Archaeal diversity and geochemical energy yields in a geothermal well on Vulcano Island, Italy

The archaeal diversity in a shallow geothermal well on Vulcano Island, Italy was characterized using culture‐independent 16S rDNA sequence analysis. Environmental DNA was extracted from 56 °C well water, and the 16S ribosomal RNA gene was amplified with archaea‐specific primers. Restriction fragment length polymorphism (RFLP) analysis of ～250 clones revealed 35 unique patterns, which were sequenced and analyzed. These yielded 17 operational taxonomic units, of which 13, 3, and 1 were unique cren‐, eury‐, and korarchaeotal sequences, respectively. The majority of the crenarchaeotal phylotypes formed a novel, deeply‐branching clade that includes sequences from other hydrothermal environments, but no cultured representatives. Three phylotypes represent novel lineages in the Thermoproteales and two phylotypes represent a novel genus of Euryarchaeota. One euryarchaeotal phylotype was nearly identical (99%) to Palaeococcus helgesonii, an aerotolerant, hyperthermophilic fermenter previously isolated from the same well. To place this diverse archaeal community in the geochemical framework of this ecosystem, we calculate values of Gibbs free energy of 145 organic and inorganic redox reactions at in situ conditions. Energy yields ranged from 0 to 125 kJ per mole of electrons transferred. The most exergonic organic reactions were organic carbon oxidation with O₂ (>100 kJ/mol e^?), followed by oxidation with (61–93 kJ/mol e^?), Fe(III) (43–60 kJ/mol e^?), and S⁰/ (6–27 kJ/mol e^?) as terminal electron acceptors. Overall, energy yields from inorganic reactions were similar to those of the organic reactions considered, but were less systematic with respect to terminal electron acceptor. The oxidation of methane coupled with Fe(III) reduction yielded the most energy (123 kJ/mol e^?). However, the most exergonic inorganic reactions were predominantly O₂, , or reduction. Reduction of , S⁰, CO₂, and CO yielded significantly less energy (0–18 kJ/mol e^?). Metabolisms of the cultured organisms identified in the Pozzo Istmo archaeal clone library were exergonic. However, most of the archaeal diversity remains uncultured and energetic calculations reveal an extensive suite of potential lithotrophic and heterotrophic metabolisms that could be exploited by these novel organisms.     

Molecular characterization of inorganic sulfur‐compound metabolism in the deep‐sea epsilonproteobacterium Sulfurovum sp. NBC37‐1

The molecular components involved in energy metabolism of deep‐sea Epsilonproteobacteria were characterized in the mesophilic hydrogen‐ and sulfur‐oxidizing chemolithoautotroph Sulfurovum sp. NBC37‐1. Previous whole‐genome analysis of strain NBC37‐1 identified key genes likely to be associated with both sulfur reduction (psr gene families) and oxidation (two sox gene clusters). However, the sox gene clusters showed unique organizations and low homologies to those in other bacteria. Therefore, the biochemical mechanism of inorganic sulfur metabolism has been uncertain. Enzymatic activity measurements and partial protein purification indicated that the Sox enzyme system was constitutively expressed, whereas the expression of sulfur‐reduction enzymes varied depending on the culture conditions. The operative Sox system in strain NBC37‐1 required membrane components. The molecular basis of energy metabolism reported in this study provides important insight into how deep‐sea Epsilonproteobacteria change their energy metabolism in response to variable physical and chemical conditions in mixing zones between hydrothermal fluid and ambient seawater.     

Barite in hydrothermal environments as a recorder of subseafloor processes: a multiple‐isotope study from the Loki's Castle vent field

Barite chimneys are known to form in hydrothermal systems where barium‐enriched fluids generated by leaching of the oceanic basement are discharged and react with seawater sulfate. They also form at cold seeps along continental margins, where marine (or pelagic) barite in the sediments is remobilized because of subseafloor microbial sulfate reduction. We test the possibility of using multiple sulfur isotopes (δ³⁴S, Δ³³S, ?³⁶S) of barite to identify microbial sulfate reduction in a hydrothermal system. In addition to multiple sulfur isotopes, we present oxygen (δ¹⁸O) and strontium (⁸⁷Sr/⁸⁶Sr) isotopes for one of numerous barite chimneys in a low‐temperature (~20 °C) venting area of the Loki's Castle black smoker field at the ultraslow‐spreading Arctic Mid‐Ocean Ridge (AMOR). The chemistry of the venting fluids in the barite field identifies a contribution of at least 10% of high‐temperature black smoker fluid, which is corroborated by ⁸⁷Sr/⁸⁶Sr ratios in the barite chimney that are less radiogenic than in seawater. In contrast, oxygen and multiple sulfur isotopes indicate that the fluid from which the barite precipitated contained residual sulfate that was affected by microbial sulfate reduction. A sulfate reduction zone at this site is further supported by the multiple sulfur isotopic composition of framboidal pyrite in the flow channel of the barite chimney and in the hydrothermal sediments in the barite field, as well as by low SO₄ and elevated H₂S concentrations in the venting fluids compared with conservative mixing values. We suggest that the mixing of ascending H₂‐ and CH₄‐rich high‐temperature fluids with percolating seawater fuels microbial sulfate reduction, which is subsequently recorded by barite formed at the seafloor in areas where the flow rate is sufficient. Thus, low‐temperature precipitates in hydrothermal systems are promising sites to explore the interactions between the geosphere and biosphere in order to evaluate the microbial impact on these systems.     

Geochemical constraints on chemolithoautotrophic reactions in hydrothermal systems

Thermodynamic calculations provide the means to quantify the chemical disequilibrium inherent in the mixing of redeuced hydrothermal fluids with seawater. The chemical energy available for metabolic processes in these environments can be evaluated by taking into account the pressure and temperature dependence of the apparent standard Gibbs free energies of reactions in the S-H₂-H₂O system together with geochemical constraints on pH, activities of aqueous sulfur species and fugacities of H₂ and/or O₂. Using present-day mixing of hydrothermal fluids and seawater as a starting point, it is shown that each mole of H₂S entering seawater from hydrothermal fluids represents about 200,000 calories of chemical energy for metabolic systems able to catalyze H₂S oxidation. Extrapolating to the early Earth, which was likely to have had an atmosphere more reduced than at present, shows that this chemical energy may have been a factor of two or so less. Nevertheless, mixing of hydrothermal fluids with seawater would have been an abundant source of chemical energy, and an inevitable consequence of the presence of an ocean on an initially hot Earth. The amount of energy available was more than enough for organic synthesis from CO₂ or CO, and/or polymer formation, indicating that the vicinity of hydrothermal systems at the sea floor was an ideal location for the emergence of the first chemolithoautotrophic metabolic systems.     

Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments

A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence on freshwater or terrestrial iron cycling. Observations of sulfate reduction in low-sulfate environments have been attributed to the presumed presence of highly crystalline iron oxides allowing sulfate reduction to be more energetically favored. Here we identified the iron-reducing processes under low-sulfate conditions within columns containing freshwater sediments amended with structurally diverse iron oxides and fermentation products that fuel anaerobic respiration. We show that despite low sulfate concentrations and regardless of iron oxide substrate (ferrihydrite, Al-ferrihydrite, goethite, hematite), sulfidization was a dominant pathway in iron reduction. This process was mediated by (re)cycling of sulfur upon reaction of sulfide and iron oxides to support continued sulfur-based respiration—a cryptic sulfur cycle involving generation and consumption of sulfur intermediates. Although canonical iron respiration was not observed in the sediments amended with the more crystalline iron oxides, iron respiration did become dominant in the presence of ferrihydrite once sulfate was consumed. Thus, despite more favorable energetics, ferrihydrite reduction did not precede sulfate reduction and instead an inverse redox zonation was observed. These findings indicate that sulfur (re)cycling is a dominant force in iron cycling even in low-sulfate systems and in a manner difficult to predict using the classical thermodynamic ladder.     

Formation of dimethylsulfide and methanethiol from methoxylated aromatic compounds and inorganic sulfide by newly isolated anaerobic bacteria

Formation of gas and of methylated sulfur compounds was observed in anaerobic enrichment cultures with methoxylated aromatic compounds as substrates. Via direct dilution of mud samples in defined reduced media supplemented with trimethoxybenzoate or syringate two new strains of anaerobic homoacetogenic bacteria (strain TMBS4 and strain SA2) were obtained in pure culture. Both strains produced dimethylsulfide and methanethiol during growth on methoxylated aromatic compounds. Growth tests and determination of stoichiometries demonstrated that the volatile sulfur compounds were formed from the methyl group at the aromatic ring and the sulfide added as reducing agent to the medium (R = aromatic residue): 2 R - O - CH₃ + H₂ S 2 R - OH + (CH₃)₂SDimethylsulfide was the major organic sulfur compound formed, whereas methanethiol appeared only as intermediate in small quantities. The isolates grew also with trihydroxybenzenes such as gallate, phloroglucinol, or pyrogallol without formation of methylated sulfur compounds. The aromatic compounds were degraded to acetate. The freshwater strain TMBS4 also fermented pyruvate. Other aliphatic or aromatic compounds were not utilized. External electron acceptors (sulfate, nitrate, fumarate) were not reduced. Both strains were mesophilic and formed rod-shaped, non-motile, Gram-negative cells. Spore formation was not observed. Tentatively, both isolates can be affiliated to the genus Pelobacter.Abbreviations TMB 3,4,5-trimethoxybenzoate - MT methanethiol - DMS dimethylsulfide     

The ecological significance of sulfur in the energy dynamics of salt marsh and coastal marine sediments

Sulfur is an important element in the metabolism of salt marshes and subtidal, coastal marine sediments because of its role as an electron acceptor, carrier, and donor. Sulfate is the major electron acceptor for respiration in anoxic marine sediments. Anoxic respiration becomes increasingly important in sediments as total respiration increases, and so sulfate reduction accounts for a higher percentage of total sediment respiration in sediments where total respiration is greater. Thus, sulfate accounts for 25% of total sediment respiration in nearshore sediments (200 m water depth or less) where total respiration rates are 0.1 to 0.3gCm^–1 day^–1 , for 50% to 70% in nearshore sediments with higher rates of total respiration (0.3 to 3gCm^–2 day^–1), and for 70% to 90% in salt marsh sediments where total sediment respiration rates are 2.5 to 5.5gcm^–2 day^–1 .During sulfate reduction, large amounts of energy from the respired organic matter are conserved in inorganic reduced sulfur compounds such as soluble sulfides, thiosulfate, elemental sulfur, iron monosulfides, and pyrite. Only a small percentage of the reduced sulfur formed during sulfate reduction is accreted in marine sediments and salt marshes. When these reduced sulfur compounds are oxidized, energy is released. Chemolithoautotrophic bacteria which catalyze these oxidations can use the energy of oxidation with efficiencies (the ratio of energy fixed in organic biomass to energy released in sulfur oxidation) of up to 21–37% to fix CO₂ and produce new organic biomass.Chemolithoautotrophic bacterial production may represent a significant new formation of organic matter in some marine sediments. In some sediments, chemolithoautotrophic bacterial production may even equal or exceed organoheterotrophic bacterial production. The combined cycle of anaerobic decomposition through sulfate reduction, energy conservation as reduced sulfur compounds; and chemolithoautotrophic production of new organic carbon serves to take relatively low-quality organic matter from throughout the sediments and concentrate the energy as living biomass in a discrete zone near the sediment surface where it can be readily grazed by animals.Contribution from a symposium on the role of sulfur in ecosystem processes held August 10, 1983, at the annual meeting of the A.I.B.S., Grand Forks, ND; Myron Mitchell, convenor.     

Oxygen isotopic composition of sulfate in deep sea pore fluid: evidence for rapid sulfur cycling

We present new data of oxygen isotopes in marine sulfate (δ¹⁸O_SO4) in pore fluid profiles through organic‐rich deep‐sea sediments from 11 ODP sites around the world. In almost all sites studied sulfate is depleted with depth, through both organic matter oxidation and anaerobic methane oxidation. The δ¹⁸O_SO4 increases rapidly near the top of the sediments, from seawater values of 9 to maxima between 22 and 25, and remains isotopically heavy and constant at these values with depth. The δ¹⁸O_SO4 in these pore fluid profiles is decoupled from variations in sulfur isotopes measured on the same sulfate samples (δ³⁴S_SO4); the δ³⁴S_SO4 increases continuously with depth and exhibits a shallower isotopic increase. This isotopic decoupling between the δ³⁴S_SO4 and the δ¹⁸O_SO4 is hard to reconcile with the traditional understanding of bacterial sulfate reduction in sediments. Our data support the idea that sulfate or sulfite and water isotopically exchange during sulfate reduction and that some of the isotopically altered sulfur pool returns to the environment. We calculate that the rapid increase in the δ¹⁸O_SO4 in the upper part of these sediments requires rates of this oxygen isotope exchange that are several orders of magnitude higher than the rates of net sulfate reduction calculated from the sulfate concentration profiles and supported by the δ³⁴S_SO4. We suggest several mechanisms by which this may occur, including ‘net‐zero’ sulfur cycling, as well as further experiments through which we can test and resolve these processes.     

C1-cycle of sulfur compounds

C₁ organic sulfides are part of many ecosystems and play an important role in the global sulfur budget and climate regulation. At this point, fluxes and conversions of these compounds are only superficially understood. Understanding of the regulating mechanisms will be necessary to quantify the role of these compounds in the global sulfur budget at their climatic role. In this review, the current knowledge of fluxes and conversions of C₁ organic sulfides in different ecosystems is presented.Abbreviations CCN cloud condensation nuclei - COS carbonylsulfide - DMS dimethylsulfide - DMDS dimethyldisulfide - DMSO dimethylsulfoxide - DMSO₂ dimethylsulfurdioxide - DMSP dimethylsulfoniopropionate - MA methylamine - 3-MPA 3-mercaptopropionate - MPPA 3-methiolpropionate - MT methanethiol     

Microbial controls on DMSP degradation and DMS formation in the Sargasso Sea

Bacterial degradation of dimethylsulfoniopropionate (DMSP) represents one of the main sources of the climatically–active trace gas dimethylsulfide (DMS) in the upper ocean. Short-term enrichment studies to stimulate specific pathways of DMSP degradation in oligotrophic waters from the Sargasso Sea were used to explore regulatory connections between the different bacterial DMSP degradation steps and determine potential biological controls on DMS formation in the open ocean. Experiments were conducted with surface water at the BATS station in the western North Atlantic Ocean. We added selected organic substrates (25 nmol L^?1 final concentration) to induce different steps of DMSP degradation in the microbial community, and then measured DMSP dynamics (assimilation and turnover rates), DMS yields (using ³⁵sulfur-DMSP tracer), and bacterial production rates. In most treatments, the main fate of consumed S-DMSP was excretion as a non-volatile S product. ³⁵S-DMSP tracer turnover rates (accumulation + assimilation + excretion of transformed products as DMS or others) increased upon addition of DMSP and glucose, but not acrylate, methymercaptopropionate (MMPA), methanethiol, DMS or glycine betaine. DMS yields from ³⁵S-DMSP never exceeded 16 % except in a short term DMSP enrichment, for which the yield reached 45 % (±17 %). Results show that availability of non-sulfur containing labile C sources (glucose, acrylate) decreased bacterial DMS production while stimulating bacterial heterotrophic production, and suggest an influence of bacterial sulfur demand in controlling DMS-yielding pathways. However, regulatory effects on ³⁵S-DMSP fate were not consistent across all reduced sulfur compounds (i.e., methanethiol or MMPA), and may reflect alternate roles of DMSP as a bacterial energy source and osmolyte.     

Isolation of a dimethylsulfide-utilizingHyphomicrobium species and its application in biofiltration of polluted air

The methylotrophic bacteriumHyphomicrobium VS was enriched and isolated, using activated sewage sludge as inoculum in mineral medium containing dimethylsulfide (DMS) at a low concentration to prevent toxicity. DMS concentrations above 1 mM proved to be growth inhibiting.Hyphomicrobium VS could use DMS, dimethylsulfoxide (DMSO), methanol, formaldehyde, formate, and methylated amines as carbon and energy source. Carbon was assimilated via the serine pathway. DMS-grown cells respired sulfide, thiosulfate, methanethiol, dimethyldisulfide and dimethyltrisulfide.To testHyphomicrobium VS for application in biofiltration of air polluted with volatile sulfur compounds two laboratory scale trickling biofilters with polyurethane and lava stone as carrier material were started up by inoculation with this bacterium. Both methanol- and DMS-grown cells could be used. Only a short adaptation period was needed. Short term experiments showed that high concentrations of DMS (1–2 µmol 1^–1) were removed very efficiently by the biofilters at space velocities up to 100 h^–1.Abbreviations VSC volatile sulfur compounds - DMS dimethylsulfide - DMDS dimethyldisulfide - DMTS dimethyltrisulfide - MT methanethiol - DMSO dimethylsulfoxide     

Ecologically and geologically relevant isotope signatures of C,N, and S: okenone producing purple sulfur bacteria part I

Purple sulfur bacteria (PSB) are known to couple the carbon, nitrogen, and sulfur cycling in euxinic environments. This is the first study with multiple strains and species of okenone‐producing PSB to examine the carbon (C), nitrogen (N), and sulfur (S) metabolisms and isotopic signatures in controlled laboratory conditions, investigating what isotopic fractionations might be recorded in modern environments and the geologic record. PSB play an integral role in the ecology of euxinic environments and produce the unique molecular fossil okenane, derived from the diagenetic alteration of the carotenoid pigment okenone. Cultures of Marichromatium purpuratum 1591 (Mpurp1591) were observed to have carbon isotope fractionations (¹³ε_{biomass – CO2}), via RuBisCO, ranging from ?16.1 to ?23.2‰ during exponential and stationary phases of growth. Cultures of Thiocapsa marina 5653 (Tmar5653) and Mpurp1591 had a nitrogen isotope fractionation (¹⁵ε_{biomass – NH4}) of ?15‰, via glutamate dehydrogenase, measured and recorded for the first time in PSB. The δ³⁴S_VCDT values and amount of stored elemental sulfur for Mpurp1591 cells grown autotrophically and photoheterotrophically were dependent upon their carbon metabolic pathways. We show that PSB may contribute to the isotopic enrichments observed in modern and ancient anoxic basins. In a photoheterotrophic culture of Mpurp1591 that switched to autotrophy once the organic substrate was consumed, there were bulk biomass δ¹³C values that span a broader range than recorded across the Late Devonian, Permian–Triassic, Triassic–Jurassic, and OAE2 mass extinction boundaries . This finding stresses the complexities in interpreting and assigning δ¹³C values to bulk organic matter preserved in the geologic record.     

Microbial diversity of Loki's Castle black smokers at the Arctic Mid‐Ocean Ridge

Hydrothermal vent systems harbor rich microbial communities ranging from aerobic mesophiles to anaerobic hyperthermophiles. Among these, members of the archaeal domain are prevalent in microbial communities in the most extreme environments, partly because of their temperature‐resistant and robust membrane lipids. In this study, we use geochemical and molecular microbiological methods to investigate the microbial diversity in black smoker chimneys from the newly discovered Loki's Castle hydrothermal vent field on the Arctic Mid‐Ocean Ridge (AMOR) with vent fluid temperatures of 310–320 °C and pH of 5.5. Archaeal glycerol dialkyl glycerol tetraether lipids (GDGTs) and H‐shaped GDGTs with 0–4 cyclopentane moieties were dominant in all sulfide samples and are most likely derived from both (hyper)thermophilic Euryarchaeota and Crenarchaeota. Crenarchaeol has been detected in low abundances in samples derived from the chimney exterior indicating the presence of Thaumarchaeota at lower ambient temperatures. Aquificales and members of the Epsilonproteobacteria were the dominant bacterial groups detected. Our observations based on the analysis of 16S rRNA genes and biomarker lipid analysis provide insight into microbial communities thriving within the porous sulfide structures of active and inactive deep‐sea hydrothermal vents. Microbial cycling of sulfur, hydrogen, and methane by archaea in the chimney interior and bacteria in the chimney exterior may be the prevailing biogeochemical processes in this system.     

Growth of sulfate-reducing bacteria and methanogenic archaea with methylated sulfur compounds: a commentary on the thermodynamic aspects

Methylated sulfur compounds such as dimethylsulfoniopropionate, dimethylsulfide, methanethiol, and other methylated sulfur compounds can act as sources of carbon and energy for the growth under anoxic conditions of a number of sulfate-reducing bacteria and methanogenic archaea. We summarise the range of degradative reactions that do or might occur in such organisms, and present thermodynamic data for these processes. These data enable estimates of the feasibility of the reactions as growth-supporting systems, and of the possible maximum growth yields of the bacteria and archaea catalysing them. We compare our new estimates with the few data that are currently available from the literature, and show that some published growth-yield assessments need reevaluation.     

Spatial variability in photosynthetic and heterotrophic activity drives localized δ13Corg fluctuations and carbonate precipitation in hypersaline microbial mats

Modern laminated photosynthetic microbial mats are ideal environments to study how microbial activity creates and modifies carbon and sulfur isotopic signatures prior to lithification. Laminated microbial mats from a hypersaline lagoon (Guerrero Negro, Baja California, Mexico) maintained in a flume in a greenhouse at NASA Ames Research Center were sampled for δ¹³C of organic material and carbonate to assess the impact of carbon fixation (e.g., photosynthesis) and decomposition (e.g., bacterial respiration) on δ¹³C signatures. In the photic zone, the δ¹³C_org signature records a complex relationship between the activities of cyanobacteria under variable conditions of CO₂ limitation with a significant contribution from green sulfur bacteria using the reductive TCA cycle for carbon fixation. Carbonate is present in some layers of the mat, associated with high concentrations of bacteriochlorophyll e (characteristic of green sulfur bacteria) and exhibits δ¹³C signatures similar to DIC in the overlying water column (?2.0‰), with small but variable decreases consistent with localized heterotrophic activity from sulfate‐reducing bacteria (SRB). Model results indicate respiration rates in the upper 12 mm of the mat alter in situ pH and concentrations to create both phototrophic CO₂ limitation and carbonate supersaturation, leading to local precipitation of carbonate minerals. The measured activity of SRB with depth suggests they variably contribute to decomposition in the mat dependent on organic substrate concentrations. Millimeter‐scale variability in the δ¹³C_org signature beneath the photic zone in the mat is a result of shifting dominance between cyanobacteria and green sulfur bacteria with the aggregate signature overprinted by heterotrophic reworking by SRB and methanogens. These observations highlight the impact of sedimentary microbial processes on δ¹³C_org signatures; these processes need to be considered when attempting to relate observed isotopic signatures in ancient sedimentary strata to conditions in the overlying water column at the time of deposition and associated inferences about carbon cycling.     

Energetics of chemolithoautotrophy in the hydrothermal system of Vulcano Island, southern Italy

The hydrothermal system at Vulcano, Aeolian Islands (Italy), is home to a wide variety of thermophilic, chemolithoautotrophic archaea and bacteria. As observed in laboratory growth studies, these organisms may use an array of terminal electron acceptors (TEAs), including O₂, , Fe(III), , elemental sulphur and CO₂; electron donors include H₂, , Fe²⁺, H₂S and CH₄. Concentrations of inorganic aqueous species and gases were measured in 10 hydrothermal fluids from seeps, wells and vents on Vulcano. These data were combined with standard Gibbs free energies () to calculate overall Gibbs free energies (ΔG_r) of 90 redox reactions that involve 16 inorganic N‐, S‐, C‐, Fe‐, H‐ and O‐bearing compounds. It is shown that oxidation reactions with O₂ as the TEA release significantly more energy (normalized per electron transferred) than most anaerobic oxidation reactions, but the energy yield is comparable or even higher for several reactions in which , or Fe(III) serves as the TEA. For example, the oxidation of CH₄ to CO₂ coupled to the reduction of Fe(III) in magnetite to Fe²⁺ releases between 94 and 123 kJ/mol e^?, depending on the site. By comparison, the aerobic oxidation of H₂ or reduced inorganic N‐, S‐, C‐ and Fe‐bearing compounds generally yields between 70 and 100 kJ/mol e^?. It is further shown that the energy yield from the reduction of elemental sulphur to H₂S is relatively low (8–19 kJ/mol e^?) despite being a very common metabolism among thermophiles. In addition, for many of the 90 reactions evaluated at each of the 10 sites, values of ΔG_r tend to cluster with differences < 20 kJ/mol e^?. However, large differences in ΔG_r (up to ～ 60 kJ/mol e^?) are observed in Fe redox reactions, due largely to considerable variations in Fe²⁺, H⁺ and H₂ concentrations. In fact, at the sites investigated, most variations in ΔG_r arise from differences in composition and not in temperature.     

基于宏基因组学重建来自深海热液喷口的Epsilonproteobacteria基因组及其代谢分析

【背景】非致病性Epsilonproteobacteria广泛存在于全球各种不同的自然环境中,特别是一些极端生境如深海热液喷口,并且经常在微生物群落中作为优势物种被发现。然而,由于现阶段培养技术的限制,仅有为数不多的深海热液Epsilonproteobacteria被分离培养,极大限制了对其生理特征、代谢方式以及生态功能的深入认识。【目的】研究深海热液未培养Epsilonproteobacteria的进化地位、代谢潜能及其在原位生态系统中可能发挥的作用。【方法】基于宏基因组学Binning的方法,从采集自东太平洋海隆深海热液烟囱体样本中构建4个高质量的Epsilonproteobacteria基因组Bin225、Bin51、Bin54和Bin189,并进行了系统发育和代谢途径的分析。【结果】Bin189在系统发育树上相对独立于其他所有已知的Epsilonproteobacteria类群,而其余3个重构基因组都与Nitratiruptor sp. SB155-2具有较近的亲缘关系。在代谢潜能方面,所有的基因组除了都含有sqr硫氧化和rTCA碳固定途径的基因以外,也同时具有脂多糖输出转运子和多种分泌系统。Bin189显示出与其它基因组显著不同的代谢特征,其中还检测到与有机物和氨基酸转运相关的功能基因。而其他的3个基因组均具有完整的反硝化途径的功能基因,其中2个还具有Sox系统、氢化酶和鞭毛移动系统。【结论】Bin189可能是一种新发现的深海热液兼性化能营养型Epsilonproteobacteria,推测其余的3个类群能够利用硫化物和氢气作为能源进行化能自养生长。考虑到它们多样的代谢潜能,这些Epsilonproteobacteria类群很可能在深海热液微生物群落的形成发展和地球化学元素循环中发挥重要作用。     

Desulfuromonas acetoxidans gen. nov. and sp. nov., a new anaerobic,sulfur-reducing,acetate-oxidizing bacterium

Anaerobic sea or fresh water media with acetate and elemental sulfur yielded enrichments of a new type of strictly anaerobic, rod-shaped, laterally flagellated, Gram-negative bacterium. Three pure culture-strains from different sulfide-containing sea water sources were characterized in detail and are described as a new genus and species Desulfuromonas acetoxidans.The new bacterium is unable to ferment organic substances; it obtains energy for growth by anaerobic sulfur respiration. Acetate, ethanol or propanol can serve as carbon and energy source for growth; their oxidation to CO₂ is stoichiometrically linked to the reduction of elemental sulfur to sulfide. Organic disulfide compounds, malate or fumarate are the only other electron acceptors used. Butanol and pyruvate are used in the presence of malate only; no other organic compounds are utilized. Biotin is required as a growth factor. The following dry weight yields per mole of substrate are obtained: in the presence of sulfur: 4.21 g on acetate, 9.77 g on ethanol; in the presence of malate: 16.5 g on acetate, 34.2 g on ethanol and 46.2 g on pyruvate. Accumulations of cells are pink; cell suspensions exhibit absorption spectra resembling those of c-type cytochromes (abs. max. at 419, 523 and 553 nm). Malate-ethanol grown cells contain a b-type cytochrome in addition.In the presence of acetate, ethanol or propanol, Desulfuromonas strains form robust growing syntrophic mixed cultures with phototrophic green sulfur bacteria.Dedicated to Prof. Roger Y. Stanier on the occasion of his 60th barthday     

A thermodynamic assessment of energy requirements for biomass synthesis by chemolithoautotrophic micro-organisms in oxic and anoxic environments

The flow of metabolic energy is arguably the most fundamental property governing ecosystem structure. In many microbial communities, particularly those that inhabit environments with little input of exogenous organic matter such as submarine hydrothermal systems and deep subsurface environments, chemolithoautotrophic organisms generate most of the organic matter available to support heterotrophic growth. In these environments, inorganic chemical reactions constitute the main source of energy input to the system, and the conversion of chemical energy to biomass by chemolithoautotrophs exerts a prominent control on the size, composition, and trophic structure of the biological community. A rigorous accounting of energy flow would aid in understanding the potential biological productivity of chemolithoautotrophic communities and help clarify the limits to habitability in geothermal and subsurface environments. In a step towards achieving a more complete accounting of energy flow in such communities, we present here computations to quantify the amount of thermodynamic energy required to synthesize the molecular components of biomass and to compare the relative energy requirements under oxic and anoxic conditions. The results suggest that only about 10% or less of the overall energy consumed during growth by chemolithoautotrophs is transformed directly into biomass. In addition, the results indicate aerobic organisms require approximately 17 kJ (g cells)⁻¹ more energy than anaerobes to synthesize the same biomass. This advantage may help explain why anaerobic organisms appear to yield greater biomass per unit energy input than aerobic organisms in laboratory growth studies, and why anaerobic micro-organisms can exist where the energy yield from catabolism is extremely low.