Search Results (202)

Invasion by Spartina alterniflora has detrimental effects on existing ecosystems. Studies have shown that microorganisms can control plant growth and development. However, the root-associated community structures of bacteria, archaea, and fungi of S. alterniflora have rarely been investigated. Here, we applied metagenomics to reveal the bacterial, archaeal, and fungal communities across four root compartments, including the bulk soil, rhizosphere, rhizoplane, and endosphere. Our findings revealed the variation in different community structures. The bacterial and fungal communities exhibited greater potential environmental flexibility than the archaeal community. The endosphere environment had the simplest microbial networks and highest stability. Additionally, we identified root-exuded metabolites from S. alterniflora, which may influence microbial community assembly. Our results indicate that the rhizoplane plays a crucial role in controlling microbial entry into the root, selectively recruiting beneficial microbes for plant growth and colonization, thereby impacting nutrient cycling and plant health. This study provides insights into microbial diversity and function within the S. alterniflora root zone and suggests potential microbial-based strategies for managing this invasive species. Full article

There is a growing demand for alternative low cost and sustainable weed management technology suitable for aerobic and organic farming. This study evaluates 915 MHz microwave heating as a potential non-chemical approach for managing weedy rice while assessing its impact on soil physicochemical properties and selected microbial groups. Microwave power levels of 10, 20, and 30 kW were applied to soil at depths of 2.5, 8.9, and 15.2 cm under controlled laboratory conditions. Weed emergence was quantified using the total germinability index (TGI), and soil physicochemical and microbial responses were analyzed in separate experiments. TGI decreased significantly with increasing microwave power and decreasing soil depth, ranging from 0.84 (10 kW at 15.2 cm) to 0 (20 kW at 2.5 cm and 30 kW at 8.9 cm). For 8.9 cm soil depth, energy levels between 176 and 265 kJ/kg resulted in 80–100% emergence suppression, while treatment of 15.2 cm soil at 30 kW for 30 s (188 kJ/kg) reduced TGI by approximately 80% and germination by 64% relative to control. Soil physicochemical properties showed minimal changes, with values remaining within agronomically acceptable ranges. Total bacterial abundance was not significantly affected, whereas ammonia-oxidizing archaea and bacteria were reduced following treatment. These results indicate that microwave heating can effectively suppress weedy rice emergence under controlled conditions, primarily through thermal effects. However, TGI reflects emergence suppression and does not distinguish underlying mechanisms such as lethality, injury, or dormancy. Additionally, limitations including low replication, lack of depth-matched controls, and limited spatial temperature measurements should be considered. Further field-scale studies are needed to validate performance, optimize energy requirements, and assess long-term soil impacts. Full article

In permanently submerged coastal wetlands, interactions between biogeochemical processes and microbial communities strongly influence greenhouse gas (GHG) fluxes. To improve our understanding of how redox-driven processes shape GHG dynamics in these ecosystems, we investigated the relationships among iron (Fe) pools, microbial dynamics, and the potential GHG production in subaqueous soils from an interdunal wetland in San Vitale Park (Italy), permanently submerged and affected by seasonal oscillations of the saline water table. Two subaqueous soil columns (WAS-2 and WAS-4), collected from similar settings, were analyzed. Surface layers of WAS-4 showed higher salinity and carbonate content, whereas WAS-2 was characterized by overall higher Fe concentrations. Distinct vertical distributions of organic matter and sulfur (S) were shown along depth. Laboratory incubations revealed that nitrous oxide (N₂O) production was up to ten times higher in WAS-2 than in WAS-4, with peaks in the top 13–14 cm, consistent with more active nitrification-denitrification in surface layers. Methane (CH₄) and carbon dioxide (CO₂) fluxes decreased with depth, reflecting reduced availability of labile carbon. Methanomicrobiales dominated CH₄-producing layers, indicating hydrogenotrophic methanogenesis, while amoA-carrying Nitrosomonadales and Thaumarchaeota, occurred in shallow, organic-rich layers where ammonia supported nitrification and denitrification. Denitrifiers mainly belonged to α- and β-Proteobacteria, consistent with their direct contribution to N₂O peaks. Spearman’s correlations showed N₂O positively correlated to sulfur and labile carbon (C), supporting denitrification under moderately reducing conditions. CH₄ and CO₂ positively correlated with organic C (Corg), total nitrogen (TN), and reactive Fe forms, reflecting redox-mediated microbial respiration and methanogenesis. Trace elements (B, Cr, Cu, Ni) acted as micronutrients or inhibitors depending on concentration. Canonical correspondence analysis indicated depth-structured links among gas fluxes, soil chemistry (Corg, TN, S/C, CaCO₃, P), and microbial distributions: surface layers, rich in labile C and nutrients, supported active bacteria and archaea involved in decomposition, nitrification, and denitrification, whereas deeper layers hosted oligotrophic archaea adapted to inorganic substrates. Overall, Fe pools appeared to be associated with soil processes relevant to GHG dynamics, although the extent of their regulatory role remains uncertain due to potential alterations of redox-sensitive Fe fractions during sample handling. These results contribute to broader efforts to predict GHG emissions in submerged wetland soils by linking redox stratification, inorganic chemistry, and microbial functional groups. Full article

In nature, a significant number of plant species form symbiotic associations with microorganisms, with arbuscular mycorrhizal fungi (AMF) and endophytic fungi being two prevalent groups of these partners. However, the ability to establish such symbioses with AMF and endophytic fungi is limited to a small fraction of native grass species. Nitrogen is a crucial nutrient for plant growth, yet it is often a limiting factor, underscoring the importance of understanding how plants acquire it. AMF enhance plant growth by improving nitrogen uptake efficiency, but the combined effects of endophytic fungi and AMF on plant physiology and ecology remain underexplored. To address this knowledge gap, in the present study, we conducted an indoor randomized block experiment to investigate the influence of endophytic fungi and AMF infection on the physiological and ecological attributes of Festuca rubra under various nitrogen regimes. The findings indicated that AMF inoculation significantly affected the total carbon content of F. rubra and the total sulfur concentration in its underground tissues across different nitrogen conditions. Additionally, dual colonization by AMF and endophytic fungi had a significant impact on the underground total nitrogen content of the plants. Furthermore, the complex interactions among AMF, endophytic fungi, and nitrogen availability emerged as critical determinants influencing underground total carbon content, transpiration rates, intercellular carbon dioxide concentrations, and the activity of soil extracellular enzymes in F. rubra. The activity of soil extracellular enzymes and pH significantly affected the structure and diversity of rhizosphere bacterial, fungal, and archaeal communities. AMF enhanced the richness of rhizosphere bacterial communities under low-nitrogen conditions, whereas endophytic fungi infection increased bacterial diversity. Soil extracellular enzyme activity and pH were closely related to the community structures and diversities of rhizosphere bacteria, fungi, and archaea. This study clarifies the effects of AMF and endophytic fungi infection on the physiological and ecological characteristics of F. rubra, significantly contributing to our understanding of the synergistic mechanisms governing the interactions among AMF, endophytic fungi, and their host plants. Full article

(1) Background: Improving nitrogen use efficiency in peanuts is essential for achieving a high yield with reduced nitrogen fertilizer input. This study investigates the role of the fungal endophyte Phomopsis liquidambaris in regulating nitrogen utilization throughout the entire growth cycle of peanuts. (2) Methods: Field pot experiments and a two-year plot trial were conducted. The effects of Ph. liquidambaris colonization on the rhizosphere microbial community, soil nitrogen forms, and peanut physiology were analyzed. (3) Results: Colonization by Ph. liquidambaris significantly suppressed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the rhizosphere at the seedling stage. This led to a transient decrease in nitrate and an increase in ammonium availability, which enhanced nodulation-related physiological responses. Concurrently, the peanut-specific rhizobium Bradyrhizobium sp. was enriched in the rhizosphere, and the root exudates induced by the fungus further stimulated nodulation activity. These early-stage effects promoted the establishment of peanut–Bradyrhizobium symbiosis. During the mid-to-late growth stages, the fungus positively reshaped the composition of key functional microbial groups (including diazotrophs, AOA, and AOB), thereby increasing rhizosphere nitrogen availability. (4) Conclusions: Under low nitrogen fertilization, inoculation with Ph. liquidambaris maintained yield stability in long-term monocropped peanuts by enhancing early nodulation and late-stage rhizosphere nitrogen availability. This study provides a promising microbe-based strategy to support sustainable legume production with reduced nitrogen fertilizer application. Full article

Marine fog is a key non-rainfall water source that sustains microbial activity and transports dissolved nutrients inland, influencing early soil development in hyperarid ecosystems. However, the mechanisms through which sustained fog inputs drive soil surface modification and biocrust formation remain poorly understood. This study evaluated the effects of long-term fog augmentation on soil surface development, biocrust dynamics, and associated microbial communities in the Atacama Desert. We implemented a four-year fog addition field experiment with three sampling times (T0, T24, T48) to assess changes in soil physicochemical properties, biocrust composition, and the integrated multi-diversity of archaea, bacteria, fungi and protist. Sustained fog input transformed bare soils into biological soil crusts, particularly lichen- and moss-dominated stages. This transition was accompanied by increases in soil nitrogen, variations in organic matter accumulation, a shift from alkaline to near-neutral pH, and improvements in soil stability and water retention. Multi-diversity increased over time and was positively associated with ecosystem variables linked to water availability, structural stabilization, and decomposition. These functions, integrated into an ecosystem multifunctionality index, also increased under prolonged fog input, revealing a positive relationship between multifunctionality and multi-diversity. Overall, the results demonstrate that sustained fog input strongly enhances early soil surface development and biocrust establishment, highlighting the ecological importance of marine fog in shaping biodiversity and ecosystem functioning in hyperarid landscapes. Full article

Nutrient additions including nitrogen (N) and phosphorus (P) are widely considered as an important strategy for enhancing grassland productivity. However, the effects of these nutrients additions on soil nitrous oxide (N₂O) emissions and the underlying mechanisms remain debated. We conducted a two-year field experiment in an alpine grassland on Kunlun Mountain in northwestern China to assess the effects of N and P additions on N₂O emissions, in relation with nitrifying enzyme activity (NEA), denitrifying enzyme activity (DEA), and key functional genes abundance responsible for nitrification (amoA and Nitrobacter-like nxrA) and denitrification (narG, nirS, nirK and nosZ). Compared to the Control without nutrient addition (CK), N addition alone substantially increased cumulative N₂O emission (ƩN₂O) by 2.0 times. In contrast, P addition or combined N and P (N+P) addition did not significantly affect ƩN₂O, though both treatments significantly increased plant aboveground biomass. Such results indicate that P addition may mitigate N-induced N₂O emission, likely by reducing soil N availability through enhanced plant and microbial N uptake. Compared to CK, N or N+P addition significantly elevated NEA but did not affect DEA. Structural equation modeling (SEM) indicated that NEA was directly influenced by the gene abundances of ammonia-oxidizing bacteria (AOB) and Nitrobacter-like nxrA but not by ammonia-oxidizing archaea (AOA). However, SEM also revealed that soil environmental variables including soil temperature, pH, and water-filled pore space (WFPS) had a stronger direct influence on N₂O emissions than the abundances of nitrifiers. These results demonstrate that soil environmental conditions play a more significant role than functional gene abundances in regulating N₂O emissions following N and P additions in semi-arid alpine grasslands. This study highlights that the N+P application can potentially decrease N₂O emissions than N addition alone, while increasing productivity in the alpine grassland ecosystems. Full article

Coastal reclamation profoundly alters soil physicochemical conditions and strongly influences soil microbial ecology; however, the millennial-scale successional patterns and assembly mechanisms of prokaryotic communities under such long-term disturbance remain insufficiently understood. In this study, we investigated archaeal and bacterial communities in the plow layer along a 0–1000-year coastal reclamation chronosequence on the southern shore of Hangzhou Bay. We analyzed community abundance, diversity, composition and assembly processes, and quantified the relative contributions of geographic distance, environmental factors and reclamation years to microbial biogeographic patterns. The results showed that reclamation markedly drove continuous soil desalination, acidification, nutrient accumulation, and particle-size refinement. Bacterial abundance exhibited a sharp decline during the early stages of reclamation, whereas archaeal abundance remained relatively stable. The α-diversity of both archaea and bacteria peaked at approximately 210–230 years of reclamation. Community assembly processes differed substantially between the two microbial domains: the archaeal communities were dominated by stochastic processes (77.78%) identified as undominated processes and dispersal limitation, whereas bacterial communities were primarily shaped by deterministic processes (70.75%) driven as variable selection. Distance–decay analysis indicated that bacterial communities were more sensitive to environmental gradients. Multiple regression and variance partitioning further demonstrated that soil pH and electrical conductivity were the key drivers of community structure. Overall, this study reveals the millennial-scale community dynamics and assembly mechanisms of archaea and bacteria in response to coastal reclamation, providing mechanistic insights into long-term microbial ecological succession and offering valuable guidance for sustainable agricultural management and ecological restoration in reclaimed coastal regions. Full article

The resident microbiota in agricultural soils strongly influences crop health and productivity. In this study, we evaluated the prokaryotic diversity of two clay soils with similar physicochemical characteristics but contrasting levels of maize (Zea mays L.) and wheat (Triticum aestivum L.) production using 16S rRNA gene sequencing. Yield records showed significant differences in grain production over five consecutive years. When comparing prokaryotic alpha diversity between the “non-productive” and “productive” soils, no major differences were found, and the abundance of ammonia-oxidizing archaea (AOA) and bacterial genera such as Arthrobacter, Neobacillus, and Microvirga remained consistent across soils. Analysis of the top 20 genera showing the greatest abundance shifts by compartment (bulk soil vs. rhizosphere) revealed that genera such as Priestia, Neobacillus, Sporosarcina, and Pontibacter decreased in the rhizosphere of the non-productive soil, while in the productive soil, these genera remained unchanged. In the non-productive soil, genera such as Flavisobacter decreased in abundance in the rhizosphere, whereas Arthrobacter increased. Principal coordinates analysis (PCoA) showed no clear clustering by compartment (bulk vs. rhizosphere), but two distinct clusters emerged when grouping by soil type (productive vs. non-productive). Interaction networks varied by soil type: non-productive soils showed positive Candidatus–Bacillus and negative Massilia links, while productive soils were dominated by Flavisolibacter and negative Pontibacter. Across soils, Rhizobium–Bradyrhizobium associations were positive, whereas Neobacillus and Priestia were negative. These findings highlight that a few potential beneficial microbiota and their interactions may be key drivers of soil productivity, representing targets for microbiome-based agricultural management. Full article

Tea plantations are a hot-spot source of nitrous oxide (N₂O) emissions in the agricultural system. Using nitrification inhibitors (NIs) is a promising way to mitigate agricultural N₂O emissions and has been widely tested in many croplands. However, the efficiency of different NIs and whether there are soil-specific effects are still unclear in tea plantations with typical acidic soil conditions. This study evaluated the effects of three widely used NIs, i.e., dicyandiamide (DCD), 3,4-dimethylpyrazole phosphate (DMPP), and 2-chloro-6-(trichloromethyl) pyridine (Nitrapyrin), through a lab incubation trial, on the nitrification suppression, N₂O emissions, and ammonia-oxidizing microbial communities in two tea plantation soils with contrasting physicochemical properties (pH and texture). During the 50-day incubation, the soil with a higher pH and coarse texture (TA) exhibited a four-times-higher apparent nitrification ratio (ANR) than the more acidic and clay soil (HZ). Nitrification inhibitor addition resulted in about a 60% and 80% reduction in the ANR in HZ and TA soils, respectively. During the entire incubation, ammonium sulfate (N) addition without NIs emitted N₂O at 64.1 ± 1.2 and 61.5 ± 0.4 μg N kg⁻¹ (mean ± standard deviation, and the same in the following text) in the HZ and TA soils, respectively. Compared with the N alone, the N₂O mitigation efficiency of DCD, DMPP, and Nitrapyrin was 38.3% ± 0.4% (standard deviation), 33.8% ± 0.99%, and 36.5% ± 0.59% in the HZ soil and 94.1% ± 0.39%, 52.8% ± 1.05%, and 95.6% ± 0.65% in the TA soil, respectively. Nitrapyrin more effectively suppressed both ammonia-oxidizing archaeal (AOA) and ammonia-oxidizing bacterial (AOB) abundance, particularly in the acidic soil (HZ), where ammonia-oxidizing archaea dominate nitrification. These results revealed the pivotal role of soil properties in controlling NI efficiency and highlighted Nitrapyrin as a potential superior nitrification inhibitor for N₂O mitigation under the tested conditions in this study. Full article

Numerous studies have shown that there are many uncertainties associated with the interactions of nitrogen with plants and microorganisms. In particular, the effects of symbioses between plants and various microorganisms on soil microbial community function remain unclear. Metagenomic sequencing was used to explore the changes in microbial community composition, function and metabolic pathways in rhizosphere soil and the associated influencing factors under different nitrogen levels caused by arbuscular mycorrhizal fungi (AMF) inoculation of F. rubra infected with endophytic fungi and nonendophytic fungi. Plant nutrient allocation (aboveground/belowground), soil pH, and enzymatic activities significantly modulated the functional profiles of the bacterial, fungal, and archaeal communities within these rhizospheres. Soil β-glucosidase activity had the greatest effect on the cluster of orthologous groups of proteins (COG) function of the rhizosphere soil bacterial community, and soil L-leucine aminopeptidase had the greatest effect on the COG function of the rhizosphere soil fungal and archaeal communities. The contributions of AMF colonization to the kyoto encyclopedia of genes and genomes (KEGG) functions of bacteria and archaea in the rhizosphere soil were greater than those of F. rubra infection with endophytic fungi, and AMF colonization improved the metabolic pathways, secondary metabolite biosynthesis, microbial metabolism, amino acid biosynthesis and carbon metabolism of bacterial and archaeal communities in the rhizosphere soil of F. rubra. The effects of endophytic fungi and AMFs on the function and metabolic pathways of symbiotic rhizosphere soil microbial communities were heterogeneous. This study revealed that considering both biotic and abiotic factors is essential for predicting the maintenance of soil ecosystem function by plant–fungal symbionts. Full article

Coal gangue (CG) dumped in open-air piles significantly impacts the surrounding soil environment. To investigate the effects of prolonged CG dumping on soil archaeal communities and their ecological functions, we used metagenomic sequencing to analyze soil samples, including control soil area not impacted by CG (CSL), undisturbed control sediment (CST), atmospheric dust fall area (ADF), and leachate flow area (LFA) samples. The results showed that the dominant phylum and genus of archaea were Thaumarchaeota (30.53–93.39%) and Candidatus Nitrosocosmicus (34.44–69.85%) in the different samples. Significant differences were observed in both α- and β-diversity (p < 0.05); archaeal community composition was primarily influenced by total nitrogen (TN), electrical conductivity (EC), Cu, As, and Cd. The contribution rate of As was the largest, about 44.8%. The metabolic functions of archaea were predominantly related to amino acid metabolism, and there were significant variations in carbon and nitrogen metabolic pathways in different areas. The ppdk gene showed considerable variation between ADF and CSL, and Euryarchaeota was the major contributing phylum to carbon fixation. However, for nitrogen metabolism, the gltB gene displayed marked differences, and the phylum of Thaumarchaeota was the major contributor. This study provides a theoretical foundation for land management and sustainable utilization in CG dump areas. Full article

Atmospheric nitrogen (N) deposition and climate warming significantly influence soil nitrogen transformation processes. Nitrification, a key step in the N cycle, is primarily driven by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, their responses to environmental changes in warm-temperate shrub tussock grasslands—a major grassland type in China—remain poorly understood. In this study, we examined the effects of N addition and warming on the community composition of ammonia oxidizers and soil nitrification potential (NP) through pot experiments simulating field conditions. Our results demonstrated that (1) the AOB community was more responsive to N addition and warming than AOA, with the genus Nitrosospira increasing by 6.30–21.75% under treatments; (2) soil pH increased significantly under warming (from 6.53 to 6.86) but remained unchanged under N addition; (3) NP increased significantly under all treatment conditions, most markedly under warming alone (2.83-fold increase compared to the control); and (4) NP was positively correlated with both soil pH and the relative abundance of Nitrosospira. These findings suggest that warming and N deposition enhance nitrification in shrub tussock soil by altering AOB community structure and increasing soil pH. This study provides new insights into the microbial mechanisms driving N cycling in warm-temperate grasslands under global change. Full article

With the transformation of industrial enterprises in China, the relocation of numerous factories has led to the emergence of retired industrial parks with serious pollution. This study investigated the contamination of benzene-based pollutants (BBPs) in soil and their relationship with soil texture, physicochemical properties, and microbial communities at a former factory site in Shanghai. The results indicated that benzene and toluene were the main pollutants in the region, accounting for 25.7–36.1% and 7.6–10.2% of the total pollutants, respectively. The horizontal contamination distribution pattern of BBPs at different sampling points were clearly related to the functional zoning of the area. Sampling points close to workshops and bathrooms possessed higher contamination levels of BBPs than those close to warehouses and office buildings. With the increase in sampling depth, the gradually rising soil density and soil porosity ratio reduced the adsorption capacity of soil for BBPs, thereby promoting the volatilization and release of BBPs in deeper soil layers to a certain extent, resulting in a “shallow > deep” trend for the content of BBPs. The abundance of norank_f__norank__o_norank__c__Bathyarchaeia in the soil may be the main functional microorganisms affecting the distribution of BBPs. Styrene and chlorobenzene exhibited significant correlations with microbial communities, primarily involving bacteria (Desulfobacterium, Thermincola, and Trichlorobacter) and archaea (including norank_f_Nitrosopumilaceae, norank_f_norank_o_norank_c_Nitrososphaeria, and Methanocella). This study identifies and analyzes the BBP contamination characteristics in a typical retired industrial park in Shanghai, providing valuable references for risk assessment and microbial remediation of such contaminated areas. Full article

The black soil region of Northeast China is crucial for agricultural productivity. Ammonia-oxidizing archaea (AOA) are key indicators of soil nitrification in this region, yet it remains unclear whether this process is driven by the entire community or by specific clusters. Here, we investigated the AOA community across a long-term fertilization Brown Soil Experimental Station and 15 sites in the Typical Black Soil Zone. Using Illumina MiSeq sequencing of the AOA amoA gene and cluster-specific primers, 14 OTUs were selected as core clusters based on relative abundance >0.1% and strong correlations (r > 0.7) with soil properties or PNR, and were further grouped into five distinct clusters according to phylogenetic analysis. Compared to the overall AOA community, core clusters responded more precisely to fertilization, straw addition, and spatial variation, with contrasting environmental responses reflected in their relationships with soil nitrification dynamics. Clusters G1 and G2 had positive correlations with soil PNR, while Clusters G4 and G5 had negative correlations. Moreover, AOA core clusters demonstrated stronger correlations with soil properties, including pH, C/N ratio, and NH₄⁺/NO₃⁻ ratio. These findings demonstrate that AOA core clusters are reliable microbial indicators of soil nitrification, and monitoring their abundance changes under nitrogen input can provide early insights into potential inhibition, informing predictive models and guiding more precise nitrogen management to support sustainable agricultural practices. Full article