Carbon isotope-labelling experiments indicate that ladderane lipids of anammox bacteria are synthesized by a previously undescribed, novel pathway

Ladderane lipids are unusual membrane lipids of bacteria that anaerobically oxidize ammonium to dinitrogen gas (anammox). Ladderane lipids contain linearly concatenated cyclobutane rings for which the pathway of biosynthesis is currently unknown. To investigate the possible biosynthetic routes of these lipids, 2-¹³C-labelled acetate was added to a culture of the anammox bacterium Candidatus Brocadia fulgida. Labelling patterns obtained by high-field ¹³C nuclear magnetic resonance spectroscopy of isolated lipids indicated that C . Brocadia fulgida synthesizes C_16:0 and iso C_16:0 fatty acids according to the known pathway of type II fatty acid biosynthesis. The ¹³C-labelling pattern of the C₈ alkyl chain of the C₂₀ [3] ladderane monoether also indicated the use of this route. However, carbon atoms in the cyclobutane rings and the cyclohexane ring were nonspecifically labelled and did not correspond to known patterns of fatty acid synthesis. Taken together, our results indicate that it is unlikely that ladderane lipids are formed from the cyclization of polyunsaturated fatty acids as hypothesized previously and suggest an alternative, although as yet unknown, pathway of biosynthesis.     

Carbon isotope ratios of plants and occurrences of C4 species under different soil moisture regimes in arid region of Northwest China

Carbon isotope ratio of leaf dry matter, δ ¹³C, was measured on species occurring within Baiyin desert community, consisting of valley, slope and ridge microhabitats, and within Shandan desert community, consisting of Gobi desert and seasonal flooded creek microhabitats, in Northwest China. δ ¹³C of C₃ species increased with a decrease in soil water availability, suggesting that water-use efficiency (WUE) increased with decreasing soil moisture, whereas for all C₄ species, δ ¹³C tended to decrease with decreasing soil water availability, suggesting that WUE also increased with decreasing soil moisture. Above results indicated that water-use pattern was conservative under drought for C₄ and C₃ plants. In this present study, C₄ species' occurrences within different microhabitats were investigated and C₄ plants were observed to be absent and/or scarce within relatively lower soil moisture microhabitats, whereas they occurred and/or even had a high abundance within relatively higher soil moisture microhabitats, suggesting limited moisture available was a key factor of limiting C₄ distribution in arid region of Northwest China.     

Photosynthesis in Salsola Species (Chenopodiaceae) from Southern Africa Relative to their C4 Syndrome Origin and their African-Asian Arid Zone Migration Pathways

Abstract: Over 60 Salsola species of Chenopodiaceae from South Africa were studied for their photosynthesis type, using δ¹³C analysis and light microscopy of leaf anatomy. These species cover about 70 % of the total list of Southern African Salsola species and grow naturally in South and Southwest African desert regions. All species are shrubby forms and belong to the single subsection Caroxylon. Only C₄ photosynthesis was found in the Salsola species determined with ¹³C/¹²C carbon isotope discrimination values that ranged from - 11.04 to - 14.03 % (PDB), plus the presence of a Kranz type assimilation tissue anatomy. The apparent absence of C₃ in Salsola in South and Southwest Africa and the known presence of C₃ and C₃ - C₄ intermediate photosynthesis in Caroxylon, Salsola species in Asia strongly indicate that the genus Salsola originated in Asia and later migrated to South Africa.     

Effect of H2 evolution on 15N2 fixation, C2H2 reduction and relative efficiency of leguminous symbionts

The (C₂H₄+ H_2(C2H₂))/¹⁵N₂ ratios of 15 clover- Rhizobium symbionts. soybean, and black medick symbionts were measured. Relative efficiency based on the C2H4 production and on ¹⁵N₂ incorporation were compared, and in most symbionts there was little difference between the two measures of relative efficiency. Total measurable electron flux through nitrogenase during acetylene reduction and ¹⁵N₂ incorporation were nearly equal for most symbionts studied. The relative efficiency and the (C₂H₄+ H_2(C2H₂))/¹⁵N₂ ratio showed an inverse correlation. Use of this ratio appears preferable to use of the ratio of C2H2 reduction/N₂ reduction. Some evolution of H₂ was observed in the presence of C₂H₂.     

Consortial N2 fixation: a strategy for meeting nitrogen requirements of marine and terrestrial cyanobacterial mats

Abstract: Four microbial mat-forming, non-axenic, strains of the non-heterocystous, filamentous, cyanobacterial genus Microcoleus were maintained in culture and examined for the ability to fix atmospheric nitrogen (N₂). Each was tested for nitrogenase activity using the acetylene reduction assay (ARA) and for the presence of the dinitrogenase reductase gene ( nifH ), an essential gene for N₂ fixation, using the polymerase chain reaction (PCR). The Microcoleus spp. cultures were incapable of growth without an exogenous nitrogen source and never exhibited nitrogenase activity. Attempts to amplify a 360-bp segment of the nifH gene using DNA purified from the cyanobacterial cultures did not produce any cyanobacteria-specific nifH sequences. However, several non-cyanobacterial homologous nifH sequences were obtained. Phylogenetic analysis showed these sequences to be most similar to sequences from heterotrophic bacteria isolated from a marine microbial mat in Tomales Bay (California, USA), and bulk DNA extracted from a cryptobiotic soil crust in Moab (Utah, USA). Microcoleus spp. dominated the biomass of both systems. Cyanobacteria-specific 16S rDNA sequences obtained from the cultured cyanobacterial strains demonstrate that the lack of cyanobacteria-specific nifH sequences was not due to inefficiency of extracting Microcoleus DNA. Hence, both the growth and genetic data indicate that, contrary to earlier reports, Microcoleus spp. appear incapable of fixing N₂ because they lack at least one of the requisite genes for this process. Furthermore, our study suggests epiphytic N₂-fixing bacteria form a diazotrophic consortium with these Microcoleus spp. and are likely key sources of fixed N₂ generated within soil crusts and marine microbial mats.     

Bacterially mediated precipitation in marine stromatolites

Stromatolites are laminated, lithified (CaCO₃) sedimentary deposits formed by precipitation and/or sediment accretion by cyanobacterial–bacterial mat communities. Stromatolites have been associated with these communities as far back as the Precambrian era some 2+ billion years ago. The means by which microbial communities mediate the precipitation processes have remained unclear, and are the subject of considerable debate and speculation. Two alternative explanations for microbially mediated precipitation include: (i) cyanobacterial photosynthesis increases pH in a system supersaturated in respect of CaCO₃, resulting in CaCO₃ precipitation and then laminated lithification, and (ii) decomposition of cyanobacterial extracellular organic matter (e.g. sheaths, mucilage and organic acids) by microheterotrophs leads to release of organic-bound Ca²⁺ ions and CaCO₃ precipitation. We evaluated these explanations by examining metabolically active, lithifying stromatolitic mat communities from Highborne Cay, Bahamas, using microautoradiography. Microautoradiographic detection of ¹⁴CO₂ fixation and ³H organic matter ( d -glucose and an amino acid mixture) utilization by photosynthetically active cyanobacteria and microheterotrophs, combined with community-level uptake experiments, indicate that bacteria, rather than cyanobacteria are the dominant sites of CaCO₃ deposition. In the oligotrophic waters in which stromatolites exist, microheterotrophs are reliant on the photosynthetic community as a main source of organic matter. Therefore, autotrophic production indirectly controls microbially mediated precipitation and stromatolite formation in these shallow marine environments.     

A survey of photosynthetic carbon metabolism in 4 ecotypes of Phragmites australis in northwest China: Leaf anatomy, ultrastructure, and activities of ribulose 1,5-bisphosphate carboxylase, phosphoenolpyruvate carboxylase and glycollate oxidase

Four ecotypes of Phragmites australis from different habitats in northwest China were examined to compare their photosynthetic characteristics. In a swamp ecotype, the Δ ¹³C value of leaf materials was −34.0‰, and bundle sheath cells contained a small amount of organelles and round-shaped chloroplasts, as being similar to typical C₃ plants. In a dune ecotype, the Δ ¹³C value was −20.9‰ and bundle sheath cells contained oval-shaped chloroplasts with poorly-developed grana. In light and heavy salt meadow ecotypes, Δ ¹³C values were −30.6‰ and −35.6‰, respectively. The shape of bundle sheath chloroplasts in the light salt meadow ecotype was intermediate between those of the swamp and dune ecotypes. Abundance of bundle sheath organelles in the heavy salt meadow ecotype was intermediate. The swamp ecotype had photosynthetic enzyme activities typical of C₃ type plants, whereas the dune ecotype had an increased activity of phosphoenolpyruvate carboxylase (PEPC), a key C₄ enzyme, and a decreased ribulose 1,5-bisphosphate carboxylase (Rubisco) activity. The light salt meadow and heavy salt meadow ecotypes had substantial activities of PEPC, which indicates potential for C₄ photosynthesis. These data suggest that this species evolved the C₃-like ecotype in swamp environments and the C₄-like C₃-C₄ intermediate in dune desert environments, and C₃-like C₃-C₄ intermediates in salt environments.     

Assimilation of methane and inorganic carbon by microbial communities mediating the anaerobic oxidation of methane

The anaerobic oxidation of methane (AOM) is a major sink for methane on Earth and is performed by consortia of methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Here we present a comparative study using in vitro stable isotope probing to examine methane and carbon dioxide assimilation into microbial biomass. Three sediment types comprising different methane-oxidizing communities (ANME-1 and -2 mixture from the Black Sea, ANME-2a from Hydrate Ridge and ANME-2c from the Gullfaks oil field) were incubated in replicate flow-through systems with methane-enriched anaerobic seawater medium for 5–6 months amended with either ¹³CH₄ or H¹³CO₃^-. In all three sediment types methane was anaerobically oxidized in a 1:1 stoichiometric ratio compared with sulfate reduction. Similar amounts of ¹³CH₄ or ¹³CO₂ were assimilated into characteristic archaeal lipids, indicating a direct assimilation of both carbon sources into ANME biomass. Specific bacterial fatty acids assigned to the partner SRB were almost exclusively labelled by ¹³CO₂, but only in the presence of methane as energy source and not during control incubations without methane. This indicates an autotrophic growth of the ANME-associated SRB and supports previous hypotheses of an electron shuttle between the consortium partners. Carbon assimilation efficiencies of the methanotrophic consortia were low, with only 0.25–1.3 mol% of the methane oxidized.     

Diurnal and seasonal variation in the carbon isotope composition of leaf dark-respired CO2 in velvet mesquite (Prosopis velutina)

We evaluated diurnal and seasonal patterns of carbon isotope composition of leaf dark-respired CO₂ ( δ ¹³C_l) in the C₃ perennial shrub velvet mesquite ( Prosopis velutina ) across flood plain and upland savanna ecosystems in the south-western USA. δ ¹³C_l of darkened leaves increased to maximum values late during daytime periods and declined gradually over night-time periods to minimum values at pre-dawn. The magnitude of the diurnal shift in δ ¹³C_l was strongly influenced by seasonal and habitat-related differences in soil water availability and leaf surface vapour pressure deficit. δ ¹³C_l and the cumulative flux-weighted δ ¹³C value of photosynthates were positively correlated, suggesting that progressive ¹³C enrichment of the CO₂ evolved by darkened leaves during the daytime mainly resulted from short-term changes in photosynthetic ¹³C discrimination and associated shifts in the δ ¹³C signature of primary respiratory substrates. The ¹³C enrichment of dark-respired CO₂ relative to photosynthates across habitats and seasons was 4 to 6‰ at the end of the daytime period (1800 h), but progressively declined to 0‰ by pre-dawn (0300 h). The origin of night-time and daytime variations in δ ¹³C_l is discussed in terms of the carbon source(s) feeding respiration and the drought-induced changes in carbon metabolism.     

Re-evaluation of proposed C4 photosynthetic characteristics in the genus Larix

It has been suggested previously that Japanese larch ( Larix kaempferi ) exhibits characteristics of C₄ photosynthesis. To further evaluate this suggestion, stable carbon isotope ratios were determined for leaf and bark tissue of Larix gmelini, L. kaempferi, L. laricina, L. Iyallii, L. occidentalis , and L. sibirica. All δ¹³C values were more negative than –22‰. Short-term labeling with ¹⁴CO₂ showed that phosphoglyceric acid and other phosphorylated compounds were the first products of photosynthesis in L. sibirica. Both of these results strongly suggest that the initial fixation of atmospheric CO₂ in these six Larix species is accomplished solely via the C₃ photosynthetic pathway.     

A Remarkable New Leaf Type With Unusual Photosynthetic Tissue in a Central Asiatic Genus of Chenopodiaceae

Abstract: From the hygrohalophyte Borszczowia aralocaspica Bunge (Chenopodiaceae), a new leaf type with 1-layered chlorenchyma is described as "borszczovoid" and compared with other leaf types in subfamily Salsoloideae. The chlorenchyma is suspected to represent a unique C₄ type. Evidence is cited from anatomical studies and documented by micrographs and Carbon isotope determinations (ä¹³C values). The 1-layered photosynthetic tissue combines all essential anatomical characters of a 2-layered chlorenchyma of regular C₄ plants and is in intimate contact with concentrically arranged peripheral bundles. The ä¹³C values are − 13.03 ‰ from young stems and − 13.78 ‰ from leaves. The results are discussed in the anatomical, physiological and taxonomic framework. In addition, from distantly-related Suaeda species of section Conosperma the conospermoid leaf type is re-described. It is characterized by typical palisade and Kranz layers and differs from the C₄ suaedoid type by an external water-storaging hypodermis and an arrangement of Kranz cells reminiscent of the atriplicoid type from subfamily Chenopodioideae. From eight other species of Chenopodiaceae ä¹³C values are given for the first time.     

Competition between anoxygenic phototrophic bacteria and colorless sulfur bacteria in a microbial mat

Abstract The populations of chemolithoautotrophic (colorless) sulfur bacteria and anoxygenic phototrophic bacteria were enumerated in a marine microbial mat. The highest population densities were found in the 0–5 mm layer of the mat: 2.0 × 10⁹ cells cm⁻³ sediment, and 4.0 × 10⁷ cells cm⁻³ sediment for the colorless sulfur bacteria and phototrophs, respectively. Kinetic parameters for thiosulfate-limited growth were assessed for Thiobacillus thioparus T5 and Thiocapsa roseopersicina M1, both isolated from microbial mats. For Thiobacillus T5, growing at a constant oxygen concentration of 43 μmol l⁻¹, μ_max was 0.336 h⁻¹ and K _s 0.8 μmol l⁻¹. Phototrophically grown Thiocapsa strain M1 displayed a μ_max of 0.080 h⁻¹ and a K _s of 8 μmol l⁻¹ when anoxically grown under thiosulfate limitation. In a competition experiment with thiosulfate as electron donor, Thiocapsa became dominant during a 10-h oxic/14-h anoxic regimen at continuous illumination, despite the higher affinity for thiosulfate of Thiobacillus .     

Methanogenesis in the hypersaline Solar Lake (Sinai)

Abstract Enrichment studies on microbial mat sediments (potential stromatolites) from the hypersaline Solar Lake (Sinai) indicated high numbers of methanogenic bacteria (up to 10⁵ ml⁻¹ sediment) in spite of the high sulfate reduction rate, sulfate concentration and salinity. Among H₂/CO₂, acetate and monomethylamine, the methylated amine was the preferred substrate. The predominant species enriched was a Methanosarcina sp. The findings indicate that methanogenic bacteria play an important role in hypersaline sulfate-enriched anoxic sediments and stromatolithic microbial mats.     

Carbon metabolism of Listeria monocytogenes growing inside macrophages

The intracellular metabolism of Listeria monocytogenes was studied by ¹³C-isotopologue profiling using murine J774A.1 macrophages as host cells. Six hours after infection, bacteria were separated from the macrophages and hydrolyzed. Amino acids were converted into tert-butyl-dimethylsilyl derivatives and subjected to gas chromatography/mass spectrometry. When the macrophages were supplied with [U-¹³C₆]glucose prior to infection, but not during infection, label was detected only in Ala, Asp and Glu of the macrophage and bacterial protein with equal isotope distribution. When [U-¹³C₆]glucose was provided during the infection period, ¹³C label was found again in Ala, Asp and Glu from host and bacterial protein, but also in Ser, Gly, Thr and Val from the bacterial fraction. Mutants of L. monocytogenes defective in the uptake and catabolism of the C₃-metabolites, glycerol and/or dihydroxyacetone, showed reduced incorporation of [U-¹³C₆]glucose into bacterial amino acids under the same experimental settings. The ¹³C pattern suggests that (i) significant fractions (50–100%) of bacterial amino acids were provided by the host cell, (ii) a C₃-metabolite can serve as carbon source for L. monocytogenes under intracellular conditions and (iii) bacterial biosynthesis of Asp, Thr and Glu proceeds via oxaloacetate by carboxylation of pyruvate.     

Demethylation and cleavage of dimethylsulfoniopropionate in marine intertidal sediments

Abstract Demethylation and cleavage of dimethylsulfoniopropionate (DMSP) was measured in three different types of intertidal marine sediments: a cyanobacterial mat, a diatom-covered tidal flat and a carbonate sediment. Consumption rates of added DMSP were highest in cyanobacterial mat slurries (59 μmol DMSP 1⁻¹) and lower in slurries from a diatom mat and a carbonate tidal sediment (24 and 9 μmol DMSP 1⁻¹ h⁻¹, respectively). Dimethyl sulfide (DMS) and 3-mercaptopropionate (MPA) were produced simultaneously during DMSP consumption, indicating that cleavage and demethylation occurred at the same time. Viable counts of DMSP-utilizing bacteria revealed a population of 2 × 10⁷ cells cm⁻³ sediment (90% of these cleaved DMSP to DMS, 10% demethylated DMSP to MPA) in the cyanobacterial mat, 7 × 10⁵ cells cm⁻³ in the diatom mat (23% cleavers, 77% demethylators), and 9 × 10⁴ cells cm⁻³ (20% cleavers and 80% demethylators) in the carbonate sediment. In slurries of the diatom mat, the rate of MPA production from added 3-methiolpropionate (MMPA) was 50% of the rate of MPA formation from DMSP. The presence of a large population of demethylating bacteria and the production of MPA from DMSP suggest that the demethylation pathway, in addition to cleavage, contributes significantly to DMSP consumption in coastal sediments.     

Stable isotope ecology of fossil hippopotamids from the Lake Turkana Basin of East Africa

The diet of African hippopotamids can be documented through δ ¹³C analyses of enamel and other tissues. Analysis of a 10-million-year sequence of hippopotamids in and near the Lake Turkana Basin of northern Kenya shows that hippos have included a substantial fraction of C₃ vegetation in their diets since the late Miocene when C₄ vegetation first appears in hippo diet as a measurable fraction. The C₄ component of vegetation becomes dominant (>50%) by Upper Burgi time ( c . 2 million years ago) but does not reach 100% for all individuals. It is therefore not unexpected that the δ ¹³C values of modern hippopotamids show a higher fraction of dietary C₃ biomass than has been estimated from traditional observations. Analysis of δ ¹⁸O of hippos from different stratigraphic levels shows no systematic trend over time; the average value for fossil hippos over the last 10 million years is similar to that of modern hippos from the Omo River system.     

Temperature-dependent changes in phospholipid and fatty acid composition and membrane lipid fluidity of Yersinia enterocolitica

Temperature-dependent compositional changes of phospholipids and their fatty acids were analysed in Yersinia enterocolitica grown at 5°, 25° and 37°C. The relative amounts of the four phospholipids, phosphatidylethanolamine (75–78%), phosphatidylglycerol (10–11%), cardiolipin (<7%) and lysophosphatidylethanolamine (<5%), were essentially the same at all growth temperatures. The degree of fatty acid unsaturation of the four phospholipids increased with decrease in growth temperature, mainly due to an increase of C_16:1 and C_18:1 and a corresponding decrease of C_16;0, C_18:0 and cyclo C_17:0. An electron spin resonance spectroscopic study of the membrane lipids showed that membrane lipid fluidity was enhanced by decreasing the growth temperatures. The changes in fatty acid composition of phospholipids in response to varied temperatures were consistent with the temperature-dependent changes in the membrane lipid fluidity of Y. enterocolitica , and were similar to those reported for other bacteria.     

Enhanced degradation of petrol (Slovene diesel) in an aqueous system by immobilized Pseudomonas fluorescens

The rate of degradation of n -alkanes C₁₂-C₁₈, in petrol (Slovene diesel) in an aqueous system, by free and immobilized Pseudomonas fluorescens in shaking flasks was investigated. Cells were immobilized to a biosupport, Biofix, and a biosorbant, Drizit. Analysis of cellular growth of the free and immobilized bacteria over 8 d of incubation with diesel as the sole carbon source, showed a reduction in the lag phase in the immobilized cultures in comparison to the free system. The free system degraded 52·3% of C₁₂ and 11·6% of C₁₃, but C₁₄-C₁₈ were not degraded. In comparison to the free system and diesel which had not been exposed to experimental conditions (unexposed), the immobilized systems degraded significantly more of C₁₃-C₁₈. Biofix-immobilized cells degraded 14·8% of C₁₂ and an average of 53·5% of C₁₃-C₁₈. Drizit-immobilized cells degraded 24·5% of C₁₂, 52·4% of C₁₃ and an average of 91·2% of C₁₄-C₁₈. This study shows the successful use of immobilized bacteria technology to enhance the degradation of diesel in an aqueous system.     

Uptake and utilization of n-octacosane and n-nonacosane by Arthrobacter nicotianae KCC B35

Arthrobacter nicotianae KCC B35 isolated from blue-green mats densely covering oil sediments along the Arabian Gulf coast grew well on C₁₀ to C₄₀ n -alkanes as sole sources of carbon and energy. Growth on C₂₀ to C₄₀ alkanes was even better than on C₁₀ to C₁₈ alkanes. Biomass samples incubated for 6 h with n -octacosane (C₂₈) or n -nonacosane (C₂₉) accumulated these compounds as the predominant constituent alkanes of the cell hydrocarbon fractions. The even chain hexadecane C₁₆ and the odd chain pentadecane C₁₅ were the second dominant constituent alkanes in C₂₈ and C₂₉ incubated cells, respectively. n -Hexadecane-incubated cells accumulated in their lipids higher proportions of C₁₆-fatty acids than control cells not incubated with hydrocarbons. On the other hand, C₂₈ and C₂₉-incubated cells did not contain any fatty acids with the equivalent chain lengths, but the fatty acid patterns of the cell lipids suggest that there should have been mid-chain oxidation of these very long chain alkanes. This activity qualifies A. nicotianae KCC B35 to be used in cocktails for bioremediating environments polluted with heavy oil sediments.     

Elevated pyruvate,orthophosphate dikinase (PPDK) activity alters carbon metabolism in C3 transgenic potatoes with a C4 maize PPDK gene

Changes in carbon metabolism and δ¹³C value of transgenic potato plants with a maize pyruvate,orthophosphate dikinase (PPDK; EC 2.7.9.1) gene are reported. PPDK catalyzes the formation of phospho enol pyruvate (PEP), the initial acceptor of CO₂ in the C₄ photosynthetic pathway. PPDK activities in the leases of transgenic potatoes were up to 5.4‐fold higher than those of control potato plants (wild‐type and treated control plants). In the transgenic potato plants, PPDK activity in leaves was negatively correlated with pyruvate content (r²= 0.81), and was positively correlated with malate content (r²= 0.88). A significant increase in the δ¹³C value was observed in the transgenic potato plants, suggesting a certain contribution of PEP carboxylase as the initial acceptor of atmospheric CO₂. These data suggest that elevated PPDK activity may alter carbon metabolism and lead to a partial operation of C₄‐type carbon metabolism. However, since parameters associated with CO₂ gas exchange were not affected, the altered carbon metabolism had only a small effect on the total photosynthetic characteristics of the transgenic plants.