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Miscanthus spp. are energy plants and excellent candidates for phytoremediation approaches of metal(loid)s-contaminated soils, especially when combined with plant growth-promoting bacteria. Forty-one bacterial strains were isolated from the rhizosphere soils and roots tissue of five dominant plants (Artemisia argyi Levl., Gladiolus gandavensis Vaniot Houtt, Boehmeria nivea L., Veronica didyma Tenore, and Miscanthus floridulus Lab.) colonizing a cadmium (Cd)-contaminated mining area (Huayuan, Hunan, China). We subsequently tested their plant growth-promoting (PGP) traits (e.g., production of indole-3-acetic acid, siderophore, and 1-aminocyclopropane-1-carboxylate deaminase) and Cd tolerance. Among bacteria, two strains, Klebsiella michiganensis TS8 and Lelliottia jeotgali MR2, presented higher Cd tolerance and showed the best results regarding in vitro growth-promoting traits. In the subsequent pot experiments using soil spiked with 10 mg Cd·kg−1, we investigated the effects of TS8 and MR2 strains on soil Cd phytoremediation when combined with M. floridulus (Lab.). After sixty days of planting M. floridulus (Lab.), we found that TS8 increased plant height by 39.9%, dry weight of leaves by 99.1%, and the total Cd in the rhizosphere soil was reduced by 49.2%. Although MR2 had no significant effects on the efficiency of phytoremediation, it significantly enhanced the Cd translocation from the root to the aboveground tissues (translocation factor > 1). The combination of K. michiganensis TS8 and M. floridulus (Lab.) may be an effective method to remediate Cd-contaminated soils, while the inoculation of L. jeotgali MR2 may be used to enhance the phytoextraction potential of M. floridulus.
Shuming Liu; Hongmei Liu; Rui Chen; Yong Ma; Bo Yang; Zhiyong Chen; Yunshan Liang; Jun Fang; Yunhua Xiao. Role of Two Plant Growth-Promoting Bacteria in Remediating Cadmium-Contaminated Soil Combined with Miscanthus floridulus (Lab.). Plants 2021, 10, 912 .
AMA StyleShuming Liu, Hongmei Liu, Rui Chen, Yong Ma, Bo Yang, Zhiyong Chen, Yunshan Liang, Jun Fang, Yunhua Xiao. Role of Two Plant Growth-Promoting Bacteria in Remediating Cadmium-Contaminated Soil Combined with Miscanthus floridulus (Lab.). Plants. 2021; 10 (5):912.
Chicago/Turabian StyleShuming Liu; Hongmei Liu; Rui Chen; Yong Ma; Bo Yang; Zhiyong Chen; Yunshan Liang; Jun Fang; Yunhua Xiao. 2021. "Role of Two Plant Growth-Promoting Bacteria in Remediating Cadmium-Contaminated Soil Combined with Miscanthus floridulus (Lab.)." Plants 10, no. 5: 912.
Accumulation of heavy metals in agricultural soils due to human production activities-mining, fossil fuel combustion, and application of chemical fertilizers/pesticides-results in severe environmental pollution. As the transmission of heavy metals through the food chain and their accumulation pose a serious risk to human health and safety, there has been increasing attention in the investigation of heavy metal pollution and search for effective soil remediation technologies. Here, we summarized and discussed the basic principles, strengths and weaknesses, and limitations of common standalone approaches such as those based on physics, chemistry, and biology, emphasizing their incompatibility with large-scale applications. Moreover, we explained the effects, advantages, and disadvantages of the combinations of common single repair approaches. We highlighted the latest research advances and prospects in phytoremediation-chemical, phytoremediation-microbe, and phytoremediation-genetic engineering combined with remediation approaches by changing metal availability, improving plant tolerance, promoting plant growth, improving phytoextraction and phytostabilization, etc. We then explained the improved safety and applicability of phytoremediation combined with other repair approaches compared to common standalone approaches. Finally, we established a prospective research direction of phytoremediation combined with multi-technology repair strategy.
Shuming Liu; Bo Yang; Yunshan Liang; Yunhua Xiao; Jun Fang. Prospect of phytoremediation combined with other approaches for remediation of heavy metal-polluted soils. Environmental Science and Pollution Research 2020, 27, 16069 -16085.
AMA StyleShuming Liu, Bo Yang, Yunshan Liang, Yunhua Xiao, Jun Fang. Prospect of phytoremediation combined with other approaches for remediation of heavy metal-polluted soils. Environmental Science and Pollution Research. 2020; 27 (14):16069-16085.
Chicago/Turabian StyleShuming Liu; Bo Yang; Yunshan Liang; Yunhua Xiao; Jun Fang. 2020. "Prospect of phytoremediation combined with other approaches for remediation of heavy metal-polluted soils." Environmental Science and Pollution Research 27, no. 14: 16069-16085.
Acidithiobacillus thiooxidans A01 is widely used in bioleaching processes and commonly thrives in most metal-rich environments. However, interactions between different heavy metals remain obscure. In this study, we elaborated the effect of ferric iron on the growth and gene expression of At. thiooxidans A01 under the stress of nickel. The results showed that 600 mM Ni2+ completely inhibited the growth and sulfur metabolism of At. thiooxidans A01. However, trace amounts of Fe3+ (0.5 mM) facilitated the growth of At. thiooxidans A01 in the presence of 600 mM Ni2+. With the addition of 5 mM Fe3+, the maximum cell density reached 1.84 × 108 cell/mL, and pH value was 0.95. In addition, metal resistance-related and sulfur metabolism genes were significantly up regulated with extra ferric iron. Taking the whole process into account, the promoting effect of Fe3+ addition can be attributed to the following: (1) alleviation of the effects of Ni2+ toxicity and restoring the growth of At. thiooxidans A01, (2) a choice of multiple pathways to export nickel ion and producing precursor of chelators of heavy metals. This can suggest that microorganisms may widely exhibit metabolic activity in iron-rich environments with heavy metals. Our study will facilitate the technique development for the processing of ore bodies with highly challenging ore compositions.
Aijia Chen; Xiaodong Hao; Yunhua Xiao; Kai Zou; Hongwei Liu; Xueduan Liu; Huaqun Yin; Guanzhou Qiu; Yili Liang. Responses of Acidithiobacillus thiooxidans A01 to Individual and Joint Nickel (Ni2+) and Ferric (Fe3+). Minerals 2019, 9, 82 .
AMA StyleAijia Chen, Xiaodong Hao, Yunhua Xiao, Kai Zou, Hongwei Liu, Xueduan Liu, Huaqun Yin, Guanzhou Qiu, Yili Liang. Responses of Acidithiobacillus thiooxidans A01 to Individual and Joint Nickel (Ni2+) and Ferric (Fe3+). Minerals. 2019; 9 (2):82.
Chicago/Turabian StyleAijia Chen; Xiaodong Hao; Yunhua Xiao; Kai Zou; Hongwei Liu; Xueduan Liu; Huaqun Yin; Guanzhou Qiu; Yili Liang. 2019. "Responses of Acidithiobacillus thiooxidans A01 to Individual and Joint Nickel (Ni2+) and Ferric (Fe3+)." Minerals 9, no. 2: 82.
Increasing evidence suggests that the gut microbiota plays vital roles in metabolic diseases. Polygonatum odoratum extract alleviates hyperglycemia and hyperlipidemia, but the underlying mechanism remains unclear. This study investigated the effects of P. odoratum polysaccharides (POPs) on high-fat diet (HFD)-induced obesity in rats and whether these effects were related to modulation of gut microbiota. POP treatment attenuated weight gain, fat accumulation, epididymal adipocyte size, liver triglycerides, and total liver cholesterol content in HFD-fed rats. POP administration also increased short-chain fatty acids (SCFAs), including isobutyric acid, butyric acid, and valeric acid. POP upregulated the expression of genes involved in adipocyte differentiation (Pparg, Cebpa, Cebpb) and lipolysis (Ppara, Atgl), and downregulated those related to lipid synthesis (Srebpf1, Fabp4, Fas), with corresponding changes in PPARγ and FABP4 protein expression. Finally, POP enhanced species richness and improved the gut microbiota community structure, reducing the relative abundances of Clostridium, Enterococcus, Coprobacillus, Lactococcus, and Sutterella. Principal coordinates analysis (PCoA) revealed a clear separation between HFD-fed rats and all other treatment groups. Correlation analysis identified negative and positive associations between obesity phenotypes and 28 POP-influenced operational taxonomic units (OTUs), including putative SCFA-producing bacteria. Our data suggest that POP supplementation may attenuate features of obesity in HFD-fed rats in association with the modulation of gut microbiota.
Yan Wang; Yanquan Fei; Lirui Liu; Yunhua Xiao; Yilin Pang; Jinhe Kang; Zheng Wang. Polygonatum odoratum Polysaccharides Modulate Gut Microbiota and Mitigate Experimentally Induced Obesity in Rats. International Journal of Molecular Sciences 2018, 19, 3587 .
AMA StyleYan Wang, Yanquan Fei, Lirui Liu, Yunhua Xiao, Yilin Pang, Jinhe Kang, Zheng Wang. Polygonatum odoratum Polysaccharides Modulate Gut Microbiota and Mitigate Experimentally Induced Obesity in Rats. International Journal of Molecular Sciences. 2018; 19 (11):3587.
Chicago/Turabian StyleYan Wang; Yanquan Fei; Lirui Liu; Yunhua Xiao; Yilin Pang; Jinhe Kang; Zheng Wang. 2018. "Polygonatum odoratum Polysaccharides Modulate Gut Microbiota and Mitigate Experimentally Induced Obesity in Rats." International Journal of Molecular Sciences 19, no. 11: 3587.
Temperature and energy resources (e.g., iron, sulfur and organic matter) usually undergo dynamic changes, and play important roles during industrial bioleaching process. Thus, it is essential to investigate their synergistic effects and the changes of their independent effects with simultaneous actions of multi-factors. In this study, we explored the synergistic effects of temperature and original mineral compositions (OMCs, energy resources) on the sphalerite bioleaching process. The microbial community structure was monitored by 16S rRNA gene sequencing technology and showed clear segregation along temperature gradients and Shannon diversity decreased at high temperature. On the contrary, the physicochemical parameters (pH and [Fe3+]) in the leachate were significantly affected by the OMCs. Interestingly, the influence of temperature on zinc recovery was greater at relatively simpler OMCs level, whereas the influence of OMCs was stronger at lower temperature. In addition, using [Fe3+], pH, relative abundances of dominant OTUs of microbial community and temperature as variable parameters, several models were constructed to predict zinc leaching efficiency, providing a possibility to predict the metal recovery efficiency under temperature change and variable energy resources.
Yunhua Xiao; Xueduan Liu; Jun Fang; Yili Liang; Xian Zhang; Delong Meng; Huaqun Yin. Responses of zinc recovery to temperature and mineral composition during sphalerite bioleaching process. AMB Express 2017, 7, 190 .
AMA StyleYunhua Xiao, Xueduan Liu, Jun Fang, Yili Liang, Xian Zhang, Delong Meng, Huaqun Yin. Responses of zinc recovery to temperature and mineral composition during sphalerite bioleaching process. AMB Express. 2017; 7 (1):190.
Chicago/Turabian StyleYunhua Xiao; Xueduan Liu; Jun Fang; Yili Liang; Xian Zhang; Delong Meng; Huaqun Yin. 2017. "Responses of zinc recovery to temperature and mineral composition during sphalerite bioleaching process." AMB Express 7, no. 1: 190.
Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.
Xian Zhang; Siyuan She; Weiling Dong; Jiaojiao Niu; Yunhua Xiao; Yili Liang; Xueduan Liu; Xiaoxia Zhang; Fenliang Fan; Huaqun Yin. Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus. Systematic and Applied Microbiology 2016, 39, 493 -502.
AMA StyleXian Zhang, Siyuan She, Weiling Dong, Jiaojiao Niu, Yunhua Xiao, Yili Liang, Xueduan Liu, Xiaoxia Zhang, Fenliang Fan, Huaqun Yin. Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus. Systematic and Applied Microbiology. 2016; 39 (8):493-502.
Chicago/Turabian StyleXian Zhang; Siyuan She; Weiling Dong; Jiaojiao Niu; Yunhua Xiao; Yili Liang; Xueduan Liu; Xiaoxia Zhang; Fenliang Fan; Huaqun Yin. 2016. "Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus." Systematic and Applied Microbiology 39, no. 8: 493-502.
Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.
Xian Zhang; Xue Feng; Jiemeng Tao; Liyuan Ma; Yunhua Xiao; Yili Liang; Xueduan Liu; Huaqun Yin. Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation. International Journal of Molecular Sciences 2016, 17, 1355 .
AMA StyleXian Zhang, Xue Feng, Jiemeng Tao, Liyuan Ma, Yunhua Xiao, Yili Liang, Xueduan Liu, Huaqun Yin. Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation. International Journal of Molecular Sciences. 2016; 17 (8):1355.
Chicago/Turabian StyleXian Zhang; Xue Feng; Jiemeng Tao; Liyuan Ma; Yunhua Xiao; Yili Liang; Xueduan Liu; Huaqun Yin. 2016. "Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation." International Journal of Molecular Sciences 17, no. 8: 1355.
The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial. By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test. Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.
Youhua Ren; Jiaojiao Niu; Wenkun Huang; Deliang Peng; Yunhua Xiao; Xian Zhang; Yili Liang; Xueduan Liu; Huaqun Yin. Comparison of microbial taxonomic and functional shift pattern along contamination gradient. BMC Microbiology 2016, 16, 110 .
AMA StyleYouhua Ren, Jiaojiao Niu, Wenkun Huang, Deliang Peng, Yunhua Xiao, Xian Zhang, Yili Liang, Xueduan Liu, Huaqun Yin. Comparison of microbial taxonomic and functional shift pattern along contamination gradient. BMC Microbiology. 2016; 16 (1):110.
Chicago/Turabian StyleYouhua Ren; Jiaojiao Niu; Wenkun Huang; Deliang Peng; Yunhua Xiao; Xian Zhang; Yili Liang; Xueduan Liu; Huaqun Yin. 2016. "Comparison of microbial taxonomic and functional shift pattern along contamination gradient." BMC Microbiology 16, no. 1: 110.
This study used an artificial enrichment microbial consortium to examine the effects of different substrate conditions on microbial diversity, composition, and function (e.g., zinc leaching efficiency) through adding pyrite (SP group), chalcopyrite (SC group), or both (SPC group) in sphalerite bioleaching systems. 16S rRNA gene sequencing analysis showed that microbial community structures and compositions dramatically changed with additions of pyrite or chalcopyrite during the sphalerite bioleaching process. Shannon diversity index showed a significantly increase in the SP (1.460), SC (1.476), and SPC (1.341) groups compared with control (sphalerite group, 0.624) on day 30, meanwhile, zinc leaching efficiencies were enhanced by about 13.4, 2.9, and 13.2 %, respectively. Also, additions of pyrite or chalcopyrite could increase electric potential (ORP) and the concentrations of Fe3+ and H+, which were the main factors shaping microbial community structures by Mantel test analysis. Linear regression analysis showed that ORP, Fe3+ concentration, and pH were significantly correlated to zinc leaching efficiency and microbial diversity. In addition, we found that leaching efficiency showed a positive and significant relationship with microbial diversity. In conclusion, our results showed that the complicated substrates could significantly enhance microbial diversity and activity of function.
Yunhua Xiao; Yongdong Xu; Weiling Dong; Yili Liang; Fenliang Fan; Xiaoxia Zhang; Xian Zhang; Jiaojiao Niu; Liyuan Ma; Siyuan She; Zhili He; Xueduan Liu; Huaqun Yin. The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system. Applied Microbiology and Biotechnology 2015, 99, 10311 -10322.
AMA StyleYunhua Xiao, Yongdong Xu, Weiling Dong, Yili Liang, Fenliang Fan, Xiaoxia Zhang, Xian Zhang, Jiaojiao Niu, Liyuan Ma, Siyuan She, Zhili He, Xueduan Liu, Huaqun Yin. The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system. Applied Microbiology and Biotechnology. 2015; 99 (23):10311-10322.
Chicago/Turabian StyleYunhua Xiao; Yongdong Xu; Weiling Dong; Yili Liang; Fenliang Fan; Xiaoxia Zhang; Xian Zhang; Jiaojiao Niu; Liyuan Ma; Siyuan She; Zhili He; Xueduan Liu; Huaqun Yin. 2015. "The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system." Applied Microbiology and Biotechnology 99, no. 23: 10311-10322.
Acidithiobacillus thiooxidans (A. thiooxidans), a chemolithoautotrophic extremophile, is widely used in the industrial recovery of copper (bioleaching or biomining). The organism grows and survives by autotrophically utilizing energy derived from the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs). However, the lack of genetic manipulation systems has restricted our exploration of its physiology. With the development of high-throughput sequencing technology, the whole genome sequence analysis of A. thiooxidans has allowed preliminary models to be built for genes/enzymes involved in key energy pathways like sulfur oxidation. The genome of A. thiooxidans A01 was sequenced and annotated. It contains key sulfur oxidation enzymes involved in the oxidation of elemental sulfur and RISCs, such as sulfur dioxygenase (SDO), sulfide quinone reductase (SQR), thiosulfate:quinone oxidoreductase (TQO), tetrathionate hydrolase (TetH), sulfur oxidizing protein (Sox) system and their associated electron transport components. Also, the sulfur oxygenase reductase (SOR) gene was detected in the draft genome sequence of A. thiooxidans A01, and multiple sequence alignment was performed to explore the function of groups of related protein sequences. In addition, another putative pathway was found in the cytoplasm of A. thiooxidans, which catalyzes sulfite to sulfate as the final product by phosphoadenosine phosphosulfate (PAPS) reductase and adenylylsulfate (APS) kinase. This differs from its closest relative Acidithiobacillus caldus, which is performed by sulfate adenylyltransferase (SAT). Furthermore, real-time quantitative PCR analysis showed that most of sulfur oxidation genes were more strongly expressed in the S0 medium than that in the Na2S2O3 medium at the mid-log phase. Sulfur oxidation model of A. thiooxidans A01 has been constructed based on previous studies from other sulfur oxidizing strains and its genome sequence analyses, providing insights into our understanding of its physiology and further analysis of potential functions of key sulfur oxidation genes.
Huaqun Yin; Xian Zhang; Xiaoqi Li; Zhili He; Yili Liang; Xue Guo; Qi Hu; Yunhua Xiao; Jing Cong; Liyuan Ma; Jiaojiao Niu; Xueduan Liu. Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans. BMC Microbiology 2014, 14, 179 -179.
AMA StyleHuaqun Yin, Xian Zhang, Xiaoqi Li, Zhili He, Yili Liang, Xue Guo, Qi Hu, Yunhua Xiao, Jing Cong, Liyuan Ma, Jiaojiao Niu, Xueduan Liu. Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans. BMC Microbiology. 2014; 14 (1):179-179.
Chicago/Turabian StyleHuaqun Yin; Xian Zhang; Xiaoqi Li; Zhili He; Yili Liang; Xue Guo; Qi Hu; Yunhua Xiao; Jing Cong; Liyuan Ma; Jiaojiao Niu; Xueduan Liu. 2014. "Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans." BMC Microbiology 14, no. 1: 179-179.