Abundance Of Bacteria In Soil Research Articles

Nitrogen Application and Rhizosphere Effect Exert Opposite Effects on Key Straw-Decomposing Microorganisms in Straw-Amended Soil.

Crop residue decomposition is an important part of the carbon cycle in agricultural ecosystems, and microorganisms are widely recognized as key drivers during this process. However, we still know little about how nitrogen (N) input and rhizosphere effects from the next planting season impact key straw-decomposing microbial communities. Here, we combined amplicon sequencing and DNA-Stable Isotope Probing (DNA-SIP) to explore these effects through a time-series wheat pot experiment with four treatments: 13C-labeled maize straw addition with or without N application (S1N1 and S1N0), and no straw addition with or without N application (S0N1 and S0N0). The results showed that straw addition significantly reduced soil microbial alpha diversity in the early stages. Straw addition changed microbial beta diversity and increased absolute abundance in all stages. Growing plants in straw-amended soil further reduced bacterial alpha diversity, weakened straw-induced changes in beta diversity, and reduced bacterial and fungal absolute abundance in later stages. In contrast, N application could only increase the absolute abundance of soil bacteria and fungi while having little effect on alpha and beta diversity. The SIP-based taxonomic analysis of key straw-decomposing bacteria further indicated that the dominant phyla were Actinobacteria and Proteobacteria, with overrepresented genera belonging to Vicinamibacteraceae and Streptomyces. Key straw-decomposing fungi were dominated by Ascomycota, with overrepresented genera belonging to Penicillium and Aspergillus. N application significantly increased the absolute abundance of key straw-decomposing microorganisms; however, this increase was reduced by the rhizosphere effect. Overall, our study identified key straw-decomposing microorganisms in straw-amended soil and demonstrated that they exhibited opposite responses to N application and the rhizosphere effect.

Nitrogen fertiliser-domesticated microbes change the persistence and metabolic profile of atrazine in soil

Pesticides and fertilisers are frequently used and may co-exist on farmlands. The overfertilisation of soil may have a profound influence on pesticide residues, but the mechanism remains unclear. The effects of chemical fertilisers on the environmental behaviour of atrazine and their underlying mechanisms were investigated. The present outcomes indicated that the degradation of atrazine was inhibited and the half-life was prolonged 6.0 and 7.6 times by urea and compound fertilisers (NPK) at 1.0 mg/g (nitrogen content), respectively. This result, which was confirmed in both sterilised and transfected soils, was attributed to the inhibitory effect of nitrogen fertilisers on soil microorganisms. The abundance of soil bacteria was inhibited by nitrogen fertilisers, and five families of potential atrazine degraders (Micrococcaceae, Rhizobiaceae, Bryobacteraceae, Chitinophagaceae, and Sphingomonadaceae) were strongly and positively (R > 0.8, sig < 0.05) related to the decreased functional genes (atzA and trzN), which inhibited hydroxylation metabolism and ultimately increased the half-life of atrazine. In addition, nitrogen fertilisers decreased the sorption and vertical migration behaviour of atrazine in sandy loam might increase the in-situ residual and ecological risk. Our findings verified the weakened atrazine degradation with nitrogen fertilisers, providing new insights into the potential risks and mechanisms of atrazine in the context of overfertilisation.

Polyethylene microplastic and nano ZnO Co-exposure: Effects on peanut (Arachis hypogaea L.) growth and rhizosphere bacterial community

Microand nano-pollutants are receiving increased research attention. However, the effects of the interactions and co-exposure to these pollutants in soil are yet to be fully elucidated. This work aimed to investigate the effects of co-exposure to polyethylene microplastics (PEMPs) and nano-ZnO (nZnO) in soil on the growth, nutrient uptake, and distribution of the peanut (Arachis hypogaea L.) and soil microbial community. Results revealed that 500 mg kg−1 nZnO significantly decreased the dry weight of peanut root, stem, leaf, and fruit by 84.4%, 79.1%, 87.3%, and 95.8%, respectively, compared with the control. Co-exposure treatments significantly alleviated this trend. Co-exposure treatments further decreased Zn concentration in peanuts by 30.3%–58.9% compared with nZnO single exposure. The distribution of Zn in peanut stems also maintained a consistent trend with the concentration and primarily occurred in the vascular bundles near the epidermis. Co-exposure and PE treatments increased the abundance of soil bacteria primarily because many PE particles entered the soil to build more living space for bacteria. These findings showed that composite pollution had a robust disturbing effect on the soil–peanut system, and the two pollutants were primarily physically adsorbed. PE particles can adsorb nZnO and then become the carrier of nanoparticles.

In-situ straw return, combined with plastic film use, influences soil properties and tomato quality and yield in greenhouse conditions

To address the challenge of disposing vegetable waste in greenhouses while mitigating white pollution associated with the use of conventional polyethylene film, we compared polyethylene (PE) film with two types of fully biodegradable film in both straw-return and no-straw-return treatments. We systematically investigated the effects of mulching on soil properties, film degradation, and tomato quality and yield. The results showed that the humic acid biodegradable film with straw-return (FZS-SR) increased the contents of lycopene, vitamin C (Vc), and soluble sugars in tomato fruit by 20.77%, 16.68%, and 25.89%, respectively, and decreased the total acid content by 8.46% compared to polyethylene film with no-straw-return (PE-NR). Additionally, FZS-SR enhanced the relative abundance of soil bacteria and fungi in Chloroflexi and Basidiomycota, while reducing the relative abundance of pathogenic fungal groups. Moreover, the biodegradable film degraded 15 days earlier in the straw-return treatment, with significantly higher characteristic peaks in Fourier transform infrared spectral analysis compared to no straw-return treatment. In a greenhouse, the straw-return model accelerated the degradation rate of biodegradable film. In summary, our results indicate that using humic acid biodegradable film with straw-return is an effective and sustainable cultivation method, improving tomato quality and yield. This approach offers insights for addressing residual plant and film pollution in vegetable production.

The impact of utilizing oyster shell soil conditioner on the growth of tomato plants and the composition of inter-root soil bacterial communities in an acidic soil environment.

The objective of this study is to examine the impact of various oyster shell soil conditioners, which are primarily composed of oyster shells, on the growth of tomatoes in acidic soil. Moreover, the aim of this investigation is to analyze the variety and structure of soil bacterial populations in close proximity to tomato roots while also contributing to the understanding of the physical, chemical, and biological mechanisms of oyster shell soil conditioners. Tomato plants were grown in acidic red soil in three groups: a control group and a treatment group that used two types of oyster shell soil conditioners, OS (oyster shell powder) and OSF (oyster shell powder with organic microbial fertilizer). A range of soil physicochemical properties were measured to study differences in inter-soil physicochemical parameters and the growth of tomato plantings. In addition, this study utilized the CTAB (Cetyltrimethylammonium Bromide) technique to extract DNA from the soil in order to investigate the effects of oyster shell soil conditioner on the composition and diversity of bacterial populations. Utilizing high-throughput sequencing technologies and diversity index analysis, the composition and diversity of bacterial populations in the soil adjacent to plant roots were then evaluated. Ultimately, correlation analysis was used in this study to explore the relationship between environmental factors and the relative abundance of soil bacteria in the inter-root zone of tomato plants. The findings indicated that the oyster shell soil conditioners were capable of modifying the physicochemical characteristics of the soil. This was evidenced by significant increases in soil total nitrogen (16.2 and 59.9%), soil total carbon (25.8 and 27.7%), pH (56.9 and 55.8%), and electrical conductivity (377.5 and 311.7%) in the OS and OSF groups, respectively, compared to the control group (p < 0.05). Additionally, data pertaining to tomato seed germination and seedling growth biomass demonstrated that both oyster shell soil conditioners facilitated the germination of tomato seeds and the growth of seedlings in an acidic red clay soil (p < 0.05). On the other hand, the application of two oyster shell soil conditioners resulted in a modest reduction in the diversity of inter-root soil bacteria in tomato plants. Specifically, the group treated with OSF exhibited the most substantial fall in the diversity index, which was 13.6% lower compared to the control group. The investigation carried out on the soil between tomato plant roots yielded findings about the identification of the ten most abundant phyla. These phyla together represented 91.00-97.64% of the overall abundance. In the inter-root soil of tomatoes, a study identified four major phyla, namely Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, which collectively accounted for up to 85% of the total abundance. At the general level, the relative abundance of Massilia increased by 2.18 and 7.93%, Brevundimonas by 5.43 and 3.01%, and Lysobacter by 3.12 and 7.49% in the OS and OSF groups, respectively, compared to the control group. However, the pathogenic bacteria unidentified_Burkholderiaceae decreased by 5.76 and 5.05%, respectively. The correlation analysis yielded conclusive evidence indicating that, which involved the use of CCA (Canonical Correlation Analysis) graphs and Spearman correlation coefficients, pH exhibited a positive correlation (p < 0.05) with Shewanella and a negative correlation (p < 0.05) with Bradyrhizobium. The relative abundance of Lysobacter and Massilia exhibited a positive correlation with the levels of total soil nitrogen. The utilization of oyster shell soil conditioner on acidic red soil resulted in several positive effects. Firstly, it raised the pH level of the inter-root soil of tomato plants, which is typically acidic. This pH adjustment facilitated the germination of tomato seeds and promoted the growth of seedlings. In addition, the application of oyster shell soil conditioner resulted in changes in the structure of the bacterial community in the inter-root soil, leading to an increase in the relative abundance of Proteobacteria and Bacteroidetes and a decrease in the relative abundance of Acidobacteria. Furthermore, this treatment fostered the proliferation of genera of beneficial bacteria like Massilia, Brevundimonas, and Lysobacter, ultimately enhancing the fertility of the red soil.

Prediction of Soil Bacterial Community Structure and Function in Minqin Desert-oasis Ecotone Artificial Haloxylon ammodendron Forest

Exploring the effects of artificial Haloxylon ammodendron forest planting on the structure and function of a desert soil bacterial community provides data reference for soil micro-ecological restoration and land quality improvement in desert oasis transition zones. Illumina high-throughput sequencing technology and PICRUSt2 functional prediction analysis were used to identify and analyze the structure and function of soil bacterial communities, and the Mantel correlation test and RDA analysis were used to explain the physicochemical factors affecting the structure and function of soil bacterial communities. The results showed that:① the soil bacterial OTU number, Chao1 index, and Shannon index were significantly higher in the H. ammodendron forest than in the mobile dune soil, and the PCoA analysis and Adonis test showed significant differences in the soil bacterial community structure between H. ammodendron and mobile dune soil (P=0.001). ② A total of 34 phyla, 89 classes, 174 orders, 262 families, and 432 genera of bacteria were detected in all samples, and the phyla Proteobacteria, Actinobacteria, Cyanobacteria, and Chloroflexi accounted for 76.05% of the relative abundance of soil bacteria, which belonged to the dominant soil bacteria, among which the relative abundance of Actinobacteria in H. ammodendron forest soil was extremely significantly higher than that in mobile dune soil (P &lt; 0.01). ③PICRUSt2 function prediction revealed that the soil bacterial community of H. ammodendron forest included six categories of primary functions and 28 categories of secondary functions, among which the metabolism of carbohydrates, metabolism of amino acids, and metabolism of cofactors and vitamins were all greater than 10% in relative abundance and were the main metabolic functions of H. ammodendron forest soil bacteria. ④ The planting of H. ammodendron forest significantly improved the nutrient content of soil organic matter and other nutrients. Soil pH, organic matter, total nitrogen, and fast-acting phosphorus were the main physicochemical factors affecting the bacterial community, with soil organic matter significantly affecting the soil bacterial community structure (P &lt; 0.05) and metabolic function (P &lt; 0.05). In conclusion, the artificial H. ammodendron forest helped to increase desert soil microbial diversity, increase the relative abundance of soil bacterial metabolic function genes, and improve the desert soil microenvironment.

Depth‐dependent responses of the soil bacterial community under vegetation restoration in soil erosion areas of southern China

AbstractSoil bacterial communities play a crucial role in the evaluation of soil ecosystem stability. Vegetation restoration is a key determinant of soil bacterial communities in areas affected by soil erosion. However, it remains unclear how the structure and diversity of soil bacterial communities vary with soil depth. In this study, we collected soil samples from 0 to 10 cm, 10 to 20 cm, 20 to 30 cm, and 30 to 40 cm depths in vegetation restoration sites located in typical soil erosion areas in China. We compared and analyzed the differences in bacterial community characteristics among different soil depths, using untreated areas as controls. Compared to the untreated areas, the abundance of soil bacteria in the 0–10 cm, 10–20 cm, and 20–30 cm depths of the vegetation restoration sites increased by 1.63, 1.04, and 1.29 times, respectively. Furthermore, vegetation restoration enhanced soil bacterial diversity at the 0–10 cm, 10–20 cm, and 20–30 cm depths. Soil organic carbon (OC) was the main explanatory factor (53.50%, p = 0.000) for the decrease in soil bacterial diversity with soil depth. Additionally, after vegetation restoration in soil erosion areas, the dominant bacterial community composition shifted from Chloroflexi to Actinobacteria at the 0–10 cm, 10–20 cm, and 20–30 cm depths and to Proteobacteria at the 30–40 cm depth. The differences in soil bacterial communities among different soil depths were primarily driven by soil total nitrogen (TN) content, which explained up to 34.5% of the variation. In conclusion, in the subsequent management of vegetation restoration sites, increasing OC and TN content can enhance soil bacterial diversity, improve bacterial community composition, and ultimately enhance the stability of soil ecosystems.

Effect of Continuous Cropping on the Physicochemical Properties, Microbial Activity, and Community Characteristics of the Rhizosphere Soil of Codonopsis pilosula

Effects of continuous cropping on rhizosphere soil physical and chemical properties, soil microbial activity, and community characteristics of Codonopsis pilosula were investigated. The C. pilosula plot(CK) fallow for five years and C. pilosula fields with different years of continuous cropping were studied using Illumina high-throughput sequencing technology combined with soil physical and chemical properties analysis. The response of rhizosphere soil physical and chemical properties, microbial activities, and microbial community characteristics to continuous cropping years of C. pilosula were investigated. The results were as follows:the contents of organic carbon, total phosphorus, total nitrogen, and salt in rhizosphere soil of C. pilosula increased with the extension of continuous cropping years. However, soil pH value decreased with the extension of continuous cropping years. Compared with that in the CK treatment, rhizosphere soil organic carbon content of C. pilosula in continuous cropping for one, two, three, and four years increased by 11.1%, 80.5%, 74.9%, and 78.2%, respectively. Total phosphorus content increased by 11.8%, 52.9%, 66.7%, and 78.4%, and total nitrogen content increased by 31.3%, 68.8%, 52.1%, and 56.3%, respectively. Soil salt content increased significantly under continuous cropping of three and four years, and soil conductivity increased by 54.2% and 84.7% compared with that in the CK treatment, respectively. The C/N ratio of microbial biomass in rhizosphere soil exhibited an increasing trend with the extension of continuous cropping years. Soil respiration entropy and microbial entropy showed a decreasing trend. With the increase in continuous cropping years, the diversity and abundance of bacteria in soil decreased, whereas the diversity and abundance of fungi increased. In addition, with the increase in continuous cropping years, the antagonistic effect between bacterial communities was enhanced, whereas the synergistic effect between fungal communities was mainly observed. Correlation analysis showed that soil total phosphorus, available potassium, carbon to nitrogen ratio of microbial biomass, soil respiration entropy, microbial biomass carbon, and electrical conductivity were the main factors affecting the changes in soil bacterial community characteristics. Soil total nitrogen, available potassium, available phosphorus, and soil respiration entropy were the main factors affecting the changes in fungal community characteristics. In conclusion, continuous cropping significantly changed the physical and chemical properties of soil and microbial activity and affected the abundance and diversity of bacteria and fungi in soil. This changed the interaction between microorganisms, which disrupted the stability of microbial communities in the soil.

Effects of Maize-Crop Rotation on Soil Physicochemical Properties, Enzyme Activities, Microbial Biomass and Microbial Community Structure in Southwest China.

Introducing cover crops into maize rotation systems is widely practiced to increase crop productivity and achieve sustainable agricultural development, yet the potential for crop rotational diversity to contribute to environmental benefits in soils remains uncertain. Here, we investigated the effects of different crop rotation patterns on the physicochemical properties, enzyme activities, microbial biomass and microbial communities in soils from field experiments. Crop rotation patterns included (i) pure maize monoculture (CC), (ii) maize-garlic (CG), (iii) maize-rape (CR) and (iv) maize-annual ryegrass for one year (Cir1), two years (Cir2) and three years (Cir3). Our results showed that soil physicochemical properties varied in all rotation patterns, with higher total and available phosphorus concentrations in CG and CR and lower soil organic carbon and total nitrogen concentrations in the maize-ryegrass rotations compared to CC. Specifically, soil fertility was ranked as CG > Cir2 > CR > Cir3 > CC > Cir1. CG decreased enzyme activities but enhanced microbial biomass. Cir2 decreased carbon (C) and nitrogen (N) acquiring enzyme activities and soil microbial C and N concentrations, but increased phosphorus (P) acquiring enzyme activities and microbial biomass P concentrations compared to CC. Soil bacterial and fungal diversity (Shannon index) were lower in CG and Cir2 compared to CC, while the richness (Chao1 index) was lower in CG, CR, Cir1 and Cir2. Most maize rotations notably augmented the relative abundance of soil bacteria, including Chloroflexi, Gemmatimonadetes and Rokubacteria, while not necessarily decreasing the abundance of soil fungi like Basidiomycota, Mortierellomycota and Anthophyta. Redundancy analysis indicated that nitrate-N, ammonium-N and microbial biomass N concentrations had a large impact on soil bacterial communities, whereas nitrate-N and ammonium-N, available P, soil organic C and microbial biomass C concentrations had a greater effect on soil fungal communities. In conclusion, maize rotations with garlic, rape and ryegrass distinctly modify soil properties and microbial compositions. Thus, we advocate for garlic and annual ryegrass as maize cover crops and recommend a two-year rotation for perennial ryegrass in Southwest China.

Responses of community traits and soil characteristics of Achnatherum inebrians-type degraded grassland to grazing systems in alpine meadows on the Qinghai-Tibet Plateau.

Scientific grazing management is of great significance for the ecological health and sustainable use of alpine meadows. To explore appropriate management methods of alpine grasslands of the Qinghai-Tibet Plateau degraded by Achnatherum inebrians (Hance) Keng ex Tzvele presence, we studied the effects of different grazing systems on the A. inebrians population, grassland vegetation community traits, soil characteristics and soil microbial community structure for cold- season grazing plus supplementary feeding pasture (CSF) and four-season open public pasture (FOP) in Tianzhu County, Gansu Province. Compared with FOP, the CSF site showed significantly inhibited reproduction of A. inebrians, especially the crown width, seed yield and number of reproductive branches per plant were as high as 50%, significantly increased the aboveground biomass of edible forage and soil water content by 57% and 43-55%, better soil nutrients, and significantly reduced soil bulk density by 10- 29%. Different grazing systems affected the composition and diversity of soil microbial communities, with a greater effect on fungi than on bacterial flora. The most abundant phyla of bacteria and fungi were Proteobacteria and Ascomycota for CSF (by 30-38% and 24-28%) and for FOP (by 67-70% and 68-73%), and the relative abundance and species of bacterial and fungal genera were greater for CSF than FOP. The α-diversity indexes of fungi were improved, and the β-diversity of fungi was significant difference between CSF and FOP. However, the grazing utilization time was prolonged in FOP, which reduced the diversity and abundance of soil bacteria and increased soil spatial heterogeneity. The use of A. inebrians-type degraded grassland in the cold season, and as a winter supplementary feeding and resting ground, could effectively inhibit expansion of A. inebrians, promote edible forage growth, enhance grassland productivity and community stability, and improve soil structure. The results guide healthy and sustainable utilization of A. inebrians-type degraded grassland in the Qinghai-Tibet Plateau.

The role of microplastics in the process of laccase-assisted phytoremediation of phenanthrene-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic organic pollutants widely distributed in terrestrial environments and laccase was considered as an effective enzyme in PAHs bioremediation. However, laccase-assisted phytoremediation of PAHs-contaminated soil has not been reported. Moreover, the overuse of plastic films in agriculture greatly increased the risk of co-existence of PAHs and microplastics in soil. Microplastics can adsorb hydrophobic organics, thus altering the bioavailability of PAHs and ultimately affecting the removal of PAHs from soil. Therefore, this study aimed to evaluate the efficiency of laccase-assisted maize (Zea mays L.) in the remediation of phenanthrene (PHE)-contaminated soil and investigate the effect of microplastics on this remediation process. The results showed that the combined application of laccase and maize achieved a removal efficiency of 83.47 % for soil PHE, and laccase significantly reduced the accumulation of PHE in maize. However, microplastics significantly inhibited the removal of soil PHE (10.88 %) and reduced the translocation factor of PHE in maize (87.72 %), in comparison with PHE + L treatment. Moreover, microplastics reduced the laccase activity and the relative abundance of some PAHs-degrading bacteria in soil. This study provided an idea for evaluating the feasibility of the laccase-assisted plants in the remediation of PAHs-contaminated soil, paving the way for reducing the risk of secondary pollution in the process of phytoremediation.

Using silkworm excrement to restore vegetation and soil ecology in heavily contaminated mining soils by multiple metal(loid)s: A recyclable sericulture measure

Ecological restoration of heavily contaminated soils by multiple metal(loid)s in mining areas is very difficult. In this study, we provided an attractive measure of using silkworm excrement (SE) and its modified materials to restore the soil heavily contaminated by arsenic (As), antimony (Sb), cadmium (Cd), lead (Pb) and chromium (Cr). We investigated the adsorption capacities and the associated remediation mechanisms for antimonite [Sb(III)] and antimonate [Sb(V)] by raw SE, biochar–modified SE (BC700), iron–modified BC700 (MBC) and sulfhydryl–modified BC700 (SH). Then, we selected SE and SH to compare their outcomes to restore the vegetations and the soil bacterial communities in the investigated soil mentioned above. The results showed that SE displayed the best characteristics for metal(loid) physical adsorption. But SH conferred the strongest capacity to adsorb Sb (max 23.92 mg g–1), suggesting the process of chemical adsorption played a key role in adsorbing Sb via functional groups (–SH). SE and SH both significantly (1) promoted the growth of pakchoi (Brassica campestris L., New Zealand No.2), community abundance of soil bacteria (283–936 OTUs), and the quantity of bacterial genera correlated with resistance, plant growth promotion and specified carbon metabolism; (2) but reduced bacterial genera correlated with pathogenicity. In this study, we suggested an attractive recyclable measure to restore the disturbed ecological environment in mining areas, i.e, using mulberry to restore the vegetation→ using leaves of mulberry to rear silkworms→ using SE to immobilize metal(loid)s in soils growing mulberry or other plants.

Composition of soil organic matter and the structure and diversity of soil bacteria and archaea, in crop systems under no-till in a subtropical ecosystem

Crop richness in crop rotation systems may modulate soil microbial activity and the diversity of community structure, driving soil organic matter (SOM) content and quality. We aimed to assess the long-term effect of crop systems on SOM composition and the structure and diversity of the bacteria and archaea in no-till subtropical soil. The study was based on samples from a subtropical Ferralsol subjected to 27 years of crop succession (wheat/soybean) or crop rotation (vetch/maize/wheat/soybean). Soil samples were analyzed in relation to C and N contents, and submitted to DNA extraction for 16 S rDNA sequencing and 13C Nuclear Magnetic Resonance spectroscopy – solid-state (CP/MAS 13C NMR). The effect of the current crop species at the time of sampling on the structure and diversity of the microbial community was predominant in relation to the long-term crop history over time (crop rotation). A greater diversity and abundance of soil bacteria and archaea was observed in the area with wheat growing in winter than with soybean growing in summer, a combined effect of crop species and season. The soil under crop rotation had a greater proportion of carbohydrate-derived C in SOM, whereas a greater proportion of alkyl-C and N/O alkyl-C was observed under crop succession. The crop species richness in crop rotation allows the maintenance of soil functions related to the formation of more biochemically labile SOM and contributes positively to soil ecosystem functioning.

Ammonia oxidation and nitrate reduction marker genes are key indicators of nitrogen losses in temperate forest catchments.

Chronic nitrogen inputs can alleviate N limitation and potentially impose N losses in forests, indicated by soil enrichment in 15 N over 14 N. However, the complexity of the nitrogen cycle hinders accurate quantification of N fluxes. Simultaneously, soil ecologists are striving to find meaningful indicators to characterise the "openness" of the nitrogen cycle. We integrate soil δ15 N with constrained ecosystem N losses and the functional gene potential of the soil microbiome in 14 temperate forest catchments. We show that N losses are associated with soil δ15 N and that δ15 N scales with the abundance of soil bacteria. The abundance of the archaeal amoA gene, representing the first step in nitrification (ammonia oxidation to nitrite), followed by the abundance of narG and napA genes, associated with the first step in denitrification (nitrate reduction to nitrite), explains most of the variability in soil δ15 N. These genes are more informative than the denitrification genes nirS and nirK, which are directly linked to N2 O production. Nitrite formation thus appears to be the critical step associated with N losses. Furthermore, we show that the genetic potential for ammonia oxidation and nitrate reduction is representative of forest soil 15 N enrichment and thus indicative of ecosystem N losses.

Characteristics of Soil Microbial Community in Different Habitats in the Process of Ecological Restoration of Haifeng Wetland in Guangdong

Soil microorganisms can respond to changes in wetland ecosystem quality and functional evolution sensitively. To explore the changes and response mechanisms of soil microorganisms under ecological restoration measures, the characteristics of the soil microbial community and their influencing factors were analyzed using high-throughput sequencing technology in four different habitats (revegetation area, native vegetation area, tidal creek, and tidal flat) during the ecological restoration process in Haifeng wetland in Guangdong. The results showed that:soil physicochemical properties of the four different habitats were significantly different; the contents of TC, TN, TOC, and TK in the tidal creek were significantly higher than those in the other habitats; and the contents of TC, TN, and TP in the revegetation restoration area were significantly higher than those in the tidal flat. The EC values in the tidal creeks and tidal flat were significantly higher than those in the revegetation area and the native vegetation area. The diversity index and abundance of soil bacteria in the tidal creek were the highest, and those in the vegetation restoration area were significantly higher than those in the bare flat. The archaea in the tidal creek were significantly more complex than those in the other three habitats, and the fungal community diversity index and abundance in the native vegetation area were significantly higher than those in the other areas, which had the most complex community structure. TN and TC were the main factors affecting the bacterial community, whereas TN and EC were the main factors affecting the archaea community, and pH, TN, and TP were the key factors affecting the fungal community. In conclusion, the planting of vegetation on the tidal flat increased the diversity and richness of the soil microbial community during the process of ecological restoration, indicating that it has resulted in positive feedback on ecological restoration so far. The results of this study can provide a theoretical basis for the selection of ecological restoration strategies for the tidal flat.

Responses of soil microbial activities to soil overburden thickness in restoring a coal gangue mound in an alpine mining area

This study analyzes the changes in soil microbial community diversity after five years of restoration in an alpine mining area using different soil overburden thicknesses, in which MiSeq high-throughput sequencing technology was applied to analyze soil microbial community diversity and its influential environmental factors. The results showed that vegetation restoration obviously changed the species composition of soil microorganisms at the OTUs (Operational Taxonomic Units) level under different soil overburden thicknesses, and the OTUs species of soil fungi and bacteria changed significantly in the 15 cm soil overburden thickness. The bacterial diversity index was higher than that of fungal microorganisms in all three soil overburden thicknesses, and the microbial diversity index without soil overburden thickness was significantly higher than that in the soil overburden thickness (P < 0.05). The dominant phyla and genera of soil bacteria and fungi were almost the same. The bacteria were Proteobacteria, Pseudoarthrobacter and Sphinomonas, and the fungi were Ascomycota and Tricharina. The relative abundance of soil bacteria and fungi varied with the soil overburden thickness. Vegetation height, coverage, moss coverage, soil temperature, moisture, organic matter, nitrogen content, pH and soil overburden thickness were the key factors affecting the soil microbial community structure. A soil overburden thickness of 10 cm was recommended as an ideal soil reconstruction measure in apline mining areas. During the restoration period of the coal gangue mound in the alpine region, significant improvement was observed in the sensitivity of soil microorganisms to thickness over the course of five years. However, in order to facilitate continuous restoration of microorganisms, it is recommended to implement measures such as covering the area with non-woven fabrics and adjusting the pH of the soil to create more favorable conditions for microbial growth.

Vegetation restoration of abandoned cropland improves soil phosphorus availability and microbial activities in the Danxia degraded region

Phosphorus is a limiting nutrient in subtropical region soils. The Danxia degraded region (DDR) is a typical ecologically degraded area in the south subtropical region of China, and mitigation measures for reconverting farmland to forest have been implemented to prevent further land degradation. However, whether vegetation restoration can alter soil P fractions (SPF) and P availability in the DDR remains unclear, and the mechanisms influencing P availability require further study. In this study, we collected soil samples from the main vegetation cover types, namely arbor forest, shrubland, and abandoned cropland, in the DDR to explore the characteristics of SPF, acid phosphatase (ACP), microbial community and their influencing factors. Results showed that vegetation restoration significantly affected soil P availability by modifying the SPF. Labile, moderately labile, and aggregate-occluded P content in the soil increased, whereas the proportion of stable P decreased. Vegetation restoration promoted the secretion of soil ACP and significantly increased the abundance of soil bacteria, fungi, actinomycetes, arbuscular mycorrhizal fungi, and the overall microbial abundance. Arbor forest soils presented higher SPF content and microbial activity than the soils from abandoned croplands and shrublands. This increases in soil microbial abundance was significantly correlated with soil microbial biomass and dissolved organic carbon. The results of redundancy and variance partitioning analyses indicated that soil nutrients and soil properties jointly drove SPF transformation in the DDR. Soil nutrient supply significantly affected soil microbial activity and SPF transformation. Vegetation restoration increased microbial activity by increasing the soil nutrient supply, and the resulting synergistic effect altered the SPF distribution and availability. This study provides a theoretical basis for the sustainable use of soil P resources in the DDR.

Crop diversification improves the diversity and network structure of the prokaryotic soil microbiome at conventional nitrogen fertilization

BackgroundSustainable agriculture seeks to optimize the application of nitrogen (N) fertilizers to reduce adverse economic and ecological effects. Crop diversification has been proposed to increase the efficiency of N fertilization. An open question is how the soil microbiome responds to these beneficial practices.MethodsIn a field study we investigated the effects of mineral N fertilizer with a 0-control, a conventional amount of 150 kg N ha−1 and an excessive application of 250 kg N ha−1 on the soil microbiome within a diversified cropping system with oil radish and undersown ryegrass over a period of 2.5 years and a non-diversified control, both in rotation of potato, winter rye and maize.ResultsN-fertilizations and crop rotations altered the pH, but differences were less pronounced with the diversified system. Compared to the crop species and season, N fertilization and crop diversification had less influence on the abundance of soil bacteria, archaea and fungi. The crop diversification showed a much stronger effect on archaeal than on bacterial or fungal abundances, while the microbial carbon use efficiency correlated strongly with bacterial abundance. At the end of the growing seasons, crop diversification increased prokaryotic richness and Shannon diversity in response to N addition, with a greater increase in the conventional N. At conventional N supply, prokaryotic co-occurrence networks revealed a much denser and complex structure in the diversified system.ConclusionsThe diversified cropping system under conventional N application rates showed positive effects on the prokaryotic soil microbiome by increasing their richness, Shannon diversity, and promoting a more elaborated network structure.

Exploration of bacterial diversity from the soil of citrus plantations applied with organic fertilizer and salicylic acid

The abundance of bacteria in citrus plantations has not been widely studied. This study aims to explore and evaluate the abundance of soil bacteria on citrus plantations. Several treatments were given to them, organic fertilizer and plant resistance inducers. The research was carried out in July - September 2022 at the Innovation Garden and at the Laboratory of Plant Protection, Politeknik Negeri Jember. This study initiated the application of treatment on citrus plantations and isolation of bacteria using multilevel dilution technique. The design used was a randomized block design, which consisted of the application of organic fertilizer and salicylic acid. Organic fertilizer application consists of control, half dose, and recommended dose. Application of 100 ppm salicylic acid watered to the plant. There were 6 treatments, with 3 replications and 2 plants each, a total of 36 plants. The results showed that 45 various bacteria were found with different morphology with a total population 20x109 - 20x1011 CFU/gr. All treatments gave almost the same results. The application of 20 kg of organic fertilizer and 100 ppm of salicylic acid gave the highest bacterial diversity as shown by the number of different bacterial isolates. The combination of organic fertilizer and salicylic acid provides new information about the abundance and diversity of bacteria in citrus plantations.

Bacterial and fungal diversities examined through high-throughput sequencing in response to lead contamination of tea garden soil.

Several studies have indicated that the heavy-metal content in tea is increasing gradually. Researchers examining the soil of more than 100 tea gardens in China have observed that lead content was higher in some soils. The effect of lead contamination on soil microorganisms in tea gardens was studied to determine the effect of lead on the essential functions of microorganisms in a tea garden soil ecosystem. Previous studies on pot experiments adopted the method of adding a single instance of pollution, which failed to comprehensively simulate the characteristics of the slow accumulation of heavy metals in soil. This study designed with two pollution modes (multistage and single instance) determined the content of soil lead in different forms according to the European Community Bureau of Reference extraction procedure. The community structure, species diversity and functional abundance of soil bacteria and fungi were examined by high-throughput sequencing. We observed that the content of four forms of lead was higher in the multistage contamination mode than in the single instance contamination mode. The effects of lead contamination on bacteria differed significantly (p < 0.05), and the abundance and diversity of bacteria were higher in the multistage contamination mode than in the single instance contamination mode. The community structure of fungi was more affected by lead than was that of bacteria. The content of each lead form was the environmental factor most strongly affecting soil bacteria and fungi. The predicted main function of the bacterial community was amino acid transport and metabolism, and the trophic mode of the fungal community was mainly pathotroph-saprotroph. This study revealed changes in soil microorganisms caused by different forms of lead and contamination methods in tea garden soil and provide a theoretical basis for examining the effects of lead contamination on soil microorganisms.