Phylogenetic analysis of aerobic anoxygenic phototrophic bacteria and their relatives based on farnesyl pyrophosphate synthase gene

The study aims to reveal phylogenetic and evolutionary relationship between aerobic anoxygenic phototrophic bacteria（AAnPB） and their relatives,anaerobic anoxygenic phototrophic bacteria（AnAnPB） and nonphototrophic bacteria（NPB,which had high homology of 16S rDNA gene with AAnPB and fell into the same genus）,and validate reliability and usefulness of farnesyl pyrophosphate synthase（FPPS） gene for the phylogenetic determination.FPPS genes with our modified primers and 16S rDNA genes with general primers,were amplified and sequenced or retrieved from GenBank database.In contrast to 16S rDNA gene phylogenetic tree,AAnPB were grouped into two clusters and one branch alone with no intermingling with NPB and AnAnPB in the tree constructed on FPPS.One branch of AAnPB,in both trees,was located closer to outgroup species than AnAnPB,which implicated that some AAnPB would be diverged earlier in FPPS evolutionary history than AnAnPB and NPB.Some AAnPB and NPB were closer located in both trees and this suggested that they were the closer relatives than AnAnPB.Combination codon usage in FPPS with phylogenetic analysis,the results indicates that FPPS gene and 16S rRNA gene have similar evolutionary pattern but the former seems to be more reliable and useful in determining the phylogenic and evolutionary relationship between AAnPB and their relatives.This is the first attempt to use a molecular marker beside 16S rRNA gene for studying the phylogeny of AAnPB,and the study may also be helpful in understanding the evolutionary relationship among phototrophic microbes and the trends of photosynthetic genes transfer.

Community structure of aerobic anoxygenic phototrophic bacteria in algae-and macrophyte-dominated areas in Taihu Lake,China

Aerobic anoxygenic phototrophic bacteria(AAPB)repre sent a major group of bacterioplankton assemblages in many water systems and some are assumed to be closely associated with phytoplankton.However,studies on relationships between AAPB and cyanobacterial blooms are in scarcity.The dynamics of the abundance and diversity of AAPB was compared based on pufM gene in Meiliang Bay(featured by cyanobacterial blooms)and East Bay(featured by macrophyte)of Taihu Lake,a shallow subtropical lake in the East China plain.AAPB abundance was not significantly different between the two sites,and they were positively correlated with dissolved organic carbon(DOC)concentration.The ratios of AAPB to total bacteria varied from 3.4%to 11.5%and peaked in winter in both site s.No significant differences of AAPB community compositions were detected between the two sites,but there was a separation between warm seasons(June,August,and October)and cold seasons(December,February,and April).Rhizobiales and Limnohabitans-like pufM sequences were significantly contributors for the difference between two seasons,and specially enriched in cold seasons.Chlorophyll a(Ch1 a)and DOC were the most significant variables influencing the AAPB community structure.Furthermore,Porphyrobacter and Rhodospirillales-like pufM sequences were positively correlated with Ch1 a,indicating potential influence of cyanobacterial blooms on these AAPB taxa.These results suggested that diverse AAPB ecotypes coexisted in Taihu Lake,and their ecological role in carbon cycling in the lake may not be ignored.

Environmental control of growth and BChl a expression in an aerobic anoxygenic phototrophic bacterium, Erythrobacter longus (DSMZ6997)

anoxygenic phototrophic bacteria （AAPB）, which form a unique functional group of heterotrophic bacteria, have the abilit,to utilize light energy. The impact of carbon source and light intensity on the growth and bacteriochlorophyn a （ BChl a） expression of a typical strain of AAPB, Erythrobacter longus strain DSMZ6997 was examined during batch culture and continuous culture. The results showed that the expression of BChl a in DSMZ6997 was regulated by both carbon-source and light conditions, and was stimulated by low availability of carbon but inhibited by light to a certain extent at 300 lx and completely at 1 500 lx. In contrast, cell abundance, and even cell size of this strain, was substantially enhanced under light/dark cycle cultivation conditions over dark conditions, indicating the promotion of growth by light. These results led to the conclusion that utilization of light through BChl a helps AAPB to survive under carbon stress, while light at high intensity is harmful to the synthesis of BChl a in AAPB.

Diversity and ecological assembly process of aerobic anoxygenic phototrophic bacteria in a low irradiation area,Three Gorges Reservoir

Aerobic anoxygenic phototrophic bacteria(AAPB)are significant bacterial groups in aquatic ecosystems,known for their rapid growth and photoheterotrophic characteristics.However,the distribution and ecological assembly process of AAPB in low irradiation freshwater basins remain unclear,warranting further investigation.In this study,we present the diversity,abundance,spatial variations,ecological process,and community interaction of AAPB in sediment of Three Gorges Reservoir(TGR)under low irradiation.Our findings demonstrate the dominant genera of AAPB community that exist in the TGR area also are appeared in different waters,with some regional preference.Moreover,the concentration of pufM gene,an indicator for AAPB,maintains a consistently high numerical level ranging from(2.21±0.44)×10^(4)to(9.98±0.30)×10^(7)gene copies/g.Although solar irradiation is suggested as the major factor affecting AAPB,it remains unclear whether and how AAPB differ between regions due to varying solar irradiation levels.Our results show spatial differences between total bacteria and AAPB communities,with significant differences observed only in AAPB.Geographical and environmental factor contributed less than 10%to the spatial difference of community,with sediment type and environmental factors being the key factors influencing microbial community structure.The stochastic process plays a dominant role in the aggregation and replacement of AAPB communities,among which the most contribution is dispersal limitation.For AAPB network,Yoonia and Gemmobacter are the hubs for modules.Those results valuable insights into the AAPB communities in TGR with low irradiation.

Diversity of the aerobic anoxygenic phototrophy gene pufM in Arctic and Antarctic coastal seawaters

Aerobic anoxygenic phototrophic（AAP） bacteria serve important functions in marine carbon and energy cycling because of their capability to utilize dissolved organic substrates and harvest light energy.AAP bacteria are widely distributed in marine environments,and their diversity has been examined in marine habitats.However,information about AAP bacteria at high latitudes remains insufficient to date.Therefore,this study determined the summer AAP bacterial diversity in Arctic Kongsfjorden and in the Antarctic coastal seawater of King George Island on the basis of puf M,a gene that encodes a pigment-binding protein subunit of the reaction center complex.Four puf M clone libraries were constructed,and 674 positive clones were obtained from four investigated stations（two in Kongsfjorden and two in the Antarctic Maxwell Bay）.Arctic clones were clustered within the Alphaproteobacteria,whereas Antarctic clones were classified into the Alphaproteobacteria and Betaproteobacteria classes.Rhodobacteraceae-like puf M genes dominated in all samples.In addition,sequences closely related to puf M encoded on a plasmid in Sulfitobacter guttiformis were predominant in both Arctic and Antarctic samples.This result indicates the transpolar or even global distribution of puf M genes in marine environments.Meanwhile,differences between the Arctic and Antarctic sequences may prove polar endemism.These results indicate the important role of Rhodobacteraceae as AAP bacteria in bipolar coastal waters.

Aerobic anoxygenic phototrophic bacteria and their roles in marine ecosystems

Aerobic anoxygenic phototrophic bacteria (AAPB) are characterized by the following physiological and ecological features. A mother AAPB cell can unusually divide into 3 daughter cells and looks like a 揧?during the division. AAPB cells sometimes adhere together forming a free-floating population. Most of the known AAPB species are obligately aerobic. Bacteriochlorophyll a (BChl a) is the only photosynthetic pigment in AAPB, and the number of BChl a molecules in an AAPB cell is much less than that in an anaerobic phototrophic bacterial cell, while the accessorial pigments carotenoids in AAPB are abundant in concentration and diverse in species. In addition to the common magnesium containing BChl a, a zinc-containing BChla was also seen in AAPB. AAPB have light harvesting complexⅠbut usually lack light harvesting complexⅡ. Although AAPB featur in photosynthesis, their growth is not necessarily light- dependent. There is a mechanism controlling the photosynthesis approach. AAPB are widely distributed in marine environments especially in oligotrophic oceans accounting for a substantial portion of the total biomass and playing a unique role in the cycle of carbon and other biogenic elements. Besides the contribution to primary production, AAPB also have great potentials in bioremediation of polluted environments. Studies on AAPB would be of great value in understanding the evolution of photosynthesis and the structure and function of marine ecosystems.

水域生境好氧不产氧光合细菌(AAPB)研究进展

好氧不产氧光合细菌(aerobic anoxygenic photosynthesis bacteria,AAPB)是广泛分布于海洋、湖泊及河流等典型水域生境中的异养原核生物,能够以环境中有机物为营养物质来获取细胞生长及代谢所需的能量,同时借助自身独特的菌绿素完成光合作用产能但不合成氧气,在物质循环与能量流动中扮演着重要角色.近年,越来越多的AAPB种属被陆续报道,基于光合基因,例如光合反应中心M亚基(pufM)的分子系统发育分析显示,大部分AAPB属于α-、β-及γ-变形菌,且丰度及多样性随生境的不同而呈现时空地理格局异质性.本文对AAPB的栖息环境与生长特性、丰度与分布、生态功能以及环境驱动因子等方面的研究进展进行了回顾和综述.目前,针对水库生态系统AAPB的研究鲜见报道,作者建议开展水库生境中AAPB多样性分布、环境驱动因素及生态功能研究,丰富对于水生生态系统中功能微生物种群生态结构与代谢功能的认识.

海洋微型生物碳泵——从微型生物生态过程到碳循环机制效应

微型生物是海洋生态系统中"看不见的主角",在资源环境以及全球变化中扮演着举足轻重的角色.本研究通过方法创新和大量现场调查,从一类特殊微型生物类群——好氧不产氧光合异养细菌(AAPB)入手,展开了微型生物生态过程与机制的系统研究,修正了国际同行AAPB计数方法的误差,获得了全球海洋AAPB的分布规律,解释了以往现场实测结果的分歧,澄清了以往理论上的偏颇认识;建立了包括不产氧光能利用途径的上层海洋碳循环模型,并通过大量现场实测揭示:细菌光能利用关系到海区碳循环的"源""汇"格局;在这些研究基础上探讨了新的海洋碳循环机制,提出了"微型生物碳泵"理论框架,为全面认识海洋储碳机制、促进学科交叉、研发海洋碳汇奠定了基础.

川西高寒森林溪流好氧不产氧光合细菌多样性

为了探明好氧不产氧光合菌(AAPB)在川西高寒森林溪流极端环境中的生态分布和群落结构及其环境影响因子,本实验结合同步温度动态和水环境特征监测,采用实时荧光定量PCR和克隆文库的方法,检测了川西高寒森林溪流季节性冻融循环3个关键时期(冻结前期、深冻期和融化期)AAPB的丰度和多样性变化及其与环境因子之间的相关性.结果表明:AAPB丰度在冻结前期非常低,仅(2.80±0.19)×10~4bp/mL;深冻期迅速增加到(4.65±0.30)×10~4bp/mL;融化期达到(5.79±0.19)×104~bp/mL.系统发育分析显示,冻结前期AAPB类群主要为α-变形菌纲细菌;而深冻期和融化期以β-变形菌纲细菌占据主要地位.相关性分析表明,在季节性冻融循环过程中,叶绿素a、可溶性有机碳和温度是AAPB菌群丰度和多样性的主要影响因子.实验结果表明冬季的川西高寒森林溪流中,AAPB类群的丰度低,但是它们高度动态变化,并且与其他淡水环境中的该类群的同源性低.

好氧不产氧光合细菌反馈作用下的五里峡水库坝前水体化学特征研究

微生物是水体生物地球化学循环的主要驱动者,也是能量代谢的主要参与者,在水体生态系统多样性与稳定性方面发挥着举足轻重的作用。好氧不产氧光合细菌(AAPB)是水体中一类分布广泛的重要功能类群,它们可利用光能补充自身能量代谢,并影响水体化学组分,其重要性被人们广泛认可并深入研究。为探讨岩溶区AAPB反馈作用下的五里峡水库坝前水体化学特征,本文对坝前不同层位水体进行实地监测,在获得不同层位水体溶解有机碳和颗粒有机碳稳定碳同位素特征的基础上,采用荧光定量PCR技术检测、研究了坝前水体不同层位AAPB分布规律。结果表明:取样期五里峡水库坝前水体为HCO_3^--Ca^(2+)-Mg^(2+)贫-中营养型;通过水体溶解氧、δ^(13)CPOC、δ^(13)CDOC和碳氮比综合分析得出,坝前水体有机碳主要由微型生物产生;AAPB占总浮游细菌的相对丰度范围在1.33%~1.60%,且AAPB在不同层位的丰度变化强度要高于总浮游细菌的丰度变化强度,表明相较于总浮游细菌,AAPB对水化学特征的反馈作用更加敏感;使用典范对应分析可揭示水体理化性质与AAPB的内在联系,结果显示AAPB和总浮游细菌均受浊度的影响较大,故基于颗粒沉降的海洋微生物泵作用也适用于陆地岩溶水库。因而,AAPB反馈作用下的水化学特征对揭示CO_2-水-碳酸盐岩-微生物代谢体系具有重要的启示意义。

台湾海峡南部海域好氧不产氧光合异养细菌对上升流的响应

国内外关于好氧不产氧光合异养细菌(AAPB)和上升流之间关系的研究甚少。本文采用“基于蓝细菌校正的时序红外显微技术”研究了台湾海峡南部近岸上升流中心区AAPB对上升流变化的响应。研究结果发现,在上升流涌升的初始阶段,AAPB和总异养细菌丰度较低;随着上升流的发展,两者丰度均增加并在上升流的成熟期达到最高值;而当上升流衰退时,AAPB和总异养细菌丰度开始下降。在上升流发展过程中,AAPB丰度与叶绿素a浓度在一定范围内呈显著正相关,但同时受环境低磷浓度的限制,总异养细菌丰度与氮、磷、硅营养盐均有显著正相关,表明叶绿素a指示的浮游植物所释放的溶解有机碳和环境中的磷限制可能对AAPB起着更为直接和重要的作用,而营养盐则可能在总异养细菌对上升流的响应中起着重要作用。本研究有助于我们理解AAPB在碳及其他生源要素循环中的作用及其调控机制。

三种碳源对乌梁素海好氧不产氧光合细菌群落结构的影响

好氧不产氧光合细菌（AAPB）营光合异养,在水体碳循环中起着重要作用.但是,碳源对AAPB群落结构的影响尚不明确.本文基于16S rDNA和光合反应中心合成中的关键基因——pufM基因,运用变性梯度凝胶电泳（DGGE）技术,比较分析了在微生物分离培养中常用的3种碳源（葡萄糖、丙酮酸钠、酵母提取物）对乌梁素海水体总细菌及AAPB群落结构的影响.结果表明,不同碳源诱导7~21 d后,水体总细菌群落丰富度及多样性指数均有不同程度的提升,AAPB群落则呈现先升后降的趋势.3种碳源中,丙酮酸钠添加后对总细菌及AAPB菌群的丰富度和多样性的提升效果最好.测序及系统发育结果表明,乌梁素海水体经诱导后新检测到了一些原环境中未发现的菌属,一些具有特殊碳代谢能力的菌属丰度得到了提升.本研究为充分认识和理解AAPB的生态学作用和意义,及其富集、分离和培养提供了基础依据.

原位PCR及其在海洋细菌检测中的应用

原位PCR技术在海洋生物研究中应用较少,尚无规范的方法步骤。将原位PCR技术应用于海洋细菌功能基因检测,通过实践探讨了影响原位PCR的关键因素,指出细胞的固定和消化是影响其成败的关键;探讨了有关的实验条件;并展望了在检测海洋细菌,尤其是对目前尚无合适方法定量检测的典型海洋功能细菌等的检测方面,原位PCR有望发挥重要作用。

舟山海域好氧不产氧光合异养细菌群落结构分析

好氧不产氧光合异养细菌(aerobic anoxygenic phototrophic bacteria,AAPB)是广泛分布在各种海洋环境中并在微生物生态学、海洋碳汇和海洋生态系统的生物地球化学循环的过程中具有潜在的重要作用的一类光合异养微生物。于2016年4月份在舟山群岛不同海洋功能区海域的八个站点采集表层海水,基于编码光合反应复合中心小亚基的puf M基因进行高通量测序,对测序结果进行分析,结果发现:除了岱山的样品测序失败以外,其它七个站点共得到192633条序列,我们进行了OTU聚类分析,相似性设为97%,可以看到,所有的数据最后一共分成4051个OTU。属于Proteobacteria的AAPB占明确分类的各细菌门的97%。Rhodobacteraceae科的Loktanella和Roseobacter两个属的AAPB在所有的采样站点中都处于优势地位。Desulfocapsa属在朱家尖站位(ZJJ)的发现非常具有研究价值,在以往的研究中还没有出现过。研究结果表明,在舟山群岛不同功能海域AAPB的群落结构和分布情况也是有差别的,而且与很多环境因素有关,这可以解释为什么目前很难准确预测水生环境总AAPB分布的问题。

环境因子对好氧不产氧光合细菌脂肪酸组成的影响

对赤杆菌属(Erythrobacter)、柠檬酸微菌属(Citromicrobium)和玫瑰杆菌(Roseobacter)分支的9株好氧不产氧光合细菌(AAPB)的脂肪酸组成进行分析,并以10株非AAPB菌为参照,从脂肪酸角度考察光照、温度、营养等重要环境因子对AAPB的影响。结果显示,AAPB的脂肪酸以C18:1 w7c为主,该成分在Roseobacter分支中含量最高,不同种脂肪酸对环境因子的响应不同,低温和寡营养条件主要作用于不饱和脂肪酸(UFA);二羟基脂肪酸在寡营养和光照双重作用下有较明显的升高。此外,结合非AAPB的比较也为AAPB脂肪酸研究提供了新的视角,如温度实验显示,由于不饱和脂肪酸的比例较高,AAPB可能在寒冷海域有更好的竞争优势,而从饥饿培养试验来看,AAPB的异养能力似乎比非AAPB更弱。

基于pufM基因的乌梁素海富营养化湖区好氧不产氧光合细菌系统发育多样性分析

好氧不产氧光合细菌(AAPB)的多样性在海洋中已经广泛研究,但在富营养化湖泊中却研究甚少。通过构建和分析AAPB光合中心合成中的关键基因pufM克隆文库,以期揭示乌梁素海富营养化湖区AAPB分布及其系统发育多样性,探讨其在富营养化湖泊中的功能和作用。对乌梁素海红圪卜湖区水体文库中的52个克隆子进行分析,产生了28个OTU,文库覆盖度达到71.4%,反映出文库有较好的代表性。同源性和系统发育分析结果表明,乌梁素海红圪卜湖区AAPB有较高的多样性,与我们之前所发现的同一湖区总细菌多样性较低形成鲜明对比。所获得的序列分属7个亚群,即γ-Proteobacteria(44.2%,含Group-1,-2和-3共3个亚群)、β-Proteobacteria(21.2%)、Rhodobacter-like(7.69%)及2个未知亚群unknown Group-1(21.2%)和Group-2(5.77%)。其中γ-Proteobacteria占到总克隆的44.2%,在低盐的乌梁素海环境中出现高比例的γ-Proteobacteria之前并未见类似报道,并且乌梁素海中存在一些可能是富营养化湖泊特有的AAPB。这表明AAPB可能在富营养化湖泊生态系统的维持和稳定中有重要作用。

渤黄海夏季表层海水中好氧不产氧光合细菌多样性分析

于2011年8月采集渤黄海表层海水样品,利用编码光合反应复合中心小亚基的puf M基因构建克隆文库,比较分析了不同生境类型海区夏季表层海水中好氧不产氧光合细菌(aerobic anoxygenic phototrophic bacteria,AAPB)的多样性。结果发现,属于α-3变形菌门(Proteobacteria)的红杆菌科(Rhodobacteraceae)在研究海区普遍存在,而且丰度较高,是研究海区AAPB的优势类群。其中渤海站位的AAPB群落结构相对较丰富,含有α-3、α-4、α-6 Proteobacteria 3个细菌类群;而渤海海峡站位和北黄海站位的AAPB群落结构相对单一,只有α-3 Proteobacteria一个类群。另外,研究表明温度最高,盐度最低的渤海站位更有利于AAPB群落的生长及组成状态。测序结果显示所占比例最大的细菌类群为未知类群,表明本文所研究的海区中可能存在着大量未知的AAPB种类,因此有进一步研究开发的价值。

赤杆菌科微生物分类研究进展

赤杆菌科微生物隶属于细菌域(Bacteria)、变形菌门(Proteobacteria)、α-变形菌纲(Alphaproteobacteria)、鞘脂单胞菌目(Sphingomonadales)。依据16S rRNA基因序列的系统发育分析结果,2005年赤杆菌科被提议建立,成立之初由3个属5个种组成;在过去10年中,该科的物种数量增加迅速;截止2015年10月,赤杆菌科合格发表6个属44个种。赤杆菌科微生物在土壤、热泉、海水和沉积物等环境中广泛分布,其在环境修复、食品工程及生物医药等领域具有重要的应用前景。此外,部分菌株具有细菌叶绿素a,营好氧异养生长兼具光合作用功能,是好养不产氧光合异养菌的一个重要类群,近年来其在全球海洋碳循环和能量代谢过程中的重要作用日益凸显,得到了国内外学者的关注。本文综述了赤杆菌科微生物的分类特征、生态分布和应用基础等方向的研究进展,并对其分类研究趋势做了分析。

玛珥湖好氧不产氧光合细菌pufM基因DNA和mRNA的定量及多样性分析

【目的】湖光岩玛珥湖是一类特殊的火山口湖,它完全封闭,地质年代久远,尚未受人类活动的剧烈影响,孕育着丰富而特殊的微生物种群。好氧不产氧光合细菌(AAPB)是以其在有氧情况下能行使光合功能而定义的一类专性异养细菌,其生理生态特征独特,进化年代久远,在水生生态系统的上层水体中广泛分布。目前,AAPB在玛珥湖水体中是否有分布仍是未知。【方法】构建和比较夏季湖水1 m、5 m、12 m三个水层的总DNA和总RNA的AAPB光合中心合成的关键基因pufM的6个克隆文库,并结合定量PCR技术,分析了不同水层AAPB的分布、系统发育多样性及其在总细菌中的比重。【结果】6个文库覆盖率和稀释曲线显示样本初步揭示了各水层优势AAPB类群的多样性。BLAST核苷酸同源性介于80%93%;多样性指数表明,湖光岩表层和底层多样性相当,中间层最低,总RNA的多样性高于总DNA。系统发育分析结果表明,OTU21 24所含的序列(占总序列的49.43%)与β-变形细菌的进化距离最接近,是湖光岩玛珥湖的优势AAPB菌群。定量PCR结果显示1 m水层中AAPB在总细菌中的比重最高,可达38.06%;而5 m水层中AAPB所占的比重最低,仅为0.85%;12 m为9.54%。【结论】湖光岩玛珥湖孕育着丰富而多样的AAPB类群。

含好氧不产氧光合基因簇和Xanthorhodopsin-like基因的Sphingomonas sp.MIM37:基因组及光促生长分析

【目的】菌株MIM37为具有两种光能利用途径的光合异养细菌,分析其基因组和光照对生长的影响,为理解光能利用途径、光营养生物多样性以及光合作用的进化和功能等提供线索。【方法】采用平板涂布划线法分离菌株,结合形态观察及16S r RNA基因和光合基因序列同源性与系统发育分析进行初步分类鉴定;以分光光度法和荧光显微观察法测定光照和黑暗培养下培养液细胞浓度和单细胞体积;构建片段长度为300-500 bp的Illumina PE文库,以Illumina Hiseq2000进行基因组测序,以SOAPdenovo和Gap Closer组装序列,以RAST在线软件注释基因组。【结果】从内蒙古腾格里沙漠天鹅湖表层水中分离获得一株细菌MIM37,经16S r RNA基因、puf M和视紫质基因同源性和系统发育分析均显示其与Sphingomonas属亲缘关系最为密切;相对黑暗培养,光照刺激下的最大细胞浓度和单细胞体积大小分别提高了1.2和5.6倍;基因组注释显示MIM37代谢途径多样,含典型好氧菌的呼吸电子传递链,具有完整的好氧不产氧细菌的光合基因簇及Xanthorhodopsin-like视紫质蛋白基因,合成铁载体,还原重金属,降解微囊藻毒素和多环芳烃类等。【结论】MIM37属于Sphingomonas属,具有两种光能利用途径,光照可明显促进其生长,多样的代谢模式可能使其在自然环境中极具竞争力、分布广泛并具有应用于修复环境污染的潜力。