Chemoautotrophic Organisms Research Articles

Assessment of the Effect of Organic Matter on Rare Earth Elements and Yttrium Using the Zhijin Early Cambrian Phosphorite as an Example

The geochemistry of rare earth elements and yttrium (REY) in phosphorite has been widely studied. However, the effect of organic matter on REY enrichment has not been well determined. We utilized paired inorganic (δ13Ccarb) and organic (δ13Ccarb) carbon isotopes, total organic carbon (TOC), and REY content (∑REY) of the Zhijin Motianchong (MTC) phosphorite and compared them with those of Meishucun (MSC) phosphorite to reveal the effect of organic matter on REY. The δ13Ccarb of the MTC area (≈0‰) is heavier than that of the MSC area (−5.23‰ to −1.13‰), whereas δ13Corg is lighter (−33.85‰ to −26.34‰) in MTC than in MSC (−32.95‰ to −25.50‰). Decoupled δ13Ccarb and δ13Corg in MTC indicate the contribution of chemoautotrophic organisms or methanotrophic bacteria. Compared to the MSC phosphorite, the MTC phosphorite has higher ∑REY and TOC, and these parameters have a positive relationship. MTC phosphorite has REY patterns resembling those of contemporary organic matter. Furthermore, dolomite cement has a higher ∑REY than dolomite in the phosphorus-bearing dolostone. Additionally, pyrites are located on the surface of fluorapatite in the Zhijin phosphorites. It is reasonable to suggest that the REY was released into the pore water owing to the anaerobic oxidation of organic matter at the interface between seawater and sediment, resulting in the REY enrichment of Zhijin phosphorites.

Transcriptomic evidences for microbial carbon and nitrogen cycles in the deoxygenated seawaters of Bohai Sea

Eutrophication-induced water deoxygenation occurs continually in coastal oceans, and alters community structure, metabolic processes, and the energy shunt, resulting in a major threat to the ecological environment. Seasonal deoxygenation events have occurred in the Bohai Sea (China), however, how these affect the functional activity of microorganisms remains unclear. Here, through the use of absolute quantification of 16S rRNA genes amplicon sequencing and metatranscriptomics approaches, we investigated the structure of the microbial community and the patterns of transcriptional activity in deoxygenated seawaters. The dominant phyla were Proteobacteria (average value, 1.4 × 106 copies ml−1), Cyanobacteria (3.7 × 105 copies ml−1), Bacteroidetes (2.7 × 105 copies ml−1), and the ammonia-oxidizing archaea Thaumarchaeota (1.9 × 105 copies ml−1). Among the various environmental factors, dissolved oxygen, pH and temperature displayed the most significant correlation with microbial community composition and functional activity. Metatranscriptomic data showed high transcriptional activity of Thaumarchaeota in the deoxygenated waters, with a significant increase in the expression of core genes representing ammonia oxidation, ammonia transport, and carbon fixation (3-hydroxypropionic acid/4-hydroxybutyric acid cycle) pathways. The transcripts of Cyanobacteria involved in photosynthesis and carbon fixation (Calvin-Benson-Bassham cycle) significantly decreased in low oxygen waters. Meanwhile, the transcripts for the ribulose bisphosphate carboxylase-encoding gene shifted from being assigned to photoautotrophic to chemoautotrophic organisms in surface and bottom waters, respectively. Moreover, the transcription profile indicated that heterotrophs play a critical role in transforming low-molecular-weight dissolved organic nitrogen. Elevated abundances of transcripts related to microbial antioxidant activity corresponded to an enhanced aerobic metabolism of Thaumarchaeota in the low oxygen seawater. In general, our transcriptional evidences showed a population increase of Thaumarchaeota, especially the coastal ecotype of ammonia oxidizers, in low oxygen aquatic environments, and indicated an enhanced contribution of chemolithoautotrophic carbon fixation to carbon flow.

Coeval Drying Across the Central Tropical Pacific Over the Last Millennium

AbstractHydroclimatic variability in the tropical Pacific reflects large‐scale ocean‐atmosphere processes that imprint on global climate, but tropical Pacific hydroclimate variability over the last millennium remains uncertain. Here we present a multi‐proxy reconstruction from a lacustrine sediment record on Kiritimati Atoll that spans the last millennium. A lake salinity reconstruction from the δ2H values of total lipid extracts, combined with changes in sediment mineralogy and the stable isotopic composition of inorganic carbonates, indicate the presence of several distinct hydrologic regimes on Kiritimati, including a period of persistent aridity from 960–1030 CE, shorter episodes of aridity from 1030–1370 CE, and extreme aridity throughout the latter half of the last millennium, from 1370–1970 CE, that drove complete evaporation of the lake. A period of wetter, variable conditions defines recent decades. Compound‐specific lipid biomarker δ2H values indicate that shifts in microbial community structure occurred in the past, from a community dominated by photoautotrophic and chemoautotrophic organisms in more arid periods to a more metabolically diverse community in the recent period. Comparison of this record with nearby sediment records from Washington Island reveals a similar pattern of aridity through the last millennium, followed by wetter conditions in the modern period. These coherent changes in hydroclimate in the central Pacific are inconsistent with a migration of the Pacific Intertropical Convergence Zone within these latitudes. Rather, past aridity was caused by reduced El Niño‐Southern Oscillation variability, observed through the low‐pass filter of lacustrine records, or by multidecadal to multi‐century strengthening of the Pacific Walker Circulation.

Geochemical and sedimentary facies study – Implication for driving mechanisms of organic matter enrichment in the lower Silurian fine-grained mudstones in the Baltic Basin (W Lithuania)

More than 100 m-long core sections from Western Lithuania (Baltic Basin), presenting an almost continuous lower Silurian fine-grained siliciclastic organic matter-rich sedimentary record from Aeronian to Homerian, were investigated to evaluate the main forces governing the organic matter enrichment. The methods applied include organic and inorganic geochemistry, organic petrology, sedimentological and petrographic studies along with framboidal pyrite analysis, as well as analysis of stable nitrogen and organic carbon isotopes. The petrographic observations showed distinct mudstone diversity reflecting a variety of paleoenvironmental depositional conditions evolving against a backdrop of post-Ordovician climate, thus, sea level variations, and progressing development of foreland basin throughout the early Silurian. Reflectance measurements on vitrinite-like particles, supported by molecular organic geochemical and Rock-Eval data prove that kerogen from the studied section reached the oil window maturity stage. Rock-Eval pyrolysis, organic geochemical and petrographical as well as δ13Corg data clearly confirm the marine origin of the organic matter. Various geochemical proxies and sedimentary features indicate that in Aeronian a period of more humid climate favored enhanced nutrient input, which in turn intensified organic matter productivity resulting in large amounts of organic matter accumulation. Redox proxies (TOC/TS ratio, trace elements enrichment, molecular organic geochemical indices, framboidal pyrite analysis, TOC/P ratio) demonstrate a rather broad spectrum of bottom water oxygenation levels in the lower Silurian sediments accumulated under oxic - dysoxic – anoxic conditions interrupted by several episodes of euxinia. A highly condensed section of Aeronian black-grey mudstones manifests a very good organic matter preservation under sediment-starved and oxygen-depleted settings. Here, the oxygen-depleted water bottom conditions are well evidenced by low values of δ15N and δ13Corg pointing to the presence of diazotrophic N-fixing and chemoautotrophic organisms. The Sheinwoodian-Homerian section of monotonous grey calcareous mudstones evenly and moderately enriched in organic matter reflects the most steady environmental settings developed under more arid climate in comparison to Llandovery. Throughout the early Silurian sedimentation rates were overall low, although probably enhanced in Wenlock, and played a role in organic matter preservation. It was a critical factor during sedimentation of grey-greenish mudstone of the Telychian characterized by comparatively the lowest organic matter preservation efficiency. Variations in the intensity of the pycnocline, thus organic matter preservation, were probably controlled by climate-triggered sea level changes, although tectonically-driven paleoenvironmantal effects, bathymetry, and, at some point, intensified paleoproductivity inducing oxygen-restricted conditions, were likely contributing. Although MoEF/UEF ratios mainly indicate fully open marine settings during the entire early Silurian, Mo–TOC covariation clearly displays strict basinal restriction in the Aeronian. The profile of δ13Corg demonstrates six carbon isotope excursions along the lower Silurian section. The identified Late Aeronian and Early Sheinwoodian Carbon Isotope Excursions are linked to global sea-level changes, thus, changes in oceanic water circulation pattern. A high percentage of tiny pyrite framboids within the interval of Early Sheinwoodian CIE could reflect an increased pyrite burial under highly reducing conditions and might be associated with an Oceanic Anoxic Event. The three positive δ13Corg excursions within the Telychian seem to be related to an early diagenetic partial oxidation of organic matter.

Intense but variable autotrophic activity in a rapidly flushed shallow-water hydrothermal plume (Kueishantao Islet, Taiwan).

Shallow-water hydrothermal plumes concomitantly host both photosynthetic and chemoautotrophic organisms in a single biotope. Yet, rate measurements to quantify the contributions of different autotrophic activity types are scarce. Herein, we measured the light and dark dissolved inorganic carbon (DIC) uptake rates in the plume water of the Kueishantao hydrothermal field using the 13 C-labeling approach. Seventy percent of the plume-water samples had chemoautotrophy as the dominant mode of carbon fixation, with the dark DIC uptake rates (up to 18.6mg C/m3 /h) within the range of the primary production in productive inner-shelf waters. When considered alongside the geochemical and microbiological observations, the rate data reveal the distribution of different trophic activities in the hydrothermal plume. The autotrophic activity at the initial phase of plume dispersal is low. This is explained by the short response time the chemoautotrophs have to the stimulation from vent-fluid discharge, and the harmful effects of hydrothermal substances on phytoplankton. As plume dispersal and mixing continue, chemoautotrophic activities begin to rise and peak in waters that have low-to-moderate Si(OH)4 content. Toward the plume margin, chemoautotrophy declines to background levels, whereas photosynthesis by phytoplankton regains importance. Our results also provide preliminary indication to the loci of enhanced heterotrophy in the plume. Results of artificial mixing experiments suggest that previously formed plume water is the primary source of microbial inoculum for new plume water. This self-inoculation mechanism, in combination with the intense DIC uptake, helps to sustain a distinct planktonic autotrophic community in this rapidly flushed hydrothermal plume.

A process economic assessment of hydrocarbon biofuels production using chemoautotrophic organisms

Economic analysis of an ARPA-e Electrofuels (http://arpa-e.energy.gov/?q=arpa-e-programs/electrofuels) process is presented, utilizing metabolically engineered Rhodobacter capsulatus or Ralstonia eutropha to produce the C30+ hydrocarbon fuel, botryococcene, from hydrogen, carbon dioxide, and oxygen. The analysis is based on an Aspen plus® bioreactor model taking into account experimentally determined Rba. capsulatus and Rls. eutropha growth and maintenance requirements, reactor residence time, correlations for gas–liquid mass-transfer coefficient, gas composition, and specific cellular fuel productivity. Based on reactor simulation results encompassing technically relevant parameter ranges, the capital and operating costs of the process were estimated for 5000 bbl-fuel/day plant and used to predict fuel cost. Under the assumptions used in this analysis and crude oil prices, the Levelized Cost of Electricity (LCOE) required for economic feasibility must be less than 2¢/kWh. While not feasible under current market prices and costs, this work identifies key variables impacting process cost and discusses potential alternative paths toward economic feasibility.

Methane-carbon flow into the benthic food web at cold seeps--a case study from the Costa Rica subduction zone.

Cold seep ecosystems can support enormous biomasses of free-living and symbiotic chemoautotrophic organisms that get their energy from the oxidation of methane or sulfide. Most of this biomass derives from animals that are associated with bacterial symbionts, which are able to metabolize the chemical resources provided by the seeping fluids. Often these systems also harbor dense accumulations of non-symbiotic megafauna, which can be relevant in exporting chemosynthetically fixed carbon from seeps to the surrounding deep sea. Here we investigated the carbon sources of lithodid crabs (Paralomis sp.) feeding on thiotrophic bacterial mats at an active mud volcano at the Costa Rica subduction zone. To evaluate the dietary carbon source of the crabs, we compared the microbial community in stomach contents with surface sediments covered by microbial mats. The stomach content analyses revealed a dominance of epsilonproteobacterial 16S rRNA gene sequences related to the free-living and epibiotic sulfur oxidiser Sulfurovum sp. We also found Sulfurovum sp. as well as members of the genera Arcobacter and Sulfurimonas in mat-covered surface sediments where Epsilonproteobacteria were highly abundant constituting 10% of total cells. Furthermore, we detected substantial amounts of bacterial fatty acids such as i-C15∶0 and C17∶1ω6c with stable carbon isotope compositions as low as −53‰ in the stomach and muscle tissue. These results indicate that the white microbial mats at Mound 12 are comprised of Epsilonproteobacteria and that microbial mat-derived carbon provides an important contribution to the crab's nutrition. In addition, our lipid analyses also suggest that the crabs feed on other 13C-depleted organic matter sources, possibly symbiotic megafauna as well as on photosynthetic carbon sources such as sedimentary detritus.

Semiconducting Mineral Photocatalytic Regeneration of Fe2+ Promotes Carbon Dioxide Acquisition by Acidithiobacillus ferrooxidans

Abstract:Chemoautotrophic organisms have once been excluded from the development of universally applicable CO2 fixation technology due to its low production yields of biomass. In this study, we used Acidithiobacillus ferrooxidans (A.f.) as a model chemoautotrophic microorganism to test the hypothesis that exogenetic photoelectrons from semiconducting mineral photocatalysis can enable the regeneration of Fe2+ that could be then used by A.f. and support its growth. In a simulated electrochemical system, where exogenetic electrons were provided by an electrochemical approach, an accelerated growth rate of A.f. was observed as compared with that in traditional batch cultivation. In a coupled system, where light‐irradiated natural rutile provided the primary electron source to feed A.f., the bacterial growth rate as well as the subsequent CO2 fixation rate was demonstrated to be in a light‐dependent manner. The sustaining flow of photogenerated electrons from semiconducting mineral to bacteria provided an inexhaustible electron source for chemoautotrophic bacteria growth and CO2 fixation. This finding might contribute to the development of novel effective CO2 fixation technology.

Compensation phenomena found in Acidithiobacillus ferrooxidans after starvation stress

Acidithiobacillus ferrooxidans showed the compensate growth and oxidation after re-feeding with sufficient ferrous materials after starvation. Compensatory phenomena were first detected in chemoautotrophic organisms. Starvation stress of Acidithiobacillus ferrooxidans was achieved via culturing in low concentrations of iron. During compensation, growth and ferrous oxidation took place faster than in controls. In addition, some genes related to ferrous oxidation (such as rus) and carbon assimilation (cbbR, csoS3) were expressed in different patterns in the low energy environments. Their expression patterns can account for this increased growth and oxidation. Other groups of genes (cspAB, feoAB, fur) were suppressed in response to starvation stress. The presence of pyrite and joint cold stress can render compensation nearly undetectable. This may be why the compensation phenomena observed under these conditions was not the same as that observed under single starvation stress conditions. Gene expression reflected a possible mechanism of tolerance to starvation in Acidithiobacillus ferrooxidans, which would allow the organism to adapt and survive in ferrous-limited environments.

The arsenic for phosphorus swap is accidental, rather than a facultative one, and the question whether arsenic is nonessential or toxic is quantitative, not a qualitative one

Arsenic shares many physicochemical properties with phosphorus, so that arsenic can be taken up inadvertently by cells through the pathways for phosphorus. As a phosphate analog, arsenate competes with phosphate and enters cells via phosphate transporters. In the cell, arsenate can be recognized as a substrate by enzymes that usually use phosphate as a substrate. The phosphate for arsenate swap results in wasteful ‘futile cycles’ in metabolic pathways, uncoupled oxidative phosphorylation and extreme DNA instability. The disrupting metabolic effects of arsenic have an evolutionary meaning, so that all living organisms—from chemoautotrophic organisms that grow by reducing or oxidizing arsenic to metazoan—carry highly conserved arsenic resistance genes. Arsenic resistance can result from different strategies including selective transport to maximize phosphate uptake and minimize entry of arsenate, active transport to export arsenate, arsenic storage in specialized compartments, enzyme selectivity toward phosphate, and increased efficiency of DNA repair systems. None of these strategies is infallible, though, and susceptibility to arsenic toxicity varies between taxa in many orders of magnitude. Even arsenic-hypertolerant organisms will stop to grow and will eventually die when exposed to arsenic over species-specific resistance limits. The arsenic for phosphorus swap is an accidental one, it does not warrant a conclusion in favor of the essentiality of arsenic to life as we know it.

The Biological Deep Sea Hydrothermal Vent as a Model to Study Carbon Dioxide Capturing Enzymes

Deep sea hydrothermal vents are located along the mid-ocean ridge system, near volcanically active areas, where tectonic plates are moving away from each other. Sea water penetrates the fissures of the volcanic bed and is heated by magma. This heated sea water rises to the surface dissolving large amounts of minerals which provide a source of energy and nutrients to chemoautotrophic organisms. Although this environment is characterized by extreme conditions (high temperature, high pressure, chemical toxicity, acidic pH and absence of photosynthesis) a diversity of microorganisms and many animal species are specially adapted to this hostile environment. These organisms have developed a very efficient metabolism for the assimilation of inorganic CO2 from the external environment. In order to develop technology for the capture of carbon dioxide to reduce greenhouse gases in the atmosphere, enzymes involved in CO2 fixation and assimilation might be very useful. This review describes some current research concerning CO2 fixation and assimilation in the deep sea environment and possible biotechnological application of enzymes for carbon dioxide capture.

Anaerobic methane oxidation by archaea/sulfate-reducing bacteria aggregates: 2. Isotopic constraints

Recent studies employing novel analytical tools provide detailed, microscopic portraits of archaea/sulfate-reducing bacteria aggregates in sediments from methane seep and vent sites. One of the most striking features of these aggregates is that lipid and cell carbon are highly depleted in ¹³C (δ¹³C < −60‰). Biogenic methane, with δ¹³C values of −50 to −110 permil, is a logical candidate for carbon source of these aggregates. Accordingly, it is widely assumed that the archaea oxidize and assimilate methane, and that methane-derived carbon is transferred to the sulfate-reducing bacteria (SRB) symbionts as CO₂ or as a partially oxidized intermediate. However, methane is not the only possible source of ¹³C-depleted carbon in archaea/SRB aggregates. ΣCO₂ in sediments at seep and vent sites tends to be isotopically “light” due to decomposition of organic matter derived from chemoautotrophic organisms. In addition, CO₂ is depleted in ¹³C by ∼10 permil compared to ΣCO₂ owing to the equilibrium isotope effect. Assimilation of this “light” CO₂ by methanogenic archaea and autotrophic SRB, combined with enzymatic isotope effects, could also yield lipid and biomass that are highly depleted in ¹³C. We derive general equations based on isotope mass-balance and calibrated with laboratory and field data to predict the isotopic composition of archaeal cell carbon and lipids derived from autotrophic methanogenesis and anaerobic methane oxidation. The calculations show that observed δ¹³C values for archaeal biomass and lipids at methane seep and vent sites are readily accounted for by isotope fractionation during methane production from CO₂, and that biomass produced during anaerobic methane oxidation is only slightly depleted in ¹³C relative to methane unless the enzymatic isotope effect associated with the anabolic arm of the assimilation-dissimilation branch point is considerably larger than the isotope effect associated with the catabolic arm. We also apply an isotope diffusion-reaction model to demonstrate that micro-gradients in δ¹³C-CO₂ cannot be maintained within archaea/SRB aggregates. However, ¹³C-depleted carbon in SRB members of the aggregate is readily explained by autotrophic sulfate-reduction with bulk porewater CO₂ as carbon source. These results illustrate that ¹³C-depleted biomass and lipids observed in sediments from methane seep and vent sites may be derived from CO₂-reducing archaea and autotrophic sulfate-reducing bacteria. The inference of anaerobic methanotrophy based on ¹³C depletion in archaeal and sulfate-reducing bacterial cell carbon and/or lipids should be considered tentative unless corroborated by independent, concordant evidence of net methane consumption.

Formation of Zn- and Fe-sulfides near hydrothermal vents at the Eastern Lau Spreading Center: implications for sulfide bioavailability to chemoautotrophs

BackgroundThe speciation of dissolved sulfide in the water immediately surrounding deep-ocean hydrothermal vents is critical to chemoautotrophic organisms that are the primary producers of these ecosystems. The objective of this research was to identify the role of Zn and Fe for controlling the speciation of sulfide in the hydrothermal vent fields at the Eastern Lau Spreading Center (ELSC) in the southern Pacific Ocean. Compared to other well-studied hydrothermal systems in the Pacific, the ELSC is notable for unique ridge characteristics and gradients over short distances along the north-south ridge axis.ResultsIn June 2005, diffuse-flow (< 50°C) and high-temperature (> 250°C) vent fluids were collected from four field sites along the ELSC ridge axis. Total and filtered Zn and Fe concentrations were quantified in the vent fluid samples using voltammetric and spectrometric analyses. The results indicated north-to-south variability in vent fluid composition. In the high temperature vent fluids, the ratio of total Fe to total Zn varied from 39 at Kilo Moana, the most northern site, to less than 7 at the other three sites. The concentrations of total Zn, Fe, and acid-volatile sulfide indicated that oversaturation and precipitation of sphalerite (ZnS(s)) and pyrite (FeS2(s)) were possible during cooling of the vent fluids as they mixed with the surrounding seawater. In contrast, most samples were undersaturated with respect to mackinawite (FeS(s)). The reactivity of Zn(II) in the filtered samples was tested by adding Cu(II) to the samples to induce metal-exchange reactions. In a portion of the samples, the concentration of labile Zn2+ increased after the addition of Cu(II), indicating the presence of strongly-bound Zn(II) species such as ZnS clusters and nanoparticles.ConclusionResults of this study suggest that Zn is important to sulfide speciation at ELSC vent habitats, particularly at the southern sites where Zn concentrations increase relative to Fe. As the hydrothermal fluids mix with the ambient seawater, Zn-sulfide clusters and nanoparticles are likely preventing sulfide oxidation by O2 and reducing bioavailability of S(-II) to organisms.

Thermodynamics of life on the planetary scale

The generation of organic matter from CO2 and H2O is a highly endothermic reaction. Energy for biological carbon fixation can be derived from chemical potential gradients in the environment by chemoautotrophic organisms or it can be harvested from photon energy by photosynthesis. On Earth, the plate tectonically driven carbon flux through the surface environment is of such a magnitude that the chemical free energy production within the Earth is insufficient to support conversion of any significant fraction of the carbon to organic matter through chemoautotrophy. Therefore, the chemical and isotopic fingerprints we observe in the Earth's surface environments are based on the invention of photosynthesis by life. We cannot a priori assume that life on any planet will invent photosynthesis and remote life detection should thus not be based exclusively on the expectations from our own ecosystem.

Bicarbonate uptake by marine Crenarchaeota

Biphytanyl membrane lipids and 16S rRNA sequences derived from marine Crenarchaeota were detected in shallow North Sea surface water in February 2002. To investigate the carbon fixation mechanism of these uncultivated archaea in situ 13C bicarbonate tracer experiments were performed with this water in the absence of light. About 70% of the detected 13C incorporation into lipids (including fatty acids and sterols) is accounted for by the crenarchaeotal biphytanyl membrane lipids. This finding indicates that marine Crenarchaeota can utilize bicarbonate or CO 2 derived thereof in the absence of light and are chemoautotrophic organisms.

西オーストラリア，ノースポール地域に産する熱水性岩脈中ケロジェンの炭素同位体組成 ３５億年前の海底下熱水系における生物圏

Abundant organic matter (kerogen) was identified in 3.5 Ga hydrothermal silica dikes from the North Pole area in the Pilbara craton, Western Australia. The silica dikes developed in the uppermost 1000 m of the ancient oceanic crust. Thus, they would have been deposited in the 3.5 Ga sub-seafloor hydrothermal system. The carbon and nitrogen isotopic compositions of the kerogen were analyzed in this study. Their highly 13C-depleted isotopic compositions (δ13C=-38 to-33%0) strongly suggest that they are originally derived from biologically produced organic matter. The remarkable similarity of the δ13C values between the kerogen and modern hydrothermal vent organisms may suggest that the kerogen was derived from chemoautotrophic organisms. This idea is also consistent with their nitrogen isotopic compositions (δ15N =-4 to + 4‰). The silica dikes consist mainly of fine-grained silica with minor pyrite and sphalerite. These mineral assemblages indicate that the silica dike was deposited from relatively low-temperature (probably less than 150 °C) reducing hydrothermal fluid. Thus, anaerobic thermophilic/hyperthermophilic organisms could have survived in the hydrothermal fluid, which formed the silica dikes. Therefore, it is plausible that a chemoautotrophic-based biosphere (possibly methanogenesis) probably existed in the Early Archean sub-seafloor hydrothermal system.

Phylogenetic relationships of the filamentous sulfur bacterium Thiothrix ramosa based on 16S rRNA sequence analysis.

The phylogeny of Thiothrix ramosa based on 16S rRNA sequences was determined. This species is the first species in this genus that has been shown to be capable of autotrophic growth with reduced sulfur compounds as sole energy sources. T. ramosa forms a monophyletic clade with Thiothrix nivea, as determined by distance, parsimony, and maximum-likelihood methods. Both of these species clearly belong to the gamma subdivision of the Proteobacteria, where they are loosely associated with other sulfur-oxidizing chemoautotrophic organisms.

Microbiological factor in acid mine drainage formation II. Further observations from a pilot plant study

Pilot plant studies examined the effect of chemoautotrophic organisms ( Ferrobacillus ferrooxidans, Ferrobacillus sulfooxidans and Thiobacillus thiooxidans) in the formation of acid mine drainage from pyritic mineral associated with coal mining. Discharges were measured for varying hydraulic flow-rates, air or nitrogen atmosphere and biological seeding or non-seeding. Under non-aerobic conditions, Fe(II) and S 2su−II mas release is constant and unaffected by organisms. Under aerobic conditions, acidity, ferrous and total iron and sulfate concentrations are zero order with respect to flow expressed in reciprocal time units, and much greater than under non-aerobic conditions. Total acidity is lower for seeded than for non-seeded aerobic conditions at higher retention times because microorganisms consume acid. Aerobic non-seeded release reaches a maximum that does not change with increasing flow. Aerobic seeded release reaches a maximum greater than that for aerobic non-seeded conditions but then decreases with increased flow. A dynamic equilibrium between pyrite dissolution and organism regeneration and flushout exists.

The biochemistry of nitrifying microorganisms.

SUMMARY Biological nitrification is mediated primarily by two genera of bacteria, Nitrosomonas and its marine form Nitrosocystis, oxidizing ammonia to nitrite, and Nitrobacter, converting nitrite into nitrate. These are chemoautotrophic organisms since they usually derive their energy for growth by oxidizing these inorganic nitrogen compounds and their carbon from carbon dioxide, carbonates or bicarbonates. The morphology and structure of these Gram‐negative bacteria studied by electron microscopy show numerous intracellular membranes reminiscent of those in photosynthetic bacteria and blue‐green algae. These structures may therefore be associated with the production of ATP. The bacteria are difficult to grow in pure cultures in sufficient amounts for biochemical work since their generation time is around 10 hr. and the yields are only about one hundredth of those obtained with heterotrophic bacteria. Thus in continuous cultures great care must be taken to avoid ‘wash‐out’ of the cells. Since Nitrosomonas and Nitrosocystis produce copious amounts of nitrous acid, which would eventually retard growth, pH stat units are used to titrate the cultures continuously with a solution of sodium carbonate, to hold the pH around 7–8. The respiratory chain which is associated with cell membranes, contains flavin, quinones and many cytochromes linking to oxygen as a terminal acceptor. In Nitro‐somonas‐Nitrosocytis hydroxylamine is oxidized by the electron transfer chain and in Nitrobacter nitrous acid is utilized. The ammonia‐oxidizing system, which in Nitrosomonas probably resides near the cell surface, does not appear to survive cell breakage. During the oxidation of hydroxylamine and nitrous acid by the respiratory chains, a phosphorylation occurs but the P/O ratios around 0–30 are low. There is little energy reserve material in the cells, possibly β‐hydroxybutyrate and some metaphosphates and as soon as the oxidative processes are impaired the cells cease dividing. Chemoautotrophic bacteria have a novel way of producing reduced nicotinamide adenine dinucleotide (NADH). This involves a reversal of electron flow from reduced cytochrome c to nicotinamide adenine dinucleotide (NAD) that is energy‐dependent, thus requiring adenosine triphosphate. Reductase enzymes, nitrate, nitrite and hydroxylamine reductases in Nitrobacter and nitrite and hydroxylamine reductases in Nitrosomonas, have been described. They appear to be readily extracted in soluble form and are probably assimilatory enzymes since 16N labelled nitrate, nitrite and hydroxylamine respectively in Nitrobacter and the last two in Nitrosomonas are readily incorporated into cell nitrogen. It has been suggested that a particulate nitrate reductase in Nitrobacter is coupled to the synthesis of adenosine triphosphate but adequate experimental evidence for this concept has not been produced. Some recent observations with Nitrobacter suggest that it grows on acetate, deriving all its energy and carbon skeletons from this source but the mean generation time for the bacterium is unchanged. Under these conditions the carbon dioxide fixing enzymes of the pentose pathway are suppressed. This then is a case of facultative chemoautotrophy but there is no increase in the biosynthesis of the TCA enzymes. Whether this is a widespread phenomenon in other chemoautotrophic bacteria remains to be established. If this does prove to be the case it would aid their survival in a variety of habitats and extend their distribution in soils and seas. The carbon dioxide fixing enzymes of the pentose pathway are found in the soluble parts of the cells. The major route is via the carboxydismutase system with only a small incorporation via the phosphoenolpyruvate carboxylase enzyme. Enzymes of the tricarboxylic acid cycle have low activities compared with those in heterotrophs and this overall slow metabolism, rather than the lack of a specific enzyme such as NADH oxidase, may well account for the slow growth of these bacteria. Although there is very active glutamic dehydrogenase in Nitrosomonas that utilizes ammonia, the enzyme has a very small activity in Nitrobacter. This poses a problem of the route of incorporation of nitrite nitrogen into cell nitrogen in the latter bacterium. A few heterotrophic fungi have been described which oxidize ammonia to nitrate but their activity is small compared with that of the nitrifying bacteria. It is concluded that the nitrifying bacteria which have many novel biochemical features not met with in other organisms merit further study.