Fungal Communities in Rhizosphere Soil under Conservation Tillage Shift in Response to Plant Growth

The Role of Soil Microbial Consortia in Sustainable Cereal Crop Residue Management

The global escalation in cereal production, essential to meet growing population demands, simultaneously augments the generation of cereal crop residues, estimated annually at approximately 3107 × 106 Mg/year. Among different crop residue management approaches, returning them to the soil can be essential for various ecological benefits, including nutrient recycling and soil carbon sequestration. However, the recalcitrant characteristics of cereal crop residues pose significant challenges in their management, particularly in the decomposition rate. Therefore, in this review, we aim to summarize the influence of different agricultural practices on enhancing soil microbial decomposer communities, thereby effectively managing cereal crop residues. Moreover, this manuscript provides indirect estimates of cereal crop residue production in Northern Europe and Lithuania, and highlights the diverse roles of lignocellulolytic microorganisms in the decomposition process, with a particular focus on enzymatic activities. This review bridges the knowledge gap and indicates future research directions concerning the influence of agricultural practices on cereal crop residue-associated microbial consortia.

Long-Term Field Application of a Plant Growth-Promoting Rhizobacterial Consortium Suppressed Root-Knot Disease by Shaping the Rhizosphere Microbiota

Root-knot nematodes (Meloidogyne spp.) are one of the most economically important plant parasitic nematodes, infecting almost all cultivated plants and resulting in severe yield losses every year. Plant growth-promoting rhizobacteria (PGPR) have been extensively used to prevent and control root-knot diseases and increase yield. In this study, the effect of a consortium of three PGPR strains (Bacillus cereus AR156, B. subtilis SM21, and Serratia sp. XY21; hereafter "BBS") on root-knot disease of cucumber was evaluated. The application of BBS significantly reduced the severity of root-knot disease by 56 to 72%, increased yield by 36 to 55%, and improved fruit quality by 14 to 90% and soil properties by 1 to 90% relative to the control in the cucumber fields of the Nanjing suburb, Jiangsu Province, from 2015 to 2018. BBS altered the rhizosphere bacterial community. Compared with the control group, it significantly (false discovery rate, P < 0.05) increased the abundance of 14 bacterial genera that were negatively correlated with disease severity. Additionally, the redundancy analysis suggested that BBS-treated rhizosphere soil samples were dominated by disease-suppressive bacteria, including the genera Iamia, Kutzneria, Salinibacterium, Mycobacterium, Kribbella, Pseudonocardia, Sporichthya, Sphaerisporangium, Actinomadura, Flavisolibacter, Phenylobacterium, Bosea, Hyphomicrobium, Agrobacterium, Sphingomonas, and Nannocystis, which were positively related to total organic carbon, total nitrogen, total organic matter, dissolved organic carbon, [Formula: see text]-N, and available phosphorus contents. This suggests that BBS suppresses root-knot nematodes and improves the soil chemical properties of cucumber by altering the rhizosphere microbial community.

Composition of fungal communities upon multiple passaging of rhizosphere microbiome for salinity stress mitigation in Vigna radiata

The top-down approach of microbiome-mediated rhizosphere engineering has emerged as an eco-friendly approach for mitigating stress and enhancing crop productivity. It has been established to mitigate salinity stress in Vigna radiata using multi-passaging approach. During the process of acclimatization under increasing levels of salinity stress, the structure of rhizospheric microbial community undergoes dynamic changes, while facilitating stress mitigation in plants. In this study, using ITS-based amplicon sequencing, the dynamics of rhizosphere fungal community was unravelled over successive passages under salinity stress in V. radiata. Clear shifts were evident among the fungal community members under stress and non-stress conditions, upon application of acclimatized rhizosphere microbiome in V. radiata across successive passages. These shifts correlated with enhanced plant biometrics and reduced stress marker levels in plant. Significant changes in the fungal community structure were witnessed in the rhizosphere across specific passaging cycles under salinity stress, which possibly facilitated stress mitigation in V. radiata.

Metagenomics reveals the abundance and accumulation trend of antibiotic resistance gene profile under long-term no tillage in a rainfed agroecosystem

Widespread soil resistance can seriously endanger sustainable food production and soil health. Conservation tillage is a promising practice for improving soil structure and health. However, the impact of long-term no-tillage on the presence of antibiotic resistance genes in agricultural soils remains unexplored. Based on the long-term (>11 yr) tillage experimental fields that include both conservation tillage practices [no tillage (ZT)] and conventional tillage practices [plough tillage (PT)], we investigated the accumulation trend of antibiotic resistance genes (ARGs) in farmland soils under long-term no-tillage conditions. We aimed to provide a scientific basis for formulating agricultural production strategies to promote ecological environment safety and human health. In comparison to PT, ZT led to a considerable reduction in the relative abundance of both antibiotic resistance genes and antibiotic target gene families in the soil. Furthermore, the abundance of all ARGs were considerably lower in the ZT soil. The classification of drug resistance showed that ZT substantially decreased the relative abundance of Ethambutol (59.97%), β-lactams (44.87%), Fosfomycin (35.82%), Sulfonamides (34.64%), Polymyxins (33.67%), MLSB (32.78%), Chloramphenicol (28.57%), Multi-drug resistance (26.22%), Efflux pump (23.46%), Aminoglycosides (16.79%), Trimethoprim (13.21%), Isoniazid (11.34%), Fluoroquinolone (6.21%) resistance genes, compared to PT soil. In addition, the abundance of the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Gemmatimonadetes decreased considerably. The Mantel test indicated that long-term ZT practices substantially increased the abundance of beneficial microbial flora and inhibited the enrichment of ARGs in soil by improving soil microbial diversity, metabolic activity, increasing SOC, TN, and available Zn, and decreasing pH. Overall, long-term no-tillage practices inhibit the accumulation of antibiotic resistance genes in farmland soil, which is a promising agricultural management measure to reduce the accumulation risk of soil ARGs.

Long-term impact of pulses crop rotation on soil fungal diversity in aerobic and wetland rice cultivation

Pulse crop rotation in rice cultivation is a widely accepted agronomic practice. Depending upon the water regime, rice cultivation has been classified into wetland and aerobic practices. However, no studies have been conducted so far to understand the impact of pulse crop rotation and rice mono-cropping on fungal diversity, particularly in aerobic soil. A targeted metagenomic study was conducted to compare the effects of crop rotations (rice-rice and rice-pulse) on fungal diversity in wetland and aerobic rice soils. Out of 445 OTUs, 41.80% was unknown and 58.20% were assigned to six phyla, namely Ascomycota (56.57%), Basidiomycota (1.32%), Zygomycota (0.22%), Chytridiomycota (0.04%), Glomeromycota (0.03%), and Blastocladiomycota (0.02%). Functional trait analysis found wetland rice-pulse rotation increased symbiotrophs (36.7%) and saprotrophs (62.1%) population, whereas higher pathotrophs were found in aerobic rice-rice (62.8%) and rice-pulse (61.4%) cropping system. Certain soil nutrients played a major role in shaping the fungal community; Ca had significant (p < 0.05) positive impact on saprotroph, symbiotroph and endophytes, whereas Cu had significant (p < 0.05) negative impact on pathotrophs. This study showed that rice-pulse crop rotation could enhance the saprophytic and symbiotic fungal diversity in wetland and reduce the population of pathogens in aerobic rice cultivation.

Characterization of the microbial community associated with the roots of joyapa (Macleania rupestris) and the effect of fungal isolates on seedling development

Macleania rupestris is a native Ericaceae with high potential benefits for health and the environment. Characterizing the interactions between M. rupestris and associated fungi is vital to supporting the plant's conservation and future domestication. However, little is known about the relationship between plant growth-promoting endophytes and M. rupestris. To learn more about the soil-associated microbiota of M. rupestris, we analyzed endophyte communities associated with the plant's rhizosphere and surrounding soil using nanopore sequencing. Additionally, fungal endophyte cultivable strains were isolated from the roots of M. rupestris to evaluate their growth-promoting activity on seedlings by applying a strain inoculation bioassay. Over 1000 genera were identified using nanopore sequencing, Bradyrhizobium and Mesorhizobium the most abundant in all samples analyzed. Similarly, six cultivable fungi were characterized by the molecular markers ITS (internal transcribed spacer) and LSU (large subunit). Amongst all isolates, Clonostachys rosea and Trichoderma paravidescens positively impacted seedlings' development. This study shows the potential of fungal strains as inoculants for the potential domestication of Macleania rupestris. Keywords: Endophyte, growth promoter, Macleania rupestris, microbial communities

Diversity of Fast-Growth Spore-Forming Microbes and Their Activity as Plant Partners

Biofertilizers are agricultural materials capable of reducing the usage amounts of chemical fertilizers. Spore-forming microorganisms (SFM) could be used for plant growth promotion or to improve plant health. Until now, biofertilizers based on SFM have been applied for rice and other crops. In this study, we isolated and characterized SFM, which were colonized on the Oryza sativa L. roots. SFM were analyzed regarding the short-term effects of biofertilization on the nursery growths. Analysis was performed without nitrogen or any inorganic fertilizer and was divided into two groups, including bacteria and fungi. SF-bacteria were dominated by the Firmicutes group, including species from Viridibacillus, Lysinibacillus, Solibacillus, Paenibacillus, Priestia, and mainly Bacillus (50%). The fungi group was classified as Mucoromycota, Basidiomycota, and mainly Ascomycota (80%), with a predominance of Penicillium and Trichoderma species. In plant performance in comparison with B. pumilus TUAT1, some bacteria and fungus isolates significantly improved the early growth of rice, based on 48 h inoculum with 10⁷ CFU mL^-1. Furthermore, several SFM showed positive physiological responses under abiotic stress or with limited nutrients such as phosphorous (P). Moreover, the metabolic fingerprint was obtained. The biofertilizer based on SFM could significantly reduce the application of the inorganic fertilizer and improve the lodging resistances of rice, interactively enhancing better plant health and crop production.

Moso bamboo (Phyllostachys edulis (Carrière) J. Houzeau) invasion affects soil microbial communities in adjacent planted forests in the Lijiang River basin, China

Introduction

Moso bamboo (Phyllostachys edulis (Carrière) J. Houz.), the most widely distributed economic bamboo species in southern China, can easily invade adjacent communities due to its clonal reproduction. However, there is little information on the effects of its establishment and expansion to adjacent forest soil communities, particularly in planted forests.

Methods

We investigated the relationships between soil properties and the microbial community during bamboo invasion under different slope directions (shady or sunny slope) and positions (bottom, middle, or top slope), in three typical stand types (bottom: pure moso bamboo, middle: mixed stands of moso bamboo and Masson pine (Pinus massoniana Lamb.), and top: pure Masson pine) in the Lijiang River Basin. This study aimed to explore the effects of key environmental factors on soil microbial composition, diversity, and abundance.

Results and Discussion

The results showed that the abundance of Acidobacteria bacterium and Acidobacteria bacterium 13_2_20CM_58_27, and Verrucomicrobia bacterium decreased as the slope increased (p < 0.05), whereas the abundance of Alphaproteobacteria bacterium, Actinobacteria bacterium, Trebonia kvetii, and Bradyrhizobium erythrophlei increased as the slope increased (p < 0.05). However, the difference of slope direction on microbial communities was not significant. The pH, organic matter (OM) and total phosphorus (TP) were the key soil environmental factors; most microorganisms (Betaproteobacteria bacterium, Candidatus Eisenbacteria bacterium, Betaproteobacteria bacterium SCGC_AG - 212 - J23, Gemmatimonadetes bacterium, Actinobacteria bacterium 13_2_20CM_2_66_6, and Myxococcaceae bacterium) showed a positive relationship with pH and a negative relationship with OM and TP. Slope position significantly affected OM, calcium (Ca), total nitrogen (TN), available phosphorus (AP), hydrolyzed nitrogen (HN), pH, and microbial abundance and composition. Slope direction significantly affected TP and magnesium (Mg). The structural equations also indicated that slope position had an effect on microbial composition, abundance, and diversity. Slope position was negatively correlated with pH (r = -0.333, p = 0.034) and positively correlated with OM (r = 0.728, p < 0.001), TN (r = 0.538, p < 0.001) and Ca (r = 0.672, p < 0.001); pH was positively correlated with microbial composition (r = 0.634, p < 0.001), abundance (r = 0.553, p < 0.001) and diversity (r = 0.412, p = 0.002), TN was positively correlated with microbial composition (r = 0.220, p = 0.014) and abundance (r = 0.206, p = 0.013), and Ca was negatively correlated with microbial composition (r = -0.358, p = 0.003) and abundance (r = -0.317, p = 0.003). Slope position can also influence microbial composition (r = 0.452, p < 0.001) directly. In addition, slope direction had an indirect effect on microbial diversity through total potassium (TK). Therefore, we proposed that the different variations in microbial community during bamboo invasion could be related to the influence of invasion on the soil properties at different invasion stages.

Climate-smart agricultural practices influence the fungal communities and soil properties under major agri-food systems

Fungal communities in agricultural soils are assumed to be affected by climate, weather, and anthropogenic activities, and magnitude of their effect depends on the agricultural activities. Therefore, a study was conducted to investigate the impact of the portfolio of management practices on fungal communities and soil physical-chemical properties. The study comprised different climate-smart agriculture (CSA)-based management scenarios (Sc) established on the principles of conservation agriculture (CA), namely, ScI is conventional tillage-based rice-wheat rotation, ScII is partial CA-based rice-wheat-mungbean, ScIII is partial CSA-based rice-wheat-mungbean, ScIV is partial CSA-based maize-wheat-mungbean, and ScV and ScVI are CSA-based scenarios and similar to ScIII and ScIV, respectively, except for fertigation method. All the scenarios were flood irrigated except the ScV and ScVI where water and nitrogen were given through subsurface drip irrigation. Soils of these scenarios were collected from 0 to 15 cm depth and analyzed by Illumina paired-end sequencing of Internal Transcribed Spacer regions (ITS1 and ITS2) for the study of fungal community composition. Analysis of 5 million processed sequences showed a higher Shannon diversity index of 1.47 times and a Simpson index of 1.12 times in maize-based CSA scenarios (ScIV and ScVI) compared with rice-based CSA scenarios (ScIII and ScV). Seven phyla were present in all the scenarios, where Ascomycota was the most abundant phyla and it was followed by Basidiomycota and Zygomycota. Ascomycota was found more abundant in rice-based CSA scenarios as compared to maize-based CSA scenarios. Soil organic carbon and nitrogen were found to be 1.62 and 1.25 times higher in CSA scenarios compared with other scenarios. Bulk density was found highest in farmers' practice (Sc1); however, mean weight diameter and water-stable aggregates were found lowest in ScI. Soil physical, chemical, and biological properties were found better under CSA-based practices, which also increased the wheat grain yield by 12.5% and system yield by 18.8%. These results indicate that bundling/layering of smart agricultural practices over farmers' practices has tremendous effects on soil properties, and hence play an important role in sustaining soil quality/health.

Differentially enriched fungal communities in root rot resistant and susceptible varieties of tobacco (Nicotiana tabacum L.) under continuous monoculture cropping

Root rot is a major disease of tobacco that causes crop losses of up to 15-20% of global tobacco production. The present study aimed to compare the fungal communities, and physicochemical properties of rhizosphere soil of root rot resistant (Yunyan 87; Y) and susceptible (Honghua Dajinyuan; H) tobacco varieties. Four treatments of each variety under continuous monocropping cultures included: control groups (HT0 and YT0); 2 years of continuous cropping (HT2 and YT2); 4 years of continuous cropping (HT4 and YT4); and 8 years of continuous cropping (YT8 and HT8). The soil physicochemical properties including available nitrogen (AN), available phosphorus (AP), available potassium (AK), and organic matter (OM) were increased (p < 0.05) from HT0 to HT8, whereas the resistant variety (Y) showed an inconsistent trend from YT0 to YT8. The pH was decreased (p < 0.05) from HT0 to HT8 and YT0 to YT8. Further, the disease incidence rate and disease index of the H variety also increased (p < 0.05) from HT0 to HT8. Alpha diversity analysis revealed that susceptible variety had higher fungal diversity from HT0 to HT8, while resistant variety exhibited lower diversity from YT0 to YT8. Ascomycota and Mortierellomycota were the dominant phyla in H and Y. Ascomycota abundance was increased (p < 0.05), whereas Mortierellomycota was decreased (p < 0.05) for continuous cropping years in H and Y. Penicillium, Fusarium, and Chrysosporium were the top three abundant genera in both varieties. The relative abundance of Penicillium spp. was increased (p < 0.05) in Y, whereas decreased (p < 0.05) in H variety. Specifically, Chrysosporium spp. was increased (p < 0.05) whereas Fusarium spp. was decreased (p < 0.05) in YT2. Redundancy analysis (RDA) revealed that fungal communities in H and Y rhizospheres were influenced by pH and carbon content, respectively. The top three highly enriched (p < 0.05) pathways in both varieties were fatty acid elongation, fatty acid β-oxidation I, and glyoxylate cycle. Our study concluded that resistant variety exhibited lower fungal diversity and functionally enriched metabolic pathways than susceptible variety that might be the result of molecular breeding practices, however, the relative abundance of Penicillium spp. were increased in resistant variety under long-term monoculture cropping.

Diversity of Root-Associated Fungi of the Terrestrial Orchids Gavilea lutea and Chloraea collicensis in a Temperate Forest Soil of South-Central Chile

The diversity of orchid mycorrhizal fungi (OMF) and other beneficial root-associated fungi in temperate forests has scarcely been examined. This study aimed to analyze the diversity of mycorrhizal and rhizosphere-associated fungal communities in the terrestrial orchids Gavilea lutea and Chloraea collicensis growing in high-orchid-population-density areas in the piedmont of the Andes Cordillera with native forest (Nothofagus-Araucaria) and Coastal Cordillera with an exotic plantation (Pinus-Eucalyptus) in south-central Chile. We focused on rhizosphere-inhabiting and peloton-associated OMF in a native forest (Andes Cordillera) and a mixed forest (Coastal Cordillera). The native terrestrial orchids G. lutea and C. collicensis were localized, mycorrhizal root segments were taken to isolate peloton-associated OMF, and rhizosphere soil was taken to perform the metabarcoding approach. The results revealed that Basidiomycota and Ascomycota were the main rhizosphere-inhabiting fungal phyla, showing significant differences in the composition of fungal communities in both sites. Sebacina was the most-abundant OMF genera in the rhizosphere of G. lutea growing in the native forest soil. In contrast, Thanatephorus was the most abundant mycorrhizal taxa growing in the rhizosphere of orchids from the Coastal Cordillera. Besides, other OMF genera such as Inocybe, Tomentella, and Mycena were detected. The diversity of OMF in pelotons differed, being mainly related to Ceratobasidium sp. and Tulasnella sp. These results provide evidence of differences in OMF from pelotons and the rhizosphere soil in G. lutea growing in the Andes Cordillera and a selection of microbial communities in the rhizosphere of C. collicensis in the Coastal Cordillera. This raises questions about the efficiency of propagation strategies based only on mycorrhizal fungi obtained by culture-dependent methods, especially in orchids that depend on non-culturable taxa for seed germination and plantlet development.

Plants Dictate Root Microbial Composition in Hydroponics and Aquaponics

The role of the microbial community in mediating fish and plant co-culture is often considered the black box of aquaponics. Despite widespread recognition regarding the dependency of plants on their rhizosphere, the extent to which upstream aquaculture influences downstream hydroponic root communities has been poorly described in the literature. In this study we performed a taxonomic survey (16S rRNA metabarcoding) of microbial communities originating in the facility water source, hydroponic nutrient solution (HNS) sump, nutrient supplemented biofilter effluent (BF) sump, and recirculating aquaculture system tanks stocked with Nile tilapia (Oreochromis niloticus). Lettuce (Lactuca sativa) was then grown using the HNS and BF effluent under sterilized or mature (prior aquaponics/hydroponics lettuce culture water) conditions, likewise, the influence of probiotic addition or inoculation with soil-grown lettuce rhizosphere was assessed. Compositional similarities across treatments suggest that under soil-less conditions, plants are able to exert a stronger discriminatory influence on their rhizosphere composition than is done by colonization from upstream sources. Furthermore, cluster dendrograms grouped the sterilized and unsterilized treatments more consistently together than hydroponics and aquaponics treatments. These findings contradict conventional beliefs that microbial communities in the water column colonize roots based on their presence alone, ignoring the role that plants play in rhizosphere community selection.

Mycobiota profile, phenology, and potential toxicogenic and pathogenic species associated with stored groundnuts (Arachis hypogaea L.) from the Volta Region, Ghana

This study updates the mycobiota resident in groundnut seeds, their phenology during storage with the view to ascertain their occurrence, potential toxigenic species, and pathologically important species in the stored samples. The moisture content of the seeds ranged from 5.7% to 6.5% within the stipulated safe moisture content of 8% for extension of shelf life. Culturing the seeds on mycological media (Sabouraud's Dextrose Agar SDA; Oxytetracycline Glucose Yeast Extract OGYE, Potato Dextrose Agar, PDA) caused a de novo growth of the quiescent spores at 28-30°C for 7-14 days. Fungal population counts on the three media ranged from 2.01 to 2.16 log₁₀ CFU/g samples to a final 6-month count of 1.67-2.60 log₁₀ CFU/g. Eighteen different fungal species belonging to ten genera were encountered on the media, namely Aspergillus, Cladosporium, Curvularia, Fusarium, Penicillium, Trichoderma, Rhizopus, Rhodotorula, Sporendonema, and Paecilomyces. Aspergillus spp. (A. niger, A. flavus, A. fumigatus, and A. terreus) were the most frequently isolated, followed by Fusarium species (F. oxysporum, F. solani, and F. verticillioides), Trichoderma (T. harzianum and T. viride), Rhizopus spp (R. oligosporus and R. stolonifer), and Penicillium verrucosum. The species which were seed borne (A. niger, A. flavus, A. terreus, A. fumigatus, F. solani, F. verticillioides, T. viride, C. herbarum, and Curvularia lunata) were isolated on both surface sterilized and non-surface sterilized seeds. The phenology of the encountered fungal species generally followed five patterns. The most frequently isolated Aspergillus niger, A. flavus, and A. fumigatus predominated throughout the 6 months sampling period, while A. ustus and A. terreus appeared sporadically and disappeared. The early colonizers (R. oligosporus, R. stolonifer, and Paecilomyces) could not be isolated after 2-3 months owing presumably to stronger antibiosis competition from the Aspergillus species. The most predominant Aspergillus species initially constituted 36%-48% of the total population but declined to 10%-36% in 6 months. Mycobiota encountered with mycotoxigenic potential and human health importance were A. niger, A. flavus, A. fumigatus, F. verticillioides, and Penicillium verrucosum. Other species of pathological importance to plants were Curvularia lunata and Fusarium oxysporum. The practical implications of these findings are discussed.

Conservation tillage improves productivity of sunflower (Helianthus annuus L.) under reduced irrigation on sandy loam soil

Sunflower production is significantly lower in arid and semi-arid regions due to various crop management problem. Conservation of tillage provides the most excellent opportunity to reduce degradation of soil reserves and increase soil productivity. The main objective of this study was to investigate the combined effects of conservation tillage and drought stress on growth and productivity of different sunflower hybrids. Experimental treatments included two sunflower hybrids ('NK-Senji' and 'S-278'), two drought stress treatments (i.e., well-watered and drought stress at flowering and grain filling stages) and three tillage practices (i.e., conservation, minimum and deep tillage). The results indicated that morphological and physiological parameters, and yield-related traits were significantly (P≤0.05) affected by all individual factors; however, their interactive effects were non-significant. Among sunflower hybrids, 'NK-Senji' performed better for morphological, physiological, and yield-related traits than 'S-278'. Similarly, conservation tillage observed better traits compared to the rest of the tillage practices included in the study. Nonetheless, conservation tillage improved growth and yield-related traits of hybrid 'NK-Senji' under drought stress. Hence, it is concluded that conservation tillage can improve the productivity of sunflower under low moisture availability. Therefore, conservation tillage could be suggested in the areas of lower water ability to improve sunflower production. Nonetheless, sunflower hybrids or varieties need thorough testing for their adaptability to conservation tillage and low moisture availability before making recommendations.

Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices

The microbial communities associated to the rhizosphere (the rhizomicrobiome) have a substantial impact on plant growth and yield. Understanding the effects of agricultural management on the rhizomicrobiome is very important for selecting efficient practices. By sequencing the V4 region of 16S rRNA for bacteria and the ITS1 regions and fungi, we investigated the influences of agronomic practices, including cucumber grafting on cucurbit hybrid (Cucurbita moschata × C. maxima), cucumber-garlic intercropping, and treatment with fungicide iprodione-carbendazim on cucumber rhizosphere microbial communities during plant growth. Soil dehydrogenase activity (DHA) and plant vegetative parameters were assessed as an indicator of overall soil microbial activity. We found that both treatments and growth stage induced significant shifts in microbial community structure. Grafting had the highest number of differentially abundant OTUs compared to control samples, followed by intercropping and fungicide treatment, while plant development stage affected both alpha and beta diversities indices and composition of the rhizomicrobiome. DHA was more dependent on plant growth stages than on treatments. Among the assessed factors, grafting and plant developmental stage resulted in the greatest changes in the microbial community composition. Grafting also increased the plant growth parameters, suggesting that this method should be further investigated in vegetable production systems.

Clary Sage Cultivation and Mycorrhizal Inoculation Influence the Rhizosphere Fungal Community of an Aged Trace-Element Polluted Soil

Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in trace element (TE)-polluted conditions and within the framework of phytomanagement approaches. The presence of high concentrations of TEs in soils can negatively affect not only microbial diversity and community composition but also plant establishment and growth. Hence, the objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community composition and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation over two successive years, combined or not with exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV), respectively, in the rhizospheric soil and roots of S. sclarea under TE-polluted conditions. Remarkably, 69 AMF species were detected at our experimental site, belonging to 12 AMF genera. Furthermore, the inoculation treatment significantly shaped the fungal communities in soil and increased the number of AMF ASVs in clary sage roots. In addition, clary sage cultivation over successive years could be one of the explanatory parameters for the inter-annual variation in both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of an aromatic plant, clary sage, grown in TE-polluted agricultural soil.

Geographical Isolation and Root-Associated Fungi in the Marine Terrains: A Step Toward Establishing a Strategy for Acquiring Unique Microbial Resources

This study aimed to understand whether the geo-ecological segregation of native plant species affects the root-associated fungal community. Rhizoplane (RP) and rhizosphere (RS) fungal microbiota of Sedum takesimense native to three geographically segregated coastal regions (volcanic ocean islands) were analyzed using culture-independent methods: 568,507 quality sequences, 1399 operational taxonomic units, five phyla, and 181 genera were obtained. Across all regions, significant differences in the phyla distribution and ratio were confirmed. The Chao's richness value was greater for RS than for RP, and this variance coincided with the number of genera. In contrast, the dominance of specific genera in the RS (Simpson value) was lower than the RP at all sites. The taxonomic identity of most fungal species (95%) closely interacting with the common host plant was different. Meanwhile, a considerable number of RP only residing fungal genera were thought to have close interdependency on their host halophyte. Among these, Metarhizium was the sole genus common to all sites. These suggest that the relationship between potential symbiotic fungi and their host halophyte species evolved with a regional dependency, in the same halophyte species, and of the same natural habitat (volcanic islands); further, the fungal community differenced in distinct geographical regions. Importantly, geographical segregation should be accounted for in national culture collections, based on taxonomical uniqueness.

Draft Genomes and Comparative Analysis of Seven Mangrove Rhizosphere-Associated Fungi Isolated From Kandelia obovata and Acanthus ilicifolius

Mangroves are one of the most productive and biologically diverse ecosystems, with unique plants, animals, and microorganisms adapted to the harsh coastal environments. Although fungi are widely distributed in the mangrove ecosystem and they are playing an important role in the decomposition of organic matter, their genomic profiles are still poorly understood. In this study, we isolated seven Ascomycota fungi (Westerdykella dispersa F012, Trichoderma lixii F014, Aspergillus tubingensis F023, Penicillium brefeldianum F032, Neoroussoella solani F033, Talaromyces fuscoviridis F034, and Arthrinium marii F035) from rhizospheres of two mangroves of Kandelia obovata and Acanthus ilicifolius. We sequenced and assembled the whole genome of these fungi, resulting in size ranging from 29 to 48 Mb, while contig N50 from 112 to 833 Kb. We generated six novel fungi genomes except A. tubingensis, and the gene completeness and genome completeness of all seven genomes are higher than 94%. Comparing with non-mangrove fungi, we found Carbohydrate-Binding Modules (CBM32), a subfamily of carbohydrate active enzymes, only detected in two mangrove fungi. Another two subfamilies, Glycoside Hydrolases (GH6) and Polysaccharide Lyases (PL4), were significantly different in gene copy number between K. obovata and A. ilicifolius rhizospheres (P-value 0.041 for GH6, 0.047 for PL4). These findings may indicate an important influence of mangrove environments or hosts on the ability of decomposition in rhizosphere fungi. Secondary metabolite biosynthesis gene clusters were detected and we found the mangrove fungi averagely contain 18 Type I Polyketide (t1pks) synthase, which was significantly higher than 13 in non-mangrove fungi (P-value 0.048), suggesting their potential roles in producing bioactive compounds that important for fungi development and ecology. We reported seven mangrove-associated fungal genomes in this study and compared their carbohydrate active enzymes and secondary metabolites (SM) genes with those of non-mangrove fungi, and the results suggest that there are differences in genetic information among fungi in different habitats.

Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to decrease the suitability of cultivated areas while potentially increasing the distribution and impact of pests and diseases. In this context, the coffee microbiota has been increasingly studied over the past decades in order to improve the sustainability of the coffee production. Therefore, coffee associated microorganisms have been isolated and characterized in order to highlight their useful characteristics and study their potential use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms (including bacteria and fungi) are able to display plant growth-promoting capacities and/or biocontrol abilities toward coffee pests and diseases. Despite that numerous studies emphasized the potential of coffee-associated microorganisms under controlled environments, the present review highlights the lack of confirmation of such beneficial effects under field conditions. Nowadays, next-generation sequencing technologies allow to study coffee associated microorganisms with a metabarcoding/metagenomic approach. This strategy, which does not require cultivating microorganisms, now provides a deeper insight in the coffee-associated microbial communities and their implication not only in the coffee plant fitness but also in the quality of the final product. The present review aims at (i) providing an extensive description of coffee microbiota diversity both at the farming and processing levels, (ii) identifying the “coffee core microbiota,” (iii) making an overview of microbiota ability to promote coffee plant growth and to control its pests and diseases, and (iv) highlighting the microbiota potential to improve coffee quality and waste management sustainability.

Changes in root-associated fungal communities in Triticum aestivum ssp. spelta L. and Triticum aestivum ssp. vulgare L. under drought stress and in various soil processing

Plant roots are inhabited by an enormous variety of microorganisms, including fungi, which can control the growth as well as regulate the health of the host plants. The mycobiome composition of the roots of wheat plants, especially spelt, under drought stress has been rarely investigated. Therefore, the aim of the present study was to examine the composition of fungal communities in the root endosphere and rhizosphere of three Triticum aestivum ssp. spelta L. cultivars and one Triticum aestivum ssp. vulgare L. cultivar, grown under drought and controlled conditions in different soil preparations. Culture-dependent fungal community profiling was performed to examine the impact of rhizocompartments (endosphere, rhizosphere), host genotype, watering status and different soil preparation on roots mycobiome structure. A total of 117 fungal strains, belonging to 22 genera, were found to colonize the internal and external parts of roots in T. aestivum ssp. spelta L. and T. aestivum ssp. vulgare L. cultivars. The results showed that the part of root and soil preparation type significantly determined the mycobiome composition of wheat roots.

Structure of Bacterial Communities in Phosphorus-Enriched Rhizosphere Soils

Although phytoremediation is the main method for P-removal and maintaining ecosystem balance in geological phosphorus-enriched soils (PES), little is known about the structure and function of microbial communities in PES. Interactions between plants and soil microorganisms mainly occur in the rhizosphere. The aim of this work was to investigate the composition and diversity of bacterial communities found in rhizosphere soils associated with the following three dominant plant species: Erianthus rufipilus, Coriaria nepalensis, and Pinus yunnanensis. In addition, we compared these rhizosphere bacterial communities with those derived from bulk soils and grassland plots in PES from the Dianchi Lake basin of southwestern China. The Illumina MiSeq platform for high-throughput sequencing of 16S rRNA was used for the taxonomy and the analysis of soil bacterial communities. The results showed higher bacterial diversity and nutrient content in rhizosphere soils as compared with bulk soils. Rhizosphere bacteria were predominantly comprised of Proteobacteria (24.43%) and Acidobacteria (21.09%), followed by Verrucomicrobia (19.48%) and Planctomycetes (9.20%). A comparison of rhizosphere soils of the selected plant species in our study and the grassland plots showed that Acidobacteria were the most abundant in the rhizosphere soil of E. rufipilus; Bradyrhizobiaceae and Rhizobiaceae in the order Rhizobiales from C. nepalensis were found to have the greatest abundance; and Verrucomicrobia and Planctomycetes were in higher abundance in P. yunnanensis rhizosphere soils and in grassland plots. A redundancy analysis revealed that bacterial abundance and diversity were mainly influenced by soil water content, soil organic matter, and total nitrogen.

Garlic Substrate Induces Cucumber Growth Development and Decreases Fusarium Wilt through Regulation of Soil Microbial Community Structure and Diversity in Replanted Disturbed Soil

Garlic substrate could influence plant growth through affecting soil microbiome structure. The relationship mechanism between changes in soil microbial communities, disease suppression and plant development, however, remains unclear, particularly in the degraded soil micro-ecological environment. In this study, garlic substrates as a soil amendment were incorporated with different ratios (1:100, 3:100 and 5:100 g/100 g of soil) in a replanted disturbed soil of long-term cucumber monoculture (annual double cropping system in a greenhouse). The results indicated that higher amount of C-amended garlic substrate significantly induced soil suppressiveness (35.9% greater than control (CK) against the foliar disease incidence rate. This inhibitory effect consequently improved the cucumber growth performance and fruit yield to 20% higher than the non-amended soil. Short-term garlic substrate addition modified the soil quality through an increase in soil organic matter (SOM), nutrient availability and enzymatic activities. Illumina MiSeq sequencing analysis revealed that soil bacterial and fungal communities in the garlic amendment were significantly different from the control. Species richness and diversity indices significantly increased under treated soil. The correlation-based heat map analysis suggested that soil OM, nutrient contents and biological activators were the primary drivers reshaping the microbial community structure. Furthermore, garlic substrate inhibited soil-borne pathogen taxa (Fusarium and Nematoda), and their reduced abundances, significantly affecting the crop yield. In addition, the host plant recruited certain plant-beneficial microbes due to substrate addition that could directly contribute to plant–pathogen inhibition and crop biomass production. For example, abundant Acidobacteria, Ascomycota and Glomeromycota taxa were significantly associated with cucumber yield promotion. Firmicutes, Actinobacteria, Bacteroidetes, Basidiomycota and Glomeromycota were the associated microbial taxa that possibly performed as antagonists of Fusarium wilt, with plant pathogen suppression potential in monocropped cucumber-planted soil.

Fungal Clusters and Their Uniqueness in Geographically Segregated Wetlands: A Step Forward to Marsh Conservation for a Wealth of Future Fungal Resources

Here, we investigated fungal microbiota in the understory root layer of representative well-conserved geographically segregated natural wetlands in the Korean Peninsula. We obtained 574,143 quality fungal sequences in total from soil samples in three wetlands, which were classified into 563 operational taxonomic units (OTU), 5 phyla, 84 genera. Soil texture, total nitrogen, organic carbon, pH, and electrical conductivity of soil were variable between geographical sites. We found significant differences in fungal phyla distribution and ratio, as well as genera variation and richness between the wetlands. Diversity was greater in the Jangdo islands wetland than in the other sites (Chao richness/Shannon/Simpson's for wetland of the Jangdo islands: 283/6.45/0.97 > wetland of the Mt. Gariwang primeval forest: 169/1.17/0.22 > wetland of the Hanbando geology: 145/4.85/0.91), and this variance corresponded to the confirmed number of fungal genera or OTUs (wetlands of Jangdo islands: 42/283 > of Mt. Gariwang primeval forest: 32/169 > of the Hanbando geology: 25/145). To assess the uniqueness of the understory root layer fungus taxa, we analyzed fungal genera distribution. We found that the percentage of fungal genera common to two or three wetland sites was relatively low at 32.3%, while fungal genera unique to each wetland site was 67.7% of the total number of identified fungal species. The Jangdo island wetland had higher fungal diversity than did the other sites and showed the highest level of uniqueness among fungal genera (Is. Jangdo wetland: 34.5% > wetland of Mt. Gariwang primeval forest: 28.6% > wetland of the Hanbando geology: 16.7%).

Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador

Coffea arabica is a highly traded commodity worldwide, and its plantations are habitat to a wide range of organisms. Coffee farmers are shifting away from traditional shade coffee farms in favor of sun-intensive, higher yield farms, which can impact local biodiversity. Using plant-associated microorganisms in biofertilizers, particularly fungi collected from local forests, to increase crop yields has gained traction among coffee producers. However, the taxonomic and spatial distribution of many fungi in coffee soil, nearby forests and biofertilizers is unknown. We collected soil samples from a sun coffee system, shade coffee system, and nearby forest from Izalco, Sonsonate, El Salvador. At each coffee system, we collected soil from the surface (upper) and 10 cm below the surface (lower), and from the coffee plant drip line (drip line) and the walkway between two plants (walkway). Forest soils were collected from the surface only. We used ITS metabarcoding to characterize fungal communities in soil and in the biofertilizer (applied in both coffee systems), and assigned fungal taxa to functional guilds using FUNGuild. In the sun and shade coffee systems, we found that drip line soil had higher richness in pathotrophs, symbiotrophs, and saprotrophs than walkway soil, suggesting that fungi select for microhabitats closer to coffee plants. Upper and lower soil depths did not differ in fungal richness or composition, which may reflect the shallow root system of Coffea arabica. Soil from shade, sun, and forest had similar numbers of fungal taxa, but differed dramatically in community composition, indicating that local habitat differences drive fungal species sorting among systems. Yet, some fungal taxa were shared among systems, including seven fungal taxa present in the biofertilizer. Understanding the distribution of coffee soil mycobiomes can be used to inform sustainable, ecologically friendly farming practices and identify candidate plant-growth promoting fungi for future studies.

Rhizospheric soil fungal community patterns of Duchesnea indica in response to altitude gradient in Yunnan, southwest China

The magnitude of the impact of altitude gradient on microbial community and diversity has been studied in recent decades. Whereas bacteria have been the focus of most studies, fungi have been given relatively less attention. As a vital part of the macro- and microscopic ecosystem, rhizosphere fungi play a key role in organic matter decomposition and relative abundance of plant species and have an impact on plant growth and development. Using Duchesnea indica as the host plant, we examined the rhizosphere soil fungal community patterns across the altitude gradient in 15 sites of Yunnan province by sequencing the fungal ITS2 region with the Illumina MiSeq platform. We determined the fungal community composition and structure. We found that, surprisingly, rhizosphere soil fungal diversity of D. indica increased with altitudinal gradient. There was a slight difference in diversity between samples from high- and medium-altitude sites, with medium-altitude sites having the greater diversity. Furthermore, the rhizosphere soil fungal community composition and structure kept changing along the altitudinal gradient. Taxonomic results showed that the extent of phylum diversity was greatest at high-altitude sites, with Ascomycota, Basidiomycota, Zygomycota, and Glomeromycota as the most dominant fungal phyla.

Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection

The bacterial and fungal communities from the olive (Olea europaea L.) root systems have not yet been simultaneously studied. We show in this work that microbial communities from the olive root endosphere are less diverse than those from the rhizosphere. But more relevant was to unveil that olive belowground communities are mainly shaped by the genotype of the cultivar when growing under the same environmental, pedological and agronomic conditions. Furthermore, Actinophytocola, Streptomyces and Pseudonocardia are the most abundant bacterial genera in the olive root endosphere, Actinophytocola being the most prevalent genus by far. In contrast, Gp6, Gp4, Rhizobium and Sphingomonas are the main genera in the olive rhizosphere. Canalisporium, Aspergillus, Minimelanolocus and Macrophomina are the main fungal genera present in the olive root system. Interestingly enough, a large number of as yet unclassified fungal sequences (class level) were detected in the rhizosphere. From the belowground microbial profiles here reported, it can be concluded that the genus Actinophytocola may play an important role in olive adaptation to environmental stresses. Moreover, the huge unknown fungal diversity here uncovered suggests that fungi with important ecological function and biotechnological potential are yet to be identified.

Interaction between arbuscular mycorrhizal fungi and Bacillus spp. in soil enhancing growth of crop plants

Soil microorganisms play an important role in enhancing soil fertility and plant health. Arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria form a key component of the soil microbial population. Arbuscular mycorrhizal fungi form symbiotic association with most of the cultivated crop plants and they help plants in phosphorus nutrition and protecting them against biotic and abiotic stresses. Many species of Bacillus occurring in soil are also known to promote plant growth through phosphate solubilization, phytohormone production and protection against biotic and abiotic stresses. Synergistic interaction between AMF and Bacillus spp. in promoting plant growth compared to single inoculation with either of them has been reported. This is because of enhanced nutrient uptake, protection against plant pathogens and alleviation of abiotic stresses (water, salinity and heavy metal) through dual inoculation compared to inoculation with either AMF or Bacillus alone.

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

Characterization and variation of the rhizosphere fungal community structure of cultivated tetraploid cotton

Rhizosphere fungal communities exert important influencing forces on plant growth and health. However, information on the dynamics of the rhizosphere fungal community structure of the worldwide economic crop cotton (Gossypium spp.) is limited. In the present study, next-generation sequencing of nuclear ribosomal internal transcribed spacer-1 (ITS1) was performed to characterize the rhizosphere fungal communities of G. hirsutum cv. TM-1 (upland cotton) and G. barbadense cv. Hai 7124 (island cotton). The plants were grown in field soil (FS) that had been continuously cropped with cotton and nutrient-rich soil (NS) that had not been cropped. The fungal species richness, diversity, and community composition were analyzed and compared among the soil resources, cotton genotypes, and developmental stages. We found that the fungal community structures were different between the rhizosphere and bulk soil and the difference were significantly varied between FS and NS. Our results suggested that cotton rhizosphere fungal community structure variation may have been primarily influenced by the interaction of cotton roots with different soil resources. We also found that the community composition of the cotton rhizosphere fungi varied significantly during different developmental stages. In addition, we observed fungi that was enriched or depleted at certain developmental stages and genotypes in FS and NS, and these insights can lay a foundation for deep research into the dynamics of pathogenic fungi and nutrient absorption of cotton roots. This research illustrates the characteristics of the cotton rhizosphere fungal communities and provides important information for understanding the potential influences of rhizosphere fungal communities on cotton growth and health.

Soil Organic Carbon Shapes AMF Communities in Soils and Roots of Cynodon dactylon under Anti-Seasonal Drying-Wetting Cycles

Anti-seasonal drying-wetting cycles since 2010 have substantially altered its soil and vegetation status in the drawdown zone of China’s Three Gorges Reservoir (TGR). Such alternations may thus affect the composition and functioning of soil microbial communities, including the beneficial arbuscular mycorrhizal fungi (AMF), which enhance plant performance. Moreover, limited information is available if AMF communities are different in soils and roots, particularly under contrasting land-use changes. By combining the Illumina Miseq sequencing with bioinformatics analyses, AMF communities in both rhizosphere soils and roots of a stoloniferous and rhizomatous C4 perennial of Cynodon dactylon were characterized under three land-use types: (1) crop cultivated, (2) non-cultivated non-disturbed, and (3) disturbed non-cultivated land. A total of 35 and 26 AMF taxa were respectively detected from C. dactylon rhizosphere soils and roots from these three land-use types, which had endured four anti-seasonal drying/summer-wetting/winter cycles. Contrasting differentiations in the AMF community composition and structure were displayed in the C. dactylon rhizosphere soils and roots, and between land-use types. Nonmetric multidimensional scaling analyses revealed that AMF communities significantly correlated to soil organic carbon in the rhizosphere soils and roots of C. dactylon, to land-use types only in rhizosphere soils, whereas to soil moisture only in roots. Our results highlight the effects of soil nutrients and land-use changes on AMF community composition and diversity under the canopy of C. dactylon in TGR. The identified dominant AMF taxa can be employed to vegetation restoration in such degraded habitats globally.

Ginkgo agroforestry practices alter the fungal community structures at different soil depths in Eastern China

Agroforestry practices aim to achieve environmentally friendly land use. Fungi play a primarily role in soil organic carbon and nutrient maintenance, while the response of the soil fungi community to land use changes is little explored. Here, a high-throughput sequencing method was applied to understand the fungal community structure distinction in ginkgo agroforestry systems and adjacent croplands and nurseries. Our results showed that the agroforestry systems achieved better soil fertility and carbon contents. The agroforestry practices significantly altered the composition of soil fungal communities comparing with pure gingko plantation, adjacent cropland, and nursery. The dominant fungal phyla were always Ascomycota and Basidiomycota. The relative abundance of Ascomycota was correlated with the TN and AP, while the abundance of Basidiomycota was negatively correlated with the TN and NN. The soil organic carbon, total nitrogen, and nitrate nitrogen explained 59.80% and 63.36% of the total variance in the fungal community composition in the topsoil and subsoil, and the available phosphorus also played a key role in the topsoil. Considering soil fertility maintenance and fungal community survival and stability, the agroforestry systems achieved better results, and the ginkgo and wheat system was the best among the five planting systems we studied. In the ginkgo and wheat system, applying readily available mineral nitrogen fertilizer either alone or in combination with organic amendments will improve the soil quality and fertility.

Broad-leaved forest types affect soil fungal community structure and soil organic carbon contents

Evergreen broad-leaved (EBF) and deciduous broad-leaved (DBF) forests are two important vegetation types in terrestrial ecosystems that play key roles in sustainable biodiversity and global carbon (C) cycling. However, little is known about their associated soil fungal community and the potential metabolic activities involved in biogeochemical processes. In this study, soil samples were collected from EBF and DBF in Shennongjia Mountain, China, and soil fungal community structure and functional gene diversity analyzed based on combined Illumina MiSeq sequencing with GeoChip technologies. The results showed that soil fungal species richness (p = 0.079) and fungal functional gene diversity (p < 0.01) were higher in DBF than EBF. Zygomycota was the most dominant phylum in both broad-leaved forests, and the most dominant genera found in each forest varied (Umbelopsis dominated in DBF, whereas Mortierella dominated in EBF). A total of 4, 439 soil fungi associated functional gene probes involved in C and nitrogen (N) cycling were detected. Interestingly, the relative abundance of functional genes related to labile C degradation (e.g., starch, pectin, hemicellulose, and cellulose) was significantly higher (p < 0.05) in DBF than EBF, and the functional gene relative abundance involved in C cycling was significantly negatively correlated with soil labile organic C (r = -0.720, p = 0.002). In conclusion, the soil fungal community structure and potential metabolic activity showed marked divergence in different broad-leaved forest types, and the higher relative abundance of functional genes involved in C cycling in DBF may be caused by release of loss of organic C in the soil.

Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere

Plant-associated microbiomes are key determinants of host-plant fitness, productivity, and function. However, compared to bacterial community, we still lack fundamental knowledge concerning the variation in the fungal microbiome at the plant niche level. In this study, we quantified the fungal communities in the rhizosphere soil, as well as leaf and root endosphere compartments of a subtropical island shrub, Mussaenda kwangtungensis, using high-throughput DNA sequencing. We found that fungal microbiomes varied significantly across different plant compartments. Rhizosphere soil exhibited the highest level of fungal diversity, whereas the lowest level was found in the leaf endosphere. Further, the fungal communities inhabiting the root endosphere shared a greater proportion of fungal operational taxonomic units (OTUs) with rhizosphere communities than with leaf fungal endophyte communities, despite significant separation in community structure between the two belowground compartments. The fungal co-occurrence networks in the three compartments of M. kwangtungensis showed scale-free features and non-random co-occurrence patterns and matched the topological properties of small-world and evidently modular structure. Additionally, the rhizosphere network was more complex and showed higher centrality and connectedness than the leaf and root endosphere networks. Overall, our findings provide comprehensive insights into the structural variability, niche differentiation, and co-occurrence patterns in the plant associated fungal microbiome.

Culturable endophytic fungal communities associated with plants in organic and conventional farming systems and their effects on plant growth

As compared to organic farming system, conventional farming system relies on higher inputs of synthetic agrochemicals, which may reduce the abundance, diversity, and beneficial effects of plant endophytic fungal communities. This study compares the diversity and abundance of culturable endophytic fungal communities associated with four plant species –corn, tomato, pepper, and watermelon grown in separate organic and conventional fields. In all, 740 fungal isolates were identified, of which 550 were from the organic fields and 190 from the conventional ones. These fungal isolates were grouped into eight orders and 22 species, with the two most abundant species being Trichoderma sp. and Pichia guilliermondi. The fungal species diversity and abundance were both significantly higher in the organic than in the conventional fields. All the isolated endophytic fungi improved tomato plants’ shoot growth and biomass significantly, as compared with the water control. Six fungal isolates also exhibited activity that enhanced tomato fruit yields. These results suggest that these endophytic fungi might be a considerable boost to sustainable agricultural production, while also reducing the agricultural application of chemicals and thus benefiting the environment and human health.

Effect of Tillage Treatment on the Diversity of Soil Arbuscular Mycorrhizal Fungal and Soil Aggregate-Associated Carbon Content

No-tillage agriculture can sustain productivity and protect the environment. A comprehensive understanding of soil arbuscular mycorrhizal (AM) fungal diversity and soil carbon distribution within aggregate fractions is essential to the evaluation of no-tillage agriculture. The long-term field experiment included two tillage treatments (1) no tillage with straw returned to the soil (NTS), and (2) conventional mouldboard-plowing tillage without straw (CT), and was conducted on the Loess Plateau, north-western China, from October 2009. The soil samples were collected from the surface layer (0-20 cm depth) at the maturation stage of the summer maize (Zea mays L.) for analyzing aggregates separated by the dry-sieving method. The organic carbon content in the bulk soil and different particle size aggregates were measured using the dichromate oxidization method. The species compositions of soil AM fungi were compared by applying high-throughput sequencing of 18S rRNA. The results showed that the NTS had 9.1-12.2% higher percentage of soil macro-aggregates, resulting in 9.8% increase in mean weight diameter and 10.0% increase in bulk soil organic carbon content as compared with CT treatment. In addition, the NTS treatment had significantly higher percentages of Septoglomus and Glomus than the CT treatment. We also found some significant differences in the fungal communities of the soils of the two treatments. There was a strong positive relationship between bulk soil organic carbon and the percentages of Septoglomus and Glomus. Our results suggested that the NTS treatment had a protective effect on AM fungal community structures, which might play a key role in the development of agricultural sustainability in the Loess Plateau of China.

Gene mutation associated with esl mediates shifts on fungal community composition in rhizosphere soil of rice at grain-filling stage

Generally, plant roots shape the rhizosphere fungal community but how individual plant genes involved in senescence affect this shaping is less studied. We used an early senescence leaf (esl) mutant rice and compared it with its isogenic wild type variety to evaluate the effect of the vacuolar H⁺-ATPase (VHA-A1) gene mutation on the rhizosphere fungal community structure and composition using a metagenomic pyrosequencing approach. The most predominate fungal phyla identified for both isogenic lines belonged to Ascomycota, Basidiomycota and Glomeromycota, where Ascomycota were more prevalent in the esl mutant than the wild type variety. Real-time quantitative PCR analysis confirmed a significant rise in the richness of Cladosporium cladosporioides in esl mutant rice than the wild type variety. Correlation analysis revealed four most abundant genera identified for the esl mutant and their close association with yield and biomass decline, lipid peroxidation, lower root vitality, chlorophyll degradation and limited VHA activity. Higher K⁺ efflux, H⁺ and a lower Ca²⁺ influx was also observed in the esl mutant which could be the reason for abnormal functioning of mutant plants. These results illustrate that besides the well-known effect of senescence on plant physiology and yield decline, it can further shape the rhizosphere fungal community.

Plant host habitat and root exudates shape fungal diversity

The rhizospheric microbiome is clearly affected by plant species and certain of their functional traits. These functional traits allow plants to adapt to their environmental conditions by acquiring or conserving nutrients, thus defining different ecological resource-use plant strategies. In the present study, we investigated whether plants with one of the two nutrient-use strategies (conservative versus exploitative) could influence fungal communities involved in soil organic matter degradation and root exudate assimilation, as well as those colonizing root tissues. We applied a DNA-based, stable-isotope probing (DNA-SIP) approach to four grass species distributed along a gradient of plant nutrient resource strategies, ranging from conservative to exploitative species, and analyzed their associated mycobiota composition using a fungal internal transcribed spacer (ITS) and Glomeromycotina 18S rRNA gene metabarcoding approach. Our results demonstrated that fungal taxa associated with exploitative and conservative plants could be separated into two general categories according to their location: generalists, which are broadly distributed among plants from each strategy and represent the core mycobiota of soil organic matter degraders, root exudate consumers in the root-adhering soil, and root colonizers; and specialists, which are locally abundant in one species and more specifically involved in soil organic matter degradation or root exudate assimilation on the root-adhering soil and the root tissues. Interestingly, for arbuscular mycorrhizal fungi analysis, all plant roots were mainly colonized by Glomus species, whereas an increased diversity of Glomeromycotina genera was observed for the exploitative plant species Dactylis glomerata.

Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields

Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.

Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques

Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS), reduced tillage (RT), full tillage (FT), and crop rotation (CR). Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation) and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation). The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates) in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895), genus level (P = 0.026, F = 3.313) and on the species level (P = 0.033, F = 2.718). This study has shown that: (1) fungal diversity was changed under the influence different cultivation techniques; (2) techniques of maize cultivation and season were an important factors that can influence the biochemical activity of soil. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, even making it more stable during seasonal changes; (3) full tillage and crop rotation may change fungal community and soil function.

Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics

Alt'itudinal gradients strongly affect plant biodiversity, but the effects on microbial patterns remain unclear, especially in the large scale. We therefore designed an altitudinal gradient experiment that covered three climate zones to monitor soil microbial community dynamics and to compare those with plant and soil characteristics. Illumina sequencing of the 16S rRNA gene and ITS gene was used to analyze soil microbial (bacterial and fungal) diversity and composition, and fumigation-extraction was used to determine microbial biomass; the plant community metrics (i.e., percent cover, Shannon-Wiener, grass biomass, and carbon/nitrogen in leaf and biomass) and soil properties (i.e., soil moisture, soil temperature, bulk density, organic carbon, total nitrogen, and available nitrogen) were determined. The results showed that carbon/nitrogen in microbial biomass was higher at medium altitude and was positively related to carbon and nitrogen in both soil and grass biomass along the altitudinal gradients. Soil bacterial alpha diversity was significantly higher at medium altitude but fungal alpha diversity did not affected by altitudinal gradients; the effect of altitudinal gradients on bacterial beta diversity was larger than that on fungal beta diversity, although both groups were significantly affected by altitudinal gradients. Moreover, Alpha-proteobacteria, Beta-proteobacteria, and Gemmatimonadetes were significantly more abundant in higher altitude than in lower altitude, both Acidobacteria and Actinobacteria significantly declined with increasing altitude; other bacterial taxa such as Chloroflexi, Nitrospirae, Gamma-proteobacteria, and Delta-proteobacteria were significantly higher at medium altitudes. For fungal taxa, Basidiomycota and Ascomycota were the dominant phyla and responded insignificantly to the altitudinal gradients. The responses of microbial alpha diversity were mostly associated with plant Shannon index, organic carbon, and total nitrogen, whereas microbial beta diversity and composition mainly depended on soil moisture and temperature. Overall, these results suggest that soil bacteria rather than fungi can reflect changes in plant and soil characteristics along altitudinal gradients.