Response of enzyme activities and microbial communities to soil amendment with sugar alcohols

Abscisic acid-polyacrylamide (ABA-PAM) treatment enhances forage grass growth and soil microbial diversity under drought stress

Drought restricts the growth of alpine grassland vegetation. This study aimed to explore a new technical system to improve the drought resistance of forage grass. Qinghai cold-land Poa pratensis seedlings were used in the drought stress experiment. A combination of abscisic acid (ABA) and polyacrylamide (PAM) were used to affect the growth, leaf physiology, soil enzyme activity, and rhizosphere microbial diversity of P. pratensis. The fresh leaf weight and root surface area were significantly increased after ABA-PAM combined treatment, while root length was significantly reduced. Besides, the leaf catalase (CAT) and superoxide dismutase (SOD) enzyme activity, proline and chlorophyll content, increased after the treatment, while malondialdehyde (MDA) content decreased. The treatment also increased sucrase, urease, and alkaline protease activities in rhizosphere soil, while decreasing acid phosphatase and neutral phosphatase enzyme activities. ABA-PAM combined treatment enhanced the rhizosphere microbial community and forage drought resistance by altering the abundance of various dominant microorganisms in the rhizosphere soil. The relative abundances of Actinobacteria, Chloroflexi, and Acidobacteria decreased, while Proteobacteria, Firmicutes, and Ascomycota increased. Unlike the relative abundance of Gibberella that decreased significantly, Komagataeibacter, Lactobacillus, Pichia, and Dekkera were significantly increased. Single-factor collinearity network analysis revealed a close relationship between the different rhizosphere microbial communities of forage grass, after ABA-PAM treatment. This study implies that ABA-PAM combined treatment can improve the drought resistance of forages. Therefore, it provides a theoretical and practical basis for restoring drought-induced grassland degradation.

The application of enzymatic fermented soybean effectively regulates associated microbial communities in tea soil and positively affects lipid metabolites in tea new shoots

Compared with traditional organic fertilizer, fermented soybean is a better fertilizer resource in tea plantations. The application of organic fertilizer is a feasible practice to mitigate the soil degradation caused by the overuse of chemical fertilizers, which can effectively regulate soil microbial communities in tea plantations. However, the effects of fermented soybean on soil microbial communities, soil metabolites and metabolites in tea new shoots have not been systematically demonstrated, and their interactions have never been studied. Here, we investigated the responses of the soil microbial community, soil metabolites and metabolites of tea new shoots to urea fertilization (UF), naturally fermented soybean fertilization (NFS) and enzymatic fermented soybean fertilization (EFS), and analyzed the relationships between soil microbes, soil metabolites and metabolites in tea new shoots. The results showed that soil bacterial communities were dominated by Pseudomonas, Romboutsia, Candidatus_Nitrosotalea and Helicobacter, and soil fungal communities were dominated by Peziza, Fusarium, Candida and Cheilymenia at the genus level. In EFS, bacterial genera (Glutamicibacter and Streptomyces) and fungal genera (Candida and Actinomucor) presented high abundances, which were correlated with soil carbohydrate and lipid including D-Mannitol, D-Sorbitol, 9,12-Octadecadienoic acid and (Z)-13-Docosenoic acid. Enzymatic fermented soybean fertilization also affected the lipid metabolites in tea new shoots. Glycerolipids and glycerophospholipids significantly increased in EFS, which positively correlated with some soil microbial communities. Besides, the application of fermented soybean fertilizer could increase the contents of TP, AP and AK, which were also important environmental factors affecting the structure of soil microbial community in tea plantation. It was concluded that fermented soybean fertilization could improve soil nutrition, regulate associated microbial communities, and positively affect lipid metabolites in tea new shoots. This study not only explores the relationships between soil microbes and metabolites in tea plants, but also provides feasible technical guidance to cultivate high-quality tea using soybean as high-grade fertilizer.

Combined application of H2S and a plant growth promoting strain JIL321 regulates photosynthetic efficacy, soil enzyme activity and growth-promotion in rice under salt stress

Salinity stress is one of the most harmful abiotic stresses that inhibit crop growth and grain yield. In this study, a salt-tolerant bacterium was isolated from the soil of the rice rhizosphere and named Myroides sp. JIL321, based on the results of the phylogenetic tree analysis. The strain JIL321 tolerated up to 1, 283.37 mM of NaCl and exhibited positive plant growth-promoting traits, such as the production of indole acetic acid (IAA) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Therefore, the effects of JIL321 on rice (Oryza sativa L.) under salinity stress were determined. The inoculation of strain JIL321 significantly increased the chlorophyll content and the accumulation of osmotic adjustment substances, such as proline and soluble sugars, in rice expose to salt stress. Additionally, strain JIL321 inoculation significantly enhanced the activities of some enzymes commonly found in soil, such as urease, invertase and catalase. Moreover, the production of hydrogen sulfide (H₂S), a pivotal signaling molecule, was also induced in rice by salt stress. Treatment with sodium hydrogen sulfide (NaHS, H₂S donor) improved salt stress tolerance of the rice, while treatment with hypotaurine (HT, H₂S scavenger) significantly suppressed it. Interestingly, NaHS treatment also improved the production of IAA and ACC deaminase in strain JIL321 under 0 mM and 150 mM salt concentrations. The combined treatment of JIL321 and NaHS could further improve the growth of salt-stressed rice seedlings, most likely due to the interaction effect between H₂S and strain JIL321. To our knowledge, this study is the first to demonstrate that the combined use of H₂S and plant growth-promoting bacteria could alleviate the adverse effects of salt stress on rice plants, and further verifies the novel role of H₂S as a signaling molecule that enhance the tolerance of plant to abiotic stresses.

Effects of Vegetation Restoration on Soil Enzyme Activity in Copper and Coal Mining Areas

Mining areas are suffering from serious environmental hazards, such as soil erosion, water pollution as well as land degradation. In this study, two types of mining areas in Anhui Province, China-one a copper mining area and the other a coal mining area-were selected to compare the soil properties under different vegetation restoration conditions, which can be generally classified into reclaimed and non-reclaimed areas. Soil catalase and urease activities and soil chemical properties were chosen to be the main indicators of soil quality. Principal component analysis was used to evaluate the overall soil fertility in the copper and coal mining areas. Results showed that in the copper mining area soil catalase activity was between 12.36 and 19.17 μg g^-1 h^-1 and urease activity was between 0.03 and 12.05 μg g^-1 h^-1. And in coal mining area, soil catalase activity was between 3.52 and 9.72 μg g^-1 h^-1 and urease activity was between 2.71 and 10.81 μg g^-1 h^-1. Moreover, soil catalase and urease activities in degraded areas were lower than those in reclaimed areas. Soil catalase activity and soil urease activity were significantly correlated with total potassium and total nitrogen, respectively. Soil quality in land types with vegetation restoration was higher than in non-reclaimed areas and old subsidence areas, while soil quality in the copper mining area was generally higher than in the coal mining area. Thus, the optimum measure in this region to ameliorate these degraded soils is vegetation restoration, which helps not only to improve the environment, but also to enhance soil quality in these degraded lands.

Taxonomic and Functional Shifts in the Sprout Spent Irrigation Water Microbiome in Response to Salmonella Contamination of Alfalfa Seeds

Despite recent advances in Salmonella-sprout research, little is known about the relationship between Salmonella and the sprout microbiome during sprouting. Sprout spent irrigation water (SSIW) provides an informative representation of the total microbiome of this primarily aquaponic crop. This study was designed to characterize the function and taxonomy of the most actively transcribed genes in SSIW from Salmonella enterica serovar Cubana-contaminated alfalfa seeds throughout the sprouting process. Genomic DNA and total RNA from SSIW was collected at regular intervals and sequenced using Illumina MiSeq and NextSeq platforms. Nucleic acid data were annotated using four different pipelines. Both metagenomic and metatranscriptomic analyses revealed a diverse and highly dynamic SSIW microbiome. A "core" SSIW microbiome comprised Klebsiella, Enterobacter, Pantoea, and Cronobacter The impact, however, of Salmonella contamination on alfalfa seeds influenced SSIW microbial community dynamics not only structurally but also functionally. Changes in genes associated with metabolism, genetic information processing, environmental information processing, and cellular processes were abundant and time dependent. At time points of 24 h, 48 h, and 96 h, totals of 541, 723, and 424 S Cubana genes, respectively, were transcribed at either higher or lower levels than at 0 h in SSIW during sprouting. An array of S Cubana genes (107) were induced at all three time points, including genes involved in biofilm formation and modulation, stress responses, and virulence and tolerance to antimicrobials. Taken together, these findings expand our understanding of the effect of Salmonella seed contamination on the sprout crop microbiome and metabolome.IMPORTANCE Interactions of human enteric pathogens like Salmonella with plants and plant microbiomes remain to be elucidated. The rapid development of next-generation sequencing technologies provides powerful tools enabling investigation of such interactions from broader and deeper perspectives. Using metagenomic and metatranscriptomic approaches, this study identified not only changes in microbiome structure of SSIW associated with sprouting but also changes in the gene expression patterns related to the sprouting process in response to Salmonella contamination of alfalfa seeds. This study advances our knowledge on Salmonella-plant (i.e., sprout) interaction.

The synergy effect of arbuscular mycorrhizal fungi symbiosis and exogenous calcium on bacterial community composition and growth performance of peanut (Arachis hypogaea L.) in saline alkali soil

Peanut (Arachis hypogaea. L) is an important oil seed crop. Both arbuscular mycorrhizal fungi (AMF) symbiosis and calcium (Ca²⁺) application can ameliorate the impact of saline soil on peanut production, and the rhizosphere bacterial communities are also closely correlated with peanut salt tolerance; however, whether AMF and Ca²⁺ can withstand high-salinity through or partially through modulating rhizosphere bacterial communities is unclear. Here, we used the rhizosphere bacterial DNA from saline alkali soil treated with AMF and Ca²⁺ alone or together to perform high-throughput sequencing of 16S rRNA genes. Taxonomic analysis revealed that AMF and Ca²⁺ treatment increased the abundance of Proteobacteria and Firmicutes at the phylum level. The nitrogen-fixing bacterium Sphingomonas was the dominant genus in these soils at the genus level, and the soil invertase and urease activities were also increased after AMF and Ca²⁺ treatment, implying that AMF and Ca²⁺ effectively improved the living environment of plants under salt stress. Moreover, AMF combined with Ca²⁺ was better than AMF or Ca²⁺ alone at altering the bacterial structure and improving peanut growth in saline alkali soil. Together, AMF and Ca²⁺ applications are conducive to peanut salt adaption by regulating the bacterial community in saline alkali soil.

Influence of Salt Stress on Growth of Spermosphere Bacterial Communities in Different Peanut (Arachis hypogaea L.) Cultivars

Background: Exposure of seeds to high salinity can cause reduced germination and poor seedling establishment. Improving the salt tolerance of peanut (Arachis hypogaea L.) seeds during germination is an important breeding goal of the peanut industry. Bacterial communities in the spermosphere soils may be of special importance to seed germination under salt stress, whereas extant results in oilseed crop peanut are scarce. Methods: Here, bacterial communities colonizing peanut seeds with salt stress were characterized using 16S rRNA gene sequencing. Results: Peanut spermosphere was composed of four dominant genera: Bacillus, Massilia, Pseudarthrobacter, and Sphingomonas. Comparisons of bacterial community structure revealed that the beneficial bacteria (Bacillus), which can produce specific phosphatases to sequentially mineralize organic phosphorus into inorganic phosphorus, occurred in relatively higher abundance in salt-treated spermosphere soils. Further soil enzyme activity assays showed that phosphatase activity increased in salt-treated spermosphere soils, which may be associated with the shift of Bacillus. Conclusion: This study will form the foundation for future improvement of salt tolerance of peanuts at the seed germination stage via modification of the soil microbes.

Nutrient enrichment induces a shift in dissolved organic carbon (DOC) metabolism in oligotrophic freshwater sediments

Dissolved organic carbon (DOC) turnover in aquatic environments is modulated by the presence of other key macronutrients, including nitrogen (N) and phosphorus (P). The ratio of these nutrients directly affects the rates of microbial growth and nutrient processing in the natural environment. The aim of this study was to investigate how labile DOC metabolism responds to changes in nutrient stoichiometry using ¹⁴C tracers in conjunction with untargeted analysis of the primary metabolome in upland peat river sediments. N addition led to an increase in ¹⁴C-glucose uptake, indicating that the sediments were likely to be primarily N limited. The mineralisation of glucose to ¹⁴CO₂ reduced following N addition, indicating that nutrient addition induced shifts in internal carbon (C) partitioning and microbial C use efficiency (CUE). This is directly supported by the metabolomic profile data which identified significant differences in 22 known metabolites (34% of the total) and 30 unknown metabolites (16% of the total) upon the addition of either N or P. ¹⁴C-glucose addition increased the production of organic acids known to be involved in mineral P dissolution (e.g. gluconic acid, malic acid). Conversely, when N was not added, the addition of glucose led to the production of the sugar alcohols, mannitol and sorbitol, which are well known microbial C storage compounds. P addition resulted in increased levels of several amino acids (e.g. alanine, glycine) which may reflect greater rates of microbial growth or the P requirement for coenzymes required for amino acid synthesis. We conclude that inorganic nutrient enrichment in addition to labile C inputs has the potential to substantially alter in-stream biogeochemical cycling in oligotrophic freshwaters.

Non-Targeted Metabolomics Reveals Sorghum Rhizosphere-Associated Exudates are Influenced by the Belowground Interaction of Substrate and Sorghum Genotype

Root exudation is an important plant process by which roots release small molecules into the rhizosphere that serve in overall plant functioning. Yet, there is a major gap in our knowledge in translating plant root exudation in artificial systems (i.e., hydroponics, sterile media) to crops, specifically for soils expected in field conditions. Sorghum (Sorghum bicolor L. Moench) root exudation was determined using both ultra-performance liquid chromatography and gas chromatography mass spectrometry-based non-targeted metabolomics to evaluate variation in exudate composition of two sorghum genotypes among three substrates (sand, clay, and soil). Above and belowground plant traits were measured to determine the interaction between sorghum genotype and belowground substrate. Plant growth and quantitative exudate composition were found to vary largely by substrate. Two types of changes to rhizosphere metabolites were observed: rhizosphere-enhanced metabolites (REMs) and rhizosphere-abated metabolites (RAMs). More REMs and RAMs were detected in sand and clay substrates compared to the soil substrate. This study demonstrates that belowground substrate influences the root exudate profile in sorghum, and that two sorghum genotypes exuded metabolites at different magnitudes. However, metabolite identification remains a major bottleneck in non-targeted metabolite profiling of the rhizosphere.

Rhizosphere Microenvironments of Eight Common Deciduous Fruit Trees Were Shaped by Microbes in Northern China

The rhizosphere microenvironment is the site of nutrient circulation and microbial community formation, and thus is an ongoing topic of research. Although research on this topic is extensive, studies into the rhizosphere microenvironment of fruit trees remain rare. To elucidate the mechanisms driving the fruit tree rhizosphere microenvironment, we assessed soil physicochemical properties, enzyme activities, the community-level physiological profile (CLPP) and microbial diversity in rhizospheric soils of eight common deciduous fruit trees in northern China. We found that the available minerals, pH, enzyme activities, microbial utilization of six types of carbon (C) substrates, and microbial diversity in the rhizosphere varied among tree species. Redundancy analysis (RDA) showed that rhizosphere microenvironmental parameters (ammonia nitrogen content, soil pH and invertase activity) were closely related to the soil microbial community. Further analysis revealed that the soil microbial utilization of six C sources, nitrate nitrogen content, and invertase activity were negatively correlated with Ambiguous species and Alternaria; however, these groups were positively correlated with pH. The ammonia nitrogen content was positively correlated with C source utilization and negatively correlated with Ambiguous, Lysobacter, Nitrospira, Alternaria, Fusarium, and Colletotrichum. Interestingly, invertase was closely linked to the microbial community, especially fungal diversity, and was positively correlated with plant-beneficial microbes such as Mortierella, Geomyces, Lysobacter, and Chaetomium, but negatively correlated with pathogenic microbes such as Alternaria, Fusarium, and Colletotrichum. Hence, rhizosphere soil physicochemical properties, enzyme activities and microbial community were significantly affected by tree species. Additionally, a variety of environmental factors were closely related to the microbial community in the rhizospheric soils of eight species of deciduous fruit trees.

Soil pH effects on the toxicity of zinc oxide nanoparticles to soil microbial community

We conducted an experiment with two agricultural soils with acidic and alkaline pH levels to assess the effects of zinc oxide nanoparticles (nZnO) on the bacterial community. The effect of the nZnO concentrations (0, 0.1, 1, 10, 100, 1000 mg Zn/kg soil) and contact time between nanoparticles and soil (180 days) was considered. We measured the microbial respiration rate, nitrogen transformation, enzymatic activities (dehydrogenase (DH), acidic phosphatase (ACP), and alkaline phosphatase (ALP)), and the community-level physiological profile (CLPP) soil parameters. Respiration potential and nitrogen transformation were negatively affected only at the highest nZnO concentration. The changes in enzymatic activities were very variable with time and between both soils. A stimulating effect of the nanoparticles on microbial activity was clearly shown at 30 days after the nZnO application in both soils, except for the 1000 mg/kg in calcareous soil, after which time in the latter, the functional richness of the bacterial community was reduced to virtually zero. However, values of the enzymatic activities demonstrated that there was self-adaptation of microbial communities over the study period (180 days). The nZnO 1000 mg/kg dose produced an increase in bacterial growth in the acidic soil, without apparent changes in their metabolic profiles over time. A good correlation was found between microbial respiration rates (calcareous and acidic soils) and microbial metabolic activity (acidic soil) based on extracted Zn concentrations. Our findings suggest the necessity of additional studies to examine the effects of nZnO in natural microorganism populations in soil with different pH levels for extended periods of time.

Response of enzyme activities and microbial communities to soil amendment with sugar alcohols

Changes in microbial community structure are widely known to occur after soil amendment with low-molecular-weight organic compounds; however, there is little information on concurrent changes in soil microbial functional diversity and enzyme activities, especially following sorbitol and mannitol amendment. Soil microbial functional diversity and enzyme activities can be impacted by sorbitol and mannitol, which in turn can alter soil fertility and quality. The objective of this study was to investigate the effects of sorbitol and mannitol addition on microbial functional diversity and enzyme activities. The results demonstrated that sorbitol and mannitol addition altered the soil microbial community structure and improved enzyme activities. Specifically, the addition of sorbitol enhanced the community-level physiological profile (CLPP) compared with the control, whereas the CLPP was significantly inhibited by the addition of mannitol. The results of a varimax rotated component matrix demonstrated that carbohydrates, polymers, and carboxylic acids affected the soil microbial functional structure. Additionally, we found that enzyme activities were affected by both the concentration and type of inputs. In the presence of high concentrations of sorbitol, the urease, catalase, alkaline phosphatase, β-glucosidase, and N-acetyl-β-d-glucosaminidase activities were significantly increased, while invertase activity was decreased. Similarly, this increase in invertase, catalase, and alkaline phosphatase and N-acetyl-β-d-glucosaminidase activities was especially evident after mannitol addition, and urease activity was only slightly affected. In contrast, β-glucosidase activity was suppressed at the highest concentration. These results indicate that microbial community diversity and enzyme activities are significantly affected by soil amendment with sorbitol and mannitol.