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A comparative analysis of the rhizosphere microbial communities among three species of the Salix genus
PeerJ Life and Environment
Abstract
Rhizosphere microorganisms exert a significant influence in counteracting diverse external stresses and facilitating plant nutrient uptake. While certain rhizosphere microorganisms associated with Salix species have been investigated, numerous rhizosphere microorganisms from various Salix species remain underexplored. In this study, we employed high-throughput sequencing to examine the rhizosphere bacterial and fungal communities composition and diversity of three Salix species: Salix zangica (SZ), Salix myrtilllacea (SM), and Salix cheilophila (SC). Furthermore, the BugBase and FUNGuild were utilized to predict the functional roles of bacterial and fungal microorganisms. The findings revealed notable variations in the alpha and beta diversities of bacterial and fungal communities among the three Salix species exhibited significant differences ( p < 0.05). The relative abundance of Flavobacterium was highest in the SZ samples, while Microvirga exhibited significant enrichment in the SM samples. Microvirga and Vishniacozyma demonstrate the highest number of nodes within their respective bacterial and fungal community network structures. The functions of bacterial microorganisms, including Gram-positive, potentially pathogenic, Gram-negative, and stress-tolerant types, exhibited significant variation among the three Salix species ( p < 0.05). Furthermore, for the function of fungal microbe, the ectomycorrhizal guild had the highest abundance of symbiotic modes. This results demonstrated the critical role of ectomycorrhizal fungi in enhancing nutrient absorption and metabolism during the growth of Salix plants. Additionally, this findings also suggested that S. zangica plant was better well-suited for cultivation in stressful environments. These findings guide future questions about plant-microbe interactions, greatly enhancing our understanding of microbial communities for the healthy development of Salix plants.
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As carriers of direct contact between plants and the atmospheric environment, the microbiomes of phyllosphere microorganisms are increasingly recognized as an important area of study. Salt secretion triggered by salt-secreting halophytes elicits changes in the community structure and functions of phyllosphere microorganisms, and often provides positive feedback to the individual plant/community environment. In this study, the contents of Na⁺ and K⁺ in the rhizosphere, plant and phyllosphere of Tamarix chinensis were increased under 200 mmol/L NaCl stress. The increase in electrical conductivity, Na⁺ and K⁺ in the phyllosphere not only decreased the diversity of bacterial and fungal communities, but also decreased the relative abundance of Actinobacteriota and Basidiomycota. Influenced by electrical conductivity and Na⁺, the bacteria–fungus co-occurrence network under salt stress has higher complexity. Changes in the structure of the phyllosphere microbial community further resulted in a significant increase in the relative abundance of the bacterial energy source and fungal pathotrophic groups. The relative abundance of Actinobacteriota and Acidobacteriota in rhizosphere showed a decreasing trend under salt stress, while the complexity of the rhizosphere co-occurrence network was higher than that of the control. In addition, the relative abundances of functional groups of rhizosphere bacteria in the carbon cycle and phosphorus cycle increased significantly under stress, and were significantly correlated with electrical conductivity and Na⁺. This study investigated the effects of salinity on the structure and physicochemical properties of phyllosphere and rhizosphere microbial communities of halophytes, and highlights the role of phyllosphere microbes as ecological indicators in plant responses to stressful environments.
This study used the ITS approach based on Illumina MiSeq sequencing to assess the endosphere and rhizosphere fungal communities in healthy and diseased faba bean plants. The findings indicate that the most predominant phyla in all samples were Ascomycota (49.89–99.56%) and Basidiomycota (0.33–25.78%). In healthy endosphere samples, Glomeromycota (0.08–1.17%) was the only predominant phylum. In diseased endosphere samples, Olpidiomycota (0.04–1.75%) was the only predominant phylum. At the genus level, Penicillium (0.47–35.21%) was more abundant in rhizosphere soil, while Paraphoma (3.48–91.16%) was predominant in the endosphere roots of faba bean plants. Significant differences were observed in the alpha diversity of rhizosphere samples from different germplasm resources (p < 0.05). The fungal community structures were clearly distinguished between rhizosphere and endosphere samples and between healthy and diseased endosphere samples (p < 0.05). Saccharomyces was significantly enriched in diseased endosphere samples, whereas Apiotrichum was enriched in healthy endosphere samples. Vishniacozyma and Phialophora were enriched in diseased rhizosphere samples, while Pseudogymnoascus was enriched in healthy rhizosphere samples. Diseased samples displayed more strongly correlated genera than healthy samples. Saprotrophs accounted for a larger proportion of the fungal microbes in rhizosphere soil than in endosphere roots. This study provides a better understanding of the composition and diversity of fungal communities in the rhizosphere and endosphere of faba bean plants as well as a theoretical guidance for future research on the prevention or control of faba bean root rot disease.
Cryobacterium spp. are Gram-positive bacteria that inhabit diverse geographical locations, particularly extremely cold environments like the Polar Regions. However, strategies that enable them to survive in harsh Antarctic environments are not fully understood. In this study, we conducted a comparative genomic analysis of the Antarctic Cryobacterium sp. SO2 as well as other members of the Cryobacterium genus. Phylogenetic analysis revealed that strain SO2 formed a distinct cluster with the validly described species: C. adonitolivorans, C. actose, C. soli, C. arcticum, and C. zongtaii. Comparative analysis based on ANI and AAI indicated that strain SO2 is a novel species. Relative Synonymous Codon Usage (RSCU) of Cryobacterium species exhibits a bias towards codon ending with G/C. The genomes of all strains harbored numerous genes associated with environmental-associated stress responses, including oxidative stress response, general stress response, heat-stress response, cold-stress response, cell envelope alteration, and osmotic stress response. Strain SO2 and related strains possess genes involved in breaking down and utilization of both plant and animal carbohydrate-containing materials. KEGG annotation indicated that strain SO2 and related species shared almost the same genes for the metabolism of trehalose (TreS, partial TPS/TPP, and TreY-TreZ pathway) and glycogen (classical and non-classical pathway). The results from this work helped us to better understand the genomic characteristics of Cryobacterium spp. in terms of genomic diversity and adaptation strategies, which may have significant implications for biotechnology and climate change research.
Nocardioides, a genus belonging to Actinomycetes, can endure various low-nutrient conditions. It can degrade pollutants using multiple organic materials such as carbon and nitrogen sources. The characteristics and applications of Nocardioides are described in detail in this review, with emphasis on the degradation of several hard-to-degrade pollutants by using Nocardioides, including aromatic compounds, hydrocarbons, haloalkanes, nitrogen heterocycles, and polymeric polyesters. Nocardioides has unique advantages when it comes to hard-to-degrade pollutants. Compared to other strains, Nocardioides has a significantly higher degradation rate and requires less time to break down substances. This review can be a theoretical basis for developing Nocardioides as a microbial agent with significant commercial and application potential.
Drought is the most important natural disaster affecting crop growth and development. Crop rhizosphere microorganisms can affect crop growth and development, enhance the effective utilization of nutrients, and resist adversity and hazards. In this paper, six spring wheat varieties were used as research material in the dry farming area of the western foot of the Greater Khingan Mountains, and two kinds of water control treatments were carried out: dry shed rain prevention (DT) and regulated water replenishment (CK). Phenotypic traits, including physiological and biochemical indices, drought resistance gene expression, soil enzyme activity, soil nutrient content, and the responses of potential functional bacteria and fungi under drought stress, were systematically analyzed. The results showed that compared with the control (CK), the leaf wilting, drooping, and yellowing of six spring wheat varieties were enhanced under drought (DT) treatment. The plant height, fresh weight (FW), dry weight (DW), net photosynthetic rate (Pn) and stomatal conductance (Gs), soil total nitrogen (TN), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), microbial biomass phosphorus (MBP), organic carbon (SOC), and soil alkaline phosphatase (S-ALP) contents were significantly decreased, among which, FW, Gs and MBC decreased by more than 7.84%, 17.43% and 11.31%, respectively. By contrast, the soil total phosphorus (TP), total potassium (TK), and soil catalase (S-CAT) contents were significantly increased (p < 0.05). TaWdreb2 and TaBADHb genes were highly expressed in T.D40, T.L36, and T.L33 and were expressed at low levels in T.N2, T.B12, and T.F5. Among them, the relative expression of the TaWdreb2 gene in T.L36 was significantly increased by 2.683 times compared with CK. Soil TN and TP are the most sensitive to drought stress and can be used as the characteristic values of drought stress. Based on this, a drought-tolerant variety (T.L36) and a drought-sensitive variety (T.B12) were selected to further analyze the changes in rhizosphere microorganisms. Drought treatment and cultivar differences significantly affected the composition of the rhizosphere microbial community. Drought caused a decrease in the complexity of the rhizosphere microbial network, and the structure of bacteria was more complex than that of fungi. The Shannon index and network modular number of bacteria in these varieties (T.L36) increased, with rich small-world network properties. Actinobacteria, Chloroflexi, Firmicutes, Basidiomycota, and Ascomycota were the dominant bacteria under drought treatment. The beneficial bacteria Bacillus, Penicillium, and Blastococcus were enriched in the rhizosphere of T.L36. Brevibacillus and Glycomyce were enriched in the rhizosphere of T.B12. In general, drought can inhibit the growth and development of spring wheat, and spring wheat can resist drought hazards by regulating the expression of drought-related genes, regulating physiological metabolites, and enriching beneficial microorganisms.
The woody plant gender difference may lead to alteration in rhizosphere microbial communities and soil physicochemical properties. In this study, we investigated the differences in rhizosphere soil properties and microbial community structures of S. linearistipularis. Rhizosphere microorganisms were analyzed by high-throughput sequencing technology. The results showed that there were significant differences in rhizosphere soil nutrition between male and female S. linearistipularis plants in saline–alkali soil. The female S. linearistipularis plants significantly reduce soil pH values and significantly increase the soil water content (SWC), available total nitrogen (TN), soil organic matter (SOM), and soil urease activity (S-UE) compared to the male plant. The ACE, Chao, and Shannon index of the female plant was significantly higher than that of the male strain. At the level of Bacteriophyta, the relative abundance of Actinobacteriota in male and female S. linearistipularis was the highest, with 34.26% and 31.03%, respectively. Among the named bacterial genera, the relative abundance of Defluviicoccus of male and female plants was the highest, with 2.67% and 5.27%, respectively. At the level of Eumycophyta, the relative abundance of Ascomycetes in male and female plants was the highest, with 54.93% and 52.10%, respectively. Among the named fungi genera, the relative abundance of male and female plants of Mortierella was the highest, with 6.18% and 9.31%, respectively. In addition, soil pH, SOM, SWC, and S-UE activities were the main driving factors of soil microbial community structures. In the process of restoring saline–alkali land in the Songnen Plain, we may prioritise the planting of female S. linearistipularis, which also provides a theoretical basis for the microorganisms restoration of saline–alkali land in the Songnen plain.
Metal mineral mining results in releases of large amounts of heavy metals into the environment, and it is necessary to better understand the response of rhizosphere microbial communities to simultaneous stress from multiple heavy metals (HMs), which directly impacts plant growth and human health. In this study, by adding different concentrations of cadmium (Cd) to a soil with high background concentrations of vanadium (V) and chromium (Cr), the growth of maize during the jointing stage was explored under limiting conditions. High-throughput sequencing was used to explore the response and survival strategies of rhizosphere soil microbial communities to complex HM stress. The results showed that complex HMs inhibited the growth of maize at the jointing stage, and the diversity and abundance of maize rhizosphere soil microorganisms were significantly different at different metal enrichment levels. In addition, according to the different stress levels, the maize rhizosphere attracted many tolerant colonizing bacteria, and cooccurrence network analysis showed that these bacteria interacted very closely. The effects of residual heavy metals on beneficial microorganisms (such as Xanthomonas, Sphingomonas, and lysozyme) were significantly stronger than those of bioavailable metals and soil physical and chemical properties. PICRUSt analysis revealed that the different forms of V and Cd had significantly greater effects on microbial metabolic pathways than all forms of Cr. Cr mainly affected the two major metabolic pathways: microbial cell growth and division and environmental information transmission. In addition, significant differences in rhizosphere microbial metabolism under different concentrations were found, and this can serve as a reference for subsequent metagenomic analysis. This study is helpful for exploring the threshold for the growth of crops in toxic HM soils in mining areas and achieving further biological remediation.
The bacterial genus Cryobacterium includes at present 14 species that live in cryospheric environments. In this study, we analyzed 101 genomes of Cryobacterium with pure cultures obtained from GenBank. They could be classified into 44 species based on average nucleotide identity (ANI) analysis, showing the diversity of Cryobacterium. Among these, 19 strains in our laboratory were isolated from the glacier samples in China. The pairwise ANI values of these 19 strains and known species were <95%, indicating that they represented 19 novel species. The comparative genomic analysis showed significant differences in gene content between the two groups with a maximum growth temperature (Tmax) of ≤ 20°C and a Tmax of >20°C. A comprehensive and robust phylogenetic tree, including 14 known species and 19 novel species, was constructed and showed five phylogenetic branches based on 265 concatenated single-copy gene sequences. The Tmax parameter had a strong phylogenetic signal, indicating that the temperature adaptation of Cryobacterium was largely through vertical transfer rather than horizontal gene transfer and was affected by selection. Furthermore, using polyphasic taxonomy combined with phylogenomic analysis, we proposed 19 novel species of the genus Cryobacterium by the following 19 names: Cryobacterium serini sp. nov., Cryobacterium lactosi sp. nov., Cryobacterium gelidum sp. nov., Cryobacterium suzukii sp. nov., Cryobacterium fucosi sp. nov., Cryobacterium frigoriphilum sp. nov., Cryobacterium cryoconiti sp. nov., Cryobacterium lyxosi sp. nov., Cryobacterium sinapicolor sp. nov., Cryobacterium sandaracinum sp. nov., Cryobacterium cheniae sp. nov., Cryobacterium shii sp. nov., Cryobacterium glucosi sp. nov., Cryobacterium algoritolerans sp. nov., Cryobacterium mannosilyticum sp. nov., Cryobacterium adonitolivorans sp. nov., Cryobacterium algoricola sp. nov., Cryobacterium tagatosivorans sp. nov., and Cryobacterium glaciale sp. nov. Overall, the taxonomy and genomic analysis can improve our knowledge of phenotypic diversity, genetic diversity, and evolutionary characteristics of Cryobacterium.
Introduction
Soil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear.
Methods
This study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress.
Results and Discussion
Compared to the control (treated with ddH2O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.
A Gram-staining-positive, heterotrophic, non-spore-forming, non-motile, rod-shaped, strain ZS14-85T belonging to the genus Cryobacterium was isolated from soil in Antarctica. Growth was observed in the presence of 0–2% (w/v) NaCl, at pH 7.0–9.0 (optimum, pH 7.0) and 4–30 ℃ (optimum, 20 ℃). Phylogenetic analysis showed that strain ZS14-85T formed a lineage in the genus Cryobacterium. The digital DNA-DNA hybridization (dDDH) values between strain ZS14-85T and its close relatives Cryobacterium psychrotolerans CGMCC 1.5382T, Cryobacterium soli MCCC 1K03549T and Cryobacterium breve NBRC 113800T were 22.5, 22.3 and 22.2%, respectively. Orthologous Average Nucleotide Identity (OrthoANI) scores between strain ZS14-85T and C. psychrotolerans CGMCC 1.5382T, C. breve NBRC 113800T and C. soli MCCC 1K03549T were 78.7, 78.1 and 77.7%, respectively. The polar lipids of strain ZS14-85T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), one unidentified glycolipid (GL) and two unidentified lipids (L). The major fatty acids were anteiso-C15:0 (60.7%), iso-C16:0 (17.0%) and anteiso-C17:0 (15.2%). MK-10, MK-11 and MK-9 were the predominant respiratory menaquinones. Based on phenotypic, phylogenetic and genotypic data, a novel species, Cryobacterium zhongshanensis sp. nov. is proposed. The type strain is ZS14-85T (= CCTCC AB 2019396T = KCTC 49384T).
Near-natural forest management plays an important role in the maintenance of the long-term productivity and soil fertility of plantations. We conducted high-throughput absolute quantitative sequencing of 16S rRNA genes to compare the structures and diversity of rhizosphere soil bacterial communities among a pure Chinese fir (Cunninghamia lanceolata) plantation (S), a Cunninghamia lanceolata-Castanopsis hystrix-Michelia hedyosperma mixed plantation (SHX), and a Cunninghamia lanceolata-Castanopsis fissa mixed plantation (SD). The results revealed that near-natural forest management improved the rhizosphere soil properties of Chinese fir, especially the phosphorus content. Rhizosphere soil bacterial communities of Chinese fir in SHX and SD contained higher total absolute abundances and more unique operational taxonomic units (OTUs) than the pure plantation forest. Planctomycetes and Actinobacteria were abundant in SD, and Actinobacteria were enriched in SHX. The tree species also had an impact on the rhizosphere soil bacterial communities. For the rhizosphere soils of different tree species of SHX, the available phosphorus (AP) content of the rhizosphere of Chinese fir significantly surpassed those of Castanopsis hystrix and Michelia hedyosperma. Bacteria related to nitrogen fixing, such as Burkholderiales and Rhizobiales, were more abundant in Chinese fir in SD than in Castanopsis fissa. Acdiobacteria and Proteobacteria underpinned the differences found in the compositions of soil bacteria. The pH and soil organic matter were key variables influencing the rhizosphere soil bacterial communities. Our results demonstrated that in Chinese fir plantations, 12 years of near-natural management of introduced broad-leaved tree species can drive alterations of the physicochemical characteristics, bacterial community structure, and composition of rhizosphere soil, with tree species identity further influencing the rhizosphere soil bacterial community. IMPORTANCE Near-natural forest management is an important way to change the soil fertility decline and productivity reduction of pure Chinese fir plantations. At present, many detailed studies have been carried out on the impact of near-natural forest management on Chinese fir plantations at home and abroad. However, there are still few studies on the response of rhizosphere bacterial communities to near-natural forest management. Our study determined absolute quantities of Chinese fir rhizosphere bacterial communities in different mixed patterns. The results underscore the importance of near-natural forest management for Chinese fir plantation rhizosphere bacterial communities and provide new information on soil factors that affect rhizosphere bacterial communities in South China.
Phytoremediation that depends on excellent plant resources and effective enhancing measures is important for remediating heavy metal-contaminated soils. This study investigated the cadmium (Cd) tolerance and accumulation characteristics of Dahlia pinnata Cav. to evaluate its Cd phytoremediation potential. Testing in soils spiked with 5–45 mg kg–1 Cd showed that D. pinnata has a strong Cd tolerance capacity and appreciable shoot Cd bioconcentration factors (0.80–1.32) and translocation factors (0.81–1.59), indicating that D. pinnata can be defined as a Cd accumulator. In the rhizosphere, Cd stress (45 mg kg–1 Cd) did not change the soil physicochemical properties but influenced the bacterial community composition compared to control conditions. Notably, the increased abundance of the bacterial phylum Patescibacteria and the dominance of several Cd-tolerant plant growth–promoting rhizobacteria (e.g., Sphingomonas, Gemmatimonas, Bryobacter, Flavisolibacter, Nocardioides, and Bradyrhizobium) likely facilitated Cd tolerance and accumulation in D. pinnata. Comparative transcriptomic analysis showed that Cd significantly induced (P < 0.001) the expression of genes involved in lignin synthesis in D. pinnata roots and leaves, which are likely to fix Cd²⁺ to the cell wall and inhibit Cd entry into the cytoplasm. Moreover, Cd induced a sophisticated signal transduction network that initiated detoxification processes in roots as well as ethylene synthesis from methionine metabolism to regulate Cd responses in leaves. This study suggests that D. pinnata can be potentially used for phytoextraction and improves our understanding of Cd-response mechanisms in plants from rhizospheric and molecular perspectives.
The Antarctic continent is one of the most inhospitable places on earth, where living creatures, mostly represented by microorganisms, have specific physiological characteristics that allow them to adapt to the extreme environmental conditions. These physiological adaptations can result in the production of unique secondary metabolites with potential biotechnological applications. The current study presents a genetic and antibacterial characterization of four Antarctic fungi isolated from soil samples collected in Pedro Vicente Maldonado Scientific Station, at Fort William Point, Greenwich Island, Antarctica. Based on the sequences of the internal transcribed spacer (ITS) region, the fungi were identified as Antarctomyces sp., Thelebolus sp., Penicillium sp., and Cryptococcus gilvescens. The antibacterial activity was assessed against four clinical bacterial strains: Escherichia coli, Klebsiella pneumoniae, Enterococcus faecalis, and Staphylococcus aureus, by a modified bacterial growth inhibition assay on agar plates. Results showed that C. gilvescens and Penicillium sp. have potential antibiotic activity against all bacterial strains. Interestingly, Thelebolus sp. showed potential antibiotic activity only against E. coli. In contrast, Antarctomyces sp. did not show antibiotic activity against any of the bacteria tested under our experimental conditions. This study highlights the importance of conservation of Antarctica as a source of metabolites with important biomedical applications.
Antarctica has a great diversity of microorganisms with biotechnological potential but is not very well Known about yeasts with phosphate solubilization activity. Thus, the aim of this study was to evaluate the ability of yeasts from Antarctica lichens to solubilize phosphate in vitro. In the screening, 147 yeasts were tested and 43 (29%) showed P solubilization in solid NBRIP medium at 15.0 °C, with a higher prevalence of positive genera Vishniacozyma, followed by Cystobasidium. Most of the positive yeasts were isolated from Usnea auratiacoatra, followed by Polycauliona regalis and Lecania brialmontii. Two strains with better activity after screening were selected for the solubilization in the liquid medium, Vishniacozyma victoriae 2.L15 and A.L6 (unidentified). Vishniacozyma victoriae 2.L15 exhibiting activities at 25.0 °C (29.91 mg/L of phosphate and pH 6.85) and at 30.0 °C (619.04 mg/L of phosphate and pH 3.73) and A.L6 strain at 25.0 °C (25.05 mg/L of phosphate and pH 6.69) and at 30.0 °C (31.25 mg/L of phosphate and pH 6.47). Of eight organic acids tested by HPLC, tartaric and acetic acids were detected during phosphate solubilization, with greater release in the period of 144 (2.13 mg/L) and 72 (13.72 mg/L) hours, respectively. Future studies to elucidate the presence of functional genes for P metabolism in lichens, as well as studies in the field of proteomics for the discovery of yeast proteins related to P solubilization are needed. Thus, the high prevalence of lichen-associated yeast communities probably contributed to the high frequency of phosphate-solubilizing isolates in this study.
Graphical abstract
BF2P4-5 was isolated from the rhizosphere soil of tomato plants, and its potential to promote plant growth was investigated in tomato plants. An in vitro test revealed that the strain could fix nitrogen, solubilize phosphate and potassium, and synthesize indole acetic acid. The bacterial strain was identified and characterized as a kind of Pseudarthrobacter chlorophenolicus based on the analysis of culture characteristics, physiological and biochemical characteristics, and 16S rRNA gene sequence (GenBank accession number OP135548.1). pH 7.0, 15% NaCl, and 35 °C temperature were ideal for optimal strain growth under culture conditions. Tomato plants grown on a cocopeat substrate were inoculated with BF2P4-5 suspension (OD600 2.0). Positive control plants were inoculated with Nitrogen Phosphorus Potassium (NPK) fertilizer. This BF2P4-5 strain and NPK treatments were complemented with a negative control, in which only tap water was applied to tomato roots, thus, establishing three distinct treatment modalities with five replications each. Two months of greenhouse trials of inoculated tomato plants improved growth parameters. Interestingly, in most of the growth metrics evaluated, tomato plants treated with strain BF2P4-5 showed little to no variation with NPK fertilizer treatment, including plant height, stem length, girth, leaf number per plant, and chlorophyll content, when compared to uninoculated plants. Furthermore, the conditions for the cocopeat plants, including pH, EC, and moisture, were within acceptable limits. Furthermore, inoculation with BF2P4-5 increased the nitrogen, phosphorus, and potassium content available in the cocopeat medium. The results showed that the strain exhibited traits for the promotion of plant growth and could be deployed as an eco-friendly microbial biofertilizer for tomatoes and probably other essential crops.
The disposal of livestock wastes is an urgent task in China. Compost is highly regarded for its ability to treat livestock wastes and protect arable land. In particular, some problems of livestock manure in cold regions, such as low efficiency because of low environmental temperature in winter, urgently need to be solved. In order to provide valuable composting information in the cold area at low environmental temperatures, the composting experiments were carried out with cow manure and corn stalk as substrates. The properties and bacterial community of compost samples in different stages were investigated. The electrical conductivity (EC), total nitrogen (TN), total phosphorus (TP), and organic matter (OM) of the final compost were 551 μS/cm, 1.12, 0.77, and 63.5%, respectively. No E. coli or Ascaris eggs were detected. The temperature was the key factor to affect the physical-co-chemical and biological properties. The absolutely dominant genera were Sporosarcina, Virgibacillus, Flavobacterium, and Steroidobacter in heating, high temperature, cooling, and maturing stages, respectively. Also, these bacteria could act as biological indicators during the composting process. Cryobacterium, Caldicoprobacter, Virgibacillus, and Sporosarcina were relatively novel genera in the compost piles in a cold environment. The biodegradation of exogenous substances mainly occurs in the initial and maturing stages. It is proven that composting can be carried out successfully in early spring or later autumn after a harvest.
Rice sheath blight pathogen, Rhizoctonia solani , produces numerous sclerotia to overwinter. As a rich source of nutrients in the soil, sclerotia may lead to the change of soil microbiota. For this purpose, we amended the sclerotia of R. solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points. At the phyla level, Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control. An increased abundance of ammonia-oxidizing bacterium (AOB) Nitrosospira and Nitrite oxidizing bacteria (NOB) i.e., Nitrospira was observed, where the latter is reportedly involved in the nitrifier denitrification. Moreover, Thiobacillus , Gemmatimonas , Anaeromyxobacter and Geobacter , the vital players in denitrification, N 2 O reduction and reductive nitrogen transformation, respectively, depicted enhanced abundance in R. solani sclerotia-amended samples. Furthermore, asymbiotic nitrogen-fixing bacteria, notably, Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control. Plant growth promoting bacteria, such as Kribbella , Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil. As per our knowledge, this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R . solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.
Bacteria communities associated with plants have been given increasing consideration because they are arguably beneficial to their host plants. To understand the ecological and evolutionary impact of these mutualistic associations, it is important to explore the vast unknown territory of bacterial genomic diversity and their functional contributions associated with the major branches of the tree-of-life. Arguably, this aim can be achieved by profiling bacterial communities by applying high throughput sequencing approaches, besides establishing model plant organisms to test key predictions. This study utilized the Illumina Miseq reads of bacterial 16S rRNA sequences to determine the bacterial diversity associated with the endosphere of the leaves of the highly specialized rock spleenwort Asplenium delavayi (Aspleniaceae). By documenting the bacterial communities associated with ferns collected in natural occurrence and cultivation, this study discovered the most species-rich bacterial communities associated with terrestrial ferns reported until now. Despite the substantial variations of species diversity and composition among accessions, a set of 28 bacterial OTUs was found to be shared among all accessions. Functional analyses recovered evidence to support the predictions that changes in bacterial community compositions correspond to functional differentiation. Given the ease of cultivating this species, Asplenium delavayi is introduced here as a model organism to explore the ecological and evolutionary benefits created by mutualistic associations between bacteria and ferns.
Plant growth-promoting rhizobacteria are known to enhance the growth and antioxidant activity of several plants. However, the effects of such rhizobacteria on Geum aleppicum, a plant with pharmacological potential in Korea are unknown. In this study, we investigated the effects of Pseudarthrobacter sp. NIBRBAC000502770 treatment (100 mL/pot, every two weeks for 55 days), in the form of culture medium, 100−fold diluted culture, culture supernatant, and pelleted cells resuspended in water, on the growth, antibacterial activity and flavonoid content of G. aleppicum. The NIBRBAC000502770 strain showed high indole-3-acetic acid (IAA) content of 461.81 μg∙mL⁻¹. The dry weight of the roots was significantly higher in the supernatant, diluted culture, and pellet-treated plants compared to that in the control plants. Additionally, the plant height, root length, leaf length, leaf width, chlorophyll content, biomass, and dry weight of the shoot were highest in the pellet-treated plants. Further, methanol extracts of pellet-treated plants showed significantly high flavonoid content compared to that in the control plants (28 mg∙g⁻¹ vs. 7.5 mg∙g⁻¹) and exhibited strong antibacterial activity against Gram-positive and negative bacteria. These results demonstrate the beneficial effects of Pseudarthrobacter sp. NIBRBAC000502770 on the growth and flavonoid content of G. aleppicum.
Bull’s-eye rot, produced by Phlyctema vagabunda, is an important postharvest disease in apples. Current measures to control infection include synthetic fungicides, in addition to the application of copper hydroxide and potassium phosphite. However, growing public concern regarding fungicide residues in food has generated interest in developing non-chemical alternative control methods; biological control is one of the most promising alternatives. In this research, native endophytic yeasts were isolated and evaluated for the biocontrol of P. vagabunda in apples. The mechanisms of action involved were also determined. Our research found 2 isolates, Vishniacozyma victoriae EPL4.5 and EPL29.5, which exhibited biocontrol activity against P. vagabunda at 20 °C in apples, the incidence of bull’s-eye rot was reduced by 39% and 61%, respectively, and the severity of the disease was decreased by 67% and 70%, respectively, when apples were inoculated with these yeasts 24 h before applying the pathogen. The main mechanisms that could be involved in the observed biocontrol activity are the ability to form biofilms and the production of volatile organic compounds.
The increasing multidrug-resistance in pathogenic microbes and the emergence of new microbial pathogens like coronaviruses have necessitated the discovery of new antimicrobials to treat these pathogens. The use of antibiotics began after the discovery of penicillin by Alexander Fleming from Penicillium chrysogenum. This has attracted the scientific community to delve deep into the antimicrobial capabilities of various fungi in general and Phoma spp. in particular. Phoma spp. such as Phoma arachidicola, P. sorghina, P. exigua var. exigua, P. herbarum, P. multirostrata, P. betae, P. fimeti, P. tropica, among others are known to produce different bioactive metabolites including polyketides, macrosporin, terpenes and terpenoids, thiodiketopiperazines, cytochalasin derivatives, phenolic compounds, and alkaloids. These bioactive metabolites have already demonstrated their antimicrobial potential (antibacterial, antifun-gal, and antiviral) against various pathogens. In the present review, we have discussed the antimicrobial potential of secondary metabolites produced by different Phoma species. We have also deliberated the biogenic synthesis of eco-friendly antimicrobial silver nanoparticles from Phoma and their role as potential antimicrobial agents. Key points • Growing multidrug-resistance and emerging pathogens need new antimicrobial drugs • Different species of Phoma produce antimicrobial metabolites • Phoma spp. are potential synthesizers of silver nanoparticles demonstrating antimicrobial activity.
Fungal-biogeography studies have shown global patterns of biotic interactions on microbial biogeography. However, the mechanisms underlying these patterns remain relatively unexplored. To determine the dominant factors affecting forest soil fungal diversity in China, soil and leaves from 33 mountain forest reserves were sampled, and their properties were measured. We tested three hypotheses and established the most realistic one for China. The results showed that the soil fungal diversity (Shannon index) varied unimodally with latitude. The relative abundance of ectomycorrhizae was significantly positively correlated with the leaf nitrogen/phosphorus. The effects of soil available phosphorus and pH on fungal diversity depended on the ectomycorrhizal fungi, and the fungal diversity shifted by 93% due to available phosphorus, potassium, and pH. Therefore, we concluded that latitudinal changes in temperature and the variations in interactions between different fungal guilds (ectomycorrhizal, saprotrophic, and plant pathogenic fungi) did not have a major influence. Forest soil fungal diversity was affected by soil pH, available phosphorus, and potassium, which are driven by the phosphorus limitation of trees.
Objective
The purpose of this study was to explore the adaptive mechanism underlying the photosynthetic characteristics and the ion absorption and distribution of white willow (Salix alba L.) in a salt stress environment in cutting seedlings. The results lay a foundation for further understanding the distribution of sodium chloride and its effect on the photosynthetic system.
Method
A salt stress environment was simulated in a hydroponics system with different NaCl concentrations in one-year-old Salix alba L.branches as the test materials. Their growth, ion absorption, transport and distribution in the roots and leaves, and the changes in the photosynthetic fluorescence parameters were studied after 20 days under hydroponics.
Results
The results show that The germination and elongation of roots are promoted in the presence of 171mM NaCl, but root growth is comprehensively inhibited under increasing salt stress. Under salt stress, Na⁺ accumulates significantly in the roots and leaves, and the Na⁺ content and the Na⁺/K⁺ and Na⁺/Ca²⁺ root ratios are significantly greater than those in the leaves. When the NaCl concentration is ≤ 342mM, Salix alba can maintain relatively stable K⁺ and Ca²⁺ contents in its leaves by improving the selective absorption and accumulation of K⁺ and Ca²⁺ and adjusting the transport capacity of mineral ions to aboveground parts, while K⁺ and Ca²⁺ levels are clearly decreased under high salt stress. With increasing salt concentrations, the net photosynthetic rate (Pn), transpiration rate (E) and stomatal conductance (gs) of leaves decrease gradually overall, and the intercellular CO2 concentration (Ci) first decreases and then increases. When the NaCl concentration is < 342mM, the decrease in leaf Pn is primarily restricted by the stomata. When the NaCl concentration is > 342mM, the decrease in the Pn is largely inhibited by non-stomatal factors. Due to the salt stress environment, the OJIP curve (Rapid chlorophyll fluorescence) of Salix alba turns into an OKJIP curve. When the NaCl concentration is > 171mM, the fluorescence values of points I and P decrease significantly, which is accompanied by a clear inflection point (K). The quantum yield and energy distribution ratio of the PSⅡ reaction center change significantly (φPo, Ψo and φEo show an overall downward trend while φDo is promoted). The performance index and driving force (PIABS, PICSm and DFCSm) decrease significantly when the NaCl concentration is > 171mM, indicating that salt stress causes a partial inactivation of the PSII reaction center, and the functions of the donor side and the recipient side are damaged.
Conclusion
The above results indicate that Salix alba can respond to salt stress by intercepting Na⁺ in the roots, improving the selective absorption of K⁺ and Ca²⁺ and the transport capacity to the above ground parts of the plant, and increasing φDo, thus shows an ability to self-regulate and adapt.
Sugarcane is an important sugar and energy crop, and its yield is greatly affected by drought. Although a large number of studies have shown that rhizosphere microorganisms can help improve the adaptability of plants to biotic or abiotic stresses, there is a lack of studies on the adaptability of sugarcane rhizosphere microbial communities to host plants. Therefore, we conducted drought stress treatment and normal irrigation treatment on three sugarcane varieties GT21, GT31, and GT42 widely cultivated in Guangxi. Using 16S rDNA sequencing technology to analyze the changes in abundance of the sugarcane rhizosphere bacterial community under different treatments, combined with the determination of soil enzyme activity, soil nutrient content, and sugarcane physiological characteristics, we explored the sugarcane rhizosphere bacterial community response to drought stress. In addition, we used the structural equation model to verify the response path of sugarcane rhizosphere bacteria. The results show that the bacterial community structure in the rhizosphere of sugarcane is stable under normal water conditions. The change in the bacterial community structure under drought stress has a 25.2% correlation with the drought adaptability of sugarcane, but the correlation with drought stress is as high as 42.17%. The changes in abundance of rhizosphere bacteria under drought stress are mainly concentrated in the phylum Rhizobiales and Streptomycetales. This change is directly related to the physiological state of the host plant under drought stress, soil available phosphorus, soil urease and soil acid protease. We investigated the response species of rhizosphere microorganisms and their response pathways under drought stress, providing a scientific basis for rhizosphere microorganisms to assist host plants to improve drought adaptability.
Wood-inhabiting fungi are crucial to wood decay and decomposition in S. psammophila sand barriers, which in turn consumingly influence nutrient dynamics in desert soils. In the case of an extremely arid desert, as opposed to forests, little of known about the fungal community composition of decaying wood and the effects of decomposing wood on soil physical and chemical properties. Combined with high-throughput gene sequencing technology, we investigated the relationships between microenvironment factors with fungal community composition and diversity during the decomposition of Salix psammophila sand barriers. The results showed that the destruction of lignocellulose components during the decay process of S. psammophila sand barrier alters the physical and chemical properties of the surrounding soil. Compared with one-year sand barrier, lignin and cellulose of seven-year S. psammophila sand barrier decreased by 40.48% and 38.33%, respectively. Soil available potassium and available nitrogen increased by 39.80% and 99.46%, respectively. We confirmed that soil available nitrogen, soil pH and soil moisture content significantly affected the fungal community distribution of S. psammophila sand barriers. Sordariomycetes are mainly affected by the positive correlation of soil pH, while Eurotiomycetes are most affected by the positive correlation of soil moisture content and soil porosity. Although our results highlighted the importance of bidirectional interactions between fungi in decayed sand barriers and soil properties, their contribution to the desert ecosystem still needs further confirmation from future studies. However, overall our findings improved the current understanding of the sand barrier-soil interactions on the process of ecological restoration.
Phytoremediation, a method of phytomanagement using the plant holobiont to clean up polluted soils, is particularly effective for degrading organic pollutants. However, the respective contributions of host plants and their associated microbiota within the holobiont to the efficiency of phytoremediation is poorly understood. The identification of plant-associated bacteria capable of efficiently utilizing these compounds as a carbon source while stimulating plant-growth is a keystone for phytomanagement engineering. In this study, we sampled the rhizosphere and the surrounding bulk soil of Salix purpurea and Eleocharis obusta from the site of a former petrochemical plant in Varennes, QC, Canada. Our objectives were to: (i) isolate and identify indigenous bacteria inhabiting these biotopes; (ii) assess the ability of isolated bacteria to utilize alkanes and polycyclic aromatic hydrocarbons (PAHS) as the sole carbon source, and (iii) determine the plant growth-promoting (PGP) potential of the isolates using five key traits. A total of 438 morphologically different bacterial isolates were obtained, purified, preserved and identified through PCR and 16S rRNA gene sequencing. Identified isolates represent 62 genera. Approximately, 32% of bacterial isolates were able to utilize all five different hydrocarbons compounds. Additionally, 5% of tested isolates belonging to genera Pseudomonas, Acinetobacter, Serratia, Klebsiella, Microbacterium, Bacillus and Stenotrophomonas possessed all five of the tested PGP functional traits. This culture collection of diverse, petroleum-hydrocarbon degrading bacteria, with multiple PGP traits, represents a valuable resource for future use in environmental bio- and phyto-technology applications.
Phytoremediation is an attractive alternative to excavating and chemically treating contaminated soils. Certain plants can directly bioremediate by sequestering and/or transforming pollutants, but plants may also enhance bioremediation by promoting contaminant-degrading microorganisms in soils. In this study, we used high-throughput sequencing of bacterial 16S rRNA genes and the fungal internal transcribed spacer (ITS) region to compare the community composition of 66 soil samples from the rhizosphere of planted willows (Salix spp.) and six unplanted control samples at the site of a former petrochemical plant. The Bray-Curtis distance between bacterial communities across willow cultivars was significantly correlated with the distance between fungal communities in uncontaminated and moderately contaminated soils but not in highly contaminated (HC) soils (>2000 mg kg(-1) hydrocarbons). The mean dissimilarity between fungal, but not bacterial, communities from the rhizosphere of different cultivars increased substantially in the HC blocks. This divergence was partly related to high fungal sensitivity to hydrocarbon contaminants, as demonstrated by reduced Shannon diversity, but also to a stronger influence of willows on fungal communities. Abundance of the fungal class Pezizomycetes in HC soils was directly related to willow phylogeny, with Pezizomycetes dominating the rhizosphere of a monophyletic cluster of cultivars, while remaining in low relative abundance in other soils. This has implications for plant selection in phytoremediation, as fungal associations may affect the health of introduced plants and the success of co-inoculated microbial strains. An integrated understanding of the relationships between fungi, bacteria and plants will enable the design of treatments that specifically promote effective bioremediating communities.The ISME Journal advance online publication, 29 August 2013; doi:10.1038/ismej.2013.149.
The fungi present during pile-fermentation of Sichuan dark tea play a pivotal role in the development of its aroma and physical characteristics. Samples of tea leaves were collected on days 0 (YC-raw material), 8 (W1-first turn), 16 (W2-second turn), 24 (W3-third turn), and 32 (W4-out of pile) during pile-fermentation. High-throughput sequencing revealed seven phyla, 22 classes, 41 orders, 85 families, 128 genera, and 184 species of fungi. During fermentation, the fungal diversity index declined from the W1 to W3 stages and then increased exponentially at the W4 stage. A bar plot and heatmap revealed that Aspergillus , Thermomyces , Candida , Debaryomyces , Rasamsonia , Rhizomucor , and Thermoascus were abundant during piling, of which Aspergillus was the most abundant. Cluster analysis revealed that the W4 stage of fermentation is critical for fungal growth, diversity, and the community structure in Sichuan dark tea. This study revealed the role of fungi during pile-fermentation in the development of the essence and physical characteristics of Sichuan dark tea. This study comes under one of the Sustainable Development Goals of United Nations Organization (UNO) to “Establish Good Health and Well-Being”.
The Willows (genus Salix), with more than 330–500 species and 200 hybrids, are trees, shrubs or prostrate plants that are widely distributed in Africa, North America, Europe, and Asia. The genus is traditionally used in folk medicine and represents a valuable source of biologically active compounds among them salicin, a prodrug for salicylic acid. Altogether, 322 secondary metabolites were characterized in the genus including flavonoids 94) (flavonols, flavones, flavanones, isoflavones, flavan-3-ols (catechins and procyanidins), chalcones, dihydrochalcone, anthocyanins, dihydroflavonols), phenolic glycosides (76), organic acids (28), and non-phenolic glycosides (17), sterols and terpenes (17), simple phenolics 13) and lignans 7) in addition to volatiles and fatty acids (69). Furthermore, willows exert analgesic, anti-inflammatory, antioxidant, anticancer, cytotoxic, antidiabetic, antimicrobial, antiobesity, neuroprotective and hepatoprotective activities. The current review provides an updated summary of the importance of willows, their chemical composition and pharmacological activities.
Background
Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry was only reported by a few studies and remains elusive. Comparison and interpretation of the characteristics of the rhizosphere microbiome of blueberry are critical important to maintain its health.
Results
In this study, a total of 20 rhizosphere soil samples, including 15 rhizosphere soil samples from three different blueberry varieties and five bulk soil samples, were sequenced with a high-throughput sequencing strategy. Based on these sequencing datasets, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities for three different blueberry varieties and compared our results with a previous study focused on the rhizosphere microbiome of blueberry varieties. Our results demonstrated significant differences in alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated, and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria , Actinobacteria , and Acidobacteria . Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective.
Conclusions
This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.
Fast growing, high biomass willows (Salix sp.) have been extensively used for the phytoremediation of trace element-contaminated environments, as they have an extensive root system and they tolerate abiotic stressors such as drought and metal toxicity. Being dual mycorrhizal plants, they can engage single or simultaneous symbiotic associations with both arbuscular mycorrhizal (AM) fungi and ectomycorrhizal (EM) fungi, which can improve overall plant health and growth. The aim of this study was to test the effect of these mycorrhizal fungi on the growth and trace element (TE) extraction potential of willows. A field experiment was carried out where we grew Salix miyabeana clone SX67 on the site of a decommissioned industrial landfill, and inoculated the shrubs with an AM fungus Rhizophagus irregularis, an EM fungus Sphaerosporella brunnea, or a mixture of both. After two growing seasons, the willows inoculated with the EM fungus S. brunnea produced significantly higher biomass. Ba, Cd and Zn were found to be phytoextracted to the aerial plant biomass, where Cd presented the highest bioconcentration factor values in all treatments. Additionally, the plots where the willows received the S. brunnea inoculation showed a significant decrease of Cu, Pb, and Sn soil concentrations. AM fungi inoculation and dual inoculation did not significantly influence biomass production and soil TE levels.
Isoprene is a climate-active gas whose wide-spread global production stems mostly from terrestrial plant emissions. The biodegradation of isoprene is carried out by a number of different bacteria from a wide range of environments. This study investigates the genome of a novel isoprene degrading bacterium Nocardioides sp. WS12, isolated from soil associated with Salix alba (Willow), a tree known to produce high amounts of isoprene. The Nocardioides sp. WS12 genome was fully sequenced, revealing the presence of a complete isoprene monooxygenase gene cluster, along with associated isoprene degradation pathway genes. Genes associated with rubber degradation were also present, suggesting that Nocardioides sp. WS12 may also have the capacity to degrade poly-cis-1,4-isoprene.
Soil microbes play important roles in plant growth and in the biogeochemical cycling of earth’s elements. However, the structure and functions of the microbial community associated with the growth of second-generation energy crops, such as Miscanthus, remain unclear. Thus, in this study, the composition and function of the bacterial and fungal communities associated with Miscanthus cultivation were analyzed by MiSeq sequencing combined with PICRUSt and FUNGUIld analyses. The results of community composition and diversity index analyses showed that Miscanthus cultivation significantly altered the bacterial and fungal community composition and reduced bacterial and fungal diversity. In addition, Miscanthus cultivation increased the soil organic matter (SOM) and total nitrogen (TN) contents. The correlation analysis between microbial community composition and environmental factors indicated that SOM and TN were the most important factors affecting bacterial and fungal communities. Miscanthus cultivation could enrich the abundances of Pseudomonas, Rhizobium, Luteibacter, Bradyrhizobium, Phenylobacterium and other common plant-promoting bacteria, while also increasing Cladophialophora, Hymenula, Magnaporthe, Mariannaea, etc., which predicted corresponded to the saprotrophic, plant pathogenic, and pathotrophic trophic modes. The PICRUSt predictive analysis indicated that Miscanthus cultivation altered the metabolic capabilities of bacterial communities, including the metabolism of carbon, nitrogen, and phosphorus cycle. In addition, FUNGUIld analysis indicated that Miscanthus cultivation altered the fungal trophic mode. The effects of Miscanthus on the communities and function of bacteria and fungi varied among Miscanthus species. Miscanthus specie Xiangdi NO 1 had the greatest impact on soil bacterial and fungal communities, whereas Miscanthus specie Wujiemang NO 1 had the greatest impact on soil bacteria and fungi functions. The results of this study provide a reference for the composition and function of microbial communities during the growth of Miscanthus.
Background:
The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in soil stability, plant biomass decomposition, and endophytic interactions with plants. They may also form symbiotic associations with biocrust components or be latent saprotrophs or pathogens that live on plant tissues. However, their functional potential in arid soils, where organic matter, nutrients and water are very low or only periodically available, is poorly characterized.
Results:
Five Ascomycota fungi were isolated from different soil crust microhabitats and rhizosphere soils around the native bunchgrass Pleuraphis jamesii in an arid grassland near Moab, UT, USA. Putative genera were Coniochaeta, isolated from lichen biocrust, Embellisia from cyanobacteria biocrust, Chaetomium from below lichen biocrust, Phoma from a moss microhabitat, and Aspergillus from the soil. The fungi were grown in replicate cultures on different carbon sources (chitin, native bunchgrass or pine wood) relevant to plant biomass and soil carbon sources. Secretomes produced by the fungi on each substrate were characterized. Results demonstrate that these fungi likely interact with primary producers (biocrust or plants) by secreting a wide range of proteins that facilitate symbiotic associations. Each of the fungal isolates secreted enzymes that degrade plant biomass, small secreted effector proteins, and proteins involved in either beneficial plant interactions or virulence. Aspergillus and Phoma expressed more plant biomass degrading enzymes when grown in grass- and pine-containing cultures than in chitin. Coniochaeta and Embellisia expressed similar numbers of these enzymes under all conditions, while Chaetomium secreted more of these enzymes in grass-containing cultures.
Conclusions:
This study of Ascomycota genomes and secretomes provides important insights about the lifestyles and the roles that Ascomycota fungi likely play in arid grassland, ecosystems. However, the exact nature of those interactions, whether any or all of the isolates are true endophytes, latent saprotrophs or opportunistic phytopathogens, will be the topic of future studies.
Isoprene is a climate-active gas and one of the most abundant biogenic volatile organic compounds (BVOC) released into the atmosphere. In the terrestrial environment, plants are the primary producers of isoprene, releasing between 500 and 750 million tons per year to protect themselves from environmental stresses such as direct radiation, heat, and reactive oxygen species. While many studies have explored isoprene production, relatively little is known about consumption of isoprene by microbes and the most well-characterized isoprene degrader is a Rhodococcus strain isolated from freshwater sediment. In order to identify a wider range of bacterial isoprene-degraders in the environment, DNA stable isotope probing (DNA-SIP) with ¹³C-labeled isoprene was used to identify active isoprene degraders associated with soil in the vicinity of a willow tree. Retrieval by PCR of 16S rRNA genes from the ¹³C-labeled DNA revealed an active isoprene-degrading bacterial community dominated by Proteobacteria, together with a minor portion of Actinobacteria, mainly of the genus Rhodococcus. Metagenome sequencing of ¹³C-labeled DNA from SIP experiments enabled analysis of genes encoding key enzymes of isoprene metabolism from novel isoprene degraders. Informed by these DNA-SIP experiments and working with leaves and soil from the vicinity of tree species known to produce high amounts of isoprene, four novel isoprene-degrading strains of the genera Nocardioides, Ramlibacter, Variovorax and Sphingopyxis, along with strains of Rhodococcus and Gordonia, genera that are known to contain isoprene-degrading strains, were isolated. The use of lower concentrations of isoprene during enrichment experiments has revealed active Gram-negative isoprene-degrading bacteria associated with isoprene-emitting trees. Analysis of isoprene-degradation genes from these new isolates provided a more robust phylogenetic framework for analysis of isoA, encoding the α-subunit of the isoprene monooxygenase, a key molecular marker gene for cultivation-independent studies on isoprene degradation in the terrestrial environment.
Fungal influence on density dependence
Tree species in highly diverse tropical forests tend to exhibit conspecific negative density dependence, a phenomenon whereby individuals of the same species tend to grow at a distance from one another. This is understood to be a key driver of species coexistence. The strength of negative density dependence varies between species, but the mechanisms driving this variation are unknown. Chen et al. studied tree species in a subtropical forest in China and found an important role for soil-dwelling fungi in this variation. Elevated accumulation of pathogenic fungi leads to stronger negative density dependence, whereas elevated accumulation of mutualistic fungi leads to weaker negative density dependence.
Science , this issue p. 124
Extensive studies have shown that plants can develop stress memories to improve their tolerance to subsequent abiotic stresses. However, the comprehensive understanding of sex-related stress memory in response to drought, low temperature, and their cross conditions remains an ongoing pursuit. In this study, we investigated plant growth, photosynthetic physiology, and the leaf metabolome in female and male Salix myrtillacea exposed to drought, low temperature, and their cross. Our results underscored the profound detrimental impact of different stresses on growth performance and the photosynthetic apparatus in both sexes. Furthermore, female willows showed greater tolerance to drought, low-temperature and cross-stress, as evidenced by their improved growth performance and higher abundance of amino acids (e.g., proline, histidine, glutamine and methionine) and sugar alcohols (e.g., melibiose, sorbitol and mannitol). Conversely, male counterparts displayed a richer diversity and abundance of flavonoids in comparison to females. In the key metabolic pathways, flavonoids (e.g., syringetin, laricitrin and isoquercitrin) were more abundant under cross-stressed conditions, suggesting that the generation of stress memory significantly enhanced the resistance of male willows at the metabolic level. Taken together, these results suggest that the enhanced resistance of female and male plants is associated with a trade-off between growth and defense. The formation of stress memory in females and males may be associated with greater plasticity in growth performance and accumulation of defensive metabolites, contributing to sex-specific patterns of adversity resistance and niche segregation.
Climate change is pushing species outside of their evolved tolerances. Plant populations must acclimate, adapt, or migrate to avoid extinction. However, because plants associate with diverse microbial communities that shape their phenotypes, shifts in microbial associations may provide an alternative source of climate tolerance. Here, we show that tree seedlings inoculated with microbial communities sourced from drier, warmer, or colder sites displayed higher survival when faced with drought, heat, or cold stress, respectively. Microbially mediated drought tolerance was associated with increased diversity of arbuscular mycorrhizal fungi, whereas cold tolerance was associated with lower fungal richness, likely reflecting a reduced burden of nonadapted fungal taxa. Understanding microbially mediated climate tolerance may enhance our ability to predict and manage the adaptability of forest ecosystems to changing climates.
Willows (Salix spp.) are promising extractors of cadmium (Cd), with fast growth, high biomass production, and high Cd accumulation capacity. However, the molecular mechanisms underlying Cd uptake and detoxification are currently poorly understood. Analysis of the Cd uptake among 30 willow genotypes in hydroponic systems showed that the S. suchowensis and S. integra hybrids, Jw8–26 and Jw9–6, exhibited distinct Cd accumulation and resistance characteristics. Jw8–26 was a high Cd-accumulating and tolerant willow, while Jw9–6 was a low Cd-accumulating and relatively Cd-intolerant willow. Therefore, these two genotypes were ideal specimens for determining the molecular mechanisms of Cd uptake and detoxification. To identify relevant genes in Cd handling, the parent S. suchowensis was treated with Cd and RNA-seq analysis was performed. SsIRT, SsHMA, and SsGST, in addition to the transcription factors SsERF, SsMYB, and SsZAT were identified as being associated with Cd uptake and resistance. Because membrane-localised heavy metal transporters mediate Cd transfer to plant tissues, a total of 17 SsIRT and 12 SsHMA family members in S. suchowensis were identified. Subsequently, a thorough bioinformatics analysis of the SsIRT and SsHMA families was conducted, and their transcript levels were analysed in the roots of the two hybrids. The transcript levels of SsIRT9 in roots were positively correlated with the observed differences in Cd accumulation in Jw8–26 versus Jw9–6. Jw8–26 displayed higher SsIRT9 expression levels and higher Cd accumulation than Jw9–6; therefore, SsIRT9 may be involved in Cd uptake. Gene expression analysis also revealed that SsHMA1 was a candidate gene associated with Cd resistance. These results lay the foundation for understanding the molecular mechanism of Cd transfer and detoxification in willows, and provide guidance for the screening and breeding of high Cd-accumulating and tolerant willow genotypes via genetic engineering.
The adverse effects of drought on plants are gradually exacerbated with global climatic change. Amelioration of the drought stress that is induced by low doses of acetic acid (AA) has been caused great interest in plants. However, whether AA can change soil microbial composition is still unknown. Here, we investigated how exogenous AA regulates the physiology, rhizosphere soil microorganisms and metabolic composition on Salix myrtillacea under drought stress. The physiological results showed that AA could improve the drought tolerance of S. myrtillacea. Azotobacter and Pseudomonas were enriched in the rhizosphere by AA irrigation. AA significantly increased the relative contents of amino acid metabolites (e.g., glycyl-L-tyrosine, l-glutamine and seryl-tryptophan) and decreased the relative contents of phenylpropane metabolites (e.g., fraxetin and sinapyl aldehyde) in soils. The enrichments of Azotobacter and Pseudomonas were significantly correlated with glycyl-L-tyrosine, l-glutamine, seryl-tryptophan, fraxetin and sinapyl aldehyde, which could increase the stress resistance by promoting nitrogen (N) uptake for willows. Furthermore, inoculation with Azotobacter chroococcum and Pseudomonas fluorescens could significantly improve willows drought tolerance. Therefore, our results reveal that the changes of plant physiology, rhizosphere soil microorganisms and metabolic composition induced by AA can improve willows drought resistance by enhancing N uptake.
Drought is a serious menace to agriculture across the world. However, it is still not clear how this will affect crop-associated microbial communities. Here, we experimentally manipulated precipitation in the field for two years and compared the bacterial communities associated with leaves, roots, and rhizosphere soils of two different wheat genotypes. The bacterial 16S rRNA gene was amplified and sequenced, while 542 microorganisms were isolated and screened for their tolerance to osmotic stress. The bacterial community was not significantly affected by the precipitation manipulation treatments but differed drastically from one plant compartment to the other. Forty-four isolates, mostly bacteria, showed high levels of resistance to osmotic stress by growing in liquid medium supplemented with 30% polyethylene glycol. The Actinobacteria were overrepresented among these isolates, and in contrast to our expectation, precipitation treatments did not influence the odds of isolating osmotic stress-resistant bacteria. However, the odds were significantly higher in the leaves as compared to the roots, the rhizosphere, or the seeds. Our results suggest that isolation efforts for wheat-compatible water stress resistant bacteria should be targeted at the leaf endosphere and that short-term experimental manipulation of precipitation does not result in a more resistant community.
Climate-related flooding poses a potential challenge to phytoremediation of metal polluted areas. In the present study, uptake, translocation and accumulation of heavy metals (Cd, Zn and Cu), and their phytoavailability in six flood-tolerant Salix genotypes were investigated under simulated seasonal flooding conditions (non-flooding conditions were kept as the control). Plants were cultivated in a greenhouse with open windows using the soil polluted with Cd, Zn and Cu for 110 days. All the control (non-flooded) genotypes did not exhibit visible toxic symptoms, whereas the flooded genotypes showed leaf chlorosis and developed both lenticels and adventitious roots. Biomass production and metal accumulation in tissues varied with Salix genotypes. The flooded genotypes dramatically decreased aerial biomass production compared with corresponding non-flooded genotypes. All the control Salix genotypes showed relatively high accumulation for Cd, Zn and Cu in aerial parts due to high EDTA-extractable metals in the rhizosphere, exhibiting phytoextraction features. In contrast, the flooded genotypes drastically decreased uptake, translocation, accumulation, and extraction capacities for Cd, Zn and Cu in aerial parts, differing with genotypes, and tended to phyto-stabilize them in roots, especially Cu. This study indicated that flooding is a leading factor on phytoremediation efficiency for contaminated sites with willows.
Wetland plants are often used as the main body of soil, and the rhizosphere is a hot spot migration and transformation. Response mechanism to rhizosphere microorganisms on chromium(Cr) stressing could help improve the phytoremediation system. Cyperus alternifolius(CA) is selected as the research object by Cr-stress treatments and uncontaminated treatments with different cultivated pattern, included sole cultivated pattern(CAI), two-cultivated pattern (CAII), three-cultivated pattern (CAIII), and the un-planted blank samples (CK). 16s rRNA gene sequencing and metagenomic sequencing are performed to measure rhizosphere microbial community. And Five common enzymes in rhizosphere soils were observed: β-1,4-glucosidase (BG), β-N-acetylglucosaminidase (NAG), β-1,4-xylosidase (BX), cellobiohydrolase (CBH) and Leucine amino peptidase (LAP) in the rhizosphere. The results show that Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, Gemmatimonadetes, Deltaproteobacteria are top five (63.97%) of the total sequence number. Wetland plants enriched a large amount of soil Cr in themselves, and the rhizosphere microorganisms don’t show significant difference in community structure after affecting. 10.48% variation of microbial community is caused by Cr-stress. Acidovorax showed a great potential for chromium resistance. BX involvement in tolerance processes indirectly affects microbial communities (P < 0.01), there is a strong linear relationship between enzyme activity and the plants accumulating Cr and microbial community within 15.58% variant. The material accumulation and microbial quantity of CAIII are relatively low, but high biodiversity remains after affecting. These results provide references for in-depth understanding of rhizosphere microbial response to heavy metal pollution in wetland phytoremediation and interaction between wetland plants and rhizosphere microorganisms.
Climate change, with its extreme temperature, weather and precipitation patterns, is a major global concern of dryland farmers, who currently meet the challenges of climate change agronomically and with growth of drought-tolerant crops. Plants themselves compensate for water stress by modifying aerial surfaces to control transpiration and altering root hydraulic conductance to increase water uptake. These responses are complemented by metabolic changes involving phytohormone network-mediated activation of stress response pathways, resulting in decreased photosynthetic activity and the accumulation of metabolites to maintain osmotic and redox homeostasis. Phylogenetically diverse microbial communities sustained by plants contribute to host drought tolerance by modulating phytohormone levels in the rhizosphere and producing water-sequestering biofilms. Drylands of the Inland Pacific Northwest, USA, illustrate the interdependence of dryland crops and their associated microbiota. Indigenous Pseudomonas spp. selected there by long-term wheat monoculture suppress root diseases via the production of antibiotics, with soil moisture a critical determinant of the bacterial distribution, dynamics and activity. Those pseudomonads producing phenazine antibiotics on wheat had more abundant rhizosphere biofilms and provided improved tolerance to drought, suggesting a role of the antibiotic in alleviation of drought stress. The transcriptome and metabolome studies suggest the importance of wheat root exudate-derived osmoprotectants for the adaptation of these pseudomonads to the rhizosphere lifestyle and support the idea that the exchange of metabolites between plant roots and microorganisms profoundly affects and shapes the belowground plant microbiome under water stress.
Leaf δ¹⁵N and δ¹³C are important functional traits in biogeographic studies of forest ecosystems. However, little is known about their relationships with soil fungal biodiversity, ectomycorrhizal and plant pathogenic abundance at large scales. In this study, leaf and soil samples were collected from 33 forest reserves along a large range across China to explore the associations between leaf δ¹⁵N and δ¹³C and soil fungal biodiversity, ectomycorrhizal and plant pathogenic relative abundance, using molecular and stable isotope techniques. Leaf δ¹⁵N was significantly positively correlated with the soil fungal Shannon index, significantly negatively correlated with the relative abundance of plant pathogens, and significantly positively correlated with the relative abundance of ectomycorrhizas. Leaf δ¹³C was significantly positively correlated with the relative abundance of ectomycorrhizas and significantly inverted unimodal correlated with the relative abundance of plant pathogens. Soil–plant–microbial interactions may contribute to variations in leaf δ¹⁵N, δ¹³C, and soil fungal communities among different types of forest ecosystems. Temperature and precipitation were the main factors that affected large-scale latitudinal and longitudinal biogeographic patterns. Leaf δ¹⁵N was mainly affected by the relative abundance of ectomycorrhizal fungi and leaf δ¹³C was affected by the mean annual temperature and mean annual precipitation. Leaf δ¹⁵N and δ¹³C may be indicators that reflect soil fungal communities in forest ecosystems.
Plant-associated microorganisms play an important role in controlling heavy metal uptake and accumulation in aerial parts. The microbial community and its interaction with Cd accumulation by willow were assessed to explore the association of phytoextraction efficiency and rhizospheric microbial populations.
Therefore, the rhizosphere microbial compositions of three willow genotypes grown in two Cd polluted sites were investigated, focusing on their interactions with phytoremediation potential. Principal coordinate analysis revealed a significant effect of genotype on the rhizosphere microbial communities. Distinct beneficial microorganisms, such as plant growth promoting bacteria (PGPB) and mycorrhizal fungi, were assembled in the rhizosphere of different willow genotypes. Linear mixed models showed that the relative abundance of PGPB was positively associated (p < 0.01) with Cd accumulation, since these microbes significantly increased willow growth. The higher abundance of arbuscular mycorrhizal fungi in the rhizosphere of Salix × aureo-pendula CL ‘J1011’ at the Kejing site, showed a negative correlation with the Cd content, but a positive correlation with biomass. Conversely, mycorrhizal fungi, were more abundant in the rhizosphere of S. × jiangsuensis CL. ‘J2345’ and positively correlated with the Cd content in willow tissues. This study provides new insights into the distinctive microbial communities in rhizosphere of different willow genotypes, which may be consistent with the phytoremediation potential.
Strains Sr36T and TMT4-23T were isolated from No. 1 glacier in Xinjiang Uygur Autonomous Region and Toumingmengke glacier in Gansu Province, PR China, respectively. They were Gram-stain-positive and rod-shaped micro-organisms. The optimum growth temperature of the two strains was 10-14 °C. Phylogenetic analysis showed that the two strains were related to members of the genus Cryobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain Sr36T and its close relatives Cryobacterium luteum Hh15T, Cryobacterium aureum Hh31T, Cryobacterium levicorallinum Hh34T and Cryobacterium flavum Hh8T were 81.16-87.24 and 28.0-32.5 %, respectively. The ANI and dDDH values between strain TMT4-23T and its close relative Cryobacterium psychrotolerans 0549T were 81.16 and 22.3 %. The polar lipids of strain Sr36T were diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid and three unidentified lipids. The polar lipids of strain TMT4-23T were diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid and six unidentified lipids. The major fatty acids of strain Sr36T were anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 1. The major fatty acids of strain TMT4-23T were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, anteiso-C15 : 1 and iso-C15 : 1. Both strains contained 2,4-diaminobutyric acid and their predominant menaquinone was MK-10. On the basis of the phenotypic, phylogenetic and genotypic data, two novel species Cryobacterium ruanii sp. nov. (type strain = Sr36T=CGMCC 1.9275T=NBRC 113797T) and Cryobacterium breve sp. nov. (type strain =TMT4-23T=CGMCC 1.9556T=NBRC 113800T) are proposed.