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Plant roots assemble unique microbial communities in rhizosphere, which are critical for plant adapting to natural environment. Given the pivotal importance of plant-microbe interactions, this study was conducted to uncover the assembly of Artemisia annua on root-associated bacterial and fungal communities and their co-occurrence networks. Soil samples were collected from a field experiment with 7-year plantation of Artemisia annua, including unplanted, bulk and rhizosphere soil. The microbial communities were investigated by amplicon sequencing targeting bacteria and fungi. The soil microbiomes were highly diverse among the three treatments. Bacterial and fungal communities were significantly influenced by AP (available phosphorus), AK (available potassium), TOC (total organic carbon), TN (total nitrogen) and WSN (water soluble nitrogen). Two plant growth-promoting bacteria, Sphingomonas and Sphingobium, and the fungal ASVs defined as Saprotroph were dramatically enriched in rhizosphere. Network analysis revealed that Artemisia annua built the less complex root-associated microbial network, compared to unplanted and bulk soils. Specially, the percentage of inter-kingdom interactions between bacteria and fungi increased in rhizosphere network, and showed the highest proportion of negative relationship. These results indicate that A. annua could assemble the specific root-associated microbial communities with increased abundance of plant growth promoting microorganisms and build inter-kingdom co-occurrence networks, which may be beneficial for the fitness of plants to natural environment. more...

Purpose Paulownia witches’ broom (WB) usually affects part of the infected tree, rarely spreading throughout the tree. WB was infected by phytoplasmas, but the associated microbiome assembly remains unknown. This study aims to clarify the possible mediating mechanism of WB outbreaks in Paulownia. Methods We collected leaves, branches, roots and rhizosphere soil of Paulownia trees with or without WB, and analyzed the bacterial community on the basis of 16S rRNA high-throughput sequencing. Results All leaf and branch samples contained phytoplasmas, but high phytoplasma levels were required for WB. Low bacterial community diversity and richness, a lack of beneficial bacteria, and an unstable bacterial network might be conducive to a WB outbreak. Phytoplasmas were more abundant in the roots of diseased trees than in the roots of healthy trees. Moreover, phytoplasma infections altered the bacterial community composition, but did not induce morphological changes. Phytoplasma did not present in the rhizosphere soil of diseased trees, but their bacterial community composition changed comparing with the corresponding samples of healthy trees. Asymptomatic leaves and branches of diseased trees recruited beneficial bacteria and increased the bacterial network stability, which might contribute to the restriction of phytoplasma infections and WB development further. The abundance of several beneficial bacteria in the endosphere was significantly negative correlation with that of phytoplasmas, implying their inhibitory effects on phytoplasmas. Conclusion Our findings have clarified the possible mechanism mediating WB outbreaks in Paulownia trees. Furthermore, we demonstrated that Paulownia trees inhibit phytoplasma infections by modulating the endosphere and rhizosphere bacterial communities. more...

A potting experiment was conducted to investigate the effect of sulfur application on the bioaccumulation by tobacco and its mechanisms of rhizospheric microorganisms. Cadmium content in tobacco was analyzed using atomic absorption spectrometer, while bacterial community and related gene in soil were analyzed via high-throughput sequencing and quantitative PCR techniques, respectively. The obtained results indicated that tobacco had the ability to accumulate cadmium under no sulfur application conditions, with cadmium contents of 35.4, 23.6, and 26.3 mg kg-1 in leaves, stems, and roots, respectively. Under high-sulfur treatment, these values increased to 66.4, 46.1, and 42.6 mg kg-1, respectively, probably due to the increase of the available cadmium content (from 1.1 to 3.3 mg kg-1) in the soil through a decrease of the soil pH value, which was contributed by the sulfur oxidation reaction. dsrA and soxB genes might play an important role in sulfur oxidation, and Thiobacillus sp. was the dominant bacterial genus during the sulfur oxidation process. In addition, sulfur application exerted little effect on the diversity and structure of the soil bacterial community. The combined results indicate that sulfur application is an effective and safe method for Cd phytoextraction by tobacco. more...

Although the plant-growth promotion by algae have been studied comprehensively, their impacts on indigenous soil microbiome remain largely unexplored. Herein we conducted a greenhouse experiment to investigate the changes in soil properties and corresponding microbial communities (bacterial, fungal and protists) after 2-year application of algae and their dynamic variation within 60 days immediately after algae addition. In comparison with Control treatment, the impact of algae on soil properties and microbial communities was huge, especially the content of nitrate was decreased however soluble organic nitrogen (SON) was increased. The increased copies of nifH gene suggested the improved potential of nitrogen fixation in algae treated soil. By constructing multitrophic ecological network, soil microorganisms were divided into several modules, and two key-stone microbial taxa (module 1 and 2) showed strong associations with the content of nitrate and SON. With addition of algae, the abundance of most microbial taxa was decreased and increased in module 1 and module 2, respectively. Particularly, module 1 and module 2 were proved to be taxonomically and functionally comprised of different microbes. Moreover, random forest analysis and structural equation model indicated that the key-stone microbial taxa were more important factors affecting the content of nitrate and SON than algae, bacterial, fungal and protistan communities and the influence of algae on soil nitrogen cycling mostly depended on their indirect effects via module 1 and 2. more...

Polycyclic aromatic hydrocarbons (PAHs) are a group of persistent organic compounds. White rot fungi (WRF) have attracted much attention due to their strong capabilities for the initial transformation of PAHs. To better understand the metabolic pathway of PAHS by WRF in the presence of ligninolytic enzymes and cytochrome P450 monooxygenase (P450s), degradation by a high laccase-producing fungus, Pycnoporus sanguineus 14, was examined in detail. This strain with high laccase activity (2516.7 U L−1) exhibited 45.6% biodegradation of phenanthrene (PHE) and 90.1% of benz[a]anthracene (BAA) under in vivo conditions. Gas chromatography–mass spectrometry (GC-MS) was used to identify 2-methylphenol as the product of PHE, and benz[a]anthracene-7,12-dione, 2,3-dihydroxy-3-phenylpropanoic acid and citramalic acid were identified as products of BAA. The results of an in vitro experiment indicated that the strain could initially transform PHE to 2-dibenzofuranol by intracellular enzymes containing P450s, or 9,10-phenanthrenedione by extracellular laccase, and could initially transform BAA to benz[a]anthracene-7,12-dione via extracellular laccase. more...

Selective inhibition (SI) has been routinely used to differentiate the contributions of bacteria and fungi to soil ecological processes. SI experiments typically measured rapid responses within hours since the addition of inhibitor, but the long-term effects of selective biocides on microbial community composition and function were largely unknown. In this study, a microcosm experiment was performed with an agricultural soil to explore the effectiveness of two bactericides (bronopol, streptomycin) and two fungicides (cycloheximide, captan), which were applied at two different concentrations (2 and 10 mg g−1). The microcosms were incubated for 6 weeks. A radiolabeled substrate, [1,2,3,4,4a,9a-14C] anthracene, was spiked to all microcosms, and the derived CO2 was monitored during the incubation. The abundance and composition of bacteria and fungi were assessed by qPCR and Miseq sequencing of ribosomal rRNA genes. It was demonstrated that only 2 mg g−1 bronopol and cycloheximide significantly changed the bacteria to fungi ratio without apparent non-target inhibition on the abundances; however, community shifts were observed in all treatments after 6 weeks incubation. The enrichment of specific taxa implicated a selection of resistant or adapted microbes by these biocides. Mineralization of anthracene was continuingly suppressed in all SI microcosms, which may result in biased estimate of bacterial and fungal contributions to pollutant degradation. These findings highlight the risks of long-term application of selective inhibition, and a preliminary assessment of biocide selection and concentration is highly recommended. more...