Deep Crustal Communities of the Juan de Fuca Ridge Are Governed by Mineralogy

Volcanic ocean crust contains a global chemosynthetic microbial ecosystem that impacts ocean productivity, seawater chemistry and geochemical cycling. We examined the mineralogical effect on community structure in the aquifer ecosystem by using a four-year in situ colonization experiment with igneous minerals and glasses in Integrated Ocean Drilling Program Hole 1301A on the Juan de Fuca Ridge. Microbial community analysis and scanning electron microscopy revealed that olivine phases and iron-bearing minerals bore communities that were distinct from iron-poor phases. Communities were dominated by Archaeoglobaceae, Clostridia, Thermosipho, Desulforudis and OP1 lineages. Our results suggest that mineralogy determines microbial composition in the subseafloor aquifer ecosystem.     

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

Despite its immense size, logistical and methodological constraints have largely limited microbiological investigations of the subseafloor basement biosphere. In this study, a unique sampling system was used to collect fluids from the subseafloor basaltic crust via a Circulation Obviation Retrofit Kit (CORK) observatory at Integrated Ocean Drilling Program borehole 1301A, located at a depth of 2667 m in the Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Here, a fluid delivery line directly accesses a 3.5 million years old basalt-hosted basement aquifer, overlaid by 262 m of sediment, which serves as a barrier to direct exchange with bottom seawater. At an average of 1.2 × 10⁴ cells ml⁻¹, microorganisms in borehole fluids were nearly an order of magnitude less abundant than in surrounding bottom seawater. Ribosomal RNA genes were characterized from basement fluids, providing the first snapshots of microbial community structure using a high-integrity fluid delivery line. Interestingly, microbial communities retrieved from different CORKs (1026B and 1301A) nearly a decade apart shared major community members, consistent with hydrogeological connectivity. However, over three sampling years, the dominant gene clone lineage changed from relatives of Candidatus Desulforudis audaxviator within the bacterial phylum Firmicutes in 2008 to the Miscellaneous Crenarchaeotic Group in 2009 and a lineage within the JTB35 group of Gammaproteobacteria in 2010, and statistically significant variation in microbial community structure was observed. The enumeration of different phylogenetic groups of cells within borehole 1301A fluids supported our observation that the deep subsurface microbial community was temporally dynamic.     

Bacteriochlorophyll-protein complexes of aerobic bacteria,Erythrobacter longus and Erythrobacter species OCh 114

Bacteriochlorophyll(Bchl)-protein complexes were isolated from obligate aerobic bacteria, Erythrobacter longus and Erythrobacter species OCh 114. The apparent molecular weights, absorption spectra and polypeptide compositions of the light-harvesting complexes were, in general, similar to those of the light-harvesting Bchl-protein complexes of purple photosynthetic bacteria. The reaction center complexes of these bacteria also showed similar properties to those of the purple bacteria except for slightly altered polypeptides. However, the following characteristic features of the light-harvesting systems were found in these aerobic bacteria. Major carotenoids were not bound to the Bchl-protein complex in E. longus. In Erythrobacter sp. OCh 114, a new type of Bchl-protein complex which showed a single absorption band in the near infrared region at 806 nm was obtained. The reaction center of strain OCh 114 was associated with a c-type cytochrome.Abbreviations Bchl bacteriochlorophyll a - RC reaction center - SDS sodium dodecylsulfate - PAGE polyacrylamide gel electrophoresis     

Isolation of tellurite- and selenite-resistant bacteria from hydrothermal vents of the Juan de Fuca Ridge in the Pacific Ocean

Deep-ocean hydrothermal-vent environments are rich in heavy metals and metalloids and present excellent sites for the isolation of metal-resistant microorganisms. Both metalloid-oxide-resistant and metalloid-oxide-reducing bacteria were found. Tellurite- and selenite-reducing strains were isolated in high numbers from ocean water near hydrothermal vents, bacterial films, and sulfide-rich rocks. Growth of these isolates in media containing K(2)TeO(3) or Na(2)SeO(3) resulted in the accumulation of metallic tellurium or selenium. The MIC of K(2)TeO(3) ranged from 1,500 to greater than 2,500 micro g/ml, and the MIC of Na(2)SeO(3) ranged from 6,000 to greater than 7,000 micro g/ml for 10 strains. Phylogenetic analysis of 4 of these 10 strains revealed that they form a branch closely related to members of the genus Pseudoalteromonas, within the gamma-3 subclass of the Proteobacteria. All 10 strains were found to be salt tolerant, pH tolerant, and thermotolerant. The metalloid resistance and morphological, physiological, and phylogenetic characteristics of newly isolated strains are described.     

Real-time PCR for quantification of aerobic anoxygenic phototrophic bacteria based on pufM gene in marine environment

The abundance of aerobic anoxygenic phototrophic bacteria (AAPB), a new functional group that plays important roles in marine carbon cycling, is determined frequently by infrared epifluorescence microscopic analysis (IREM) or high-performance liquid chromatography (HPLC) based on detecting BChl a (bacteriochlorophyll a) fluorescence signal at 880 nm. Unfortunately, the fluorescence signal is often influenced by environmental variables and physiological state of cell. Here we developed a real-time quantitative PCR (qPCR) assay based on pufM gene to specifically quantify AAPB in marine environments. High specificity and sensitivity for estimation of AAPB abundance were revealed by analysis of amplification products, melting curves and target sequences. The phylogenetic tree indicated that this primer set is suitable for a wide genetic diversity of AAPB, including α-3, α-4 Proteobacteria and clones of unclear taxonomic position. In contrast, no amplicon was obtained from green non-sulphur bacteria and oxygenic phototrophic bacteria such as Cyanobacterial genomic DNA. The melting behavior could indicate predominant phenotypes in AAPB community in addition to validating the products of qPCR. The AAPB was estimated to range from 1.3 × 10⁴ cell/ml to 3.4 × 10⁵ cell/ml in our 10 tested water samples by this qPCR assay. Further investigations on the abundance distribution of AAPB in marine environments using the qPCR assay may provide new insight into their ecological functions.     

Feeding and territorial behavior of Paralvinella sulfincola, a polychaete worm at deep-sea hydrothermal vents of the Northeast Pacific Ocean

Behavioral adaptations to the severe nature and high faunal densities of hydrothermal vent habitats have received little attention from researchers. In this study, video and digital still imagery were analyzed to document the feeding and general behavior of the polychaete Paralvinella sulfincola at deep-sea vents on the Juan de Fuca ridge (North-East Pacific). This worm lives in mucous tubes on the actively growing portions of sulphide mineral chimneys and is considered to be the pioneering macrofaunal species in this habitat. We identified 6 recurrent behavior patterns, including antagonistic territoriality between neighboring conspecifics. The latter likely explains the regular spatial distribution of P. sulfincola populations on the substratum they colonize, and the observed confinement of feeding and exploration activities to a definable territory around the tube opening. Territory size, territorial overlap and density were significantly related to body weight, further supporting the importance of size and aggressive encounters in the maintenance of the worm's feeding area. During feeding, P. sulfincola uses its buccal tentacles to gather particles from the substratum using two different capture modes: seizing single macro-particles and aggregation of small particles.     

Anoxygenic phototrophic bacteria of the high-altitude meromictic Lake Gek-Gel,Azerbaijan

The anoxygenic phototrophic bacterial community of the high-altitude meromictic Lake Gek-Gel (Azerbaijan) was investigated in September 2003. The highest concentration of bacteriochlorophyll e (48 μg/l) was detected at a depth of 30 m; the peak of bacteriochlorophyll a (4.5 μg/l) occurred at 29 m. Phylogenetic analysis revealed that brown-colored green sulfur bacteria Chlorobium phaeobacteroides predominated in the lake. Nonsulfur purple bacteria phylogenetically close to Blastochloris sulfoviridis were found in insignificant amounts; these organisms have not been previously reported in Lake Gek-Gel.     

Purification and characterization of reaction centers from the obligate aerobic phototrophic bacteria Erythrobacter litoralis,Erythromonas ursincola and Sandaracinobacter sibiricus

Reaction centers (RC) from the species Erythrobacter (Eb.) litoralis, Erythromonas (Em.) ursincola and Sandaracinobacter (S.) sibiricus have been purified by LDAO treatment of light-harvesting-reaction center complexes and DEAE chromatography. The content and overall organisation of the RCs' chromophores, determined by linear dichroism (LD) and absorption spectroscopy, are similar to those isolated from anaerobic photosynthetic bacteria. The redox properties of the primary electron donor are pH-independent and very similar to those determined for anaerobic photosynthetic bacteria with midpoint potential values equal to 445 (± 10), 475 and 510 mV for Eb. litoralis, S. sibiricus and Em. ursincola, respectively. The RC purified from Eb. litoralis does not contain bound cytochrome (cyt), whereas RCs isolated from S. sibiricus and Em. ursincola possess a tetraheme cyt c. Each of these tetraheme cyts contains two high potential hemes and two low potential hemes. Their redox properties are very similar, with midpoint potentials equal to 385 (± 10), 305, 40, -40 mV for Em. ursincola and 355, 285, 30, -48 mV for S. sibiricus. At physiological pH, the midpoint potential of the primary electron acceptor (Q_A) varies with a slope of -60 mV/pH unit. The reduced form of Q_A presents pK values of 9, 9.8, 10.5 for S. sibiricus, Em. ursincola and Eb. litoralis, respectively. The main difference observed between RCs isolated from anaerobic photosynthetic and from obligate aerobic bacteria is the _Emvalues of Q_A which are 65 to 120 mV higher in the last case. This difference is proposed to be a major reason for the inability of these species to grow under anaerobic photosynthetic conditions.     

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。     

Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria

Based upon their photosynthetic nature and the presence of a unique light-harvesting antenna structure, the chlorosome, the photosynthetic green bacteria are defined as a distinctive group in the Bacteria. However, members of the two taxa that comprise this group, the green sulfur bacteria (Chlorobi) and the filamentous anoxygenic phototrophic bacteria (Chloroflexales), are otherwise quite different, both physiologically and phylogenetically. This review summarizes how genome sequence information facilitated studies of the biosynthesis and function of the photosynthetic apparatus and the oxidation of inorganic sulfur compounds in two model organisms that represent these taxa, Chlorobium tepidum and Chloroflexus aurantiacus. The genes involved in bacteriochlorophyll (BChl) c and carotenoid biosynthesis in these two organisms were identified by sequence homology with known BChl a and carotenoid biosynthesis enzymes, gene cluster analysis in Cfx. aurantiacus, and gene inactivation studies in Chl. tepidum. Based on these results, BChl a and BChl c biosynthesis is similar in the two organisms, whereas carotenoid biosynthesis differs significantly. In agreement with its facultative anaerobic nature, Cfx. aurantiacus in some cases apparently produces structurally different enzymes for heme and BChl biosynthesis, in which one enzyme functions under anoxic conditions and the other performs the same reaction under oxic conditions. The Chl. tepidum mutants produced with modified BChl c and carotenoid species also allow the functions of these pigments to be studied in vivo.     

Dynamics of aerobic anoxygenic phototrophic bacteria in the East China Sea

Aerobic anoxygenic phototrophic bacteria (AAPB) are a group of heterotrophic bacteria capable of photosynthesis. The dynamics of AAPB in the East China Sea, a typical marginal sea characterized by diverse physical-chemical and ecological conditions, were investigated from April 2002 to September 2003. The results showed that the abundance of AAPB varied from 0.16 to 7.9 x 10(4) cells mL(-1) and the percentage of AAPB (AAPB%) in the total heterotrophic bacterial abundance varied from 0.5% to 11.6% over a gradient of environmental conditions. The abundance of AAPB and AAPB% was higher in coastal and continental shelf waters than in oceanic waters. An interesting seasonal pattern was observed in the Yangtze River estuary: the abundance of AAPB was highest in summer and lowest in winter; however, AAPB% was higher in winter than in the other seasons. Throughout the investigation period, variation of AAPB abundance with temperature was much less than that of nonAAPB abundance, suggesting that low temperature was not a limiting factor for AAPB in this case. Close correlation between AAPB and chlorophyll a was observed in each season, suggesting that dependence of AAPB on dissolved organic carbon produced by phytoplankton (PDOC) may be one key factor controlling AAPB distribution.     

On the natural selection and evolution of the aerobic phototrophic bacteria

This contribution gives a brief survey of the short history since the discovery of the aerobic phototrophic bacteria to focus on a general evolutionary scenario. Most of the citations are of reviews that have covered the earlier literature and to which the reader is directed at appropriate places in the following text. The data summarized in these reviews are supplemented with information from recent or otherwise key primary publications in order to support a synthesis that addresses vexing questions about bacteria containing photosynthetic pigment-protein complexes, but which are incapable of growth with light as the sole, or even the major source of energy. This revised version was published online in June 2006 with corrections to the Cover Date.     

Vertical distribution in and isolation of bacteria from Lake Vanda: an Antarctic lake

Vertical distribution of bacteria in Lake Vanda, an Antarctic meromictic lake, was examined by the acridine orange epifluorescence direct count method. Total bacteria were 10⁴–10⁵ cells · ml^–1 in the water at 55 m depth and above, and increased drastically to 10⁷ cells · ml^–1 in the bottom water. Filamentous or long rodshaped bacteria occurred at a high frequency in the upper layers, but in the bottom layers most bacteria were coccoidal or short rods. Mean bacterial cell volume in water of between 10 m and 60 m deep was fairly large compared with common bacterial populations in seawater and lake water. Aerobic heterotrophic bacteria were recovered from the water of a depth of 30 m and above, and were assumed to belong to Caulobacter. Viable heterotrophic bacteria were not recovered from the high salinity deep water by media prepared with the same deep water. Phototrophic purple non-sulphur bacteria were isolated by enrichment cultures from water at 55 m depth.     

Isolation of Aerobic Anoxygenic Photosynthetic Bacteria from Black Smoker Plume Waters of the Juan de Fuca Ridge in the Pacific Ocean

A strain of the aerobic anoxygenic photosynthetic bacteria was isolated from a deep-ocean hydrothermal vent plume environment. The in vivo absorption spectra of cells indicate the presence of bacteriochlorophyll a incorporated into light-harvesting complex I and a reaction center. The general morphological and physiological characteristics of this new isolate are described.     

Some factors controlling the biosynthesis of chlorosome antenna bacteriochlorophylls in green filamentous anoxygenic phototrophic bacteria of the family Oscillochloridaceae

We determined the concentrations of bacteriochlorophylls (BChl) in the light-harvesting antennae of Oscillochloris trichoides (of the family Oscillochloridaceae belonging to green filamentous mesophilic bacteria) cultivated either with gabaculine, an inhibitor of the C-5 pathway of BChl biosynthesis in a number of bacteria, or at various illumination intensities. We determined the BChl c: BChl a molar ratios in intact cells, in chlorosome-membrane complexes, and in isolated chlorosomes. We revealed that BChl c synthesis in Osc. trichoides was more gabaculine-sensitive than BChl a synthesis. Accordingly, an increase in gabaculine concentrations in the medium resulted in a decrease in the BChl c: BChl a ratio in the tested samples. We suggest that BChl synthesis in Osc. trichoides proceeds via the C-5 pathway, similar to representatives of other families of green bacteria (Chlorobium limicola and Chloroflexus aurantiacus). We demonstrated that the BChl c: BChl a ratio in the chlorosomes varied from 55: 1 to 110: 1, depending on light intensity. This ratio is, therefore, closer to that of Chlorobiaceae, and it significantly exceeds the BChl c: BChl a ratio in Chloroflexaceae.     

Isolation and characterization of<Emphasis Type="Italic"> Erythrobacter</Emphasis> sp. strains from the upper ocean

Seven strains of marine aerobic anoxygenic phototrophs belonging to the genus Erythrobacter were isolated. The strains were characterized regarding their physiological and biochemical properties, 16S rDNA and pufM gene sequences, morphological features, substrate preference, as well as pigment and lipid composition. All strains had functional type-2 reaction centers containing bacteriochlorophyll, served by small, light-harvesting complex 1, and were photosynthetically competent. In addition, large pools of carotenoids were found, but only some of the accessory pigments transfer energy to the reaction centers. All of the isolates were facultative photoheterotrophs. They required an organic carbon substrate for growth; however, they are able to supplement a significant fraction of their metabolic requirements with photosynthetically derived energy.Abbreviations BChl Bacteriochlorophyll - Chl Chlorophyll - Erb. Erythrobacter - Erm. Erythromicrobium - FAMEs Fatty acid methyl esters - IRFRR Infrared fast repetition rate - LH1, LH2 Light-harvesting complex 1 and 2, respectively - Por. Porphyrobacter - PUFAs Polyunsaturated fatty acids - Rsb. Roseobacter - RubisCO Ribulose-1,5-bisphosphate carboxylase/oxygenase - µ Growth rate - ₄₇₀ Functional cross-section of the photosynthetic unit at 470 nm     

Characterization of the chlorosome antenna of the filamentous anoxygenic phototrophic bacterium<Emphasis Type="Italic"> Chloronema</Emphasis> sp. strain UdG9001

The absorption and fluorescence properties of chlorosomes of the filamentous anoxygenic phototrophic bacterium Chloronema sp. strain UdG9001 were analyzed. The chlorosome antenna of Chloronema consists of bacteriochlorophyll (BChl) d and BChl c together with -carotene as the main carotenoid. HPLC analysis combined with APCI LC-MS/MS showed that the chlorosomal BChls comprise a highly diverse array of homologues that differ in both the degree of alkylation of the macrocycle at C-8 and/or C-12 and the alcohol moiety esterified to the propionic acid group at C-17. BChl c and BChl d from Chloronema were mainly esterified with geranylgeraniol (33% of the total), heptadecanol (24%), octadecenol (19%), octadecanol (14%), and hexadecenol (9%). Despite this pigment heterogeneity, fluorescence emission of the chlorosomes showed a single peak centered at 765 nm upon excitation at wavelengths ranging from 710 to 740 nm. This single emission, assigned to BChl c, indicates an energy transfer from BChl d to BChl c within the same chlorosome. Likewise, incubation of chlorosomes under reducing conditions caused a weak increase in fluorescence emission, which indicates a small redox-dependent fluorescence. Finally, protein analysis of Chloronema chlorosomes using SDS-PAGE and MALDI-TOF-MS revealed the presence of a chlorosomal polypeptide with a molecular mass of 5.7 kDa, resembling the CsmA protein found in Chloroflexus aurantiacus and Chlorobium tepidum chlorosomes. Several minor polypeptides were also detected but not identified. These results indicate that, compared with other members of filamentous anoxygenic phototrophic bacteria and green sulfur bacteria, Chloronema possesses an antenna system with novel features that may be of interest for further investigations.Abbreviations APCI LC-MS/MS Atmospheric pressure chemical ionization liquid chromatography mass spectrometry - BChl Bacteriochlorophyll - Chl. Chlorobium - Cfl. Chloroflexus - MALDI-TOF-MS Matrix assisted laser desorption/ionization time-of-flight mass spectrometry - [Et] Ethyl - [i-Bu] Isobutyl - [Me] Methyl - [neo-Pent] Neopentyl - [n-Pr] Propyl - t _R Retention time     

Biological N2 fixation by heterotrophic and phototrophic bacteria in association with straw

Much of the crop residues, including cereal straw, that are produced worldwide are lost by burning. Plant residues, and in particular straw, contain large amounts of carbon (cellulose and hemicellulose) which can serve as substrates for the production of microbial biomass and for biological N₂ fixation by a range of free-living, diazotrophic bacteria. Microorganisms with the dual ability to utilise cellulose and fix N₂ are rate, but some strains that utilize hemicellulose and fix N₂ have been found. Generally, cellulolysis and diazotrophy are carried out by a mixed microbial community in which N₂-fixing bacteria utilise cellobiose and glucose produced from straw by cellulolytic microorganisms. N₂-fixing bacteria include heterotrophic and phototrophic organisms and the latter are apparently more prominent in flooded soils such as rice paddies than in dryland soils. The relative contributions of N₂ fixed by heterotrophic diazotrophic bacteria compared with cyanobacteria and other phototrophic bacteria depend on the availability of substrates from straw decomposition and on environmental pressures. Measurements of asymbiotic N₂ fixation are limited and variable but, in rice paddy systems, rates of 25 kg N ha^-1 over 30 days have been found, whereas in dryland systems with wheat straw, in situ measurements have indicated up to 12 kg N ha^-1 over 22 days. Straw-associated N₂ fixation is directly affected by environmental factors such as temperature, moisture, oxygen concentration, soil pH and clay content as well as farm management practices. Modification of managements and use of inoculants offer ways of improving asymbiotic N₂ fixation.In laboratory culture systems, inoculation of straws with cellulolytic and diazotrophic microorganisms has resulted in significant increases in N₂ fixation in comparison to uninoculated controls and gains of N of up to 72 mg N fixed g^-1 straw consumed have been obtained, indicating the potential of inoculation to improve N gains in composts that can then be used as biofertilisers. Soils, on the other hand, contain established, indigenous microbial populations which tend to exclude inoculant microorganisms by competition. As a consequence, improvements in straw-associated N₂ fixation in soils have been achieved mostly by specific straw-management practices which encourage microbial activity by straw-decomposing and N₂-fixing microorganisms.Further research is needed to quantify more accurately the contribution of asymbiotic N₂ fixation to cropping systems. New strains of inoculants, including those capable of both cellulolytic and N₂-fixing activity, are needed to improve the N content of biofertilisers produced from composts. Developments of management practices in farming systems may result in further improvements in N₂ fixation in the field.     

黄河滩地和稻田土中铁还原菌、不产氧光合细菌分布机制

【目的】探讨沿黄流域土壤中铁还原菌(ferric reducing bacteria, Fe RB)、不产氧光合细菌(anoxygenic phototrophic bacteria, An PB)的分布机制。【方法】以沿黄流域(原阳段)为研究对象,采集黄河滩地和稻田土样,利用16Sr RNA基因高通量测序和实时荧光定量分析技术,结合统计学分析,揭示Fe RB、An PB菌群结构、丰度和主要环境影响因子。【结果】二者中的优势Fe RB在科(属)水平为Hydrogenophilaceae(Thiobacillus)、 Bacillaceae(Bacillus)、 Clostridiaceae、Rhodobactereace(Rhodobacter)、 Geobacteraceae(Geobacter),优势An PB为Rhodobactereace(Rhodobacter)、 Chloroflexaceae(Chloronema)、 Acetobacteraceae(Roseomonas)。An PB中Rhodobacteraceae与Fe RB中Bacillaceae、 Clostri...