Bacterial Shannon Index Research Articles

Applicability of soil health assessment dominated by biological indicators in facility agriculture

The minimum data set (MDS) is widely used for soil health index (SHI) assessment, with the selection of indicators being crucial. However, biological indicators are less frequently used compared to physical and chemical indicators. This study aimed to establish a biologically-centered MDS for assessing soil health in tomato facility agriculture in Ningbo. Using biochemical, microbiological, and nematode data from 60 continuous cropping soils, we identified key indicators for the MDS. Principal component analysis revealed a strong correlation between the MDS and the total data set (TDS), with the final MDS including available phosphorus, electrical conductivity, β-glucosidase, urease, bacterial Chao1 index, bacterial Shannon index, Ralstonia solanacearum, nematode Shannon index, structure index, and channel index. Random forest modeling showed that the predicted SHI had a high fit with the MDS-SHI, with bacterial and nematode Shannon indices being the most influential predictors, emphasizing the critical role of biological communities in maintaining soil health. Furthermore, the study identified three distinct phases in soil health during long-term continuous cropping: healthy (0–10 years), sub-healthy (11–15 years), and recovery (16–20 years), demonstrating the soil's potential for self-recovery. By incorporating biodiversity as a core component, this biologically-focused MDS provides a more comprehensive and precise method for evaluating soil health in facility agriculture. The findings suggest that this MDS could inform future research and applications in similar agricultural systems. Moreover, the results highlight the vital role of biodiversity in agroecosystem stability, suggesting that future soil health assessments should place greater emphasis on biological indicators to better capture the complexity of soil functions.

Synergistic regulation of salinity and nutrients on organic carbon mineralization in a 700-year cultivated saline soil chronosequence

Long-term cultivation in reclaimed mudflats significantly impacts soil properties through changes in salinity and organic carbon (OC) inputs, which subsequently affect soil physical, chemical, and biological characteristics. In addition, long-term rice cultivation can help optimize soil health and fertility management in paddy fields, mitigate climate change, and enhance ecosystem services. However, the impact of long-term cultivation on OC mineralization across a salinity gradient remains unclear. During an 80-d incubation experiment, we assessed 13C-labeled glucose mineralization in soils cultivated for 5, 20, 200, and 700 years, each with varying salinity levels. Our results demonstrated that glucose mineralization declined linearly with increasing soil salinity, from 76 % in low-salinity soils to 31 % in high-salinity soils, reflecting a clear physical impact. This process was closely linked with chemical properties, showing a positive correlation with Olsen P and levels of microbial biomass carbon and nitrogen. Soil organic carbon (SOC) mineralization was primarily controlled by dissolved OC regardless of soil salinity. Further investigation revealed significant shifts in the biological properties, notably the bacterial community composition, which varied with the duration of soil cultivation. The bacterial Shannon index increased steadily from 50 to 700 years, forming distinct clusters, influenced primarily by electrical conductivity and pH in high-salinity soils and by soil-labile nutrients in low-salinity soils. The abundance of Acidobacteria, Proteobacteria, and Verrucomicrobia—dominant phyla in soil cultivated for 700 years—is negatively correlated with soil salinity and pH and positively with labile nutrients, glucose, and OC mineralization, whereas the opposite was true for Bacteroidetes and Firmicutes dominant phyla in soil cultivated for 5 years, was affected positively by soil salinity and pH and negatively by labile nutrients and glucose mineralization. In conclusion, soil salinity and nutrients synergistically regulate OC mineralization in a 700-year cultivated saline soil chronosequence. Addressing these factors is critical to enhancing microbial activity and OC accumulation in saline soils, underscoring the importance of integrating measures to reduce salt and increase the import and accumulation of exogenous organic matter.

Effects of Selenium Application on Fermentation Quality, Chemical Composition, and Bacterial Community of Hybrid Pennisetum Silage

The primary objective of this study is to facilitate the conversion of inorganic selenium (Se) into organic Se within plants via assimilation, subsequently feeding it to livestock and poultry to enhance healthy animal production and yield Se-enriched livestock and poultry products. Therefore, it is imperative to first investigate the impact of varying Se doses on the agronomic traits of plants as well as their forage storage and processing. This experiment investigated the effect of Se fertilizer application on the fermentation quality, chemical composition, and bacterial community of Pennisetum americanum × Pennisetum purpureum cv Minmu 7 (HPM7). There were nine Se fertilizer dissolution levels of HPM7 treated, which were 0 mg/kg (Se0), 0.50 mg/kg (Se1), 1.00 mg/kg (Se2), 2.00 mg/kg (Se3), 5.00 mg/kg (Se4), 10.00 mg/kg (Se5), 20.00 mg/kg (Se6), 30.00 mg/kg (Se7), 40.00 mg/kg (Se8), and 50.00 mg/kg (Se9). The results showed that after silage, the water-soluble carbohydrates of Se1, Se2, and Se3 were lower than Se0, and the pH of Se3, Se4, and Se6 were lower than the Se0. The number of OTUs in the nine groups was sequentially Se1 > Se2 > Se3 > Se8 > Se6 > Se5 > Se7 > Se4 > Se0. The dominant bacterial phyla in silage samples were Firmicutes and Proteobacteria. Compared with Se0, Bacterial Shannon index in Se1 and Se2 were higher, while Chao1 and ACE indices of Se1, Se2, Se3, Se5, and Se6 were higher. A beta diversity analysis indicated that the Se1 exhibited the highest number of significant biomarkers. Escherichia coli between Se0 and Se3 and Clostridium sardiniense and Clostridium perfringens between Se0 and Se1 exhibited significant differences at a species level. The most abundant pathways for metabolism were membrane transport, carbohydrate metabolism, translation, replication, repair, and amino acid metabolism. The correlation analysis indicated that the dry matter content was negatively correlated with Bacillus (p < 0.01), Lactobacillus (p < 0.05), Pediococcus (p < 0.05), and Hirschia (p < 0.05); the contents of neutral detergent fiber and hemi-cellulose were positively correlated with Lactobacillus (p < 0.05, p < 0.01). The protein content was negatively correlated with proteus (p < 0.05). This study demonstrated that the application of Se fertilizer could enhance the Se content in HPM7. The optimal fertilization concentration was found to range from 0.50 to 2.00 mg/kg, which facilitates the metabolism of soluble carbohydrates and enhances both the fermentation quality and microbial relative abundance of HPM7 silage.

Development of root rot in Zanthoxylum bungeanum is closely linked to changes in soil microbial communities, enzyme activities, and physicochemical factors

Due to the emergence of root rot (RR), it can cause harm to the health of Zanthoxylum bungeanum (Z. bungeanum) plants. However, the reason for this is not clear, and further research is needed. We selected healthy and RR-affected 6-year-old Z. bungeanum trees (infected for 1 year), collected their rhizosphere and bulk soils, and analyzed soil microbial communities, enzyme activities, and physicochemical properties. When the plants were diseased, soil water content (SWC), available potassium (AK), organic matter (OM) contents, β-1,4-glucosidase (β-G) activity, and fungal Shannon index significantly decreased, while bacterial Shannon index significantly increased in the rhizosphere soil. Soil total nitrogen (TN), SWC, AK, OM contents, and β-G and N-acetyl-glucosamine (NAG) activity significantly reduced, while fungal Simpson index significantly increased in the bulk soil. There were significant differences in the bacterial communities of bulk and rhizosphere soil. However, there were no obvious differences in the fungal communities. Pearson's correlation analysis showed that changes in soil microbial communities were significantly correlated with changes in the contents of TN, AK, OM, and SWC, as well as the activities of β-G and NAG. In summary, changes in soil AK, OM, SWC, and TN resulted in changes in microbial community composition, as well as changes in β-G and NAG activities, and these alterations may lead to RR in Z. bungeanum.

Changes in soil microbial community and function across stand age of Cryptomeria japonica var. sinensis plantations in subtropical China

Microbial communities are important influencing factors in soil biogeochemical cycling. Differences in stand age can affect microbial communities and functions by altering soil biochemical characteristics. Studying the changes in soil microbial communities and functions at different ages of Cryptomeria japonica var. sinensis can provide a theoretical basis for the scientific management of plantations. Therefore, we collected soil samples from different soil depths from 7- (7a), 13- (13a), 24- (24a), 33- (33a), and 53-year (53a) C. japonica var. sinensis plantations, to assess the differences in soil biochemical characteristics, soil bacterial and fungal communities, soil enzyme activity, and soil respiration rate. Results showed that as the stand age increases, the ACE and Shannon indices of fungal communities showed an initial increase followed by a decrease, whereas the Chao 1 index showed an increasing trend. The ACE and Shannon indices of bacterial communities did not change with stand age, but the Chao1 index decreased with an increase in stand age. In addition, the fungal ACE and Chao1 indices and bacterial Shannon index were higher at the 0–15 cm depth than at the 15–30 cm depth. Soil microbial community composition varied with stand age and soil depth, including Proteobacteria and Unclassified_k_Fungi relative abundances, and their functional groups' (nitrogen cycling-related bacteria, saprophytic fungi, pathogens, and ectomycorrhizal fungi) relative abundances. In addition, stand age will indirectly affect soil microbial function by influencing soil biochemical characteristics and microbial communities at the 0–15 cm depth, whereas at the 15–30 cm depth, there is no direct or indirect impact on the above indicators. In summary, significant variations exist in soil microbial communities and their functions across stand ages, and these differences will further vary between soil depths. Our research contributes to a better understanding of the impact of different ages of afforestation on soil biogeochemical cycling, providing valuable microbial information for the sustainable management of C. japonica var. sinensis forests in the future.

Rhizosphere microbial community construction during the latitudinal spread of the invader Chromolaena odorata

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu’ er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata.

Bacteria, Fungi, and Protists Exhibit Distinct Responses to Managed Vegetation Restoration in the Karst Region.

Bacteria, fungi, and protists occupy a pivotal position in maintaining soil ecology. Despite limited knowledge on their responses to managed vegetation restoration strategies in karst regions, we aimed to study the essential microbial communities involved in the process of vegetation restoration. We compared microbial characteristics in four land use types: planted forests (PF), forage grass (FG), a mixture of plantation forest and forage grass (FF), and cropland (CR) as a reference. Our findings revealed that the richness of bacteria and protists was higher in FF compared to PF, while fungal richness was lower in both PF and FF than in CR. Additionally, the bacterial Shannon index in FF was higher than that in CR and PF, while the fungal and protist Shannon indices were similar across all four land use types. Significant differences were observed in the compositions of bacterial, fungal, and protist communities between FF and the other three land use types, whereas bacterial, fungal, and protist communities were relatively similar in PF and FG. In FF, the relative abundance of bacterial taxa Acidobacteria, Firmicutes, and Gemmatimonadetes was significantly higher than in PF and CR. Fungal communities were dominated by Ascomycota and Basidiomycota, with the relative abundance of Ascomycota significantly higher in FF compared to other land use types. Regarding protistan taxa, the relative abundance of Chlorophyta was higher in FF compared to CR, PF, and FG, while the relative abundance of Apicomplexa was higher in CR compared to FF. Importantly, ammonium nitrogen, total phosphorus, and microbial biomass nitrogen were identified as key soil properties predicting changes in the diversity of bacteria, fungi, and protists. Our results suggest that the microbial community under FF exhibits greater sensitivity to vegetation restoration compared to PF and FG. This sensitivity may stem from differences in soil properties, the formation of biological crusts and root systems, and management activities, resulting in variations in bacterial, fungal, and protist diversity and taxa in PF. As a result, employing a combination restoration strategy involving plantation forest and forage grass proves to be an effective approach to enhance the microbial community and thereby improve ecosystem functionality in ecologically fragile areas.

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.

Biodegradable film mulching increases soil microbial network complexity and decreases nitrogen-cycling gene abundance

Biodegradable plastic films have emerged as a substitute for conventional plastic films. Nevertheless, responses of plant-associated microbiomes to the application of biodegradable film mulching at field scale have received little attention. A field experiment was conducted to assess the influence of different film mulching treatments on various microbial attributes and nitrogen (N) cycling functional genes in bulk and rhizosphere soils. Biodegradable film mulching raised the bacterial Shannon index in bulk soils but not in rhizosphere soils. Biodegradable film mulching has led to an increase in the complexity and connectivity of microbial networks, as well as an enhancement in the positive association among microorganisms owing to raised soil nutrients and increased crop biomass. In biodegradable film-treated soils, both bacterial and fungal communities were primarily influenced by stochastic processes associated with dispersal limitation. Moreover, conventional plastic film mulching increased denitrification, anammox, N fixation, and dissimilatory nitrate-reduction (DNRA) gene abundance in bulk soils. In rhizosphere soils, biodegradable film mulching reduced nitrification, denitrification, anammox, N fixation, and DNRA gene abundance. Furthermore, keystone genera (e.g., Nitrosospira, Truepera, Adhaeribacter, Opitutus, and Fusarium) were affected by edaphic variables, contributing to decreased N-cycling gene abundance in biodegradable film-treated soils. Collectively, biodegradable film mulching transformed soil microbiome assembly and functional adaptation, and soil nutrient availability and plant biomass were the critical factors influencing the microbial community. These findings present a novel perspective on the diverse impacts of biodegradable and conventional film mulching on soil microbiome and N-cycling processes.

Elevated Altitude and Limestone Soil Promoted Fungal Diversity in Rhizosphere Soil of Sophora japonica

Soil microorganisms play a crucial role in mediating material transformation and nutrient cycling. However, little attention has been paid to the relationships between microbial communities and altitude and lithology in karst regions. Sophora japonica cv. Jinhuai is an officinal plant cultivated in karst areas, and there is a correlation between the dynamics of microbial community and ecological factors. This study examined the diversity of microbial communities in the rhizosphere of S. japonica under different lithologies and altitudes in karst regions of northern Guangxi, China using high-throughput sequencing technology. It was found that the bacterial community consisted of 37 phyla, including Proteobacteria. The fungal community mainly comprised 15 phyla, including Ascomycota. The fungal Shannon and Chao1 indices increased with altitude, while the bacterial Shannon index decreased. The fungal Shannon indices in limestone soil were higher than those in dolomite. The soil’s microbial Shannon and Chao1 indices were positively affected by pH, while the available phosphorus and potassium had the opposite effect. Research shows that altitude, lithology, pH, and available phosphorus were the crucial factors influencing the rhizosphere soil microbial community. This study provides references for understanding the relationship between plants and microorganisms and the microbial distribution strategy of rocky desertification habitats in the future.

Effect of Intertidal Vegetation (Suaeda salsa) Restoration on Microbial Diversity in the Offshore Areas of the Yellow River Delta.

The coastal wetlands in the Yellow River Delta play a vital role in the ecological function of the area. However, the impact of primary restoration on microbial communities is not yet fully understood. Hence, this study aimed to analyze the bacterial and archaeal communities in the soil. The results indicated that Marinobacter and Halomonas were predominant in the bacterial community during spring and winter. On the other hand, Muribaculaceae and Helicobacter were prevalent during the core remediation of soil, while Inhella and Halanaerobium were predominant in non-vegetation-covered high-salinity soil. The bacterial Shannon index showed significant differences in vegetation-covered areas. For archaea, Salinigranum, Halorubrum, and Halogranum were dominant in vegetation areas, while Halolamina, Halogranum, and Halorubrum were prevalent in non-vegetation areas. The colonization of Suaeda salsa led to differences in the composition of bacteria (22.6%) and archaea (29.5%), and salt was one of the significant reasons for this difference. The microflora was more diverse, and the elements circulated after vegetation grounding, while the microbial composition in non-vegetation areas was similar, but there was potential competition. Therefore, vegetation restoration can effectively restore soil ecological function, while the microorganisms in the soil before restoration provide germplasm resources for pollutant degradation and antimicrobial development.

Comparing struvite, K-struvite and hydroxyapatite for the remediation of lead and cadmium contaminated soil

Heavy metal pollution leads to severe soil contamination and raises environmental concerns. Phosphorus-bearing minerals have been identified as effective and environmentally friendly agents for remediating contaminated soil. However, using recycled phosphorus for metal remediation remains limited. In this study, we investigated the potential use of recovered magnesium ammonium phosphate (MAP), potassium magnesium phosphate hydrate (KMP), and hydroxyapatite (HAP) to immobilize lead (Pb) and cadmium (Cd) in contaminated soil. The effectiveness of MAP, KMP, and HAP in modifying the chemical composition of Pb and Cd in the soil and reducing their mobility was demonstrated by the results. When added at dosages of 5:1 and 10:1, the extractable fraction of Pb decreased to 0.43–13.43 % of the control group. Similarly, the extractable fraction of Cd decreased to 49.18–76.44 % of the control group at the same dosages. Moreover, the application of these products resulted in an increase in soil pH value, urease activity, and bacterial Shannon index, thereby enhancing soil properties. The immobilization effects were more significant in Pb-contaminated soil compared to Cd-contaminated soil, and MAP and KMP exhibited a stronger passivation effect on Pb in comparison to HAP. For soil fertility improvement, a molar ratio of 10:1 was recommended, whereas a ratio of 5:1 effectively passivated Pb in contaminated soil. These findings provide evidence for the feasibility of utilizing MAP, KMP, and HAP in the immobilization of heavy metals in polluted soil.

Microbial-driven mechanisms for the effects of heavy metals on soil organic carbon storage: A global analysis

Heavy metal (HM) enrichment is closely related to soil organic carbon (SOC) pools in terrestrial ecosystems, which are deeply intertwined with soil microbial processes. However, the influence of HMs on SOC remains contentious in terms of magnitude and direction. A global analysis of 155 publications was conducted to integrate the synergistic responses of SOC and microorganisms to HM enrichment. A significant increase of 13.6 % in SOC content was observed in soils exposed to HMs. The response of SOC to HMs primarily depends on soil properties and habitat conditions, particularly the initial SOC content, mean annual precipitation (MAP), initial soil pH, and mean annual temperature (MAT). The presence of HMs resulted in significant decreases in the activities of key soil enzymes, including 31.9 % for soil dehydrogenase, 24.8 % for β-glucosidase, 35.8 % for invertase, and 24.3 % for cellulose. HMs also exerted inhibitory effects on microbial biomass carbon (MBC) (26.6 %), microbial respiration (MR) (19.7 %), and the bacterial Shannon index (3.13 %) but elevated the microbial metabolic quotient (qCO2) (20.6 %). The HM enrichment-induced changes in SOC exhibited positive correlations with the response of MBC (r = 0.70, p < 0.01) and qCO2 (r = 0.50, p < 0.01), while it was negatively associated with β-glucosidase activity (r = 0.72, p < 0.01) and MR (r = 0.39, p < 0.01). These findings suggest that the increase in SOC storage is mainly attributable to the inhibition of soil enzymes and microorganisms under HM enrichment. Overall, this meta-analysis highlights the habitat-dependent responses of SOC to HM enrichment and provides a comprehensive evaluation of soil carbon dynamics in an HM-rich environment.

Linking soil organic carbon mineralization to soil physicochemical properties and bacterial alpha diversity at different depths following land use changes

BackgroundAnthropogenic land use changes (LUCs) impart intensifying impacts on soil organic carbon (SOC) turnover, leading to uncertainty concerning SOC mineralization patterns and determining whether soils act as “source” or “sink” in the global carbon budget. Therefore, understanding the SOC mineralization characteristics of different LUC patterns and their potential influencing factors is crucial. An indoor incubation experiment was conducted to study the SOC mineralization patterns and their relevance to soil physicochemical properties, soil enzyme activity, SOC fractions, and bacterial alpha diversity. The soils were collected from two layers of five typical LUC patterns in Yellow Sea Forest Park, including four that were converted from wheat–corn rotation systems [a gingko plantation (G), a metasequoia plantation (M), a gingko–wheat–corn agroforestry system (GW), and a gingko–metasequoia system (GM)] and a traditional wheat–corn system (W).ResultsLUCs had significant and diverse impacts on the SOC content and SOC fraction contents and on soil enzyme activity. The cumulative SOC mineralization was significantly higher in the M systen than in the W and GW systems at 0–20 cm depth and higher in the G system than in the GW system at 20–40 cm depth after 60-day incubation. The mineralization ratio was highest in the W system and lowest in the GW system. The soil pH and bulk density had a significant negative correlation with the cumulative SOC mineralization, while the soil bacterial Shannon index had a significant positive correlation with cumulative SOC mineralization. Multiple stepwise linear regression analysis showed that the SOC mineralization potential was dominantly explained by the bacterial Shannon index and operational taxonomic units (OTUs). The GW system had lower potentially mineralizable SOC and higher SOC stability. Additionally, the incubation time and cumulative SOC mineralization were well fitted by the first-order kinetic equation.ConclusionsLUCs significantly changed SOC mineralization characteristics and the results highlighted the important roles of the bacterial community in soil carbon cycling, which contributes to the fundamental understanding of SOC turnover regulation.

Differences in Juniperus przewalskii Rhizosphere Microbiomes across Age Classes: Community Diversity and Assembly.

Evidence shows that biotic and abiotic factors have apparent diversity at different forest ages, leading to changes in rhizosphere microbiomes. However, the difference in diversity, co-occurrence pattern, and assembly of the rhizosphere microbial community among the different forest ages is still unclear. A total of 24 Juniperus przewalskii rhizosphere soil samples were selected from four representative age classes, using diameter at breast height (DBH) as a proxy for tree age (age class I: 5 < DBH ≤ 12.5 cm, age class II: 12.5 < DBH ≤ 22.5 cm, age class III: 22.5 < DBH ≤ 32.5 cm, and age class IV: DBH > 32.5 cm), and analyzed the structural characteristics of the soil microbial community by high-throughput amplicon sequencing. With the increase in age class, the microbial community α-diversity and β-diversity had an increased trend. The bacterial Shannon index in class II and class III were markedly higher than in class I. From class I to class IV, the relative abundances of dominant phyla such as Actinobacteria and Ascomycota decreased, and the relative abundances of Proteobacteria and Basidiomycota increased in contrast. The complexity and association stability of the bacteria and fungi community network structure increase with forest age. Stochastic processes mediated the assembly of soil bacterial communities, while deterministic processes played a more significant role in the assembly of fungal communities. In addition, the relative importance of deterministic components in the microbial community increased significantly with age class. Random forests suggested that soil pH, plant Shannon-Wiener index (H), and Pielou's evenness index (J) were the most important driving factors of bacterial and fungal community assembly. Overall, these results provide information useful for understanding the generation and maintenance mechanisms of rhizosphere microbial communities across age classes.

Soil properties and microbial functional attributes drive the response of soil multifunctionality to long-term fertilization management

Fertilization is a vital management practice to improve soil fertility and promote agricultural production. However, there is limited knowledge about the interactive effects between soil abiotic and biotic factors and soil multifunctionality after long-term fertilization. There has been little research on determining whether the application of organic fertilizers can improve the functional potential of microorganisms to maintain multifunctional stability. In this study, we integrated soil physicochemical properties, extracellular enzyme activities, bacterial community characteristics, and the abundance of functional genes related to carbon (C) and nitrogen (N) cycling to evaluate the mechanism of soil functional potential response to 13 years of fertilization management. Four treatments were compared, including no fertilizer (CK), conventional fertilization (CF), formulated fertilization by soil testing (SF), SF with organic fertilizer (SFO). The addition of organic fertilizer enhanced the soil electrical conductivity, N-cycling enzyme activities, contents of macroaggregate and associated C, and soil nutrients, while decreasing the content of microaggregates compared with other treatments. The co-application of chemical and organic fertilizer led to significant increases in soil multifunctionality and the bacterial Shannon index compared with the CK and CF treatments. Soil abiotic factors are the key predictors for shaping soil multifunctionality. The addition of organic fertilizer could increase the abundance of functional genes related to C- and N-cycling mediated by the contents of nutrients and the aggregates associated with nutrients. Additionally, treatment with organic fertilizer can mitigate the decrease in genes for C-cycling function caused by the long-term application of chemical fertilizer (SF). In addition, the structural equation models revealed that the fertilization positively affected soil multifunctionality indirectly by changing the bacterial diversity and community composition, as well as the functional potential related to N-cycling. Overall, soil properties and microbial functional attributes jointly drive the response of soil multifunctionality to long-term fertilization management. These results suggest that the combination of organic and chemical fertilizer is worth popularizing to improve multifunctionality and its stability to maintain agricultural sustainability.

Soil nutrients and the responses of microbial community structure to pine bark and vinegar residues in blueberry cultivation

The addition of suitable acidic organic materials to improve the soil for blueberry (Vaccinium spp.) cultivation is the foundation for ensuring the sustainable development of blueberry industry in China. However, the effects of managing orchards with different inputs of organic material to improve the soil nutrients varied substantially. To unearth the best types of organic material to improve the soil fertility for blueberry cultivation and the rates to use in their application, a cultivation experiment used rooting zone restriction container and one-year-old seedlings of highbush blueberry (Vaccinium corymbosum L. variety “Legacy”) as the test materials and pure soil as the control (CK) in this study. We compared the effects of three rates of application of pine bark and vinegar residue on the soil nutrients and microbial community structures, three concentrations of 1884, 3768, and 5652 m3 km−2 of pine bark and three of 2826, 5652, and 8478 m3 km−2 vinegar residue were designed to add to the soil, and they were designated PB1, PB2, and PB3 and VR1, VR2, and VR3, respectively. Surface soil samples were collected for analysis after the blueberry shrubs had been planted for one year. The results showed that compared with the CK, the PB1 treatment significantly increased the total potassium (TK), alkaline hydrolyzed nitrogen (AN) and available phosphorus (AP) contents in the soil. The PB2 and PB3 treatments significantly enhanced the soil organic matter (SOM), total phosphorus (TP), AN, and AP contents but significantly reduced the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and microbial biomass phosphorus (MBP) contents. The VR1, VR2 and VR3 treatments significantly increased the contents of soil pH, total nitrogen (TN), available potassium (AK), SOM, AN, MBC and MBP. The PB1, PB2, VR1, VR2, and VR3 treatments markedly enhanced the bacterial Shannon index. However, the VR3 treatment markedly reduced the number of fungal species and the Chao 1, ACE, Simpson, and Shannon indices when compared with those of the CK. The soil fungal diversity was more easily regulated by soil nutrients than the bacterial diversity. A redundancy analysis showed that the dominant bacterial phyla were primarily regulated by the soil AN, while the dominant fungal phyla were primarily regulated by the SOM and MBN. In conclusion, the vinegar residue was more effective than the pine bark at improving the soil nutrients. The VR2 treatment not only significantly improved the soil nutrients but also maintained the soil microbial diversity, which rendered it the best organic material to improve the cultivation of blueberry soil.

Associations of soil bacterial diversity and function with plant diversity in Carex tussock wetland.

Some species of Carex can form tussocks, which are usually distributed in valleys and flood plains. The soil microbial community diversity and function of micro-habitats formed by tussocks are associated with plant diversity, and research on these associations can guide Carex tussock wetland restoration. In this study, we selected tussock wetlands dominated by Carex appendiculata, including natural wetlands (NW), artificially restored wetlands (ARW), and naturally restored wetlands (NRW), and investigated plant diversity. Soil samples were collected from the quadrats of each sample plot with the maximum (ma), median (me), and minimum (mi) plant Shannon index values, and high-throughput sequencing was used to analyze the bacterial community composition, diversity, and functions. The plant diversity indexes of neither ARW nor NRW significantly differed from that of NW, but the companion species in NRW were hygrophytes and mesophytes, in contrast to only hygrophytes serving as companion species in NW and ARW. The soil bacterial communities at the operational taxonomic unit level of the nine quadrats with different plant Shannon index values significantly (p < 0.01) differed. The relative abundances of the dominant phyla (Proteobacteria, Chloroflexi, and Bacteroidetes) and the dominant genera (Geobacter, Sideroxydans, and Clostridium except for unassigned genera) significantly (p < 0.05) differed under the different levels of plant diversity. The plant Shannon index, soil moisture content, total organic carbon, N, and P were significantly (p < 0.05 or p < 0.01) correlated with the bacterial Shannon index. The phylogenetic diversity of the bacterial community in NW was significantly (p < 0.0001) different from those in ARW and NRW, and that in ARW was also significantly (p < 0.05) different from that in NRW. The functional groups of bacterial communities associated with plant diversity. In the NWme, ARWme, and NRWme bacterial communities, the relative proportions of functional groups related to soil N cycle were higher, but those related to soil S and C cycles were lower. Considering the rehabilitation of both plant and microbial communities, the methods used for establishing the ARW are recommended for Carex tussock wetland restoration.

Daylily intercropping: Effects on soil nutrients, enzyme activities, and microbial community structure.

The daylily (Hemerocallis citrina Baroni)/other crop intercropping system can be a specific and efficient cropping pattern in a horticultural field. Intercropping systems contribute to the optimization of land use, fostering sustainable and efficient agriculture. In the present study, high-throughput sequencing was employed to explore the diversity in the root-soil microbial community in the intercropping of four daylily intercropping systems [watermelon (Citrullus lanatus)/daylily (WD), cabbage (Brassica pekinensis)/daylily (CD), kale (Brassica oleracea)/daylily (KD), watermelon/cabbage/kale/daylily (MI)], and determine the physicochemical traits and enzymatic activities of the soil. The results revealed that the contents of available potassium (2.03%-35.71%), available phosphorus (3.85%-62.56%), available nitrogen (12.90%-39.52%), and organic matter (19.08%-34.53%), and the urease (9.89%-31.02%) and sucrase (23.63%-50.60%) activities, and daylily yield (7.43%- 30.46%) in different intercropping soil systems were significantly higher compared to those in the daylily monocropping systems (CK). The bacterial Shannon index increased significantly in the CD and KD compared to the CK. In addition, the fungi Shannon index was also increased significantly in the MI, while the Shannon indices of the other intercropping modes were not significantly altered. Different intercropping systems also caused dramatic architectural and compositional alterations in the soil microbial community. A prominently higher relative richness of Bacteroidetes was noted in MI compared to that in CK, while Acidobacteria in WD and CD and Chloroflexi in WD were pronouncedly less abundant compared to those in CK. Furthermore, the association between soil bacteria taxa and soil characteristic parameters was stronger than that between fungi and soil. In conclusion, the present study demonstrated that the intercropping of daylily with other crops could significantly improve the nutrient levels of the soil and optimize the soil bacterial microflora composition and diversity.

The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales

Microorganisms exist throughout the soil profile and those microorganisms living in deeper soil horizons likely play key roles in regulating biogeochemical processes. However, the vertical differentiations of microbes along soil depth and their global biogeographical patterns remain poorly understood. Herein, we conducted a global meta-analysis to clarify the vertical changes of microbial biomass, diversity, and microbial relative abundance across the soil profiles. Data was collected from 43 peer-reviewed articles of 110 soil profiles (467 observations in total) from around the world. We found soil microbial biomass and bacterial diversity decreased with depth in soils. Among examined edaphic factors, the depth variation in soil pH exhibited significant negative associations with the depth change in microbial biomass and bacterial Shannon index, while soil total organic carbon (TOC) and total nitrogen (TN) exhibited significant positive associations. For the major bacteria phyla, the relative abundances of Proteobacteria and Bacteroidetes decreased with soil depth, while Chloroflexi, Gemmatimonadetes, and Nitrospirae increased. We found both parallels and differences in the biogeographical patterns of microbial attribute of topsoil vs. subsoil. Microbial biomass was significantly controlled by the soil nutrient concentrations in both topsoil and subsoil compared with climatic factors, while bacterial Shannon index was significantly controlled by the edaphic factors and across latitudes or climatic factors. Moreover, mean annual precipitation can also be used as a predictor of microbial biomass in subsoil which is different from topsoil. Collectively, our results provide a novel integrative view of how microbial biomass and bacterial community response to soil depth change and clarify the controlling factors of the global distribution patterns of microbial biomass and diversity, which are critical to enhance ecosystem simulation models and for formulating sustainable ecosystem management and conservation policies.