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Publications
Publications (111)
Nitrogen (N) is an essential element for living organisms that limits the productivity of biospheres through time. It has been suggested that ferruginous anoxic waters could enhance the fraction of dissimilatory nitrate reduction to ammonium (DNRA) and conserve the biologically available N in the ecosystems. However, the role of mixed-valent iron [...
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...
A Gram-stain-positive, moderately halophilic, aerobic, endospore-forming, rod-shaped bacterium, designated strain DP4-553-S T , was isolated from hypersaline sediment collected from the Dalangtan Playa in the Qaidam Basin, Northwest PR China. Growth occurred within 0–21.6% (w/v) NaCl (optimum 7.2%) at pH 5.5–9.0 (optimum pH 7.0) and at 4–45 °C (opt...
Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane‐oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption...
Karst caves are a natural oligotrophic subsurface biosphere widely distributed in southern China. Despite the progress in bacterial and fungal diversity, the knowledge about interactions between bacteria, fungi, and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on we...
Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene inte...
Microbiomes play fundamental roles in ecological function of peatlands. Despite the confirmed role of hydrology in the modulation of microbial communities in peatlands, its impact on microbial functional groups involved in methane cycle has remained poorly defined particularly at subtropical peatlands. To this end, prokaryotic communities and metha...
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...
Bacterial communities in antimony (Sb) polluted soils have been well addressed, whereas the important players fungal communities are far less studied to date. Here, we report different responses of bacterial and fungal communities to Sb contamination and the ecological processes controlling their community assembly. Soil samples in the Xikuangshan...
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...
The genesis of sedimentary dolomite remains an unresolved issue. Protodolomite has been considered as a metastable precursor for some sedimentary dolomites. Through laboratory experiments, much has been learnt about the transformation of protodolomite into dolomite under hydrothermal conditions mimicking those in open diagenetic systems. However, i...
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.
On Earth, salt environments are the most relevant analogues to Martian salt deposits with regard to the search for preserved biomolecules. In this study, we analyzed the distribution of lipids in salt samples from Dalangtan and Qarhan in the Qaidam Basin, which is the most important area to carry out analog research of Mars in China. Furthermore, w...
Karst caves have recently been demonstrated to be a potential atmospheric methane sink, presumably due to consumption by methane-oxidizing bacteria. However, the sparse knowledge about the diversity, distribution, and community interactions of methanotrophs requires us to seek further understanding of the ecological significance of methane oxidatio...
The level of water table and temperature are two environmental variables shaping soil bacterial communities, particularly in peatland ecosystems. However, discerning the specific impact of these two factors on bacterial communities in natural ecosystems is challenging. To address this issue, we collected pore water samples across different months (...
Karst caves are widely distributed subsurface systems, and the microbiomes therein are proposed to be the driving force for cave evolution and biogeochemical cycling. In past years, culture-independent studies on the microbiomes of cave systems have been conducted, yet intensive microbial cultivation is still needed to validate the sequence-derived...
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...
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...
The genesis of dolomite is a contentious issue partly due to the difficulty in its synthesis at ambient temperature. Certain types of microorganisms have been demonstrated to be effective in promoting the precipitation of disordered dolomite, an important precursor of sedimentary ordered dolomite. In contrast to a growing body of research on the ca...
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 (...
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...
The origin of dolomite has long puzzled geologists. It has recently been documented that sulfate-reducing bacteria (SRB) are capable of catalyzing the formation of protodolomite, a previously proposed precursor of ordered sedimentary dolomite. However, the catalytic mechanism of SRB remains incompletely understood. This experimental study is aimed...
Dolomite nucleation and subsequent crystallization are kinetically-controlled processes. Modern dolomite-forming environments provide clues to the trigger factors that facilitate dolomite formation under Earth surface conditions. It has been documented that certain types of benthic microorganisms promoted the precipitation of protodolomite from sed...
Sphagnum microbiomes play an important role in the northern peatland ecosystems. However, information about above and belowground microbiomes related to Sphagnum at subtropical area remains largely limited. In this study, microbial communities from Sphagnum palustre peat, S. palustre green part, and S. palustre brown part at the Dajiuhu Peatland, i...
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...
To investigate the vertical variation of microbial functional groups particular nitrogen fixers and ammonia oxidizers, sediment samples from a 155 cm deep peat profile were collected from the acidic Dajiuhu Peatland and subsequently subjected to clone library construction and quantification. Results showed that nifH gene abundance varied between 10...
In the past several decades, sulfate concentration and salinity have been considered to be the two essential hydrochemical factors in the formation of dolomite, yet arguments against this hypothesis have existed simultaneously. To clarify the effects of sulfate concentration and salinity in the mineralization of dolomite, we conducted experiments o...
Caves are natural laboratories to study the subsurface deep biosphere, where drip water connect the caves with outside environments. Drip water may bring microorganisms and DOC from the outside environments into caves which subsequently play a fundamental role in sustaining the oligotrophic subsurface ecosystem. To understand the seasonal dynamics...
Microorganisms are thought to play a critical role in methane consumption in karst caves, however, the presence and diversity of methane-oxidizing bacteria (MOB) are still mysterious. In Heshang Cave, CH4 concentration decreases from 1.9 ppm at the entrance to 0.65 ppm into the cave. To explore the presence and diversity of MOB in this cave, weathe...
Dalangtan Playa is the second largest salt playa in the Qaidam Basin, north-western China. The hyper saline deposition, extremely arid climate and high UV radiation make Dalangtan a Mars analogue both for geomorphology and life preservation. To better understand microbial life at Dalangtan, both culture-dependent and culture-independent methods wer...
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 (...
Ingredients of Arq medium used for archaeal isolation in this study.
(DOCX)
SEM images of bacterial isolates from Dalangtan Playa cultured in the modified growth media (MGM) with salinities of 18% (a, c, d, e, and f) and 3% (b).
(TIF)
Deciphering of the mycobiome in pristine karst caves has been impeded by constraints of remote locations, inaccessibility to specimens and technical limitations, which greatly restricted in-depth understanding of mycobiomes in subterranean ecosystem. Here, mycobiomes of Heshang Cave in south-western karst region of China were investigated by Illumi...
Arsenic (As) and antinomy (Sb) usually coexist in natural environments where both of them pollute soils and water. Microorganisms that oxidize arsenite [As(III)] and tolerate Sb have great potential in As and Sb bioremediation, In this study, a Gram-negative bacterial strain, Bosea sp. AS-1, was isolated from a mine slag sample collected in Xikuang...
To investigate the microbial utilization of organic carbon in peatland ecosystem, water samples were collected from the Dajiuhu Peatland and nearby lakes, central China across the year of 2014. The acridine orange (AO) staining and Biolog Eco microplates were used to numerate microbial counts and determine the carbon utilization of microbial commun...
Qaidam Basin (Tibetan Plateau) is considered an applicable analogue to Mars with regard to sustained extreme aridity and abundant evaporites. To investigate the possibility of the preservation of microbial lipids under these Mars analog conditions, we conducted a mineralogical and organic geochemistry study on samples collected from two Quaternary...
Although most modern dolomites occur in hypersaline environments, the effects of elevated salinity on the microbial mediation of dolomite precipitation have not been fully evaluated. Here we report results of dolomite precipitation in association with a batch culture of Haloferax volcanii DS52, a halophilic archaeon, under various salinities (from...
High abundance and widespread distribution of the archaeal phylum Bathyarchaeota in marine environment have been recognized recently, but knowledge about Bathyarchaeota in terrestrial settings and their correlation with environmental parameters is fairly limited. Here we reported the abundance of Bathyarchaeota members across different ecosystems a...
The Mg²⁺ content is essential in determining different Mg-CaCO3 minerals. It has been demonstrated that both microbes and the organic matter secreted by microbes are capable of allocating Mg²⁺ and Ca²⁺ during the formation of Mg-CaCO3, yet detailed scenarios remain unclear. To investigate the mechanism that microbes and microbial organic matter pot...
Enhanced monsoon duration and soil acidification from acid rain are expected to impact the distribution of microbial communities in surface and subsurface environments, although these impacts are poorly understood for most systems. In central China, soluble carbonate bedrock forms extensive karst landscapes. Current predictions are that the amount...
Humic substances are a chemically heterogeneous class of organic macromolecules ubiquitous in the environment and have been reported to function as an electron shuttle for microbial iron reduction. In most experimental research, synthetic quinone compounds (e.g., anthraquinone-2.6-disulfonate, AQDS) were used as the surrogate for humic substances....
Nitrification represents one of the key steps in the global nitrogen cycle. While originally considered an exclusive metabolic capability of bacteria, the identification of the Thaumarchaeota revealed that ammonia-oxidizing archaea (AOA) are also important contributors to this process, particularly in acidic environments. Nonetheless, the relative...
Arsenic contamination in groundwater has been reported in the Jianghan Plain of China since 2005, yet little is known about the microbial communities involved in As mobilization in this area, especially the dissimilatory arsenate reducing bacteria (DARB) communities. Here, we conducted a cultivation-independent investigation on core sediments colle...
Hyalospheniids are among the most common and conspicuous testate amoebae in high-latitude peatlands and forest humus. These testate amoebae were widely studied as bioindicators, and are increasingly used as models in microbial biogeography. However, data on their diversity and ecology are still very unevenly distributed geographically: notably, dat...
Chemical weathering of fluorine-bearing minerals is widely accepted as the main mechanism for the release of fluorine (F) to groundwater. Here we propose a potential mechanism of F release via microbial dissolution of fluoroapatite (Ca5(PO4)3F) which has been neglected previously. Batch culture experiments were conducted at 30°C with a phosphate-so...
With increased concentration of methane in the atmosphere and its impact on climate, effective mitigation of methane emission is of global importance. Recent studies have shown the inhibition of microbial methanogenesis upon addition of ferruginous clay minerals. To better elucidate the mechanism of the inhibitory effect of clay minerals on methano...
Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent metho...
Microbial lipids in stalagmites are increasingly used to reconstruct the paleoclimate change,
necessitating the investigations on microbial communities in dripping waters. A pilot molecular
survey was conducted on bacterial communities of dripping waters at two sites (1D and 3D) in
Heshang Cave of Hubei province in central China for a period of 200...
Biogenic mineral assemblages that form from circumneutral microbial reduction of iron in smectite have been suggested as biosignatures in the geological record. However, mineralogical transformation of smectite mediated by microbes under extreme pH condition is still poorly known. The objective of this study was to understand the reduction capacity...
Sediment and tailings samples were collected from sites with a contrasting physicochemical gradient to investigate microbial squalene-hopene cyclase (sqhC) composition and distribution in terrestrial environments. Acidobacteria (66%), Alphaproteobacteria (96%) and Gammaproteobacteria (55%) were found to dominate sqhC communities, respectively, at t...
Symbiotic methanotrophic bacteria are prevalent on the stems or in the hyaline cells of Sphagnum spp. in peat-moss ecosystems and can contribute a significant amount of isotopically light carbon for moss photosynthesis. Despite this, the influence of the methanotrophs on the δ13C values of Sphagnum-derived lipids is poorly known, especially in peat...
Exogenous electron transfer mediators employed by Fe(III)-reducing bacteria are believed to govern the kinetics and equilibrium of bioreduction of Fe(III) in solid phase. In contrast to a large number of studies on humic substances and analog anthraquinone-2,6-disulfonate (AQDS), our knowledge of other potential electron shuttles involved in Fe(III...
Testate amoebae are a diverse and abundant group of protozoa that constitute a large proportion of biomass in many ecosystems and probably fill important roles in ecosystem function. These microorganisms have attracted the interest of paleoecologists because the preserved shells of testate amoebae and their known hydrological preferences enable rec...
