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Nitrification and nitrogen (N) immobilization are important pathways in soil N transformations, involving soil N loss and retention, respectively. The ratio of nitrification to N immobilization generally reflects the potential risk of soil N loss. However, little is known about the response of this ratio to anthropogenic carbon (C) and N inputs, but also climate and soil conditions. Here, we aimed to elucidate, for the first time, the impacts of chemical fertilizer and manure application on the ratio of gross nitrification to N immobilization by using 15N dilution technology, based on ten long-term fertilization trials spanning multiple climatic zones in eastern China. Results showed that manure application differentially increased gross N immobilization rather than nitrification compared to the chemical fertilizer treatment, leading to manure-induced decreases in gross nitrification to N immobilization ratio ranging from 1.2 to 93% across the sites. The decreased gross nitrification to N immobilization ratio in the manure treatment was mainly due to the increased ratio of bacteria to nitrifiers abundance. Manuring was more effective for a decrease in the gross nitrification to N immobilization ratio at sites characterized by high rainfall and low soil pH, as it prevented soil pH decline thereby favoring bacterial abundance and N immobilization. Consequently, manure application resulted in a substantial increase in soil total N accumulation, facilitated by increased microbial N immobilization that promoted microbial biomass. These findings suggest that substituting manure for chemical fertilizer in the areas with high rainfall and acidic soils promisingly reduces soil N loss risk, with positive consequences for soil N retention. This knowledge highlights the potential to reconcile soil N loss and fertility improvement through optimizing regional manure management, which offers valuable insights for the development of a tailored regional fertilization management strategy. [ABSTRACT FROM AUTHOR]

Soil microbes are crucial for regulating biogeochemical cycles and maintaining forest ecosystem sustainability; however, the understanding of microbial communities and enzyme activity under natural and plantation forests in plateau regions remains limited. Using soil samples from 15-, 30-, and 50-year-old Picea crassifolia plantations and a natural forest (NF) in eastern Qinghai, China, this study assessed physicochemical properties, microbial communities, and enzyme activity across three soil layers. Microbial composition was characterized using the phospholipid fatty acid (PLFA) method, which is sensitive to structural changes. The PLFAs of bacteria, fungi, and actinomycetes accounted for 58.31%–74.20%, 8.91%–16.83%, and 3.41%–10.41% of the total PLFAs in all forests, respectively. There were significant differences between the NF and plantations, with the NF exhibiting higher PLFA abundance and enzyme activities than plantations, except for fungal PLFAs. PLFAs in plantations increased with the plantation age. However, the fungi-to-bacteria ratio was lower in the NF than in plantations. Finally, a redundancy analysis revealed that soil properties influence microbial composition and enzyme functionality significantly. These findings highlight the influence of stand age on microbial communities and structure, offering valuable insights for forest management practices aimed at conserving natural forests. [ABSTRACT FROM AUTHOR]

Background: Soil microbes drive the carbon cycle, yet are understudied in relation to long-term fire regimes in tropical savannas. Aim: Explore the impact of fire regime on soil microbes and organic carbon. Methods: We sampled topsoils (0–10 cm) of a tropical savanna near Darwin, Australia, where the frequency and season of fire had been experimentally managed for 17 years. We measured the effects of fire regime on microbial abundance, fungal-to-bacterial (F:B) ratio, soil physicochemistry (organic carbon, total nitrogen, C:N ratio, pH) and vegetative ground cover (grasses, leaf litter). Key results: Microbial abundance was most influenced by fire season, minimally affected by fire frequency and reduced by both grass and litter cover; the magnitude of grass cover effect differed among paleoecological groups (i.e. ancient and modern). Soil organic carbon was not affected by fire treatments, nor was the F:B ratio. Conclusions: Our data indicate that soil organic carbon, microbial abundance and F:B ratio are slow to change in a tropical savanna despite 17 years of imposed fire regimes. Implications: Soil microbes in savanna ecosystems may have evolved resilience to variable fire regimes and the potential for soil carbon sequestration in Australia from fire suppression is likely limited within human timescales. In an Australian tropical savanna, soil microbial abundance was more affected by burn season than fire frequency. Grass and litter cover reduced microbial abundance; modern grasses had a greater impact on microbes than ancient endemic species. Soil organic carbon and coarse-scale microbial community structure were unaffected by fire regime. This article belongs to the collection: Savanna burning. [ABSTRACT FROM AUTHOR]

Poorly-treated wastewater harbors harmful microorganisms, posing risks to both the environment and public health. To mitigate this, it is essential to implement robust disinfection techniques in wastewater treatment plants. The use of performic acid (PFA) oxidation has emerged as a promising alternative, due to its powerful disinfection properties and minimal environmental footprint. While PFA has been used to inactivate certain microbial indicators, its potential to tackle the entire microbial community in effluents, particularly resistant bacterial strains, remains largely unexplored. The present study evaluates the efficacy of PFA disinfection on the microbial communities of a WWTP effluent, through microbial resistance mechanisms due to their membrane structure. The effluent microbiome was quantified and identified. The results showed that the number of damaged cells increases with CT, reaching a maximum for CT = 240 mg/L•min and plateauing around 60 mg/L•min, highlighting the optimal conditions for PFA-disinfection against microbial viability. A low PFA level with a 10-min contact time significantly affected the microbial composition. It is worth noting the sensitivity of several bacterial genera such as Flavobacterium, Pedobacter, Massilia, Exiguobacterium, and Sphingorhabdus to PFA, while others, Acinetobacter, Leucobacter, Thiothrix, Paracoccus, and Cloacibacterium, showed resistance. The results detail the resistance and sensitivity of bacterial groups to PFA, correlated with their Gram-positive or Gram-negative membrane structure. These results underline PFA effectiveness in reducing microbial levels and remodeling bacterial composition, even with minimal concentrations and short contact times, demonstrating its suitability for widespread application in WWTPs. [ABSTRACT FROM AUTHOR]

Cyanobacterial biofertilizers provide soil fertility and productivity gains at varying levels in paddy rice cultivation. The colonization and influences of introduced strains in different soil types with characteristic compositions of native cyanobacteria remain largely unknown. In this work, seven paddy rice soils with the composition of indigenous cyanobacteria described by amplicon sequencing analysis were inoculated with the cyanobacterial biofertilizer. The microbial abundance and the cyanophage concentrations were evaluated under light-dark or continuous dark cycles using quantitative polymerase chain reaction (qPCR) assays. The copies of cyanobacterial-16S rRNA gene markers varied from 5.65 × 106 to 9.22 × 107 g-1 soil, and their abundance increased significantly in the inoculated soils. The cyanophage concentrations, quantified using the capsid assembly protein gene g20 in the soils tested, ranged from 3.04 × 108 to 9.24× 108 g-1 soil on 30 days after incubation. There were significant increases in the abundance of the nifH gene copies, about 1.54×105 to 1.35×106 g-1, in the inoculated soils, albeit with soil type-specific responses. The gene markers of C and N cycling (i.e., cbbL and nifH, respectively), taxonomic markers (of archaea, bacteria, and cyanobacteria), and cyanophage-specific gene copies showed strong and positive correlation with the cyanobacterial biofertilizer inoculation. However, the genes related to nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, narG, and nosZ) were clustered together in the uninoculated soils. The rice rhizospheres in three representative paddy soil types, using metatranscriptomics analysis, showed distinctive colonization by cyanobacteria, with several members yet to be described. These results indicate the potential for improving cyanobacterial biofertilizers for their contributions to plant growth and fertility gains in a soil-specific way. [ABSTRACT FROM AUTHOR]

Anaerobic digestion (AD) presents a promising avenue for efficiently reducing sewage sludge and generating renewable energy. The success of AD systems largely relies upon the microbial community composition, which is associated with various process parameters. This review aims to investigate the correlations among the microbiota abundances, digestion performances, and process parameters based on 233 datasets in 69 publications. Statistical analysis of the datasets uncovers significant correlations between process parameters with dominant bacterial phyla and archaeal genera. The evolution of microbial relative abundance (RA) reveals that Chloroflexi are positively correlated with Actinobacteria, Spirochaetes, and Synergistetes, while Firmicutes exhibit negative correlations with Proteobacteria, Chloroflexi, and Spirochaetes. Methanosarcina have negative correlations with Methanothrix, Methanobacterium, and Methanomassiliicoccus. Bacteria and archaea exhibit potential competitive (between syntrophic acetate-oxidizing bacteria and acetoclastic archaea) and syntrophic (between hydrogen-producing bacteria and hydrogenotrophic archaea) relationships. Furthermore, the volatile solids reduction and methane yield are significantly correlated with microbiota RAs and the ratio of Bacteroidetes and Firmicutes. This review sheds light on microbial interactions and thus AD performance by establishing the correlations between process parameters and microbiota composition. Future research directions should emphasize the significance of rare taxa, the necessity for experimental validation, and the potential of advanced modeling approaches to optimize sludge AD systems. [ABSTRACT FROM AUTHOR]

Agriculture is a major source of greenhouse gas (GHG) emissions. Biochar has been recommended as a potential strategy to mitigate GHG emissions and improve soil fertility and crop productivity. However, few studies have investigated the potential of biochar co-compost (BCC) in relation to soil properties, rice productivity, and GHG emissions. Therefore, we examined the potential of BC, compost (CP), and BCC in terms of environmental and agronomic benefits. The study comprised four different treatments: control, biochar, compost, and biochar co-compost. The application of all of the treatments increased the soil pH; however, BC and BCC remained the top performers. The addition of BC and BBC also limited the ammonium nitrogen (NH4+-N) availability and increased soil organic carbon (SOC), which limited the GHG emissions. Biochar co-compost resulted in fewer carbon dioxide (CO2) emissions, while BC resulted in fewer methane (CH4) emissions, which was comparable with BCC. Moreover, BC caused a marked reduction in nitrous oxide (N2O) emissions that was comparable to BCC. This reduction was attributed to increased soil pH, nosZ, and nirK abundance and a reduction in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) abundance. The application of different amendments, particularly BCC, favored rice growth and productivity by increasing nutrient availability, soil carbon, and enzymatic activities. Lastly, BCC and BC also increased the abundance and diversity of soil bacteria, which favored plant growth and caused a reduction in GHG emissions. Our results suggest that BCC could be an important practice to recycle organic sources while optimizing climate change and crop productivity. [ABSTRACT FROM AUTHOR]

Prebiotics, a subset of biostimulants, have garnered attention for their potential to enhance soil conditions and promote plant growth, offering a promising alternative to conventional agricultural inputs. This study explores how two commercial prebiotics, K1® and NUTRIGEO L® (SPK and SPN), impact soil functions compared to a control (SP). The experiment involved agricultural soil amended with organic wheat straws and cultivated with Zea mays L. Previous research demonstrated substantial effects of these prebiotics on plant biomass, soil parameters, and microbial community ten weeks after application. The present study delves deeper, focusing on soil microbial abundance, enzyme activities, and metabolic diversity. Analysis revealed that SPN notably increased the fungi-to-bacteria ratio, and both prebiotics elevated the activity of several key enzymes. SPN enhanced α-glucosidase and β-galactosidase activities, while SPK increased arylsulfatase, phosphatase, alkaline phosphatase, and urease activities. Enzymatic indexes confirmed the positive impact on soil functional diversity and fertility. Additionally, prebiotic treatments showed distinct metabolic profiles, with SPK degrading eleven carbon sources more rapidly across five groups and SPN accelerating the decomposition rate of four carbon sources from three groups. These findings highlight the ability of prebiotics to shape microbial communities and enhance soil fertility by modulating their functional activity and diversity. [ABSTRACT FROM AUTHOR]

Simple Summary: In China, high-grain diets for ruminants due to forage scarcity cause metabolic disorders. Yeast culture promotes rumen health by stabilizing microbial composition and enhancing nutrition and immunity. Therefore, the objective of this experiment was mainly to investigate the effect of the addition of two different species of yeast culture on goat production performance, rumen fermentation profile, microbial balance, and immunity under high-grain conditions. The results indicated that the incorporation of yeast culture into a high-grain diet significantly enhanced the production performance of goats, augmented their immunity, and stabilized the rumen environment. However, different types of yeast cultures acted by different mechanisms. The results provide a reference for the rational application of yeast culture in production. It is a common practice among farmers to utilize high-grain diets with the intention of promoting ruminant growth. However, this approach bears the risk of inducing rumen disorders and nutrient metabolism diseases. Yeast culture (YC) showed advantages in ruminant applications. The objective of this study was to evaluate the effects of adding two different types of YC to high-grain conditions on production performance, rumen fermentation profile, microbial abundance, and immunity in goats. A total of 30 male goats with similar body condition were randomly distributed into 3 dietary treatments with 10 replicates per treatment as follows: basic diet group (CON); basic diet + 0.5% yeast culture 1 (YC1) group; basic diet + 0.5% yeast culture 2 (YC2) group. The trial lasted for 36 days. The results demonstrated that dietary YC supplementation led to an increase in the average daily gain and a reduction in feed intake and weight gain ratio in goats. It increased the apparent digestibility of crude protein, NDF, and ADF (p < 0.05). The serum concentrations of interleukin (IL)-1β, IL-6, and Tumor Necrosis Factor-α in the control group were significantly higher than those of the YC groups (p < 0.05). The serum concentrations of Immunoglobulin (Ig)A and IgG in the control group were significantly lower than those in the YC groups (p < 0.05). The rumen concentration of microbial protein (MCP) in the control group was significantly lower than that in the YC groups (p < 0.05). There was a negative correlation between the concentration of IL-10 and Bacteroidota, Spirochaetota, and Succinivibrio, while there was a positive correlation between concentrations of IL-10 and Firmicutes. Nevertheless, discrepancies were observed in the impact of the two different types of YC on the physiological and biochemical indicators of the animals. The concentration of triglyceride in the YC1 group was significantly higher than that of the CON and YC2 groups, while the concentration of urea in the YC2 group was significantly higher than that of the CON and YC1 groups (p < 0.05). At the phylum level, the addition of YC2 to the diet significantly increased the relative abundance of Bacteroidota and Fibrobacterota and significantly decreased Firmicutes compared to the control. At the genus level, the addition of YC1 to the HGD significantly reduced the relative abundance of Rikenellaceae_RC9_gut_group, while the addition of YC2 to the HGD significantly increased the relative abundance of Prevotellace-ae_UCG-001, Fibrobacter, and Prevotellaceae_UCG-003 (p < 0.05). The addition of YC significantly improved growth performance, increased nutrient digestibility, beneficially manipulated ruminal fermentation and microbial diversity, and improved immune function. The choice of yeast cultures can be customized according to specific production conditions. [ABSTRACT FROM AUTHOR]

Changes in gut microbiome composition have been implicated in the pathogenesis of graft-versus-host disease (GvHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Our objective was to explore the microbial abundance in patients with GvHD after allo-HSCT. We conducted a single-center, prospective study in patients who underwent allo-HSCT and developed grade II or higher acute GvHD and/or moderate or severe chronic GvHD, to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected fecal specimens at −2 to +2 (T1), +11 to +17 (T2), +25 to +30 (T3), +90 (T4), and +180 (T5) days to assess changes in gut microbiota, with day 0 being the day of allo-HSCT. We included 20 allo-HSCT recipients in the study. Compared with timepoint T1, at timepoint T4 we found a significant decrease in the abundance of Proteobacteria phylum (14.22% at T1 vs. 4.07% at T4, p = 0.01) and Enterobacteriaceae family (13.3% at T1 vs. <0.05% at T4, p < 0.05), as well as a significant increase in Enterococcus species (0.1% at T1 vs. 12.8% at T4, p < 0.05) in patients who developed acute GvHD. Regarding patients who developed chronic GvHD after allo-HSCT, there was a significant reduction in the abundance of Eurobactereaceae family (1.32% at T1 vs. 0.53% at T4, p < 0.05) and Roseruria genus (3.97% at T1 vs. 0.09% at T4, p < 0.05) at T4 compared with T1. Alpha and beta diversity analyses did not reveal a difference in the abundance of bacteria at the genus level in GvHD patients at T4 compared with T1. Our study reinforces results from previous studies regarding changes in gut microbiota in patients with acute GvHD and provides new data regarding the gut microbiome changes in chronic GvHD. Future studies will need to incorporate clinical parameters in their analyses to establish their association with specific changes in gut microbiota in patients with GvHD after allo-HSCT. [ABSTRACT FROM AUTHOR]

The aim of this experiment was to reveal the effects of dietary soybean hulls content on growth performance, abundance of microbial species in rumen and the diversity of bacterial colonies in rumen of Hu sheep. Ninty-six healthy Hu male sheep (with the bodyweight was about 30 kg) were randomly assigned to 4 groups, with 24 sheep in each group. Sheep in the 4 groups were fed experimental diets which supplemented with 0 (group O), 10% (group A), 20% (group B), 30% (group C) soybean hulls. The trail lasted for 10 days for adaption, and 60 days for test. The growth performance, abundance of rumen microbial species and rumen microbial diversity of sheep were measured. The results were showed as follows: ADG and ADFI of group A and B were significantly higher than group O, C (P<0.05). When the soybean hulls content was 20% in the feed, and F/G was the lowest. The main ruminal microbial community of Hu sheep based on phylum level were Bacteroidetes, Firmicutes, Proteobacteria. The abundance of Bacteroidetes in group B,C were higher than group O, A. The abundance of Firmicutes in group O,A were higher than group B C. The main ruminal microbial community of Hu sheep based on genus level were Prevolella, Erysipelotrichaceae_UCG-002, Acetitomaculum. In the aspect of biodiversity, the amount of species in group O was significantly higher than group B, C (P<0.01). The Shannon index of group O, A were significantly higher than group B, C (P<0.01). There was no significant difference in Simpson index (P>0.05). Principal component analysis based on unweighted distance, the cluster of group O, A were the best, it was distributed in group B, C, and it was showed that there were different structural differences between communities. Result: the soybean hulls content in feed was 10%-20%, the growth performance of Hu sheep was higher. Different additition of soybean hulls in feed influenced the abundance of Bacteroidetes, Firmicutes and Prevolella. Species diversity was affected by different proportion of soybean hulls .The abundance of microbial species and diversity decreased with the increase of soybean hulls. [ABSTRACT FROM AUTHOR]

Carbon source addition is an important way improving the carbon and nitrogen transformation in aquaculture system; however, its effectiveness of algal–bacterial-based aquaponics (AA) through carbon source addition is still vague. In this study, the influences of organic carbon (OC-AA system) and inorganic carbon (IC-AA system) addition and without carbon source addition (C-AA system) on the operational performance of AA system were investigated. Results showed that 10.1–19.5% increase of algal–bacterial biomass enhanced the purifying effect of ammonia nitrogen in OC-AA system and IC-AA system relative to C-AA system. Moreover, extra electron donor supply in the OC-AA system obtained the lowest NO3−-N concentration. However, that was at the cost of aggravated N2O conversion ratio, which increased by more than 2.0-folds than other systems, attributing to 2.9-folds increase of nirS gene abundance. In addition, carbon source addition increased the pH and then decreased the fish biomass production of AA system. The results of this study would provide theoretical supports of carbon source addition on the performance of nutrient transformation and greenhouse gas effect in AA system. [ABSTRACT FROM AUTHOR]

Soil amendment with biochar from oil palm biomass has been found to improve the quality of the infertile weathered soils and enhance crop productivity in the humid tropics. Meanwhile, the field information on microbial responses to oil palm-derived biochar application and its residual effect in acidic tropical soils is still limited. A field study was carried out over three cropping cycles of sweet corn on a Haplic Acrisol of Peninsular Malaysia. The soil was amended once with oil palm kernel shell (OPKS) biochar before the first cropping cycle, with or without inorganic fertiliser. Soil samples were taken at each harvesting stage and analysed for soil pH, cation exchange capacity (CEC), organic C, total N, available P, microbial biomass (C (MBC), N (MBN), and P (MBP)). Microbial biomass ratios (MBC : MBN, MBC : MBP) were calculated. The total bacterial and fungal populations were quantified from soil genomic DNA, employing qPCR amplification of the 16S rDNA and ITS gene. The sole application of biochar and its combined application with fertiliser, increased soil pH, CEC, organic C and N. Coapplication of OPKS biochar and NPK fertiliser hindered N loss in the second cycle. The bacterial and fungal abundance was stimulated following biochar treatment majorly due to the elevation of soil pH and CEC. The ratio of MBC : MBN had a significant negative correlation with N, signifying that this ratio could reflect soil N content and be used as a soil fertility indicator. [ABSTRACT FROM AUTHOR]

Although nitrogen (N) enrichment is known to threaten the temporal stability of aboveground net primary productivity, it remains unclear how it alters that of belowground microbial abundance and whether its impact can be regulated by grassland degradation. Using data from N enrichment experiments at temperate grasslands with no, moderate, severe, and extreme degradation degrees, we quantified the temporal stability of soil microbial abundance (hereafter 'microbial community stability') using the ratio of the mean quantitative PCR to its standard deviation over 4 years. Both bacterial and fungal community stability sharply decreased when N input exceeded 30 g N m−2 year−1 in non‐degraded grasslands, whereas a reduction in this threshold occurred in degraded grasslands. Microbial species diversity, species asynchrony, and species associations jointly altered microbial community stability. Interestingly, the linkages between plant and microbial community stability were strengthened in degraded grasslands, suggesting that plants and soil microbes might depend on each other to keep stable communities in harsh environments. Our findings highlighted the importance of grassland degradation in regulating the responses of microbial community stability to N enrichment and provided experimental evidence for understanding the relationships between plant and microbial community stability. [ABSTRACT FROM AUTHOR]

Aim: The accumulation of microbial necromass carbon has gained increasing attention due to its slow decomposition. However, it remains unclear what induces the accumulation of microbial necromass carbon via reiterated community turnover on large spatial scales. This study explores the characteristics of soil necromass carbon accumulation in terrestrial ecosystems. Location: Global. Time Period: Contemporary (1999–2022). Major Taxa Studied: Soil microorganisms. Methods: A dataset was compiled using 993 observations from 82 peer‐reviewed papers on the effects of coefficients of microbial necromass accumulation (hereafter NAC) in equilibrium. Linear mixed‐effect models and structural equation models were used to ascertain the controlling factors of the NAC. Results: The average NAC was higher in croplands (28.2) and forests (26.8) than in grasslands (21.1). Edaphic factors seemingly affected the NAC, which was lower in soils with high pH and clay content on a global scale. Biotic factors, particularly those related to living microorganism abundance and microbial biomass nitrogen content, were the pivotal drivers of NAC and accounted for approximately 43.6% of its geographic variability. More organic carbon was likely to be preserved in soil with a higher NAC, regardless of ecosystem type. Conclusions: Novel findings regarding the overriding controls for the living microorganism abundance and microbial biomass nitrogen that drive the NAC highlight an urgent need for viable strategies to manipulate microbial attributes for enhancing carbon sequestration. [ABSTRACT FROM AUTHOR]

The paper presents the study of the soil quality and health expressed by the chemical and biological properties in a research field placed at Varciorog, Bihor County, Romania. The soil samples were collected from 3 soil variants in March 2023. In each soil variant, some soil chemical parameters and the abundance of bacteria were determined. The frequency and intensity of colonization, along with arbuscules and vesicles, were scored to determine the mycorrhizal potential of each soil. The community-level physiological profile was used to determine the functional microbiome and its ability to decompose a specific set of substrates. In the control variant (CTRL), which is a functional forest cultivated with beech in a proportion of 90%, the soil properties were compared with those determined from Site 1 (a declined mixed forest) and from Site 2 (chestnut forest in a stage of complete drying). The data were statistically processed with a one-way ANOVA test, followed by the Duncan post-hoc test, which revealed significant variation in the potential of microbial functional communities across the analyzed sites. Also, the soil parameters that significantly varied in the 3 soil variants were bacterial number, pH, humus, exchangeable aluminum, coarse sand, dust, and fine sand. The Pearson correlation was computed to study the links between bacterial numbers and chemical parameters. The results showed strong correlations between most of the studied soil properties. The Ecoplates approach to soil functional microbiome highlighted various differences between the microbial communities of the three tested sites. Mycorrhizal colonization shows different potentials for symbiosis formation. The peak of mycorrhizal colonization was in declined forest, with 43.36% colonization frequency and 24.56% intensity. Arbuscules reached 11.36% in declined forest, while in control and decayed sites, the indicator was under 4%. Vesicles are more associated with control and decayed forests, with values of presence over 1.30%. As an indicator of microbial general activity, the sum of recorded activities was higher in declined and decayed forests. At these sites, the activity of the functional microbiome was amplified. The decline process activates a higher diversity of functional groups and is associated with a larger area of substrate decomposition capacity, which indicates a more extensive range of microbial functions related to breaking down organic matter. [ABSTRACT FROM AUTHOR]

Prebiotics, a subset of biostimulants, have garnered attention for their potential to enhance soil conditions and promote plant growth, offering a promising alternative to conventional agricultural inputs. This study explores how two commercial prebiotics, K1® and NUTRIGEO L® (SPK and SPN), impact soil functions compared to a control (SP). The experiment involved agricultural soil amended with organic wheat straws and cultivated with Zea mays L. Previous research demonstrated substantial effects of these prebiotics on plant biomass, soil parameters, and microbial community ten weeks after application. The present study delves deeper, focusing on soil microbial abundance, enzyme activities, and metabolic diversity. Analysis revealed that SPN notably increased the fungi-to-bacteria ratio, and both prebiotics elevated the activity of several key enzymes. SPN enhanced α-glucosidase and β-galactosidase activities, while SPK increased arylsulfatase, phosphatase, alkaline phosphatase, and urease activities. Enzymatic indexes confirmed the positive impact on soil functional diversity and fertility. Additionally, prebiotic treatments showed distinct metabolic profiles, with SPK degrading eleven carbon sources more rapidly across five groups and SPN accelerating the decomposition rate of four carbon sources from three groups. These findings highlight the ability of prebiotics to shape microbial communities and enhance soil fertility by modulating their functional activity and diversity.

Agronomic practices can have a negative impact on soil health and quality and ecosystem resilience. The objectives of the study were (1) to evaluate the soil chemical properties and microbial abundance under short-term application of organic and mineral fertilizers and different cultivated crops and (2) to observe the antifungal efficacy of microorganisms isolated from the studied soil. A field trial was conducted in the 2021–2022 period on a preluvosoil-type soil in four randomized blocks with eight fertilizer treatments based on manure compost (MC) and MC + mineral fertilizer (V1—control-soil; V2—NPK only; V3—15 t/ha MC; V4—15 t/ha MC + NPK; V5—30 t/ha MC; V6—30 t/ha MC + NPK; V7—60 t/ha MC; and V8—60 t/ha MC +NPK) and four crops (winter wheat—Triticum aestivum L., maize—Zea mays L., soybean—Glycine max L., and a mixture of perennial grasses and legumes). In almost all treatments, the soil pH decreased during the summer–autumn period. The organic carbon (Corg) and humus contents increased compared to the initial state of the soil after the application of different doses of MC and MC + NPK fertilization in almost all treatments. The microbial load of the soil was influenced by the fertilization regime and crop species, but there were no significant differences between the variants. The highest bacterial load was recorded in soil cultivated with a mixture of perennial grasses and grain legumes, i.e., in the variant with 15 t/ha MC, followed by soil cultivated with maize and fertilized with 30 t/ha and 60 t/ha MC. A higher number of fungi was observed in the mixture of perennial grasses and legumes, and Rhizobium population was higher, especially in the winter wheat plots, despite the fertilization regime. The antifungal efficacy of the microorganisms isolated from the samples was medium to low, except in the winter wheat experiment, where the efficacy against Fusarium culmorum was medium to high and against other pathogens was medium. In the other crops within the experiment, the antagonistic activity of the soil microorganisms was medium to low. [ABSTRACT FROM AUTHOR]

Aims: Partially substituting organic fertilizer for chemical fertilizer is becoming more commonly recognized as a feasible technique for achieving sustainable agriculture. Nonetheless, the effects of partial replacement of artificial nitrogen (N) with organic fertilizer derived from food waste on rice production, N use efficiency (NUE), soil N pools, and microbial activity are unknown. Methods: Over the 2020 and 2021 rice growing seasons, the following four treatments were investigated: CK, no fertilizer; CF, chemical fertilizer; C20, food waste organic fertilizer replacing 20% chemical N; and C50, food waste organic fertilizer replacing 50% chemical N. Under various treatments, we compared rice production, NUE, soil N pools, enzyme activities, and microbial abundance. Results: The results demonstrated that substituting food waste organic fertilizer for chemical N ensured rice yield and improved NUE compared to chemical fertilizer alone. Food waste organic fertilizer substitution exhibited greater potential for enhancing soil organic matter (SOM), total N (TN), dissolved organic N (DON), microbial biomass N (MBN), ammonium N (NH4+-N), and nitrate N (NO3−-N) contents compared to the use of chemical fertilizer alone. Fertilization significantly increased the activities of N-acquiring enzymes and led to increased abundances of bacteria and fungi compared to no fertilizer application. Food waste organic fertilizer substitution resulted in higher levels of protease and leucine aminopeptidase compared to chemical fertilizer, while activities of urease and β-N-acetylglucosaminidase, as well as bacterial and fungal abundances, did not show significant differences between food waste organic fertilizer substitution and chemical fertilizer. Moreover, our findings indicate that organic substitution maintains rice production primarily by regulating soil N sources. Conclusions: Our findings imply that substituting food waste organic fertilizer for artificial N enhances soil N availability, soil bacteria and fungus abundances, and N-acquiring enzyme activities while also maintaining rice output. [ABSTRACT FROM AUTHOR]

Shallow-water hydrothermal vents are extreme environments characterized by high temperatures, low pH, and high CO2 concentrations; therefore, they are considered as suitable laboratories for studying the effect of global changes on marine microbes. We hypothesized a direct effect of vents on prokaryotic community structure and functioning in the Panarea Island's hydrothermal system. Sampling was conducted along a 9-station transect characterized by three active emission points. The water column was stratified with a thermocline at 25 m depth and a deep chlorophyll maximum between 50 and 100 m. Prokaryotic abundance ranged from 0.2 to 1.5 × 109 cells L−1, prokaryotic carbon production from 2.4 to 75.4 ng C L−1 h−1, and exoenzymatic activities degrading proteins, phosphorylated compounds, and polysaccharides were on the order of 4–28, 2–31 and 0.2–4.16 nM h−1, respectively. While microbial abundance and production were shaped by the water column's physical structure, alkaline phosphatase and beta-glucosidase activities seemed to be enhanced by hydrothermal fluids. The 16S rRNA gene amplicon sequencing analysis identified a surface, a deep, and a vent-influenced microbial community. In terms of relative abundance members of the SAR11 group dominated the water column, alongside Synechococcus and Prochlorococcus in surface and bottom samples, respectively. Vent-influenced stations were characterized by the presence of Thiomicrorhabdus, a sulfur-oxidizer chemolithoautotroph. Overall, this study provides insights on the coupling between microbial community structure and the biogeochemical cycling of nutrients in low-pH conditions (CO2 and H2S-based), thus addressing some of the opened questions about the response of microbes to acidification. [ABSTRACT FROM AUTHOR]

Link for citation: Soldatova E.A., Sidkina E.S., Kiriukhin B.A., Maximov P.N., Krivenok L.A., Ivanov V., Tananaev N.I. Geochemical conditions of Sullar spring: formation of authigenic minerals and methane fluxes. Bulletin of the Tomsk Polytechnic University. Geo Аssets Engineering, 2023, vol. 334, no. 10, рр. 16-33. In Rus. Relevance and the research object. Interpermafrost aquifers and areas of their discharge with seasonal ice covers are special permafrost-hydrogeological and hydrochemical systems that are not typical for the thick continuous permafrost zone of Central Yakutia. Differences in chlorofluorocarbon content indicate the anaerobic conditions of some springs suggesting microbial degradation of these compounds by methanogenic bacteria. In the discharge area of such springs, a sharp change in the geochemical conditions takes place leading to a transformation in the water chemical composition and boosting the processes of authigenic mineral formation in this buffer area. In current work we considered the geochemical system of the Sullar spring – the most northern and the least studied among interpermafrost groundwater discharge zones of the Lena River right bank. Intensive accumulation of authigenic minerals was found in the Sullar discharge area during field research. It was Fe compounds with bacterial mats as an opalescent film. Some researchers state the connection between the transformation of Fe compounds during permafrost melting and the migration and transformation of organic matter, including its consumption by microorganisms with further methane emission. We assumed that there is a relationship between the authigenic mineral formation and the content and emission of methane in the discharge area of the spring. This research is the first comprehensive description of the hydrochemistry of the interpermafrost water of the Sullar spring. The aim of the research was to explore influence of geochemical conditions and microbial communities on formation of authigenic minerals and methane fluxes, in particular the effect of the change of geochemical conditions due to groundwater discharge on Fe precipitation and to analyze the relation of that process with methane fluxes. For this purpose, we study water chemical composition of the Sullar spring, measure methane fluxes from water surface and analyze mineral and microbial composition of secondary mineral crusts and bottom eluvium collected near water sampling points. Methods. The main element content was determined by ion chromatography. The concentrations of the bicarbonate ion and dissolved carbon dioxide were calculated by the equilibrium modeling method based on the pH and Eh values of the system. The content of trace elements was measured by mass spectrometry with inductively coupled plasma. To identify seasonal and annual variability, a retrospective analysis of the water chemical composition of the Sullar spring for the period from 1962 to 2020 was carried out. Methane fluxes were measured using the chamber method. The methane concentration was determined by gas chromatography with a flame ionization detector. The features of the secondary mineral crusts and bottom eluvium were determined using a petrographic microscope. The chemical composition of individual mineral phases was evaluated using a scanning electron microscope equipped with a detector for energy dispersive X-ray spectral microanalysis. The DNA concentration was measured on a fluorimeter. Amplicon libraries were generated by polymer chain reaction with universal primers for the V4 region. Equilibrium modeling was carried out using the HCh software.

This study presents the distribution of bacterial and fungal abundances in long-term copper (Cu) contaminated soils in Topolnitsa-Pirdop valley - a highly industrialized zone with a number of mines and processing plants for copper and other non-ferrous metals. The bacterial (16S rRNA gene copies) and fungal (ITS rRNA gene copies) were estimated using quantitative PCR technique in five topsoils, differently Cu contaminated (ranging from 28.05 to 198.9 mg kg-1). Bacterial abundance varied in a range of 1.68 × 1011 to 3.24 × 101116S rRNA genes, whereas fungi amounted from 1.95 × 108 to 6.71 × 108 ITS rRNA genes. Fungal and bacterial abundances were significantly (fungi) and insignificantly (bacteria) influenced by Cu contamination. The fungal/bacterial ratio related negatively with soil Cu, which shifted microbial communities' structure towards bacterial dominance. Since the ratio between bacteria and fungi are vital in explaining many soil functions, the calculated changes in this ratio indicated deterioration in soil quality, being of primary importance for plant production. [ABSTRACT FROM AUTHOR]

The application of fungicides has become a recurring method of modern agriculture. However, its frequent application could inhibit key processes in agroecosystems, particularly in the soil. Captan is a broad-spectrum, organochlorine, non-systemic fungicide widely used in agriculture. This study aimed to evaluate how different dosages of the fungicide captan affect the microbiota of soil subjected to different types of management and with a degradation gradient associated with the soil organic matter (SOM) content. The trial was conducted in a greenhouse and included soils with three types of management: pristine forest soil (L1), 2:1 rotation (soybean-corn) under no-tillage management (L2), and soybean monoculture under conventional tillage management (L3). The treatments were: control (0x), dosage 1.0 mg/kg soil (1x), and dosage 10 mg/kg soil (10x). Sampling was carried out 30 days after the application of captan. Enzymatic activities related to C, N, and P cycles, phospholipid fatty acid profiles (PLFA), and a quantification method for ribosomal RNA gene copy numbers (16S and 18S) were evaluated to assess the impact of captan on the structure and activities of microbial communities. Our results showed increases in enzyme activities and biomass in L1 soils at 1x doses compared to the control, except for gram-negative bacteria that increased at 10x dosages. However, the application of 10x dosages produced losses in activity and microbial biomass in the three types of soil. The lowest values of 16S and 18S rRNA copies were registered in the treatments with fungicide. The 16S bacterial rRNA did not present differences between the treatments in the L3 soils. In conclusion, the L1 soil presented greater sensitivity in its response to captan compared to the L2 and L3 soils under agricultural management. [ABSTRACT FROM AUTHOR]

The ingestion of cold water in winter results in fluctuating decreases in rumen temperature, impacting rumen fermentation function and methane production. This study aimed to investigate the impact of calcium propionate (CaP) on rumen fermentation characteristics, methane production, and microbial microbiome under different in vitro incubation temperatures. A 2 × 2 factorial experiment was conducted over 72 h, with or without 2.5% CaP (dry matter [DM] basis) in substrate under a constant incubation temperature (39 °C, CIT) or shifting incubation temperatures (12 cycles in total, with each cycle consisting of 4 h of incubation at 39 °C followed by immediate transfer to 30 °C for 2 h, ITS). The results showed that ITS inhibited the gas production, methane production, and methane concentration at 12 and 72 h (p < 0.05), and reduced the concentration of ammonium nitrogen (−14.25%), propionate (−16.14%), butyrate (−12.67%), and total volatile fatty acid (−8.50%) at 72 h more than the CIT groups (p < 0.05). The addition of 2.5% CaP significantly increased the gas production at 72 h (+4.84%), asymptotic gas production (+5.08%, per 0.2 g DM substrate), concentration of propionate (+18.05%), and valerate (+9.45%) (p < 0.05) compared to CaP-free groups, while it had no observable effect on the production or concentration of methane. Furthermore, the addition of 2.5% CaP yielded a significant increase in the relative abundance of Bacteroides (p < 0.05). Under the ITS condition, the relative abundance of Methanomicrobiales decreased and was positively correlated with methane production at 72 h (r = 0.47, p < 0.05). Additionally, CaP decreased the abundance of Prevotella_UCG_003 (p < 0.05), which was negatively correlated with the asymptotic gas production (r = 0.45, p < 0.05). Overall, our study suggests that the addition of 2.5% CaP can alleviate the adverse effects of ITS on in vitro fermentation parameters by regulating microbial composition and sustaining a reduction in methane production. [ABSTRACT FROM AUTHOR]

The importance of denitrification and anaerobic ammonium oxidation (anammox) in removing nitrogen (N) from upland runoff has been well documented in riparian wetlands. However, the relative contributions of denitrification and anammox to N removal in the rhizosphere and non‐rhizosphere soils of riparian zones remain unclear. Here, we explored the denitrification and anammox rates in the rhizosphere and bulk soils (0–5 and 10–15 cm) of 39 riparian wetlands along the Yangtze River using the 15N isotope pairing technique. Additionally, we used a quantitative polymerase chain reaction assay to determine the abundance of soil denitrifying and anammox bacteria using nosZ and hzsB genes, respectively. The results showed that both denitrification and anammox rates were significantly higher in rhizosphere soils than in bulk soils, suggesting that the rhizosphere environment is favorable for N removal. The contribution of anammox constituted over half (62.53% ± 1.49%) of the N loss and was greater in bulk soils (68.57% ± 1.42%) than in rhizosphere soils (55.64% ± 2.42%). Higher nosZ and hzsB gene abundances were also observed in rhizosphere soils than in bulk soils. Denitrification and anammox rates were significantly regulated by edaphic properties, microbial abundance, and plant biomass. The structural equation model further revealed that soil pH and N availability could affect denitrification and anammox rates both directly and indirectly by altering nosZ and hzsB gene abundance. Overall, this study highlights that the rhizosphere is a control point for N removal and harbors more functional microbes than bulk soils. Therefore, revegetation may effectively enhance the N removal function of riparian wetlands along the Yangtze River. Key Points: Denitrification and anammox rates were higher in rhizosphere soils than in bulk soilsThe contribution of anammox constituted over 60% of the N loss in the riparian zoneSoil pH and N availability regulated denitrification and anammox rates directly and indirectly [ABSTRACT FROM AUTHOR]

Microorganisms in the soil have a very important role because they participate in numerous processes. Intensive and/or inadequate use of the soil leads to disturbance of the plant - microbial interactions, a decline in productivity, and degradation. The abundance and microbiological activity of a certain ecosystem are considered indicators of soil fertility. In this paper, surface (0-20 cm) and subsurface (20-40 cm) samples of grassland, agricultural soil, forest soil and coal-mine-affected soil at the Banovići municipality (Tuzla Canton, Bosnia and Herzegovina) taken in October 2021 and April 2022 were used for chemical and microbiological characterization. Chemical analyses were performed using the standard methodology, while the microbial count was determined using the agar plate method. Enzyme production was expressed through dehydrogenase activity. The lowest pH value was recorded in forest soil, while the highest in the grassland. In all samples, microbial abundance decreased with increasing soil depth. The lowest microbial activity was observed in coal mine-affected soil. The highest value of the total number of bacteria and ammonifiers was recorded in forest soil. Oligonitrophiles were most abundant in agricultural soil, while the number of actinomycetes was highest in grassland. Dehydrogenase activity was highest in forest and agricultural soil. In most of samples, microbial abundance was higher in spring, while dehydrogenase activity was higher in autumn. This research confirms the impact of land use on microbial abundance as parameter of soil quality. [ABSTRACT FROM AUTHOR]

Purpose: Plant inputs provide the main food and energy for soil organisms. Considering substantial aboveground litter on the soil surface but few belowground input in the non-growing season, we hypothesize that aboveground input would have an important role in sustaining microbial abundance and community at this period. Methods: We initiated a manipulative temperate grass experiment with four types of plant inputs, i.e., no input (NI), only belowground input (+B), only aboveground input (+A), and both aboveground and belowground inputs (+A +B) in 2018. We tested whether plant aboveground input plays an important role in maintaining soil microorganisms in the non-growing season, i.e., before and after the growing season of 2019. Results: Microbial activities, abundance, composition, and diversity were all similar among the four plant treatments before the growing season. However, after the growing season, microbial activity and diversity were higher at the plots with belowground input (+B and +A +B) than at those without belowground input (+A and NI). Similarly, the abundance of saprophytic fungi, AM fungi, and gram-positive bacteria were larger in the plots with belowground input than NI plot. Microbial community composition was similar between +B and +A +B plots (with belowground input), but they were different with those at +A and NI plots (without belowground input). These results indicated that belowground plant input plays a determining role in maintaining soil microorganisms after the growing season. This may link with the legacy of the rhizodeposition carbon in the growing season. Conclusion: We demonstrate that aboveground input does not play a substantial role in maintaining soil microbial community in the non-growing season, although aboveground input amount dominates relative to belowground input. [ABSTRACT FROM AUTHOR]

Polar marine environments host a complex assemblage of cold-adapted auto- and heterotrophic microorganisms that affect water biogeochemistry and ecosystem functions. However, due to logistical difficulties, remote regions like those in close proximity to glaciers have received little attention, resulting in a paucity of microbiological data. To fill these gaps and obtain novel insights into microbial structure and function in Arctic regions, a survey of microbial communities in an area close to the Blomstrandbreen glacier in Kongsfjorden (Svalbard Archipelago; Arctic Ocean) was carried out during an early summer period. An Unmanned Autonomous Vehicle designed to safely obtain seawater samples from offshore-glacier transects (PROTEUS, Portable RObotic Technology for Unmanned Surveys) was equipped with an automatic remotely-controlled water multi-sampler so that it could sample just beneath the glacier, where access from the sea is difficult and dangerous. The samples were analysed by image analysis for the abundance of total prokaryotes, viable and respiring cells, their morphological traits and biomass; by flow cytometry for autotrophic and prokaryotic cells (with high and low nucleic acid contents) as well as virus-like particle counts; by BIOLOG ECOPLATES for potential community metabolism; and by fluorimetry for potential enzymatic activity rates on organic polymers. Contextually, the main physical and chemical (temperature, salinity, pH, dissolved oxygen and nutrients) parameters were detected. Altogether, besides the PROTEUS vehicle's suitability for collecting samples from otherwise inaccessible sites, the multivariate analysis of the overall dataset allowed the identification of three main sub-regions differently affected by the haline gradient (close to the glacier) or terrigenous inputs coming from the coast. A complex microbiological scenario was depicted by different patterns of microbial abundance and metabolism among the transects, suggesting that ice melting and Atlantic water inflow differently supported microbial growth. [ABSTRACT FROM AUTHOR]

Introduction: Nitrous oxide (N2O) emission from soil is a major concern due to its contribution to global climate change and its function as a loss mechanism of plant-available nitrogen (N) from the soil. This is especially true in intensive agricultural soils with high rates of N fertilizer application such as those on the semi-arid Southern High Plains, USA. Methods: This study examined emissions of N2O, pore-space concentrations of N2O and nitric oxide (NO), soil chemical properties, water content, and the genetic potential for N cycling five years after conservation system and N management implementation. Results: For these semi-arid soils with low N, carbon, and water contents, large soil N2O emissions (up to 8 mL N2O-N m-2 day-1) are directly related to the application of N fertilizer which overwhelms the N2O reducing capacity of the soil. When this fertilizer N is depleted, N2O flux is either low, non-existent, or net-negative and has been observed as early as mid-season for preplant applied N fertilizer (-0.1 mL N2O-N m-2 day-1). Soil pore-space gas concentrations (N2O and NO) remained relatively constant across the growing season (average N2O: 0.78 µL N2O L-1 soil air; NO: 3.3 μL NO L-1 soil air, indicating a base-level of N-cycle activity, but was not directly related to surface emissions of N2O which decreased across the growing season. In addition, genetic potential for N cycle activities increased across the growing season simultaneously with stagnant/reduced N cycle activity. This reflects the difficulty in relating genetic potential to in-situ activity in field research. Conclusion: It is likely that in a nutrient and carbon-poor soil, such as the semiarid agricultural soil in this study, the microbial processes associated with N cycling are mostly limited by inorganic-N and less directly related to genetic potential at the time of sampling. [ABSTRACT FROM AUTHOR]

Shallow underwater hydrothermal systems are often overlooked despite their potential contribution to marine diversity and biogeochemistry. Over a decade after its eruption, the Tagoro submarine volcano continues to emit heat, reduced compounds, and nutrients into shallow waters, serving as a model system for studying the effects of diffuse hydrothermal fluids on surface microbial communities. The impact on both phytoplankton and bacterial communities was examined through experimental manipulations mimicking dilution levels up to ~100 m from the primary crater of Tagoro. Chlorophyll a concentration doubled in the presence of hydrothermal products, with peak levels detected about a day earlier than in controls. Picoeukaryotes and Synechococcus cell abundances moderately increased, yet small eukaryotic phytoplankton (≤ 5 μm) predominated in the hydrothermally enriched bottles. Dinoflagellates, diatoms, small green algae and radiolarians particularly benefited from the hydrothermal inputs, along with phototrophic and chemoautotrophic bacteria. Our results indicate that hydrothermal products in shallow waters enhance primary production driven by phototrophic microbes, potentially triggering a secondary response associated with increased organic matter availability. Additionally, protistan grazing and parasitism emerged as key factors modulating local planktonic communities. Our findings highlight the role of shallow submarine hydrothermal systems in enhancing local primary production and element cycling., (© 2025 The Author(s). Environmental Microbiology published by John Wiley & Sons Ltd.)

IntroductionNitrous oxide (N2O) emission from soil is a major concern due to its contribution to global climate change and its function as a loss mechanism of plant-available nitrogen (N) from the soil. This is especially true in intensive agricultural soils with high rates of N fertilizer application such as those on the semi-arid Southern High Plains, USA.MethodsThis study examined emissions of N2O, pore-space concentrations of N2O and nitric oxide (NO), soil chemical properties, water content, and the genetic potential for N cycling five years after conservation system and N management implementation.ResultsFor these semi-arid soils with low N, carbon, and water contents, large soil N2O emissions (up to 8 mL N2O-N m-2 day-1) are directly related to the application of N fertilizer which overwhelms the N2O reducing capacity of the soil. When this fertilizer N is depleted, N2O flux is either low, non-existent, or net-negative and has been observed as early as mid-season for preplant applied N fertilizer (-0.1 mL N2O-N m-2 day-1). Soil pore-space gas concentrations (N2O and NO) remained relatively constant across the growing season (average N2O: 0.78 µL N2O L-1 soil air; NO: 3.3 µL NO L-1 soil air, indicating a base-level of N-cycle activity, but was not directly related to surface emissions of N2O which decreased across the growing season. In addition, genetic potential for N cycle activities increased across the growing season simultaneously with stagnant/reduced N cycle activity. This reflects the difficulty in relating genetic potential to in-situ activity in field research.ConclusionIt is likely that in a nutrient and carbon-poor soil, such as the semi-arid agricultural soil in this study, the microbial processes associated with N cycling are mostly limited by inorganic-N and less directly related to genetic potential at the time of sampling.

Soil microbial abundance is a key factor to predict soil organic carbon dynamics in peatlands. However, little is known about the effects of altitude and soil depth and their interaction on soil microbial abundance in peatlands. In this study, we measured the microbial abundance and soil physicochemical properties at different soil depths (0–30 cm) in peatlands along an altitudinal gradient (from 200 to 1,500 m) on Changbai Mountain, China. The effect of soil depth on soil microbial abundance was stronger than the altitude. The total microbial abundance and different microbial groups showed the same trend along the soil depth and altitudinal gradients, respectively. Microbial abundance in soil layer of 5–10 cm was the highest and then decreased with soil depth; microbial abundance at the altitude of 500–800 m was the highest. Abiotic and biotic factors together drove the change in microbial abundance. Physical variables (soil water content and pH) and microbial co-occurrence network had negative effects on microbial abundance, and nutrient variables (total nitrogen and total phosphorus) had positive effects on microbial abundance. Our results demonstrated that soil depth had more effects on peatland microbial abundance than altitude. Soil environmental change with peat depth may lead to the microorganisms receiving more disturbances in future climate change. [ABSTRACT FROM AUTHOR]

Permafrost affected soils are highly vulnerable to climate change. These soils store huge amounts of organic carbon (C), and a significant proportion of this carbon is stored in subsoil horizons where it might become available to microbial decomposition under global warming. An important factor in understanding and quantifying the C release from soils include the limitation of resources for microbes. Microbes decompose soil organic matter (SOM) by secreting extracellular enzymes into the soil, thus enzyme activity and their ratios are considered important indicators of soil nutrient availability and microbial substrate limitation. To evaluate nutrient limitation and the limitation of microbial substrate utilization, we investigated the potential enzyme activity from whole soil profiles, including topsoil, cryoturbated organic matter, mineral subsoil, and permafrost of Herschel Island (Canada) and Disko Island (Greenland). We included seven enzymes (five hydrolytic and two oxidative) and related them to bacterial and fungal gene abundance. The results showed hydrolytic enzymatic activity was strongly influenced by soil type, whereas oxidative enzymes varied between different localities. The enzyme ratios indicated that the topsoil microbial communities were C and phosphorus (P) co-limited in both localities, whereas the subsoil communities were nitrogen (N) limited from HI and C, P limited from DI. A strong positive correlation between all measured enzymes and bacterial gene abundance compared to that of fungi suggested that bacteria might play a more important role in SOM decomposition in permafrost soil horizons. This study suggests that Arctic permafrost microbial communities were not only limited by N, but also by C, P, and their co-limitation under specific conditions (i.e., higher abundance of bacteria and lower abundance of fungi). [ABSTRACT FROM AUTHOR]

Abstract Background The chicken gut microbiota passes through different stages of maturation; therefore, strengthening it with well characterised probiotics increases its resilience required for optimum gut health and wellbeing. However, there is limited information on the interaction of Bacillus based probiotics with gut microbial community members in cage free laying chickens both in rearing and production phases of life. In the current study, we investigated the changes in the gut microbiome of free range hens in the field after Bacillus based probiotic supplementation. Results Overall, at phylum level, probiotic supplementation increased the populations of Bacteroidetes and Proteobacteria mainly at the expense of Firmicutes. The population of Bacteroidetes significantly increased during the production as compared to the rearing phase, and its higher population in the probiotic-supplemented chickens reflects the positive role of Bacillus based probiotic in gut health. Core differences in the beta diversity suggest that probiotic supplementation decreased microbial compositionality. The non-significant difference in alpha diversity between the probiotic and control chickens showed that the composition of community structure did not change. No Salmonella spp. were isolated from the probiotic supplemented birds. Egg internal quality was significantly higher, while egg production and body weight did not differ. Functional prediction data showed that probiotic supplementation enriched metabolic pathways, such as vitamin B6 metabolism, phenylpropanoid biosynthesis, monobactam biosynthesis, RNA degradation, retinol metabolism, pantothenate and CoA biosynthesis, phosphonate and phosphinate metabolism, AMPK signaling pathway, cationic antimicrobial peptide (CAMP) resistance and tyrosine metabolism. Conclusions Overall, age was the main factor affecting the composition and diversity of gut microbiota, where probiotic supplementation improved the abundance of many useful candidates in the gut microbial communities. The generated baseline data in the current study highlights the importance of the continuous use of Bacillus based probiotic for optimum gut health and production.

The SOC and carbon mineralization were highest under no grazing. As grazing intensity increased, trampling by sheep broke up large soil aggregates, leading to a loss of SOC and a decrease in carbon mineralization. Light grazing maintained high SOC content, but reduced carbon mineralization, which was associated with reduced plant carbon inputs and bacterial abundance. The main reasons for the reduction in carbon mineralization was due to the dramatic reductions in plant carbon inputs, fungal and bacterial abundance under both moderate and heavy grazing. [Display omitted] • Soil carbon mineralization decreased by 15–55% under different grazing intensities. • Light grazing reduced carbon mineralization but maintained high soil organic carbon. • Soil carbon mineralization was modulated by the environment and microbial interactions. Fencing off grassland soils emits massive amounts of carbon into the atmosphere. Whether grazing management in desert steppes with fragile ecosystems can mitigate this trend remains highly uncertain. Here, we examined how soil carbon mineralization, as well as its underlying mechanisms, varied with grazing intensity by sheep in a long-term (17 − year) experiment in the desert steppe. Carbon mineralization decreased by 15 % − 55 % under different grazing intensities compared to fencing controls. Soil organic carbon (SOC) maintained high levels under light grazing, whereas it decreased with increasing grazing intensity. Reductions in plant carbon and absolute microbial abundance due to grazing, coupled with changes in soil carbon quality and the environment, drove the reduction in carbon mineralization. We suggest that mechanisms of carbon mineralization can be integrated into predictive modelling efforts to better understand the impact of grazing on carbon fluxes in ecologically fragile, but globally important, arid and semi-arid grasslands. [ABSTRACT FROM AUTHOR]

Simple Summary: Saponins are famous for their anti-methane effects; however, due to their structural differences that have different fates of antimicrobial activity in the rumen, their effects are not consistent in the literature. Thus, the current study used polymeric media-coated gynosaponin (PMCG) to estimate the time-dependent effects on the methanogenesis, rumen fermentation properties and microbial abundance in goats. We used Xinjiang goats (n = 8) that were divided into two groups, i.e., the PMCG group (8 g/kg DMI) and a control group (0 g/kg DMI). Ruminal contents were analyzed for rumen fermentation properties and microbial abundance. Protozoa numbers were counted to calculate the abundance of methanogens, rumen fungi and cellulolytic bacteria using real-time PCR. The results indicated that PMCG significantly reduced the methane production, and decreased the acetate to propionate ratio and total VFA concentration. The protozoa numbers and gene copies of methanogens, total bacteria and F. succinogens relative to the 16 s rDNA were all slightly decreased. Overall, the addition of PMCG had an inhibitory effect on methane production. Gynosaponin is known to modulate rumen methanogenesis and microbial fermentation characteristics in ruminants. The current experiment aimed to determine the time-dependent effects of intraruminal polymeric media-coated gynosaponin (PMCG) supplementation on the methanogenesis, rumen fermentation properties and microbial abundance in Xinjiang goats. Eight goats were used in a 2 × 2 crossover arrangement with a PMCG group (8 g/kg DMI) and a control group (0 g/kg DMI). The experiment was divided into four phases, each lasted 21 d. Ruminal contents were obtained for analysis of rumen fermentation properties and microbial abundance. Protozoa numbers were counted by microscope and the abundance of methanogens, rumen fungi and cellulolytic bacteria were quantified by real-time PCR. The results indicated that PMCG significantly reduced methane production (p < 0.05) during the first two phases but this increased to baseline again during the last two phases. Meanwhile, the concentration of acetate decreased remarkably, which resulted in a significant reduction in the acetate to propionate ratio and total VFA concentration (p < 0.05). However, other rumen properties and dry matter intake were not affected (p > 0.05). During the first and second phases, the protozoa numbers and gene copies of methanogens, total bacteria and F. succinogens relative to the 16 s rDNA were all slightly decreased, but the statistical results were not significant. However, the ruminal supplementation of PMCG had little effect on other tested microbes. Accordingly, it was concluded that the addition of PMCG had an inhibitory effect on methane production probably due to a decline in methanogen numbers. [ABSTRACT FROM AUTHOR]

Wetland ecosystems have low plant diversity, dominated only by one or two types of vegetation. Species with high biomass can easily invade wetlands and the effect of plant invasion on ecosystem process rates has drawn considerable attention within the field of microbial ecology. However, the effects of high biomass plants on microbes, which play a central role in wetland biogeochemistry, are notably understudied. This study investigates the relationship between plant species and their enzyme activities with microbial diversity in wetland ecosystems. Samples were collected from both natural and constructed wetlands to test whether high and low biomass species of submerged aquatic plants would have significant effects on microbial activity and diversity. This study found that plant species with high biomass increased activities of hydrolase activities such as β-glucosidase and N-acetyl-glucosaminidase. Microbial diversity was higher in rhizosphere with two high biomass plant species present compared to one plant species, due to niche competition, as indicated by a higher Shannon–Weaver index value. [ABSTRACT FROM AUTHOR]

Climate warming affects the carbon cycle of northern peatlands through temperature rises and a changing carbon availability. To clarify the effects of elevated temperature and labile carbon addition on SOC mineralization, as well as their microbial driving mechanisms, topsoil (0–10 cm) and subsoil (10–20 cm) were collected from a peatland in the Great Hing'an Mountains and incubated with or without 13C-glucose at 10 °C and 15 °C for 42 days. The results showed that 5 °C warming significantly stimulated SOC mineralization along with NH4+-N and NO3−-N content increases, as well as a decrease in invertase and urease activities. Glucose addition triggered a positive priming effect (PE) in the early stage of the incubation but changed to a negative PE in the late stage of the incubation. Glucose likely regulates carbon dynamics by altering fungi: bacteria, soil invertase, and β-glucodase activities, and MBC, DOC, NH4+-N contents. Glucose addition increased fungal abundance in 0–10 cm at 10 °C and 15 °C, and 10–20 cm at 10 °C, respectively, but significantly decreased fungal abundance in 10–20 cm at 15 °C. Glucose addition decreased bacterial abundance in 0–10 cm at 10 °C but increased bacterial abundance in 10–20 cm soil at 10 °C, and in 0–10 and 10–20 cm soils at 15 °C, respectively. Glucose addition significantly decreased the fungi: bacteria ratio in 0–20 cm soils at 15 °C. In addition, Q10 was significantly positively correlated with the changes in soil DOC, NH4+-N contents, invertase, and β-glucosidase activities, while negatively correlated with fungi: bacteria and urease activities after 5 °C of warming, and glucose addition significantly increased the Q10. Labile carbon may decrease carbon losses in northern peatlands that inhibit warming-induced carbon emission increase, thus partially buffering soil carbon content against change. [ABSTRACT FROM AUTHOR]