Liyuan Ma

• PhD
• Professor at China University of Geosciences

Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological dif ferences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb grad...

Colloids may play an important role in the geochemical cycle of antimony (Sb). However, the controlling behaviors of colloids on Sb fate in contaminated groundwater are not available. To investigate the effects of colloids on Sb mobility, groundwater samples from Xikuangshan Sb Mine's two main aquifers (the D3s2 aquifer and the D3x4 aquifer) were s...

Acidithiobacillus ferrooxidans serves as a model chemolithoautotrophic organism in extremely acidic environments, which has attracted much attention due to its unique metabolism and strong adaptability. However, little was known about the divergences along the evolutionary process based on whole genomes. Herein, we isolated six strains of A. ferroo...

Background The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of int...

Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathe...

Microbial communities composed of few abundant and many rare species are widely involved in the biogeochemical cycles of elements. Yet little is known about the ecological roles of rare taxa in antimony (Sb) contaminated groundwater. Groundwater samples were collected along a Sb concentration gradient in the Xikuangshan antimony mine area and subje...

The exploitation of polymetallic deposits produces large amounts of mine drainage, which poses great challenges to the surrounding aquatic ecosystem. However, the prokaryotic microbial community assembly and co-existence patterns in the polluted area are poorly understood, especially in high-altitude localities. Herein, we investigated the prokaryo...

Understanding cell-cell communication QS is highly relevant for comprehending the regulatory and adaptive mechanisms among acidophiles in extremely acidic ecosystems. Previous studies focused on the existence and functionality of a single QS system in several acidophilic strains.

Acidiferrobacter spp. are facultatively anaerobic acidophiles that belong to a distinctive Acidiferrobacteraceae family, which are similar to Ectothiorhodospiraceae phylogenetically, and are closely related to Acidithiobacillia class/subdivision physiologically. The limited genome information has kept them from being studied on molecular taxonomy a...

Bosea sp. AS-1 is an arsenite [As(III)] and antimonite [Sb(III)] oxidizer previously isolated by our group from the Xikuangshan Antimony (Sb) Mine area. Our previous study showed that Bosea sp. AS-1 had a preference for oxidizing As(III) or Sb(III) with different carbon sources, which suggested that different metabolic mechanisms may be utilized by...

Soils and waters are heavily contaminated by antimony in Xikuangshan (XKS) mine area. It is widely accepted that oxidative dissolution of sulfide minerals and aqueous dissolution are the most prevalent geochemical mechanisms for the release of Sb to the environment. Bosea sp. AS-1 is an antimonite-oxidizer isolated from the mine slag in Xikuangshan...

Re-inoculation was an effective way to improve bioleaching efficiency by enhancing the synergetic effects of biogenic Fe³⁺ coupling with S⁰ oxidation. However, the complex microbial interactions after re-inoculation have received far less attention, which was crucial to the bioleaching performances. Herein, the enriched ferrous oxidizers (FeO) or s...

Heavy metal contamination is widespread in the environment and has resulted in numerous adverse consequences for the ecosystem. Ureolytic microorganisms are known to immobilize heavy metals by co-precipitation with calcium carbonates, which are formed during microbial hydrolysis of urea. In this work, we described a novel halophilic ureolytic bacte...

In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors.

The dissimilatory Fe(III)-reducing bacteria play a significant role in the mobility of antimony (Sb) under reducing environment. Sb-rich smelting slag is iron (Fe)-containing antimonic mine waste, which is one of the main sources of antimony pollution. In this study, the soluble antimony reacted with Fe(III) by S. oneidensis (Shewanella oneidensis...

Structure and assembly processes of soil bacterial communities under different land use at karst areas remained poorly understood to date. To address this issue, soil samples from arable land and pristine forest over a karst cave, located in the acid rain impacted area, Hubei province, were collected and subjected to high-throughput sequencing and...

By analyzing the shift of microbial communities under different iron/sulfur ratios, the response of metallurgical microorganisms to energy substrates was investigated based on molecular ecological networks. High-throughput sequencing of microbial samples from different domesticated batches was conducted to analyze the changes in community compositi...

Adsorption of microorganisms (bacteria, fungi and microalgae, etc.) and biomacromolecules (humic substances, extracellular substances, proteins and nuclear acids, etc.) to minerals are universal in the nature environments. These processes also governed the inorganic and organic pollutants migration and conversion. This chapter discusses the interfa...

With the increase of the frequency and intensity of extreme precipitation in the context of global warming, the subsequent impact on groundwater ecosystem is urgently needed to be investigated. To understand the impact of heavy rain event (HRE) on groundwater microbial communities, sampling campaigns were conducted at Xikuangshan (XKS), the world l...

Sphagnum-associated microbiomes are crucial to Sphagnum growth and peatland ecological functions. However, roles of rare species in bacterial communities across Sphagnum compartments are poorly understood. Here the structures of rare taxa (RT) and conditionally abundant and rare taxa (CART) from Sphagnum palustre peat (SP), S. palustre ectosphere (...

Diverse metabolic behaviors endow microorganisms with various ecological functions, and metabolic activities of microbial species may affect the environmental conditions of their habitats. In this study, genome-guided analysis of Planktothrix spp. first divided these strains into six distinct groups, and comparisons of Planktothrix genomes revealed...

In this study, we demonstrate that a bacterial isolate Paraccocus versutus XT0.6 from the Xikuangshan antimony mine, the world largest antimony deposit, is capable of stibnite dissolution, oxidation of Sb(III), and formation of secondary Sb(V) bearing mineral. The isolate could oxidize dissolved Sb(III) aerobically and anaerobically. It was able to...

Chalcopyrite bioleaching by 2, 4 and 6 acidophilic strains with the same inoculation density were studied, respectively. The results indicated that the 6-strain community firstly adapted to bioleaching environment, dissolved the chalcopyrite rapidly and maintained an efficient work until late stage. Transcriptome profiles of the 6-strain community...

Fluoride toxicity to microorganisms was a predominant factor contributing to the failure of a commercial scale bioleach heap. An integrated control strategy for fluoride complexation without jarosite generation by stepwise adding ferric ions was first proposed to enable the bioleaching of the chalcopyrite associated with fluoride-bearing gangue min...

Introducing exogenous species into an environment is an effective method to strengthen ecological functions. The traits of the exogenous species and the indigenous communities, as well as the resistance and subsequent succession of the community to exogenous species, are not well-understood. Here, three different functional consortia were introduce...

Introducing exogenous species into an environment is an effective method to strengthen ecological functions. The traits of the exogenous species and the indigenous communities, as well as the resistance and subsequent succession of the community to exogenous species, are not well-understood. Here, three different functional consortia were introduce...

The chalcopyrite bioleaching by enriched ferrous or sulfur oxidizers was investigated. The bioleaching was also intensified three times by the enriched communities. The results indicated that copper recoveries extracted by the enriched ferrous and sulfur oxidizers (Fe-O and S-O) were 38.87% and 43.13%, compared with that by the original community (...

Anionic ion species occur in gangue minerals and impact the bioleaching efficiency even at low concentrations. Recently, the detrimental influence of fluoride ions on bioleaching microorganisms has caused great attention in research. However, the tolerance mechanisms of bioleaching microorganisms for fluoride are still unclear. In order to reveal f...

We used Illumina HiSeq technology to sequence the whole genome of Pseudomonas stutzeri LH-42, a bacterium isolated from petroleum-contaminated soil in Liaoning Province, China. The bacterium contains a series of specific genes involved in the oxidation of organic sulfur compounds.

This study used an artificial microbial community with four known moderately thermophilic acidophiles (three bacteria including Acidithiobacillus caldus S1, Sulfobacillus thermosulfidooxidans ST and Leptospirillum ferriphilum YSK, and one archaea, Ferroplasma thermophilum L1) to explore the variation of microbial community structure, composition, d...

Acidithiobacillus ferrivorans is an acidophile that often occurs in low temperature acid mine drainage, e.g., that located at high altitude. Being able to inhabit the extreme environment, the bacterium must possess strategies to copy with the survival stress. Nonetheless, information on the strategies is in demand. Here, genomic and transcriptomic...

Growth curves of A. ferrivorans YL15 at 6°C and 28°C. Filtration sterilized ferrous sulfate was used as an energy source. (TIF)

Selected genes and primers for quantitative real-time PCR. (DOCX)

Identification of CRISPR-associated (Cas) proteins in strain YL15. (DOCX)

Genes predicted to involved in metal resistance, pH homeostasis and UVR-resistance. The symbol ‘/’means the genes has no specific functions. (DOCX)

Functional genes with differential transcritpts based on analysis by TopHat and Cufflinks packages. There were 199 and 173 genes with significantly higher and lower RNA transcripts out of the total 2,798 protein-coding genes in genome of strain YL15. Classification of protein functions was based on KEGG annotation. (DOCX)

Physicochemical properties of the acid mine drainage sample for strain YL15. (DOCX)

Comparison of CRISPRs loci among acidophilic bacteria. CRISPRs loci of YL15 were annotated using CRISPRFinder while those of other strains were retrieved from CRISPRs database. (DOCX)

Correlation analysis of RNA-seq and qRT-PCR. (TIF)

Comparison of number of genes in main categories with higher transcripts levels at low temperatures between results from Christel et al. and this study. The bold and regular letters represent categories and sub-categories, respectively. Sub-categories were based on classification of protein functions as listed in S6 Table. (DOCX)

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the po...

Taxus chinensis is a rare and endangered shrub, highly sensitive to temperature changes and widely known for its potential in cancer treatment. How gene expression of T. chinensis responds to low temperature is still unknown. To investigate cold response of the genus Taxus, we obtained the transcriptome profiles of T. chinensis grown under normal a...

Importance: Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional n...

The use of green manures in agriculture can provide nutrients, affect soil microbial communities, and be a more sustainable management practice. The activities of soil microbes can effect crop growth, but the extent of this effect on yield remains unclear. We investigated soil bacterial communities and soil properties under four different green man...

Toxic ions accumulation in leachate is one of the limitations for bioleaching application. The effects of fluoride ions on microbial growth relevant to bioleaching have been extensively emphasized. However, the reasons that the microorganisms present different fluoride tolerance in bioleaching of different minerals have not yet been proposed. A fun...

It is known that excess fines may reduce heap permeability and block channelings of leachate flow in heap bioleaching operation, and further cause low metal recovery. The purpose of this investigation was to compare the effects of three potential heap construction methods including layered heap construction method (Method A), agglomerate heap const...

Although the taxonomical/phylogenetic diversity of microbial communities in biological heap leaching systems has been investigated, the diversity of functional genes was still unclear, and, especially, the differentiation and the relationships of diversity and functions of microbial communities in leaching heap (LH) and leaching solution (LS) were...

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. Phylog...

The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial co...

Acidophilic microorganisms involved in uranium bioleaching are usually suppressed by dissolved fluoride ions, eventually leading to reduced leaching efficiency. However, little is known about the regulation mechanisms of microbial resistance to fluoride. In this study, the resistance of Acidithiobacillus ferrooxidans ATCC 23270 to fluoride was inve...

Solution chemical calculation, zeta potential measurement and flotation test were introduced to verify the effective inhibiting component and illustrate the inhibition mechanism of ZnSO4 and Na2CO3 as a combined inhibitor for talc. Solution chemical speciation calculations indicated that the formation of solid state Zn(OH)2 occurred in all initial...

The draft genome of newly isolated Acidithiobacillus ferrivorans ZB-1 and DX-1 were deciphered to obtain a comprehensive insight into the genetic information and to discover the cellular mechanisms during its high activity in low temperature environment. Genome analysis speculated that Acidithiobacillus ferrivorans ZB-1 and DX-1 could fix carbon di...

In the bioleaching process, many factors in ore, water and sediments are important contributors as driving forces to improve leaching efficiency. In this study, FeSO4·7H2O and S⁰ as energy substrates were added to an oxide-rich, low-grade copper ore to explore the influence of biological and environmental factors on leaching efficiency. Mantel test...

Extraction of zinc from sphalerite using bio-hydrometallurgical technologies has become more and more popular. This study used an artificial microbial community with five known microorganisms to examine the relationship among microbial diversity, composition, and function (e.g., zinc extraction rates) in sphalerite bioleaching systems with addition...

In order to investigate the effect of initial proportions of microorganisms on chalcopyrite leaching, six typical bioleaching strains were used to rebuild different co-culture systems. According to their different energy use types, Acidithiobacillus ferrooxidans DX2012 (ferrous and sulfur), Sulfobacillus thermosulfidooxidnas DX2012 (ferrous and sul...

The effects of galvanic interaction between galena and pyrite on their flotation and electrochemical characters were studied by electrochemical, adsorption, flotation and FTIR techniques, respectively. Electrochemical tests indicate that galena is electrochemically more active than pyrite and serves as an anode in galvanic combination with pyrite....

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...

The microbial community in a biological heap leaching (BHL) system is crucial for the decomposition of ores. However, the microbial community structure and functional differentiation in different parts of a biological heap leaching system are still unknown. In this study, metagenomic sequencing was used to fully illuminate the microbial community d...

The electrochemical characteristics, surface properties and collectorless flotation behavior of galena with and without the presence of pyrite have been studied. Electrochemical tests confirmed previous reports in the literature that galena is electrochemically more active than pyrite and serves as the anode in galvanic combinations with pyrite. Cy...

Background 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, t...

The genus Sulfobacillus is a cohort of mildly thermophilic or thermotolerant acidophiles within the phylum Firmicutes and requires extremely acidic environments and hypersalinity for optimal growth. However, our understanding of them is still preliminary partly because few genome sequences are available. Here, the draft genome of Sulfobacillus ther...

In order to explore the fluoride tolerance and the community dynamics of mixed bioleaching microorganisms, a co-culture including five typical bioleaching strains (Acidithiobacillus ferrooxidans ATCC 23270, Leptospirillum ferriphilum YSK, Sulfobacillus thermosulfidooxidans ST, Acidithiobacills thiooxidans A01, Acidithiobacills caldus S1) was constr...

A defined mixed bioleaching consortium (constructed by Acidithiobacills ferrooxidans ATCC 23270, Leptospirillum ferriphilum YSK, Sulfobacillus thermosulfidooxidans ST, Acidithiobacills thiooxidans A01 and Acidithiobacills caldus S1) was used to investigate the fluoride stress response. The results showed that its growth and iron oxidation rate were...

In the bioleaching of uranium ore, fluoride that ever accreted with the ore floats into solution, inhibiting the growth and metabolic processes of microorganism or even killing them Ell, further reducing the efficiency of uranium leaching. In order to study the fluoride tolerance of the bioleaching microorganisms, five typical bioleaching strains i...

The effect of Ni(2+) on the growth and functional gene expression of the pure culture and co-culture of Acidithiobacillus thiooxidans and Leptospirillum ferriphilum has been studied. Compared with the pure culture, the co-culture showed a stronger sulfur and ferrous ion oxidation activity. At 100 mM, A. thiooxidans in co-culture grew faster and had...