土著浸矿微生物群落引种机制研究
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摘要
在生物冶金领域,为了构建和优化浸矿微生物群落,常常需要引入具有一定特性的嗜酸微生物。关于土著浸矿微生物群落引种机制的研究还没有相关报道。本文利用构建的共培养体系或驯化后的自然嗜酸微生物群落作为土著群落,在其不同的生长时期,引入不同代谢类型的外来浸矿菌种。对土著浸矿微生物群落的引种机制进行了研究,为找出浸矿过程中对土著群落引种的最佳类型和时间提供理论依据。
采用液体梯度稀释分离法从不同酸性矿坑水样品中分离到4株弧状或螺旋状菌株。对四株分离物的纯度、生理特征、16S rDNA和gyrB基因序列、形态学以及对黄铁矿浸出能力的分析后,最终确定四株分离物均为嗜铁钩端螺旋菌(L. ferriphilum)。
构建了一个包括At. caldus、L. ferriphilum、Ferroplasma、At. ferrooxidans、Acidiphillum spp和S. thermosulfidooxidans的共培养体系,其在40℃、pH为1.5和矿浆浓度为0.5%(g/100m1)时对黄铁矿的浸出效率相对较好；在此条件下,At. caldus、L. ferriphilum和Ferroplasma为共培养体系中的优势种群,而At. ferrooxidans、 Acidiphillum spp.和S. thermosulfidooxidans为劣势种群；其各个生长时期可划分为：0-48小时为生长适应期；48-96小时为快速生长期；96-192小时为稳定生长期；192-240小时为衰亡期。
以上述共培养体系作为土著群落,At. thiooxidans A01作为外来菌种分别在第66和138小时引入土著群落后,对黄铁矿浸出效率分别提高了10%和13%。实时定量PCR结果显示：At. thiooxidans A01的引入促进L. ferriphilum、Ferroplasma和Acidiphillum spp.的生长；在一定程度上抑制At. caldus的生长；而对At. ferrooxidans和S. thermosulfidooxidans的影响不大。功能基因芯片结果表明：来自L.ferriphilum的编码protoheme ferrolyase、formate hydrogenlyase、ADP heptose、phosphoheptose isomerase和glycosyltransferase的基因,以及来自Ferroplasma sp的编码ferredoxin oxidoreductase的基因和来自Acidiphillum spp编码acetyl-CoA carboxylase的基因,在引种后0-20小时表达水平上调；来自At. caldus的doxD基因和来自S.thermosulfidooxidans编码ribulose-1,5-bisphosphate carboxylase/oxygenase的基因,在引种后0-20小时表达水平都下调；来自At.ferrooxidans编码ADP-heptose Synthase的基因在引种后0-12小时表达水平上调,而在12-20小时下调。
对上述共培养体系的组分进行微调(At. thiooxidans A01加入,而L. ferriphilum YSK移除,其他组分不变),在相同实验条件下,L.ferriphilum YSK作为外来菌种分别在第0、66和138小时引入后,对黄铁矿的浸出效率分别提高了9%、14%和19%。实时定量PCR结果显示：L. ferriphilum YSK引入后,促进At. caldus、At. thiooxidans和Acidiphillum spp.的生长；抑制Ferroplasma和S. thermosulfidooxidans的生长；而对At. ferrooxidans的影响不大。运用功能基因芯片对第138小时引种后功能基因表达水平的变化进行分析后发现：来自L.ferriphilum的编码ADPheptose、phosphoheptose isomerase glycosyltransferase、Biotin carboxylase和protoheme ferrolyase的基因,以及来自Acidiphillum spp编码acetyl-CoA carboxylase的基因和来自At. caldus的doxD基因,在引种后0-20小时表达水平上调；来自At.ferrooxidans编码lipid A disaccharide synthase LpxB、glycosyl transferase和ADP-heptose Synthase的基因,在引种后0-8小时表达水平上调,而在8-20小时下调；来自Ferroplasma sp的编码ferredoxin oxidoreductase的基因在引种后0-4小时表达水平上调,而4-16小时下调,16-20小时上调；来自At. ferrooxidans的CbbS基因,在引种后0-20小时表达水平下调。
对来自不同酸性矿坑水中的嗜酸微生物混合,在低品位黄铜矿的浸矿体系中经过连续五次驯化后,其对黄铜矿的浸出效率提高了近45%。RFLP结果显示：驯化前的群落中共检测到八种常见浸矿微生物,包括At. ferrooxidans, At. caldus, Sulfobacillus sp., L. ferriphilum, S. thermosulfidooxidans, Acidiphilium sp., Alicyclobacillus sp.和Pseudomonas sp.;而在驯化后的群落中,只检测到了At. ferrooxidans, At. caldus, Sulfobacillus sp., L.ferriphilum和Acidiphilium的存在。功能基因芯片结果表明：At. caldus、L. ferriphilum、Sulfobacillus sp.、 Sulfolobus sp.和Acidiphilium sp.在群落中的丰度随着驯化而逐渐增多；而S. thermosulfidooxidans、Alicyclobacillus sp.和At. ferrooxidans的丰度逐渐减少。来自At. caldus和Sulfolobus sp.的与硫代谢相关的功能基因的丰度逐渐增多,而来自At. ferrooxidans的与硫代谢相关的功能基因的丰度逐渐减少；来自L. ferriphilum的与铁代谢相关的编码protoheme ferrolyase的基因的丰度逐渐增加；来自At. ferrooxidans, At. caldus, L. ferriphilum, Sulfolobus spp.和Acidiphilium sp.的与金属抗性相关的功能基因的丰度逐渐增加。
以上述从酸性矿坑水中驯化所得群落作为土著群落,At.thiooxidans A01作为外来菌种分别在第0、24和36天引入(浸矿周期为48天)。结果表明：在没有引种,以及第0、24和36天引种的各个浸矿体系中,最终Cu2+浸出浓度依次为：204.3、215.1、230.8和251.5mg/l。运用RFLP方法对在第36天引种后的土著群落进行分析后发现：在引种前第36天和引种后第48天的群落中,虽然同时检测到L. ferriphilum, At. ferrooxidans, At. caldus, Sulfobacillus sp., At. albertensis和Acidiphilium的存在,但优势种群At. caldus、 L.ferriphilum和At. ferrooxidans在群落中所占比例分别由38.4%、30.4%和17.6%相应变化为29.6%、40%和12%。而在没有引种的第48天的对照组中,我们只检测到了除At. albertensis外的其他5个种群,且At. caldus、L. ferriphilum和At. ferrooxidans的比例为43.2%、36%和10.4%。实时定量PCR和功能基因芯片结果显示：At.thiooxidansA01在第36天引入后首先主要吸附在矿石表面,并在第42天吸附量达到最大值,随后逐渐下降；而浮游的At. thiooxidans A01开始时菌体浓度较低,直到第45天才达到最大值,随后逐渐下降。吸附和浮游的At. caldus和Sulfobacillus sp在引种后的群落中的丰度都相对下降；而L. ferriphilum、At. ferrooxidans和Acidiphilium sp都相对上升。来自L. ferriphilum的编码protoheme ferrolyase和来自At.ferrooxidans的编码sulfide-quinone reductase的基因的丰度不管是在吸附还是浮游样品中,在引种后的群落中都显著增加；相反,来自At. caldus和Sulfolobus sp.的与硫代谢相关的一些基因(如doxD基因)却表现为丰度的下降。而来自At. ferrooxidans, L. ferriphilum和Acidiphilium sp等与金属抗性相关的基因都表现为丰度的增加。
Special acidophilic species are usually introduced into the bioleaching systems for constructing and optimizing microbial community during bioleaching process. However, little is known about the mechanism of species introduction into original bioleaching consortia. The built co-culture system or nature bioleaching microbial community, after adaptation, functioned as the original bacterial consortium. In this study, exogenous bacteria, belonging to different metabolic type, were introduced into original bioleaching systems at different growth periods. The introduction mechanism was studied in order to determine the most appropriate introduction type and time for the original bioleaching microbial community, as well as provide some theoretical basis.
Four vibrio or spiral-shaped bacteria strains were isolated from acid mineral drainage (AMD) using liquor gradient dilution method. Based on the analysis of purity, physiological property,16S rDNA and gyrB gene sequence, morphology, and bioleaching capacity towards pyrite, the four strains were identified as L. ferriphilum.
A co-culture system consisted of At. caldus、L. ferriphilum、 Ferroplasma、Acidiphillum spp.、S. thermosulfidooxidans and At. ferrooxidans was built. It was found that the co-culture system demonstrated superior pyrite bioleaching capacity under the condition (40℃, pH1.5and0.5%(g/100ml) pulp density). Besides, At. caldus、L. ferriphilum and Ferroplasma were the dominant groups compared with At. ferrooxidans、Acidiphillum spp. and S. thermosulfidooxidans. The growth period can be divided into four phases:adaptation phase from0to48hours, rapid-growth phase from48to96hours, stable growth phase from96to192hours, and decline phase from192to240hours.
The above co-culture system served as the indigenous community. At. thiooxidans A01, the exogenous species, was introduced into the original consortium at66and138hours, and the pyrite bioleaching rate increased by10%and13%, respectively. Based on the real-time PCR analysis, the introduction of At. thiooxidans A01promoted the growth of L. ferriphilum, Ferroplasma and Acidiphillum spp., inhibited the growth of At. Caldus, and demonstrated inconspicuous effect on the growth of At. ferrooxidans and S. thermosulfidooxidans. Based on the functional gene arrays data, protoheme ferrolyase、 formate hydrogenlyase、ADP heptose、 phosphoheptose isomerase and glycosyltransferase genes of L. ferriphilum, ferredoxin oxidoreductase gene of Ferroplasma sp. and acetyl-CoA carboxylase gene of Acidiphillum spp. were up-regulated from0to20hours after the introduction. In contrast, the doxD gene of At. caldus and ribulose-1,5-bisphosphate carboxylase/oxygenase gene of S. thermosulfidooxidans were down-regulated from0to20hours after the introduction. The ADP-heptose Synthase gene of At. ferrooxidans was up-regulated from0to12hours after the introduction, and then down-regulated from12to20hours.
The composition of the above co-culture was slightly adjusted in the following experiment. To be specific, along with the removal of L. ferriphilum, At. thiooxidans was added in the system. Under the same experimental condition, L. ferriphilum YSK serving as the exogenous species, was introduced into the indigenous consortium at0,66and138hours, and the pyrite bioleaching rate increased by9%,14%and19%, respectively. Based on the real-time PCR analysis, the introduction of L. ferriphilum YSK promoted the growth of At. caldus, At. thiooxidans and Acidiphillum spp., inhibited the growth of Ferroplasma and S. thermosulfidooxidans, and demonstrated inconspicuous effect on the growth of At. ferrooxidans. The shift of functional gene expression level from "138hours introduction" was analyzed using the functional gene arrays. It was found that ADP heptose、phosphoheptose isomerase、 glycosyltransferase、Biotin carboxylase and protoheme ferrolyase genes of L. ferriphilum, acetyl-CoA carboxylase gene of Acidiphillum spp. and doxD gene of At. caldus were up-regulated from0to20hours after the introduction. In addition, lipid A disaccharide synthase LpxB、glycosyl transferase and ADP-heptose Synthase genes of At. ferrooxidans showed up-regulated expression from0to8hours after the introduction, and then down-regulated expression from8to20hours. The situation was more complex with ferredoxin oxidoreductase gene of Ferroplasma sp. In detail, this gene was up-regulated from0to4hours, down-regulated from16to20hours, and then up-regulated again from16to20hours after the introduction. CbbS gene of At. ferrooxidans showed down-regulated expression from0to20hours after the introduction.
The acidophilic microorganism mixture from different AMD environment was adapted for five generations in chalcopyrite bioleaching system, and then was used in chalcopyrite bioleaching. An increase by45%of the bioleaching rate was observed. According to the RFLP analysis, the microbial community consisted of eight common bioleaching microorganisms, including At. ferrooxidans, At. caldus, Sulfobacillus sp., L. ferriphilum, S. thermosulfidooxidans, Acidiphilium sp., Alicyclobacillus sp. and Pseudomonas sp., however, only the existence of At. ferrooxidans, At. caldus, Sulfobacillus sp., L ferriphilum and Acidiphilium was detected after adaptation. Based on the analysis of functional gene arrays, functional gene abundance of At. Caldus, L.ferriphilum, Sulfobacillus sp., Sulfolobus sp. and Acidiphilium sp. was increased along with the adaptation, however, the abundance of S. thermosulfidooxidans、Alicyclobacillus sp. and At. ferrooxidans was through a decline. The functional genes of At. caldus and Sulfolobus sp. involved in sulfur metabolism, demonstrated increasing gene abundance, while the functional genes of At. ferrooxidans involved in sulfur metabolism showed decreasing abundance. In addition, protoheme ferrolyase gene, functional genes involved in iron metabolism of L. ferriphilum showed increasing abundance. The functional genes involved in metal resistance of At. ferrooxidans, At. caldus, L. ferriphilum, Sulfolobus spp. and Acidiphilium sp. also demonstrated increasing abundance.
At. thiooxidans A01, the exogenous species, was introduced into the indigenous consortium, the adapted microbial community from AMD environment, respectively at the0th,24th and36th day (bioleaching cycle spanned48days). The results showed that the copper ion concentration was respectively204.3,215.1,230.8and251.5mg/L in the bioleaching system without and with introduction of At. thiooxidans A01at0th,24th and36th day. Microbial community structure was analyzed using RFLP method. After the inroduciton of At. thiooxidans A01, it suggested that L. ferriphilum, At. ferrooxidans, At. caldus, Sulfobacillus sp., At. albertensis and Acidiphilium were together detected in bioleaching all the way. Moreover, the proportion of dominant groups, namely, At. caldus、L. ferriphilum and At. ferrooxidans, in these two systems, changed from38.4%,30.4%and17.6%at36th day to29.6%,40%and12%at48th day, respectively. However, only five microbial species except for At. albertensis were detected in the control group without introduction of At. thiooxidans A01. The real-time PCR and functional gene arrays data suggested that At. thiooxidans A01, introduced at the the36th day, primarily attached on the mineral surface, and the adsorbance reached the peak at the42th day, followed by the decreasing amount. For the supernatant At. thiooxidans A01, the cell number was initially low, reached the peak at the45th day, and then turned into a decreasing tendency. The abundance of both attached and free At. caldus and Sulfobacillus sp. was decreased after the introduction, while, that of L. ferriphilum, At. ferrooxidans and Acidiphilium sp. were all increased. The abundance of protoheme ferrolyase gene of L. ferriphilum and sulfide-quinone reductase gene of At. ferrooxidans were increased after introduction in both attached and free bacteria. However, the genes involved in sulfur metabolism, such as doxD gene, showed decreasing abundance. Moreover, the metal resistance genes of At. ferrooxidans, L. ferriphilum and Acidiphilium sp. showed an increasing abundance.
采用液体梯度稀释分离法从不同酸性矿坑水样品中分离到4株弧状或螺旋状菌株。对四株分离物的纯度、生理特征、16S rDNA和gyrB基因序列、形态学以及对黄铁矿浸出能力的分析后,最终确定四株分离物均为嗜铁钩端螺旋菌(L. ferriphilum)。
构建了一个包括At. caldus、L. ferriphilum、Ferroplasma、At. ferrooxidans、Acidiphillum spp和S. thermosulfidooxidans的共培养体系,其在40℃、pH为1.5和矿浆浓度为0.5%(g/100m1)时对黄铁矿的浸出效率相对较好；在此条件下,At. caldus、L. ferriphilum和Ferroplasma为共培养体系中的优势种群,而At. ferrooxidans、 Acidiphillum spp.和S. thermosulfidooxidans为劣势种群；其各个生长时期可划分为：0-48小时为生长适应期；48-96小时为快速生长期；96-192小时为稳定生长期；192-240小时为衰亡期。
以上述共培养体系作为土著群落,At. thiooxidans A01作为外来菌种分别在第66和138小时引入土著群落后,对黄铁矿浸出效率分别提高了10%和13%。实时定量PCR结果显示：At. thiooxidans A01的引入促进L. ferriphilum、Ferroplasma和Acidiphillum spp.的生长；在一定程度上抑制At. caldus的生长；而对At. ferrooxidans和S. thermosulfidooxidans的影响不大。功能基因芯片结果表明：来自L.ferriphilum的编码protoheme ferrolyase、formate hydrogenlyase、ADP heptose、phosphoheptose isomerase和glycosyltransferase的基因,以及来自Ferroplasma sp的编码ferredoxin oxidoreductase的基因和来自Acidiphillum spp编码acetyl-CoA carboxylase的基因,在引种后0-20小时表达水平上调；来自At. caldus的doxD基因和来自S.thermosulfidooxidans编码ribulose-1,5-bisphosphate carboxylase/oxygenase的基因,在引种后0-20小时表达水平都下调；来自At.ferrooxidans编码ADP-heptose Synthase的基因在引种后0-12小时表达水平上调,而在12-20小时下调。
对上述共培养体系的组分进行微调(At. thiooxidans A01加入,而L. ferriphilum YSK移除,其他组分不变),在相同实验条件下,L.ferriphilum YSK作为外来菌种分别在第0、66和138小时引入后,对黄铁矿的浸出效率分别提高了9%、14%和19%。实时定量PCR结果显示：L. ferriphilum YSK引入后,促进At. caldus、At. thiooxidans和Acidiphillum spp.的生长；抑制Ferroplasma和S. thermosulfidooxidans的生长；而对At. ferrooxidans的影响不大。运用功能基因芯片对第138小时引种后功能基因表达水平的变化进行分析后发现：来自L.ferriphilum的编码ADPheptose、phosphoheptose isomerase glycosyltransferase、Biotin carboxylase和protoheme ferrolyase的基因,以及来自Acidiphillum spp编码acetyl-CoA carboxylase的基因和来自At. caldus的doxD基因,在引种后0-20小时表达水平上调；来自At.ferrooxidans编码lipid A disaccharide synthase LpxB、glycosyl transferase和ADP-heptose Synthase的基因,在引种后0-8小时表达水平上调,而在8-20小时下调；来自Ferroplasma sp的编码ferredoxin oxidoreductase的基因在引种后0-4小时表达水平上调,而4-16小时下调,16-20小时上调；来自At. ferrooxidans的CbbS基因,在引种后0-20小时表达水平下调。
对来自不同酸性矿坑水中的嗜酸微生物混合,在低品位黄铜矿的浸矿体系中经过连续五次驯化后,其对黄铜矿的浸出效率提高了近45%。RFLP结果显示：驯化前的群落中共检测到八种常见浸矿微生物,包括At. ferrooxidans, At. caldus, Sulfobacillus sp., L. ferriphilum, S. thermosulfidooxidans, Acidiphilium sp., Alicyclobacillus sp.和Pseudomonas sp.;而在驯化后的群落中,只检测到了At. ferrooxidans, At. caldus, Sulfobacillus sp., L.ferriphilum和Acidiphilium的存在。功能基因芯片结果表明：At. caldus、L. ferriphilum、Sulfobacillus sp.、 Sulfolobus sp.和Acidiphilium sp.在群落中的丰度随着驯化而逐渐增多；而S. thermosulfidooxidans、Alicyclobacillus sp.和At. ferrooxidans的丰度逐渐减少。来自At. caldus和Sulfolobus sp.的与硫代谢相关的功能基因的丰度逐渐增多,而来自At. ferrooxidans的与硫代谢相关的功能基因的丰度逐渐减少；来自L. ferriphilum的与铁代谢相关的编码protoheme ferrolyase的基因的丰度逐渐增加；来自At. ferrooxidans, At. caldus, L. ferriphilum, Sulfolobus spp.和Acidiphilium sp.的与金属抗性相关的功能基因的丰度逐渐增加。
以上述从酸性矿坑水中驯化所得群落作为土著群落,At.thiooxidans A01作为外来菌种分别在第0、24和36天引入(浸矿周期为48天)。结果表明：在没有引种,以及第0、24和36天引种的各个浸矿体系中,最终Cu2+浸出浓度依次为：204.3、215.1、230.8和251.5mg/l。运用RFLP方法对在第36天引种后的土著群落进行分析后发现：在引种前第36天和引种后第48天的群落中,虽然同时检测到L. ferriphilum, At. ferrooxidans, At. caldus, Sulfobacillus sp., At. albertensis和Acidiphilium的存在,但优势种群At. caldus、 L.ferriphilum和At. ferrooxidans在群落中所占比例分别由38.4%、30.4%和17.6%相应变化为29.6%、40%和12%。而在没有引种的第48天的对照组中,我们只检测到了除At. albertensis外的其他5个种群,且At. caldus、L. ferriphilum和At. ferrooxidans的比例为43.2%、36%和10.4%。实时定量PCR和功能基因芯片结果显示：At.thiooxidansA01在第36天引入后首先主要吸附在矿石表面,并在第42天吸附量达到最大值,随后逐渐下降；而浮游的At. thiooxidans A01开始时菌体浓度较低,直到第45天才达到最大值,随后逐渐下降。吸附和浮游的At. caldus和Sulfobacillus sp在引种后的群落中的丰度都相对下降；而L. ferriphilum、At. ferrooxidans和Acidiphilium sp都相对上升。来自L. ferriphilum的编码protoheme ferrolyase和来自At.ferrooxidans的编码sulfide-quinone reductase的基因的丰度不管是在吸附还是浮游样品中,在引种后的群落中都显著增加；相反,来自At. caldus和Sulfolobus sp.的与硫代谢相关的一些基因(如doxD基因)却表现为丰度的下降。而来自At. ferrooxidans, L. ferriphilum和Acidiphilium sp等与金属抗性相关的基因都表现为丰度的增加。
Special acidophilic species are usually introduced into the bioleaching systems for constructing and optimizing microbial community during bioleaching process. However, little is known about the mechanism of species introduction into original bioleaching consortia. The built co-culture system or nature bioleaching microbial community, after adaptation, functioned as the original bacterial consortium. In this study, exogenous bacteria, belonging to different metabolic type, were introduced into original bioleaching systems at different growth periods. The introduction mechanism was studied in order to determine the most appropriate introduction type and time for the original bioleaching microbial community, as well as provide some theoretical basis.
Four vibrio or spiral-shaped bacteria strains were isolated from acid mineral drainage (AMD) using liquor gradient dilution method. Based on the analysis of purity, physiological property,16S rDNA and gyrB gene sequence, morphology, and bioleaching capacity towards pyrite, the four strains were identified as L. ferriphilum.
A co-culture system consisted of At. caldus、L. ferriphilum、 Ferroplasma、Acidiphillum spp.、S. thermosulfidooxidans and At. ferrooxidans was built. It was found that the co-culture system demonstrated superior pyrite bioleaching capacity under the condition (40℃, pH1.5and0.5%(g/100ml) pulp density). Besides, At. caldus、L. ferriphilum and Ferroplasma were the dominant groups compared with At. ferrooxidans、Acidiphillum spp. and S. thermosulfidooxidans. The growth period can be divided into four phases:adaptation phase from0to48hours, rapid-growth phase from48to96hours, stable growth phase from96to192hours, and decline phase from192to240hours.
The above co-culture system served as the indigenous community. At. thiooxidans A01, the exogenous species, was introduced into the original consortium at66and138hours, and the pyrite bioleaching rate increased by10%and13%, respectively. Based on the real-time PCR analysis, the introduction of At. thiooxidans A01promoted the growth of L. ferriphilum, Ferroplasma and Acidiphillum spp., inhibited the growth of At. Caldus, and demonstrated inconspicuous effect on the growth of At. ferrooxidans and S. thermosulfidooxidans. Based on the functional gene arrays data, protoheme ferrolyase、 formate hydrogenlyase、ADP heptose、 phosphoheptose isomerase and glycosyltransferase genes of L. ferriphilum, ferredoxin oxidoreductase gene of Ferroplasma sp. and acetyl-CoA carboxylase gene of Acidiphillum spp. were up-regulated from0to20hours after the introduction. In contrast, the doxD gene of At. caldus and ribulose-1,5-bisphosphate carboxylase/oxygenase gene of S. thermosulfidooxidans were down-regulated from0to20hours after the introduction. The ADP-heptose Synthase gene of At. ferrooxidans was up-regulated from0to12hours after the introduction, and then down-regulated from12to20hours.
The composition of the above co-culture was slightly adjusted in the following experiment. To be specific, along with the removal of L. ferriphilum, At. thiooxidans was added in the system. Under the same experimental condition, L. ferriphilum YSK serving as the exogenous species, was introduced into the indigenous consortium at0,66and138hours, and the pyrite bioleaching rate increased by9%,14%and19%, respectively. Based on the real-time PCR analysis, the introduction of L. ferriphilum YSK promoted the growth of At. caldus, At. thiooxidans and Acidiphillum spp., inhibited the growth of Ferroplasma and S. thermosulfidooxidans, and demonstrated inconspicuous effect on the growth of At. ferrooxidans. The shift of functional gene expression level from "138hours introduction" was analyzed using the functional gene arrays. It was found that ADP heptose、phosphoheptose isomerase、 glycosyltransferase、Biotin carboxylase and protoheme ferrolyase genes of L. ferriphilum, acetyl-CoA carboxylase gene of Acidiphillum spp. and doxD gene of At. caldus were up-regulated from0to20hours after the introduction. In addition, lipid A disaccharide synthase LpxB、glycosyl transferase and ADP-heptose Synthase genes of At. ferrooxidans showed up-regulated expression from0to8hours after the introduction, and then down-regulated expression from8to20hours. The situation was more complex with ferredoxin oxidoreductase gene of Ferroplasma sp. In detail, this gene was up-regulated from0to4hours, down-regulated from16to20hours, and then up-regulated again from16to20hours after the introduction. CbbS gene of At. ferrooxidans showed down-regulated expression from0to20hours after the introduction.
The acidophilic microorganism mixture from different AMD environment was adapted for five generations in chalcopyrite bioleaching system, and then was used in chalcopyrite bioleaching. An increase by45%of the bioleaching rate was observed. According to the RFLP analysis, the microbial community consisted of eight common bioleaching microorganisms, including At. ferrooxidans, At. caldus, Sulfobacillus sp., L. ferriphilum, S. thermosulfidooxidans, Acidiphilium sp., Alicyclobacillus sp. and Pseudomonas sp., however, only the existence of At. ferrooxidans, At. caldus, Sulfobacillus sp., L ferriphilum and Acidiphilium was detected after adaptation. Based on the analysis of functional gene arrays, functional gene abundance of At. Caldus, L.ferriphilum, Sulfobacillus sp., Sulfolobus sp. and Acidiphilium sp. was increased along with the adaptation, however, the abundance of S. thermosulfidooxidans、Alicyclobacillus sp. and At. ferrooxidans was through a decline. The functional genes of At. caldus and Sulfolobus sp. involved in sulfur metabolism, demonstrated increasing gene abundance, while the functional genes of At. ferrooxidans involved in sulfur metabolism showed decreasing abundance. In addition, protoheme ferrolyase gene, functional genes involved in iron metabolism of L. ferriphilum showed increasing abundance. The functional genes involved in metal resistance of At. ferrooxidans, At. caldus, L. ferriphilum, Sulfolobus spp. and Acidiphilium sp. also demonstrated increasing abundance.
At. thiooxidans A01, the exogenous species, was introduced into the indigenous consortium, the adapted microbial community from AMD environment, respectively at the0th,24th and36th day (bioleaching cycle spanned48days). The results showed that the copper ion concentration was respectively204.3,215.1,230.8and251.5mg/L in the bioleaching system without and with introduction of At. thiooxidans A01at0th,24th and36th day. Microbial community structure was analyzed using RFLP method. After the inroduciton of At. thiooxidans A01, it suggested that L. ferriphilum, At. ferrooxidans, At. caldus, Sulfobacillus sp., At. albertensis and Acidiphilium were together detected in bioleaching all the way. Moreover, the proportion of dominant groups, namely, At. caldus、L. ferriphilum and At. ferrooxidans, in these two systems, changed from38.4%,30.4%and17.6%at36th day to29.6%,40%and12%at48th day, respectively. However, only five microbial species except for At. albertensis were detected in the control group without introduction of At. thiooxidans A01. The real-time PCR and functional gene arrays data suggested that At. thiooxidans A01, introduced at the the36th day, primarily attached on the mineral surface, and the adsorbance reached the peak at the42th day, followed by the decreasing amount. For the supernatant At. thiooxidans A01, the cell number was initially low, reached the peak at the45th day, and then turned into a decreasing tendency. The abundance of both attached and free At. caldus and Sulfobacillus sp. was decreased after the introduction, while, that of L. ferriphilum, At. ferrooxidans and Acidiphilium sp. were all increased. The abundance of protoheme ferrolyase gene of L. ferriphilum and sulfide-quinone reductase gene of At. ferrooxidans were increased after introduction in both attached and free bacteria. However, the genes involved in sulfur metabolism, such as doxD gene, showed decreasing abundance. Moreover, the metal resistance genes of At. ferrooxidans, L. ferriphilum and Acidiphilium sp. showed an increasing abundance.
引文
[1]Johnson DB. Biodiversity and ecology of acidophilic microoganisms. FEMS Microbiol Ecol,1998,27:307-317.
[2]Bond PL, Druschel GK, Banfield JF. Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems[J]. Applied and environmental microbiology,2000,66(11):4962-4971.
[3]Johnson DB, Hallberg K B. The microbiology of acidic mine waters[J]. Research in Microbiology,2003,154:466-473.
[4]Johnson, DB. and Rang L. Ejects of acidophilic protozoa on populations of metal-mobilising bacteria during the leaching of pyritic coal[J]. J. Gen. Microbiol,1993,139:1417-1423.
[5]Kelly DP, Wood AP. Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov, Halothiobacillus gen. nov, and Thermithiobacillus gen. nov. Int J Syst Evol Microbiol,2000,50:511-516.
[6]Hiraishi A, Nagashima KV, Matsuura K, Shimada K, Takaichi S, Wakao N, Katayama Y. Phylogeny and photosynthetic features of Thiobacillus acidophilus and related acidophilic bacteria:its transfer to the genus Acidiphilium as Acidiphilium acidophilum comb. nov. Int J Syst Bacteriol,1998,48:1389-1398.
[7]Coram NJ, Rawlings DE. Molecular relationship between two groups of the genus Leptospirillum and the finding that Leptospirillum ferriphilum sp. nov. dominates South African commercial biooxidation tanks that operate at 40 degrees C. Appl Environ Microbiol,2002,68:838-845.
[8]Clark DA, Norris PR. Acidimicrobium ferrooxidans gen. nov, sp. nov.: mixed-culture ferrous iron oxidation with Sulfobacillus species. Microbiology, 1996,142:785-790.
[9]Johnson B, Roberto FF. Heterotrophic acidophiles and their roles in the bioleaching of sulfide minerals. In:Rawlings DE (ed) Biomining:theory, microbes and industrial processes. Springer, Berlin Heidelberg New York, pp 1997:259-279.
[10]Fuchs T, Huber H, Teiner K, Burggraf S, Stetter KO. Metallosphaera prunae, sp. nov, a novel metal-mobilizing, thermoacidophilic archaeum, isolated from a uranium mine in Germany. Syst Appl Microbiol,1995,18:560-566.
[11]Fuchs T, Huber H, Burggraf S, Stetter KO.16S rDNA-based phylogeny of the archaeal order Sulfolobales and reclassification of Desulfurolobus ambivalens as Acidianus ambivalens comb. nov. Syst Appl Microbiol,1996,19:56-60.
[12]Pronk JT, de Bruyn JC, Bos P, Kuenen JG. Anaerobic growth of Thiobacillus ferooxidans. Appl Environ Microbiol,1992,58:2227-2230.
[13]Das A, Mishra AK, Roy P. Anaerobic growth on elemental sulfur using dissimilar iron reduction by autotrophic Thiobacillus ferrooxidans. FEMS Microbiol Lett, 1992,97:167-172.
[14]Hiraishi A, Shimada K. Aerobic anoxygenic photo synthetic bacteria with zinc-bacteriochlorophyll. J Gen Appl Microbiol,2001,47:161-180.
[15]Norris PR. University of Warwick, UK, personal communication.
[16]Torma AE. The role of Thiobacillus ferrooxidans in hydro-metallurgical processes[A]. In Advances in Biochemical Engineering[C], ed. TK Ghose, A Fretcher, N Blackebrough, New York:Springer,1977,6:1-37.
[17]Suzuki I. Microbial leaching of metals from sulfide minerals[J]. Biotechnology advances,2001,19:119-132.
[18]Duncan DW, Trussell PC and Walden CC. Leaching of Chalcopyrite with Thiobacillus ferrooxidans:Effect of Surfactants and Shaking[J]. Appl Environ Microbiol,1964,12(2):122-126.
[19]Jerez CA, Arrendondo RA. Sensitive immunological method to enumerate Lepto spirillum ferrooxidans in the presence of Thiobacillus ferrooxidans[J]. Microbiology Letters,1991,78:99-102.
[20]Femandez MG, Mustin C. Occurences at mineral-bacteria interface during oxidation of arsenopyrite by thiobacillus ferrooxidans[J]. Biotechnology and Bioengineering,1995,48:13-211.
[21]Escoba BJ, Jedlicki E, Vargas T. A method for evaluating the proportion of free and attached bacteria in the bioleaching of chalcopyrite with thiobacillus ferrooxidans[J], Hydrometallurgy,1996,40:1-10.
[22]Fowler TA, Crundwell FK. Leaching of Zn sulfide by thiobacillus ferrooxidans: experiments with a controlled redox potential indicate no direct bacterial mechanism[J].Appl Environ Microbiol,1998,64:3570-3575.
[23]Ehrlich HL. Past, present and future of biohydrometallurgy[A]. In:Amils R, Ballester A, editors. Biohydrometallurgy and the environment toward the mining of the 21st century PT-A-1999[C], New Yoek:Wiiey,1999,9:51-60.
[24]Sand W, Gehrke T, Hallmann R, et al. Sulfur chemistry, biofilm, and the (in)direct attack mechanism-a critical evalution of bacterial leaching[J]. Applied and microbiological biotechnology,1995,43:961-966.
[25]Schippers A, Sand W. Bacterial leaching of metal sulfides proceeds by two indirect mechanisms via thiosulfate or via polysulfides and sulfur[J]. Appl Environ Microbiol,1999,65:319-321.
[26]Rawlings DE. The molecular genetics of Thiobacillus ferrooxidans and other mesophilic, acidophilic, chemolithotrophic, iron-or sulfur-oxidizing bacteria[J]. Hydrometallurgy,2001,59:187-201.
[27]Rawlings DE. Heavy metal mining using microbes[J]. Annual review of microbiology,2002,56:65-91.
[28]Donati E, Curutchet G. et al. Bioleaching of covellite using pure and mixed cultures of Thiobacillus ferroxidans and Thiobacillus thiooxidans. Process Biochem,1996,31(2):129-134.
[29]Falco L, Pogliani C. A comparison of bioleaching of covellite using pure cultures of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans or a mixed culture of Leptospirillum ferrooxidans and Acidithiobacillus thiooxidans. Hydrometallurgy,2003,71:31-36.
[30]Shi SY, Fang ZX. Bioleaching of marmatite flotation concentrate by Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans. Trans Nonferrous Metal Soc China,2004,14 (3):569-575.
[31]Hugues D, Foucher P. et. al. Continuous bioleaching of chalcopyrite using a novel extremely thermophilic mixed culture. Int J Min Processing,2002,66(1): 107-119.
[32]Stott MB, Sutton DC. Comparative leaching of chalcopyrite by selected Acidophilic bacteria and Archaea. Geomicrobiol J,2003,20 (3):215-230.
[33]Devecia H, Akcilb A. I. Alpa. Bioleaching of complex zinc sulphides using mesophilic and thermophilic bacteria:comparative importance of pH and iron. Hydrometallurgy,2004,73:293-303.
[34]Battaglia-Brunet F, d'Hugues P. The mutual effect of mixed Thiobacillus and Leptospirillum populations on pyrite bioleaching[J]. Min Eng,1998,11(2): 195-205.
[35]Okibe N, Johnson DB. Biooxidation of pyrite by defined mixed culture of moderately thermophilic acidophiles in pH-controlled bioreactor:significance of microbial interaction [J]. Biotechnol. Bioeng,2004,87:574-583.
[36]Dopson M, Lindstrom EB. Potential role of Thiobacilcaldus in arsenopyrite bioleaching[J]. Appl Environ Microbiol,1999,65:36-40.
[37]Colmer AR, Hinckle ME. The Role of Microorganism in Acid Mine Drainage. A Preliminary Report, Science.1947,106:253-256.
[38]Norris PR. Acidophilic bacteria and their activity in metal sulfide oxidation[J]. In Microbial Mineral Recover.1990,3-27.
[39]Hector M, Lizama IS. Bacterial Leaching of a Sulfide Ore By Thiobacillus Ferrooxidans and Thiobacillus Thiooxidans, Part II:Column leaching studies [J]. hydrometallurgy,1989,22:301-310.
[40]Schrenk MO, Edwards KJ, GoodmanRM, et al. Distribution of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans:implications for generation of acid mine drainage[J]. Science,1998,279:1519-1521.
[41]Johnson DB, Biological desulfurization of coal using mixed populations of mesophilic and moderately thermophilic acidophilic bacteria[C]. In:Processing and Utilization of High Sulfur Coals (Dugan PR, Quigley DR, and Attia YA, Eds.), 1991, pp.567-580. Elsevier, Amsterdam.
[42]Liu Y, Yin HQ, Zeng WM, et al. The effect of the introduction of exogenous strain Acidithiobacillus thiooxidans A01 on functional gene expression, structure and function of indigenous consortium during pyrite bioleaching. Bioresource Technology,2011,102(17):8092-8098.
[43]Johnson DB, and Roberto FF, Heterotrophic acidophiles and their roles in the bioleaching of sulfide minerals[C]. In:Biomining:Theory, Microbes and Industrial Processes (Rawlings DE, Ed.), pp.1997,259-280. Springer-Verlag/Landes Bioscience, Georgetown, TX.
[44]Hallmann R, Friedrich A, Koops H P, et al, Physiological characteristics of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans and physicochemical factors infuence microbial metal leaching[J]. Geomicrobiol. J,1992,10:193-206.
[45]McGinness S and Johnson DB. Grazing of acidophilic bacteria by a fagellate protozoan[J]. Microbiol. Ecol,1992,23:75-86.
[46]Ojumu TV, Hansford G, Petersen J. The kinetics of ferrous-iron oxidation by Leptospirillum ferriphilum in continuous culture:The effect of temperature. Biochem. Eng. J,2009,46:161-168.
[47]Konishi Y, Yoshida S, Asai S. Bioleaching of pyrite by acidophilic thermophile Acidianus brierleyi. Biotechnol. Bioeng,1995,48:592-600.
[48]Johnson DB and Hallberg KB. The microbiology of acidic mine waters. Res. Microbiol,2003,154:466-473.
[49]Rawlings DE, Johnson DB. The microbiology of biomining:development and optimization of mineral-oxidizing microbial consortia[J]. Microbiology,2007, 153:315-324.
[50]Johnson DB, Roberto FF. Heterotrophic acidophiles and their roles in the bioleaching of sulfide minerals. In Biomining:Theory, Microbes and Industrial Processes, pp. Edited by D. E. Rawlings. Georgetown, TX:Springer/Landes Bioscience,1997,259-280.
[51]Okibe, N, Gericke, M, Hallberg, K. B. & Johnson, D. B. Enumeration and characterization of acidophilic microorganisms isolated from a pilot plant stirred tank bioleaching operation. Appl Environ Microbiol,2003,69,1936-1943.
[52]Bacelar-Nicolau P, Johnson DB. Leaching of pyrite by acidophilic heterotrophic iron-oxidizing bacteria in pure and mixed cultures. Appl Environ Microbiol, 1999,65:585-590.
[53]Akcil A, Ciftci H, Deveci H. Role and contribution of pure and mixed cultures of mesophiles in bioleaching of a pyritic chalcopyrite concentrate. Minerals Engineering,2007,20:310-318.
[54]Demergasso CS, Galleguillos P PA, Escudero G LV, Zepeda A VJ, Danny C, Casamayor EO. Molecular characterization of microbial populations in a low-grade copper ore bioleaching test heap. Hydrometallurgy,2005,80: 241-253.
[55]Rawlings DE. Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates. Microbial Cell Factories,2005,4(13):1-15.
[56]Sebastian J. Schreiber, Andrew P. Gutierrez. A supply:demand perspective of species invasions and coexistence:applications to biological control. Eco model. 1998,106:27-45.
[57]Theresa N. Mgidi, David C. Le Maitre, et al. Alien plant invasions-incorporating emerging invaders in regional prioritization:A pragmatic approach for Southern Africa. J Environ Manag.2007,84:173-187.
[58]Boonchan S, Britz ML, Stanley GA. Degradation and mineralization of high-molecular-weight polycyclic aromatic hydrocarbons by defined fungal-bacteria cocultures. Appl. Environ. Microbiol,2000,66:1007-1019.
[59]Juhasz AL, Naidu R. Bioremediation of high molecular weight polycyclic aromatic hydrocarbons:a review of the microbial degradation of benzo[a]pyrene. Int. Biodeterior. Biodegrad,2000,45:57-88.
[60]Crooks J, Ruiz G. Biological invasions of marine ecosystems. In:Gallaugher P, Bendell-Young L (Eds) Waters in peril.2001,42:3-18.
[61]Moseman SM, Zhang R, Qian PY, Levin LA. Diversity and functional responses of nitrogen-fixing microbes to three wetland invasions. Biol. Invasions,2009,11:225-239.
[62]Rodriguez CF, Becares E, Fernandez-Alaez M, Fernandez-Alaez C. Loss of diversity and degradation of wetlands as a result of introducing exotic crayfish. Biol. Invas,2005,7:75-85.
[63]Branch GM, Steffani CN. Can we predict the effects of alien species? A casehistory of the invasion of South Africa by Mytilus galloprovincialis (Lamarck). J. Exp. Mar. Biol. Ecol,2004,300:189-215.
[64]Cerda M, Castilla JC. Diversidad biologica y biomasa de macro-invertebratos en matrices intermareales de Pyura praeputialis. Rev. Chil. Hist. Nat,1999,74: 841-853.
[65]Olivier P, Etienne V, Catherine R. Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by Cladosporium sphaerospermum isolated from an aged PAH contaminated soil. FEMS Microbiol. Ecol,2004,51:71-79.
[66]Vander Gast CJ, Whiteley AS, Thompson IP. Temporal dynamics and degradation activity of an bacterial inoculum for treating waste metal-working fluid. Environ Microbiol,2004,6:254-263.
[67]Hippe H. Leptospirillum gen. nov. (ex Markosyan 1972), nom. rev, including Leptospirillum ferrooxidans sp. nov. (ex Markosyan 1972), nom. rev. and Leptospirillum. Int. J. Syst. Evol. Microbiol,2000,2:501-503.
[68]Goebel BM and Stackebrandt E. Cultural and phylo genetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl. Environ. Microbiol.1994,60:1614-1621.
[69]Bond P.L., Smriga S.P. and Banfield J.F.. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol.2000,66:3842-3849.
[70]Edwards KJ, Bond PL, Gihring TM and Banfield JF. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science,2000,287: 1796-1799.
[71]Darland G, Brock T.D, Samsonoj W and Conti SF. A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science,1970,170:1416-1418.
[72]Segerer A, Langworthy TA and Stetter KO. Thermoplasma acidophilum and Thermoplasma volcanium sp. nov. from Solfatare Fields. Syst. Appl. Microbiol, 1988,10:161-171.
[73]Burton NP and Norris PR. Microbiology of acidic, geothermal springs of Montserrat:environmental rDNA analysis. Extremophiles,2000,4:315-320.
[74]Zhou, JZ, and Thompson, DK. Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol.2002,13:202-204.
[75]Ye RW, Tao W, Bedzyk L, et al, Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions[J]. J. Bacteriol,2000,182: 4458-4465.
[76]Zhou J. Microarrays for bacterial detection and microbial community analysis[J]. Current Opinion in Microbiology,2003,6:288-294.
[77]Cho JC. and James MT. Quantitative detection of microbial genes by using DNA microarrays[J]. Appl Environ Microbiol,2002,68(3):1425-1430.
[78]Wu L, Thompson DK, Li G, et al. Development and evalution of functional gene arrays for detection of selected genes in the environmental studies in microbiology[J]. Appl Environ Microbiol,2001,67:5780-5790.
[79]Zhou J and Thompson DK. Microarrays:applications in environmental microbiology[C]. In Encyclopedia of Environmental Microbiology, Edited by Bitton G. New Youk:John Wiley & Sons,2002,14:1968-1979.
[80]Loy, A., A. Lehner, N. Lee, J. Adamczyk, H. Meier, J. Ernst, K.-H. Schleifer, and M. Wagner.2002. Oligonucleotide microarray for 16S rRNA-based detections of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol.68:5064-5081.
[81]Valinsky, L., G. D. Vedova, A. J. Scupham, A. Figueroa, B. Yin, R. J. Hartin, M. Chroback, D. E. Crowley, T. Jiang, and J. Borneman.2002. Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl. Environ. Microbiol.68:3243-3250.
[82]Yin H, Cao L, Qiu G, Wang D, Laurie K, Zhou J, Dai Z, Liu X. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in acid mine drainages and bioleaching systems. Journal of Microbiological Methods,2007,70:165-178.
[83]Chen QJ, Yin HQ, Luo HL et al. Ming Xie, Guanzhou Qiu, Xueduan Liu. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms in acid mine drainage and bioleaching systems. Hydrometallurgy,2009,95(1-2):96-103.
[84]Zhang, QG,Zhang DY. Species richness destabilizes ecosystem functioning in experimental aquatic microcosms. Oikos,2006,112:218-226.
[85]Li Q, Shen L, Luo HL, Yin HQ, Liao LQ, Qiu GZ, Liu XD. Development and evaluation of whole-genome oligonucleotide array for Acidithiobacillus ferrooxidans ATCC 23270. transactions of nonferrous metals society of china. 2008,18(6):1343-1351.\
[86]Baker BJ. and JF Banfield. Microbial communities in acid mine drainage. FEMS Microbiology Ecology,2003,44:139-152.
[87]Yin HQ, Cao LH, Xie M, Chen QJ, Qiu GZ, Zhou JZ, Wu LY, Wang DZ, Liu XD. "Bacterial diversity based on 16S rRNA and gyrB genes at Yinshan mine, China" Systematic and Applied Microbiology,2008,31:302-311.
[88]Rawlings DE, Tributsch H and Hansford GS. "Reasons why 'Leptospirillum'-like species rather than Thiobacillus ferrooxidans are the dominant iron-oxidizing bacteria in many commercial processes for biooxidation of pyrite and related ores," Microbiology,1999,145(3):5-13.
[89]Johnson DB. "Genus Ⅱ Leptospirillum Hippe 2000 (ex Markosyan 1972,26)," in Bergey's manual of systematic bacteriology,2nd ed, vol. Ⅰ. Garrity, ed. Berlin: Springer-Verlag,2001:453-457.
[90]Tuovinen OH, Niemela SI and Gyllenberg HG. "Effect of mineral nutrients and organic substances on the development of Thiobacillus ferrooxidans," Biotechnol. Bioeng,1971,13(4):517-527.
[91]Chin KJ, Hahn D, Hengstmann U, Liesack W, and Janssen PH. "Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms," Appl Environ Microbiol,1999,65: 5042-5049.
[92]J. Versalovic, M. Schneider, F. de Bruijn, J. Lupski, Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction, Meth. Mol. Cell Biol,1994,5:25-40.
[93]J Versalovic, FJ de Bruijn, JR Lupski, Repetitive sequence-based PCR (rep-PCR) DNA fingerprinting of bacterial genomes, in:F.J. de Bruijn, J.R. Lupski, G.M. Weinstock (Eds.), Bacterial Genomes:Physical Structure and Analysis, Chapman and Hall,1997, pp,437-453.
[94]Schneider M and De Bruijin FJ. "Rep-PCRmediated genomic fingerprinting of rhizobia and computer-assisted phylogenetic pattern analysis," World J. Microbiol. Biotechnol,1996,12:163-174.
[95]Gao J, Zhang C, Wu X, Wang H and Qiu G. "Isolation and identification of a strain of Leptospirillum ferriphilum from an extreme acid mine drainage site," Annals of Microbiology,2007,57(2):171-176.
[96]Silverman MP, Lundgren DC. Study on the chemoautotrophic iron bacterium thiobacillus ferrooxidans:I. an improved medium and harvesting procedure for securing high cell yield. J. Bacteriol,1959,77:642-647.
[97]Xie M, Yin H, Liu Y, Liu J, Liu X. "Repetitive sequence based polymerase chain reaction to differentiate close bacteria strains in acidic sites," Trans. Nonferrous Met. Soc. China,2008,18,1392-1397.
[98]Marchesi JR, T. Sato, AJ Weightman, TA Martin, JC Fry, SJ Hiom, D Dymock and WG Wade. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA (Vol 64, Pg 795,1998). Applied and Environmental Microbiology,1998,64:2333.
[99]Yamamoto S, PJ Bouvet, and S Harayama. Phylogenetic structures of the genus Acinetobacter based on gyrB sequences:comparison with the grouping by DNA-DNA hybridization. Int. J. Syst. Bacteriol,1999,49:87-95.
[100]Yamamoto S, Harayama S. PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of pseudomonas putida strains[J]. Applied and environmental microbiology,1995,61(3):1104-1109.
[101]Yamamoto S, Harayama S. Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD, and 16S rRNA genes[J]. Int J Syst Bacteriol,1998,48:813-819.
[102]Venkateswaran K, Moser DP, Dollhopf, et al. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp.nov[J]. Int J Syst Bacteriol,1999,49:705-724.
[103]Kasai H, Ezaki T, Harayama S. Differentiation of phylogenetically related slowly growing Mycobacteria by their gyrB sequences[J]. J Clin Microbiol, 2000,38:301-308.
[104]Ochman H, Wilson AC. Evolution in bacteria:evidence for a universal substitution rate in cellar genomes[J]. J. Mol Evol,1987,26:74-86.
[105]Zhang RY, Xia JL, Peng JH, Zhang Q, Zhang CG, Nie ZY, Qiu GZ. A new strain Leptospirillum ferriphilum YTW315 for bioleaching of metal sulfides ores. Trans. Nonferrous Met. Soc. China,2010,20:135-141.
[106]Fournier D, Lemieux R, et al. Essential Interaction between Thiobacillus ferrooxidans and heterotrophic microoganisms during a wastewater sludge bioleaching process[J]. Environ Pollution,1998,101:303-309.
[107]Li QH, Tian Y, Fu X et al. The community dynamics of major bioleaching microorganisms during chalcopyrite leaching under the effect of organics. Current Microbiology,2011, doi:10.1007/S00284-011-9960-y.
[108]Rohwerder T, Gehrke T, Kinzler K, Sand W. Bioleaching review part A: Progress in bioleaching:Fundamentals and mechanisms of bacterial metal sulfide oxidation. Applied Microbiology and Biotechnology,2003,63:239-248.
[109]Johnson DB. Biodiversity and interactions of acidophiles:Key to understanding and optimizing microbial processing of ores and concentrates. Transactions of the Nonferrous Metals Society of China,2008,18:1367-1373.
[110]Wallentinus I, Nyberg CD. Introduced marine organisms as habitat modifiers. Mar Pollut Bull,2007,55:323-332.
[111]Serena M, Rui Z, Pei Y, Lisa A, Levin. Diversity and functional responses of nitrogen-fixing microbes to three wetland invasions Biol Invasions,2009, 11:225-239.
[112]Frgione J, Brown CS, Tilman D. Community assembly and invasion:An experimental test of neutral versus niche processes. Proc. Nat. Acad. of Sci. USA.2004.101:414-414.
[113]Fu B, Zhou HB, Zhang Q, Qiu GZ. Isolation and characterization of three strains of Acidithiobacillus thiooxidans and its bioleaching of chalcopyrite. Journal of Microbiology,2008,28 (1),12-19.
[114]Nemati M, Harrison STL. A comparative study on thermophilic and mesophilic biooxidation of ferrous iron[J].Minerals Engineering,2000,13(1):19-24.
[115]Verdnik DS. Handran, and S. Pickett. Key considerations for accurate microarray scanning and image analysis, p.2002,89-98. In G. Kamberova, (Ed.), DNA Image Analysis:Nuts & Bolts. DNA Press LLC, Salem, MA.
[116]Zhou HB, Zeng WM, Yang ZH, Xie YJ, Qiu GZ. Bioleaching of chalcopyrite concentrate by a moderately thermophilic culture in a stirred tank reactor. Bioresource Technology,2009,2:515-520.
[117]Rodriguez Y, Balleste A, Bla'zquez ML, Gonza'lez F, Munoz JA. New information on the pyrite bioleaching mechanism at low and high temperature. Hydrometallurgy.2003,71:37-46.
[118]Plumb JJ, Muddle R, Franzmann PD. Effect of pH on rates of iron and sulfur oxidation by bioleaching organisms. Minerals Engineering,2008,21:76-82.
[119]Sand W, Gehrke T. Extracellular polymeric substances mediate bioleaching/biocorrosion via interfacial processes involving iron(Ⅲ) ions and acidophilic bacteria. Research in Microbiology,2006,157 (1):49-56.
[120]Rzhepishevska OI, Valde's J, Marcinkeviciene L, Gallardo CA, Meskys R, Bonnefoy V, Holmes DS, Dopson M. Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds. Applied and Environmental Microbiology,2007,73:7367-7372.
[121]Johnson DB, Hallberg KB. Carbon iron and sulfur metabolism in acidophilic micro-organisms. Advances in Microbial Physiology,2009,54:202-245.
[122]Kinzler K, Gehrke T, Telegdi J, Sand W. Bioleaching-a result of interfacial processes caused by extracellular polymeric substances (EPS). Hydrometallurgy,2003,71 (1-2):83-88.
[123]Zeng W, Qiu G, Zhou H, Peng J, Chen M, Tan S, Chao W, Liu X, Zhang Y. Community structure and dynamics of the free and attached microorganisms during moderately thermophilic bioleaching of chalcopyrite concentrate. Bioresource Technol,2010,101:7068-7075.
[124]Hackl RP, Dreisinger DB, Peters E. Passivation of chalcopyrite during oxidative leaching in sulfate media. Hydrometallurgy,1995,39 (1):25-48.
[125]Sandstorm A, Petersson S. Bioleaching of a complex sulphide ore with moderate thermophilic and extreme thermophilic microorganism. Hydrometallurgy,1997,46 (1-2):181-190.
[126]Sand W, Rohde K, Sobotke B and Zenneck C. Evaluation of Leptospirillum ferrooxidans for leaching. Appl Environ Microbiol,1992,58:85-94.
[127]Gehrke T, Telegdi J, Thierry D, Sand W. Importance of extracellular polymeric substances from Thiobacillus ferrooxidans for bioleaching. Applied and Environmental Microbiology,1998,64 (7):2743-2747.
[128]Stott MB, Waliting HR, Franzmann PD, Sutton D. The role of ironhydroxy precipitates in the passivation of chalcopyrite during bioleaching. Minerals Engineering,2000,13(10):1117-1127.
[129]Rodriguez Y, Ballester A, Bla'zquez ML, Gonzalez F, Munoz JA. New information on the chalcopyrite bioleaching mechanism at low and high temperature. Hydrometallurgy,2003,71:47-56.
[130]Franzmann PD, Haddad CM, Hawkes RB, Robertson WJ, Plumb JJ. Effects of temperature on the rates of iron and sulfur oxidation by selected bioleaching Bacteria and Archaea:Application of the Ratkowsky equation. Minerals Engineering,2005,18(13-14):1304-1314.
[131]Zeng WM, Tan S, Chen M, Qiu GZ. Detection and analysis of attached microorganisms on the mineral surface during bioleaching of pure chalcopyrite with moderate thermophiles. Hydrometallurgy. In press.2011.
[132]Golyshina OV, Pivovarova TA, Karavaiko GI, Kondrateva TF, Moore ER, Abraham WR, Lunsdorf H, Timmis KN, Yakimov MM, Golyshin PN. Ferroplasma acidiphilum gen. nov, sp. nov, an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov, comprising a distinct lineage of the Archaea. Int J Syst Evol Microbiol,2000,50:997-1006
[133]Edwards KJ, Goebel BM, Rodgers TM, Schrenk MO, Gihring TM, Cardona MM, Hu B, McGuire MM, Hamers RJ, Pace NR. and Banfield JF. Geomicrobiology of pyrite(FeS2) dissolution:Case Study at Iron Mountain, California. Geomicrobiol J,1999,16:155-179.
[134]Colmer AR, KL Temple, and ME Hinkle. An iron-oxidizing bacterium from the acid drainage of some bituminous coal mines. Journal of Bacteriology,1950,59: 317-328.
[135]Druschel GK, Baker BJ, Gihring T. and Banfield JF. Acid mine drainage biogeochemistry at Iron Mountain, California, in review.
[136]Schrenk MO, Edwards KJ, Goodman RM, Hamers RJ, and Banfield JF. Distribution of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans: implications for generation of acid mine drainage. Science,1998,279: 1519-1522.
[137]Yahya A, Roberto FF, and Johnson DB. Novel mineraloxidizing bacteria from Montsterrat (W.I.):physiological and phylogenetic characteristics. In: Biohydrometallurgy and the Environment Toward the Mining of the 21st Century Process Microbiology 9A (Amils, R. and Ballester, A, Eds.), pp.1999, 729-740. Elsevier, Amsterdam.
[138]Peccia J, Marchand EA, Silverstein J. and Hernandez M. Development and application of small-subunit rRNA probes for assessment of selected Thiobacillus species and members of the genus Acidiphilum. Appl. Environ. Microbiol,2000,66:3065-3072.
[139]Watling HR. The bioleaching of sulphide minerals with emphasis on copper sulphides-a review. Hydrometallurgy,2006 84,81-108.
[140]Lane DJ.16S/23S rRNA sequencing[C], STACKEBRANDT E, GOODFELLOW M. Nucleic Acid Techniques in Bacterial Systematics. Chichester:John Wiley & Sons,1991:115-175.
[141]Romero J, Yanez C, Vasquez M. Characterization and identification of an iron-oxidizing, Leptospirillum-like bacterium, present in the high sulfate leaching solution of a commercial bioleaching plant. Research in Microbiology, 2003,154 (5),:353-359.
[142]Dopson M, Lindstrom EB. Analysis of community composition during moderately thermophilic bioleaching of pyrite, arsenical pyrite, and chalcopyrite. Microbial Ecology,2004,48(1):19-28.
[143]Foucher S, Battaglia F, D'Hugues P. Evolution of the bacterial population during the batch bioleaching of a cobaltiferous pyrite in a suspended-solids bubble column and comparison with a mechanically agitated reactor.Hydrometallurgy,2003,71(1-2):5-12.
[144]Johnson DB. Importance of microbial ecology in the development of new mineral technologies. Hydrometallurgy,2001,59(2-3):147-157.
[145]Mousavi SM, Jafari A, Yaghmaei S, Vossoughi M. Bioleaching of low-grade sphalerite using a column reactor. Hydrometallurgy,2006,82(1-2):75-82.
[146]Klocke M, Mahnert P, Mundt K, Souidi K, Linke B. Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate. Systematic and Applied Microbiology,2007,30(2):139-151.
[147]Gomez C, Blazquez ML. Bioleaching of a Spanish complex sulphide ore bulk concentrate. Minerals Engineering,1999,12(1):93-106.
[2]Bond PL, Druschel GK, Banfield JF. Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems[J]. Applied and environmental microbiology,2000,66(11):4962-4971.
[3]Johnson DB, Hallberg K B. The microbiology of acidic mine waters[J]. Research in Microbiology,2003,154:466-473.
[4]Johnson, DB. and Rang L. Ejects of acidophilic protozoa on populations of metal-mobilising bacteria during the leaching of pyritic coal[J]. J. Gen. Microbiol,1993,139:1417-1423.
[5]Kelly DP, Wood AP. Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov, Halothiobacillus gen. nov, and Thermithiobacillus gen. nov. Int J Syst Evol Microbiol,2000,50:511-516.
[6]Hiraishi A, Nagashima KV, Matsuura K, Shimada K, Takaichi S, Wakao N, Katayama Y. Phylogeny and photosynthetic features of Thiobacillus acidophilus and related acidophilic bacteria:its transfer to the genus Acidiphilium as Acidiphilium acidophilum comb. nov. Int J Syst Bacteriol,1998,48:1389-1398.
[7]Coram NJ, Rawlings DE. Molecular relationship between two groups of the genus Leptospirillum and the finding that Leptospirillum ferriphilum sp. nov. dominates South African commercial biooxidation tanks that operate at 40 degrees C. Appl Environ Microbiol,2002,68:838-845.
[8]Clark DA, Norris PR. Acidimicrobium ferrooxidans gen. nov, sp. nov.: mixed-culture ferrous iron oxidation with Sulfobacillus species. Microbiology, 1996,142:785-790.
[9]Johnson B, Roberto FF. Heterotrophic acidophiles and their roles in the bioleaching of sulfide minerals. In:Rawlings DE (ed) Biomining:theory, microbes and industrial processes. Springer, Berlin Heidelberg New York, pp 1997:259-279.
[10]Fuchs T, Huber H, Teiner K, Burggraf S, Stetter KO. Metallosphaera prunae, sp. nov, a novel metal-mobilizing, thermoacidophilic archaeum, isolated from a uranium mine in Germany. Syst Appl Microbiol,1995,18:560-566.
[11]Fuchs T, Huber H, Burggraf S, Stetter KO.16S rDNA-based phylogeny of the archaeal order Sulfolobales and reclassification of Desulfurolobus ambivalens as Acidianus ambivalens comb. nov. Syst Appl Microbiol,1996,19:56-60.
[12]Pronk JT, de Bruyn JC, Bos P, Kuenen JG. Anaerobic growth of Thiobacillus ferooxidans. Appl Environ Microbiol,1992,58:2227-2230.
[13]Das A, Mishra AK, Roy P. Anaerobic growth on elemental sulfur using dissimilar iron reduction by autotrophic Thiobacillus ferrooxidans. FEMS Microbiol Lett, 1992,97:167-172.
[14]Hiraishi A, Shimada K. Aerobic anoxygenic photo synthetic bacteria with zinc-bacteriochlorophyll. J Gen Appl Microbiol,2001,47:161-180.
[15]Norris PR. University of Warwick, UK, personal communication.
[16]Torma AE. The role of Thiobacillus ferrooxidans in hydro-metallurgical processes[A]. In Advances in Biochemical Engineering[C], ed. TK Ghose, A Fretcher, N Blackebrough, New York:Springer,1977,6:1-37.
[17]Suzuki I. Microbial leaching of metals from sulfide minerals[J]. Biotechnology advances,2001,19:119-132.
[18]Duncan DW, Trussell PC and Walden CC. Leaching of Chalcopyrite with Thiobacillus ferrooxidans:Effect of Surfactants and Shaking[J]. Appl Environ Microbiol,1964,12(2):122-126.
[19]Jerez CA, Arrendondo RA. Sensitive immunological method to enumerate Lepto spirillum ferrooxidans in the presence of Thiobacillus ferrooxidans[J]. Microbiology Letters,1991,78:99-102.
[20]Femandez MG, Mustin C. Occurences at mineral-bacteria interface during oxidation of arsenopyrite by thiobacillus ferrooxidans[J]. Biotechnology and Bioengineering,1995,48:13-211.
[21]Escoba BJ, Jedlicki E, Vargas T. A method for evaluating the proportion of free and attached bacteria in the bioleaching of chalcopyrite with thiobacillus ferrooxidans[J], Hydrometallurgy,1996,40:1-10.
[22]Fowler TA, Crundwell FK. Leaching of Zn sulfide by thiobacillus ferrooxidans: experiments with a controlled redox potential indicate no direct bacterial mechanism[J].Appl Environ Microbiol,1998,64:3570-3575.
[23]Ehrlich HL. Past, present and future of biohydrometallurgy[A]. In:Amils R, Ballester A, editors. Biohydrometallurgy and the environment toward the mining of the 21st century PT-A-1999[C], New Yoek:Wiiey,1999,9:51-60.
[24]Sand W, Gehrke T, Hallmann R, et al. Sulfur chemistry, biofilm, and the (in)direct attack mechanism-a critical evalution of bacterial leaching[J]. Applied and microbiological biotechnology,1995,43:961-966.
[25]Schippers A, Sand W. Bacterial leaching of metal sulfides proceeds by two indirect mechanisms via thiosulfate or via polysulfides and sulfur[J]. Appl Environ Microbiol,1999,65:319-321.
[26]Rawlings DE. The molecular genetics of Thiobacillus ferrooxidans and other mesophilic, acidophilic, chemolithotrophic, iron-or sulfur-oxidizing bacteria[J]. Hydrometallurgy,2001,59:187-201.
[27]Rawlings DE. Heavy metal mining using microbes[J]. Annual review of microbiology,2002,56:65-91.
[28]Donati E, Curutchet G. et al. Bioleaching of covellite using pure and mixed cultures of Thiobacillus ferroxidans and Thiobacillus thiooxidans. Process Biochem,1996,31(2):129-134.
[29]Falco L, Pogliani C. A comparison of bioleaching of covellite using pure cultures of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans or a mixed culture of Leptospirillum ferrooxidans and Acidithiobacillus thiooxidans. Hydrometallurgy,2003,71:31-36.
[30]Shi SY, Fang ZX. Bioleaching of marmatite flotation concentrate by Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans. Trans Nonferrous Metal Soc China,2004,14 (3):569-575.
[31]Hugues D, Foucher P. et. al. Continuous bioleaching of chalcopyrite using a novel extremely thermophilic mixed culture. Int J Min Processing,2002,66(1): 107-119.
[32]Stott MB, Sutton DC. Comparative leaching of chalcopyrite by selected Acidophilic bacteria and Archaea. Geomicrobiol J,2003,20 (3):215-230.
[33]Devecia H, Akcilb A. I. Alpa. Bioleaching of complex zinc sulphides using mesophilic and thermophilic bacteria:comparative importance of pH and iron. Hydrometallurgy,2004,73:293-303.
[34]Battaglia-Brunet F, d'Hugues P. The mutual effect of mixed Thiobacillus and Leptospirillum populations on pyrite bioleaching[J]. Min Eng,1998,11(2): 195-205.
[35]Okibe N, Johnson DB. Biooxidation of pyrite by defined mixed culture of moderately thermophilic acidophiles in pH-controlled bioreactor:significance of microbial interaction [J]. Biotechnol. Bioeng,2004,87:574-583.
[36]Dopson M, Lindstrom EB. Potential role of Thiobacilcaldus in arsenopyrite bioleaching[J]. Appl Environ Microbiol,1999,65:36-40.
[37]Colmer AR, Hinckle ME. The Role of Microorganism in Acid Mine Drainage. A Preliminary Report, Science.1947,106:253-256.
[38]Norris PR. Acidophilic bacteria and their activity in metal sulfide oxidation[J]. In Microbial Mineral Recover.1990,3-27.
[39]Hector M, Lizama IS. Bacterial Leaching of a Sulfide Ore By Thiobacillus Ferrooxidans and Thiobacillus Thiooxidans, Part II:Column leaching studies [J]. hydrometallurgy,1989,22:301-310.
[40]Schrenk MO, Edwards KJ, GoodmanRM, et al. Distribution of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans:implications for generation of acid mine drainage[J]. Science,1998,279:1519-1521.
[41]Johnson DB, Biological desulfurization of coal using mixed populations of mesophilic and moderately thermophilic acidophilic bacteria[C]. In:Processing and Utilization of High Sulfur Coals (Dugan PR, Quigley DR, and Attia YA, Eds.), 1991, pp.567-580. Elsevier, Amsterdam.
[42]Liu Y, Yin HQ, Zeng WM, et al. The effect of the introduction of exogenous strain Acidithiobacillus thiooxidans A01 on functional gene expression, structure and function of indigenous consortium during pyrite bioleaching. Bioresource Technology,2011,102(17):8092-8098.
[43]Johnson DB, and Roberto FF, Heterotrophic acidophiles and their roles in the bioleaching of sulfide minerals[C]. In:Biomining:Theory, Microbes and Industrial Processes (Rawlings DE, Ed.), pp.1997,259-280. Springer-Verlag/Landes Bioscience, Georgetown, TX.
[44]Hallmann R, Friedrich A, Koops H P, et al, Physiological characteristics of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans and physicochemical factors infuence microbial metal leaching[J]. Geomicrobiol. J,1992,10:193-206.
[45]McGinness S and Johnson DB. Grazing of acidophilic bacteria by a fagellate protozoan[J]. Microbiol. Ecol,1992,23:75-86.
[46]Ojumu TV, Hansford G, Petersen J. The kinetics of ferrous-iron oxidation by Leptospirillum ferriphilum in continuous culture:The effect of temperature. Biochem. Eng. J,2009,46:161-168.
[47]Konishi Y, Yoshida S, Asai S. Bioleaching of pyrite by acidophilic thermophile Acidianus brierleyi. Biotechnol. Bioeng,1995,48:592-600.
[48]Johnson DB and Hallberg KB. The microbiology of acidic mine waters. Res. Microbiol,2003,154:466-473.
[49]Rawlings DE, Johnson DB. The microbiology of biomining:development and optimization of mineral-oxidizing microbial consortia[J]. Microbiology,2007, 153:315-324.
[50]Johnson DB, Roberto FF. Heterotrophic acidophiles and their roles in the bioleaching of sulfide minerals. In Biomining:Theory, Microbes and Industrial Processes, pp. Edited by D. E. Rawlings. Georgetown, TX:Springer/Landes Bioscience,1997,259-280.
[51]Okibe, N, Gericke, M, Hallberg, K. B. & Johnson, D. B. Enumeration and characterization of acidophilic microorganisms isolated from a pilot plant stirred tank bioleaching operation. Appl Environ Microbiol,2003,69,1936-1943.
[52]Bacelar-Nicolau P, Johnson DB. Leaching of pyrite by acidophilic heterotrophic iron-oxidizing bacteria in pure and mixed cultures. Appl Environ Microbiol, 1999,65:585-590.
[53]Akcil A, Ciftci H, Deveci H. Role and contribution of pure and mixed cultures of mesophiles in bioleaching of a pyritic chalcopyrite concentrate. Minerals Engineering,2007,20:310-318.
[54]Demergasso CS, Galleguillos P PA, Escudero G LV, Zepeda A VJ, Danny C, Casamayor EO. Molecular characterization of microbial populations in a low-grade copper ore bioleaching test heap. Hydrometallurgy,2005,80: 241-253.
[55]Rawlings DE. Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates. Microbial Cell Factories,2005,4(13):1-15.
[56]Sebastian J. Schreiber, Andrew P. Gutierrez. A supply:demand perspective of species invasions and coexistence:applications to biological control. Eco model. 1998,106:27-45.
[57]Theresa N. Mgidi, David C. Le Maitre, et al. Alien plant invasions-incorporating emerging invaders in regional prioritization:A pragmatic approach for Southern Africa. J Environ Manag.2007,84:173-187.
[58]Boonchan S, Britz ML, Stanley GA. Degradation and mineralization of high-molecular-weight polycyclic aromatic hydrocarbons by defined fungal-bacteria cocultures. Appl. Environ. Microbiol,2000,66:1007-1019.
[59]Juhasz AL, Naidu R. Bioremediation of high molecular weight polycyclic aromatic hydrocarbons:a review of the microbial degradation of benzo[a]pyrene. Int. Biodeterior. Biodegrad,2000,45:57-88.
[60]Crooks J, Ruiz G. Biological invasions of marine ecosystems. In:Gallaugher P, Bendell-Young L (Eds) Waters in peril.2001,42:3-18.
[61]Moseman SM, Zhang R, Qian PY, Levin LA. Diversity and functional responses of nitrogen-fixing microbes to three wetland invasions. Biol. Invasions,2009,11:225-239.
[62]Rodriguez CF, Becares E, Fernandez-Alaez M, Fernandez-Alaez C. Loss of diversity and degradation of wetlands as a result of introducing exotic crayfish. Biol. Invas,2005,7:75-85.
[63]Branch GM, Steffani CN. Can we predict the effects of alien species? A casehistory of the invasion of South Africa by Mytilus galloprovincialis (Lamarck). J. Exp. Mar. Biol. Ecol,2004,300:189-215.
[64]Cerda M, Castilla JC. Diversidad biologica y biomasa de macro-invertebratos en matrices intermareales de Pyura praeputialis. Rev. Chil. Hist. Nat,1999,74: 841-853.
[65]Olivier P, Etienne V, Catherine R. Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by Cladosporium sphaerospermum isolated from an aged PAH contaminated soil. FEMS Microbiol. Ecol,2004,51:71-79.
[66]Vander Gast CJ, Whiteley AS, Thompson IP. Temporal dynamics and degradation activity of an bacterial inoculum for treating waste metal-working fluid. Environ Microbiol,2004,6:254-263.
[67]Hippe H. Leptospirillum gen. nov. (ex Markosyan 1972), nom. rev, including Leptospirillum ferrooxidans sp. nov. (ex Markosyan 1972), nom. rev. and Leptospirillum. Int. J. Syst. Evol. Microbiol,2000,2:501-503.
[68]Goebel BM and Stackebrandt E. Cultural and phylo genetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl. Environ. Microbiol.1994,60:1614-1621.
[69]Bond P.L., Smriga S.P. and Banfield J.F.. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol.2000,66:3842-3849.
[70]Edwards KJ, Bond PL, Gihring TM and Banfield JF. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science,2000,287: 1796-1799.
[71]Darland G, Brock T.D, Samsonoj W and Conti SF. A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science,1970,170:1416-1418.
[72]Segerer A, Langworthy TA and Stetter KO. Thermoplasma acidophilum and Thermoplasma volcanium sp. nov. from Solfatare Fields. Syst. Appl. Microbiol, 1988,10:161-171.
[73]Burton NP and Norris PR. Microbiology of acidic, geothermal springs of Montserrat:environmental rDNA analysis. Extremophiles,2000,4:315-320.
[74]Zhou, JZ, and Thompson, DK. Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol.2002,13:202-204.
[75]Ye RW, Tao W, Bedzyk L, et al, Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions[J]. J. Bacteriol,2000,182: 4458-4465.
[76]Zhou J. Microarrays for bacterial detection and microbial community analysis[J]. Current Opinion in Microbiology,2003,6:288-294.
[77]Cho JC. and James MT. Quantitative detection of microbial genes by using DNA microarrays[J]. Appl Environ Microbiol,2002,68(3):1425-1430.
[78]Wu L, Thompson DK, Li G, et al. Development and evalution of functional gene arrays for detection of selected genes in the environmental studies in microbiology[J]. Appl Environ Microbiol,2001,67:5780-5790.
[79]Zhou J and Thompson DK. Microarrays:applications in environmental microbiology[C]. In Encyclopedia of Environmental Microbiology, Edited by Bitton G. New Youk:John Wiley & Sons,2002,14:1968-1979.
[80]Loy, A., A. Lehner, N. Lee, J. Adamczyk, H. Meier, J. Ernst, K.-H. Schleifer, and M. Wagner.2002. Oligonucleotide microarray for 16S rRNA-based detections of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol.68:5064-5081.
[81]Valinsky, L., G. D. Vedova, A. J. Scupham, A. Figueroa, B. Yin, R. J. Hartin, M. Chroback, D. E. Crowley, T. Jiang, and J. Borneman.2002. Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl. Environ. Microbiol.68:3243-3250.
[82]Yin H, Cao L, Qiu G, Wang D, Laurie K, Zhou J, Dai Z, Liu X. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in acid mine drainages and bioleaching systems. Journal of Microbiological Methods,2007,70:165-178.
[83]Chen QJ, Yin HQ, Luo HL et al. Ming Xie, Guanzhou Qiu, Xueduan Liu. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms in acid mine drainage and bioleaching systems. Hydrometallurgy,2009,95(1-2):96-103.
[84]Zhang, QG,Zhang DY. Species richness destabilizes ecosystem functioning in experimental aquatic microcosms. Oikos,2006,112:218-226.
[85]Li Q, Shen L, Luo HL, Yin HQ, Liao LQ, Qiu GZ, Liu XD. Development and evaluation of whole-genome oligonucleotide array for Acidithiobacillus ferrooxidans ATCC 23270. transactions of nonferrous metals society of china. 2008,18(6):1343-1351.\
[86]Baker BJ. and JF Banfield. Microbial communities in acid mine drainage. FEMS Microbiology Ecology,2003,44:139-152.
[87]Yin HQ, Cao LH, Xie M, Chen QJ, Qiu GZ, Zhou JZ, Wu LY, Wang DZ, Liu XD. "Bacterial diversity based on 16S rRNA and gyrB genes at Yinshan mine, China" Systematic and Applied Microbiology,2008,31:302-311.
[88]Rawlings DE, Tributsch H and Hansford GS. "Reasons why 'Leptospirillum'-like species rather than Thiobacillus ferrooxidans are the dominant iron-oxidizing bacteria in many commercial processes for biooxidation of pyrite and related ores," Microbiology,1999,145(3):5-13.
[89]Johnson DB. "Genus Ⅱ Leptospirillum Hippe 2000 (ex Markosyan 1972,26)," in Bergey's manual of systematic bacteriology,2nd ed, vol. Ⅰ. Garrity, ed. Berlin: Springer-Verlag,2001:453-457.
[90]Tuovinen OH, Niemela SI and Gyllenberg HG. "Effect of mineral nutrients and organic substances on the development of Thiobacillus ferrooxidans," Biotechnol. Bioeng,1971,13(4):517-527.
[91]Chin KJ, Hahn D, Hengstmann U, Liesack W, and Janssen PH. "Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms," Appl Environ Microbiol,1999,65: 5042-5049.
[92]J. Versalovic, M. Schneider, F. de Bruijn, J. Lupski, Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction, Meth. Mol. Cell Biol,1994,5:25-40.
[93]J Versalovic, FJ de Bruijn, JR Lupski, Repetitive sequence-based PCR (rep-PCR) DNA fingerprinting of bacterial genomes, in:F.J. de Bruijn, J.R. Lupski, G.M. Weinstock (Eds.), Bacterial Genomes:Physical Structure and Analysis, Chapman and Hall,1997, pp,437-453.
[94]Schneider M and De Bruijin FJ. "Rep-PCRmediated genomic fingerprinting of rhizobia and computer-assisted phylogenetic pattern analysis," World J. Microbiol. Biotechnol,1996,12:163-174.
[95]Gao J, Zhang C, Wu X, Wang H and Qiu G. "Isolation and identification of a strain of Leptospirillum ferriphilum from an extreme acid mine drainage site," Annals of Microbiology,2007,57(2):171-176.
[96]Silverman MP, Lundgren DC. Study on the chemoautotrophic iron bacterium thiobacillus ferrooxidans:I. an improved medium and harvesting procedure for securing high cell yield. J. Bacteriol,1959,77:642-647.
[97]Xie M, Yin H, Liu Y, Liu J, Liu X. "Repetitive sequence based polymerase chain reaction to differentiate close bacteria strains in acidic sites," Trans. Nonferrous Met. Soc. China,2008,18,1392-1397.
[98]Marchesi JR, T. Sato, AJ Weightman, TA Martin, JC Fry, SJ Hiom, D Dymock and WG Wade. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA (Vol 64, Pg 795,1998). Applied and Environmental Microbiology,1998,64:2333.
[99]Yamamoto S, PJ Bouvet, and S Harayama. Phylogenetic structures of the genus Acinetobacter based on gyrB sequences:comparison with the grouping by DNA-DNA hybridization. Int. J. Syst. Bacteriol,1999,49:87-95.
[100]Yamamoto S, Harayama S. PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of pseudomonas putida strains[J]. Applied and environmental microbiology,1995,61(3):1104-1109.
[101]Yamamoto S, Harayama S. Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD, and 16S rRNA genes[J]. Int J Syst Bacteriol,1998,48:813-819.
[102]Venkateswaran K, Moser DP, Dollhopf, et al. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp.nov[J]. Int J Syst Bacteriol,1999,49:705-724.
[103]Kasai H, Ezaki T, Harayama S. Differentiation of phylogenetically related slowly growing Mycobacteria by their gyrB sequences[J]. J Clin Microbiol, 2000,38:301-308.
[104]Ochman H, Wilson AC. Evolution in bacteria:evidence for a universal substitution rate in cellar genomes[J]. J. Mol Evol,1987,26:74-86.
[105]Zhang RY, Xia JL, Peng JH, Zhang Q, Zhang CG, Nie ZY, Qiu GZ. A new strain Leptospirillum ferriphilum YTW315 for bioleaching of metal sulfides ores. Trans. Nonferrous Met. Soc. China,2010,20:135-141.
[106]Fournier D, Lemieux R, et al. Essential Interaction between Thiobacillus ferrooxidans and heterotrophic microoganisms during a wastewater sludge bioleaching process[J]. Environ Pollution,1998,101:303-309.
[107]Li QH, Tian Y, Fu X et al. The community dynamics of major bioleaching microorganisms during chalcopyrite leaching under the effect of organics. Current Microbiology,2011, doi:10.1007/S00284-011-9960-y.
[108]Rohwerder T, Gehrke T, Kinzler K, Sand W. Bioleaching review part A: Progress in bioleaching:Fundamentals and mechanisms of bacterial metal sulfide oxidation. Applied Microbiology and Biotechnology,2003,63:239-248.
[109]Johnson DB. Biodiversity and interactions of acidophiles:Key to understanding and optimizing microbial processing of ores and concentrates. Transactions of the Nonferrous Metals Society of China,2008,18:1367-1373.
[110]Wallentinus I, Nyberg CD. Introduced marine organisms as habitat modifiers. Mar Pollut Bull,2007,55:323-332.
[111]Serena M, Rui Z, Pei Y, Lisa A, Levin. Diversity and functional responses of nitrogen-fixing microbes to three wetland invasions Biol Invasions,2009, 11:225-239.
[112]Frgione J, Brown CS, Tilman D. Community assembly and invasion:An experimental test of neutral versus niche processes. Proc. Nat. Acad. of Sci. USA.2004.101:414-414.
[113]Fu B, Zhou HB, Zhang Q, Qiu GZ. Isolation and characterization of three strains of Acidithiobacillus thiooxidans and its bioleaching of chalcopyrite. Journal of Microbiology,2008,28 (1),12-19.
[114]Nemati M, Harrison STL. A comparative study on thermophilic and mesophilic biooxidation of ferrous iron[J].Minerals Engineering,2000,13(1):19-24.
[115]Verdnik DS. Handran, and S. Pickett. Key considerations for accurate microarray scanning and image analysis, p.2002,89-98. In G. Kamberova, (Ed.), DNA Image Analysis:Nuts & Bolts. DNA Press LLC, Salem, MA.
[116]Zhou HB, Zeng WM, Yang ZH, Xie YJ, Qiu GZ. Bioleaching of chalcopyrite concentrate by a moderately thermophilic culture in a stirred tank reactor. Bioresource Technology,2009,2:515-520.
[117]Rodriguez Y, Balleste A, Bla'zquez ML, Gonza'lez F, Munoz JA. New information on the pyrite bioleaching mechanism at low and high temperature. Hydrometallurgy.2003,71:37-46.
[118]Plumb JJ, Muddle R, Franzmann PD. Effect of pH on rates of iron and sulfur oxidation by bioleaching organisms. Minerals Engineering,2008,21:76-82.
[119]Sand W, Gehrke T. Extracellular polymeric substances mediate bioleaching/biocorrosion via interfacial processes involving iron(Ⅲ) ions and acidophilic bacteria. Research in Microbiology,2006,157 (1):49-56.
[120]Rzhepishevska OI, Valde's J, Marcinkeviciene L, Gallardo CA, Meskys R, Bonnefoy V, Holmes DS, Dopson M. Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds. Applied and Environmental Microbiology,2007,73:7367-7372.
[121]Johnson DB, Hallberg KB. Carbon iron and sulfur metabolism in acidophilic micro-organisms. Advances in Microbial Physiology,2009,54:202-245.
[122]Kinzler K, Gehrke T, Telegdi J, Sand W. Bioleaching-a result of interfacial processes caused by extracellular polymeric substances (EPS). Hydrometallurgy,2003,71 (1-2):83-88.
[123]Zeng W, Qiu G, Zhou H, Peng J, Chen M, Tan S, Chao W, Liu X, Zhang Y. Community structure and dynamics of the free and attached microorganisms during moderately thermophilic bioleaching of chalcopyrite concentrate. Bioresource Technol,2010,101:7068-7075.
[124]Hackl RP, Dreisinger DB, Peters E. Passivation of chalcopyrite during oxidative leaching in sulfate media. Hydrometallurgy,1995,39 (1):25-48.
[125]Sandstorm A, Petersson S. Bioleaching of a complex sulphide ore with moderate thermophilic and extreme thermophilic microorganism. Hydrometallurgy,1997,46 (1-2):181-190.
[126]Sand W, Rohde K, Sobotke B and Zenneck C. Evaluation of Leptospirillum ferrooxidans for leaching. Appl Environ Microbiol,1992,58:85-94.
[127]Gehrke T, Telegdi J, Thierry D, Sand W. Importance of extracellular polymeric substances from Thiobacillus ferrooxidans for bioleaching. Applied and Environmental Microbiology,1998,64 (7):2743-2747.
[128]Stott MB, Waliting HR, Franzmann PD, Sutton D. The role of ironhydroxy precipitates in the passivation of chalcopyrite during bioleaching. Minerals Engineering,2000,13(10):1117-1127.
[129]Rodriguez Y, Ballester A, Bla'zquez ML, Gonzalez F, Munoz JA. New information on the chalcopyrite bioleaching mechanism at low and high temperature. Hydrometallurgy,2003,71:47-56.
[130]Franzmann PD, Haddad CM, Hawkes RB, Robertson WJ, Plumb JJ. Effects of temperature on the rates of iron and sulfur oxidation by selected bioleaching Bacteria and Archaea:Application of the Ratkowsky equation. Minerals Engineering,2005,18(13-14):1304-1314.
[131]Zeng WM, Tan S, Chen M, Qiu GZ. Detection and analysis of attached microorganisms on the mineral surface during bioleaching of pure chalcopyrite with moderate thermophiles. Hydrometallurgy. In press.2011.
[132]Golyshina OV, Pivovarova TA, Karavaiko GI, Kondrateva TF, Moore ER, Abraham WR, Lunsdorf H, Timmis KN, Yakimov MM, Golyshin PN. Ferroplasma acidiphilum gen. nov, sp. nov, an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov, comprising a distinct lineage of the Archaea. Int J Syst Evol Microbiol,2000,50:997-1006
[133]Edwards KJ, Goebel BM, Rodgers TM, Schrenk MO, Gihring TM, Cardona MM, Hu B, McGuire MM, Hamers RJ, Pace NR. and Banfield JF. Geomicrobiology of pyrite(FeS2) dissolution:Case Study at Iron Mountain, California. Geomicrobiol J,1999,16:155-179.
[134]Colmer AR, KL Temple, and ME Hinkle. An iron-oxidizing bacterium from the acid drainage of some bituminous coal mines. Journal of Bacteriology,1950,59: 317-328.
[135]Druschel GK, Baker BJ, Gihring T. and Banfield JF. Acid mine drainage biogeochemistry at Iron Mountain, California, in review.
[136]Schrenk MO, Edwards KJ, Goodman RM, Hamers RJ, and Banfield JF. Distribution of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans: implications for generation of acid mine drainage. Science,1998,279: 1519-1522.
[137]Yahya A, Roberto FF, and Johnson DB. Novel mineraloxidizing bacteria from Montsterrat (W.I.):physiological and phylogenetic characteristics. In: Biohydrometallurgy and the Environment Toward the Mining of the 21st Century Process Microbiology 9A (Amils, R. and Ballester, A, Eds.), pp.1999, 729-740. Elsevier, Amsterdam.
[138]Peccia J, Marchand EA, Silverstein J. and Hernandez M. Development and application of small-subunit rRNA probes for assessment of selected Thiobacillus species and members of the genus Acidiphilum. Appl. Environ. Microbiol,2000,66:3065-3072.
[139]Watling HR. The bioleaching of sulphide minerals with emphasis on copper sulphides-a review. Hydrometallurgy,2006 84,81-108.
[140]Lane DJ.16S/23S rRNA sequencing[C], STACKEBRANDT E, GOODFELLOW M. Nucleic Acid Techniques in Bacterial Systematics. Chichester:John Wiley & Sons,1991:115-175.
[141]Romero J, Yanez C, Vasquez M. Characterization and identification of an iron-oxidizing, Leptospirillum-like bacterium, present in the high sulfate leaching solution of a commercial bioleaching plant. Research in Microbiology, 2003,154 (5),:353-359.
[142]Dopson M, Lindstrom EB. Analysis of community composition during moderately thermophilic bioleaching of pyrite, arsenical pyrite, and chalcopyrite. Microbial Ecology,2004,48(1):19-28.
[143]Foucher S, Battaglia F, D'Hugues P. Evolution of the bacterial population during the batch bioleaching of a cobaltiferous pyrite in a suspended-solids bubble column and comparison with a mechanically agitated reactor.Hydrometallurgy,2003,71(1-2):5-12.
[144]Johnson DB. Importance of microbial ecology in the development of new mineral technologies. Hydrometallurgy,2001,59(2-3):147-157.
[145]Mousavi SM, Jafari A, Yaghmaei S, Vossoughi M. Bioleaching of low-grade sphalerite using a column reactor. Hydrometallurgy,2006,82(1-2):75-82.
[146]Klocke M, Mahnert P, Mundt K, Souidi K, Linke B. Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate. Systematic and Applied Microbiology,2007,30(2):139-151.
[147]Gomez C, Blazquez ML. Bioleaching of a Spanish complex sulphide ore bulk concentrate. Minerals Engineering,1999,12(1):93-106.
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