Continuous cropping system altered soil microbial communities and nutrient cycles

Understanding the response of microbial communities and their potential functions is essential for sustainability of agroecosystems under long-term continuous cropping. However, limited research has focused on investigating the interaction between soil physicochemical factors and microbial community dynamics in agroecosystems under long-term continuous cropping. This study probed into the physicochemical properties, metabolites, and microbial diversity of tobacco rhizosphere soils cropped continuously for 0, 5, and 20 years. The relative abundance of bacterial genera associated with nutrient cycling (e.g., Sphingomonas) increased while potential plant pathogenic fungi and beneficial microorganisms showed synergistic increases with the duration of continuous cropping. Variations in soil pH, alkeline nitrogen (AN) content, and soil organic carbon (SOC) content drove the shifts in soil microbial composition. Metabolites such as palmitic acid, 3-hydroxypropionic acid, stearic acid, and hippuric acid may play a key role in soil acidification. Those results enhance our ability to predict shifts in soil microbial community structure associated with anthropogenic continuous cropping, which can have long-term implications for crop production.

Intercropping system modulated soil-microbe interactions that enhanced the growth and quality of flue-cured tobacco by improving rhizospheric soil nutrients, microbial structure, and enzymatic activities

As the promotive/complementary mechanism of the microbe-soil-tobacco (Nicotiana tabacum L.) interaction remains unclear and the contribution of this triple interaction to tobacco growth is not predictable, the effects of intercropping on soil nutrients, enzymatic activity, microbial community composition, plant growth, and plant quality were studied, and the regulatory mechanism of intercropping on plant productivity and soil microenvironment (fertility and microorganisms) were evaluated. The results showed that the soil organic matter (OM), available nitrogen (AN), available phosphorus (AP), available potassium (AK), the urease activity (UE) and sucrase activity (SC), the diversity, abundance, and total and unique operational taxonomic units (OTUs) of bacteria and fungi as well as plant biomass in T1 (intercropping onion), T2 (intercropping endive), and T3 (intercropping lettuce) treatments were significantly higher than those of the controls (monocropping tobacco). Although the dominant bacteria and fungi at the phylum level were the same for each treatment, LEfSe analysis showed that significant differences in community structure composition and the distribution proportion of each dominant community were different. Proteobacteria, Acidobacteria, and Firmicutes of bacteria and Ascomycota and Basidiomycetes of fungi in T1, T2, and T3 treatments were higher than those of the controls. Redundancy analysis (RDA) suggested a close relation between soil characteristic parameters and microbial taxa. The correlation analysis between the soil characteristic parameters and the plant showed that the plant biomass was closely related to soil characteristic parameters. In conclusion, the flue-cured tobacco intercropping not only increased plant biomass and improved chemical quality but also significantly increased rhizospheric soil nutrient and enzymatic activities, optimizing the microbial community composition and diversity of rhizosphere soil. The current study highlighted the importance of microbe-soil-tobacco interactions in maintaining plant productivity and provided the potential fertilization practices in flue-cured tobacco production to maintain ecological sustainability.

Esterification with a Long-Chain Fatty Acid Elevates the Exposure Toxicity of Tigliane Diterpenoids from Euphorbia fischeriana Roots against Nematodes

In this study, two tigliane diterpenoids, 12-deoxyphorbol-13-hexadecanoate and 12-deoxyphorbol-13-acetate (prostratin), were identified from the methanol extract of the roots of Euphorbia fischeriana and were found to have the ability to significantly reduce the survival of Caenorhabditis elegans. It was determined that exposure to these two compounds had toxic effects on the growth, reproduction, locomotion behavior, and accumulation of lipids and lipofuscin of the nematodes. Moreover, the transcription levels of the genes associated with lipid accumulation, apoptosis, insulin, and nuclear hormone synthesis in C. elegans were significantly influenced. Interestingly, 12-deoxyphorbol-13-hexadecanoate produced exposure toxicity at lower concentrations than that of prostratin. Pearson correlation analysis indicates that the elevated exposure toxicity of 12-deoxyphorbol-13-hexadecanoate may be the result of differing transcription levels, which result from the differential expression of fat-6, egl-38, and cep-1. These results reveal that esterification with a long-chain fatty acid elevates the exposure toxicity of this tigliane diterpenoid, thus providing a basis for the application of tigliane diterpenoids in plant-derived nematicides.

Ecological Diversity of Bacterial Rhizomicrobiome Core during the Growth of Selected Wheat Cultivars

One of the latest ecological concepts is the occurrence of a biased rhizosphere of microorganisms recruited mostly through interactions among various components of the rhizosphere, including plant roots and the bulk soil microbiome. We compared the diverse attributes of the core microbiome of wheat rhizosphere communities with wheat (W) and legume (L) forecrops determined by three different methods in this study (membership, composition, and functionality). The conclusions of the three methods of microbiome core definition suggest the presence of generalists, i.e., some representative microorganisms from Proteobacteria, Actinobacteria, Hypomicrobiaceae, Bradyrhizobiaceae, Sphingomonas sp., in the wheat rhizomicrobiome. The relative abundance of the core microbiome accounted for 0.1976% (W) and 0.334% (L)-membership method and 6.425% (W) and 4.253% (L)-composition method. Additionally, bacteria of the specialist group, such as Rhodoplanes sp., are functionally important in the rhizomicrobiome core. This small community is strongly connected with other microbes and is essential for maintenance of the sustainability of certain metabolic pathways.

GC-MS Based Characterization, Antibacterial, Antifungal and Anti-Oncogenic Activity of Ethyl Acetate Extract of Aspergillus niger Strain AK-6 Isolated from Rhizospheric Soil

Rhizospheric soil is the richest niche of different microbes that produce biologically active metabolites. The current study investigated the antimicrobial, antifungal and anticancer activities of ethyl acetate extract of the potent rhizospheric fungus Aspergillus niger AK6 (AK-6). A total of six fungal isolates were isolated, and isolate AK-6 was selected based on primary screening. Further, it exhibited moderate antimicrobial activity against pathogens such as Klebsiella pneumonia, Candida albicans, Escherichia coli, Shigella flexneri, Bacillus subtilis and Staphylococcus aureus. The morphological and molecular characterization (18S rRNA) confirmed that the isolate AK-6 belonged to Aspergillus niger. Further, AK-6 showed potent antifungal activity with 47.2%, 59.4% and 64.1% of inhibition against Sclerotium rolfsii, Cercospora canescens and Fusarium sambucinum phytopathogens. FT-IR analysis displayed different biological functional groups. Consequently, the GC-MS analysis displayed bioactive compounds, namely, n-didehydrohexacarboxyl-2,4,5-trimethylpiperazine (23.82%), dibutyl phthalate (14.65%), e-5-heptadecanol (8.98%), and 2,4-ditert-butylphenol (8.60%), among the total of 15 compounds isolated. Further, the anticancer activity of AK-6 was exhibited against the MCF-7 cell line of human breast adenocarcinoma with an IC₅₀ value of 102.01 μg/mL. Furthermore, flow cytometry depicted 17.3%, 26.43%, and 3.16% of early and late apoptosis and necrosis in the AK-6 extarct treated MCF-7 cell line, respectively. The results of the present analysis suggest that the isolated Aspergillus niger strain AK-6 extract has the potential to be explored as a promising antimicrobial, antifungal and anticancer drug for medical and agricultural applications.

nov., a new member of the genus Solitalea isolated from rhizospheric soil of a jujube tree

A Gram-stain negative, aerobic, rod-shaped and creamy pink-coloured bacterium, designated MAHUQ-68^T, was isolated from rhizospheric soil of a jujube tree. Colonies grew at 10-40 °C (optimum, 28 °C), pH 6.0-9.0 (optimum pH, 7.0) and in the presence of 0-1.5 % NaCl (optimum 0-0.5 %). Positive for both catalase and oxidase activity. Strain MAHUQ-68^T hydrolysed casein, starch, aesculin and l-tyrosine. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-68^T clustered together within the genus Solitalea. The closest members were Solitalea longa HR-AV^T (98.8 % sequence similarity), Solitalea canadensis DSM 3403^T (96.9 %) and Solitalea koreensis R2A36-4^T (94.0 %). The genome of strain MAHUQ-68 ^T was 4 250 173 bp long with 68 scaffolds and 3 570 protein-coding genes. The genomic DNA G+C content of the type strain was 38.0 mol%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain MAHUQ-68^T and its closest relatives were 72.0-81.4% and 19.8-24.3 %, respectively. The major cellular fatty acids were iso-C_15 : 0 and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c). The main respiratory quinone was menaquinone-7. The polar lipids comprised phosphatidylethanolamine, an unidentified aminolipid and four unidentified lipids. Based on these data, strain MAHUQ-68^T represents a novel species in the genus Solitalea, for which the name Solitalea agri sp. nov. is proposed. The type strain is MAHUQ-68^T (=KACC 22249^T=CGMCC 1.19062^T).

Paenibacillus rhizolycopersici sp. nov., an oligotrophic bacterium isolated from a tomato plant in China

A Gram-positive, rod-shaped, motile, endospore-forming strain, DXFW5^T, was isolated from the rhizosphere soil of tomato. Strain DXFW5^T grew at 20-50 °C (optimum, 25-37 °C), pH 5-8 (optimum, pH 7) and in the presence of 3 % NaCl. It was positive for catalase and oxidase. Phylogenetic analysis using 16S rRNA gene sequences showed this strain was most closely related to Paenibacillus timonensis DSM 16943^T (98.0 %) and Paenibacillus barengoltzii DSM 22255^T (97.4 %). The DNA G+C content was 52.9 mol%. The digital DNA-DNA hybridization values between strain DXFW5^T and P. timonensis DSM 16943^T, P. barengoltzii DSM 22255^T and P. macerans DSM 24^T were 33.1, 24.9 and 21.2 %, respectively. The average nucleotide identity values between strain DXFW5^T and P. timonensis DSM 16943^T , P. barengoltzii DSM 22255^T and P. macerans DSM 24^T were 86.93, 81.77 and 75.98 %, respectively. The major fatty acids were anteiso-C_15 : 0 (55.1 %), iso-C_16 : 0 (13.2 %) and C_16 : 0 (10 %). The polar lipids of strain DXFW5^T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine two unidentified phospholipids and three unidentified lipids. MK-7 was the major isoprenoid quinone. Based on these results, it was concluded that the isolate represents a novel species of the genus Paenibacillus, for which the name Paenibacillus rhizolycopersici sp. nov. is proposed, with DXFW5^T (=ACCC 61751^T=JCM 34488^T) as the type strain.

Effects of the Long-Term Continuous Cropping of Yongfeng Yam on the Bacterial Community and Function in the Rhizospheric Soil

Replant disease caused by continuous cropping commonly occurs in yam with consecutive monoculture. However, little is known about how the continuous cropping of yam affects the rhizospheric soil bacterial community structure. In this study, the effects of continuous cropping on rhizospheric soil characteristics, bacterial diversity, and community structure were investigated in the Yongfeng yam fields under monoculture for 1, 5, 10, 15, and 20 years. Long-term monoculture caused soil acidification and increased the concentration of available potassium (AK) and available phosphorus (AP), and soil bacterial richness, but decreased the soil bacterial diversity. An exception was for the field under monoculture for 20 years as it showed the highest bacterial diversity. The relative abundance of beneficial bacteria, such as Proteobacteria, Actinobacteria, and Chloroflexi decreased while the relative abundance of harmful bacteria, including Gemmatimonadetes and Acidobacteria, increased with an extended continuous cultivation time. The networks varied among yams with different cultivation years and became complex with the increase in cultivation years. However, after time in monoculture, the bacterial network decreased gradually and existed stably. These changes in bacterial community composition and co-occurrence of networks may increase the potential risk of soil-borne disease and reduce the yield and quality of Yongfeng yam.

Impacts of Biogas Slurry Fertilization on Arbuscular Mycorrhizal Fungal Communities in the Rhizospheric Soil of Poplar Plantations

The majority of terrestrial plants are symbiotic with arbuscular mycorrhizal fungi (AMF). Plants supply carbohydrates to microbes, whereas AMF provide plants with water and other necessary nutrients-most typically, phosphorus. Understanding the response of the AMF community structure to biogas slurry (BS) fertilization is of great significance for sustainable forest management. This study aimed to look into the effects of BS fertilization at different concentrations on AMF community structures in rhizospheric soil in poplar plantations. We found that different fertilization concentrations dramatically affected the diversity of AMF in the rhizospheric soil of the poplar plantations, and the treatment with a high BS concentration showed the highest Shannon diversity of AMF and OTU richness (Chao1). Further analyses revealed that Glomerales, as the predominant order, accounted for 36.2-42.7% of the AMF communities, and the relative abundance of Glomerales exhibited negligible changes with different BS fertilization concentrations, whereas the order Paraglomerales increased significantly in both the low- and high-concentration treatments in comparison with the control. Furthermore, the addition of BS drastically enhanced the relative abundance of the dominant genera, Glomus and Paraglomus. The application of BS could also distinguish the AMF community composition in the rhizospheric soil well. An RDA analysis indicated that the dominant genus Glomus was significantly positively correlated with nitrate reductase activity, while Paraglomus showed a significant positive correlation with available P. Overall, the findings suggest that adding BS fertilizer to poplar plantations can elevate the diversity of AMF communities in rhizospheric soil and the relative abundance of some critical genera that affect plant nutrient uptake.

Different Fertilizers Applied Alter Fungal Community Structure in Rhizospheric Soil of Cassava (Manihot esculenta Crantz) and Increase Crop Yield

Soil microbes play an important role in the ecosystem and have a relationship with plant growth, development, and production. There are only a few reports on the effects of planting patterns of cassava on the microbial community structure in the rhizospheric soil. Here, we investigated the effects of different fertilization on the microbial community structure in the cassava rhizospheric soil. SC205 cultivar was used in this study as the experimental material. Compound fertilizer (CF) and reduced fertilizer (RF) were applied to the soil prior to planting. Soil samples were collected before harvest, and fungi were analyzed using IonS5^TMXL sequencing platform. Results showed that CF and RF treatments significantly increased cassava yield. Amplicon sequencing result indicated that the fungi richness in rhizospheric soil of cassava was increased after CF was applied, and the diversity was decreased. However, the fungal diversity and richness were decreased in rhizospheric soil after RF was applied. The most dominant fungal phylum was Ascomycota, which increased after fertilization. In addition, the abundance of beneficial fungi such as Chaetomium increased after fertilization, while that of pathogenic fungi such as Fusarium solani was decreased. The composition of the fungal community in rhizospheric soil with CF and RF applied was similar, but the richness and diversity of fungi were different. Canonical correspondence analysis (CCA) indicates there was a positive correlation between soil nutrition and fungal community structure. Overall, our results indicate that fertilization alters the fungal community structure of cassava rhizospheric soil, such that the abundance of potentially beneficial fungi increased, while that of potentially pathogenic fungi decreased, thereby significantly promoting plant growth and yield of cassava. Thus, during actual production, attention should be paid to maintain the stability of cassava rhizospheric soil micro-ecology.

nov., a novel actinobacterium isolated from rhizospheric soil of the wild plant Elymus tsukushiensis

An actinobacterial strain, designated KUDC0627^T, was isolated from rhizospheric soil that contained Elymus tsukushiensis on the Dokdo Islands, Republic of Korea. Cells were Gram-stain-positive, facultative anaerobic, non-motile and non-endospore-forming cocci. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KUDC0627^T belongs to the genus Microlunatus and is most closely related to Microlunatus soli DSM 21800^T (98.5 %), Microlunatus endophyticus DSM 100019^T (97.7 %) and Microlunatus ginsengisoli Gsoil 633^T (96.5 %). The average nucleotide identity scores and average amino acid identity values were all below the 95.0 % cut-off point. In silico DNA-DNA hybridization, using the Genome-to-Genome Distance Calculator, estimated that there is 22.3 % DNA relatedness between KUDC0627^T and M. soli DSM 21800^T. The genomic DNA G+C content was 66.9 mol%. The major menaquinone was MK-9(H₄) and the major diagnostic diamino acid in the cell-wall peptidoglycan was ll-diaminopimelic acid. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids and unidentified lipids. The major cellular fatty acids were iso-C_15 : 0, anteiso-C_15 : 0 and iso-C_16 : 0. Based on phenotypic, chemotaxonomic, and phylogenetic data, strain KUDC0627^T (=KCTC 39853^T=JCM 32702^T) represents a novel species, for which the name Microlunatus elymi sp. nov. is proposed.

Effects of Continuous Cropping of Sweet Potato on the Fungal Community Structure in Rhizospheric Soil

Soil microorganisms play an important role in the ecosystem, and have a certain relationship with the continuous cropping obstacles, which are common with sweet potato. However, there are few reports on the effects of continuous cropping of sweet potato on the microbial community structure in the rhizospheric soil. Here, we investigated the effects of continuous cropping of sweet potato on the fungal community structure in rhizospheric soil, in order to provide theoretical basis for prevention and control of continuous cropping obstacles. This study used X18 and Y138 varieties as experimental materials. Soil samples were collected during the early period of planting and harvest in two consecutive years, and fungi were analyzed using Illumina Miseq. Results showed that the fungi diversity and richness in rhizospheric soil of X18 and Y138 were significantly increased after continuous cropping; the most dominant fungi phylum was Ascomycota, which decreased significantly after continuous cropping. In addition, the content of beneficial fungi such as Chaetomium was reduced, while that of harmful fungi such as Verticillium, Fusarium, and Colletotrichum were increased. The composition of X18 and Y138 fungal community in the same sampling period after continuous cropping was similar, although that of the same sweet potato variety significantly differed with the sampling period. Overall, our results indicate that continuous cropping alters the fungal community structure of the sweet potato rhizospheric soil, such that the content of beneficial fungi decrease, while that of harmful fungi increase, thereby increasing soil-borne diseases and reducing the yield and quality of sweet potato. Furthermore, these effects are different for different sweet potato varieties. Thus, during actual production, attention should be paid to maintain the stability of sweet potato rhizospheric soil micro-ecology through rotation or application of microbial fertilizers and soil amendments to alleviate continuous cropping obstacles.

in Spain

During a study on biodiversity of bacteria inhabiting rhizospheric soil of rockrose (Cistus ladanifer L.), we isolated a strain coded RD25^T in a soil from Northern Spain. The 16S rRNA gene sequence showed 99.5 % identity with respect to the closest related species Pseudomonas brenneri DSM15294^T, and 99.4 % with respect to P. paralactis WS4672^T. The following related Pseudomonas species showed 99.3 % or less identity, and therefore RD25^T was classified within genus Pseudomonas. The phylogenetic analysis of 16S rRNA and the housekeeping genes rpoB, rpoD and gyrB suggested that this strain could be a novel species. The strain RD25^T has several polar-subpolar flagella. It can grow at 36 °C, at 0-6 % NaCl concentration and a range of pH 5-9. Positive for arginine dihydrolase and urease production, and negative for reduction of nitrate. The strain is catalase and oxidase positive. Major fatty acids are C_16 : 1 ω7c / C_16 : 1 ω6c in summed feature 3, C_16 : 0, and C_18 : 1 ω7c / C_18 : 1 ω6c in summed feature 8. The respiratory ubiquinone is Q9. The DNA G+C content was 59.9 mol%. The digital DNA-DNA hybridisation average values (dDDH) ranged between 30-61.2 % relatedness and the ANIb values ranged between 93.9-80.5 % with respect to the type strains of the closely related species. Therefore, the genotypic, genomic, phenotypic and chemotaxonomic data support the classification of strain RD25 as a novel species of genus Pseudomonas, for which the name P. edaphica sp. nov. is proposed. The type strain is RD25^T (=LMG 30152^T=CECT 9373^T).

Actinophytocola glycyrrhizae sp. nov. isolated from the rhizosphere of Glycyrrhiza inflata

A Gram-stain-positive, aerobic actinomycete, designated strain BMP B8152^T, was isolated from the rhizosphere of Glycyrrhiza inflata collected ashore, in Kashi, Xinjiang province, northwest PR China. A polyphasic approach was used to establish the taxonomic position of this strain. BMP B8152^T was observed to form non-fragmented substrate mycelium, and relatively scanty aerial mycelium with rod-shaped spores. Cell-wall hydrolysates contained meso-diaminopimelic acid, galactose, arabinose, glucose and rhamnose (trace). Mycolic acids were not detected. The diagnostic phospholipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, ninhydrin-positive phosphoglycolipid and phosphatidylinositol. The predominant menaquinone and fatty acid were MK-9(H4) and iso-branched hexadecanoate (iso-C16 : 0), respectively. The phylogenetic analyses based on the 16S rRNA gene sequences indicated that BMP B8152^T formed a distinct monophyletic clade clustered with Actinophytocola timorensisID05-A0653^T (98.8 % 16S rRNA gene sequence similarity), Actinophytocola oryzaeGMKU 367^T (98.6 %), Actinophytocola corallinaID06-A0464^T (98.2 %) and Actinophytocola burenkhanensisMN08-A0203^T (97.5 %). In addition, DNA-DNA hybridization values between BMP B8152^T and A. timorensisID05-A0653^T(44.2±3.6 %) and A. oryzaeGMKU 367^T(36.7±2.3 %) were well below the 70 % limit for species identification. The combined phenotypic and genotypic data indicate that the isolate represents a novel species of the genus Actinophytocola, for which the name Actinophytocola glycyrrhizae sp. nov., is proposed, with the type strain BMP B8152^T (=KCTC 49002^T=CGMCC 4.7433^T).

[Effects of elevated ozone concentrations on enzyme activities and organic acids content in wheat rhizospheric soil.]

The elevated concentration of tropospheric ozone (O₃) is an important global climate change driver, with adverse impacts on soil ecological environment and crop growth. In this study, a pot experiment was carried out in an open top chamber (OTC), to investigate the effects of elevated ozone concentration on soil enzyme activities (catalase, polyphenol oxidase, dehydrogenase and invertase), organic acids contents (oxalic acid, citric acid and malic acid) at different growth stages (tillering, jointing, heading and ripening stages) of wheat, and combined with the rhizospheric soil physicochemical properties and plant root characteristics to analyze the underlying reasons. The results showed that, elevated ozone concentration increased soil catalase, polyphenol oxidase, dehydrogenase and invertase activities at wheat ripening period to different degrees, with the effects on the activities of catalase and polyphenol oxidase being statistically significant. At the heading stage, activities of dehydrogenase and invertase were significantly increased by up to 76.7%. At the ripening stage, elevated ozone concentration significantly increased the content of citric acid and malic acid and redox potential (Eh) in rhizospheric soil, but reduced soil pH, electrical conductivity, total carbon and nitrogen. For root characteristics, elevated ozone concentrations significantly reduced the wheat root biomass, total root length and root surface area but increased the average root diameter.

Thailandins A and B, New Polyene Macrolactone Compounds Isolated from Actinokineospora bangkokensis Strain 44EHW(T), Possessing Antifungal Activity against Anthracnose Fungi and Pathogenic Yeasts

Two new polyene macrolactone antibiotics, thailandins A, 1, and B, 2, were isolated from the fermentation broth of rhizosphere soil-associated Actinokineospora bangkokensis strain 44EHW(T). The new compounds from this strain were purified using semipreparative HPLC and Sephadex LH-20 gel filtration while following an antifungal activity guided fractionation. Their structures were elucidated through spectroscopic techniques including UV, HR-ESI-MS, and NMR. These compounds demonstrated broad spectrum antifungal activity against fungi causing anthracnose disease (Colletotrichum gloeosporioides DoA d0762, Colletotrichum gloeosporiodes DoA c1060, and Colletotrichum capsici DoA c1511) as well as pathogenic yeasts (Candida albicans MT 2013/1, Candida parasilopsis DKMU 434, and Cryptococcus neoformans MT 2013/2) with minimum inhibitory concentrations ranging between 16 and 32 μg/mL. This is the first report of polyene antibiotics produced by Actinokineospora species as bioactive compounds against anthracnose fungi and pathogenic yeast strains.