Rhizosphere Soil Bacterial Communities Research Articles

Effects of soil microbial ecology on ginsenoside accumulation in Panax ginseng across different cultivation years

The quality of ginseng is greatly influenced by ecological factors, especially soil factors. However, there are few reports on the association between the physicochemical properties of ginseng rhizosphere soil, enzyme activity, microbial bacterial community, and ginsenoside content accumulation in ginseng planted at different ages. In order to investigate the relationship between the soil microbial ecology of ginseng and the content of ginsenosides, this study compared the differences in the rhizosphere soil microecological environment and ginsenoside accumulation between ginseng planted for one, two, and three years, using soil without ginseng cultivation as a control. The results showed that monomer saponins Ro, Re, Rf, Rb1, and total ginsenoside content increased significantly (P < 0.05), while monomer saponins Rb2, Rd, Rh2, and Rg3 content decreased significantly in three-year-old ginseng, (P < 0.05). And soil pH, soil bulk weight and soil enzyme activity in ginseng rhizosphere soils altered the abundance and diversity of rhizosphere soil bacterial community. Redundancy analysis and Pearson correlation analysis revealed that soil pH, soil bulk density, soil urease, and protease were the primary factors influencing the bacterial community in the soil around roots of one, two, three years old ginseng. Co-occurrence network visualization analysis indicated that seven bacterial communities, Planctomycetota, Methylomirabilota, Verrucomicrobiota and Acidobacteriota at the phylum level, Vicinamibacterales_unclassified, Vicinamibacteraceae_unclassified and Candidatus_Udaeobacter at the genus level, had a significant effect on the synthesis of ginsenosides. In summary, soil urease, pH, and soil bulk density in agricultural soils can regulate soil physicochemical properties, soil enzymatic activities, and soil bacterial community abundance. These factors are key drivers of the ginseng soil microbial ecology in ginseng cultivation. These studies will provide a scientific basis for subsequent optimization of soil improvement techniques for cultivated ginseng in farmland by improving the soil microbial ecology.

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.

Phthalate ester (PAEs) accumulation in wheat tissues and dynamic changes of rhizosphere microorganisms in the field with plastic-film residue

Phthalates acid esters (PAEs) have accumulated in soil and crops like wheat as a result of the widespread usage of plastic films. It is yet unclear, nevertheless, how these dynamic variations in PAE accumulation in wheat tissues relate to rhizosphere bacteria in the field. In this work, a field root-bag experiment was conducted to examine the changes of PAEs accumulation in the rhizosphere soil and wheat tissues under film residue conditions at four different growth stages of wheat, and to clarify the roles played by the microbial community in the alterations. Results showed that the plastic film residues significantly increased the concentrations of PAEs in soils, wheat roots, straw and grains. The maximum ΣPAEs concentration in soils and different wheat tissues appeared at the maturity, with the ΣPAEs concentration of 1.57 mg kg−1, 4.77 mg kg−1, 5.21 mg kg−1, 1.81 mg kg−1 for rhizosphere soils, wheat roots, straw and grains, respectively. The plastic film residues significantly changed the functions and components of the bacterial community, increased the stochastic processes of the bacterial community assembly, and reduced the complexity and stability of the bacterial network. In addition, the present study identified some bacteria associated with plastic film residues and PAEs degradation in key-stone taxa, and their relative abundances were positive related to the ΣPAEs concentration in soils. The PAEs content and key-stone taxa in rhizosphere soil play a crucial role in the formation of rhizosphere soil bacterial communities. This field study provides valuable information for better understanding the role of microorganisms in the complex system consisting of film residue, soil and crops.

Diversity and growth-promoting characteristics of rhizosphere bacteria of three naturally growing plants at the sand iron ore restoration area in Qinghe County

It is a great challenge to restore northern mines after mining and achieve optimal results due to the extremely harsh environment and climate, as in Qinghe County of Xinjiang Province, China. Qinghe County has a climate of drought, cold, strong winds, and high altitude. After sand and iron mining, the soil in this area contains a large amount of sand and gravel with extremely low organic matter, nitrogen deficiency, and a high pH of 9.26. Our preliminary studies disclosed that only three plants, including Caligonum junceum, Atraphaxis virgata, and Melilotus albus Medic, can grow naturally in this environment without any artificial management. For effective ecology restoration, this study explored the mechanism of plant-microbial interaction and stress resistance in this environment. It was found that although the soil condition in the sand iron ore landfill area is extreme, the bacterial diversity remained high, with Shannon and Simpson indices reaching 9.135 and 0.994, respectively. The planting of three types of remediation plants did not significantly improve, or even decreased, the soil bacterial diversity index, but greatly changed the composition of dominant bacterial genera. Significant differences in the composition of rhizosphere soil bacterial communities among these three remediation plants were observed. Potential new bacterial species accounted for 9.8 %, and the proportion of unique genera reached 30 % or 50 %, respectively. Among all the isolated strains, 74 % had nitrogen fixation and other growth-promoting properties. In summary, the soil microbial community structure in this extreme environment is unique and diverse. The types of remediation plants play a major role in the composition of the rhizosphere bacterial community structure, and the recruited growth-promoting bacteria are diverse and functional. This study may offer valuable information for further studies in vegetation restoration and aid in ecology restoration, especially under extreme conditions.

Impacts of AlaAT3 transgenic poplar on rhizosphere soil chemical properties, enzyme activity, bacterial community, and metabolites under two nitrogen conditions

ABSTRACT Poplar stands as one of the primary afforestation trees globally. We successfully generated transgenic poplar trees characterized by enhanced biomass under identical nutrient conditions, through the overexpression of the pivotal nitrogen assimilation gene, pxAlaAT3. An environmental risk assessment was conducted for investigate the potential changes in rhizosphere soil associated with these overexpressing lines (OL). The results show that acid phosphatase activity was significantly altered under ammonium in OL compared to the wild-type control (WT), and a similar difference was observed for protease under nitrate. 16SrDNA sequencing indicated no significant divergence in rhizosphere soil microbial community diversity between WT and OL. Metabolomics analysis revealed that the OL caused minimal alterations in the metabolites of the rhizosphere soil, posing no potential harm to the environment. With these findings in mind, we anticipate that overexpressed plants will not adversely impact the surrounding soil environment.

Microbial Diversity and Functional Profiles of Three Commercial Biofertilizers and Impacts on the Bacterial Communities of Avocado’s Soil Rhizosphere

Chilean avocado (Persea americana Mill.) exports have accounted for 60 % of the total production and are recognized for their high quality worldwide. However, avocado production has significantly decreased in recent years, which is mainly attributed to abiotic and biotic factors, among which are high and low temperatures, intense and sudden rains, unavailability of water resources, and agricultural salinity. Secondary factors include pests and diseases. Applying plant growth promoting microorganisms (PGPM)-based commercial biofertilizers is a potential practice to increase avocado production and resistance to edaphoclimatic factors. In this study, to determine the functionality of microbial communities present in three commercial biofertilizers (Biofert A, Biofert B, and Biofert C) and thus offer a structure of associated microbial communities, the rhizospheric soil of avocado was analysed using the Biolog EcoPlate™ technique, providing information on the community level physiologic profiles (CLPP) and biodiversity indices by denaturing gradient gel electrophoresis (DGGE). The findings revealed that the microbial diversity in the three commercial biofertilizers is highly different, showing a SIMPER overall dissimilarity of 83.9 % in the catabolic capacity. Concerning the impact on avocados’ rhizosphere soil bacterial communities, the results demonstrated significant changes in their composition, particularly with Biofert A and C. In contrast, Biofert B did not show significant changes, especially on days 15 and 30. Long-term studies are recommended to develop sustainable agricultural practices for Chilean avocados.

Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil.

Antibiotic contamination in soil has become a major concern worldwide. At present, it is not clear how two co-existed antibiotics with environmentally relevant concentrations would affect soil bacterial community structure, the abundances of antibiotic resistance genes (ARGs) and functional genes, and whether the effects of antibiotics would differ between rhizosphere and bulk soil. We conducted a greenhouse pot experiment to grow maize in a loess soil treated with oxytetracycline (OTC) or sulfadiazine (SDZ) or both at an environmentally relevant concentration (1 mg kg-1) to investigate the effects of OTC and SDZ on the rhizosphere and bulk soil bacterial communities, abundances of ARGs and carbon (C)-, nitrogen (N)-, and phosphorus (P)-cycling functional genes, and on plant growth and plant N and P nutrition. The results show that the effects of environmentally relevant concentrations of OTC and SDZ on bacterial communities and abundances of ARGs and functional genes differ between maize rhizosphere and bulk soil. The effects of two antibiotics resulted in a higher absolute abundances of accA, tet(34), tnpA-04, and sul2 in the rhizosphere soil than in the bulk soil and different bacterial community compositions and biomarkers in the rhizosphere soil and the bulk soil. However, OTC had a stronger inhibitory effect on the abundances of a few functional genes in the bulk soil than SDZ did, and their combination had no synergistic effect on plant growth, ARGs, and functional genes. The role of co-existed OTC and SDZ decreased shoot height and increased root N concentration. The results demonstrate that environmentally relevant concentrations of antibiotics shift soil microbial community structure, increase the abundances of ARGs, and reduce the abundances of functional genes. Furthermore, soil contamination with antibiotics can diminish agricultural production via phytotoxic effects on crops, and combined effects of antibiotics on plant growth and nutrient uptake should be considered.

Effects of intercropping teak with Alpinia katsumadai Hayata and Amomum longiligulare T.L. Wu on rhizosphere soil nutrients and bacterial community diversity, structure, and network.

Teak is a precious hardwood species in tropical and subtropical regions with a long growth cycle and slow economic returns. Intercropping medicinal plants is an effective method for obtaining early returns during the growth period of teak. However, currently, we lack sufficient knowledge about the impact of intercropping on the soil microenvironment, especially on rhizosphere soil bacterial communities. We selected two medicinal plants Alpinia katsumadai Hayata and Amomum longiligulare T.L. Wu, for an intercropping experiment with teak, and the non-intercropping teak forest area was used for comparison. By collecting soil rhizosphere samples and conducting 16S rDNA sequencing and property analysis, we aimed to investigate the influence of teak intercropping on soil microbial communities. The results showed that intercropping significantly improved soil nutrients contents, such as soil organic matter, soil total potassium and soil available nitrogen, and significantly altered bacterial community structure. Co-occurrence network analysis revealed that intercropping tightened the connections of the soil bacterial network and increased its complexity (by increasing the number of nodes and the proportion of positive edges). Teak intercropping with Amomum longiligulare T.L. Wu resulted in tighter network connections than teak intercropping with A. katsumadai Hayata. Changes in the soil bacterial community structure may related to environmental factors such as total potassium content and pH. These results demonstrated that the introduction of medicinal plants exerts a significant impact on the soil bacterial community of teak, fostering the enrichment of specific bacterial taxa (such as Firmicutes and Methylomirabilota), and makes the rhizosphere bacterial network denser and more complex. This study provides valuable insights for the management of teak plantations.

Biochar and nano-hydroxyapatite combined remediation of soil surrounding tailings area: Multi-metal(loid)s fixation and soybean rhizosphere soil microbial improvement

The soil near tailings areas is relatively barren and contaminated by multi-metal(loid)s, seriously threatening the safety of crop production. Here, biochar and nano-hydroxyapatite (nHAP) were combined to improve the sterilized and unsterilized polymetallic contaminated soil, and soil incubation and soybean pot experiments were designed. Results showed that biochar and nHAP not only increased soil C, N, and P but also effectively reduced multi-metal bioavailability, wherein the combined application of the two amendments had the best effect on metal immobilization. The synergistic effect of the two amendments decreased the acid-soluble contents of Co, Cu, Fe, and Pb in rhizosphere soils up to 86.75%, 80.69%, 89.09%, and 96.70%, respectively. The ameliorant reduced the accumulation of metal(loid)s in soybean plants, and rhizosphere microorganisms inhibited the migration of soil metals to plants. Additionally, biochar and nHAP regulated the rhizosphere soil microbial community. The rhizosphere soil of the sterilization group tended to prioritize the restoration of the original dominant bacteria. As, Pb, Fe, Urease, OM, TN, and TP were the critical environmental variables affecting rhizosphere soil bacterial communities. Therefore, combining biochar and nHAP is an environmentally friendly strategy to reduce polymetallic mobility in tailings soil and crops and improve soil microbial community structure.

Sesame bacterial wilt significantly alters rhizosphere soil bacterial community structure, function, and metabolites in continuous cropping systems

Bacterial wilt is the leading disease of sesame and alters the bacterial community composition, function, and metabolism of sesame rhizosphere soil. However, its pattern of change is unclear. Here, the purpose of this study was to investigate how these communities respond to three differing severities of bacterial wilt in mature continuously cropped sesame plants by metagenomic and metabolomic techniques, namely, absence (WH), moderate (WD5), and severe (WD9) wilt. The results indicated that bacterial wilt could significantly change the bacterial community structure in the rhizosphere soil of continuously cropped sesame plants. The biomarker species with significant differences will also change with increasing disease severity. In particular, the gene expression levels of Ralstonia solanacearum in the WD9 and WD5 treatments increased by 25.29% and 33.61%, respectively, compared to those in the WH treatment (4.35 log10 copies g-1). The occurrence of bacterial wilt significantly altered the functions of the bacterial community in rhizosphere soil. KEEG and CAZy functional annotations revealed that the number of significantly different functions in WH was greater than that in WD5 and WD9. Bacterial wilt significantly affected the relative content of metabolites, especially acids, in the rhizosphere soil, and compared with those in the rhizosphere soil from WH, 10 acids (including S-adenosylmethionine, N-acetylleucine, and desaminotyrosine, etc.) in the rhizosphere soil from WD5 or WD9 significantly increased. In comparison, the changes in the other 10 acids (including hypotaurine, erucic acid, and 6-hydroxynicotinic acid, etc.) were reversed. The occurrence of bacterial wilt also significantly inhibited metabolic pathways such as ABC transporter and amino acid biosynthesis pathways in rhizosphere soil and had a significant impact on two key enzymes (1.1.1.11 and 2.6.1.44). In conclusion, sesame bacterial wilt significantly alters the rhizosphere soil bacterial community structure, function, and metabolites. This study enhances the understanding of sesame bacterial wilt mechanisms and lays the groundwork for future prevention and control strategies against this disease.

Kitchen compost-derived humic acid application promotes ryegrass growth and enhances the accumulation of Cd: An analysis of the soil microenvironment and rhizosphere functional microbes

Phytoremediation is an environmentally friendly and safe approach for remediating environments contaminated with heavy metals. Humic acid (HA) has high biological activity and can effectively complex with heavy metals. However, whether HA affects available Cd storage and the Cd accumulation ability of plants by altering the soil microenvironment and the distribution of special functional microorganisms remains unclear. Here, we investigated the effects of applying kitchen compost-derived HA on the growth and Cd enrichment capacity of ryegrass (Lolium perenne L.). Additionally, the key role of HA in regulating the structure of rhizosphere soil bacterial communities was identified. HA promoted the growth of perennial ryegrass and biomass accumulation and enhanced the Cd enrichment capacity of ryegrass. The positive effect of HA on the soil microenvironment and rhizosphere bacterial community was the main factor promoting the growth of ryegrass, and this was confirmed by the significant positive correlation between the ryegrass growth index and the content of SOM, AP, AK, and AN, as well as the abundance of rhizosphere growth-promoting bacteria such as Pseudomonas, Steroidobacter, Phenylobacterium, and Caulobacter. HA passivated Cd and inhibited the translocation capacity of ryegrass. The auxiliary effect of resistant bacteria on plants drove the absorption of Cd by ryegrass. In addition, HA enhanced the remediation of Cd-contaminated soil by ryegrass under different Cd levels, which indicated that kitchen compost-derived HA could be widely used for the phytoremediation of Cd-contaminated soil. Generally, our findings will aid the development of improved approaches for the use of kitchen compost-derived HA for the remediation of Cd-contaminated soil.

Effects of Combined Stress of High Density Polyethylene Microplastics and Chlorimuron-ethyl on Soybean Growth and Rhizosphere Bacterial Community

With the vigorous development of agriculture in China， plastic mulch film and pesticides are widely used in agricultural production. However， the accumulation of microplastics （formed by the degradation of plastic mulch film） and pesticides in soil has also caused many environmental problems. At present， the environmental biological effects of microplastics or pesticides have been reported， but there are few studies on the combined effects on crop growth and the rhizosphere soil bacterial community. Therefore， in this study， the high density polyethylene microplastics （HDPE， 500 mesh） were designed to be co-treated with sulfonylurea herbicide chlorimuron-ethyl to study their effects on soybean growth. In addition， the effects of the combined stress of HDPE and chlorimuron-ethyl on soybean rhizosphere soil bacterial community diversity， structure composition， microbial community network， and soil function were investigated using high-throughput sequencing technology， interaction network， and PICRUSt2 function analysis to clarify the combined toxicity of HDPE and chlorimuron-ethyl to soybean. The results showed that the half-life of chlorimuron-ethyl in soil was prolonged by the 1% HDPE treatment （from 11.5 d to 14.3 d）， and the combined stress of HDPE and chlorimuron-ethyl had more obvious inhibition effects on soybean growth than that of the single pollutant or control. The HiSeq 2 500 sequencing showed that the rhizosphere bacterial community of soybean was composed of 20 phyla and 312 genera under combined stress， the number of phyla and genera was significantly less than that of the control and single pollutant treatment， and the relative abundances of bacteria with potential biological control and plant growth-promoting characteristics （such as Nocardioides and Sphingomonas） were reduced. Alpha diversity analysis showed that the combined stress significantly reduced the richness and diversity of the soybean rhizosphere bacterial community， and Beta diversity analysis showed that the combined stress significantly changed the structure of the bacterial community. The dominant flora of the rhizosphere bacterial community were regulated， and the abundances of secondary functional layers such as amino acid metabolism， energy metabolism， and lipid metabolism were reduced under combined stress by the analysis of LEfSe and PICRUSt2. It was inferred from the network analysis that the combined stress of HDPE and chlorimuron-ethyl reduced the total number of connections and network density of soil bacteria， simplified the network structure， and changed the important flora species to maintain the stability of the network. The results above indicated that the combined stress of HDPE and chlorimuron-ethyl significantly affected the growth of soybean and changed the rhizosphere bacterial community structure， soil function， and network structure. Compared with that of the single pollutant treatment， the potential risk of combined stress was greater. The results of this study can provide guidance for evaluating the ecological risks of polyethylene microplastics and chlorimuron-ethyl and for the remediation of contaminated soil.

Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China

Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.

Changes in rhizosphere soil bacterial, fungal, and protistan communities during tomato (Solanum lycopersicum) growth after reductive soil disinfestation

Changes in rhizosphere soil bacterial, fungal, and protistan communities during tomato (Solanum lycopersicum) growth after reductive soil disinfestation

Effects of Different Planting Years on Soil Physicochemical Indexes, Microbial Functional Diversity and Fruit Quality of Pear Trees

This study explores the interaction between pear fruit quality and the soil environment over four different planting years (5, 20, 30, and 40 years), focusing on the fruit’s chemical properties, rhizosphere soil properties, microbial communities, and both microbiomass and functional diversity. The results found that reducing sugar, sucrose, and vitamin C contents in pears initially increased with planting years before declining, while total acidity showed an inverse trend. Analysis of the soil physicochemical index revealed that rhizosphere soil physicochemical indexes were significantly different between different planting years, but there was no obvious regularity. Correlation analysis found that total phosphorus, total potassium, organic matter, and available nitrogen were significantly and positively correlated with pear quality indexes. Soil microbiomass carbon decreased before increasing with increasing planting year, while soil microbial nitrogen was irregular. Results of functional diversity of rhizosphere soil bacterial communities showed that the relationship of carbon source utilization among the six groups was 20 years &gt; 5 years &gt; 30 years &gt; 40 years. Interestingly, the 20-year group had the most core differences in microbial communities. The study suggests that as pear trees age, adequate plant nutrition during peak fruiting periods can improve soil fertility, microbial functional diversity, and ultimately enhance fruit quality.

Bacterial communities in the potato tuberosphere share similarities with bulk soil and rhizosphere communities, yet possess distinct features

To date, a paucity of studies have examined bacterial communities in tuberospheres. However, the function of these bacterial communities in healthy potato plants is still largely unknown. Here, we aimed to describe the structure and composition of tuberosphere bacteriomes and its capability to make organosulfur plant available using the rhizosphere and bulk soil bacterial community characteristics as a reference. Rhizosphere, tuberosphere and bulk soil was collected from two field grown potato varieties. Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Bacterial organosulfur mobilization indicators were evaluated with cultivation dependent and independent methods and were correlated (Spearman) with the relative abundance of bacterial families. The structure of tuberosphere bacterial communities either overlapped with the bulk soil or had similarities with the rhizosphere. Relative abundance of specific bacterial families were distinct between bulk soil, tuberosphere and rhizosphere. Tuberospheres had a tendency for higher arylsulfonate utilization compared to bulk soil. The families Sphingomonadaceae, Sphingobacteriaceae and Rhizobiaceae which presented a decline in their relative abundances from the rhizosphere to tuberosphere and bulk soil had positive correlations with organosulfur mobilizing indicators. Potato variety and soil characteristics played a role in structuring the tuberosphere bacterial communities. Tuberospheres represent an environment in-between bulk soil and rhizosphere indicative from the intermediate relative abundances of specific bacterial families. A moderately higher bacterial organosulfur mobilization activity in tuberospheres suggests that this microbial function may serve specific biological roles for potato tubers.

Interdomain ecological network analysis infers the endophytic bacteria protect against Fusarium root rot invasion

Fungi and bacteria coexist assembling complex communities in plant rhizosphere and endosphere that are important for plant health and agricultural productivity, however, the influence of root rot pathogen on bacterial-fungal interactions in plant ecological settings remains unclear. Here, bacterial communities from soil to endophyte of tobacco during Fusarium root rot invasion were comprehensively investigated. The bacterial community diversity and composition of stem endophytes were significantly altered by Fusarium root rot invasion. Molecular ecological network analysis revealed that the interactions among bacterial microbes in infected plant soils exhibit more intricate network structures compared to those found in healthy plants. The pathogens invasion led to changes in the crucial species within both the rhizosphere soil and plant endophytic bacterial communities. Furthermore, the interactions among fungal and bacterial species indicated that diseased samples, encompassing both the rhizosphere and endosphere, exhibited more complicated interdomain networks compared to their healthy counterparts. Importantly, the endophytic bacterial species Bacillus, Paenibacillus, Lactococcus, and two unclassified bacteria (OTU11999 and OTU730) from infected roots, and Bacillus, Raoultella, Leminorella, Pseudomonas, and three unclassified bacteria (OTU12058, OTU3 and OTU11435) from infected stems were negatively correlated with the pathogen Fusarium oxysporum f sp. psidii. It suggested that these endophytic bacteria may be associated with anantagonist effect and resistant against Fusarium root rot.

Soil plastisphere interferes with soil bacterial community and their functions in the rhizosphere of pepper (Capsicum annuum L.)

With a growing number of research reports on microplastics (MPs), there is increasing concern regarding MPs-induced contamination in soil ecological systems. Notwithstanding, the interaction between the plastisphere and rhizosphere microbial hotspots in soil-plant systems, as well as the diversity and composition of plastisphere microbial communities in such systems, remain largely unexplored. This study evaluated the response of rhizosphere bacterial communities to MPs at three growth stages of pepper and examined the bacterial communities present on MPs (plastisphere). The 16 S rRNA revealed that, under the stress of MPs, the Chao1 and Shannon index of the pepper soil bacterial community decreased. Meanwhile the relative abundance of Actinobacteriota was decreased, and that of Proteobacteria was increased. Furthermore, the plastisphere serves as a unique microbial habitat (niche) that recruits the colonization of specific bacterial groups, including potential plastic-degrading bacteria and potential pathogens (e.g., Massilia and Pseudomonas). Simultaneously, the plastisphere recruits specific bacteria that may impact the rhizosphere soil bacterial communities, thus indirectly affecting plant growth. Functional prediction using PICRUSt2 revealed higher activity in the plastisphere for Metabolism of terpenoids and polyketides, Human diseases, and Xenobiotics biodegradation and metabolism. Notably, the human diseases metabolic pathway exhibited increased activity, suggesting potential ecological risks associated with pathogens. These results highlighted that the plastisphere serves as a unique microbial habitat (niche) in the soil ecological systems, recruiting specific bacteria and potentially interfering with the surrounding soil microbial community, thereby influencing the functional characteristics of the soil ecological systems.

Differential Responses of Bacterial Communities in Rhizosphere and Bulk Soils of Cotton to Long-Term Amelioration Practices Based on Freezing Saline Water Irrigation and Plastic Mulching in a Coastal Saline Soil

Soil amelioration in coastal saline areas plays an important role in alleviating land resource shortages, improving regional ecological environments, ensuring food security, and promoting economic development. Plastic mulching (M) and the combination of freezing saline water irrigation and plastic mulching (WIM) are successful amelioration practices that dramatically reduce the salinity of surface soil and facilitate plant growth in coastal saline soil. However, the bacterial responses that are closely related to these amelioration practices in coastal saline soil remain poorly understood. In this study, bacterial richness and diversity, community composition, and potential ecological functions in the rhizosphere and bulk soils of cotton in M and WIM treatments, along with a control treatment, were investigated using high-throughput sequencing in a coastal saline field. The results showed that both the M and WIM treatments increased bacterial richness and alpha diversity, which were in general significantly higher in bulk soil than in rhizosphere soil. Non-metric multidimensional scaling and the Bray–Curtis dissimilarity analysis revealed that the bacterial community in rhizosphere soil was assembled far from those in the control and bulk soils and behaved more specifically in rhizosphere soil than in bulk soil. The relative abundances of most of the dominant phyla showed opposite trends of variation in bulk and rhizosphere soils compared to those in control soil in both M and WIM treatments; in particular, the specific bacterial groups of Proteobacteria and Actinobacteria decreased in bulk soil but significantly increased in rhizosphere soil. Functional groups of chemoheterotrophy, aerobic chemoheterotrophy, and nitrate reduction were predominant in rhizosphere rather than bulk soil, according to the Functional Annotation of Prokaryotic Taxa. These findings improve the understanding of the mechanism of bacterial responses to amelioration practices M and WIM in coastal saline soils and provide valuable information for the development of amelioration techniques based on agricultural practices and soil microbiome to enhance plants’ adaptability to saline soil in the future.

Root-knot nematode infections and soil characteristics significantly affected microbial community composition and assembly of tobacco soil microbiota: a large-scale comparison in tobacco-growing areas.

Tobacco root-knot nematode (RKN) is a highly destructive soil-borne disease worldwide. However, there is a lack of research on the relationship between RKN and tobacco root microbial community composition under large-scale geographical conditions in China. In this study, we collected 65 samples from 28 main tobacco-growing areas across 10 provinces in China and conducted 16S rDNA sequencing to investigate the dynamic microbial changes in tobacco soil infected by RKN compared to healthy tobacco soil. Based on the analysis of rhizosphere soil bacterial communities, changes after RKN infection, and soil environmental factors. We found the 28 tobacco-growing areas could be divided into two distinct groups with different microbial compositions and varying responses to RKN infection. In group1 of the provinces of Anhui, Henan, Shanxi, and Heilongjiang, Vicinamibacteria dominated the bacterial community, while Acidobacteriae was present in low abundance. In contrast, group2 of the other six provinces (Yunnan, Guizhou, Chongqing, Guangxi, Hubei, and Shandong) exhibited an opposite pattern. After infected by RKN, the genera Chitinophaga increased significant in group 1, while the genera Rhodococcus in group 2 exhibited a substantial increase. Alpha-diversity analysis revealed that RKN-infected tobacco exhibited a richer and more diverse rhizosphere soil bacterial community compared to healthy tobacco in most growing areas. A total of 12 kinds of soil environmental factors were measured in healthy and RKN-infected tobacco soil, and based on the co-occurrence and correlation analysis between environmental factors and microbial species, the pH level, calcium (Ca), magnesium (Mg), phosphorus (P), iron (Fe), and sodium (Na) were identified as key environmental factors influencing the population composition of rhizosphere microorganisms during RKN infection. We observed that RKN infection further increased the pH in weakly alkaline group 1 soil, while weakly acidic group 2 soil experienced a further decrease in pH. Furthermore, we identified three genera as potential biocontrol or plant growth-promoting bacteria for tobacco. These findings provide valuable reference data for managing RKN disease in different tobacco-growing areas and contribute to the exploration of new and effective biological control methods.