Shaohua Shi's research while affiliated with Chinese Academy of Sciences and other places

Publications (30)

Article
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Background The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the co...
Article
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Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the...
Article
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AimsSpecific soil bacteria can sense and respond to the selective rhizosphere recruitment of root exudates using unique systems of chemotaxis that mediate plant-microbe and microbe-microbe interactions. This study investigates how the bacterial chemotaxis systems have been impacted by selection during the domestication of rice (Oryza species).Metho...
Article
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The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipo...
Article
Soybean is considered as one of the most important food for both humans and animals; unfortunately, it faces soil-borne diseases caused by bacteria or fungi, leading to severe yield losses. Hybridization has helped the soybean to obtain beneficial genes from wild species that can resist some adverse conditions. However, the influences of hybridizat...
Preprint
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Background Rice root-inhabited microbial communities are seriously affected by domestication as evidenced by comparing the rhizomicrobiomes of wild and related cultivated rice species. While earlier studies focused on the structures of the rhizomicrobiomes, here, we compared the functioning of the microbial communities in the rhizosphere of wild ve...
Article
Continuous cropping of soybean often causes significant declines in yields of soybean because of the outbreaks of soil-borne fungal diseases. It has been reported that wild crops often harbour a unique microbiome to benefit the host plants. Thus, it is necessary to find the different community structures of the rhizomicrobiomes associated with cult...
Article
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Little known the connections between soybeans mitogen-activated protein kinase (MAPK) gene expression and the rhizomicrobiome upon invasion of the root pathogen Fusarium oxysporum. To address this lack of knowledge, we assessed the rhizomicrobiome and root transcriptome sequencing of wild and cultivated soybean during the invasion of F. oxysporum....
Article
Full-text available
Plant domestication was a pivotal accomplishment in human history, which led to a reduction in genetic diversity of crop species; however, there was less research focus on how this reduced genetic diversity of crops in affecting rhizosphere microbial communities during crop domestication process. Here, we used high-throughput sequencing to explore...
Article
This study presents evidence that strigolactones (SLs) promote defense against devastating rice blast fungal pathogen Magnaporthe oryzae. Impairment in either SL-biosynthetic dwarf17 (d17) or -signaling (d14) led to increased susceptibility towards M. oryzae. Comparative transcriptome profiling of the SL-signaling d14 mutant and WT plants revealed...
Article
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The fungicides used to control diseases in cereal production can have adverse effects on non-target microbial communities, with possible consequences for plant health and productivity. Although we know that fungicides affect microbial community structure and soil activities, it is unclear how crop cultivars have altered the impact of fungicides on...
Article
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Asian cultivated rice (Oryza sativa L), the important cereal crop, has low resistance to numerous biotic and abiotic stresses compared to its ancestral wild rice (Oryza rufipogon). Although genetic studies have shown that the susceptibility of cultivated rice towards various environmental stresses is due to its narrow genetic diversity caused by do...
Data
Species analysis of AMF based on high-throughput sequencing in the original rhizospheric soil of 2-yr-old ginseng planting root. (A) The percentage of AMF in total fungi of the original rhizospheric soil taken from 2-yr-old ginseng. X-axis and Y-axis indicate group and the ratio of AMF in total fungi, respectively. (B) AMF species of the original r...
Data
HPLC curve of standard ginsenoside monomers. Six standard ginsenoside monomers, Re, Rg1, Rb1, Rb2, Rc, and Rd were mixed together and made to a concentration of 2 μg/mL. The mobile phase solution was (A) acetonitrile and (B) water. The program used was as follows: 0–20 min, 22% acetonitrile; 20–25 min, 22–30% acetonitrile; 25–45 min, 30–46% acetoni...
Article
Soil salinization is one of the key factors that threatens plant existence worldwide and is a major challenge to sustain crop production and soil quality. However, there has been limited research on the responses of microbial communities and enzyme activities under soil amendments application in saline alkaline soils. Here, we explored the response...
Article
Soil ameliorants can improve soil physico-chemical properties and activate microbial communities in saline-sodic soils. However, there has been less focus on how aggregate fractions affect soil microbial communities under different ameliorant applications. Here, we used the phospholipid fatty acid (PLFA) analysis to explore the effects of soil amel...
Article
Full-text available
Panax ginseng is an important medicinal herb due to its ability to strengthen the human immune system. However, due to the increasing needs of ginseng in medicine, the continuous cropping of ginseng has become more common and has resulted in increased problems with fungal decay. Thus, chemical fungicides are commonly used in ginseng plantings, whic...
Article
The rhizomicrobiome plays a key role in suppressing soil-borne plant diseases. It remains unclear if crop domestication has altered the rhizomicrobiome and reduced the resistance of domesticated crops to pathogens. To investigate this question, the pathogenic fungus Magnaporthe oryzae was administered to the rhizosphere of plants of cultivated and...
Article
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Soil microbes play critical roles in global biogeochemical cycles, but their succession patterns across long temporal scales have rarely been studied. In this study, soil samples were collected from three volcanoes in Wudalianchi, northeastern China: Laoheishan (LH, approximately 240 years old), Dongjiaodebushan (DJ, 0.45–0.6 million years old), an...
Article
The plant and root-associated microbiomes are closely related. Plant metabolic substances can serve as a nutrient source for the microbiome, and in return, the microbiome can regulate the production of plant metabolic substances. Wild rice (Oryza rufipogon), as the ancestor of cultivated rice (Oryza sativa), has changed several metabolic pathways a...
Article
Full-text available
Background: Magnaporthe oryzae, the causal fungus of rice blast disease, negatively impacts global rice production. Wild rice (Oryza rufipogon), a relative of cultivated rice (O. sativa), possesses unique attributes that enable it to resist pathogen invasion. Although wild rice represents a major resource for disease resistance, relative to curren...
Article
Full-text available
Background Glomus intraradices is a species of arbuscular mycorrhizal fungi that, as an obligate endomycorrhiza, can form mutually beneficial associations with plants. Panax ginseng is a popular traditional Chinese medicine; however, problems associated with ginseng planting, such as pesticide residues, reduce the ginseng quality. Methods In this...

Citations

... In addition, iron respiration coincides with strong suppression of methanogenesis [56]. The microbial iron respiration function of the wild rice core rhizobacterial community might suppress methane production, which would corroborate our earlier finding that methane metabolism is higher in the rhizosphere of domesticated rice than in the rhizosphere of wild rice [57]. Interestingly, nitrogen fixation was identified as a function of the core rhizobacterial community in both in situ and ex situ wild rice, suggesting that wild rice growth relies on the rhizomicrobiome for nitrogen nutrient uptake. ...
... Each of these methods has specific drawbacks; for example, Venn diagrams only identify ASVs that are detected in all treatments and do not consider relative abundances [22]. Co-occurrence analysis investigates the rhizosphere microbial community under a compositional constraint (the limitation imposed by sequencing) using Spearman and Pearson correlation analyses, resulting in a lack of independence of the correlation analysis [33]. ...
... Domestication has been shown to alter the diversity of microbes in the rhizosphere of crops such as corn [45], tomato [46], wheat [47], and rice [48,49]. Chang et al. [50] compared the bacterial communities of wild and domesticated rice genotypes and found that Frankiaceae was enriched in the rhizosphere of cultivated Oryza sativa but absent from the rhizosphere of wild Oryza rufipogon. This result highlights that unique microbes that are not recruited by wild relatives are enriched in the rhizosphere of domesticated cultivars. ...
... The 50 µL PCR reaction system had the following components all included in the kit: dNTPs (2.5 mmol/L), forward and reverse primers (10 µmol/L each), 10 Pyrobest buffer (5 µL), Pyrobest DNA polymerase (2 U/µL), and dissolved DNA in ddH 2 O (36.7 µL, 1 ng/µL). Temperature was set to 95 • C for five minutes, followed by 25 cycles at 95 • C for 30 s, 56 • C for 30 s, and 72 • C for 40 s in the PCR process [21]. Paired-end sequencing was performed on the Illumina-MiSeq platform, and the raw data were filtered by truncating the end sequences of reads with quality values lower than 20, removing junction-contaminated reads, removing N-containing reads, and removing low-complexity reads (Adjustment of Short reads, v1.2.11). ...
... This higher network complexity in wild pearl millet may result in a more stable mycobiome that could contribute to higher plant resilience to environmental perturbations 57,58 . On the other hand, plant genotype and/or agriculture practices may account for the lower network complexity in cultivated pearl millet 59,60 . We identified four different potential hub taxa in the core mycobiome of cultivated (Bipolaris, Cochliobolus, Curvularia and Penicillium #1) and wild (Helminthosporium, Paecilomyces, Penicillium #1 and Penicillium #2) plants. ...
... The Chytridiomycota phylum comprises zoosporic fungi that occur in soil as saprophytes growing on organic material [111]. Spizellomyces have been identified in soybean rhizosphere as a plant pathogen infecting soybean during farm cultivation [112]. Schlatter et al. [113] reported that glyphosate, by compromising the plant defense system, promotes the colonization of root pathogens, and can result in a "green bridge" between weeds and crop hosts. ...
... Differences between rhizobacterial communities increase with the phylogenetic distance between Poaceae (Bouffaud et al., 2016), but this is not apparent when considering phyla abundance. For example, Verrucomicrobia are found at the same level of magnitude in the rhizospheres of millet, rice and wheat ( Figure 3A; Shi et al., 2019), even though the former two are distant from the Triticeae tribe. Moreover, rice (the closest to wheats in Figure 3C) displays a higher abundance of Chytridiomycota in the rhizosphere than Triticeae, whereas maize (although more distant) exhibits rhizosphere levels of Chytridiomycota closer to those of the Triticeae. ...
... Among these, strigolactones (SLs) serve as important bioactive molecules, stimulating the branching and metabolism of pre-symbiotic hyphae in AMF [109]. At the same time, SLs also influence the growth of several plant pathogens [110]. Flavonoids also play a significant role in AMF spore germination, hyphal growth, differentiation, and root colonization in AMF-plant interactions, as well as in promoting the growth of host-specific rhizobia by serving as chemoattractants [111]. ...
... 57,59 For instance, a decreased abundance of benecial bacteria belonging to Nitrosomonadaceae and Rhodanobacter was observed in strigolactone-decient rice mutants. 60 Similarly, soybeans accumulating more strigolactones harbor altered rhizosphere microbial compositions (enriched Shinella and Bdellovibrio genera) compared to its wild-type controls. 61 Sorghum genotypes producing different ratios of orobanchol (28) to 5-deoxystrigol (29) could recruit different sets of bacterial families in the rhizosphere. ...
... Soil pH was determined by the leaching potential method (soil-water ratio of 1:5) [18]; soil total phosphorus (TP) was determined by H 2 SO 4 ablation-molybdenum sulfate inverse colorimetric method; total nitrogen (TN) was determined by the Kjeldahl methodcontinuous-flow analyzer; soil organic matter (SOM) was determined by the external heating method-potassium dichromate volumetric method [19]. Soil effective phosphorus (AP) was determined by 0.5 mol-L −1 NaHCO 3 extraction-molybdenum sulfate inverse colorimetric method; fast-acting potassium (AK) was determined by 1 mol-L −1 CH3COONH4 extraction-inductively coupled plasma-emission spectroscopy (ICPS-7500) ICP-AES method [20]. Soil fast-acting nitrogen (NH 4 + -N) was determined by 2 mol·L −1 KCl extraction with a flow analyzer. ...