Soil Bacterial Community Structure Research Articles

Linking phosphorus fertility to soil microbial diversity and network complexity in citrus orchards: Implications for sustainable agriculture

Continuous input of chemical fertilizers causes soil acidification, land degradation, and water eutrophication, but its impact on soil microbial communities and co-occurrence patterns of microboes is unclear. In this study, we evaluated the impact of chemical fertilizer on bacterial community diversity and ecological network at 75 citrus sites in a watershed where chemical fertilizer is continuously applied. In addition, 25 natural forest sites adjacent to citrus sites were used as references to compare the potential effects of land conversion from natural forests to citrus orchards on soil bacterial diversity and microbial network. The results showed that the cultivation of citrus results in soil phosphorus (P) accumulation, with significantly higher available and mineral-bound phosphate contents than those found in soils of natural forests. Citrus soil average soil available P was 73.2 mg/kg, which was 20 times higher than that in forest soils. As the P content accumulates, soil bacterial Shannon index linearly decreases from 7.06 to 5.93 and is significantly lower than that of adjacent natural forest soils (7.13). Low P fertility soils have higher microbial network complexity and stability, containing more microbial communities and tighter relationships between microbes compared to higher P fertility soils. Soil P content and soil pH regulates soil microbial network complexity and stability. In addition, soil bacterial community structure in soils of natural forests is significantly different from that in citrus soils, and the bacterial community structure in high P soils is different from that in medium and low P soils. Soil P fertility reduces the relative abundance of dominant communities including Proteobacteria, Bacteroidetes, and Gemmatimonadetes, and also changes the relative abundance of some functional microbial communities, such as some phosphorus cycling microorganisms, including Acetobacteraceae and Beijerinckiaceae. In conclusion, soil phosphate accumulation severely alters soil bacterial community diversity, complexity, stability, and functionality. This could have negative impacts on soil functional stability and the sustainability of citrus orchards.

Long Term Fertilization on Soil Nutrient Dynamics, Soil Quality and Soil Bacterial Community Structure in an Inceptisol Under Semi-arid Tropics of Finger Millet (Eleusine coracana) - Maize (Zea Mays) Cropping Sequence

Long Term Fertilization on Soil Nutrient Dynamics, Soil Quality and Soil Bacterial Community Structure in an Inceptisol Under Semi-arid Tropics of Finger Millet (Eleusine coracana) - Maize (Zea Mays) Cropping Sequence

Effects of soil conditioners on vineyard saline soil physicochemical properties and bacterial community in arid areas

AbstractSoil salinization adversely affects soil quality and ecosystem. Many researches have tried to ameliorate saline soils by soil conditioners. However, little is known about the differences in the responses of soil bacterial communities to natural and artificial conditioners applied to saline soils. Therefore, in this study, the effects of natural humic acid (IK), synthetic polymer (IP), and composite material (IF) (mixture of IK and IP (1:1)) on bacterial community structure and functional genes in saline soil were evaluated to clarify their differences. The results showed that the application of the three soil conditioners significantly reduced soil pH and Na+ content but increased soil alkaline phosphatase, urease, invertase and catalase activities, bacterial diversity, and nutrients, compared to the control (no conditioner). IK application increased bacterial relative abundance (e.g., Subgroup_6, RB41, MND1, and KD4‐96) and metabolic functions (e.g., Two‐component system and Biosynthesis of amino acids) by increasing soil nitrogen and maintaining K+ and Na+ balance. IP application increased soil alkaline phosphatase and urease activities as well as bacterial relative abundance (e.g., Subgroup_6, RB41, MND1, Gemmatimonadaceae, and KD4‐96) and metabolic functions (e.g., Quorum sensing and carbon metabolism) by increasing soil organic carbon/nitrogen content. IF application increased the bacterial relative abundance of Subgroup_6, RB41, and MND1 by increasing soil available nitrogen and regulated their metabolic pathways (e.g., ABC transporters and microbial metabolism). On the whole, IK, IP, and IF could regulate the structure and function of soil bacterial community in saline soils. This study clarifies difference in the effects of different soil conditioners on the amelioration of saline soils from the perspective of soil microbiology, and provides a reference for the amelioration of saline soils in arid areas.

Combined contamination of microplastic and antibiotic alters the composition of microbial community and metabolism in wheat and maize rhizosphere soil

The widespread application of antibiotics and plastic films in agriculture has led to new characteristics of soil pollution. The impacts of combined contamination of microplastics and antibiotics on plant growth and rhizosphere soil bacterial community and metabolisms are still unclear. We conducted a pot experiment to investigate the effects of polyethylene (0.2%) and norfloxacin/doxycycline (5mgkg–1), as well as the combination of polyethylene and antibiotics, on the growth, rhizosphere soil bacterial community and metabolisms of wheat and maize seedlings. The results showed that combined contamination caused more serious damage to plant growth than individual contamination, and aggravated root oxidative stress responses. The diversity and structure of soil bacterial community were not markedly altered, but the composition of the bacterial community, soil metabolisms and metabolic pathways were altered. The co-occurrence network analysis indicated that combined contamination may inhibit the growth of wheat and maize seedings by simplifying the interrelationships between soil bacteria and metabolites, and altering the relative abundance of specific bacteria genera (e.g. Kosakonia and Sphingomonas) and soil metabolites (including sugars, organic acids and amino acids). The results help to elucidate the potential mechanisms of phytotoxicity of the combination of microplastic and antibiotics.

Competitive relationships due to similar nutrient preferences reshape soil bacterial metacommunities

Paddy soil, as an ecosystem with alternating drained and flooded conditions, microorganisms in it can maintain the stability of the ecosystem by regulating the composition and diversity of its species when disturbed by external biotic or abiotic factors, and the regulatory mechanism in this process is a controversial topic in ecological research. In this study, we investigate the effects of pigeon feces addition on bacterial communities in three textured soils, two conditions (drained and flooded) based on microcosm experiment using high-throughput sequencing techniques. Our results show that pigeon feces addition reduced environmental heterogeneity and community diversity, both under flooded and drained conditions and in all textured soils, thereby decreasing the effectiveness of environmental selection and increasing diffusion limitations among bacterial communities. Bacterial communities are altered by environmental factors including total organic carbon, available nitrogen, total phosphorus, available phosphorus and available potassium, resulting in the formation of new community structures and dominant genera. Bacteria from pigeon feces did not colonize the original soil in large numbers, and the soil bacterial community structure changed, with some species replaced the indigenous ones as new dominant genera. As nutrient diffusion increases the nutrient content of the soil, this does not lead to species extinction; however, nutrient diffusion creates new nutrient preferences of the bacterial community, which causes direct competition between species, and contributes to the extinction and immigration species. Our results suggest that species replacement is an adaptive strategy of soil bacterial community in response to dispersal of pigeon feces, and that bacterial community regulate diversity and abundance of the community by enhancing species extinction and immigration, thereby preventing bacteria in pigeon feces from colonizing paddy soils and maintaining ecosystem stability.

Changes in soil bacterial community structure in a short-term trial with different silicate rock powders

BackgroundThe use of rock powders in soil has emerged as a nature-based technology to improve soil properties relevant to crop development and for atmospheric carbon dioxide removal (CDR) via enhanced rock weathering (ERW). Although modeling this process is crucial, the soil microbiome has been identified as the main reason why several experimental and field results do not fit the geochemical and kinetic theoretical models. Here, the hypothesis that the bacterial community structure is modulated by the application of different silicate rock powders was tested. One phonolite, three basalt variations and one granite, as well as KCl treatments, were applied to a Ferralsol cultivated with Brachiaria in short-term pedogeochemical experiments and assessed after 1 (1M), 4 (4M) and 8 (8M) months.ResultsThe main changes in soil bacterial structure were observed at 8M and found to be modulated according to rock type, with petrochemistry and mineralogy acting as the main drivers. The content of microbial biomass carbon tended to decrease over time in the Control and KCl treatments, especially at 4M, while the rock treatments showed constant behavior. The sampling time and treatment affected the richness and diversity indices. The Si, Ca and Fe from mafic minerals were the main chemical elements related to the soil bacterial changes at 8M.ConclusionsThe type (acidity) of silicate rock powder modulated the soil bacterial community (SBC) in a pot experiment with tropical soil. The specificity of the SBC for each rock type increased with time until the end of the experiment at 8 months (8M). The carbon content in the microbial biomass was lower in the rock powder treatments in the first month (1 M) than in the control and KCl treatments and was equal to or higher than that in the 8 M treatment. This result illustrates the challenge of modeling rock powder dissolution in soil since the soil medium is not inert but changes concurrently with the dissolution of the rock.Graphical

Characteristics of Bacterial Communities under Different Tree Species and Their Response to Soil Physicochemical Properties

This study investigates the structure of soil bacterial communities in the brown mountain soils beneath the deciduous broadleaf forests of Dongling Mountain and their response to soil physicochemical properties. Aiming to provide a scientific basis for soil conservation and sustainable forest development under deciduous broadleaf forests, this research utilized high-throughput sequencing technology to examine the diversity and community structure of bacteria in soil under different tree species, alongside assessing soil physicochemical properties. The results revealed significant differences in nutrient content between the 0–20 cm and 20–40 cm soil layers. Additionally, the N:P in the brown mountain soils of Dongling Mountain was found to be below the national average, indicating potential nitrogen limitation. Dominant bacterial phylum included Actinobacteria, Proteobacteria, and Acidobacteria. The study also found that soil bacterial community structure was similar under different tree species at the same depth but varied significantly with soil depth. Furthermore, redundancy analysis (RDA) showed that the available potassium (AK), total nitrogen (TN), and ammonium nitrogen (NH4+-N) significantly influenced the structural changes in the soil bacterial community. This research highlights the characteristics of soil bacterial community structure beneath deciduous broadleaf forests and its relationship with soil physicochemical properties, offering valuable insights for regional soil ecosystem conservation and forest management.

Soil Fertility and Bacterial Community Composition in Response to the Composting of Biochar-Amended Chicken Manure

Amidst the burgeoning expanse of the poultry sector, the escalation of chicken manure production has ensued, potentially exacerbating ecological contamination. However, the application of chicken manure is bound to transmute the habitat of edaphic microorganisms, precipitating an alteration in the soil’s microbial consortium. The composting of biochar-amended chicken manure and wood chips (biochar composting products, BCPs) was used to improve Chinese cabbage (Brassica campestris L.) production and regulate soil properties and bacterial community structure. On the 40th day of Chinese cabbage growth, soil and Chinese cabbage were collected for laboratory analysis. The effects of different proportions of BCPs (0, 1%, 3%, 5% and 7% biochar) on soil fertility, enzyme activity, the microbial community and the growth of Chinese cabbage were studied under facility conditions. The results showed that the growth performance and quality of Chinese cabbage were significantly increased with increasing BCP ratios. Soil fertility indicators including pH, AN, AP, AK and SOM were significantly increased, except for the pH value in the 1% BCP group. The activities of phosphatase, catalase and urease were increased for all groups of BCP treatment. The soil microbial community response was significantly different, and the application of 5% and 7% BCPs reduced the abundance, diversity and evenness of soil bacteria. Chinese cabbage growth performance was positively correlated with an increase in BCP supplemental levels in the range of 3–5%. Also, the abundance, diversity and uniformity of the soil microbial community were improved in the 3% BCP treatment group. Therefore, the dominant bacterial phyla were Bacteroidetes, Actinobacteriota, Gemmatimonadota, Myxococcota, Bdellovibrionota and Firmicutes, especially the Bradyrhizobium of Proteobacteria. BCP treatment reduced the degradation of soil organic matter. In addition, it also improved the relative abundance of sequences associated with improving soil fertility. Collectively, these findings offer insights for the re-evaluation of application management strategies for BCP organic fertilizers.

Soil bacterial community structure and co‐occurrence networks in response to the succession of secondary forests in subtropical regions

AbstractA large amount of secondary successional vegetation (subtropical evergreen broadleaved forests) has formed after the extensive deforestation and cultivation of coniferous forests in Wuyi Mountain, Southeast China. However, we lack a detailed understanding of the dynamic changes in microbial community structure and its co‐occurrence network during succession. The features that are responsible for alterations in the soil bacterial community remain poorly defined. Therefore, we compared the soil physicochemical properties, enzyme activities, and bacterial diversity among three different forests (a coniferous forest [CF], early stage of succession; a mixed conifer‐broadleaf forest [CBMF], middle stage of succession; an evergreen broadleaf forest [EBF]; late stage of succession). Results indicated that the contents of soil organic carbon and microbial biomass carbon (MBC) in CBMF were higher compared with those in CF. The alpha diversity indices were the highest in CBMF. Functional annotation of prokaryotic taxa predicted the relative abundances of chemoheterotrophy and aerobic chemoheterotrophy were lower in CF than in the other two forests. Bacterial network topology was affected by forest succession, with CBMF having more complex bacterial networks. Mantel's test indicated the soil nitrate nitrogen content (P = 0.03) was the most important property that shaped the bacterial community composition, bacterial diversity was influenced by soil pH (P = 0.026), and the contents of available phosphorus (P = 0.04) and MBC (P = 0.022) during the succession process. In conclusion, the succession of secondary forests promoted soil nutrient accumulation and improved bacterial diversity and network complexity.

Emissions of N2O AND CH4 gases and soil bacterial community under integrated systems in the tropical region

The use of integrated production systems is widespread, mainly in tropical areas. This practice could contribute to soil conservation, increasing biodiversity and environmental services while reducing greenhouse gases emissions. The present work assessed bacterial biodiversity and correlations with nitrous oxide (N2O) and methane (CH4) emissions in soils under integrated production systems. Analyses of bacterial diversity and community structure were carried out using DGGE (denaturing gradient gel electrophoresis). Samples for the evaluation of greenhouse gases were collected in the field and measured using a gas chromatograph. The assessed treatments in a rainy and dry season were: crop (L), pasture (P), planted eucalypt forests (F), pasture followed by crop (IPL), crop followed by pasture (ILP), crop with forest (ILF); pasture with forests (IPF); crop with forest followed by pasture with forests, pasture with forests followed by crop with forest and crop, grassland and forest. In the rainy season, most N2O emissions occurred in the ILP with an average flow of 42.33 µg N m−2 h−1, and the lowest flow was observed in the ILF, with an average flow of 5.53 µg N m−2 h−1. In the dry season, higher emission occurred in the IPL, with an average flow of 4.17 ug N m−2 h−1. In this period, we observed gas consumption in F, the highest N2O consumer with a flow of −4.14 µg N m−2 h−1. In both seasons, CH4 was consumed, with IPF as the most significant consumer with an average flow of −14.19 µg C m−2 h 1(dry); F was the most significant consumer with an average flow −12.32 µg of C m−2 h−1. Bacterial community structure was affected by the agricultural production system and the seasons. Methane emissions and pH showed a correlation with bacterial diversity in different treatments. In contrast, nitrous oxide was negatively correlated with bacterial diversity. Based on our results, we suggest that integrated production systems and plant coverage modulate soil bacterial community structure and biodiversity which, in turn, affect soil processes related to higher or lower methane and nitrous oxide emissions.

Sheep dung deposition disrupted the soil microbiome in degraded grassland but not in non-degraded grassland

Grazing is the most extensive land use in grassland worldwide, wherein the soil microbiome is known to support multiple ecosystem functions. Yet, the experimental impact of livestock grazing and dung deposits on the soil microbiome in degraded grassland remains poorly understood. We examined the effects of sheep dung depositions on the bacterial and fungal microbiome of two grasslands: non-degraded and degraded (long-term overgrazing) in northern China. Specifically, sheep dung was experimentally added to the soil and its effects on the soil microbial community were determined 3 months later (corresponding to livestock excreta deposited throughout the entire growing season of grassland, June to September). Our results showed that sheep dung additions showed negative effects on the soil microbiome of already degraded grassland, while with a diminished impact on the non-degraded grassland. In particular, dung deposition decreased soil microbial Shannon index, notably significantly reducing fungal diversity in degraded grassland. Moreover, sheep dung deposition modifies soil bacterial community structure and diminishes bacterial community network complexity. The alteration of soil pH caused by sheep dung deposition partially explains the decline in microbial diversity in degraded grassland. However, sheep dung did not alter the relative abundance and community composition of bacterial and fungal dominant phyla either in the non-degraded or in the degraded grassland. In conclusion, the short-term deposition of sheep dung exerted a detrimental influence on the microbial community in degraded grassland soil. It contributes new experimental evidence regarding the adverse effects of livestock grazing, particularly through dung deposition, on the soil microbiome in degraded grassland. This knowledge is crucial for guiding managers in conserving the soil microbiome in grazed grasslands.

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems.

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

Differential response patterns of soil fungal and bacterial communities to typical vegetation types in the Yellow River floodplain ecosystem

Soil microorganisms are one of the primary driving factors of biogeochemical cycles in floodplain ecosystems. Vegetation type has an impact on the activities of soil microorganisms. However, it is currently unclear whether the composition and structure of soil bacterial and fungal communities in floodplain ecosystems have a consistent response pattern to vegetation communities. In this research, Illumina Mi-Seq sequencing technology was employed to study the soil fungal and bacterial communities covered by three typical vegetation communities in the Yellow River floodplain ecosystem. Our results showed that the underground biomass, total carbon (TC) and nitrogen (TN) were significantly different between the three vegetation communities. In the surface soil of summer, the Shannon index of fungi community was the highest in Tamarix chinensis (T. chinensis) and the lowest in Phragmites australis (P.australis). In autumn, the Shannon and Simpson indices of bacterial communities in surface soil were the highest in the P.australis and the lowest in the Sonchus arvensis (S.arvensis), but there was no significant difference in the β-diversity of bacterial community among the three vegetation communities. In autumn, the Chao1 index of fungal community in subsoil was the highest in P.australis and the lowest in S.arvensis, while there was no significant difference in the α-diversity of bacterial community among the three vegetation communities. In addition, there were considerable disparities in the fungal and bacteria community structure in various vegetation soils. Redundancy analysis (RDA analysis) showed that TN, TC, AP, pH, NO3 -, NH4 + and moisture content were key factors driving bacterial community structure, while TP, NH4 +, pH and moisture content were essential factors driving fungal community composition. These outcomes help to improve our understanding of the ecological model of soil fungal and bacterial community in floodplain ecosystems and give assistance in improving the role of an ecological barrier and floodplain service possibilities.

Effect of Forest Fires on the Alpha and Beta Diversity of Soil Bacteria in Taiga Forests: Proliferation of Rare Species as Successional Pioneers

Forest fires are among the most influential drivers of changes in forest soil bacterial diversity. Nevertheless, little is known regarding the effects of forest fires on maintaining the complex interactions that preserve forest ecosystem stability. Therefore, this study characterized alterations in soil bacterial community composition and diversity within taiga forests subjected to varying disturbance intensities. Particularly, this study examined the bacterial community within a Larix gmelinii fire-burnt site in Daxinganling, analyzing the changes in bacterial community structure and function across light, moderate, and heavy fire-burnt sites, as well as a control sample site, utilizing Illumina MiSeq technology. Through an assessment of bacterial community diversity and soil physicochemical properties (moisture content (MC), pH, microbial biomass carbon (MBC), organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AP)), we explored the influence of the soil microenvironment on the soil bacterial community structure at the burnt site under different disturbance intensities. Our findings demonstrated that (1) there was no significant change in the Chao index of soil bacteria in the burnt site under different disturbance intensities, whereas the Shannon index decreased significantly (p < 0.05) and the Simpson index increased significantly (p < 0.05) in the burnt site under light and moderate disturbance. (2) The relative abundance of dominant phyla, such as Proteobacteria, Proteobacteria, and Actinobacteriota, did not change significantly in the fire-burnt site under different disturbance intensities, whereas rare species, such as Acidipila, Occallatibacter, and Acidibacter, experienced a significant increase in relative abundance at the genus level. (3) The results of principal coordinates analysis (PCoA) and canonical correlation analysis (CCA) revealed significant differences in the Beta diversity of soil bacteria in the fire-burnt site under varying interference intensities. The Beta diversity of soil bacteria exhibited significant differences (p = 0.001), with MC, pH, TN, AN, and AK identified as significant influencing factors. (4) FAPROTAX functional prediction analyses were conducted to assess the changes in soil bacteria involved in Cellulolysis, Chemoheterotrophy, and Aerobic_Chemoheterotrophy in the fire-burnt site, with the relative abundance of bacteria involved in Chemoheterotrophy being significantly increased (p < 0.05) under different disturbance intensities. Collectively, our findings demonstrated that different disturbance intensities caused by fires significantly affected the Alpha diversity, Beta diversity, and functional abundance of soil bacterial communities in taiga forests, with MC, pH, TN, AN, and AK being identified as key influencing factors. Additionally, the presence of numerous rare species suggests their role as pioneer communities in the succession of soil bacterial communities.

Site properties, environmental factors, and crop identify influence soil bacterial communities more than municipal biosolid application

Reducing the environmental impact of Canadian field crop agriculture, including the reliance on conventional synthesised fertilisers, are key societal targets for establishing long-term sustainable practices. Municipal biosolids (MSB) are an abundant, residual organic material, rich in phosphate, nitrogen and other oligo-nutrients, that could be used in conjunction with conventional fertilisers to decrease their use. Though MBS have previously been shown to be an effective fertiliser substitute for different crops, including corn and soybean, there remain key knowledge gaps concerning the impact of MBS on the resident soil bacterial communities in agro-ecosystems. We hypothesised that the MBS fertiliser amendment would not significantly impact the structure or function of the soil bacterial communities, nor contribute to the spread of human pathogenic bacteria, in corn or soybean agricultural systems. In field experiments, fertiliser regimes for both crops were amended with MBS, and compared to corn and soybean plots with standard fertiliser treatments. We repeated this across four different agricultural sites in Quebec, over 2021 and 2022. We sampled MBS-treated, and untreated soils, and identified the composition of the soil bacterial communities via 16S rRNA metabarcoding. We found no indication that the MBS fertiliser amendment altered the structure of the soil bacterial communities, but rather that the soil type and crop identities were the most significant factors in structuring the bacterial communities. Moreover, there was no evidence that the MBS-treated soils were enriched in potential human bacterial pathogens over the two years of our study. Our analysis indicates that not only can MBS function as substitutes for conventional, synthesised fertilisers, but that they also do not disrupt the structure of the resident soil bacterial communities in the short term. Finally, we suggest that the use of MBS in agro-ecosystems poses no greater concern to the public than existing soil bacterial communities. This highlights the significant role MBS could potentially have in reducing the use of conventional industrial fertilisers and improving agricultural production, without risking environmental contamination.

Biochar's role in improving pakchoi quality and microbial community structure in rhizosphere soil.

Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes. The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq. The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significantly negatively correlated with the relative abundance of Ilumatobacter. Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application. Overall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (e.g., Gemmatimonadetes and Ilumatobacter), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better.

Responses of soil bacterial and fungal community structure and functions to different plant species in a mixed forest plantation in a semi-arid region of China

Soil microbial communities play important roles in biogeochemical cycles and ecosystem functioning. However, how tree and grass species affect soil microbial structure and functions in semi-arid regions is poorly understood. In this study, we used sequencing of representative genes and bioinformatic analysis to compare the soil bacterial and fungal communities and their functional groups among legume and non-legume broad-leaved plantations, conifer plantations, artificial grassland, and adjacent farmland in a semi-arid area of Northern China. We found that soil bacterial diversity and abundance were significantly increased by legume plantations, especially Robinia pseudoacacia, compared to farmland. Soil bacterial communities were dominated by K-strategists in plantation soils and by r-strategists in farmland and grassland soils. Soil fungal communities showed contrasting patterns between Ascomycetes and Basidiomycota across treatments, and the highest abundance of nutrient indicator taxa Mortierellomycota was observed in plantation soils. Functional analysis revealed that afforestation altered the capacity of soil bacteria for organic compound mineralization and C and N cycling, and that different plant species enriched different types of ectomycorrhizal and saprophytic fungi. Moreover, we found that plantations and grasslands formed more connected but less complex and stable bacterial co-occurrence networks than farmland, and that conifer plantations increased the closeness of soil fungal networks compared to broad-leaved plantations. Our results suggest that tree and grass species play a key role in shaping the soil microbial community structure and functional groups, and provide valuable information for choosing suitable tree and grass species for ecosystem restoration and management in semi-arid regions.

Synergistic effects of rhizosphere effect and combined organic and chemical fertilizers application on soil bacterial diversity and community structure in oilseed rape cultivation.

The combined application of chemical and organic fertilizers has been recognized to enhance soil fertility and foster the soil microbial ecosystem. However, the optimal ratio of chemical and organic fertilizers in oilseed rape cultivation is still uncertain, and the role of rhizosphere effect is still unclear. Thus, this study aimed to elucidate the impacts of varying ratios of chemical and organic fertilizers on the structure and potential functionalities of rhizosphere and non-rhizosphere soil microbial communities. The interplay of microbial communities with soil properties and oilseed rape root exudates was investigated in controlled pot cultivations receiving varying ratios of chemical and organic fertilizers. Results indicated clear segregation in the soil bacterial community, influenced by both fertilization treatments and rhizosphere effects. The bacterial community structure significantly correlated with nitrate nitrogen, organic acids, and dissolved organic carbon (DOC) content. Rhizosphere effects led to increased bacteria abundance, reduced diversity, and decreased network stability. Notably, F3 treatment receiving 25% chemical and 75% organic fertilizers showed a significantly higher abundance at 1.43 × 1011 copies g-1 dry soil, accompanied by increased species and genetic diversity, and ecological network complexity. This treatment also yielded the highest aboveground biomass of oilseed rape. However, the application of organic fertilizers also increased the risk of plant pathogenicity. This study reveals the impact of fertilizers and rhizosphere effects on soil microbial community structure and function, shedding light on the establishment of more effective fertilization schemes for oilseed rape agriculture.

‘Fertile island’ effects on the soil microbial community beneath the canopy of Tetraena mongolica, an endangered and dominant shrub in the West Ordos Desert, North China

BackgroundThe fertile islands formed by shrubs are major drivers of the structure and function of desert ecosystems, affecting seedling establishment, plant–plant interactions, the diversity and productivity of plant communities, and microbial activity/diversity. Although an increasing number of studies have shown the critical importance of soil microbes in fertile island formation, how soil microbial community structure and function are affected by the different fertile island effect intensities is still unknown. As an endangered and dominant shrub species in the West Ordos Desert, Tetraena mongolica was selected for further exploration of its fertile island effect on the soil microbial community in the present study to test the following two hypotheses: (1) T. mongolica shrubs with different canopy sizes exert fertile island effects of different strengths; (2) the soil microbial community structure and function beneath the T. mongolica canopy are affected by the fertile island, and the strength of these effects varies depending on the shrub canopy size.ResultsThe contents of soil total nitrogen (TN) and available phosphorus (AVP) were significantly greater beneath T. mongolica shrub canopy than outside the shrub canopy. With increasing shrub canopy size, the enrichment of soil TN and AVP increased, indicating a stronger fertile island effect. The structure and function of soil microbial communities, including fungal, archaeal and bacterial communities, are affected by the fertile island effect. An increase in canopy size increased the relative abundance of Ascomycota (Fungi) and Thaumarchaeota (Archaea). For the soil microbial functional groups, the relative abundance of endophytes in the fungal functional groups; steroid hormone biosynthesis, sphingolipid metabolism, and steroid biosynthesis genes in the bacterial functional groups; and nonhomologous end-joining and bisphenol degradation functional genes in the archaeal functional groups increased significantly with increasing T. mongolica canopy size.ConclusionsThese results revealed that T. mongolica had a fertile island effect, which affected the soil microbial community structure and functions, and that the fertile island effect might increase with increasing shrub canopy size. The fertile island effect may strengthen the interaction between T. mongolica shrubs and microbes, which may be beneficial to the growth and maintenance of T. mongolica.

Impacts of florfenicol on soil bacterial community structure and diversity by high throughput sequencing analysis

Impacts of florfenicol on soil bacterial community structure and diversity by high throughput sequencing analysis