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.

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.

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.

Abundance and Diversity of the Phototrophic Microbial Mat Communities of Sulphur Mountain Banff Springs and Their Significance to the Endangered Snail, <i>Physella johnsoni</i>

Seasonal population fluctuations and diversity of anoxygenic phototrophs and cyanobacteria at the Sulphur Mountain thermal springs, Banff, Canada were investigated and compared to drastic population changes of the endangered snail Physella johnsoni. The microbial community revealed new species of anoxygenic phototrophic bacteria with novel spectral and morphological characteristics. Major mat-forming organisms included densely growing Thiothrix-like species, oxygenic phototrophs of the genera Spirulina, Oscillatoria, and Phormidium and purple nonsulfur bacteria Rhodobacter, Rhodopseudomonas and Rhodomicrobium. Aerobic anoxygenic phototrophs comprised a significant portion, upwards of 9.6 × 104 CFU/cm2 of mat or 18.9% of total aerobic heterotrophic isolates, while PNSB and purple sulfur bacteria were quantified at maximum abundance of 3.2 × 105 and 2.0 × 106 CFU/cm2 of mat, respectively. Photosynthetic activity revealed incredibly productive carbon fixation rates, averaging 40.5 mg C/cm2/day at one studied spring system. A temporal mismatch was observed for mat area and available organics to the fluctuation of P. johnsoni population in a tracking inertia manner. Mat chlorophyll a content appeared directly proportional to snail numbers making it an appropriate indicator of population. This survey of the Sulphur springs microbial communities suggests that phototrophic species are among the main determinants to the proliferation of P. johnsoni.

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.

Significance of the carbon sink produced by H_2O–carbonate–CO_2–aquatic phototroph interaction on land

One of the most important questions in the science of global change is how to balance the atmospheric CO2 budget. There is a large terrestrial missing carbon sink amounting to about one billion tonnes of carbon per annum. The locations, magnitudes, variations, and mechanisms responsible for this terrestrial missing carbon sink are uncertain and the focus of much continuing debate. Although the positive feedback between global change and silicate chemical weathering is used in geochemical models of atmospheric CO2, this feedback is believed to operate over a long timescale and is therefore generally left out of the current discussion of human impact upon the carbon budget. Here, we show, by synthesizing recent findings in rock weathering research and studies into biological carbon pump effects in surface aquatic ecosystems, that the carbon sink produced by carbonate weathering based on the H2O- carbonate-CO2-aquatic phototroph interaction on land not only totals half a billion tonnes per annum, but also displays a significant increasing trend under the influence of global warming and land use change; thus, it needs to be included in the global carbon budget.

Enhanced metronidazole removal by binary-species photoelectrogenic biofilm of microaglae and anoxygenic phototrophic bacteria

High efficient removal of antibiotics during nutriments recovery for biomass production poses a major technical challenge for photosynthetic microbial biofilm-based wastewater treatment since antibiotics are always co-exist with nutriments in wastewater and resist biodegradation due to their strong biotoxicity and recalcitrance.In this study,we make a first attempt to enhance metronidazole(MNZ)removal from wastewater using electrochemistry-activated binary-species photosynthetic biofilm of Rhodopseudomonas Palustris(R.Palustris)and Chlorella vulgaris(C.vulgaris)by cultivating them under different applied potentials.The results showed that application of external potentials of-0.3,0 and 0.2 V led to 11,33 and 26-fold acceleration in MNZ removal,respectively,as compared to that of potential free.The extent of enhancement in MNZ removal was positively correlated to the intensities of photosynthetic current produced under different externally applied potentials.The binary-species photoelectrogenic biofilm exhibited 18 and 6-fold higher MNZ removal rate than that of single-species of C.vulgaris and R.Palustris,respectively,due to the enhanced metabolic interaction between them.Application of an external potential of 0V significantly promoted the accumulation of tryptophan and tyrosine-like compounds as well as humic acid in ex-tracellular polymeric substance,whose concentrations were 7.4,7.1 and 2.0-fold higher than those produced at potential free,contributing to accelerated adsorption and reductive and photosensitive degradation of MNZ.

Enhanced biohydrogen generation from organic wastewater containing NH^(+)_(4)by phototrophic bacteria Rhodobacter sphaeroides AR-3

NH^(+)_(4)is typically an inhibitor to hydrogen production from organic wastewater by photo-bacteria.In this experiment,biohydrogen generation with wild-type anoxygenic phototrophic bacterium Rhodobacter sphaeroideswas found to be sensitive to NH^(+)_(4)due to the significant inhibition of NH^(+)_(4)to its nitrogenase.In order to avoid the inhibition of NH^(+)_(4)to biohydrogen generation by R.sphaeroides,a glutamine auxotrophic mutant R.sphaeroides AR-3 was obtained by mutagenizing with ethyl methane sulfonate.The AR-3 mutant could generate biohydrogen efficiently in the hydrogen production medium with a higher NH^(+)_(4)concentration,because the inhibition of NH^(+)_(4)to nitrogenase of AR-3 was released.Under suitable conditions,AR-3 effectively produced biohydrogen from tofu wastewater,which normally contains 50–60 mg/L NH^(+)_(4),with an average generation rate of 14.2 mL/L$h.This generation rate was increased by more than 100%compared with that from wild-type R.sphaeroides.

Metagenomic analysis reveals wide distribution of phototrophic bacteria in hydrothermal vents on the ultraslow-spreading Southwest Indian Ridge

Deep-sea hydrothermal vents are known as chemosynthetic ecosystems.However,high temperature vents emit light that hypothetically can drive photosynthesis in this habitat.Metagenomic studies have sporadically reported the occurrence of phototrophic populations such as cyanobacteria in hydrothermal vents.To determine how geographically and taxonomically widespread phototrophs are in deep-sea hydrothermal vents,we collected samples from three niches in a hydrothermal vent on the Southwest Indian Ridge and carried out an integrated metagenomic analysis.We determined the typical community structures of microorganisms found in active venting fields and identified populations of known potential chlorophototrophs and retinalophototrophs.Complete chlorophyll biosynthetic pathways were identified in all samples.By contrast,proteorhodopsins were only found in active beehive smoker diffusers.Taxonomic groups possessing potential phototrophy dependent on semiconductors present in hydrothermal vents were also found in these samples.This systematic comparative metagenomic study reveals the widespread distribution of phototrophic bacteria in hydrothermal vent fields.Our results support the hypothesis that the ocean is a seed bank of diverse microorganisms.Geothermal vent light may provide energy and confer a competitive advantage on phototrophs to proliferate in hydrothermal vent ecosystems.

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.

负碳人工光合群落的设计、优化与应用

CO_(2)生物转化技术的开发为解决能源转型和气候变化问题提供了可能。人工光合群落是由密切协作的光合自养微生物与异养微生物组成的新一代生物炼制平台,能够通过群落成员间的互利代谢分工,高效地利用光能将CO_(2)直接转化为生物质和多种化学品,是实现负碳生物制造的潜在途径之一,因其在适用性和鲁棒性方面的优势受到了广泛的关注。近年来,随着系统生物学研究和合成生物技术的快速发展,多种研究策略被用于人工光合群落的设计与优化,取得了长远的进展,促进了对光合群落生产的理解。本文综述了光合群落的互作机制、独到优势和系统生物学研究方法,着重介绍人工光合群落的底盘升级、固定化/区室化技术、加强内部多层次调控等设计与优化策略以及在不同领域的应用进展。在此基础上,探讨了进一步将人工光合群落规模化应用所面临的光合效率和中间碳水化合物限制以及外源生物污染等潜在挑战,对纳米半导体材料杂合、物种间精细互作关系调控、基于多组学数据的群落模型构建等未来的改造方向和研究策略进行了展望。

不产氧光合细菌的分类学进展

不产氧光合细菌(APB)一直是研究生命起源与进化、光合作用和固氮机理的良好模式生物。近年来,APB资源研究发展迅速,不断发现新的物种、模式种及特殊功能物种,不断提出新的分类单元,APB分类系统发生了较大变化,同时引起了一定混乱。本文对不产氧光合细菌定义、分类系统和分类指征最新进展进行了系统述评,对分类系统中存在的问题和发展趋势也进行了评述。

还原亚硒酸盐产生红色单质硒光合细菌菌株的筛选与鉴定

从实验室保藏的光合细菌中筛选出一株对亚硒酸钠还原效率较高的菌株S3,其亚硒酸钠还原产物通过透射电子显微镜及EDX(Electron-Dispersive X-ray)分析确定为红色单质硒。菌株S3的形态学特征、生理生化特征及光合色素扫描结果与固氮红细菌(Rhodobacter azotoformans)的特征基本一致;16S rDNA序列(GenBank登录号为DQ402051)在系统发育树中与固氮红细菌同属一个类群,序列同源性为99%。根据上述结果将菌株S3鉴定为固氮红细菌。初步研究了该菌株还原亚硒酸钠的特性,首次报道固氮红细菌具有还原亚硒酸盐产生红色单质硒的能力,为今后利用微生物方法治理环境中硒污染、利用微生物方法获得活性红色单质硒以及对微生物还原亚硒酸盐产生红色单质硒的机理研究奠定了良好的基础。

水生光合生物对茂兰拉桥泉及其下游水化学和δ^(13)C_(DIC)昼夜变化的影响

碳酸盐风化能否形成稳定持久碳汇很大程度上取决于风化产生的溶解无机碳(DIC)能否被水生光合生物利用及其利用程度,后者可通过地表水水化学和?13CDIC的昼夜变化进行探讨。本研究对冬季茂兰拉桥表层岩溶泉及其中游和下游池水的温度、pH、电导率(EC)和溶解氧(DO)进行了为期30 h(1月27日10:00至1月28日16:00)高分辨率(15 min/次)的昼夜动态监测和?13CDIC定期取样(白天每隔2 h,夜间每隔4 h)测定,以了解水生光合生物对水化学和?13CDIC昼夜动态变化的影响。同时,结合水面静态箱CO2测定获得的岩溶水与空气CO2交换通量,对生物碳泵效应进行了估算。结果表明,在少有沉水植物生长的泉口及其下游水池,水化学和?13CDIC的昼夜变化明显偏小,而在沉水植物(轮藻为主)大量生长的中游水池,水的DO、pH、SIC(方解石饱和指数)和?13CDIC在白天呈逐渐增加趋势,而在夜间逐渐降低,与水生生物的新陈代谢进程(白天以光合作用为主,晚上以呼吸作用占优势)相一致;另一方面,水的EC、3HCO?、Ca2+和p(CO2)(二氧化碳分压)呈现相反的变化趋势,即白天下降,晚上上升。计算得到中游水池因类似海洋"生物碳泵"效应固定下来的有机碳通量达到336 t C/(a·km2),是海洋的51倍,表明陆地水生生态系统应该作为"遗失碳汇"的一个重要方面继续进行研究。

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.

生物产氢技术研究进展

Hydrogen is noted widely because it is a clean energy. Many countries in the world are studying and developing new methods for hydrogen production. Biological hydrogen production is one of such new methods with the advantages of utilizing renewable energy and wastes, and of low cost. In this paper, the characteristics of 5 modes of biological hydrogen production were summarized and compared according to hydrogen metabolic energetic. Furthermore, the molecular mechanism of biological hydrogen production by anoxygenic phototrophic bacteria was described. Finally, the newest progress of hydrogen production by anoxygenic phototrophic bacteria in the aspects of electronic donor, coupling to light energy, inhibition of ammonium, and genetic manipulation and exploiting of application system was reviewed. Fig 1, Tab 1, Ref

北京红篓菌合成聚羟基烷酸的研究

报道从污水处理厂回流池废水中分离到的北京红篓菌 (Rcs.pekingensisstrain 3 p)合成PHAs的研究结果。实验结果表明 ,3 p菌株生长及积累PHAs的最佳培养条件为 :0 0 1 %酵母膏 ,0 0 1 %NH4 Cl,乙酸钠 5g L ;培养基最适pH值为 7 0～ 7 2。在此培养条件下 ,细胞内PHAs积累量达菌体干重的 60 %以上。酶活测定表明菌株 3 p含有与PHAs合成相关的β 酮硫解酶 ,乙酰乙酰CoA还原酶 ,PHA聚合酶 ,初步推断此菌株的代谢途径为 :乙酸 (或其他脂肪酸 )—乙酰CoA—乙酰乙酰CoA—羟基丁酰CoA—PHAs。

光合细菌生物膜反应器葡萄糖降解及产氢特性实验

The biodegradation performance of a novel photosynthetic bacterial biofilm reactor for hydrogen production using glucose as the sole carbon source during the start-up stage and steady operation stage was investigated experimentally.The effects of operation parameters,such as light intensity,light wave length,inlet substrate concentration,temperature and pH of the substrate medium on the biodegradation efficiency of the photosynthesis hydrogen production biofilm reactor were studied respectively.The experimental results showed that the glucose elimination capacity of the bioreactor increased rapidly in the biofilm formation stage,then fluctuated in the growth stage,and finally kept almost constant in the stabilization stage.The biodegradation efficiency of the photosynthesis hydrogen production biofilm reactor increased with the increase in light intensity,inlet substrate concentration,temperature and pH till the biodegradation efficiency reached a maximum value.Then the biodegradation efficiency decreased with the increase in these parameters.In addition,light wave length had significant influence on the biodegradation efficiency.

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。