Relative Abundance Of Fusarium Research Articles

Assessing the biodiversity of rhizosphere and endophytic fungi in Knoxia valerianoides under continuous cropping conditions

BackgroundRhizosphere and endophytic fungi play important roles in plant health and crop productivity. However, their community dynamics during the continuous cropping of Knoxia valerianoides have rarely been reported. K. valerianoides is a perennial herb of the family Rubiaceae and has been used in herbal medicines for ages. Here, we used high-throughput sequencing technology Illumina MiSeq to study the structural and functional dynamics of the rhizosphere and endophytic fungi of K. valerianoides.ResultsThe findings indicate that continuous planting has led to an increase in the richness and diversity of rhizosphere fungi, while concomitantly resulting in a decrease in the richness and diversity of root fungi. The diversity of endophytic fungal communities in roots was lower than that of the rhizosphere fungi. Ascomycota and Basidiomycota were the dominant phyla detected during the continuous cropping of K. valerianoides. In addition, we found that root rot directly affected the structure and diversity of fungal communities in the rhizosphere and the roots of K. valerianoides. Consequently, both the rhizosphere and endophyte fungal communities of root rot-infected plants showed higher richness than the healthy plants. The relative abundance of Fusarium in two and three years old root rot-infected plants was significantly higher than the control, indicating that continuous planting negatively affected the health of K. valerianoides plants. Decision Curve Analysis showed that soil pH, organic matter (OM), available K, total K, soil sucrase (S_SC), soil catalase (S_CAT), and soil cellulase (S_CL) were significantly related (p < 0.05) to the fungal community dynamics.ConclusionsThe diversity of fungal species in the rhizosphere and root of K. valerianoides was reported for the first time. The fungal diversity of rhizosphere soil was higher than that of root endophytic fungi. The fungal diversity of root rot plants was higher than that of healthy plants. Soil pH, OM, available K, total K, S_CAT, S_SC, and S_CL were significantly related to the fungal diversity. The occurrence of root rot had an effect on the community structure and diversity of rhizosphere and root endophytic fungi.

The Combination of Biochar and Bacillus subtilis Biological Agent Reduced the Relative Abundance of Pathogenic Bacteria in the Rhizosphere Soil of Panax notoginseng.

In the continuous cropping of Panax notoginseng, the pathogenic fungi in the rhizosphere soil increased and infected the roots of Panax notoginseng, resulting in a decrease in yield. This is an urgent problem that needs to be solved in order to effectively overcome the obstacles associated with the continuous cropping of Panax notoginseng. Previous studies have shown that Bacillus subtilis inhibits pathogenic fungi in the rhizosphere of Panax notoginseng, but the inhibitory effect was not stable. Therefore, we hope to introduce biochar to help Bacillus subtilis colonize in soil. In the experiment, fields planted with Panax notoginseng for 5 years were renovated, and biochar was mixed in at the same time. The applied amount of biochar was set to four levels (B0, 10 kg·hm-2; B1, 80 kg·hm-2; B2, 110 kg·hm-2; B3, 140 kg·hm-2), and Bacillus subtilis biological agent was set to three levels (C1, 10 kg·hm-2; C2, 15 kg·hm-2; C3, 25 kg·hm-2). The full combination experiment and a blank control group (CK) were used. The experimental results show that the overall Ascomycota decreased by 0.86%~65.68% at the phylum level. Basidiomycota increased by -73.81%~138.47%, and Mortierellomycota increased by -51.27%~403.20%. At the genus level, Mortierella increased by -10.29%~855.44%, Fusarium decreased by 35.02%~86.79%, and Ilyonectria increased by -93.60%~680.62%. Fusarium mainly causes acute bacterial wilt root rot, while Ilyonectria mainly causes yellow rot. Under different treatments, the Shannon index increased by -6.77%~62.18%, the Chao1 index increased by -12.07%~95.77%, the Simpson index increased by -7.31%~14.98%, and the ACE index increased by -11.75%~96.12%. The good_coverage indices were all above 0.99. The results of a random forest analysis indicated that Ilyonectria, Pyrenochaeta, and Xenopolyscytalum were the top three most important species in the soil, with MeanDecreaseGini values of 2.70, 2.50, and 2.45, respectively. Fusarium, the primary pathogen of Panax notoginseng, ranked fifth, and its MeanDecreaseGini value was 2.28. The experimental results showed that the B2C2 treatment had the best inhibitory effect on Fusarium, and the relative abundance of Fusarium in Panax notoginseng rhizosphere soil decreased by 86.79% under B2C2 treatment; the B1C2 treatment had the best inhibitory effect on Ilyonectria, and the relative abundance of Ilyonectria in the Panax notoginseng rhizosphere soil decreased by 93.60% under B1C2 treatment. Therefore, if we want to improve the soil with acute Ralstonia solanacearum root rot, we should use the B2C2 treatment to improve the soil environment; if we want to improve the soil with yellow rot disease, we should use the B1C2 treatment to improve the soil environment.

Response of the rhizosphere soil microbial diversity to different nitrogen and phosphorus application rates in a hulless barley and pea mixed-cropping system

The mixed-cropping mode of hulless barley (Hordeum vulgare L) and peas (Pisum sativum L) can optimize the planting system, effectively enhancing crop nitrogen and phosphorus utilization and increasing yield. This mode has been widely applied in Qinghai Province, China. In this study, a split-plot experimental design was employed to investigate the bacterial and fungal communities in the rhizosphere soil of monocropping and mixed-cropping treatments under different fertilization levels. The Illumina MiSeq sequencing technology was used for the research, and the physicochemical properties of the soil were measured. The results indicated that with the increase in the application of nitrogen and phosphorus, the bacterial α-diversity in the rhizosphere of the mixed-cropping system initially increased and then decreased after reaching a peak. The α-diversity index of soil bacteria was higher under the mixed-cropping mode than under the monocropping mode. For the rhizosphere soil fungi in the mixed-cropping system, the Shannon index initially increased and then decreased, while the Chao1 and ACE indices decreased initially and then increased. Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Sphingomonas, and Pseudomonas comprised the predominant bacterial genera in the rhizosphere soil of the hulless barley–pea intercropping treatment, whereas Fusarium, Metarhizium, and Cladosporium dominated among the fungal genera across the 12 treatments. Under the same fertilization levels, the relative abundances of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium in the rhizosphere soil of the mixed-cropping treatment increased by 8.4 %, 7.1 %, 5.7 %, and 5.6 %, respectively, compared to the monoculture of hulless barley, with a decreasing trend as nitrogen and phosphorus levels increased. Compared to the monoculture of hulless barley, the relative abundance of Fusarium in the mixed-cropping treatment decreased by 37.3 %, 43.8 %, 56.8 %, and 40.3 %, respectively. Redundancy and correlation analyses suggested that the variation in bacterial and fungal diversity and community composition in the mixed-cropping zone due to the interaction between hulless barley and peas under different nitrogen and phosphorus fertilizer application levels was significantly correlated with changes in soil organic matter, available phosphorus, and alkaline hydrolyzable nitrogen.

Fusarium Wilt Invasion Results in a Strong Impact on Strawberry Microbiomes.

Plant-endophytic microbes affect plant growth, development, nutrition, and resistance to pathogens. However, how endophytic microbial communities change in different strawberry plant compartments after Fusarium pathogen infection has remained elusive. In this study, 16S and internal transcribed spacer rRNA amplicon sequencing were used to systematically investigate changes in the bacterial and fungal diversity and composition in the endophytic compartments (roots, stems, and leaves) of healthy strawberries and strawberries with Fusarium wilt, respectively. The analysis of the diversity, structure, and composition of the bacterial and fungal communities revealed a strong effect of pathogen invasion on the endophytic communities. The bacterial and fungal community diversity was lower in the Fusarium-infected endophytic compartments than in the healthy samples. The relative abundance of certain bacterial and fungal genera also changed after Fusarium wilt infection. The relative abundance of the beneficial bacterial genera Bacillus, Bradyrhizobium, Methylophilus, Sphingobium, Lactobacillus, and Streptomyces, as well as fungal genera Acremonium, Penicillium, Talaromyces, and Trichoderma, were higher in the healthy samples than in the Fusarium wilt samples. The relative abundance of Fusarium in the infected samples was significantly higher than that in the healthy samples, consistent with the field observations and culture isolation results for strawberry wilt. Our findings provide a theoretical basis for the isolation, identification, and control of strawberry wilt disease.

Impact of Bacillus subtilis and Pseudomonas fluorescens beneficial bacterial agents on soil-borne diseases, growth, and economics of continuous cropping of flue-cured tobacco

Employing beneficial bacteria as fungicides is an effective strategy for improving crop and soil health. Despite its effectiveness, the investigation of appropriate beneficial bacterial candidates for tackling the challenges posed by the continuous cropping of field tobacco remains a neglected area. This study addressed this gap by conducting field experiments at two distinct sites to ascertain the effects of introducing beneficial bacterial agents (CK, devoid of bacterial agent; B, Bacillus subtilis agent; P, Pseudomonas fluorescens agent; and a mixture of both bacterial agents [B + P]) on soil-borne pathogen abundance, disease occurrence, and economic effects in the context of the continuous cropping of flue-cured tobacco. The results revealed that the application of bacterial agents (B, P, and B + P) contributed to varying degrees of reduction in the relative abundance of Fusarium spp. within the continuous cropping flue-cured tobacco soil, while enhancing the abundance of Bacillus spp. and Pseudomonas spp. Notably, the B + P treatment demonstrated a superior performance. In terms of disease management, B + P treatment significantly inhibited the incidence of black shank disease and root black rot disease by over 50.0%, with a significant reduction in severity exceeding 34.3%. The relative control effects reached 48.7%–66.7% and 39.1%–63.2%, respectively. In addition, the mixed application of bacterial agent (B + P) exerted a substantial positive influence on various agronomic attributes of flue-cured tobacco, such as leaf dimensions, leaf count, and dry matter accumulation. Chemical component contents and economic parameters, such as yield, high-quality tobacco leaf proportion, and medium-to high-quality tobacco leaf proportion, also demonstrated excellent enhancement. This comprehensive improvement ultimately achieved disease mitigation and increased yield. Overall, the integration of B. subtilis and P. fluorescens can improve soil health and promote crop growth. The mixed application strategy (B + P) is an effective approach for mitigating soil-borne diseases, augmenting yields, and elevating economic returns.

Biochar preparation and its effects with reduced compound fertilizer on nutrients, phenolic acid and fungal community in tobacco rhizosphere soil

Biochar is a carbon-rich soil conditioner produced from pyrolysis of biomass, it has been widely used to enhance soil quality because of its physical adsorption as well as water and fertilizer conservation functions. This work aimed to improve the soil quality of continuously cropped flue-cured tobacco fields using biochar prepared from agricultural waste. To explore the impact of reduced compound fertilizer with biochar application on nutrients, phenolic acid contents and fungi diversity in the rhizosphere soil, 4 treatments were set: regular compound fertilizer application (T1), and biochar with reduced compound fertilizer in different proportions (T2, T3, T4, with 100, 75, 50% of compound fertilizer, respectively). The physicochemical properties of the prepared biochar were characterized and observed using electron microscopy. The results indicated that, a noticeable increase in the content of soil organic matter (SOM) and soil organic carbon (SOC) in T2 treatment compared to T1 treatment. Moreover, T2 treatment demonstrated a significant improvement in the contents of alkali-hydrolyzable nitrogen (AN), available phosphorus (AP), and available potassium (AK), with increases of 9.29%, 15.85% and 25.42% compared to T1 treatment, respectively. While a gradual decrease in soil AN, AP, and AK content was observed with the reduction of compound fertilizer application (T2–T4), there was no obvious difference between T3 and T1. For total phenolic acid, the content in T2 treatment significantly decreased by 35.99% compared to T1 treatment, while T3 and T4 treatments showed significant reductions of 15.30 and 18.73% respectively, compared to T2 treatment. Biochar application could enhance the fungal community’s abundance and diversity in the rhizosphere soil. Fungal community exhibited the highest richness under T3 treatment, while the relative abundance ofFusariumandMortierellareduced as the decrease of compound fertilizer (T2–T4). In conclusion, the reduced compound fertilizer with biochar application could reduce nutrient loss, phenolic acids accumulation, and improving the abundance of fungal community in the rhizosphere soil. This paper provides a reference for biochar combined with compound fertilizer to improve soil from the regulation of allelochemicals and soil fungi.

A Meta-Analysis in Nine Different Continuous Cropping Fields to Find the Relationship between Plant Species and Rhizosphere Fungal Community

Plant species and cropping systems influence rhizospheric fungal communities’ composition, diversity, and structure. The fungus community is one of the main factors behind soil health and quality. Yet, there is insufficient evidence and research on the effect of plant species with continuous cropping histories on the rhizospheric fungal community. In order to investigate how the fungal community responds to the various plant species and cropping systems, we have chosen one field that is left fallow along with eight continuously farmed areas to research. Among the eight phyla, the relative abundance of Ascomycota was significantly higher in Polygonum multiflorum, which was continuously cropped in fields for two years (P2). Basidiomycota was considerably higher in the fallow field (CK). Among the 1063 genera, the relative abundance of Fusarium was significantly higher in maize continuous-cropped fields for six years (M6), followed by Fritillaria thunbergii continuous-cropped fields for two years (F2), and found lower Fusarium abundance in CK. The alpha diversity observed in taxa, Chao1, and phylogenetic diversity indices were significantly higher in M2. β-diversity found that the fungal communities in the samples clustered from the fields in the same year were quite similar. In all the soil samples, the saprotrophic trophic type was the most common among the OTUs that had been given a function. Our studies have proved that continuous cropping and plant species changed the fungal community’s composition, diversity, and structure. This research may serve as a guide for overcoming significant agricultural challenges and advancing the industry’s sustainable growth.

Identification and characterization of pathogens causing saffron corm rot in China.

Corm rot is the most important disease of saffron, for which fungi from several genus such as Fusarium spp. Penicillium spp. and Botrytis spp., have been previously reported to be the pathogens. In this research, we used a combination of amplicon sequencing and traditional isolation methods to identify the causal agents, main infection source. The diversity of microbial communities in diseased saffron corms and soil decreased significantly compared with healthy corms and soil. The contents of Penicillium and Botrytis in healthy and diseased corms were similarly high, indicating that them were not directly related to the occurrence of corm rot. But the relative abundance of Fusarium, Cadophora and Fusicolla were significantly higher in the diseased corms than healthy ones. The abundance of Fusarium increased, while the abundance of Oidiodendron, Paraphaeosphaeria and the endophytic beneficial bacteria Pseudomonas decreased, which may relate to the occurrence of the disease. The co-occurrence network diagram showed that the correlation between fungal and bacterial communities was mainly positive. Plant pathogens were relatively abundant in the diseased soil, according to functional gene prediction. At the same time, we also collected 100 diseased corms from the fields in Jiande, where is known as the "hometown of saffron." All isolated pathogenic strains were identified as Fusarium oxysporum through morphological observation and phylogenetic tree analysis of ITS, Tef-1α and β-tubulin. To better clarify the biological characteristics of F. oxysporum, we cultured the isolates at different temperatures and pH values. The optimum temperature for mycelial growth and sporulation was 25°C, pH 6，carbon sources sorbitol and nitrogen sources, peptone. In short, our results suggests that F. oxysporum was the pathogen causing corm rot in Jiande and corms other than soils are the main primary infection source. These new understanding of saffron corm rot will provide the theoretical basis for its better and efficiently management.

Fungal gut microbiota dysbiosis in systemic lupus erythematosus.

Despite recent developments in our comprehension of how the gut microbiota and systemic lupus erythematosus (SLE) are related. The mycobiome: which is a small but crucial part of the gut microbiota and is involved in hosts' homeostasis and physiological processes, remained unexplored in SLE. We profiled the gut fungal mycobiota based on internal transcribed spacer region 1 (ITS1) sequencing for the gut microbial DNA from the SLE individuals with lupus nephritis (LN) (n = 23), SLE without LN (n = 26) and healthy controls (n = 14) enrolled in Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School. The ITS sequencing generated a total of 4.63 million valid tags which were stratified into 4,488 operational taxonomic units (OTUs) and identified about 13 phyla and 262 genera. Patients with SLE were characterized with unique fungal flora feature. The fungal microbiomes of the three groups displayed distinct beta diversity from each other. Compared with HC group, the abundance of fungal dysbiosis was reflected in a higher ratio of opportunistic fungi in SLE or LN group, as well as the loss of Rhizopus and Malassezia. The main principal components of the flora between the SLE and LN group were generally consistent. The relative abundance of Vanrija in the fecal fungal community was higher in LN group, while the relative abundance of Fusarium was higher in SLE group. Moreover, our data revealed superior diagnostic accuracy for SLE with the fungal species (e.g. Candida, Meyerozyma). Correlations between gut fungi and clinical parameters were identified by Spearman's correlation analysis. Interestingly, Aspergillus in SLE patients was positively correlated with ACR, 24 h proteinuria, proteinuria, anti-dsDNA, ANA, and SLEDAI, while Rhizopus was negatively correlated with lymphocytes and Hb. Finally, we successfully cultured the fungi and identified it as Candida glabrata by microscopic observation and mass spectrometry. We first explored the highly significant gut fungal dysbiosis and ecology in patients with SLE, and demonstrated the applicability of fungal species as SLE diagnostic tools, signifying that the gut fungal mycobiome-host interplay can potentially contribute in disease pathogenesis.

Biocontrol mechanisms of Bacillus velezensis against Fusarium oxysporum from Panax ginseng

Root rot caused by Fusarium oxysporum severely reduces ginseng root yield and quality, leading to large economic losses. Biological control has attracted extensive attention because it is safe, environmentally friendly, and sustainable. Screening for biocontrol strains to suppress soil-borne diseases is important for improving ginseng quality. A Bacillus velezensis strain was isolated from the forest rhizosphere of Pinus sylvestris could inhibited F. oxysporum in ginseng. To explore the strain’s biocontrol effects and mechanism of action against F. oxysporum, four treatments were established in pot experiments: no inoculation (CK), F. oxysporum inoculation (F), B. velezensis YW 17 (B), and mixed inoculation of B. velezensis and F. oxysporum (BF). After 4 months of cultivation, the ginseng plants in the F treatment grew more slowly, and the withering degree was most serious among all the treatments. The results from high-throughput sequencing showed that the relative abundance of Fusarium in the roots of the BF treatment was significantly lower than that of the F treatment. B. velezensis inoculation improved the relative abundance of other beneficial microorganisms in the ginseng rhizosphere, such as Arthrobacter and Mortierella. The experimental results indicated that YW17 had strong abilities to produce biofilms and IAA, and could colonize roots. The whole genome sequencing results showed that some genes (trpA-C, gatA) were involved in the synthesis of the plant growth-promoting hormone IAA and other genes (efp, hfq, epsA-O, spo0A, sinI/sinR, lysC, yjbB, flgK, fliD, srfABC) were involved in biofilm formation and root colonization. The results of whole genome sequencing showed that there are 18 gene clusters related to the synthesis of secondary metabolite with antifungal activities. In addition, some genes involved in the biosynthetic pathway of acetoin, such as ilvB and alsD, were also found. Based on the above results, we infer that B. velezensis YW17 could inhibit pathogenic F. oxysporum by secreting antifungal lipopeptides, proteins and volatile substances, thereby indirectly protecting ginseng from pathogenic fungal infections. These results indicated that B. velezensis could control ginseng root rot indirectly by regulating the root and rhizosphere microbial community structures and directly by secreting antifungal substances.

Diversity of Fungal Endophytes in American Ginseng Seeds.

Seeds play a critical role in the production of American ginseng. Seeds are also one of the most important media for the long-distant dissemination and the crucial way for pathogen survival. Figuring out the pathogens carried by seeds is the basis for effective management of seedborne diseases. In this paper, we tested the fungi carried by the seeds of American ginseng from the main production areas of China using incubation and highly throughput sequencing methods. The seed-carried rates of fungi in Liuba, Fusong, Rongcheng, and Wendeng were 100, 93.8, 75.2, and 45.7%, respectively. Sixty-seven fungal species, which belonged to 28 genera, were isolated from the seeds. Eleven pathogens were identified from the seed samples. Among the pathogens, Fusarium spp. were found in all of the seed samples. The relative abundance of Fusarium spp. in the kernel was higher than that in the shell. Alpha index showed that the fungal diversity between seed shell and kernel differed significantly. Nonmetric multidimensional scaling analysis revealed that the samples from different provinces and between seed shell and kernel were distinctly separated. The inhibition rates of four fungicides to seed-carried fungi of American ginseng were 71.83% for Tebuconazole SC, 46.67% for Azoxystrobin SC, 46.08% for Fludioxonil WP, and 11.11% for Phenamacril SC. Fludioxonil, a conventional seed treatment agent, showed a low inhibitory effect on seed-carried fungi of American ginseng.

Crop diversity promotes the recovery of fungal communities in saline-alkali areas of the Western Songnen Plain.

Phytoremediation is an effective strategy for saline land restoration. In the Western Songnen Plain, northeast China, soil fungal community recovery for saline phytoremediation has not been well documented among different cropping patterns. In this study, we tested how rotation, mixture, and monoculture cropping patterns impact fungal communities in saline-alkali soils to assess the variability between cropping patterns. The fungal communities of the soils of the different cropping types were determined using Illumina Miseq sequencing. Mixture and rotation promoted an increase in operational taxonomic unit (OTU) richness, and OTU richness in the mixture system decreased with increasing soil depth. A principal coordinate analysis (PCoA) showed that cropping patterns and soil depths influenced the structure of fungal communities, which may be due to the impact of soil chemistry. This was reflected by soil total nitrogen (TN) and electrical conductivity (EC) being the key factors driving OTU richness, while soil available potassium (AK) and total phosphorus (TP) were significantly correlated with the relative abundance of fungal dominant genus. The relative abundance of Leptosphaerulina, Alternaria, Myrothecium, Gibberella, and Tetracladium varied significantly between cropping patterns, and Leptosphaerulina was significantly associated with soil chemistry. Soil depth caused significant differences in the relative abundance of Fusarium in rotation and mixture soils, with Fusarium more commonly active at 0-15 cm deep soil. Null-model analysis revealed that the fungal community assembly of the mixture soils in 0-15 cm deep soil was dominated by deterministic processes, unlike the other two cropping patterns. Furthermore, fungal symbiotic networks were more complex in rotation and mixture than in monoculture soils, reflected in more nodes, more module hubs, and connectors. The fungal networks in rotation and mixture soils were more stable than in monoculture soils, and mixture networks were obviously more connected than rotations. FUNGuild showed that the relative proportion of saprotroph in rotation and mixture was significantly higher than that in monocultures. The highest proportion of pathotroph and symbiotroph was exhibited in rotation and mixture soils, respectively. Overall, mixture is superior to crop rotation and monocultures in restoring fungal communities of the saline-alkali soils of the Western Songnen Plain, northeast China.

Soybean continuous cropping affects yield by changing soil chemical properties and microbial community richness.

In agroecosystems, different cropping patterns cause changes in soil physicochemical properties and thus in microbial communities, which in turn affect crop yields. In this study, the yields of soybean continuous cropping for 5 years (C5), 10 years (C10), and 20 years (C20) and of soybean-corn rotational cropping (R) treatments were determined, and samples of the tillage layer soil were collected. High-throughput sequencing technology was used to analyze the diversity and composition of the soil bacterial and fungal communities. The factors influencing microbial communities, along with the effects of these communities and those of soil chemical indexes on yield, were further evaluated. The results showed that the community richness index of bacteria was higher in C20 than in R and that of fungi was highest in C5. The differences in the bacterial and fungal communities diversity indexes were not significant among the different continuous cropping treatments, respectively. The soil microbial community composition of all continuous cropping treatments differed significantly from R. The dominant bacterial phylum was Actinobacteriota and the dominant fungal phylum was Ascomycota. The relative abundance of Fusarium did not differ significantly among the continuous cropping treatments, while that of the plant pathogen fungi Lectera sp., Plectosphaerella sp., and Volutella sp. increased with continuous cropping years. Soil pH, SOM, N, and TP had significant effects on both bacterial and fungal communities, and TK and C/N had highly significant effects on fungal communities. The yield of C5 was significantly lower than that of R, and the differences in yield between C10, C20, and R were not significant. TN, TP, and pH had significant effects on yield, and fungal community abundance had a greater negative effect on yield than bacterial community abundance.

Mechanism underlying the response of fungi and their Fusarium symbiotic networks to the rotations of soybean and corn

Fusarium oxysporum and Fusarium solani are the main soybean root rot pathogens in northern China. We investigated the distribution and driving factors of Fusarium under different cropping systems to evaluate and regulate soil health. The factors affecting Fusarium in soybean cropping systems were assessed using high-throughput sequencing of ITS1 to identify soil microbial population diversity, and then the soil physicochemical properties were assessed to determine the levels of various elements present in the environment. According to the results, the abundance of Fusarium was obviously reduced in the corn–soybean rotation and uncultivated soil systems. The relative abundance of Fusarium in the soil and the abundance and diversity of fungal communities were significantly positively associated with the abundance of Ascomycota. Additionally, the relative abundance of Fusarium was significantly positively correlated with the zinc (Zn) content. When the Zn content was high, the abundance of Fusarium increased, and the correlations with Chaetomium, Cryptococcus, Penicillium and Trichoderma significantly decreased. Soybean yield was significantly negatively correlated with fungal community abundance and diversity. Based on our results, the uncultivated soil and corn–soybean rotation cropping systems improved the organizational structure of the soil fungal community and were conducive to the health and production of soybean.

Soil microbiome and metabolome analysis reveals beneficial effects of ginseng–celandine rotation on the rhizosphere soil of ginseng-used fields

Ginseng (Panax ginseng C.A.Meyer) cultivation is hindered by the continuous cropping obstacle, whereby without appropriate rotations yield decline and fields must be abandoned. Organism interactions in the rhizosphere alleviate and improve the obstacles to continuous cropping of ginseng. In this study, high-throughput sequencing and gas chromatography coupled with time-of-flight mass spectrometry (GC–TOF-MS) in combination with analysis of soil chemical properties were used to investigate soil microecological changes after 5 years of celandine (Chelidonium majus L.) cultivation in land previously planted with ginseng for 6 years. Comparison of data for the ginseng–celandine rotation (experimental group) and ginseng–fallow (control group) revealed that the celandine rhizosphere TOC, AN, and AK contents as well as PPO activity and Cat activity were significantly increased. Rotation increased the abundance of some bacteria and fungal in the rhizosphere of celandine rhizosphere soil, such as Arthrobacter, Metarhizium, and Exophiala. The relative abundance of Fusarium in ginseng–celandine rotation soil was lower than that of ginseng–fallow soil, which may effectively reduce the incidence of ginseng root rot. The non-targeted metabolites and microbial community structure of the rhizosphere soil were changed with celandine cultivation. In celandine rhizosphere soil, the abundance of the bacterial and fungal communities was positively or negatively correlated with rhizosphere soil metabolites. Pathway enrichment analysis showed that starch and sucrose metabolism were significantly enriched in the celandine rhizosphere soil, a result consistent with the results shown in bacterial community function prediction and non-targeted metabolomics. The present combined analysis of the soil microbiome and non-targeted metabolome provided insight into the effects and mechanism of ginseng–celandine rotation on the soil micro-ecosystem of ginseng-used fields. Briefly, crop rotation with celandine was beneficial to soil quality, and it is a good option to alleviate Ginseng continuous cropping obstacles.

Reductive soil disinfestation with biochar amendment modified microbial community composition in soils under plastic greenhouse vegetable production

Reductive soil disinfestation (RSD) and biochar amendment are considered sustainable management practices to improve degraded vegetable soil. However, the combined effects of these two remediation methods on soil microbial communities and vegetable yields remain unclear. In the present field study, the interactive impacts of conventional RSD treatment and biochar were tested in plastic greenhouse soils under a continuous vegetable cultivation system. Six treatments consisted of different management practices: soil untreated (CK), soil amended with biochar (BC), soil flooded (SF), soil flooded and mulched with plastic film (SFM), soil amended with alfalfa residue, flooded and mulched with plastic film (RSD), and soil amended with alfalfa residue plus biochar, flooded and mulched with plastic film (RSD+BC). Analysis of the soil samples collected at 0–20 cm for a range of physicochemical and microbial properties revealed that both RSD and RSD+BC treatments decreased soil nitrate (NO3-) concentrations while increasing soil pH, ammonium (NH4+), dissolved organic carbon (DOC), and the low-valent ion (Fe2+, Mn2+) concentrations (P < 0.05). Unlike the BC, SF and SFM treatments, the RSD and RSD+BC treatments decreased the bacterial and fungal diversity (P < 0.05) compared to the CK, and altered microbial community composition. The RSD treatment significantly reduced the relative abundance of genus Fusarium while increasing the relative abundances of genera Bacillus and Clostridium, and the increase was more evident in the RSD+BC treatment, suggesting the potential of the latter to suppress pathogenic fungi while increasing beneficial bacteria. The structural equation model revealed the key role of soil redox potential (Eh) and NH4+ concentration in the regulation of microbial community composition. Furthermore, BC, RSD, and RSD+BC treatments increased pepper yield by 27.4%, 55.3% and 44.4%, respectively, compared to CK. The yield of pepper was positively correlated with the contents of DOC, NH4+, and the relative abundance of Bacillus and Clostridium in soil (P < 0.01), and negatively correlated with NO3- and relative abundance of Fusarium (P < 0.05). This study provides evidence for the efficiency of the combined application of RSD and biochar to amend the quality of degraded soils in plastic sheds under continuous cultivation.

Effects of Trichoderma asperellum 6S-2 on Apple Tree Growth and Replanted Soil Microbial Environment.

Trichoderma asperellum strain 6S-2 with biocontrol effects and potential growth-promoting properties was made into a fungal fertilizer for the prevention of apple replant disease (ARD). 6S-2 fertilizer not only promoted the growth of Malus hupehensis Rehd seedlings in greenhouse and pot experiments, but also increased the branch elongation growth of young apple trees. The soil microbial community structure changed significantly after the application of 6S-2 fertilizer: the relative abundance of Trichoderma increased significantly, the relative abundance of Fusarium (especially the gene copy numbers of four Fusarium species) and Cryptococcus decreased, and the relative abundance of Bacillus and Streptomyces increased. The bacteria/fungi and soil enzyme activities increased significantly after the application of 6S-2 fertilizer. The relative contents of alkenes, ethyl ethers, and citrullines increased in root exudates of M. hupehensis Rehd treated with 6S-2 fertilizer and were positively correlated with the abundance of Trichoderma. The relative contents of aldehydes, nitriles, and naphthalenes decreased, and they were positively correlated with the relative abundance of Fusarium. In addition, levels of ammonium nitrogen (NH4-N), nitrate nitrogen (NO3-N), available phosphorus (AP), available potassium (AK), organic matter (SOM), and pH in rhizosphere soil were also significantly related to changes in the microbial community structure. In summary, the application of 6S-2 fertilizer was effective in alleviating some aspects of ARD by promoting plant growth and optimizing the soil microbial community structure.

Microbial diversity and associated metabolic potential in the supraglacial habitat of a fast-retreating glacier: a case study of Patsio glacier, North-western Himalaya.

In the present study, we investigated the microbial community composition and their associated metabolic potentials using the 16S rRNA gene (V3-V4) and ITS (ITS1) amplicon sequencing approach in the Patsio glacier. The bacterial community composition was mainly dominated by Bacteroidota (18%-38% of total reads) and Cyanobacteria (9%-30%), along with a rare Candidate phylum Patescibacteria. Ferruginibacter (13%) and Polaromonas (8%) were the most dominant genera identified across the samples known to have potential ecological roles in colonization, driving the functioning of supraglacial habitats. The prevalence of metabolic genes associated with nitrogen, carbon and sulfur cycling processes was identified in the present study. The fungal diversity was dominated by members of unclassified phyla, followed by Ascomycota (up to 6%) and Basidiomycota (up to 4%), in terms of its relative abundance. The relative abundance of Fusarium and Didymella (8%-14%) was higher among the high altitude, cryoconite samples (P1-P5), while Rhodotorula (12%-29%) dominated in the glacial ice debris samples (P6-P8). Thus, our study provides significant insights into dynamics of microbial communities and its potential ecological roles in the changing climate.

Rhizosphere Microbial Communities Are Significantly Affected by Optimized Phosphorus Management in a Slope Farming System.

Soil rhizosphere microorganisms play crucial roles in promoting plant nutrient absorption and maintaining soil health. However, the effects of different phosphorus (P) managements on soil microbial communities in a slope farming system are poorly understood. Here, rhizosphere microbial communities under two P fertilization levels—conventional (125 kg P2O5 ha–1, P125) and optimal (90 kg P2O5 ha–1, P90)—were compared at four growth stages of maize in a typical sloped farming system. The richness and diversity of rhizosphere bacterial communities showed significant dynamic changes throughout the growth period of maize, while different results were observed in fungal communities. However, both the P fertilization levels and the growth stages influenced the structure and composition of the maize rhizosphere microbiota. Notably, compared to P125, Pseudomonas, Conexibacter, Mycobacterium, Acidothermus, Glomeromycota, and Talaromyces were significantly enriched in the different growth stages of maize under P90, while the relative abundance of Fusarium was significantly decreased during maize harvest. Soil total nitrogen (TN) and pH are the first environmental drivers of change in bacterial and fungal community structures, respectively. The abundance of Gemmatimonadota, Proteobacteria, and Cyanobacteria showed significant correlations with soil TN, while that of Basidiomycota and Mortierellomycota was significantly related to pH. Additionally, P90 strengthened the connection between bacteria, but reduced the links between fungi at the genus level. Our work helps in understanding the role of P fertilization levels in shaping the rhizosphere microbiota and may manipulate beneficial microorganisms for better P use efficiency.

Chiral enantiomers of the plant growth regulator paclobutrazol selectively affect community structure and diversity of soil microorganisms

Paclobutrazol is a triazole plant growth regulator with a wide range of applications in crop and fruit tree production. Paclobutrazol is used as a racemic mixture in agriculture. However, the effects of paclobutrazol enantiomers on soil microbial community structure and diversity are unclear. In the present study, Illumina high-throughput sequencing was used to study the enantioselective effects of two paclobutrazol enantiomers on soil microbial community. S-paclobutrazol was more persistent than R-paclobutrazol. The half-lives of the S- and R-isomers were 80 d and 50 d, respectively. No interconversion between the two isomers occurred in soils. In addition, the enantiomers had significant enantiomeric effects on soil microbial community and the paclobutrazol degradation was probably attributed to the presence of Pseudomonas and Mycobacterium. Notably, the relative abundance of Fusarium, a genus of filamentous fungi producing gibberellins, could be enantioselectively affected by the chiral enantiomers. Paclobutrazol enantiomers exhibited greater effects on the fungal community structure than bacterial community structure due to the fungicidal activity of paclobutrazol. Finally, R-paclobutrazol had a significant effect on the microbial networks. The findings of the present study suggest that the use of S-paclobutrazol may accomplish both plant growth regulation and the minimization of effects of paclobutrazol on soil microbial communities.