Min Hu

Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings

In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e. primary tailings (T1), slightly acidic tailings (T2), extremely acidic tailings (T3, T4 and T5) and orange-coloured oxidized tailings (T6). Geochemical results showed that the six tailings (from T1 to T6) likely represented sequential stages of the acidification process of the mine tailings. 16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%. Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively. The microbial communities in T2 and T6 harboured more genes suggesting diverse metabolic capacities for sulfur oxidation/heavy metal detoxification and tolerating low pH respectively.

Identification of two suites of cyclotide precursor genes from metallophyte Viola baoshanensis: cDNA sequence variation, alternative RNA splicing and potential cyclotide diversity

Cyclotides are a novel family of plant-derived defense peptides that are biosynthetically produced via the processing of cyclotide precursor (CP) proteins containing one, two or three cyclotide domains. By screening a cDNA library of Viola baoshanensis roots and using RACE and RT-PCR methods, 23 cDNA clones were identified and then used to deduce full CP proteins containing one (VbCP1S-5), two (VbCP6S), or three (VbCP7S) cyclotide domains. RT-PCR and sequence analyses suggested that VbCP6S were resulted from the alternative splicing of VbCP7S RNA. The significance of VbCP7S RNA splicing is that it provides a mechanism for increasing the diversity of cyclotide expression via the recombination of N-terminal repeat (NTR) regions and cyclotide domains. After analyzing the full endoplasmic reticulum (ER) signals of known and novel CPs associated with RT-PCR tests, three primers encoding the conserved sequence ALVLIATFA, AAFALPA-LA and AAFALPA-AFA were proposed to be more efficient in cloning CP genes than the well-applied primer encoding AAFALPA. Cyclotide sequence analyses indicated that the cDNA clones encoded a variety of Möbius and bracelet cyclotides, which were likely involved in the known bioactivities of cyclotides, and also might play a previously unreported role in mediating the metal tolerance of V. baoshanensis. Overall, this study shows that CP genes are varied in V. baoshanensis and cyclotide expression is subject to transcriptional and post-transcriptional regulation in this plant.

Accumulation of Zinc, Cadmium, and Lead in Four Populations of Sedum alfredii Growing on Lead/Zinc Mine Spoils

Sedum alfredii Hance is a newly reported zinc (Zn) and cadmium (Cd) hyperaccumulator native to China. In this study, four populations of S. alfredii were collected from Yejiwei (YJW), Jinchuantang (JCT) and Qiaokou (QK) lead (Pb)/Zn mines located in Hunan Province as well as Quzhou (QZ) Pb/Zn mine located in Zhejiang Province for exploring the intraspecies difference of this plant in metal accumulation. Although they grew in the Pb/Zn spoils with relatively similar levels of Zn, Cd and Pb, remarkable differences among the four populations in tissue heavy metal concentrations were observed. The shoot Zn concentration of QZ population (11,116 mg/kg) was highest and nearly five times higher than that of the JCT population (1930 mg/kg). Furthermore, the shoot Cd concentration observed in the QZ population (1090 mg/kg) was also highest and 144 times higher than that found in the JCT population (7.5 mg/kg). As for Pb concentrations in the shoot of different populations, a fourfold difference between the highest and the lowest was also found. Such difference on metal accumulation was population-specific and may be significantly explained by differences in the soil properties such as pH, organic matter (OM), and electrical conductivity (EC). Taking biomass and metal concentration in plants into consideration, the QZ, YJW and QK populations may have high potential for Zn phytoremediation, the QZ population may have the highest potential in Cd phytoremediation, and the QK population may be the most useful in Pb phytoremediation.

A transcriptional profile of metallophyte Viola baoshanensis involved in general and species-specific cadmium-defense mechanisms.

Viola baoshanensis Shu, Liu et Lan is a newly identified metallophyte, and its defensive strategies against heavy metals are still unclear. In the present study, we firstly constructed a root cDNA library of the plant subjected to 300muM Cd for 48h by using suppression subtractive hybridization (SSH), and 43 unique cDNA fragments were further isolated from the library. Sequence homology analysis showed that half of the identified genes were involved in general stress defense, such as antioxidative enzymes, protein degradation and stress signal transduction. After RT-PCR and RACE analysis, a Cd-responsive gene Vb40 was identified, which could deduce a novel cysteine-rich mini-protein. Meanwhile, five cyclotide precursor genes (VbCP1-VbCP5) were also identified. The Vb40 and the VbCP1-VbCP5 were further investigated by yeast expression analysis, and they could improve copper (Cu) tolerance in hosted yeast, indicating that these species-specific genes possibly functioned in V. baoshanensis heavy metals tolerance. Our results suggested that heavy metal tolerance in V. baoshanensis relied on both general and species-specific defense.

Contrasting patterns of genetic divergence in two sympatric pseudo-metallophytes: Rumex acetosa L. and Commelina communis L.

BackgroundPatterns of genetic divergence between populations of facultative metallophytes have been investigated extensively. However, most previous investigations have focused on a single plant species making it unclear if genetic divergence shows common patterns or, conversely, is species-specific. The herbs Rumex acetosa L. and Commelina communis L. are two pseudo-metallophytes thriving in both normal and cupriferous soils along the middle and lower reaches of the Yangtze River in China. Their non-metallicolous and metallicolous populations are often sympatric thus providing an ideal opportunity for comparative estimation of genetic structures and divergence under the selective pressure derived from copper toxicity.ResultsIn the present study, patterns of genetic divergence of R. acetosa and C. communis , including metal tolerance, genetic structure and genetic relationships between populations, were investigated and compared using hydroponic experiments, AFLP, ISSR and chloroplast genetic markers. Our results show a significant reduction in genetic diversity in metallicolous populations of C. communis but not in R. acetosa . Moreover, genetic differentiation is less in R. acetosa than in C. communis , the latter species also shows a clustering of its metallicolous populations.ConclusionsWe propose that the genetic divergences apparent in R. acetosa and C. communis , and the contrasting responses of the two species to copper contamination, might be attributed to the differences in their intrinsic physiological and ecological properties. No simple and generalised conclusions on genetic divergence in pseudo-metallophytes can thus be drawn.

Development of eight polymorphic microsatellite markers by FIASCO-based strategy for a arsenic-hyperaccumulator Chinese brake fern

Chinese Brake fern (Pteris vittata) is the first identified and well-known arsenic-hyperaccumulator. It is widely distributed in areas of temperate zone as diploid and of subtropics-tropics zone as tetraploid. Screening 60 individuals from Southern China, eight polymorphic microsatellite markers were developed for the first time by employing fast isolation by AFLP of sequences containing repeats protocol (FIASCO). The number of alleles for each marker ranged from two to seven and one to four bands per individual. Furthermore, five of the loci possess more than two alleles per individual. The results suggested these microsatellite markers provide a useful tool for studying the ongoing genetic variability of this specie as well as mating systems.