Search Results (28)

Water scarcity is driving increased use of treated wastewater in agriculture while also leading to an increase in concerns about the presence of active pharmaceutical active compounds (PhACs) and their impact on soil ecosystems. This study provides novel field-scale evidence on the combined impact of tertiary-treated wastewater (TWW) irrigation and short-term tomato/wheat crop succession on soil microbial communities, nitrogen-cycling functional groups, and crop productivity. Over two consecutive years in southern Italy, TWW was compared with freshwater (FW) using integrated chemical, microbiological, and metagenomic approaches. TWW irrigation significantly increased tomato and wheat yields (+14% and +20%, respectively) without negatively affecting crop quality. Several PhACs were detected in soil and showed moderate accumulation under TWW, particularly sitagliptin and flecainide, which reached 10 ng/g. However, limited effects were observed in terms of total microbial abundance, nitrogen-cycle gene markers, or overall microbiome structure. The fungal population of Bionectria was found to be a potential biomarker since it was negatively affected by TWW (−56%). In contrast, time and crop succession emerged as the primary driver of microbial dynamics, inducing marked shifts in bacterial and fungal community composition and diversity, with wheat promoting higher diversity than tomato. Nitrogen-fixing bacteria were higher in tomato crop seasons. Ammonia oxidizing increased in the wheat crop season, while denitrifiers were more influenced by sampling time. These findings demonstrate that, under compliant treatment conditions, TWW reuse can enhance crop productivity with limited short-term ecological risks, supporting sustainable agricultural water management. Full article

Microbial communities regulate the transformation and stabilization of nutrients during composting; however, current knowledge on their specific functional roles across composting stages remains poorly integrated. This review examines the pivotal role of microbial mediation in nitrogen (N) and phosphorus (P) dynamics during composting and their subsequent impact on soil health. We analyze how biotechnological interventions—specifically the inoculation of functional microbial consortia (phosphate-solubilizing bacteria, phosphate-accumulating bacteria, and nitrifiers) and the application of physicochemical additives such as biochar—reconfigure microbial succession patterns to mitigate gaseous losses and enhance nutrient bioavailability. Several studies have reported substantial reductions in ammonia (NH₃) and nitrous oxide (N₂O) emissions under specific composting conditions, while simultaneously promoting the stabilization of labile P into more recalcitrant forms, including polyphosphates. Furthermore, the application of mature compost to agricultural systems induces a profound ecological reassembly of the soil microbiome, shifting community composition toward copiotrophic dominance (Pseudomonadota and Bacteroidota) and increasing functional redundancy. These microbial and functional shifts enhance soil resilience to environmental stressors—such as drought and temperature fluctuations—by stabilizing extracellular enzyme activity and reinforcing microbial co-occurrence networks. We conclude that managing microbial interactions along the compost–soil continuum is essential for developing organic amendments optimized for specific soil and crop requirements. This integrated approach represents a cornerstone of precision sustainable agriculture and contributes to climate change mitigation through soil health restoration. Full article

Climate change-induced drought threatens the persistence of Araucaria araucana, an endangered and endemic conifer of the Southern Andes. Beneficial plant–microbe interactions may contribute to drought resilience. Here, we evaluated the effects of a root-endophytic bacterium with the capacity to produce N-acyl homoserine lactones (AHLs) on the growth and drought tolerance of A. araucana. For this, a root endophytic bacterium was isolated from A. araucana and identified as Erwinia billingiae. It was characterized for plant growth-promoting traits, and inoculated into A. araucana seedlings under drought conditions). The bacteria produced N-butyryl-L-homoserine lactone (C4-HSL) under control conditions and C4-HSL and N-hexanoyl-L-homoserine lactone (C6-HSL) under drought stress. The strain also produces indoleacetic acid, ammonia, siderophores and solubilizes phosphate. Under drought stress, non-inoculated seedlings showed marked reductions in shoot and root biomass, chlorophyll content, relative water content (RWC), and soluble sugars. In contrast, inoculated seedlings under drought displayed significantly higher shoot and root biomass, reaching levels comparable to those of well-watered controls. Chlorophyll content increased from 5.42 to 9.35 mg L⁻¹, and RWC increased from 62% to 71% in inoculated plants under drought conditions. Soluble sugar content increased from 25.74 to 36.34 mg g⁻¹ fresh weight following inoculation. Drought-induced oxidative stress was significantly alleviated in inoculated seedlings, with lower malondialdehyde and proline accumulation compared to non-inoculated drought-stressed plants. Antioxidant responses were modulated, indicating improved redox balance under water limitation. These results demonstrate that a root-endophytic bacterium with AHL production can enhance drought tolerance in A. araucana seedlings. This study provides novel evidence supporting the role of beneficial endophytes in microbiome-based strategies for conserving native forest species under climate change. Full article

Bacterial communities in the rhizosphere and endorhizosphere of plants show distinct composition, function, and ecological roles during adaptation to diverse habitats. This study examines how rhizosphere and endophytic microbes associated with Aeluropus sinensis—a salt-excreting halophyte—contribute to its salt tolerance across saline-alkali environments. Microbial diversity and composition were analyzed via 16S rRNA gene amplicon sequencing. Soil physicochemical properties were measured to evaluate environmental effects. Linear regression assessed microbial–environment relationships, and co-occurrence networks identified key taxa and their adaptive strategies along environmental gradients. Soil salinity significantly affected rhizosphere bacterial diversity, with moderate levels increasing richness. Proteobacteria dominated both root and rhizosphere microbiomes across habitats. The endorhizosphere community strongly correlated with soil nutrients such as available phosphorus (AP) and total nitrogen (TN). Co-occurrence analysis reveals that chemoheterotrophic microbes in the A. sinensis rhizosphere employ distinct adaptive strategies across gradients, and ammonia-oxidizing bacteria (AOB) may support nitrogen cycling in the Yellow River Delta saline–alkaline ecosystem. This study underscores microbial adaptability in salt-tolerant grasses, demonstrating that comparing rhizosphere and endorhizosphere microbiomes in Poaceae under stress improves understanding of microbial functions in harsh environments. 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

The lotus–fish co-culture (LFC) system leverages plant–fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal–fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC’s ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation. Full article

Global agricultural intensification has exacerbated soil compaction and nitrogen (N) inefficiency, thereby threatening sustainable crop production. Sub-soiling, a tillage technique that fractures subsurface layers while preserving surface structure, offers potential solutions by modifying soil physical properties and enhancing microbial-mediated N cycling. This study investigated the effects of subsoiling depth (0, 20, and 40 cm) on soil microbial communities and N transformations in a semi-arid maize system in China. The results demonstrated that subsoiling to a depth of 40 cm (D2) significantly enhanced the retention of nitrate-N and ammonium-N, which correlated with improved soil porosity and microbial activity. High-throughput 16S rDNA sequencing revealed subsoiling depth-driven reorganization of microbial communities, with D2 increasing the abundance of Proteobacteria (+11%) and ammonia-oxidizing archaea (Nitrososphaeraceae, +19.9%) while suppressing denitrifiers (nosZ gene: −41.4%). Co-occurrence networks indicated greater complexity in microbial interactions under subsoiling, driven by altered aeration and carbon redistribution. Functional gene analysis highlighted a shift from denitrification to nitrification-mineralization coupling, with D2 boosting maize yield by 9.8%. These findings elucidate how subsoiling depth modulates microbiome assembly to enhance N retention, providing a mechanistic basis for optimizing tillage practices in semi-arid agroecosystems. Full article

In recent years, gut microbiota has emerged as a critical regulator of gastrointestinal health and disease, with its role in inflammatory bowel disease (IBD)—including Crohn’s disease and ulcerative colitis—being particularly significant. Among the many factors influencing the gut microbiota, dietary components such as fibers, fats, and polyphenols have received substantial attention. However, nitrogen-containing compounds, such as amino acids, nitrates, urea, and even nucleic acids, such as purines, remain underexplored despite their integral role in shaping microbial ecology, host metabolism, and immune responses. Some of these compounds are metabolized by gut bacteria into bioactive molecules such as short-chain fatty acids, ammonia, and nitric oxide, which exert diverse effects on mucosal integrity and inflammation. IBD pathophysiology is characterized by chronic inflammation, microbial dysbiosis, and compromised epithelial barriers. Nitrogen metabolism contributes significantly to these processes by influencing microbial composition, metabolite production, and host immune pathways. The breakdown of various nitrogen-containing compounds in the body leads to the production of byproducts, such as ammonia and hydrogen sulfide, which have been implicated in mucosal damage and immune dysregulation. At the same time, nitrogen-derived molecules, such as short-chain fatty acids and nitric oxide, exhibit protective effects, underscoring the dual role of dietary nitrogen in health and disease. This narrative review highlights the complex interactions between dietary nitrogen sources, gut microbiota, and IBD pathogenesis. We summarize the mechanisms by which nitrogen compounds influence microbial dynamics, identify their contributions to inflammation and barrier dysfunction, and explore their therapeutic potential. Multidisciplinary approaches integrating clinical, metabolomic, and microbiome research are essential to unravel the full scope of nitrogen’s role in gut health and identify novel therapeutic targets. Full article

Ammonia nitrogen is a common contaminant in aquatic environments, and its potential toxicity to organisms has attracted extensive attention. However, few studies have comprehensively evaluated the negative impacts of ammonia stress on cold-water fish. In this study, liver, gill, and intestine specimens of Amur grayling (Thymallus grubii) from three treatment groups (control (0 mg/L), low ammonia (43.683 mg/L), and high ammonia (436.8 mg/L)), were collected for histological observation, biochemical examination, and transcriptomic, metabolomic, and intestinal microbiome analysis. Our results showed that excessive ammonia nitrogen blocked the normal immune function and compromised the integrity of liver and gill tissues through oxidative stress-mediated differential cell death pathways. Meanwhile, the multi-omics analysis revealed that ammonia exposure predominantly altered the carbohydrate, lipid, and amino acid metabolism modes. In addition, it was also demonstrated that ammonia nitrogen stress affected the composition of intestinal microbiota taxa. This study provides insights into the potential risks and hazards of ammonia stress on cold fish in natural waters and provides a reference for the environment control of the water quality in aquaculture. Full article

Nitrification plays a crucial role in aquatic ecosystems and in the biofilters used in fish farms. Despite their importance, the role of canonical nitrifiers, comammox bacteria, and archaea has not yet been sufficiently investigated. The aim of this study was to characterize the microbiome of the external canister biofilter in a freshwater fish aquarium, with particular focus on the role of comammox Nitrospira and their competition with other nitrifiers. To achieve this, a comprehensive approach combining metagenome sequencing and co-occurrence network analysis was used to study the interactions between microorganisms in portable biofilter. The fish were subjected to a changing feeding regime that affected the ecological relationships and abundance of different microbial taxa. The results showed the presence of two types of nitrifiers in the biofilter: comammox Nitrospira and ammonia-oxidizing archaea (AOA). Five comammox Nitrospira genomes were reconstructed, with comammox clade B being the most abundant with an average abundance of 7.8 ± 0.4%. In addition, two families of archaea were identified: Nitrosopumilaceae and Nitrososphaeraceae, with an average abundance of 4.3 ± 0.4%. Heterotrophs were also abundant in the bacterial community, particularly in the genera Actinomycetota, Planctomycetota, and Pseudomonadota. Network analysis indicated competitive interactions between comammox and heterotrophs, whereas no competition was observed between comammox and AOA. The predominance of comammox Nitrospira, and AOA over canonical nitrifiers emphasizes their better adaptation to oligotrophic environments. This study highlights the importance of competition within the biofilter microbiome and the role of ecological interaction networks, which can contribute to the optimization of water purification systems in RASs. Full article

Certain plant species have developed the ability to express biological nitrification inhibition (BNI), suppressing the activity of nitrifying microbes and thereby reducing the conversion of ammonium to nitrate. This study assessed the BNI capacity and the rhizosphere ammonia-oxidizing microbiome of two grass species: the endemic Australian Barley Mitchell grass (Astrebla pectinata) and the introduced koronivia grass (Urochloa humidicola), using soils from both agricultural land and native vegetation. In agricultural soil, koronivia grass exhibited significantly higher BNI capacity compared with Barley Mitchell grass. However, in native soil, this trend was reversed, with Barley Mitchell grass demonstrating a significantly greater BNI capacity than koronivia grass (52% vs. 38%). Koronivia grass significantly altered the composition of the ammonia-oxidizing bacteria community in its rhizosphere, leading to a decrease in the Shannon index and bacteria number. Conversely, Barley Mitchell grass reduced the Shannon index (1.2 vs. 1.7) and population size (3.28 × 10⁷ vs. 7.43 × 10⁷ gene copy number g⁻¹ dry soil) of the ammonia-oxidizing archaea community in its rhizosphere to a greater extent. These findings suggest that Australian Barley Mitchell grass may have evolved mechanisms to suppress soil archaeal nitrifiers, thereby enhancing its BNI capacity and adapting to Australia’s nutrient-poor soils. Full article

Struvite and ammonium nitrate (AN), as wastewater-recovered products, are possible alternatives as raw materials for nutrient solutions. However, their impact on the rhizosphere microbiota and N₂O emissions is scarcely known. Therefore, the present research studies the ecological changes in the bulk-substrate microbiome and its correlation with N₂O emissions in a perlite-based system tomato crop under (i) conventional synthetic fertigation management; (ii) fertigation with struvite; and (iii) struvite and AN. A high bacterial diversity and the natural presence of plant-growth-promoting rhizobacteria in a soilless system are highlighted. However, the different N-NH₄⁺:N-NO₃⁻ ratios influence the ecological niches of ammonia-oxidizing archaea (AOA) and bacteria (AOB), with a stronger response by AOB community, while AOA kept constant regarding the fertilization applied. Despite this, enrichment of N-transforming bacterial phylotypes was relatively enhanced (mainly Nitrosomonas, Nitrosospira, and Nitrospira) concomitant with the production of N₂O emissions when ammonium fertilization was overapplied. In the absence of a plant, N₂O emissions were positively correlated, respectively, with Nitrosospira and AOB:AOA ratio, suggesting potential indicators for ammonium availability in the substrate. Fertilizer blends using recovered nutrients are a feasible alternative for increasing circularity in horticulture. Nevertheless, optimum fertilizer management is needed due to its influence on rhizosphere microbiota and N₂O emissions. Full article

Beside natural factors, human activities are important for the development of microbiomes. Thus, local soil bacterial communities are affected by recent activities such as agriculture, mining and industry. In addition, ancient human impacts dating back centuries or millennia have changed soils and can emboss the recent bacterial communities up to now, representing a certain long-term “memory of soil”. Soil samples from five different archaeological excavation places were investigated for the presence of Archaea with a Next Generation Sequencing (NGS) analysis of the DNA coding for 16S r-RNA sequences. It was found that the abundance of Archaea differs strongly between less than one and more than 40 percent of bacteria. A Principal Component Analysis (PCA) of all samples shows that the archaeological excavation places can be distinguished from each other by the archaeal component of soil bacterial communities, which presents a typical pattern for each place. Most samples are marked by the dominance of Crenarchaeota, which are presented mainly by ammonia-related types. High contents of Nanoarchaeaota have been observed in one ash deposit of a historical saline and all samples of a historical tannery area. These samples are also marked by a significant presence of Dadabacteria. The specific abundancies of special Archaea—among them ammonia-oxidizing and sulphur-related types—are due obviously to former human activities and support the concept of the “ecological memory of soil”. Full article

Although winter cover crops (WCCs) have demonstrated positive effects on soil properties, relatively little is known about the responses of the soil and plant microbiomes to the introduction of WCCs and their associated management. Our objective was to evaluate the effects of WCC suppression methods on the rhizosphere microbiome of oats under field conditions. Rhizospheric soil was extracted to quantify the abundances of amoA gene of ammonia-oxidizing bacteria and archaea, and nitrite reductase genes (nirK and nirS), and to determine potential nitrification activity. The bacterial 16S rRNA V4 region and fungal ITS regions were sequenced with the Illumina MiSeq system. Overall, our results indicated that the composition of the bacterial and fungal communities of the rhizosphere were sensitive to the WCC suppression methods. Some bacterial genera, including fungal antagonists and chitin degraders, and two fungi associated with plant potential pathogens, were favored by both suppression methods, yet both methods negatively affected other genera associated with plant growth promotion characteristics. Our work contributes to a more complete understanding of the interactions between WCC management practices, soil properties, and microbial communities in the rhizosphere, which is essential for choosing management strategies that maintain soil health and promote environmental sustainability. Full article