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

Synergistic interactions between AMF and MHB communities in the rhizospheric microenvironment facilitated endemic hyperaccumulator plants growth thrive under heavy metal stress in ultramafic soil

Ultramafic outcrop settings are characterized by long-term heavy metal (HM) stress and nutrient imbalances, making plant resilience highly challenging. This study investigated that how native plant types in the serpentine environment influence the variation of synergistic interactions between rhizosphere arbuscular mycorrhizal fungi (AMF) and mycorrhizal helper bacteria (MHB) communities under HM stress and nutrient-deficient conditions, which support native plant endemism and their HM accumulation potential. The results displayed significant enrichment of key MHB (Rhizobium_tropici, Bacillus_subtilis, Pseudomonas_parafulva, Pseudomonas_akapagensis) and AMF species (Glomus_constrictum, Glomus_aggregatum, Rhizophagus_intraradices, Rhizophagus_irregularis) in rhizosphere soils (q < 0.05). Pseudomonas_chlororaphis and Burkholderia_cepacia were strongly associated with Rhizophagus_irregularis and Glomus_mosseae in Panicum maximum Jacq (PMJ) and Bidens pilosa (BP) under chromium (Cr), and cadmium (Cd) and arsenic (As) stress. Pseudomonas_fluorescens and Bacillus_pabuli were linked to Geosiphon_pyriformis and Glomus_aggregatum in Pueraria montana (PM) under nickel (Ni), lead (Pb), and cobalt (Co) stress, while Arthrobacter_globiformis and Rhizobium_leguminosarum were associated with Glomus_intraradices under copper (Cu) stress in Leucaena leucocephala (LL). Pathways related to nitrogen, phosphorous and potassium (NPK) cycling, HM detoxification, and resistance were enriched, with AMF predominantly symbiotrophic root-endophytic, except for one as lichenized nostoc endosymbiont. Canonical correspondence analysis (CCA) showed HM stress and nutrients influence MHB-AMF symbiosis, while pH moisture content (MC) and electric conductivity (EC) significantly regulate their distribution. Rhizobium_leguminosarum, Rhizobium_tropici, Nitrospira_japonica, and Rhizobium_cauense with Glomus_mosseae and Rhizophagus_irregularis drive NPK cycling in HM-stressed rhizosphere soils. This finding suggested that association between plants type and their functional rhizosphere microbiome promote an eco-friendly strategy for HM recovery from serpentine soil.

Fine-scale diazotroph community structure in the continental slope of the northern South China sea

Diazotrophs have made significant contributions to marine nitrogen cycles. However, their distribution patterns and determined mechanisms have not been fully understood, particularly at the small regional scales. Here, the diazotrophic community structure by different sample sizes (0.2-10 μm and >10 μm), evaluated using high-throughput sequencing of the nifH gene, and the abundance of four typical diazotroph phylotypes, estimated by quantitative PCR of the nifH gene, were investigated on the continental slope of the northern South China Sea at a horizontal spatial resolution of 47.19-71.63 km. The results showed that Proteobacteria and Cyanobacteria were the dominant diazotrophic groups, which mainly contributed by Gamma-proteobacteria and Trichodesmium, respectively. Trichodesmium occupied the large-particle samples in the surface water, while other diazotrophs were nonuniformly distributed across water depths, particle sizes, and stations, indicating the heterogeneous distribution of diazotrophs at fine scales. Vertical profiles of environmental factors, especially the profile data of Fe concentration, were investigated, and the results indicated that temperature, dissolved inorganic nitrogen, and N:Fe were strongly correlated to diazotroph abundance and distribution of Trichodesmium and γ-24774A11. In the transect influenced by the Pearl River plume, γ-24774A11 nifH gene abundance significantly decreased than in other stations, indicating the important role of Pearl River plume in shaping the diazotrophic community structure. These findings advance our understanding of diazotrophic biogeography at the smaller regional scales.

Aquatic macrophytes mitigate the conflict between nitrogen removal and nitrous oxide emissions during tailwater treatments

Tailwater from wastewater treatment plants (WWTP) usually reduces the nitrogen (N) removal efficiency while simultaneously elevates nitrous oxide (N2O) emissions due to the low carbon-nitrogen (C/N) ratio. Conflicts between N removal and N2O emissions require mitigation by selecting appropriate aquatic plants for tailwater treatment. In this study, a simulated tailwater mesocosm was established using three aquatic plants including Eichhornia crassipes, Myriophyllum aquaticum and Pistia stratiotes. Results of the 15N isotope mass balance analysis revealed the considerable contributions from plant uptake and benthic retention to overall N removal. It was demonstrated that the N assimilation efficiency of aquatic plants depended more on the root-shoot ratio rather than on growth rate. Furthermore, aquatic plants indirectly influence microbial N removal and N2O emissions by altering the water quality parameters. Additionally, aquatic plants could regulate the N transformation through affecting the structure of bacterial community, including microbial abundance, diversity and association networks. Overall, the study underlined the enormous capacities of E. crassipes and P. stratiotes for N uptake and N2O mitigation in tailwater treatment. Utilizing these two aquatic plants for phytoremediation may help mitigate the conflict between tailwater purification and N2O production.

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.

Mitigated N2O emissions from submerged-plant-covered aquatic ecosystems on the Changjiang River Delta

Submerged plants affect nitrogen cycling in aquatic ecosystems. However, whether and how submerged plants change nitrous oxide (N2O) production mechanism and emissions flux remains controversial. Current research primarily focuses on the feedback from N2O release to variation of substrate level and microbial communities. It is deficient in connecting the relative contribution of individual N2O production processes (i.e., the N2O partition). Here, we attempted to offer a comprehensive understanding of the N2O mitigation mechanism in aquatic ecosystems on the Changjiang River Delta according to stable isotopic techniques, metagenome-assembly genome analysis, and statistical analysis. We found that the submerged plant reduced 45 % of N2O emissions by slowing down the dissolved inorganic nitrogen conversion velocity to N2O in sediment (Vf-[DIN]sed). It was attributed to changing the N2O partition and suppressing the potential capacity of net N2O production (i.e., nor/nosZ). The dominated production processes showed a shift with increasing excess N2O. Meanwhile, distinct shift thresholds of planted and unplanted habitats reflected different mechanisms of stimulated N2O production. The hotspot zone of N2O production corresponded to high nor/nosZ and unsaturated oxygen (O2) in unplanted habitat. In contrast, planted habitat hotspot has lower nor/nosZ and supersaturated O2. O2 from photosynthesis critically impacted the activities of N2O producers and consumers. In summary, the presence of submerged plants is beneficial to mitigate N2O emissions from aquatic ecosystems.

Biogeography and impact of nitrous oxide reducers in rivers across a broad environmental gradient on emission rates

Microbial communities that reduce nitrous oxide (N2O) are divided into two clades, nosZI and nosZII. These clades significantly differ in their ecological niches and their implications for N2O emissions in terrestrial environments. However, our understanding of N2O reducers in aquatic systems is currently limited. This study investigated the relative abundance and diversity of nosZI- and nosZII-type N2O reducers in rivers and their impact on N2O emissions. Our findings revealed that stream sediments possess a high capacity for N2O reduction, surpassing N2O production under high N2O/NO3- ratio conditions. This study, along with others in freshwater systems, demonstrated that nosZI marginally dominates more often in rivers. While microbes containing either nosZI and nosZII were crucial in reducing N2O emissions, the net contribution of nosZII-containing microbes was more significant. This can be attributed to the nir gene co-occurring more frequently with the nosZI gene than with the nosZII gene. The diversity within each clade also played a role, with nosZII species being more likely to function as N2O sinks in streams with higher N2O concentrations. Overall, our findings provide a foundation for a better understanding of the biogeography of stream N2O reducers and their effects on N2O emissions.

Arbuscular mycorrhizal fungi offset NH3 emissions in temperate meadow soil under simulated warming and nitrogen deposition

Most soil ammonia (NH3) emissions originate from soil nitrogen (N) that has been in the form of exchangeable ammonium. Emitted NH3 not only induces nutrient loss but also has adverse effects on the cycling of N and accelerates global warming. There is evidence that arbuscular mycorrhizal (AM) fungi can alleviate N loss by reducing N2O emissions in N-limited ecosystems, however, some studies have also found that global changes, such as warming and N deposition, can affect the growth and development of AM fungi and alter their functionality. Up to now, the impact of AM fungi on NH3 emissions, and whether global changes reduce the AM fungi's contribution to NH3 emissions reduction, has remained unclear. In this study, we examined how warming, N addition, and AM fungi alter NH3 emissions from high pH saline soils typical of a temperate meadow through a controlled microscopic experiment. The results showed that warming significantly increased soil NH3 emissions, but N addition and combined warming plus N addition had no impact. Inoculations with AM fungi strongly reduced NH3 emissions both under warming and N addition, but AM fungi effects were more pronounced under warming than following N addition. Inoculation with AM fungi reduced soil NH4+-N content and soil pH, and increased plant N content and soil net N mineralization rate while increasing the abundance of ammonia-oxidizing bacterial (AOB) gene. Structural equation modeling (SEM) shows that the regulation of NH3 emissions by AM fungi may be related to soil NH4+-N content and soil pH. These findings highlight that AM fungi can reduce N loss in the form of NH3 by increasing N turnover and uptake under global changes; thus, AM fungi play a vital role in alleviating the aggravation of N loss caused by global changes and in mitigating environmental pollution in the future.

Arbuscular mycorrhizal fungi alleviate erosional soil nitrogen loss by regulating nitrogen cycling genes and enzymes in experimental agro-ecosystems

Nutrient losses from agricultural ecosystems are increasingly threatening global environmental and human health. Although arbuscular mycorrhizal (AM) fungi have the potential to regulate soil nitrogen (N) loss by enhancing plant uptake and soil particle immobilization, the microbial mechanism behind such mycorrhizal effect is unknown. Herein, by conducting a simulated erosion experiment, we compared the effects of exogenous AM fungal inoculation (Funneliformis mosseae) on the gene abundances and enzyme activities of N-cycling processes, and associated such effect to N uptake and loss. The experiment was composed of combinations of two AM fungal treatments (control vs. AM fungal inoculation), two crops (maize vs. soybean) and two slopes of the plots (6° vs. 20°). The experimental plots subjected to natural rainfalls to simulate the erosion events. We showed that the effects of AM fungi were greater in the maize soils than in the soybean soils. In the maize soils, AM fungi increased the abundances of N-fixing (+81.1 %) and nitrifying genes (+200.7 %) and N cycling enzyme activity (+22.3 %). In the soybean soils, AM fungi increased the N-fixing gene abundance (+36.9 %) but decreased the abundance of nitrifying genes (-18.9 %). The abundance of N-fixing gene was positively correlated with N uptake but negatively correlated with N loss. Additionally, AM fungi enhanced the effects of mycorrhizal colonization and moisture but decreased the effects of nutrients on soil microbial metrics related to N-cycling processes. Therefore, AM fungal inoculation enhanced N uptake and reduced N loss by increasing N-fixing gene abundance, and that AM fungi should be preferably used for the low N environments or for the ecosystems highly limited by or competing for N.

Spatial distribution characteristics of denitrification functional genes and the environmental drivers in Liaohe estuary wetland

Genes nirS, nirK, and nosZ are specific for the denitrification process, which is associated with greenhouse gas N2O emission. The abundances and diversities of community containing these three genes are usually used as a common index to reflect the denitrification process, and they would be affected by differences in environmental factors caused by changes from warm to cold conditions. The quantification of denitrification in natural wetlands is complex, and straightforward identification of spatial distribution and drivers affecting the process is still developing. In this study, the bacterial communities, gene diversities, and relative abundances involved in denitrification were investigated in Liaohe Estuary Wetland. We analyzed the relative abundances, diversities, and communities of bacteria containing the three genes at warm and cold conditions using Illumina MiSeq sequencing and detected the potential environmental factors influencing their distribution by using a random forest algorithm. There are great differences in the community composition of the bacteria containing genes nirS, nirK, and nosZ. All the abundant taxa of nirS and nirK communities belonged to phylum Proteobacteria. Compared with the community composition of bacteria containing nirS and nirK, the community of bacteria containing nosZ is more diverse, and the subdivision taxa of phylum Euryarchaeota was also abundant in the community containing nosZ. The distribution characteristics of the relative abundance of nirS and nirK showed obvious differences both at warm and cold climate conditions. The oxidation-reduction potential, nitrite nitrogen, and salinity were detected as potential variables that might explain the diversity of nirS. The total nitrogen and nitrite nitrogen were the important variables for predicting the relative abundance of nirS at warm climate condition, while oxidation-reduction potential and pH contributed to the diversity of nirS at cold condition. The bulk density of sediment was detected as a potential variable affecting the relative abundance of nirK at warm and cold conditions, and diversity of nirK at warm condition, while nitrite nitrogen was detected as an important environmental factor for predicting the diversity of nirK at cold condition. Overall, our results show that the key environmental factors, which affect the relative abundance, diversity, and community of bacteria containing the functional denitrification genes, are not exactly the same, and the diversities of nirS, nirK, and nosZ have a higher environmental sensitivity than their relative abundances.

Mycorrhiza-mediated recruitment of complete denitrifying Pseudomonas reduces N2O emissions from soil

BACKGROUND

Arbuscular mycorrhizal fungi (AMF) are key soil organisms and their extensive hyphae create a unique hyphosphere associated with microbes actively involved in N cycling. However, the underlying mechanisms how AMF and hyphae-associated microbes may cooperate to influence N₂O emissions from "hot spot" residue patches remain unclear. Here we explored the key microbes in the hyphosphere involved in N₂O production and consumption using amplicon and shotgun metagenomic sequencing. Chemotaxis, growth and N₂O emissions of isolated N₂O-reducing bacteria in response to hyphal exudates were tested using in vitro cultures and inoculation experiments.

RESULTS

AMF hyphae reduced denitrification-derived N₂O emission (max. 63%) in C- and N-rich residue patches. AMF consistently enhanced the abundance and expression of clade I nosZ gene, and inconsistently increased that of nirS and nirK genes. The reduction of N₂O emissions in the hyphosphere was linked to N₂O-reducing Pseudomonas specifically enriched by AMF, concurring with the increase in the relative abundance of the key genes involved in bacterial citrate cycle. Phenotypic characterization of the isolated complete denitrifying P. fluorescens strain JL1 (possessing clade I nosZ) indicated that the decline of net N₂O emission was a result of upregulated nosZ expression in P. fluorescens following hyphal exudation (e.g. carboxylates). These findings were further validated by re-inoculating sterilized residue patches with P. fluorescens and by an 11-year-long field experiment showing significant positive correlation between hyphal length density with the abundance of clade I nosZ gene.

CONCLUSIONS

The cooperation between AMF and the N₂O-reducing Pseudomonas residing on hyphae significantly reduce N₂O emissions in the microsites. Carboxylates exuded by hyphae act as attractants in recruiting P. fluorescens and also as stimulants triggering nosZ gene expression. Our discovery indicates that reinforcing synergies between AMF and hyphosphere microbiome may provide unexplored opportunities to stimulate N₂O consumption in nutrient-enriched microsites, and consequently reduce N₂O emissions from soils. This knowledge opens novel avenues to exploit cross-kingdom microbial interactions for sustainable agriculture and for climate change mitigation. Video Abstract.