Bicarbonate Assimilation Research Articles

Primary producing prokaryotic communities of brine, interface and seawater above the halocline of deep anoxic lake L'Atalante, Eastern Mediterranean Sea

Meso- and bathypelagic ecosystems represent the most common marine ecological niche on Earth and contain complex communities of microorganisms that are for the most part ecophysiologically poorly characterized. Gradients of physico-chemical factors (for example, depth-related gradients of light, temperature, salinity, nutrients and pressure) constitute major forces shaping ecosystems at activity 'hot spots' on the ocean floor, such as hydrothermal vents, cold seepages and mud volcanoes and hypersaline lakes, though the relationships between community composition, activities and environmental parameters remain largely elusive. We report here results of a detailed study of primary producing microbial communities in the deep Eastern Mediterranean Sea. The brine column of the deep anoxic hypersaline brine lake, L'Atalante, the overlying water column and the brine-seawater interface, were characterized physico- and geochemically, and microbiologically, in terms of their microbial community compositions, functional gene distributions and [(14)C]bicarbonate assimilation activities. The depth distribution of genes encoding the crenarchaeal ammonia monooxygenase alpha subunit (amoA), and the bacterial ribulose-1,5-biphosphate carboxylase/oxygenase large subunit (RuBisCO), was found to coincide with two different types of chemoautotrophy. Meso- and bathypelagic microbial communities were enriched in ammonia-oxidizing Crenarchaeota, whereas the autotrophic community at the oxic/anoxic interface of L'Atalante lake was dominated by Epsilonproteobacteria and sulfur-oxidizing Gammaproteobacteria. These autotrophic microbes are thus the basis of the food webs populating these deep-sea ecosystems.

A proposed citramalate cycle for acetate assimilation in the purple non-sulfur bacterium Rhodospirillum rubrum

During phototrophic growth on acetate and CO2Rhodospirillum rubrum 2R contained malate synthase but lacked isocitrate lyase. Acetate assimilation by R. rubrum cells was stimulated by pyruvate, propionate glyoxylate, CO2 and H2. Acetate photoassimilation by R. rubrum cells in the presence of bicarbonate was accompanied by glyoxylate secretion, which increased after addition of fluoroacetate and decreased after addition of malonate. When acetyl-CoA was incubated with pyruvate in cell-free extracts, citramalate was formed. Citramalate was also formed from propionyl-CoA and glyoxylate. The existence in R. rubrum of a CO2-dependent cyclic pathway of acetate oxidation to glyoxylate with citramalate as an intermediate is proposed. Inhibitor analysis of acetate and bicarbonate assimilation indicated that pyruvate synthase is not involved in acetate assimilation in R. rubrum. The possible anaplerotic sequences employed by R. rubrum during phototrophic growth on acetate are discussed.

Temperature characteristics of bacterial iron solubilisation and 14C assimilation in naturally exposed sulfide ore material at Citronen Fjord, North Greenland (83°N)

The presence of iron-solubilising bacteria in the weathered, naturally exposed part of a large sulfide ore deposit (gossan) in the High Arctic (eastern North Greenland, 83°N) was demonstrated. Microscopic examination of ore material and enrichment cultures in minimal medium containing FeS2 or Fe2+ as sole inorganic electron donors revealed the presence of rod-shaped Thiobacillus-like bacteria. When glucose was added as a supplementary energy source to the same enrichment medium, growth of spherical or filamentous acidophilic heterotrophs was observed. Growth kinetics and iron solubilisation activity of acidophilic autotrophs and heterotrophs, respectively, in samples of gossan material were investigated in the temperature range between 0 and 32.5°C. Assimilation of 14C-labelled bicarbonate and glucose occurred at low temperatures (down to 0°C) in both types of enrichments but was optimal around 21°C. It is noteworthy that the rate of dissolved iron (DI=Fe2++Fe3+) production from ore material at 0°C constituted as much as 30% of the maximal value at 21°C. The bacteria involved thus exhibited iron-dissolving activity at the lowest temperature ever reported. An activation energy for DI production of 56 kJ mol−1 K−1 was calculated in the temperature interval from 0 to 17°C. The corresponding H14CO−3 incorporation into biomass at 0°C only amounted to about 5% of the incorporation measured at 21°C. Rates of production were reduced by approximately 25% in incubations amended with glucose as compared to incubations solely containing inorganic compounds. These results indicate that autotrophic bacteria were involved in the solubilisation of iron from the gossan samples.

Vertical and temporal shifts in microbial communities in the water column and sediment of saline meromictic Lake Kaiike (Japan), as determined by a 16S rDNA‐based analysis, and related to physicochemical gradients

The vertical and temporal changes in microbial communities were investigated throughout the water column and sediment of the saline meromictic Lake Kaiike by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Marked depth-related changes in microbial communities were observed at the chemocline and the sediment-water interface. However, no major temporal changes in the microbial community below the chemocline were observed during the sampling period, suggesting that the ecosystem in the anoxic zone of Lake Kaiike was nearly stable. Although the sequence of the most conspicuous DGGE band throughout the anoxic water and in the top of the microbial mat was most similar to that of an anoxic, photosynthetic, green sulphur bacterium, Pelodyction luteolum DSM273 (97% similarity), it represented a new phylotype. A comparison of DGGE banding patterns of the water column and sediment samples demonstrated that specific bacteria accumulated on the bottom from the anoxic water layers, and that indigenous microbial populations were present in the sediment. The measurements of bicarbonate assimilation rates showed significant phototrophic assimilation in the chemocline and lithoautotrophic assimilation throughout the anoxic water, but were not clearly linked with net sulphide turnover rates, indicating that sulphur and carbon metabolisms were not directly correlated.

A proposed citramalate cycle for acetate assimilation in the purple non-sulfur bacterium Rhodospirillum rubrum

During phototrophic growth on acetate and CO 2 Rhodospirillum rubrum 2R contained malate synthase but lacked isocitrate lyase. Acetate assimilation by R. rubrum cells was stimulated by pyruvate, propionate glyoxylate, CO 2 and H 2. Acetate photoassimilation by R. rubrum cells in the presence of bicarbonate was accompanied by glyoxylate secretion, which increased after addition of fluoroacetate and decreased after addition of malonate. When acetyl-CoA was incubated with pyruvate in cell-free extracts, citramalate was formed. Citramalate was also formed from propionyl-CoA and glyoxylate. The existence in R. rubrum of a CO 2-dependent cyclic pathway of acetate oxidation to glyoxylate with citramalate as an intermediate is proposed. Inhibitor analysis of acetate and bicarbonate assimilation indicated that pyruvate synthase is not involved in acetate assimilation in R. rubrum. The possible anaplerotic sequences employed by R. rubrum during phototrophic growth on acetate are discussed.

Temperature characteristics of bacterial iron solubilisation and 14C assimilation in naturally exposed sulfide ore material at Citronen Fjord, North Greenland (83°N)

The presence of iron-solubilising bacteria in the weathered, naturally exposed part of a large sulfide ore deposit (gossan) in the High Arctic (eastern North Greenland, 83°N) was demonstrated. Microscopic examination of ore material and enrichment cultures in minimal medium containing FeS 2 or Fe 2+ as sole inorganic electron donors revealed the presence of rod-shaped Thiobacillus-like bacteria. When glucose was added as a supplementary energy source to the same enrichment medium, growth of spherical or filamentous acidophilic heterotrophs was observed. Growth kinetics and iron solubilisation activity of acidophilic autotrophs and heterotrophs, respectively, in samples of gossan material were investigated in the temperature range between 0 and 32.5°C. Assimilation of 14C-labelled bicarbonate and glucose occurred at low temperatures (down to 0°C) in both types of enrichments but was optimal around 21°C. It is noteworthy that the rate of dissolved iron (DI=Fe 2++Fe 3+) production from ore material at 0°C constituted as much as 30% of the maximal value at 21°C. The bacteria involved thus exhibited iron-dissolving activity at the lowest temperature ever reported. An activation energy for DI production of 56 kJ mol −1 K −1 was calculated in the temperature interval from 0 to 17°C. The corresponding H 14CO − 3 incorporation into biomass at 0°C only amounted to about 5% of the incorporation measured at 21°C. Rates of production were reduced by approximately 25% in incubations amended with glucose as compared to incubations solely containing inorganic compounds. These results indicate that autotrophic bacteria were involved in the solubilisation of iron from the gossan samples.

Seasonal variation of nitrification along a salinity gradient in an urban estuary

The rates of water column nitrification measured as nitrapyrin-sensitive rates of bicarbonate assimilation were monitoredalong the salinity gradient of the estuary of the RiverNervion (Bay of Biscay) from January to November 1993.Highest nitrapyrin-sensitive rates of bicarbonate assimilationwere found in the deep layer at stations located in the innerestuary during summer and autumn, coinciding with dissolvedoxygen concentrations generally lower than 1 mg O2 l−1. Possible explanation for this spatial distributionpattern are discussed. Axial and depth distribution of ammonia,nitrite and nitrate suggests that in the deep layer of theinner zone of the estuary nitrification and nitrate and nitritereduction are occurring concurrently. Nitrification showed asignificant positive correlation with temperature, but thiscorrelation was not very strong. It is argued that the wash outof nitrifying bacteria by rainfalls also plays a role in theseasonal variation of nitrification rates.

Chemical and isotopic composition of karstic lakes in Jamaica, West Indies

Lakes in the limestone region of Jamaica exhibit a range of chemical characteristics that reflect varying inputs from precipitation, surface runoff and groundwater, together with the subsequent evolution of the water within the limnic environment. Detailed spatial and temporal sampling was conducted on one lake, Wallywash Great Pond. Chemical data, together with D/H, 18O/16O, 13C/12C and 87Sr/86Sr ratios confirm that the karstic spring waters entering the lake evolve chemically through degassing, mixing with rainfall and runoff, biogenic decalcification (resulting mainly from bicarbonate assimilation by the high biomass of submerged macrophytes), and evaporation. Modern carbonate sedimentation in Wallywash Great Pond is largely of high-Mg calcite. This is consistent with Mg/Ca molar ratios >2 within much of the lake. However, aragonite forms on the adaxial leaf surfaces of Potamogeton spp. This may be explained either as a result of locally elevated Mg concentrations or a high degree of supersaturation favouring very rapid carbonate precipitation. Two small lakes to the north of Wallywash Great Pond show minor influence of the Na-Cl dominated coastal aquifer, suggesting that coastal lakes are sensitive to variations in the boundary between fresh and brackish groundwater caused by changes in climate or sea level. Their 13C/12C ratios are strongly influenced by biogenic CO2 derived from plant respiration or decay.

Late Quaternary palaeolimnology of a tropical marl lake: Wallywash Great Pond, Jamaica

Wallywash Great Pond (17° 57′ N, 77° 48 W, 7 m a.s.l.) is the largest perennial lake in Jamaica. It occupies a fault trough within the karstic White Limestone. The Great Pond is a hardwater lake with a pH of 8.2–8.6 and an alkalinity of 3.6–3.9 meq 1−1. Its chemistry is strongly influenced by the spring discharge from the limestone. The lake water is subject to degassing, evaporation and bicarbonate assimilation by submerged plants and algae, resulting in marl precipitation. A 9.23 m core (WGP2), taken from a water depth of 2.8 m, was analysed for magnetic susceptibility, loss-on-ignition, carbonate content, mole % MgCO3 in calcite, and stable isotopes in the fine carbonate fraction. The chronology is based on ten14C and four U/Th dates. Four main sediment types alternate in the core: marl; organic, calcareous mud; organic mud or peat; and earthy, brown, calcareous mud. The marls represent periods of wet/warm climate during sea-level highstands and the organic deposits, shallower, swampy conditions. In contrast, the brown, calcareous muds were laid down when the lake was dry or ephemeral. The last interglacial (120 000- 》 106 000 yr BP) is represented by three distinct marl units. After a dry interval, stable, wet/warm conditions set in from 106 000 to 93 000 yr BP. A dry/cool climate prevailed between 93 000 and at least 9500 yr BP. Three subsequent cycles of alternating wet and dry conditions culminated in flooding of the basin by the Black River during the late Holocene. These recent events cannot be accurately dated by14C due to significant and temporally-variable inputs of ‘dead’ carbon from the springs.

Calcification in Chara corallina: CO2 hydroxylation generates protons for bicarbonate assimilation

The alga Chara corallina (Charophyta, Charophyceae) apparently generates protons through the hydroxylation and precipitation of CO2, which leaks from the cell into highly alkaline pericellular regions. Under mildly alkaline conditions, the loss of CO2 to calcification is compensated by the production of twice as much CO2 from HCO3−, using the protons generated during calcification.Experiments capitalize on Chara’s large cells with their alternating alkaline (calcareous) and acidic (noncalcareous) pericellular zones. 14C uptake into carbonate and organic phases is fastest when the isotope is applied to the acidic zones. The ratio of calcification to photosynthesis is ∼ 1 at pH 8 and increases with pH approximately as simulated by a model in which both calcification and photosynthesis use carbon assimilated in the acidic zones. PIPES buffer (pKa = 6.8) inhibits calcification and photosynthesis equally, suggesting competition with bicarbonate as a proton acceptor in the acidic zones. CAPS buffer (pKa = 10.4) has little effect, suggesting that exogenous bicarbonate is not very important for calcification. Divalent Sr and Mn added to the medium precipitate primarily between the cell and calcareous encrustations, but phosphate does not. This result is consistent with the use of cellular Ca and CO2 in extracellular calcification.

Anoxygenic microbial mats of hot springs: thermophilic Chlorobium sp.

Non-laminated, green to yellow-green microbial mats, with Chlorobium sp. as the only phototroph, occurred from 55 to about 40°C in hot springs in and near Rotorua, New Zealand. The pH ranged from 4.3 to 6.2 and sulfide from 0.2 to 1.8 mM. This Chlorobium sp. is unique in its ability to form populations at temperatures as high as 55°C. Spectroradiometric measurements with a fiber-optic microprobe in the intact Chlorobium mass showed great opacity with less than 0.1% of the incident radiation (at photosynthetically usable wavelengths) available at 0.7 mm depth within the mat, although the concentrated Chlorium population sometimes extended to 3 mm depth. Sulfide-dependent, anoxygenic photosynthesis was demonstrated by [14C]bicarbonate assimilation in mat suspensions and in intact mats by a sulfide-specific microelectrode. No oxygen evolution occurred and no O2 was present within the mat. A light-enhanced uptake of [14C]acetate also occurred in cell suspensions. This rate was not enhanced by sulfide.

Anoxygenic microbial mats of hot springs: thermophilic Chlorobium sp

Non-laminated, green to yellow-green microbial mats, with Chlorobium sp. as the only phototroph, occurred from 55 to about 40°C in hot springs in and near Rotorua, New Zealand. The pH ranged from 4.3 to 6.2 and sulfide from 0.2 to 1.8 mM. This Chlorobium sp. is unique in its ability to form populations at temperatures as high as 55°C. Spectroradiometric measurements with a fiber-optic microprobe in the intact Chlorobium mass showed great opacity with less than 0.1% of the incident radiation (at photosynthetically usable wavelengths) available at 0.7 mm depth within the mat, although the concentrated Chlorium population sometimes extended to 3 mm depth. Sulfide-dependent, anoxygenic photosynthesis was demonstrated by [14C]bicarbonate assimilation in mat suspensions and in intact mats by a sulfide-specific microelectrode. No oxygen evolution occurred and no O2 was present within the mat. A light-enhanced uptake of [14C]acetate also occurred in cell suspensions. This rate was not enhanced by sulfide.

PHYSIOLOGICAL MODIFICATIONS RELATED TO DENSITY INCREASE IN PERIPHYTIC ASSEMBLAGES 1

ABSTRACT Periphytic communities in running waters were examined as they developed on granite rocks, concrete balls and glass slides. At equivalent cell densities, no differences in pigment concentrations, species diversity or production levels were found among the different substrata examined. Development of the assemblage appeared to result from the elongation of short algal filaments which had initially settled on the surface. As these communities matured, a distinct canopy and understory developed. Cellular metabolisms were comparable among the communities. In the understory of the communities, even though the cellular content of chl a and b did not differ, chl c and carotenoid pigment concentrations were higher than those in the over‐story. Bicarbonate assimilation of Tabellaria fenestrata (Lyng.) Külz. and Eunotia pectinalisi var. pectinalis (O. F. Müll?) Rabh. was higher than that of the more abundant Tabellaria flocculosa (Roth.)Kütz. var. flocculosa IV (sensu Koppen) at both high and low cell densities. This probably reflects a seasonal succession of colonizing species. Glucose assimilation appeared to be mainly attributable to bacterial activity, and algal cells of the upper layer were less active than those of the bottom. The small amount of glucose that was incorporated by the algal cells was probably absorbed passively since its amount was in direct proportion to cell volumes.

Studies on the Absorption of Dissolved Carbon Dioxide through Roots of Rice Plant (Part 6) The Relative Ability of Assimilation and Absorption of Bicarbonate through Roots and the Reties of These Amounts to Carbon Balance in Each Seedlings of Rice, Maize

Studies on the Absorption of Dissolved Carbon Dioxide through Roots of Rice Plant (Part 6) The Relative Ability of Assimilation and Absorption of Bicarbonate through Roots and the Reties of These Amounts to Carbon Balance in Each Seedlings of Rice, Maize

Studies on the Absorption of Dissolved Carbon Dioxide through Roots of Rice Plant (Part 5) The Transfer Forms and the Assimilation and Absorption of Bicarbonate through Roots of Rice, Maize and Wheat Seedlings

Studies on the Absorption of Dissolved Carbon Dioxide through Roots of Rice Plant (Part 5) The Transfer Forms and the Assimilation and Absorption of Bicarbonate through Roots of Rice, Maize and Wheat Seedlings

Studies on Nelumbo lutea (Willd.) Pers. II. Effects of pH on photosynthetic carbon assimilation

Analyses of carbon assimilation rates as a function of pH were conducted on shoot sections of the floating-leaved aquatic vascular plant Nelumbo lutea (Willd.) Pers., which were grown from seed under axenic conditions in acidic (pH 5.5) or alkaline (pH 8.2) liquid media. Collectively, the data suggest that while Nelumbo may be capable of limited bicarbonate assimilation at alkaline pH, CO 2 represents the preferred dissolved carbon source in this species. Photosynthetic carbon assimilation rates in submersed shoots at pH 4.5 (ca. 1.45 × 10 3 μmol C mg −1 Chl a h −1) were about 50-fold higher than rates at pH 8.5 (ca. 30 μmol C mg −1 Chl a h −1). pH-dependent C-assimilation curves in sections from plants grown in acidic or alkaline media were statistically similar. C-assimilation rates at alkaline pH, although lower than published rates for some bicarbonate-using aquatic macrophytes, could not be accounted for solely by equilibrium CO 2 concentrations or by CO 2 resupply to media by dissociation of bicarbonate to CO 2. Experiments utilizing filtered lake water, with or without added buffers (Hepes, Tris or Tricine), in place of artificial media demonstrated that the loss of C-assimilatory capacity at circumneutral to alkaline pH was not due to buffer inhibition. Analyses conducted in the presence of inhibitors of photosynthetic electron flow, respiration and plasmalemma ATPase, and various cyclic nucleotide derivatives, supported the view that a portion of C-assimilation at alkaline pH, but not acidic pH, was energy-dependent and sensitive to nucleotide modulation, as has been reported in several bicarbonate-using macrophytic and algal taxa.

Bicarbonate assimilation in aquatic angiosperms. Significance of the apoplast and unstirred layer

Bicarbonate assimilation in aquatic angiosperms. Significance of the apoplast and unstirred layer

The physiological ecology of cyclic adenosine 3′:5′-monophosphate (cAMP) in vascular aquatic plants II. cAMP as a modulator of carbon assimilation

Laboratory and in situ experiments on the submersed aquatic macrophyte species Scirpus subterminalis Torr., Potamogeton praelongus Wulf. and Najas flexilis (Willd.) Rostk. & Schmidt were conducted to test the hypothesis that exogenous or endogenous cyclic adenosine 3′:5′-monophosphate (cAMP) may serve as a positive or negative modulator of carbon assimilation in macrophytes. Leaf sections or discs were incubated in artificial media amended with quantities of cAMP found in lake water (0.2–10 nmol 1 −1). In both short-term (30 s) and long term (3 h) experiments, 14C-assimilation rates in Scirpus and Potamogeton were significantly stimulated by inclusion of as little as 0.2 nM cAMP in incubation media. Najas leaf sections were unaffected by cAMP addition. Our evidence indicated that the putative modulation process involved exogenous cAMP and not tissue cAMP alterations. Stimulation of C-assimilation by cAMP was blocked by the photosynthetic uncoupler DCMU, did not occur in dark-incubated plants or in senescent leaves, and commenced immediately upon addition of nucleotide to incubation media. A synergistic relationship between media Ca 2+ ion concentration and cAMP addition was found in Scirpus and cAMP stimulated C-assimilation over a wide range of photosynthetically-available carbon concentrations. Collectively, the data were consistent with the view that cAMP and similar cyclic nucleotides may interact directly with active bicarbonate assimilation complexes at the surface of macrophyte leaves, thereby modulating carbon assimilation rates.

Effects of senescence on somatic cell physiology in the green alga Volvox carteri

In every generation resulting from asexual reproduction, the somatic cells of the green alga Volvox carteri undergo synchronous senescence and cell death. Although the somatic cells of the asexual and sexual (female) generations of V. carteri f. weismannia ceased growth 72–96 h after the cells had stopped dividing, the somatic cells in the sexual spheroid remained alive approx. 96 h longer than comparable cells in the asexual spheroid. Measurement of several environmental factors demonstrated that senescence was not caused by extrinsic factors, such as changes in the light period, temperature, or culture medium. If these factors (light, temperature) were purposely altered, the timing of viability decline changed. Other changes occurring with senescence included a decreased rate of [ 14C ]bicarbonate assimilation after 96 h and a rapid decline in total soluble cell protein. The addition of the protein synthesis inhibitor, cycloheximide, prolonged the onset of senescence and delayed the decline in somatic cell viability. By adding cycloheximide at different times during senescence, we were able to show that the drug had less effect after 96 h than it did when added at 72 h. These results rule out extrinsic events governing senescence and are consistent with our idea that senescence in V. carteri is due to an intrinsic, sequential genetic program.

The mechanism of bicarbonate assimilation by the polar leaves of Potamogeton and Elodea. CO2 concentrations at the leaf surface

Abstract. Photosynthetic utilization of HCO, in leaves of Poiamogeton and Elodea occurs at the lower leaf side, with subsequent OH∼ release at the upper side. It is accompanied by transport of cations, in the present experiment K +, across the leaf. The resulting pH and K+ concentration changes near the leaf surface were recorded with miniature electrodes. From the pH and K+ concentration the concentrations of the different inorganic carbon species were calculated and compared with photosynthetic O, production. HCO−3 utilization is accompanied by a drastic increase in the free CO2 concentration near the lower epidermis. Experiments with CO2− and HCO3−free solutions showed an oscillating acidification near the lower epidermis and alkalinization near the upper epidermis. It is concluded that the acidification results from the activity of light‐dependent H+ pumps. The finding that an increase in pH at the upper side always coincided with a decrease at the lower in these experiments shows that the H+ pumps and the OH− extruding mechanism are coupled although occurring in different cell layers. Previously we have suggested that the first step in the process of photosynthetic HCO3− utilization is external conversion of HCO3−” by acidification caused by light‐dependent H+ pumps. The present results strongly support this hypothesis. Two possible pathways for the accompanying K + transport are discussed. The model presented here explains the known inhibiting effects of buffers and high pH on photosynlhetic HCO3− utilization.