Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates

Arbuscular mycorrhizal fungi reduce soil N2O emissions by altering root traits and soil denitrifier community composition

Arbuscular mycorrhizal fungi (AMF) increase the ability of plants to obtain nitrogen (N) from the soil, and thus can affect emissions of nitrous oxide (N2O), a long-lived potent greenhouse gas. However, the mechanisms underlying the effects of AMF on N2O emissions are still poorly understood, particularly in agroecosystems with different forms of N fertilizer inputs. Utilizing a mesocosm experiment in field, we examined the effects of AMF on N2O emissions via their influence on maize root traits and denitrifying microorganisms under ammonia and nitrate fertilizer input using 15N isotope tracer. Here we show that the presence of AMF alone or both maize roots and AMF increased maize biomass and their 15N uptake, root length, root surface area, and root volume, but led to a reduction in N2O emissions under both N input forms. Random forest model showed that root length and surface area were the most important predictors of N2O emissions. Additionally, the presence of AMF reduced the (nirK + nirS)/nosZ ratio by increasing the relative abundance of nirS-Bradyrhizobium and Rubrivivax with ammonia input, but reducing nosZ-Azospirillum, Cupriavidus and Rhodopseudomonas under both fertilizer input. Further, N2O emissions were significantly and positively correlated with the nosZ-type Azospirillum, Cupriavidus and Rhodopseudomonas, but negatively correlated with the nirS-type Bradyrhizobium and Rubrivivax. These results indicate that AMF reduce N2O emissions by increasing root length to explore N nutrients and altering the community composition of denitrifiers, suggesting that effective management of N fertilizer forms interacting with the rhizosphere microbiome may help mitigate N2O emissions under future N input scenarios.

Effects of N levels on land productivity and N2O emissions in maize-soybean relay intercropping

BACKGROUND

Relay intercropping of maize and soybean can improve land productivity. However, the mechanism behind N2O emissions in this practice remains unclear. A two-factor randomized block field trial was conducted to reveal the mechanism of N2O emissions in a full additive maize-soybean relay intercropping. Factor A was three cropping systems - that is, monoculture maize (Zea mays L.), monoculture soybean (Glycine max L. Merr.) and maize-soybean relay intercropping. Factor B was different N supply, containing no N, reduced N and conventional N. Differences in N2O emissions, soil properties, rhizosphere bacterial communities and yield advantage were evaluated.

RESULTS

The land equivalent ratio was 1.55-2.44, and the cumulative N2O emission (C E N 2 O $$ \mathrm{C}{\mathrm{E}}_{{\mathrm{N}}_2\mathrm{O}} $$ ) was notably lower by 60.2% in intercropping than in monoculture, respectively. Reduced N declinedC E N 2 O $$ \mathrm{C}{\mathrm{E}}_{{\mathrm{N}}_2\mathrm{O}} $$ without penalty on the yield advantages. The relay intercropping shifted soil properties - for example, soil organic matter, total N,NH 4 + $$ {\mathrm{NH}}_4^{+} $$ and protease activity - and improved the soil microorganism community - for example, Proteobacteria and Acidobacteria. Intercropping reducedC E N 2 O $$ \mathrm{C}{\mathrm{E}}_{{\mathrm{N}}_2\mathrm{O}} $$ by directly suppressing nirS- and amoA-regulated N2O generation during soil N cycling, or nirS- and amoA-mediated soil properties shifted to reduceC E N 2 O $$ \mathrm{C}{\mathrm{E}}_{{\mathrm{N}}_2\mathrm{O}} $$ indirectly. Reduced N directly reducedC E N 2 O $$ \mathrm{C}{\mathrm{E}}_{{\mathrm{N}}_2\mathrm{O}} $$ by decreasing soil N content and reducing soil microorganism activities to alleviate N2O produced in soil N cycling.

CONCLUSION

Conducting a full additive maize-soybean relay intercropping with reduced nitrogen supply provides a way to alleviate N2O emissions without the penalty on the yield advantage by changing rhizosphere bacterial communities and soil N cycling. © 2024 Society of Chemical Industry.

Process of mercury accumulation in urban strip river artificial wetland ecosystems: a case study of Changchun, a typical industrial city in Northeast China

Mercury (Hg), as a global pollutant, is persistent, migratory, insidious, highly biotoxic and highly enriched, and is widely distributed in the atmosphere, hydrosphere, biosphere and lithosphere. Wetland ecosystems, as active mercury reservoirs, have become the most important sources and sinks of heavy metal mercury. Distinguished from natural wetlands, artificial wetlands located in urban sections of rivers face problems such as diverse urban pollution sources and complex spatial and temporal changes. Therefore, in this study, five intermittently distributed artificial wetlands were selected from the upstream to the downstream of the Changchun section of the Yitong River, a tributary of the Songhua River basin in the old industrial base of Northeast China. The mercury levels in the water bodies, sediments and plants of the artificial wetlands were collected and tested in four quarters from April 2023 to analyse the spatial and temporal distribution characteristics of total mercury. The results showed that the mercury levels in the water bodies, sediments and plants of the five wetlands showed a fluctuating trend with the river flow direction and had certain spatial and temporal distribution characteristics. This phenomenon was attributed to the sinking of external mercury pollution sources. In general, the wetland ecosystems showed a decreasing trend in the total Hg output of the downstream watershed. This may be due to the retention of particulate matter by aquatic plants in artificial wetlands to regular salvage of dead aquatic plants. At the same time urbanization and industrialization affect mercury levels in aquatic environments, so the risk of residential exposure needs to be looked at.

Biological inhibition of denitrification (BDI): an early plant strategy for Fallopia × bohemica seedling development

BACKGROUND AND AIMS

The successful plant Fallopia × bohemica presents interesting capacities for control of the soil nitrogen cycle at the adult stage, termed biological inhibition of denitrification (BDI). The BDI strategy allows the plant, via the production of secondary metabolites (procyanidins), to compete with the denitrifying microbial community and to divert nitrate from the soil for its benefit. In this study, we analysed whether seedlings of F. × bohemica can implement BDI at the seedling stage. We also determined whether soil nitrogen availability influences the implementation of BDI and seedling growth.

METHODS

We sowed achenes of F. × bohemica in soils representing a nitrogen gradient (six treatments) and harvested seedlings after 20 or 40 days of growth. The denitrification and related microbial communities (i.e. functional gene abundances of nirK and nirS), soil parameters (nitrate content and humidity) and plant performance (biomass, growth and root morphology) were determined.

KEY RESULTS

On soil without addition of nitrogen, BDI was observed after 20 days of growth, whereas a stimulation of denitrification was found after 40 days. The increase of soil N content had few effects on the activity and structure of the soil denitrifying community and on the plant biomasses or the relative growth rates. Correlations between plant and microbial parameters were observed after 20 days of growth, reflecting early and strong chemical interactions between plants and the denitrifying community, which decreased with plant growth after 40 days.

CONCLUSIONS

This study shows that an early BDI enhances the efficiency of nitrogen acquisition in the first weeks of growth, allowing for a conservative root strategy after 40 days. This switch to a conservative strategy involved resource storage, an altered allocation to above- and below-ground parts and an investment in fine roots. It now seems clear that this storage strategy starts at a very young age with early establishment of BDI, giving this clonal plant exceptional capacities for storage and multiplication.

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development

IMPORTANCE

Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.

Coupling of soil methane emissions at different depths under typical coastal wetland vegetation types

As an important source of atmospheric methane, methane emissions from coastal wetlands are affected by many factors. However, the methane emission process and interrelated coupling mechanisms in coastal wetland soils of a variety of environments remain unclear owing to complex interactions between intensified anthropogenic activities and climate change in recent years. In this study, we investigated methane cycling processes and the response mechanisms of environmental and microbial factors in soils at different depths under four typical coastal wetland vegetation types of the Yellow River Delta, China, using laboratory culture and molecular biology techniques. Our results show that methane generation pathways differed among the different soil layers, and that the methane emission process has a special response to soil N compounds (NO3-, NH4+). We found that nitrogen can indirectly affect methane emission by impacting key physicochemical properties (pH, oxidation reduction potential, etc.) and some functional communities (mcrA, ANME-2d, sulfate-reducing bacteria (SRB), narG, nosZII). Methane production processes in shallow soils compete closely with sulfate reduction processes, while methane emissions facilitated in deeper soils due to denitrification processes. We believe that our results provide a reference for future research and wetland management practices that seek to mitigate the global greenhouse effect and climate change.

Bacillus paralicheniformis 2R5 and its impact on canola growth and N-cycle genes in the rhizosphere

Chemical fertilization has a negative impact on the natural environment. Plant growth-promoting (PGP) rhizobacterial biofertilizers can be a safer alternative to synthetic agrochemicals. In this research, a culture-based method was used to assess the population size of rhizobacteria at the vegetative, flowering, and maturity stages of canola. Rhizobacteria were then isolated from each of the canola growth stages, and their seven PGP traits were determined. The highest abundance of culturable bacteria was found at the vegetative stage of the plants. Furthermore, four out of seven PGP traits were produced by the highest % of isolates at the vegetative stage. In the greenhouse experiment that included six rhizobacterial strains with best PGP traits, the greatest canola growth promotion ability under sterile conditions was observed after the introduction of Bacillus paralicheniformis 2R5. Moreover, under nonsterile conditions, 2R5 significantly increased canola growth. The presence of the trpA, B, C, D, E, F and pstA, and S genes in the 2R5 genome could be associated with canola growth promotion abilities. The chiA and mbtH genes could contribute to 2R5 antifungal activity against fungal pathogens. Moreover, the introduction of 2R5 significantly increased the abundance of the narG, nosZ, nifH, and nirS genes, which can prove that the 2R5 strain may be an important member of the soil bacterial community.

Sunlight Significantly Enhances Soil Denitrification via an Interfacial Biophotoelectrochemical Pathway

Denitrification is an essential step of the nitrogen cycle in soil. However, although sunlight is an important environmental factor for soil, the investigation of the influence of sunlight on soil denitrification is limited to plant photosynthesis-mediated processes. Herein, a new pathway, denoted as a biophotoelectrochemical process, which is induced by the direct photoexcitation of soil, was found to greatly enhance soil denitrification. Using red soil as the research object, the soil with irradiation showed nitrate reduction that was 2.6-4.7 times faster than that without irradiation. The irradiation of soil accelerated the reduction of nitrite and enhanced the conversion of nitrous oxide to nitrogen, indicating that more electron sources were generated. This resulted from the photoinduced generation of ferrous substrates and photoelectrons. The contribution of irradiation to soil denitrification was almost half (45.4%), of which 30.9% was from photoinduced ferrous substrates and 14.5% was from photoelectrons. Moreover, a designed biophotoelectrochemical cell provided solid evidence for direct photoelectron transfer from soil photosensitive substrates to microorganisms. Irradiation promoted the enrichment of Alicyclobacillus, which participates in iron oxidation and electroautotrophy. This finding reveals a role of sunlight in soil denitrification that has been thus seriously overlooked and provides solid evidence for the natural occurrence of photoelectrotrophic effects.

Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China

Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH₄). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO₃^-), sulfate (SO₄^2-), and nitrous oxide (N₂O) flux, among them, soil N substances (TN, NO₃^-, N₂O) have essential regulatory roles in the AOM process, while NO₃^- and N₂O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH₄ sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH₄ biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.

Soil net N mineralization and hydraulic properties of carbonate-derived laterite under different vegetation types in Karst forests of China

Soil net nitrogen (N) mineralization (N_min) is a key process in the forest N cycle regulating the N availability of plant growth. However, it is unclear how N transformation responds to soil hydraulic properties changes. The soil inorganic N pools and N transformation in the early growing season in karst forestlands were investigated by using an intact soil core in situ incubation method. Three different typical vegetation types were selected. The results showed that the mean values of NH₄⁺-N, NO₃^--N, and inorganic N were 1.05-1.36, 1.55-3.85, and 1.05-2.34 times greater for ferns than for shrubs. NO₃^--N and NH₄⁺-N mainly occur at soil depths of 0-5 cm and 5-15 cm, respectively. The soil N_min was 2.21-232.03 times higher at 0-5 cm than at the 10-15 cm. Net N immobilization was found for the juvenile ferns and shrubs at 5-15 cm. The N_min of juvenile and mature ferns was 1.90-11.78 times and 1.17-16.20 times higher than shrubs, respectively, and shrubs had the highest K_s (69.91 mm h^-1) but the lowest water-holding capacity. Both ferns and shrubs were able to hold more water and available water was richest in mature fern soil, which provided an extra water source for fern growth. Principal component analysis (PCA) was used to test whether the measured variables affected N_min, and the results showed that soil organic matter (SOM), pH, and saturated volumetric water content (θ_s) were the main soil factors affecting N_min. In addition, the NH₄⁺-N, NO₃^--N, and inorganic N stocks were reduced by 3.98 %-59.04 %, 48.07 %-63.30 % and 8.18 %-57.37 % after rainwater input, respectively. Our findings suggest that soil inorganic N and N_min in the karst forest were regulated by soil hydraulic properties. Changes in the soil hydraulic properties might therefore influence the functioning of soil N transformation.

Arbuscular Mycorrhizae Shift Community Composition of N-Cycling Microbes and Suppress Soil N2O Emission

Mycorrhizae are ubiquitous symbiotic associations between arbuscular mycorrhizal fungi (AMF) and terrestrial plants, in which AMF receive photosynthates from and acquire soil nutrients for their host plants. Plant uptake of soil nitrogen (N) reduces N substrate for microbial processes that generate nitrous oxide (N₂O), a potent greenhouse gas. However, the underlying microbial mechanisms remain poorly understood, particularly in agroecosystems with high reactive N inputs. We examined how plant roots and AMF affect N₂O emissions, N₂O-producing (nirK and nirS) and N₂O-consuming (nosZ) microbes under normal and high N inputs in conventional (CONV) and organically managed (OM) soils. Here, we show that high N input increased soil N₂O emissions and the ratio of nirK to nirS microbes. Roots and AMF did not affect the (nirK + nirS)/nosZ ratio but significantly reduced N₂O emissions and the nirK/nirS ratio. They reduced the nirK/nirS ratio by reducing nirK-Rhodobacterales but increasing nirS-Rhodocyclales in the CONV soil while decreasing nirK-Burkholderiales but increasing nirS-Rhizobiales in the OM soil. Our results indicate that plant roots and AMF reduced N₂O emission directly by reducing soil N and indirectly through shifting the community composition of N₂O-producing microbes in N-enriched agroecosystems, suggesting that harnessing the rhizosphere microbiome through agricultural management might offer additional potential for N₂O emission mitigation.

Root exudate chemistry affects soil carbon mobilization via microbial community reassembly

Plant roots are one of the major mediators that allocate carbon captured from the atmosphere to soils as rhizodeposits, including root exudates. Although rhizodeposition regulates both microbial activity and the biogeochemical cycling of nutrients, the effects of particular exudate species on soil carbon fluxes and key rhizosphere microorganisms remain unclear. By combining high-throughput sequencing, q-PCR, and NanoSIMS analyses, we characterized the bacterial community structure, quantified total bacteria depending on root exudate chemistry, and analyzed the consequences on the mobility of mineral-protected carbon. Using well-controlled incubation experiments, we showed that the three most abundant groups of root exudates (amino acids, carboxylic acids, and sugars) have contrasting effects on the release of dissolved organic carbon (DOC) and bioavailable Fe in an Ultisol through the disruption of organo-mineral associations and the alteration of bacterial communities, thus priming organic matter decomposition in the rhizosphere. High resolution (down to 50 nm) NanoSIMS images of mineral particles indicated that iron and silicon co-localized significantly more organic carbon following amino acid inputs than treatments without exudates or with carboxylic acids. The application of sugar strongly reduced microbial diversity without impacting soil carbon mobilization. Carboxylic acids increased the prevalence of Actinobacteria and facilitated carbon mobilization, whereas amino acid addition increased the abundances of Proteobacteria that prevented DOC release. In summary, root exudate functions are defined by their chemical composition that regulates bacterial community composition and, consequently, the biogeochemical cycling of carbon in the rhizosphere.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Assembly of root-associated N2O-reducing communities of annual crops is governed by selection for nosZ clade I over clade II

The rhizosphere is a hotspot for denitrification. The nitrous oxide (N2O) reductase among denitrifiers and nondenitrifying N2O reducers is the only known N2O sink in the biosphere. We hypothesized that the composition of root-associated N2O-reducing communities when establishing on annual crops depend on soil type and plant species, but that assembly processes are independent of these factors and differ between nosZ clades I and II. Using a pot experiment with barley and sunflower and two soils, we analyzed the abundance, composition, and diversity of soil and root-associated N2O reducing communities by qPCR and amplicon sequencing of nosZ. Clade I was more abundant on roots compared to soil, while clade II showed the opposite. In barley, this pattern coincided with N2O availability, determined as potential N2O production rates, but for sunflower no N2O production was detected in the root compartment. Root and soil nosZ communities differed in composition and phylogeny-based community analyses indicated that assembly of root-associated N2O reducers was driven by the interaction between plant and soil type, with inferred competition being more influential than habitat selection. Selection between clades I and II in the root/soil interface is suggested, which may have functional consequences since most clade I microorganisms can produce N2O.

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.

Effects of exogenous organic acids and flooding on root exudates, rhizosphere bacterial community structure, and iron plaque formation in Kandelia obovata seedlings

The rhizosphere of coastal wetland plants is the active interface of iron (Fe) redox transformation. However, coupling mechanism between organic acids (OAs) exuded by plant roots and Fe speciation transformation participated by Fe redox cycling bacteria in the rhizosphere is still unclear. Effects of four common OAs (citric acid, malic acid, tartaric acid, and oxalic acid) on root exudation, rhizosphere bacterial community structure, root Fe plaque, and Fe redox cycling bacterial communities of Kandelia obovata were investigated in this study. Long-term flooding (10 h) was conducive to K. obovata seedlings exuding additional dissolved organic carbon (DOC) and nitrogen and phosphorus organic matter (NH₄⁺-N, NO₃^--N, and dissolved inorganic phosphorus [DIP]) under each OA level. DOC, NH₄⁺-N, NO₃^--N, and DIP in root exudates increased significantly with the increase of exogenous OA level. Notably, long flooding time corresponds to an evidently increasing trend. Exogenous OAs also significantly increased contents of formic and oxalic acids in root exudates. Exogenous OAs and flooding enhanced the rhizosphere effect of K. obovata and significantly enhanced bacterial diversity of the rhizosphere and relative abundance of dominant bacteria in rhizoplane. Bacterial diversity in the rhizosphere of K. obovata seedlings was significantly higher than that in the rhizoplane under the same level of OAs and flooding. Fe plaque content of K. obovata root decreased significantly and the relative abundance of typical Fe-oxidizing bacteria, such as Gallionella, unclassified_f__Gallionellaceae, and Sideroxydans, decreased significantly in the rhizosphere but increased significantly in the rhizoplane with the increase of the treatment level of exogenous OAs. This finding is likely due to the Fe³⁺ reduction caused by acidification of rhizosphere environment after exogenous OA treatment rather than the result of chemotactic colonization of Fe redox cycling bacteria in the rhizoplane.

Influence of Leguminous Cover Crops on Soil Chemical and Biological Properties in a No-Till Tropical Fruit Orchard

South Florida’s agricultural soils are traditionally low in organic matter (OM) and high in carbonate rock fragments. These calcareous soils are inherently nutrient-poor and require management for successful crop production. Sunn hemp (SH, Crotalaria juncea) and velvet bean (VB, Mucuna pruriens) are highly productive leguminous cover crops (CCs) that have shown potential to add large quantities of dry biomass to nutrient- and organic-matter-limited systems. This study focuses on intercropping these two CCs with young carambola (Averrhoa carambola) trees. The objective was to test the effectiveness of green manure crops in providing nutrients and supplementing traditional fertilizer regimes with a sustainable soil-building option. Typically, poultry manure (PM) is the standard fertilizer used in organic or sustainable production in the study area. As such, PM treatments and fallow were included for comparison. The treatments were fallow control (F), fallow with PM (FM), sunn hemp (SH), SH with PM (SHM), velvet bean (VB), and VB with PM (VBM). Sunn hemp and VB were grown for two summer growing seasons. At the end of each 90-day growing period, the CCs were terminated and left on the soil surface to decompose in a no-till fashion. The results suggest that SH treatments produced the greatest amount of dry biomass material ranging from 48 to 71% higher than VB over two growing seasons. As a result, SH CCs also accumulated significantly higher amounts of total carbon (TC) and total nitrogen (TN) within their dry biomass that was added to the soil. Sunn hemp, SHM, and FM treatments showed the greatest accumulation of soil OM, TC, and TN. Soil inorganic N (NH₄⁺ + NO3− + NO2) fluctuated throughout the experiment. Our results indicate that generally, VB-treated soils had their highest available N around 2 months post termination, while SH-treated soils exhibited significantly higher N values at CC termination time. Sunn hemp + PM (SHM)treatments had highest soil N availability around 4 months after CC termination. Soil enzyme activity results indicate that at CC termination, SHM exhibited the highest levels of β-1-4- glucosidase and β-N-acetylglucosaminidase among all treatments. Overall, SH, SHM, and FM treatments showed the greatest potential for supplementing soil nutrients and organic matter in a no-till fruit production setting.

Effects of rumen undegradable protein sources on nitrous oxide, methane and ammonia emission from the manure of feedlot-finished cattle

The effects of sources of rumen undegradable protein (RUP) in diets on methane (CH₄), nitrous oxide (N₂O) and ammonia (NH₃) emissions from the manure of feedlot-finished cattle were evaluated. We hypothesized that the use of different RUP sources in diets would reduce N loss via urine and contribute to reduced N₂O, CH₄ and NH₃ emissions to the environment. Nellore cattle received different diets (18 animals/treatment), including soybean meal (SM, RDP source), by-pass soybean meal (BSM, RUP source) and corn gluten meal (CGM, RUP source). The protein source did not affect the N and C concentration in urine, C concentration in feces, and N balance (P > 0.05). The RUP sources resulted in a higher N₂O emission than the RDP source (P = 0.030), while BSM resulted in a higher N₂O emission than CGM (P = 0.038) (SM = 633, BSM = 2521, and CGM = 1153 g ha⁻² N–N₂O); however, there were no differences in CH₄ and NH₃ emission (P > 0.05). In conclusion, the use of RUP in diets did not affect N excretion of beef cattle or CH₄ and NH₃ emission from manure, but increased N₂O emission from the manure.

Soil Inoculation With Beneficial Microbes Buffers Negative Drought Effects on Biomass, Nutrients, and Water Relations of Common Myrtle

Common myrtle (Myrtus communis L.) occurs in (semi-)arid areas of the Palearctic region where climate change, over-exploitation, and habitat destruction imperil its existence. The evergreen shrub is of great economic and ecological importance due to its pharmaceutical value, ornamental use, and its role in urban greening and habitat restoration initiatives. Under greenhouse conditions, we investigated the effect of soil inoculation with arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) on biomass allocation, water relations, and nutritional status of drought-stressed myrtle seedlings. Single and dual AMF (Funneliformis mosseae and Rhizophagus irregularis) and PGPR (Pseudomonas fluorescens and P. putida) soil inoculations were applied to myrtle seedlings growing under different soil water regimes (100, 60, and 30% of field capacity) for 6 months using a full factorial, completely randomized design. AMF and PGPR treatments, especially dual inoculations, alleviated negative drought effects on biomass and morpho-physiological traits, except for water-use efficiency, which peaked under severe drought conditions. Under the greatest soil water deficit, dual inoculations promoted leaf biomass (104%-108%), root biomass (56%-73%), mesophyll conductance (58%), and relative water content (1.4-fold) compared to non-inoculated controls. Particularly, dual AMF and PGPR inoculations stimulated nutrient dynamics in roots (N: 138%-151%, P: 176%-181%, K: 112%-114%, Ca: 124%-136%, and Mg: 130%-140%) and leaves (N: 101%-107%, P: 143%-149%, K: 83%-84%, Ca: 98%-107%, and Mg: 102%-106%). Our findings highlight soil inoculations with beneficial microbes as a cost-effective way to produce highly drought resistant seedling stock which is vital for restoring natural myrtle habitats and for future-proofing myrtle crop systems.

Effects of nitrogen and phosphorus enrichment on soil N2O emission from natural ecosystems: A global meta-analysis

Nitrogen (N) and phosphorous (P) enrichment play an important role in regulating soil N₂O emission, but their interactive effect remains elusive (i.e. whether the effect of P or N enrichment on soil N₂O emission varies between ambient and elevated soil N or P conditions). Here, we conducted a Bayesian meta-analysis across the global natural ecosystems to determine this effect. Our results showed that P enrichment significantly decreased soil N₂O emission by 13.9% at ambient soil N condition. This N₂O mitigation is likely due to the decreased soil NO₃^--N content (-17.6%) derived by the enhanced plant uptake when the P limitation was alleviated by P enrichment. However, this P-induced N₂O (and NO₃^--N) mitigation was not found at elevated soil N condition. Additionally, N enrichment significantly increased soil N₂O emission by 101.4%, which was associated with the increased soil NH₄⁺-N (+41.0%) and NO₃^--N (+82.3%). However, the effect of N enrichment on soil N₂O emission did not differ between ambient and elevated soil P subgroups, indicating that the P-derived N₂O mitigation could be masked by N enrichment. Further analysis showed that manipulated N rate, soil texture, soil dissolved organic nitrogen, soil total nitrogen, soil organic carbon, soil pH, aboveground plant biomass, belowground plant biomass, and plant biomass nitrogen were the main factors affecting soil N₂O emission under N enrichment. Taken together, our study provides evidence that P enrichment has the potential to reduce soil N₂O emission from natural ecosystems, but this mitigation effect could be masked by N enrichment.

Substrate pH Influences the Nutrient Absorption and Rhizosphere Microbiome of Huanglongbing-Affected Grapefruit Plants

The substrate pH directly affects nutrient availability in the rhizosphere and nutrient uptake by plants. Macronutrients such as nitrogen, potassium, calcium, magnesium, and sulfur are highly available at pH 6.0-6.5, while micronutrients become less available at higher, alkaline pH (pH > 7.0). Recent research has indicated that low pHs can enhance nutrient uptake and improve sweet orange (Citrus sinensis) tree health. We designed a study to understand the influence of a wide range of substrate pH values on plant size and biomass, nutrient availability, leaf gas exchange, and rhizosphere microbiome of grapefruit (Citrus paradisi) affected by Huanglongbing (HLB). Two-year-old "Ray Ruby" grapefruit plants grafted on sour orange (Citrus aurantium) rootstock were cultivated indoors in 10-cm wide × 40-cm tall pots with peat:perlite commercial substrate (80:20 v/v). We tested two disease statuses [HLB-free or healthy (negative, HLB-) and HLB-affected (positive, HLB+)] and six substrate pH values (4, 5, 6, 7, 8, 9) in a 2 × 6 factorial arranged on a complete randomized design with four replications. The canopy volume of HLB+ plants was 20% lower than healthy plants, with pHs 7 and 9 resulting in 44% less canopy volume. The root and shoot ratio of dry weight was 25.8% lower in HLB+ than in healthy plants. Poor root growth and a decrease in fibrous roots were found, especially in pH 5 and 6 treatments in HLB+ plants (p < 0.0001). The disease status and the substrate pHs influenced the leaf nutrient concentration (p < 0.05). High substrate pH affects nutrient availability for root uptake, influencing the nutrient balance throughout the plant system. pH values did not affect plant photosynthesis, indicating that pH does not recover HLB+ plants to the photosynthetic levels of healthy plants-even though high pH positively influenced internal CO₂. There were collectively over 200 rhizobacterial identified by the 16S rRNA gene sequencing in individual phylogenetic trees. Most rhizobacteria reads were identified in pH 9. Our results indicated no effect of substrate pHs on the plant disease status induced by enhanced nutrient uptake.

Pathways of soil N2O uptake, consumption, and its driving factors: a review

Nitrous oxide (N₂O) is an important greenhouse gas that plays a significant role in atmospheric photochemical reactions and contributes to stratospheric ozone depletion. Soils are the main sources of N₂O emissions. In recent years, it has been demonstrated that soil is not only a source but also a sink of N₂O uptake and consumption. N₂O emissions at the soil surface are the result of gross N₂O production, uptake, and consumption, which are co-occurring processes. Soil N₂O uptake and consumption are complex biological processes, and their mechanisms are still worth an in-depth systematic study. This paper aimed to systematically address the current research progress on soil N₂O uptake and consumption. Based on a bibliometric perspective, this study has highlighted the pathways of soil N₂O uptake and consumption and their driving factors and measurement techniques. This systematic review of N₂O uptake and consumption will help to further understand N transformations and soil N₂O emissions.

Promotion mechanism of self-transmissible degradative plasmid transfer in maize rhizosphere and its application in naphthalene degradation in soil

Rhizospheres can promote self-transmissible plasmid transfer, however, the corresponding mechanism has not received much attention. Plant-microbe remediation is an effective way to promote pollutant biodegradation; however, some pollutants, such as naphthalene, are harmful to plants and result in inefficient plant-microbe remediation. In this study, transfer of a TOL-like plasmid, a self-transmissible plasmid loaded with genetic determinants for pollutant degradation, among different bacteria was examined in bulk and rhizosphere soils as well as addition of maize root exudate and its artificial root exudate (ARE). The results showed that the numbers of transconjugants and recipients as well as bacterial metabolic activities, such as xylE mRNA expression levels and catechol 2,3-dioxygenase (C23O) activities of bacteria, remained high in rhizosphere soils, when compared with bulk soils. The number of transconjugants and bacterial metabolic activities increased with the increasing exudate and ARE concentrations, whereas the populations of donor and recipient bacteria were substantially unaltered at all concentrations. All the experiments consistently showed that a certain number of bacteria is required for self-transmissible plasmid transfer, and that the increased plasmid transfer might predominantly be owing to bacterial metabolic activity stimulated by root exudates and ARE. Furthermore, ARE addition increased naphthalene degradation by transconjugants in both culture medium and soil. Thus, the combined action of a wide variety of components in ARE might contribute to the increased plasmid transfer and naphthalene degradation. These findings suggest that ARE could be an effectively alternative for plant-microbe remediation of pollutants in environments where plants cannot survive.

Unconventional microbial mechanisms for the key factors influencing inorganic nitrogen removal in stormwater bioretention columns

Bioretention systems are environmentally friendly measures to control the amount of water and pollutants in urban stormwater runoff, and their treatment performance for inorganic N strongly depends on various microbial processes. However, microbial responses to variations of N mass reduction in bioretention systems are complex and poorly understood, which is not conducive to management designs. In the present study, a series of bioretention columns were established to monitor their fate performance for inorganic N (NH4+and NO3-) by using different configurations and by dosing with simulated stormwater events. The results showed that NH4+ was efficiently oxidized to NO3-, mainly by ammonia- and nitrite-oxidizing bacteria in the oxic media, regardless of the configurations of the bioretention systems or stormwater conditions. In contrast, NO3- removal pathways varied greatly in different columns. The presence of vegetation efficiently improved NO3-mass reduction through root assimilation and enhancement of microbial NO3- reduction in the rhizosphere. The construction of an organic-rich saturation zone can make the redox potential too low for heterotrophic denitrification to occur, so as to ensure high NO3- mass reduction mainly via stimulating chemolithotrophic NO3- reduction coupled with oxidation of reductive sulfur compounds derived from the bio-reduction of sulfate. In contrast, in the organic-poor saturation zone, multiple oligotrophic NO3- reduction pathways may be responsible for the high NO3- mass reduction. These findings highlight the necessity of considering the variation of N bio-transformation pathways for inorganic N removal in the configuration of bioretention systems.

CH4 and N2O Emissions From Cattle Excreta: A Review of Main Drivers and Mitigation Strategies in Grazing Systems

Cattle production systems are an important source of greenhouse gases (GHG) emitted to the atmosphere. Animal manure and managed soils are the most important sources of emissions from livestock after enteric methane. It is estimated that the N2O and CH4 produced in grasslands and manure management systems can contribute up to 25% of the emissions generated at the farm level, and therefore it is important to identify strategies to reduce the fluxes of these gases, especially in grazing systems where mitigation strategies have received less attention. This review describes the main factors that affect the emission of GHG from manure in bovine systems and the main strategies for their mitigation with emphasis on grazing production systems. The emissions of N2O and CH4 are highly variable and depend on multiple factors, which makes it difficult to use strategies that mitigate both gases simultaneously. We found that strategies such as the optimization of the diet, the implementation of silvopastoral systems and other practices with the capacity to improve soil quality and cover, and the use of nitrogen fixing plants are among the practices with more potential to reduce emissions from manure and at the same time contribute to increase carbon capture and improve food production. These strategies can be implemented to reduce the emissions of both gases and, depending on the method used and the production system, the reductions can reach up to 50% of CH4 or N2O emissions from manure according to different studies. However, many research gaps should be addressed in order to obtain such reductions at a larger scale.

A review of root exudates and rhizosphere microbiome for crop production

Increasing crop yields and ensuring food security is a major global challenge. In order to increase crop production, chemical fertilizers and pesticides are excessively used. However, the significance of root exudates is understudied. Beneficial interactions between plant and rhizosphere microbiome are critical for plant fitness and health. In this review, we discuss the application and progress of current research methods and technologies in terms of root exudates and rhizosphere microbiome. We summarize how root exudates promote plant access to nitrogen, phosphorus, and iron, and how root exudates strengthen plant immunity to cope with biotic stress by regulating the rhizosphere microbiome, and thereby reducing dependence on fertilizers and pesticides. Optimizing these interactions to increase plant nutrient uptake and resistance to biotic stresses offers one of the few untapped opportunities to confront sustainability issues in food security. To overcome the limitations of current research, combination of multi-omics, imaging technology together with synthetic communities has the potential to uncover the interaction mechanisms and to fill the knowledge gap for their applications in agriculture to achieve sustainable development.

No Tangible Effects of Field-Grown Cisgenic Potatoes on Soil Microbial Communities

DNA modification techniques are increasingly applied to improve the agronomic performance of crops worldwide. Before cultivation and marketing, the environmental risks of such modified varieties must be assessed. This includes an understanding of their effects on soil microorganisms and associated ecosystem services. This study analyzed the impact of a cisgenic modification of the potato variety Desirée to enhance resistance against the late blight-causing fungus Phytophthora infestans (Oomycetes) on the abundance and diversity of rhizosphere inhabiting microbial communities. Two experimental field sites in Ireland and the Netherlands were selected, and for 2 subsequent years, the cisgenic version of Desirée was compared in the presence and absence of fungicides to its non-engineered late blight-sensitive counterpart and a conventionally bred late blight-resistant variety. At the flowering stage, total DNA was extracted from the potato rhizosphere and subjected to PCR for quantifying and sequencing bacterial 16S rRNA genes, fungal internal transcribed spacer (ITS) sequences, and nir genes encoding for bacterial nitrite reductases. Both bacterial and fungal communities responded to field conditions, potato varieties, year of cultivation, and bacteria sporadically also to fungicide treatments. At the Dutch site, without annual replication, fungicides stimulated nirK abundance for all potatoes, but with significance only for cisgenic Desirée. In all other cases, neither the abundance nor the diversity of any microbial marker differed between both Desirée versions. Overall, the study demonstrates environmental variation but also similar patterns of soil microbial diversity in potato rhizospheres and indicates that the cisgenic modification had no tangible impact on soil microbial communities.

Effect of perfluorooctanesulfonate (PFOS) on the rhizosphere soil nitrogen cycling of two riparian plants

Here, we examined the effects of low and high concentrations of perfluorooctanesulfonate (PFOS) on rhizosphere soil N cycling processes in the presence of Lythrum salicaria and Phragmites communis over 4 months. Compared with the control group, the nitrate nitrogen (NO₃^--N) content of the bulk soil in the low PFOS (0.1 mg kg^-1) treatment significantly decreased (27.7%), the ammonium nitrogen (NH₄⁺-N) content significantly increased (8.7%), and the pH value and total organic carbon (TOC) content slightly increased (0.3% and 1.1%, respectively). Compared with the low PFOS treatment, the content of NO₃^-N, NH₄⁺-N and pH value in the bulk soil of the high PFOS treatment (50 mg kg^-1) significantly increased (1.0%, 53.8% and 61.8%, respectively), and the TOC content significantly decreased (8.2%). Soil protease levels were high in the low PFOS treatment, but low in the high PFOS treatment. PFOS produced inverted U-shaped responses in the potential nitrification (1.5, 3.0, and 1.1 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively), denitrification (0.19, 0.30, and 0.22 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively), and N₂O emission rates (0.01, 0.03, and 0.02 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively) of bulk soil. The abundance of the archaea amoA gene decreased with increasing PFOS concentration, whereas that of bacterial amoA increased; inverted U-shaped responses were observed for narG, nirK, nirS, and nosZ. In the PFOS-contaminated rhizosphere soil, the observed changes differed from those in the bulk soil and differed between treatments. P. communis tended to upregulate each step of the nitrogen cycle under low PFOS conditions, whereas L. salicaria tended to inhibit them. Under high PFOS conditions, both test plants tended to act as inhibitors of the soil N-cycle; thus, the effects of PFOS on soil N transformation were plant-specific.

Structure of greenhouse gas-consuming microbial communities in surface soils of a nitrogen-removing experimental drainfield

Septic systems represent a source of greenhouse gases generated by microbial processes as wastewater constituents are degraded. Both aerobic and anerobic wastewater transformation processes can generate nitrous oxide and methane, both of which are potent greenhouse gases (GHGs). To understand how microbial communities in the surface soils above shallow drainfields contribute to methane and nitrous oxide consumption, we measured greenhouse gas surface flux and below-ground concentrations and compared them to the microbial communities present using functional genes pmoA and nosZ. These genes encode portions of particulate methane monooxygenase and nitrous oxide reductase, respectively, serving as a potential sink for the respective greenhouse gases. We assessed the surface soils above three drainfields served by a single household: an experimental layered passive N-reducing drainfield, a control conventional drainfield, and a reserve drainfield not in use but otherwise identical to the control. We found that neither GHG flux, below-ground concentration or soil properties varied among drainfield types, nor did methane oxidizing and nitrous oxide reducing communities vary by drainfield type. We found differences in pmoA and nosZ communities based on depth from the soil surface, and differences in nosZ communities based on whether the sample came from the rhizosphere or surrounding bulk soils. Type I methanotrophs (Gammaproteobacteria) were more abundant in the upper and middle portions of the soil above the drainfield. In general, we found no relationship in community composition for either gene based on GHG flux or below-ground concentration or soil properties (bulk density, organic matter, above-ground biomass). This is the first study to assess these communities in the surface soils above an experimental working drainfield, and more research is needed to understand the dynamics of greenhouse gas production and consumption in these systems.

Edaphic factors and plants influence denitrification in soils from a long-term arable experiment

Factors influencing production of greenhouse gases nitrous oxide (N₂O) and nitrogen (N₂) in arable soils include high nitrate, moisture and plants; we investigate how differences in the soil microbiome due to antecedent soil treatment additionally influence denitrification. Microbial communities, denitrification gene abundance and gas production in soils from tilled arable plots with contrasting fertilizer inputs (no N, mineral N, FYM) and regenerated woodland in the long-term Broadbalk field experiment were investigated. Soil was transferred to pots, kept bare or planted with wheat and after 6 weeks, transferred to sealed chambers with or without K¹⁵NO₃ fertilizer for 4 days; N₂O and N₂ were measured daily. Concentrations of N₂O were higher when fertilizer was added, lower in the presence of plants, whilst N₂ increased over time and with plants. Prior soil treatment but not exposure to N-fertiliser or plants during the experiment influenced denitrification gene (nirK, nirS, nosZI, nosZII) relative abundance. Under our experimental conditions, denitrification generated mostly N₂; N₂O was around 2% of total gaseous N₂ + N₂O. Prior long-term soil management influenced the soil microbiome and abundance of denitrification genes. The production of N₂O was driven by nitrate availability and N₂ generation increased in the presence of plants.

Characteristics and Driving Factors of the Aerobic Denitrifying Microbial Community in Baiyangdian Lake, Xiong'an New Area

Here, the ion-exchangeable form of nitrogen (IEF-N), weak-acid extractable form of nitrogen (WAEF-N), strong-alkali extractable form of nitrogen (SAEF-N), strong-oxidant extractable form of nitrogen (SOEF-N), residue nitrogen (Res-N), and total nitrogen (TN) showed spatial differences, and most of the sediment nitrogen fractions exhibited positive correlations in Baiyangdian Lake. High-throughput sequencing analysis revealed that the aerobic denitrification microbial community was composed of proteobacteria (42.04%–99.08%) and unclassified_bacteria (0.92%–57.92%). Moreover, the microbial community exhibited significant differences (R² = 0.4422, P < 0.05) on the basis of the adonis analysis. T(temperature), Moisture content (MC), sediment total phosphorus (STP), ion-exchangeable form of ammonia (IEF-NH₄⁺-N), weak-acid extractable form of ammonia (WAEF-NH₄⁺-N), weak-acid extractable form of nitrate (WAEF-NO₃⁻-N), and strong-alkali extractable form of ammonia (SAEF-NH₄⁺-N) were the dominant environmental factors and explained 11.1%, 8.2%, 10.7%, 6.9%, 9.3%, 8.1%, 10.5%, 7.5%, and 7% variation, respectively, of the total variation in the microbial community. Furthermore, the network analysis showed that symbiotic relationships accounted for a major percentage of the microbial networks. The keystone aerobic denitrifying bacteria belonged to Comamonas, Rhodobacter, Achromobacter, Aeromonas, Azoarcus, Leptothrix_Burkholderiales, Pseudomonas, Thauera, unclassified_Burkholderiales, and unclassified_bacteria. The composition of the keystone aerobic denitrifying microbial community also exhibited significant differences (R² = 0.4534, P < 0.05) on the basis of the adonis analysis. T, STP, IEF-NH₄⁺-N, ion-exchangeable form of nitrate (IEF-NO₃⁻-N), WAEF-NO₃⁻-N, SAEF-NH₄⁺-N, and TN were the dominant environmental factors that explained 8.4%, 6.2%, 4.6%, 5.9%, 5.9%, 4.5%, and 9.4% variation, respectively, of the total variation in the keystone aerobic denitrifying microbial community. The systematic investigation could provide a theoretical foundation for the evolution mechanism of the aerobic denitrifying microbial community in Baiyangdian Lake.

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.

Changes of Soil Microbes Related with Carbon and Nitrogen Cycling after Long-Term CO2 Enrichment in a Typical Chinese Maize Field

Elevated atmospheric CO2 concentration (eCO2) has been the most important driving factor and characteristic of climate change. To clarify the effects of eCO2 on the soil microbes and on the concurrent status of soil carbon and nitrogen, an experiment was conducted in a typical summer maize field based on a 10-year mini FACE (Free Air Carbon Dioxide Enrichment) system in North China. Both rhizospheric and bulk soils were collected for measurement. The soil microbial carbon (MBC), nitrogen (MBN), and soil mineral N were measured at two stages. Characteristics of microbes were assayed for both rhizospheric soil and bulk soils at the key stage. We examined the plasmid copy numbers, diversities, and community structures of bacteria (in terms of 16s rRNA), fungi (in terms of ITS-internal transcribed spacer), ammonia oxidizing bacteria (AOB) and denitrifiers including nirK, nirS, and nosZ using the Miseq sequencing technique. Results showed that under eCO2 conditions, both MBC and MBN in rhizospheric soil were increased significantly. The quantity of ITS was increased in the eCO2 treatment compared with that in the ambient CO2 (aCO2) treatment, while the quantity of 16s rRNA in rhizospheric soil showed decrease in the rhizospheric soil in the eCO2 treatment. ECO2 changed the relative abundance of microbes in terms of compositional proportion of some orders or genera particularly in the rhizospheric soil-n particular, Chaetomium increased for ITS, Subgroups 4 and 6 increased for 16s rRNA, Nitrosospira decreased for AOB, and some genera showed increase for nirS, nirK, and nosZ. Nitrate N was the main inorganic nitrogen form at the tasseling stage and both quantities of AOB and denitrifiers, as well as the nosZ/(nirS+nirK) showed an increase under eCO2 conditions particularly in the rhizospheric soil. The Nitrosospira decreased in abundance under eCO2 conditions in the rhizospheric soil and some genera of denitrifiers also showed differences in abundance. ECO2 did not change the diversities of microbes significantly. In general, results suggested that 10 years of eCO2 did affect the active component of C and N pools (such as MBC and MBN) and both the quantities and relative abundance of microbes which are involved in carbon and nitrogen cycling, possibly due to the differences in both the quantities and component of substrate for relevant microbes in the rhizospheric soils.

A comparison of nitrate removal and denitrifying bacteria populations among three wetland plant communities

Reed canary grass (Phalaris arundinacea L.) is an invasive, cool-season grass commonly dominating wetlands with high nutrient loads. Its impact on nitrogen removal via denitrification in wetlands is unknown. Most studies of denitrification in treatment wetlands have focused on the effects of physical or chemical variables and not on the effects of plant roots on the soil environment. The purpose of this study was to measure effects of plant type on denitrification rates in typical wetland soils of the midwestern United States by comparing wet prairie mix, switchgrass-dominated, and reed canary grass plant communities. Nitrate (NO₃ ^- ) removal and other parameters were measured in miniature wetlands, or mesocosms, containing each plant community transplanted from a small agricultural treatment wetland in southern Minnesota. Quantitative polymerase chain reaction analysis was used to quantify the total bacteria population (measured with 16S rRNA genes) and denitrifying gene abundance (measured with nosZ genes) from the rhizosphere of each plant community. The wet prairie mix mesocosms on average removed the most NO₃ ^- in each test (p = .01 and .08). Whereas the wet prairie mix removed the most NO₃ ^- from the surface water (p < .01), reed canary grass removed more from the subsurface (p < .01). Ratios of denitrifying to total bacteria were higher in the wet prairie mix than in the other communities' root zones (p < .05). Results suggest that reed canary grass invasion could reduce denitrification in wetlands, especially during the spring and fall when it is growing but other plants are dormant.

Effects of antibiotics on microbial community structure and microbial functions in constructed wetlands treated with artificial root exudates

In the rhizosphere, plant root exudates can mediate the toxicity of antibiotics on microorganisms, yet the mechanisms are poorly understood. To simulate the antibiotic contamination of global rivers and lakes, the current study investigated the effects of two antibiotics (ofloxacin at 8.69 × 10⁴ ng L^-1 and tetracycline at 8.62 × 10⁴ ng L^-1) and their binary combination (8.24 × 10⁴ ng L^-1 ofloxacin and 7.11 × 10⁴ ng L^-1 tetracycline) on bacterial communities in micro-polluted constructed wetlands with and without artificial root exudates. The two antibiotics had no significant effects on the removal of excess carbon and nitrogen from the microcosms treated with and without exudates. Furthermore, with regard to bacterial community structure, antibiotic exposure increased the bacterial richness of bulk and exudate treated microcosms (P < 0.05). However, a significant increase (P < 0.05) in bacterial diversity elicited by ofloxacin and antibiotic mixture exposure was only observed in microcosms with exudates. In exudate treated microcosms, ofloxacin promoted the relative abundance of Arthrobacter spp., which are ofloxacin-resistant bacterial species, which significantly varied from what was observed in microcosms free of exudates. Moreover, tetracycline, ofloxacin and their combination all significantly increased the relative abundance of nitrogen cycling bacteria Rhizobacter spp. and Rhizobium spp., and decreased the relative abundance of antibiotic-resistant bacteria Pseudomonas spp. Simultaneously, with regard to bacterial community functions, the functional profiles (Kyoto Encyclopedia of Genes and Genomes) showed that the pathways of amino acid and carbohydrate metabolism were enhanced by antibiotics in microcosms with exudates. The findings illustrate that antibiotics not only alter the bacterial structure and composition but also change their functional properties in constructed wetlands, and these interruption effects could be affected by root exudates of plants, which may further reveal the ecological implication of plants in constructed wetlands.

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

BACKGROUND

Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes.

RESULTS

Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system.

CONCLUSIONS

Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.

Shifts in the Composition and Activities of Denitrifiers Dominate CO2 Stimulation of N2O Emissions

Elevated atmospheric CO₂ (eCO₂) often increases soil N₂O emissions, but the underlying mechanisms remain largely unknown. One hypothesis suggests that high N₂O emissions may stem from increased denitrification induced by CO₂ enhancement of plant carbon (C) allocation belowground. However, direct evidence illustrating linkages among N₂O emissions, plant C allocation, and denitrifying microbes under eCO₂ is still lacking. We examined the impact of eCO₂ on plant C allocation to roots and their associated arbuscular mycorrhizal fungi and its subsequent effects on N₂O emissions and denitrifying microbes in the presence of two distinct N sources, ammonium nitrogen (NH₄⁺-N) and nitrate nitrogen (NO₃^--N). Our results showed that the form of the N inputs dominated the effects of eCO₂ on N₂O emissions: eCO₂ significantly increased N₂O emissions with NO₃^--N inputs but had no effect with NH₄⁺-N inputs. eCO₂ increased plant biomass N more with NH₄⁺-N than with NO₃^--N inputs, likely reducing microbial access to available N under NH₄⁺-N inputs and/or contributing to higher N₂O emissions under NO₃^--N inputs. eCO₂ enhanced root and mycorrhizal N uptake and also increased N₂O emissions under NO₃^--N inputs. Further, eCO₂ enhancement of N₂O emissions under NO₃^--N inputs concurred with a shift in the soil denitrifier community composition in favor of N₂O-producing (nirK- and nirS-type) over N₂O-consuming (nosZ-type) denitrifiers. Together, these results indicate that eCO₂ stimulated N₂O emissions mainly through altering plant N preference in favor of NH₄⁺ over NO₃^- and thus stimulating soil denitrifiers and their activities. These findings suggest that effective management of N sources may mitigate N₂O emissions by negating the eCO₂ stimulation of soil denitrifying microbes and their activities.

Conversion of monoculture cropland and open grassland to agroforestry alters the abundance of soil bacteria, fungi and soil-N-cycling genes

Integration of trees in agroforestry systems can increase the system sustainability compared to monocultures. The resulting increase in system complexity is likely to affect soil-N cycling by altering soil microbial community structure and functions. Our study aimed to assess the abundance of genes encoding enzymes involved in soil-N cycling in paired monoculture and agroforestry cropland in a Phaeozem soil, and paired open grassland and agroforestry grassland in Histosol and Anthrosol soils. The soil fungi-to-bacteria ratio was greater in the tree row than in the crop or grass rows of the monoculture cropland and open grassland in all soil types, possibly due to increased input of tree residues and the absence of tillage in the Phaeozem (cropland) soil. In the Phaeozem (cropland) soil, gene abundances of amoA indicated a niche differentiation between archaeal and bacterial ammonia oxidizers that distinctly separated the influence of the tree row from the crop row and monoculture system. Abundances of nitrate (napA and narG), nitrite (nirK and nirS) and nitrous oxide reductase genes (nosZ clade I) were largely influenced by soil type rather than management system. The soil types’ effects were associated with their differences in soil organic C, total N and pH. Our findings show that in temperate regions, conversion of monoculture cropland and open grassland to agroforestry systems can alter the abundance of soil bacteria and fungi and soil-N-cycling genes, particularly genes involved in ammonium oxidation.

Phosphorus availability and plants alter soil nitrogen retention and loss

Availability of phosphorus (P) can directly and/or indirectly affect nitrogen (N) retention and loss from soil by stimulating microbial and plant root activities. However, it is not clear how P availability and plant presence interact on nitrous oxide (N₂O) emission and nitrate (NO₃^-) leaching in soil. A mesocosm experiment was conducted to investigate the effect of P addition (0, 10 and 20 mg P kg^-1) with and without plant presence (Phalaris aquatica, C3 grass) on N₂O emission, NO₃^- leaching and ¹⁵N recovery. Our results showed large variation in N₂O emission with significant increases after leaching events. We observed that initially low but later (after 53 days of sowing) high levels of P addition increased N₂O emission rates, possibly by stimulating nitrifiers and/or denitrifiers in soil. Plant presence decreased N₂O emission at times when plants reduced water and NO₃^- in the soil, but increased N₂O emission at times when both water and NO₃^- in the soil were abundant, and where plants may have stimulated denitrification through supply of labile organic C. Furthermore, an increase in net N mineralization, possibly due to increased decomposition stimulated by root derived C, may also have contributed to the higher cumulative N₂O emission with plant presence. P addition increased ¹⁵N recovery in soil, but reduced it in leachates, suggesting increased ¹⁵N fixation in microbial biomass. Our results showed that both P addition and plant presence stimulated N loss as N₂O, but also increased N retention in the soil-plant system and thus reduced N loss through leaching.

Estimation of methane and nitrous oxide emission from wetland rice paddies with reference to global warming potential

Methane (CH₄) and nitrous oxide (N₂O) are two important greenhouse gases (GHG) and contribute largely to global warming and climate change. The impact of physiological characteristics of rice genotypes on global warming potential (GWP) and greenhouse gas intensity (GHGI) is not well documented. A 2-year field experiment was conducted with eight summer rice varieties: Dinanath, Joymoti, Kanaklata, Swarnabh, IR 64, Tapaswami (modern varieties), Number 9, and Jagilee Boro (indigenous varieties) for two successive seasons (December-June, 2015-2016 and December-June, 2016-2017) to estimate their GWP and GHGI. The GWP of the rice varieties ranged from 841.52 to 1288.67 kg CO₂-equiv. ha^-1 and GHGI from 0.184 to 0.854 kg CO₂-equiv. kg^-1 grain yield. Significant differences (p < 0.05) in seasonal GHG emission, GWP, GHGI, CEE (carbon equivalent emission), photosynthetic efficiency, stomatal conductance, transpiration rate, and grain productivity among the rice varieties were observed during the investigation. A good correlation of GWP (p < 0.01) was recorded with rate of stomatal conductance and transpiration rate of the varieties. The present study reveals a strong relationship between plant biomass (p < 0.01) with GWP and CEE of the rice varieties. The variety IR 64 and Number 9 are identified as the most suitable variety with lowest GWP (909.85 and 876.68 kg CO₂-equiv. ha^-1 respectively) and GHGI (0.192 and 0.227 kg CO₂-equiv. kg^-1 grain yield respectively) accompanied by higher grain productivity (4839 and 3867 kg ha^-1 respectively). Observations from the study suggest that agricultural productivity and GHG mitigation can be simultaneously achieved by proper selection of rice genotypes.

Effect of plants and their root exudate on bacterial activities during rhizobacterium-plant remediation of phenol from water

We investigated remediation of phenol from water using microbe-plant partnerships. Co-introduction of maize seedlings, Pseudomonas fluorescens rifampicin-resistant P13 and P. stutzeri P7 carrying self-transmissible TOL-like plasmids reduced phenol content in water at lower phenol concentrations (25, 50, and 75 mg/L), similar to individual introduction of the bacteria. Co-introduction of plants and bacteria significantly reduced phenol content in water at higher phenol concentrations (100, 125, and 150 mg/L) compared to using individual introduction of the bacteria. Moreover, TOL-like plasmids were transferred from P7 to P13. Addition of plants promoted the growth of both strains, leading to increased plasmid transfer. At higher phenol concentrations, addition of plants resulted in increases of catechol 2, 3-dioxygenase (C23O) activity and reduction in level of reactive oxygen species (ROS) of bacteria in the degradation experiments. Increased plasmid transfer and C23O activity and reduction in ROS level might be the major reasons why plants promote bacterial degradation of phenol at higher phenol concentrations. Furthermore, root exudate of maize seedlings and artificial root exudate (ARE) constructed using major components of the root exudate had the same effects on bacterial activities. Unlike the ARE, deletion of glucose, arabinose, or fructose or all the monosaccharides from ARE resulted in no increase in numbers of both strains and in plasmid transfer. At the higher phenol concentrations, deletion of glutamic acid, aspartic acid, alanine, or glycine or all the amino acids did not stimulate bacterial C23O activity. Deletion of fumaric, oxaloacetic or citric acids still reduced bacterial ROS level as ARE did, but, deletion of all the organic acids or DIMBOA, a hydroxamic acid, did not reduce bacterial ROS level as ARE did. The data showed that each monosaccharide might be important for sufficient numbers of plant-associated bacteria and increased plasmid transfer while each amino acid might be important for maintaining bacterial C23O activity and that DIMBOA might be responsible for the decrease in ROS levels. These results are the basis for efficient remediation of phenol from water by microbe-plant partnerships and further studies on the mechanism of rhizobacterium-plant interaction.

Altering N2O emissions by manipulating wheat root bacterial community

Nitrous oxide (N₂O) is a greenhouse gas and a potent ozone-depleting substance in the stratosphere. Agricultural soils are one of the main global sources of N₂O emissions, particularly from cereal fields due to their high areal coverage. The aim of this study was to isolate N₂O-reducing bacteria able to mitigate N₂O emissions from the soil after inoculation. We isolated several bacteria from wheat roots that were capable of N₂O reduction in vitro and studied their genetic potential and activity under different environmental conditions. Three of these isolates- all carrying the nitrous oxide reductase-encoding clade I nosZ, able to reduce N₂O in vitro, and efficient colonizers of wheat roots- presented different N₂O-reduction strategies when growing in the root zone, possibly due to the different conditions in situ and their metabolic preferences. Each isolate seemed to prefer to operate at different altered oxygen levels. Isolate AU243 (related to Agrobacterium/Rhizobium) could reduce both nitrate and N₂O and operated better at lower oxygen levels. Isolate AU14 (related to Alcaligenes faecalis), lacking nitrate reductases, operated better under less anoxic conditions. Isolate NT128 (related to Pseudomonas stutzeri) caused slightly increased N₂O emissions under both anoxic and ambient conditions. These results therefore emphasize the importance of a deep understanding of soil–plant–microbe interactions when environmental application is being considered.

An evaluation of primers for detecting denitrifiers via their functional genes

Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.

Adequate vegetative cover decreases nitrous oxide emissions from cattle urine deposited in grazed pastures under rainy season conditions

A decline in pasture productivity is often associated with a reduction in vegetative cover. We hypothesize that nitrogen (N) in urine deposited by grazing cattle on degraded pastures, with low vegetative cover, is highly susceptible to losses. Here, we quantified the magnitude of urine-based nitrous oxide (N₂O) lost from soil under paired degraded (low vegetative cover) and non-degraded (adequate vegetative cover) pastures across five countries of the Latin America and the Caribbean (LAC) region and estimated urine-N emission factors. Soil N₂O emissions from simulated cattle urine patches were quantified with closed static chambers and gas chromatography. At the regional level, rainy season cumulative N₂O emissions (3.31 versus 1.91 kg N₂O-N ha^-1) and emission factors (0.42 versus 0.18%) were higher for low vegetative cover compared to adequate vegetative cover pastures. Findings indicate that under rainy season conditions, adequate vegetative cover through proper pasture management could help reduce urine-induced N₂O emissions from grazed pastures.