stimulated dynamic of the nitrogen cycling-related genes in the bulk soil inferred that the bulk soil was likely to be the hotspot where the inoculated bacterial fertilizers dominated the nitrogen cycle. Furthermore, a network analysis showed that bulk soil microbial communities were more cooperative than those in the rhizosphere after biofertilization, suggesting that the microbiome of the bulk soils were more efficient for nutrient cycling. In addition, the relatively abundant ammonia-oxidizing bacteria and archaea present in the networks of bulk soil microbial communities further indicated that the bulk soil was the plausible hotspot after the application of the biofertilizers. Therefore, our research provides a new insight into the explicit practice of plant fertilization and agricultural management, which may improve the implementational efficiency of biofertilization.

Mitigation of greenhouse gas emissions from a red acidic soil by using magnesium-modified wheat straw biochar

To mitigate greenhouse gas (GHG) emissions, different strategies have been proposed, including application of dolomite, crop straw and biochar, thus contributing to cope with the increasing global warming affecting the planet. In the current study, pristine wheat straw biochar (WBC) and magnesium (MgCl₂.6H₂O) modified wheat straw biochar (MWBC) were used. Treatments included control (CK), two WBC dosages (1% and 2.5%), and two MWBC doses (1% and 2.5%). After 90 days of incubation, WBC and MWBC improved the soil physiochemical properties, being more pronounced with increasing rates of biochar. MWBC_2.5 significantly decreased microbial biomass carbon (MBC), while microbial biomass nitrogen (MBN) increased when both biochar materials (WBC₁ and MWBC₁) were applied at low rate. Compared to control soil, Urease and Alkaline phosphatase activities increased with the increasing rate of WBC and MWBC. The activities of dehydrogenase and β-glucosidase decreased with the WBC and MWBC application, compared to CK. The fluxes of all the three GHGs evaluated (CO₂, CH₄ and N₂O) decreased with time for both biochar amendments, while cumulative emission of CO₂ increased by 58% and 45% for WBC, and by 54% and 41% for MWBC, as compared to CK. The N₂O cumulative emissions decreased by 18 and 34% for WBC, and by 25 and 41% for MWBC, compared to CK, whereas cumulative methane emission showed non-significant differences among all treatments. These findings indicate that Mg-modified wheat straw biochar would be an appropriate management strategy aiding to reduce GHG emissions and improving the physiochemical properties of affected soils, and specifically of the red dry land soil investigated in the current work.

Efficiency and mechanism of reducing ammonia volatilization in alkaline farmland soil using Bacillus amyloliquefaciens biofertilizer

Ammonia volatilization from the farmland caused by the application of synthetic nitrogen fertilizer is the most important source of anthropogenic ammonia emissions. Biofertilizer application has been considered as an alternative option for agriculture sustainability and soil improvement. In this study, field trials were carried out to investigate the efficiency of Bacillus amyloliquefaciens (BA) biofertilizer on alleviating ammonia volatilization in alkaline farmland soil and increasing crop yield and nitrogen utilization. Potential response mechanisms were investigated from soil enzyme, nitrogen cycle function genes and microbial community levels. Compared with conventional fertilization, BA biofertilizer application reduced the ammonia volatilization by 68%, increased the crop yield and nitrogen recovery by 19% and 19%, respectively. Soil enzyme activity analysis showed that BA biofertilizer inhibited the urease activity and enhanced the potential ammonia oxidation (PAO). In addition, BA biofertilizer application also increased the bacterial amoA gene abundance, while decreased the ureC gene abundance. BA biofertilizer also significantly altered the community structure and composition, and especially raised the abundance of ammonia oxidation bacteria (AOB), while no changes were observed in abundance of nitrite oxidation bacteria (NOB). Briefly, BA biofertilizer was approved to reduce the transformation of fertilizer nitrogen to NH₄⁺-N, simultaneously accelerating NH₄⁺-N into the nitrification process, thus decreasing the NH₄⁺-N content remained in alkaline soil and consequently alleviating the ammonia volatilization. Thus, these results suggested that the application of BA biofertilizer is a feasible strategy to improve crop yields and reduce agricultural ammonia emissions.

Acetic Acid-Producing Endophyte Lysinibacillus fusiformis Orchestrates Jasmonic Acid Signaling and Contributes to Repression of Cadmium Uptake in Tomato Plants

Diverse signaling pathways regulated by phytohormones are essential for the adaptation of plants to adverse environments. Root endophytic bacteria can manipulate hormone-related pathways to benefit their host plants under stress conditions, but the mechanisms underlying endophyte-mediated plant stress adaptation remain poorly discerned. Herein, the acetic acid-producing endophytic bacteria Lysinibacillus fusiformis Cr33 greatly reduced cadmium (Cd) accumulation in tomato plants. L. fusiformis led to a marked increase in jasmonic acid (JA) content and down-regulation of iron (Fe) uptake-related genes in Cd-exposed roots. Accordantly, acetic acid treatment considerably increased the JA content and inhibited root uptake of Cd uptake. In addition, the Cr33-inoculated roots displayed the increased availability of cell wall and rhizospheric Fe. Inoculation with Cr33 notably reduced the production of nitric oxide (NO) and suppressed Fe uptake systems in the Cd-treated roots, thereby contributing to hampering Cd absorption. Similar results were also observed for Cd-treated tomato plants in the presence of exogenous JA or acetic acid. However, chemical inhibition of JA biosynthesis greatly weakened the endophyte-alleviated Cd toxicity in the plants. Collectively, our findings indicated that the endophytic bacteria L. fusiformis effectively prevented Cd uptake in plants via the activation of acetic acid-mediated JA signaling pathways.

Unraveling Mechanisms and Impact of Microbial Recruitment on Oilseed Rape (Brassica napus L.) and the Rhizosphere Mediated by Plant Growth-Promoting Rhizobacteria

Plant growth-promoting rhizobacteria (PGPR) are noticeably applied to enhance plant nutrient acquisition and improve plant growth and health. However, limited information is available on the compositional dynamics of rhizobacteria communities with PGPR inoculation. In this study, we investigated the effects of three PGPR strains, Stenotrophomonas rhizophila, Rhodobacter sphaeroides, and Bacillus amyloliquefaciens on the ecophysiological properties of Oilseed rape (Brassica napus L.), rhizosphere, and bulk soil; moreover, we assessed rhizobacterial community composition using high-throughput Illumina sequencing of 16S rRNA genes. Inoculation with S. rhizophila, R. sphaeroides, and B. amyloliquefaciens, significantly increased the plant total N (TN) (p < 0.01) content. R. sphaeroides and B. amyloliquefaciens selectively enhanced the growth of Pseudomonadacea and Flavobacteriaceae, whereas S. rhizophila could recruit diazotrophic rhizobacteria, members of Cyanobacteria and Actinobacteria, whose abundance was positively correlated with inoculation, and improved the transformation of organic nitrogen into inorganic nitrogen through the promotion of ammonification. Initial colonization by PGPR in the rhizosphere affected the rhizobacterial community composition throughout the plant life cycle. Network analysis indicated that PGPR had species-dependent effects on niche competition in the rhizosphere. These results provide a better understanding of PGPR-plant-rhizobacteria interactions, which is necessary to develop the application of PGPR.

Bacillus subtilis biofertilizer mitigating agricultural ammonia emission and shifting soil nitrogen cycling microbiomes

Excessive ammonia (NH₃) emitted from nitrogen fertilizer application in farmland have caused serious disturbance to global environment, including reduction of visibility, formation of regional haze, and increase of nitrogen deposition. Application of biofertilizer has been considered as an effective approach for soil improvement and agriculture sustainability. In this study, a field experiment was conducted to evaluate the potential of B. subtilis biofertilizer on mitigating NH₃ volatilization and to investigate the underlying mechanisms. Compared with organic fertilizer, the incorporation of B. subtilis biofertilizer reduced NH₃ volatilization by up to 44%. Moreover, the application of B. subtilis biofertilizer reduced the abundance of ureC gene, and increased the abundance of functional genes (bacterial amoA and comammox amoA) and ammonia-oxidizing bacteria (AOB). This indicated that the conversion of fertilizer nitrogen to NH₄⁺-N was decreased and the nitrification process was increased. In brief, the application of B. subtilis biofertilizer reduced the "source" and increased the "sink" of NH₄⁺-N, thus reducing the retention of NH₄⁺-N in alkaline soil, and mitigating NH₃ volatilization. These results indicated that B. subtilis biofertilizer is an effective control strategy for agricultural NH₃ emission, maintaining high crop yield and mitigating environmental disturbance.

Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials

The identification of microorganisms in closely related groups is challenging. The present work focused on the different molecular methodology for the accurate microbial identification in the five commercially available organic agriculture materials enriched with effective microorganisms. From the tested five organic agricultural materials, a total of seven distinct bacterial colonies (A-1, B-1, C-1, D-1, E-1, E-2, and E-3) were isolated and processed for sequential identification utilizing HiCrome™ Bacillus agar, biochemical tests with API CHB50, 16S rRNA gene analysis, random amplified polymorphic DNA (RAPD), and species-specific PCR analysis. All the isolated microorganisms were Gram-positive rods and spore former belonging to Bacillus group and appeared as a differential characteristic feature on HiCrome™ Bacillus agar. All isolates showed high-percentage similarities with the different members of Bacillus species in biochemical testing and 16S rRNA gene analysis. The collective identification results revealed isolates, A-1, B-1, and C-1, close to B. velezensis. Further RAPD-PCR and species-specific PCR discriminated and provided confirmatory evidence for D-1 as B. thuringiensis and E-1, E-2, and E-3 as B. licheniformis, respectively. In addition, presence of B. thuringiensis was also confirmed by toxin crystal protein staining. In conclusion, the species-specific primers could be used as a rapid and accurate identification tool to discriminate closely related Bacillus species such as B. subtilis, B. licheniformis, and B. thuringiensis.

Characterization of nitrous oxide reduction by Azospira sp. HJ23 isolated from advanced wastewater treatment sludge

A new nitrous oxide (N₂O)-reducing bacterium was isolated from a consortium that was enriched using advanced wastewater treatment sludge as an inoculum and N₂O as the sole nitrogen source. The isolated facultative anaerobe was identified as Azospira sp. HJ23. Azospira sp. HJ23 exhibited optimum N₂O-reducing activity with a C/N ratio of 62 at pH 6 in the temperature range of 37 °C to 40 °C. The optimum carbon source for N₂O reduction was a mixture of glucose and acetate. The maximum rate of N₂O reduction by Azospira sp. HJ23 was 4.8 mmol·g-dry cell^-1·h^-1, and its N₂O-reducing activity was higher than other known N₂O reducers. Azospira sp. HJ23 possessed several functional genes for denitrification. These included narG (NO₃^- reductase), nirK (NO₂^- reductase), norB (NO reductase), and nosZ (N₂O reductase) genes. These results suggest that Azospira sp. HJ23 can be applied in the denitrification process to minimalize N₂O emission.

Paenibacillus polymyxa biofertilizer application in a tea plantation reduces soil N2O by changing denitrifier communities

Increasing the use of nitrogen fertilizers in tea orchards has led to intense nitrous oxide (N₂O) emissions. Foliar application of Paenibacillus polymyxa biofertilizer has been proven to be beneficial for organic tea production. In this study, tea yield and quality were significantly improved after application of P. polymyxa biofertilizer compared with the control but were not significantly different from chemical fertilizer treatments. However, the average N₂O fluxes in tea fields treated with chemical fertilizers and biofertilizers (225 kg N·ha^-1·year^-1 for both) were 50.6-973.7 and 0.6-29.1 times higher than those in the control treatment, respectively. Pot experiments conducted to explore the mechanism of N₂O reduction induced by P. polymyxa biofertilizer showed that applying P. polymyxa in addition to urea could reduce N₂O fluxes by 36.5%-73.1%. Quantitative PCR analysis suggested that a significant increase in the quantity of nirK and nosZ genes was linked to the reduction of N₂O, and high-throughput sequencing of nosZ revealed active and potentially efficient denitrifiers in different treatments. Our findings suggest that P. polymyxa biofertilizer is in line with the requirements of modern agriculture, which aims to increase product yield and quality while reducing negative environmental impacts.

Biocontrol Potential of a Novel Endophytic Bacterium From Mulberry (Morus) Tree

Mulberry (Morus) is an economically important woody tree that is suitable for use in sericulture as forage and in medicine. However, this broad-leaved tree is facing multiple threats ranging from phytopathogens to insect pests. Here, a Gram-positive, endospore-forming bacterium (ZJU1) was frequently isolated from healthy mulberry plants by screening for foliar endophytes showing antagonism against pathogens and pests. Whole-genome sequencing and annotation resulted in a genome size of 4.06 Mb and classified the bacterium as a novel strain of Bacillus amyloliquefaciens that has rarely been identified from tree leaves. An integrative approach combining traditional natural product chemistry, activity bioassays, and high-resolution mass spectrometry confirmed that strain ZJU1 uses a blend of antimicrobials including peptides and volatile organic compounds to oppose Botrytis cinerea, a major phytopathogenic fungus causing mulberry gray mold disease. We showed that the inoculation of endophyte-free plants with ZJU1 significantly decreased both leaf necrosis and mortality under field conditions. In addition to the direct interactions of endophytes with foliar pathogens, in planta studies suggested that the inoculation of endophytes also induced plant systemic defense, including high expression levels of mulberry disease resistance genes. Moreover, when applied to the generalist herbivore Spodoptera litura, ZJU1 was sufficient to reduce the pest survival rate below 50%. A previously undiscovered crystal toxin (Cry10Aa) could contribute to this insecticidal effect against notorious lepidopteran pests. These unique traits clearly demonstrate that B. amyloliquefaciens ZJU1 is promising for the development of successful strategies for biocontrol applications. The search for new plant-beneficial microbes and engineering microbiomes is therefore of great significance for sustainably improving plant performance.

Bacterial nitrous oxide respiration: electron transport chains and copper transfer reactions

Biologically catalyzed nitrous oxide (N₂O, laughing gas) reduction to dinitrogen gas (N₂) is a desirable process in the light of ever-increasing atmospheric concentrations of this important greenhouse gas and ozone depleting substance. A diverse range of bacterial species produce the copper cluster-containing enzyme N₂O reductase (NosZ), which is the only known enzyme that converts N₂O to N₂. Based on phylogenetic analyses, NosZ enzymes have been classified into clade I or clade II and it has turned out that this differentiation is also applicable to nos gene clusters (NGCs) and some physiological traits of the corresponding microbial cells. The NosZ enzyme is the terminal reductase of anaerobic N₂O respiration, in which electrons derived from a donor substrate are transferred to NosZ by means of an electron transport chain (ETC) that conserves energy through proton motive force generation. This chapter presents models of the ETCs involved in clade I and clade II N₂O respiration as well as of the respective NosZ maturation and maintenance processes. Despite differences in NGCs and growth yields of N₂O-respiring microorganisms, the deduced bioenergetic framework in clade I and clade II N₂O respiration is assumed to be equivalent. In both cases proton motive quinol oxidation by N₂O is thought to be catalyzed by the Q cycle mechanism of a membrane-bound Rieske/cytochrome bc complex. However, clade I and clade II organisms are expected to differ significantly in terms of auxiliary electron transport processes as well as NosZ active site maintenance and repair.

Linking N2O Emissions from Biofertilizer-Amended Soil of Tea Plantations to the Abundance and Structure of N2O-Reducing Microbial Communities

Nitrous oxide (N₂O) contributes up to 8% of global greenhouse gas emissions, with approximately 70% from terrestrial sources; over one-third of this terrestrial emission has been linked to increased agricultural fertilizer use. Much of the nitrogen in fertilizers is converted to N₂O by microbial processes in soil. However, the potential mechanism of biofertilizers and the role of microbial communities in mitigating soil N₂O emissions are not fully understood. Here, we used a greenhouse-based pot experiment with tea plantation soil to investigate the effect of Trichoderma viride biofertilizer on N₂O emission. The addition of biofertilizer reduced N₂O emissions from fertilized soil by 67.6%. Quantitative PCR (qPCR) analysis of key functional genes involved in N₂O generation and reduction ( amoA, nirK, nirS, and nosZ) showed an increased abundance of nirS and nosZ genes linked to the pronounced reduction in N₂O emissions. High-throughput sequencing of nosZ showed enhanced relative abundance of nosZ-harboring denitrifiers in the T. viride biofertilizer treatments, thus linking greater N₂O reduction capacity to the reduced emissions. Our findings showed that biofertilizers can affect the microbial nitrogen transformation process and reduce N₂O emissions from agroecosystems.