封闭环境下酸性矿坑水中微生物生态多样性的研究

铜绿山铜矿是世界开采时间最长的矿井之一,在开采过程中有许多矿井被废弃,许多废弃的矿井内产生了大量的对环境有害的酸性矿坑水.酸性矿坑水取自铜绿山铜矿某废弃矿井,利用限制性酶切片断多样性分析(RFLP分析)对酸性矿坑水中的微生物生态多样性进行了研究.研究表明,酸性矿坑水呈酸性,相对于其他极端与非极端生态环境,酸性矿坑水中的细菌与古菌的群落多样性较低.RFLP分析与系统发育分析表明,酸性矿坑水中细菌主要由A.fcrrooxidans(属于gamma-Proteobacteria)和L.ferrooxidans(属于Nitospira)成;古菌主要由Thermoplasma相关古菌组成.在这种封闭环境的酸性矿坑水中首次发现了类似于产甲烷古菌的克隆片断,其占古菌种群的四分之一左右.本研究将促进对酸性矿坑水中细菌及古菌群落组成及其对酸性矿坑水产生的作用的研究.     

Palatability of Leaves Conditioned in Streams Affected by Mine Drainage: A Feeding Experiment with Gammarus Pulex (L.)

Both the absence of leaf shredding macroinvertebrates and low microbial activity are of major importance in determining slow and incomplete leaf decay in extremely acidic (pH<3.5) mining streams. These streams are affected by a heavy ochre deposition causing the formation of massive iron plaques on leaf surfaces that hinder microbial exploitation. An investigation was carried out to determine whether iron plaques and leaf conditioning status (acid conditioned with and without iron plaques, neutral conditioned, unconditioned) affect the feeding preference of the shredder Gammarus pulex (L.). Leaf respiration rates and fungal biomass (ergosterol contents) were measured to determine microbial colonization. Neutral conditioned leaves had significantly higher microbial colonization than acid conditioned leaves with iron plaques. Notwithstanding, leaves of both conditioning types were consumed at high rates by G. pulex. The microbial colonization had no influence on feeding preference in the experiment. It is presumed that iron adsorbed organic material caused the high palatability of leaves with iron plaques. The results indicate that the large deposits of leaves coated with iron plaques will be available to the stream food web when water quality will be restored to neutral as planed in scenarios for the future development of mining streams.     

A Novel Community of Acidophiles in an Acid Mine Drainage Sediment

A sediment sample (pH 2.5) was collected at an acid mine drainage site in Anhui, China. The present acidophilic microbial community in the sediment was studied with a 16S rRNA gene clone library. Small-subunit rRNA genes were PCR amplified, cloned and screened by amplified rDNA restriction analysis (ARDRA). Subsequently, 10 different clones were identified and they were affiliated with Acidobacteria, β/γ-Proteobacteria, δ-Proteobacteria, Nitrospira, Candidate division TM7, and Low G + C Gram-positives. Phylogenetic analysis of 16S rRNA gene sequences revealed a diversity of acidophiles in the sediment that were mostly novel. Unexpectedly, 16S rRNA gene sequences affiliated with δ-Proteobacteria were found to constitute more than 60% of clone library. To our knowledge, this is the first occasion that bacteria of δ-Proteobacteria have been found dominant in the acidic habitat. Anaerobic sulfate- or metal reduction is the predominant physiological trait of bacteria of this subdivision. The high sulfate, ferric iron and the presence of bioavailable carbon in the anaerobic microenvironment may result in the dominance of bacteria of δ-Proteobacteria.     

Changes in the Bacterial Community of Soil from a Neutral Mine Drainage Channel

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments.     

Bacterial Community Succession in Natural River Biofilm Assemblages

Temporal bacterial community changes in river biofilms were studied using 16S rRNA gene-based polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) followed by sequence analysis. Naturally occurring biofilms were sampled in 2001 during an undisturbed 7-month low-water period in the River Garonne (SW France). During the sampling period epilithic biomass exhibited a particular pattern: two 3-month periods of accumulation that resulted in two peaks in summer and fall, each at about 25 g ash-free dry mass per square meter. Bacterial community DGGE profiles differed between the summer and fall biomass peaks and shared only 30% common operational taxonomic units (OTUs), suggesting the influence of seasonal factors on these communities. During the second biomass accrual phase, bacterial richness and the appearance of new OTUs fitted a conceptual model of bacterial biofilm succession. During succession, five OTUs (corresponding to Dechloromonas sp., Nitrospira sp., and three different Spirosoma spp.) exhibited particular patterns and were present only during clearly defined successional stages, suggesting differences in life-history strategies for epilithic bacteria. Co-inertia analysis of DGGE banding patterns and physical–chemical data showed a significant relationship between community structure and environmental conditions suggesting that bacterial communities were mainly influenced by seasonal changes (temperature, light) and hydrodynamic stability. Within the periods of stability, analysis of environmental variables and community patterns showed the dominant influence of time and maturation on bacterial community structure. Thus, succession in these naturally occurring epilithic biofilm assemblages appears to occur through a combination of allogenic (seasonal) and autogenic changes.     

Bacterial Community Structure Along Moisture Gradients in the Parafluvial Sediments of Two Ephemeral Desert Streams

Microorganisms inhabiting stream sediments mediate biogeochemical processes of importance to both aquatic and terrestrial ecosystems. In deserts, the lateral margins of ephemeral stream channels (parafluvial sediments) are dried and rewetted, creating periodically wet conditions that typically enhance microbial activity. However, the influence of water content on microbial community composition and diversity in desert stream sediments is unclear. We sampled stream margins along gradients of wet to dry sediments, measuring geochemistry and bacterial 16S rRNA gene composition, at streams in both a cold (McMurdo Dry Valleys, Antarctica) and hot (Chihuahuan Desert, New Mexico, USA) desert. Across the gradients, sediment water content spanned a wide range (1.6–37.9% w/w), and conductivity was highly variable (12.3–1,380 μS cm⁻²). Bacterial diversity (at 97% sequence similarity) was high and variable, but did not differ significantly between the hot and cold desert and was not correlated with sediment water content. Instead, conductivity was most strongly related to diversity. Water content was strongly related to bacterial 16S rRNA gene community composition, though samples were distributed in wet and dry clusters rather than as assemblages shifting along a gradient. Phylogenetic analyses showed that many taxa from wet sediments at the hot and cold desert site were related to, respectively, halotolerant Gammaproteobacteria, and one family within the Sphingobacteriales (Bacteroidetes), while dry sediments at both sites contained a high proportion of taxa related to the Acidobacteria. These results suggest that bacterial diversity and composition in desert stream sediments is more strongly affected by hydrology and conductivity than temperature.     

Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10⁹ cells g⁻¹ dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.     

云南东川黄铜矿酸性浸矿废水中微生物群落分析

利用限制性片段长度多态性和16s rRNA PCR扩增及其序列分析来研究中国云南东川黄铜矿酸性浸矿废水(AMD)中微生物群落结构。基于建立16s rRNA克隆文库的分子方法常常被用来研究AMD中微生物生态。一小部分的rRNA被PCR扩增,克隆,然后用限制性片段长度多态性来筛选出其不同种类。在三个样地中,共挑选了357个克隆子,经限制性酶切分析后聚为100个可操作分类单元(OTU)。一个OTU代表各个样地中出现的同一种酶切图谱。有58个OTU被测序分析,结果在基因数据库中比对分析,其系统发育分析表明它们聚类为六大类:γ-proteobacteria,Acidobacteria,Clostridia,Actinobacteria,Nitrospira,α-pro- teobacteria。其中,γ-proteobacteria为最大的群落,在三个样地DCK-Ⅰ,DCN-Ⅰand DC-Ⅱ中分别占36%,57%,62%的比例。但与浸矿相关的微生物如At.ferrooxidans;L ferrooxidans等却发现的很少,仅在两个样地中各发现四个相关的OTUs。在这个AMD环境中浸矿相关的微生物都不是优势种群。     

Stability and Change in Estuarine Biofilm Bacterial Community Diversity

Biofouling communities contribute significantly to aquatic ecosystem productivity and biogeochemical cycling. Our knowledge of the distribution, composition, and activities of these microbially dominated communities is limited compared to other components of estuarine ecosystems. This study investigated the temporal stability and change of the dominant phylogenetic groups of the domain Bacteria in estuarine biofilm communities. Glass slides were deployed monthly over 1 year for 7-day incubations during peak tidal periods in East Sabine Bay, Fla. Community profiling was achieved by using 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes in combination with ribotyping, cloning, and sequencing to evaluate diversity and to identify dominant microorganisms. Bacterial community profiles from biofilms grown near the benthos showed distinct periods of constancy within winter and summer sampling periods. Similar periods of stability were also seen in T-RFLP patterns from floating biofilms. Alternating dominance of phylogenetic groups between seasons appeared to be associated with seasonal changes in temperature, nutrient availability, and light. The community structure appeared to be stable during these periods despite changes in salinity and in dissolved oxygen.     

Denitrification in Agriculturally Impacted Streams: Seasonal Changes in Structure and Function of the Bacterial Community

Denitrifiers remove fixed nitrogen from aquatic environments and hydrologic conditions are one potential driver of denitrification rate and denitrifier community composition. In this study, two agriculturally impacted streams in the Sugar Creek watershed in Indiana, USA with different hydrologic regimes were examined; one stream is seasonally ephemeral because of its source (tile drainage), whereas the other stream has permanent flow. Additionally, a simulated flooding experiment was performed on the riparian benches of the ephemeral stream during a dry period. Denitrification activity was assayed using the chloramphenicol amended acetylene block method and bacterial communities were examined based on quantitative PCR and terminal restriction length polymorphisms of the nitrous oxide reductase (nosZ) and 16S rRNA genes. In the stream channel, hydrology had a substantial impact on denitrification rates, likely by significantly lowering water potential in sediments. Clear patterns in denitrification rates were observed among pre-drying, dry, and post-drying dates; however, a less clear scenario was apparent when analyzing bacterial community structure suggesting that denitrifier community structure and denitrification rate were not strongly coupled. This implies that the nature of the response to short-term hydrologic changes was physiological rather than increases in abundance of denitrifiers or changes in composition of the denitrifier community. Flooding of riparian bench soils had a short-term, transient effect on denitrification rate. Our results imply that brief flooding of riparian zones is unlikely to contribute substantially to removal of nitrate (NO₃ ^-) and that seasonal drying of stream channels has a negative impact on NO₃ ^- removal, particularly because of the time lag required for denitrification to rebound. This time lag is presumably attributable to the time required for the denitrifiers to respond physiologically rather than a change in abundance or community composition.     

Selection of a Microbial Community in the Course of Formation of Acid Mine Drainage

Microbiology - Changes in microbial community composition during formation of an acid mine drainage were studied on a model of two water reservoirs located in the Ozernoye open-cast mine for...     

Microbial Community Composition in Acid Mine Drainage Lake of Xiang Mountain Sulfide Mine in Anhui Province,China

Acid mine drainage (AMD) lake of Xiang Mountain in Anhui Province, China, was characterized by acidic waters (pH around 2.8) containing high concentrations of soluble metals and sulfate. To investigate the function and dynamics of this extreme ecosystem, four water samples were collected from the lake in the fall of 2010. The acidophilic community structure was analyzed by molecular approaches, and bacterial and archaeal clone libraries of 16S rRNA genes were constructed. In contrast to dominance of chemolithotrophic acidophiles in typical AMD environments, autotrophic iron/sulfur-oxidizing bacteria were detected in only one sample with low abundance. Unexpectedly, the Cyanobacteria group was the predominant in all four samples (54.9%?77%). Chemoheterotrophs Acidiphilium and Acidisphaera were also abundant. These two heterotrophic groups contain bacteriochlorophyll that can perform photosynthesis, an advantage to grow and survive in such oligotrophic acidic environments. Only two clone sequences related to Legionella (2.8% of the total clones) were recovered from one sample in sharp contrast to its higher abundance (12.7%) in the summer of 2009. All archaeal sequences were affiliated to the phylum Crenarchaeota. The results of statistical analysis suggested that the water chemistry of the AMD lake controlled microbial composition of the AMD ecosystem.     

Assessment of the Microbial Community in a Constructed Wetland that Receives Acid Coal Mine Drainage

Constructed wetlands are used to treat acid drainage from surface or underground coal mines. However, little is known about the microbial communities in the receiving wetland cells. The purpose of this work was to characterize the microbial population present in a wetland that was receiving acid coal mine drainage (AMD). Samples were collected from the oxic sediment zone of a constructed wetland cell in southeastern Ohio that was treating acid drainage from an underground coal mine seep. Samples comprised Fe(III) precipitates and were pretreated with ammonium oxalate to remove interfering iron, and the DNA was extracted and purified by agarose gel electrophoresis prior to amplification of portions of the 16S rRNA gene. Amplified products were separated by denaturing gradient gel electrophoresis and DNA from seven distinct bands was excised from the gel and sequenced. The sequences were matched to sequences in the GenBank bacterial 16S rDNA database. The DNA in two of the bands yielded matches with Acidithiobacillus ferrooxidans and the DNA in each of the remaining five bands was consistent with one of the following microorganisms: Acidithiobacillus thiooxidans, strain TRA3-20 (a eubacterium), strain BEN-4 (an arsenite-oxidizing bacterium), an Alcaligenes sp., and a Bordetella sp. Low bacterial diversity in these samples reflects the highly inorganic nature of the oxic sediment layer where high abundance of iron- and sulfur-oxidizing bacteria would be expected. The results we obtained by molecular methods supported our findings, obtained using culture methods, that the dominant microbial species in an acid receiving, oxic wetland are A. thiooxidans and A. ferrooxidans.     

Sulfate Reduction in Freshwater Sediments Receiving Acid Mine Drainage

One arm of Lake Anna, Va., receives acid mine drainage (AMD) from Contrary Creek (SO₄²⁻ concentration = 2 to 20 mM, pH = 2.5 to 3.5). Acid-volatile sulfide concentrations, SO₄²⁻ reduction rates, and interstitial SO₄²⁻ concentrations were measured at various depths in the sediment at four stations in four seasons to assess the effects of the AMD-added SO₄²⁻ on bacterial SO₄²⁻ reduction. Acid-volatile sulfide concentrations were always an order of magnitude higher at the stations receiving AMD than at a control station in another arm of the lake that received no AMD. Summer SO₄²⁻ reduction rates were also an order of magnitude higher at stations that received AMD than at the control station (226 versus 13.5 mmol m⁻² day⁻¹), but winter values were inconclusive, probably due to low sediment temperature (6°C). Profiles of interstitial SO₄²⁻ concentrations at the AMD stations showed a rapid decrease with depth (from 1,270 to 6 μM in the top 6 cm) due to rapid SO₄²⁻ reduction. Bottom-water SO₄²⁻ concentrations in the AMD-receiving arm were highest in winter and lowest in summer. These data support the conclusion that there is a significant enhancement of SO₄²⁻ reduction in sediments receiving high SO₄²⁻ inputs from AMD.     

Spatial Variation and Fractionation of Bed Sediment-Borne Copper,Zinc, Lead,and Cadmium in a Stream System Affected by Acid Mine Drainage

An investigation was conducted to examine the spatial variation and fractionation of bed sediment-borne Cu, Zn, Pb, and Cd in a stream system affected by acid mine drainage. The pH had a major control on the spatial variation pattern of soluble, exchangeable, and carbonate-bound Cu, Zn, and Cd. There was a prominent concentration peak of carbonate-bound, oxide-bound, and organic-bound metals at the 29 km station, as controlled by the abundance of organic C, carbonate C, and oxides of manganese and iron. In general, the residual fraction was the dominant form for all four investigated metals. It was likely that oxide-Mn played a more important role in binding Zn and Cd than oxide-Fe did. In contrast, Cu had a higher affinity for iron hydrous oxides than for manganese oxide. Pb had a higher affinity for oxides of iron and manganese than for carbonates and organic matter. The presence of organic-bound metals in both the acidic upstream reach and non-acidic downstream reach suggests that the binding of these metals by organic matter was not markedly affected by pH, while the correspondence of organic C peak and organic-bound metal peaks at the 29 km station indicates a strong control by organic matter abundance on the quantity of organic-complexed metals.     

Spatial Variation in the Bacterial and Denitrifying Bacterial Community in a Biofilter Treating Subsurface Agricultural Drainage

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples. In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria. Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect, while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics. Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically inundated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.     

Bacterial Community Structure and Location in Stilton Cheese

The microbial diversity occurring in Stilton cheese was evaluated by 16S ribosomal DNA analysis with PCR-denaturing gradient gel electrophoresis. DNA templates for PCR experiments were directly extracted from the cheese as well as bulk cells harvested from a variety of viable-count media. The variable V3 and V4-V5 regions of the 16S genes were analyzed. Closest relatives of Lactococcus lactis, Enterococcus faecalis, Lactobacillus plantarum, Lactobacillus curvatus, Leuconostoc mesenteroides, Staphylococcus equorum, and Staphylococcus sp. were identified by sequencing of the DGGE fragments. Fluorescently labeled oligonucleotide probes were developed to detect Lactococcus lactis, Lactobacillus plantarum, and Leuconostoc mesenteroides in fluorescence in situ hybridization (FISH) experiments, and their specificity for the species occurring in the community of Stilton cheese was checked in FISH experiments carried out with reference cultures. The combined use of these probes and the bacterial probe Eub338 in FISH experiments on Stilton cheese sections allowed the assessment of the spatial distribution of the different microbial species in the dairy matrix. Microbial colonies of bacteria showed a differential location in the different parts of the cheese examined: the core, the veins, and the crust. Lactococci were found in the internal part of the veins as mixed colonies and as single colonies within the core. Lactobacillus plantarum was detected only underneath the surface, while Leuconostoc microcolonies were homogeneously distributed in all parts observed. The combined molecular approach is shown to be useful to simultaneously describe the structure and location of the bacterial flora in cheese. The differential distribution of species found suggests specific ecological reasons for the establishment of sites of actual microbial growth in the cheese, with implications of significance in understanding the ecology of food systems and with the aim of achieving optimization of the fermentation technologies as well as preservation of traditional products.     

Study of the Response of a Biofilm Bacterial Community to UV Radiation

We have developed a bioluminescent whole-cell biosensor that can be incorporated into biofilm ecosystems. RM4440 is a Pseudomonas aeruginosa FRD1 derivative that carries a plasmid-based recA-luxCDABE fusion. We immobilized RM4440 in an alginate matrix to simulate a biofilm, and we studied its response to UV radiation damage. The biofilm showed a protective property by physical shielding against UV C, UV B, and UV A. Absorption of UV light by the alginate matrix translated into a higher survival rate than observed with planktonic cells at similar input fluences. UV A was shown to be effectively blocked by the biofilm matrix and to have no detectable effects on cells contained in the biofilm. However, in the presence of photosensitizers (i.e., psoralen), UV A was effective in inducing light production and cell death. RM4440 has proved to be a useful tool to study microbial communities in a noninvasive manner.