Soil pH: a key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard

Understanding and exploring the diversity of soil microorganisms in tea (Camellia sinensis) gardens: toward sustainable tea production

Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes' function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production.

Unveiling the driving role of pH on community stability and function during lignocellulose degradation in paddy soil

Introduction

Crop straw, a major by-product of agricultural production, is pivotal in maintaining soil health and preserving the ecological environment. While straw incorporation is widely recognized as a sustainable practice, the incomplete decomposition of crop residues poses challenges to plant growth, increasing the risk of pests and diseases. This necessitates a comprehensive investigation.

Methods

The current study employs a 28-day pot experiment to simulate the degradation of rice straw in paddy soils. The impacts of bioaugmentation and biostimulation on lignocellulose degradation are systematically evaluated.

Results

Results indicate a high lignocellulose degradation ability in paddy soil, with over 80% straw weight loss within 28 days. Bioaugmentation with a lignocellulolytic microbial consortium enhances straw degradation during the initial stage (0-14 days). In contrast, biostimulation with readily available nutrients leads to soil acidification, hindering straw degradation and reducing microbial diversity. Furthermore, pH emerges as a critical factor influencing microbial community stability and function during lignocellulose degradation. Microbial co-occurrence network analysis reveals that microorganisms occupy ecological niches associated with different cellulose components. Notably, Module M2, comprising Proteobacteria, Firmicutes, Gemmatimonadota, Actinobacteriota, Bacteroidota, Myxococcota, Halobacterota, and Acidobacteriota, positively correlates with pH and weight loss.

Discussion

This study significantly advances our understanding of microbial mechanisms in soil decomposition, emphasizing the pivotal role of pH in community stability and function in paddy soil. These findings can inform future strategies for managing rice straw while safeguarding soil ecosystem health.

More N fertilizer, more maize, and less alfalfa: maize benefits from its higher N uptake per unit root length

Root plasticity is fundamental to soil nutrient acquisition and maximizing production. Different soil nitrogen (N) levels affect root development, aboveground dry matter accumulation, and N uptake. This phenotypic plasticity is well documented for single plants and specific monocultures but is much less understood in intercrops in which species compete for the available nutrients. Consequently, the study tested whether the plasticity of plant roots, biomass and N accumulation under different N levels in maize/alfalfa intercropping systems differs quantitatively. Maize and alfalfa were intercropped for two consecutive years in large soil-filled rhizoboxes and fertilized with 6 different levels of N fertilizer (0, 75, 150, 225, 270, and 300 kg ha-1). Root length, root surface area, specific root length, N uptake and yield were all increased in maize with increasing fertilizer level, whereas higher N rates were supraoptimal. Alfalfa had an optimal N rate of 75-150 kg ha-1, likely because the competition from maize became more severe at higher rates. Maize responded more strongly to the fertilizer treatment in the second year when the alfalfa biomass was much larger. N fertilization contributes more to maize than alfalfa growth via root plasticity responses. Our results suggest that farmers can maximize intercropping yield and economic return by optimizing N fertilizer management.

Unraveling two decades of phyllosphere endophytes: tracing research trends and insights through visualized knowledge maps, with emphasis on microbial interactions as emerging frontiers

Phyllosphere endophytes play a critical role in a myriad of biological functions, such as maintaining plant health and overall fitness. They play a determinative role in crop yield and quality by regulating vital processes, such as leaf functionality and longevity, seed mass, apical growth, flowering, and fruit development. This study conducted a comprehensive bibliometric analysis aiming to review the prevailing research trajectories in phyllosphere endophytes and harness both primary areas of interest and emerging challenges. A total of 156 research articles on phyllosphere endophytes, published between 2002 and 2022, were retrieved from the Web of Science Core Collection (WoSCC). A systematic analysis was conducted using CiteSpace to visualize the evolution of publication frequency, the collaboration network, the co-citation network, and keywords co-occurrence. The findings indicated that initially, there were few publications on the topic of phyllosphere endophytes. However, from 2011 onwards, there was a notable increase in the number of publications on phyllosphere endophytes, gaining worldwide attention. Among authors, Arnold, A Elizabeth is widely recognized as a leading author in this research area. In terms of countries, the USA and China hold the highest rankings. As for institutional ranking, the University of Arizona is the most prevalent and leading institute in this particular subject. Collaborative efforts among the authors and institutions tend to be confined to small groups, and a large-scale collaborative network needs to be established. This study identified the influential journals, literature, and hot research topics. These findings also highlight the interconnected nature of key themes, e.g., phyllosphere endophyte research revolves around the four pillars: diversity, fungal endophytes, growth, and endophytic fungi. This study provides an in-depth perspective on phyllosphere endophytes studies, revealing the identification of biodiversity and microbial interaction of phyllosphere endophytes as the principal research frontiers. These analytical findings not only elucidate the recent trajectory of phyllosphere endophyte research but also provide invaluable insights for similar studies and their potential applications on a global scale.

Environmental factors influencing the diversity and distribution of dictyostelid cellular slime molds in forest and farmland soils of western China

IMPORTANCE

Soil protists are an essential yet seriously understudied component of the soil microbiome. In this study, 11 new records of dictyostelids belonging to 2 orders, 3 families, and 4 genera were identified from 99 soil samples collected from different elevations and habitats in central Gansu and the southeastern and southcentral portions of Guizhou Province, China. We found that dictyostelid communities were significantly different between Gansu and Guizhou Provinces, apparently in response to different environmental factors. Moreover, dictyostelids were found to have the highest species diversity in mixed forests. Soil pH, temperature, and elevation were determined to be the primary factors that affect the distribution and occurrence of dictyostelids in Guizhou and Gansu Provinces. This work supplements the survey data available for dictyostelids elsewhere in China. These new findings have significant implications for our understanding of the diversity of soil microorganisms.

Improvement in gravel-mulched land soil nutrient and bacterial community diversity with Lonicera japonica

Gravel-mulched land in China suffers from poor natural resources and fragile ecological environment, posing a challenge to effective restoration of ecological function. Lonicera japonica, a traditional Chinese herb used for treating human diseases, is a highly adaptable and resilient plant species, can effectively improve the soil properties, and may have important implications for the ecology and economy of gravel-mulched land. A study was conducted in a gravel-mulched field to measure the impact of planting the L. japonica (including control (CK), 1-year, 2-year, and 4-year cultivation of plants) on (i) dynamic changes in soil nutrient and enzyme activity properties, and (ii) soil rhizosphere microbial community structure characteristics. We found that the concentration of soil organic carbon, available nitrogen, available phosphorus and available potassium in L. japonica soil after cultivation for 1-4 years increased by 11-409%. The urease, phosphatase and catalase activities were increased by 11-560%, with the highest nutrient concentration and enzyme activity in 4-year plants. The pH value gradually decreased after cultivation. The improved soil environments increased soil bacterial community diversity. Planting L. japonica significantly increased the bacterial ACE, Chao1 index, Simpson index, and Shannon-Wiener index. The Firmicutes, Proteobacteria and Bacteroidetes were observed in dominant phyla. The relative abundance of eight genera, including Streptococcus, Veillonella and Rothia, was significantly reduced by more than 1%. Taken together, these soil indicators suggest that planting L. japonica in the short term would be a cost-effective strategy to combat soil degradation in a gravel-mulched ecosystem.

Co-existing antibiotics alter the enantioselective dissipation characteristics of zoxamide and drive combined impact on soil microenvironment

Co-existence of antibiotics (ABX) in soil may expand the environmental harm of pesticide pollution. Our study investigated the combined effects of five antibiotics chlortetracycline (CTC), oxytetracycline (OTC), tetracycline (TC), sulfamethoxazole (SMX), enrofloxacin (ENR) on enantioselective fate of zoxamide (ZXM) and soil health. The results showed that S-(+)-ZXM preferentially dissipated in soil. ABX prolonged dissipation half-life and reduced enantioselectivity of ZXM. Soil was detected to be more acidic after long-term treatment of ZXM and ABX. Lowest soil available N, P, K were found in ZXM + SMX, ZXM + OTC and ZXM + SMX groups at 80 days, respectively. ABX had demonstrated effective promotion of catalase (S-CAT), urease (S-UE) and negative impact on dehydrogenase (S-DHA), sucrase (S-SC) activities. Bacteria Lysobacter, Sphingomonas and fungus Mortierella were identified as the most dominant genera, which possessed as potential microbial resources for removal of composite pollution from ZXM and ABX. SMX and TC, SMX, ENR, respectively, contributed to the alteration of bacteria and fungi community abundance. Soil acidity, available N and enzyme activity showed stronger correlations with bacteria and fungi compared to other environmental factors. Our findings highlighted the interactions between ZXM and ABX from the perspective of soil microenvironment changes. Moreover, a theoretical basis for the mechanism was actively provided.

Impact of Red Imported Fire Ant Nest-Building on Soil Properties and Bacterial Communities in Different Habitats

The red imported fire ant (Solenopsis invicta Buren) is a highly adaptable invasive species that can nest and reproduce in different habitat soils. We aimed to explore the adaptability of red imported fire ants in different habitats by analyzing changes in the physicochemical properties of nest soils and bacterial communities. Five habitat types (forest, tea plantation, rice field, lawn, and brassica field) were selected. The results showed that the pH of the nest soils increased significantly in all five habitats compared to the control soils of the same habitat. A significant increase in nitrogen content was detected in the nests. The Cr, Pb, Cu, and Ni levels were significantly reduced in the soils of the five habitats, due to nesting activities. Analysis of the composition and diversity of the soil microbial community showed that, although the richness and diversity of bacteria in the nest soils of red imported fire ants in the five habitats varied, the relative abundance of Actinobacteria significantly increased and it emerged as the dominant bacterial group. These results indicate that red imported fire ants modify the physicochemical properties of nest soils and bacterial communities to create a suitable habitat for survival and reproduction.

Contrasting effects of organic materials versus their derived biochars on maize growth, soil properties and bacterial community in two type soils

The objective of this study was to assess the benefit of applying biochar instead of its feedstock in enhancing soil quality. To accomplish this, we investigated the short-term effects of two organic materials and their derived biochars on maize growth, soil properties, and microbial community in fluvo-aquic and red soil with a pot experiment. Five treatments were applied to each soil, namely, the addition of straw, manure, straw-derived biochar, manure-derived biochar, and the control with no addition of any organic materials and biochar. Our results revealed that straw decreased the shoot biomass of maize in both soils, while straw-derived biochar, manure and manure-derived biochar increased it by 51.50, 35.47 and 74.95% in fluvo-aquic soil and by 36.38, 117.57 and 67.05% in red soil compared with the control, respectively. Regarding soil properties, although all treatments increased soil total organic carbon, straw and manure exhibited more pronounced effects on improving permanganate-oxidizable carbon, basal respiration, and enzyme activity compared with their derived biochars. Manure and its biochar had more significant effects on improving soil available phosphorus, whereas straw and its biochar exhibited more ameliorating effects on available potassium. Straw and manure consistently decreased bacterial alpha diversity (Chao1 and Shannon index) and altered bacterial community composition in the two soils by increasing the relative abundances of Proteobacteria, Firmicutes, and Bacteroidota and decreasing those of Actinobacteriota, Chloroflexi, and Acidobacteriota. More specifically, straw had a greater effect on Proteobacteria, whereas manure affected Firmicutes more. While straw-derived biochar had no effect on bacterial diversity and bacterial community composition in both soils, manure-derived biochar increased bacterial diversity in the fluvo-aquic soil and altered bacterial community composition in the red soil by increasing the relative abundances of Proteobacteria and Bacteroidota and decreasing that of Firmicutes. In summary, owing to the input of active organic carbon, straw and manure exhibited more pronounced short-term effects on soil enzyme activity and bacterial community compared with their derived biochar. Furthermore, straw-derived biochar was found to be a better option than straw in promoting maize growth and nutrient resorption, while the choice of manure and its biochar should be determined by the soil type.

Contributions of Beneficial Microorganisms in Soil Remediation and Quality Improvement of Medicinal Plants

Medicinal plants (MPs) are important resources widely used in the treatment and prevention of diseases and have attracted much attention owing to their significant antiviral, anti-inflammatory, antioxidant and other activities. However, soil degradation, caused by continuous cropping, excessive chemical fertilizers and pesticide residues and heavy metal contamination, seriously restricts the growth and quality formation of MPs. Microorganisms, as the major biota in soil, play a critical role in the restoration of the land ecosystem. Rhizosphere microecology directly or indirectly affects the growth and development, metabolic regulation and active ingredient accumulation of MPs. Microbial resources, with the advantages of economic efficiency, harmless to environment and non-toxic to organisms, have been recommended as a promising alternative to conventional fertilizers and pesticides. The introduction of beneficial microbes promotes the adaptability of MPs to adversity stress by enhancing soil fertility, inhibiting pathogens and inducing systemic resistance. On the other hand, it can improve the medicinal quality by removing soil pollutants, reducing the absorption and accumulation of harmful substances and regulating the synthesis of secondary metabolites. The ecological and economic benefits of the soil microbiome in agricultural practices are increasingly recognized, but the current understanding of the interaction between soil conditions, root exudates and microbial communities and the mechanism of rhizosphere microecology affecting the secondary metabolism of MPs is still quite limited. More research is needed to investigate the effects of the microbiome on the growth and quality of different medicinal species. Therefore, the present review summarizes the main soil issues in medicinal plant cultivation, the functions of microbes in soil remediation and plant growth promotion and the potential mechanism to further guide the use of microbial resources to promote the ecological cultivation and sustainable development of MPs.

Diversity in rhizospheric microbial communities in tea varieties at different locations and tapping potential beneficial microorganisms

Soil microenvironments and plant varieties could largely affect rhizosphere microbial community structure and functions. However, their specific effects on the tea rhizosphere microbial community are yet not clear. Beneficial microorganisms are important groups of microbial communities that hold ecological functionalities by playing critical roles in plant disease resistance, and environmental stress tolerance. Longjing43 and Zhongcha108 are two widely planted tea varieties in China. Although Zhongcha108 shows higher disease resistance than Longjing43, the potential role of beneficial tea rhizosphere microbes in disease resistance is largely unknown. In this study, the structure and function of rhizosphere microbial communities of these two tea varieties were compared by using the Illumina MiSeq sequencing (16S rRNA gene and ITS) technologies. Rhizosphere soil was collected from four independent tea gardens distributed at two locations in Hangzhou and Shengzhou cities in eastern China, Longjing43 and Zhongcha108 are planted at both locations in separate gardens. Significant differences in soil physicochemical properties as demonstrated by ANOVA and PCA, and distinct rhizosphere microbial communities by multiple-biotech analyses (PCoA, LEfSe, Co-occurrence network analyses) between both locations and tea varieties (p < 0.01) were found. Functions of bacteria were annotated by the FAPROTAX database, and a higher abundance of Nitrososphaeraceae relating to soil ecological function was found in rhizosphere soil in Hangzhou. LDA effect size showed that the abundance of arbuscular mycorrhizal fungi (AMF) was higher in Zhongcha108 than that in Longjing43. Field experiments further confirmed that the colonization rate of AMF was higher in Zhongcha108. This finding testified that AMF could be the major beneficial tea rhizosphere microbes that potentially function in enhanced disease resistance. Overall, our results confirmed that locations affected the microbial community greater than that of tea varieties, and fungi might be more sensitive to the change in microenvironments. Furthermore, we found several beneficial microorganisms, which are of great significance in improving the ecological environment of tea gardens and the disease resistance of tea plants. These beneficial microbial communities may also help to further reveal the mechanism of disease resistance in tea and potentially be useful for mitigating climate change-associated challenges to tea gardens in the future.

Responsive change of crop-specific soil bacterial community to cadmium in farmlands surrounding mine area of Southeast China

In arable soils co-influenced by mining and farming, soil bacteria significantly affect metal (Cadmium, Cd) bioavailability and accumulation. To reveal the soil microecology response under this co-influence, three intersection areas (cornfield, vegetable field, and paddy field) were investigated. With a similar nutrient condition, the soils showed varied Cd levels (0.31-7.70 mg/kg), which was negatively related to the distance from mining water flow. Different soils showed varied microbial community structures, which were dominated by Chloroflexi (19.64-24.82%), Actinobacteria (15.49-31.96%), Acidobacteriota (9.46-20.31%), and Proteobacteria (11.88-14.57%) phyla. A strong correlation was observed between functional microbial taxon (e. g. Acidobacteriota), soil physicochemical properties, and Cd contents. The relative abundance of tolerant bacteria including Vicinamibacteraceae, Knoellia, Ardenticatenales, Lysobacter, etc. elevated with the increase of Cd, which contributed to the enrichment of heavy metal resistance genes (HRGs) and integration genes (intlI), thus enhancing the resistance to heavy metal pollution. Cd content rather than crop species was identified as the dominant factor that influenced the bacterial community. Nevertheless, the peculiar agrotype of the paddy field contributed to its higher HRGs and intlI abundance. These results provided fundamental information about the crop-specific physiochemical-bacterial interaction, which was helpful to evaluate agricultural environmental risk around the intersection of farmland and pollution sources.

Differential response of bacterial diversity and community composition to different tree ages of pomelo under red and paddy soils

Rhizosphere soil microbial communities substantially impact plant growth by regulating the nutrient cycle. However, dynamic changes in soil microbiota under different tree ages have received little attention. In this study, changes in soil physicochemical properties, as well as bacterial diversity and community structures (by high-throughput Illumina MiSeq sequencing), were explored in pomelo trees of different ages (i.e., 10, 20, and 30 years) under red and paddy soils cultivated by farmers with high fertilizer input. Moreover, soil factors that shape the bacterial community, such as soil pH, AP (available phosphorous), AK (available potassium), and AN (available nitrogen), were also investigated. Results showed that pH significantly decreased, while AP, AK, and AN increased with increasing tree age under red soil. For paddy soil, pH was not changed, while AP was significantly lower under 10-year-old pomelo trees, and AK and AN contents were minimum under 30-year-old pomelo trees. Both soil types were dominated by Proteobacteria, Acidobacteria, and Actinobacteria and showed contrasting patterns of relative abundance under different tree age groups. Bacterial richness and diversity decreased with increasing tree age in both soil types. Overall, bacterial community composition was different under different tree ages. RDA analysis showed that soil pH, AP, and AN in red soil, and pH and AP in paddy soil showed the most significant effects in changing the bacterial community structure. A random forest model showed Sinomonas and Streptacidiphilus in red soil, while Actinoallomurus and Microbacterium in paddy soil were the most important genera explaining the differences among different age groups. The ternary plot further revealed that genera enrichment for Age_30 was higher than that for Age_10 and Age_20 in red soil, whereas specific genera enrichment decreased with increasing tree age under paddy soil. Co-occurrence network revealed that bacterial species formed a complex network structure with increasing tree age, indicating a more stable microbial association under 20 and 30 years than 10-year-old pomelo trees. Hence, contrasting patterns of changes in soil physicochemical properties and soil microbial communities were recorded under different tree ages, and tree ages significantly affected the bacterial community structure and richness. These findings provide valuable information regarding the importance of microbes for the sustainable management of pomelo orchards by optimizing fertilizer input for different ages of trees.

The Application of Mixed Organic and Inorganic Fertilizers Drives Soil Nutrient and Bacterial Community Changes in Teak Plantations

Appropriate fertilization can enhance forest productivity by maintaining soil fertility and improving the structure of the bacterial community. However, there is still uncertainty surrounding the effects of combined application of organic and inorganic fertilizers on soil nutrient status and bacterial community structure. A fertilization experiment was set up in an eight-year-old teak plantation with five treatments involved: mixed organic and NPK compound fertilizers (OCF), mixed organic and phosphorus fertilizers (OPF), mixed organic, NPK and phosphorus fertilizers (OCPF), mixed NPK and phosphorus fertilizers (CPF) and no fertilization (CK). Soil chemical properties and bacterial communities were investigated, and the co-occurrence pattern of the bacterial community under different fertilization treatments was compared. The results showed that the contents of soil organic matter and nitrate nitrogen, and the soil pH values were the highest after OCPF treatment, which were 20.39%, 90.91% and 8.16% higher than CK, respectively. The richness and diversity of bacteria underwent no obvious changes, but the structure of the soil’s bacterial community was significantly altered by fertilization. Of the dominant bacteria taxa, the relative abundance increased for Gemmatimonadetes, Myxococcota, ADurb.Bin063-13 and Candidatus_Koribacter, and decreased for Chloroflexi, Proteobacteria, JG30-KF-AS9 and Acidothermus under OCPF treatment in comparison to CK. The number of nodes and edges, the average degree and the network density of bacterial community co-occurrence networks were the greatest in OCPF treatment, indicating that application of OCPF could make the network structure of soil bacteria more stable and complex. Moreover, soil pH and organic matter were significantly correlated with bacterial community structure and were considered the main influencing factors. These findings highlight that the combined application of organic, NPK and phosphorus fertilizers is highly beneficial for improving soil quality and optimizing bacterial community structure in teak plantations.