Utilization Of Different Carbon Sources Research Articles

Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages

Abstract. Isotopes of dissolved inorganic carbon (DIC) are used to indicate both transit times and biogeochemical evolution of groundwaters. These signals can be complicated in carbonate aquifers, as both abiotic (i.e., carbonate equilibria) and biotic factors influence the δ13C and 14C of DIC. We applied a novel graphical method for tracking changes in the δ13C and 14C of DIC in two distinct aquifer complexes identified in the Hainich Critical Zone Exploratory (CZE), a platform to study how water transport links surface and shallow groundwaters in limestone and marlstone rocks in central Germany. For more quantitative estimates of contributions of different biotic and abiotic carbon sources to the DIC pool, we used the NETPATH geochemical modeling program, which accounts for changes in dissolved ions in addition to C isotopes. Although water residence times in the Hainich CZE aquifers based on hydrogeology are relatively short (years or less), DIC isotopes in the shallow, mostly anoxic, aquifer assemblage (HTU) were depleted in 14C compared to a deeper, oxic, aquifer complex (HTL). Carbon isotopes and chemical changes in the deeper HTL wells could be explained by interaction of recharge waters equilibrated with post-bomb 14C sources with carbonates. However, oxygen depletion and δ13C and 14C values of DIC below those expected from the processes of carbonate equilibrium alone indicate considerably different biogeochemical evolution of waters in the upper aquifer assemblage (HTU wells). Changes in 14C and 13C in the upper aquifer complexes result from a number of biotic and abiotic processes, including oxidation of 14C-depleted OM derived from recycled microbial carbon and sedimentary organic matter as well as water–rock interactions. The microbial pathways inferred from DIC isotope shifts and changes in water chemistry in the HTU wells were supported by comparison with in situ microbial community structure based on 16S rRNA analyses. Our findings demonstrate the large variation in the importance of biotic as well as abiotic controls on 13C and 14C of DIC in closely related aquifer assemblages. Further, they support the importance of subsurface-derived carbon sources like DIC for chemolithoautotrophic microorganisms as well as rock-derived organic matter for supporting heterotrophic groundwater microbial communities and indicate that even shallow aquifers have microbial communities that use a variety of subsurface-derived carbon sources.

XC_0531 encodes a c-type cytochrome biogenesis protein and is required for pathogenesis in Xanthomonas campestris pv. campestris

BackgroundThe phytopathogenic Xanthomonas campestris pv.campestris is a gram-negative bacterium and the causal agent of black-rot disease of cruciferous crops. Many gram-negative bacteria possess a family of proteins, called Dsbs, which are involved in disulfide bond formation in certain periplasmic proteins. In our preliminary screening of the virulence to the plants we identified that gene XC_0531 which annotated gene dsbD of Xanthomonas campestris pv. campestris (Xcc) is related to the virulence to the host plants.ResultsHere, we found XC_0531 encoded a DsbD like protein. Its deletion is sensitive to DTT and copper, decreased accumulation of free thiols in periplasm. Its deletion also affected heme synthesis, position of Soret band and the production of peak c550. This suggests that XC_0531 is related to c-type cytochromes biogenesis. XC_0531 mutation decreased the utilization of different carbon sources (such as galactose, xylose, maltose, saccharose and glucose), reduced extracellular polysaccharide (EPS) production, decreased extracellular enzyme activities (protease, cellulose and amylase), slowed down growth rate of Xcc and weakened virulence to the plants. These results suggest that these phenotypes caused by XC_0531 mutation is possibly due to deficient biosynthesis of c-type cytochromes in respiration chain and the formation of disulfide bonds. Our work confirmed the function of XC_0531 and provide theory basis for scientists working on molecular mechanisms of cytochrome c biogenesis, pathogenesis of Xcc, development of EPS commercial values and protecting plant from black rot.ConclusionWe confirmed the function of gene XC_0531, which encodes a DsbD like protein, a protein correlated with c-type cytochrome biogenesis. This gene is related to the virulence to plants by affecting funtion of cytochromes c and probably disulfide bonds modification of proteins in type II secretion system (T2SS).

Pelistega suis sp. nov., isolated from domestic and wild animals

Biochemical and molecular genetic studies were performed on three novel Gram-stain-negative, catalase- and oxidase-positive, bacilli-shaped organisms isolated from the tonsils of two pigs and one wild boar. The micro-organism was identified as a species of the genus Pelistega based on its cellular morphological and biochemical tests. The closest phylogenetic relative of the novel bacilli was Pelistega indica HM-7T (98.2 % 16S rRNA gene sequence similarity to the type strain). groEL and gyrB sequence analysis showed interspecies divergence from the closest 16S rRNA gene phylogenetic relative, P. indica of 87.0.% and 69 %, respectively. The polyamine pattern contains predominantly putrescine and 2-hydroxyputrescine. The major quinone is ubiquinone Q-8 and in the polar lipid profile, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid are predominant. The novel bacterial isolate can be distinguished from P. indica by several biochemical characteristics, such as the production of l-pyrrolydonil arylamidase but not gamma-glutamyl-transferase, and the utilization of different carbon sources. Based on both phenotypic and phylogenetic findings, the novel bacterium is classified as representing a novel species of the genus Pelistega, for which the name Pelistega suis sp. nov. is proposed. The type strain is 3340-03T ( = CECT 8400T = CCUG 64465T).

Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis.

Cross-feeding is an important metabolic interaction mechanism of bacterial groups inhabiting the human colon and includes features such as the utilization of acetate by butyrate-producing bacteria as may occur between Bifidobacterium and Faecalibacterium genera. In this study, we assessed the utilization of different carbon sources (glucose, starch, inulin and fructooligosaccharides) by strains of both genera and selected the best suited combinations for evidencing this cross-feeding phenomenon. Co-cultures of Bifidobacterium adolescentis L2-32 with Faecalibacterium prausnitzii S3/L3 with fructooligosaccharides as carbon source, as well as with F. prausnitzii A2-165 in starch, were carried out and the production of short-chain fatty acids was determined. In both co-cultures, acetate levels decreased between 8 and 24 h of incubation and were lower than in the corresponding B. adolescentis monocultures. In contrast, butyrate concentrations were higher in co-cultures as compared to the respective F. prausnitzii monocultures, indicating enhanced formation of butyrate by F. prausnitzii in the presence of the bifidobacteria. Variations in the levels of acetate and butyrate were more pronounced in the co-culture with fructooligosaccharides than with starch. Our results provide a clear demonstration of cross-feeding between B. adolescentis and F. prausnitzii.

O3浓度升高和太阳辐射减弱对小麦根际土壤微生物功能多样性的影响

PDF HTML阅读 XML下载 导出引用 引用提醒 O3浓度升高和太阳辐射减弱对小麦根际土壤微生物功能多样性的影响 DOI: 10.5846/stxb201308052029 作者: 作者单位: 南京信息工程大学环境科学与工程学院,南京信息工程大学环境科学与工程学院,南京信息工程大学环境科学与工程学院,南京信息工程大学环境科学与工程学院,南京信息工程大学环境科学与工程学院 作者简介: 通讯作者: 中图分类号: 基金项目: 教育部高等学校博士学科点专项科研基金(20123228110003); 国家自然科学基金(41075114) Effects of ozone fumigation and depressed solar irradiance on soil microbial functional diversity in winter wheat rhizosphere Author: Affiliation: Nanjing University of Information Science Technology,Jiangsu Key Laboratory of Atmospheric environmental monitoring and Pollution control high-tech research,Nanjing University of Information Science Technology,Jiangsu Key Laboratory of Atmospheric environmental monitoring and Pollution control high-tech research,Nanjing University of Information Science Technology,Jiangsu Key Laboratory of Atmospheric environmental monitoring and Pollution control high-tech research,Nanjing University of Information Science Technology,Jiangsu Key Laboratory of Atmospheric environmental monitoring and Pollution control high-tech research,Nanjing University of Information Science Technology,Jiangsu Key Laboratory of Atmospheric environmental monitoring and Pollution control high-tech research Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:采用开顶箱(OTC)法和遮光网技术,设置100 nL/L臭氧熏气与3个辐射减弱梯度结合,模拟臭氧浓度升高和太阳辐射减弱的复合大气背景。用BIOLOG生态测试板,采用孔平均颜色变化率法(AWCD)测定冬小麦根际土壤微生物利用不同碳源的能力,计算微生物群落多样性指数,对不同碳源的利用率进行了主成分分析。两年试验结果显示,臭氧熏气与太阳辐射减弱复合作用,降低了土壤微生物对碳源的利用速度和利用总量;除了聚合物以外其它碳源利用率显著降低;对土壤微生物多样性没有直接的影响;对碳源降解的抑制效应大于增强的O3与减弱的太阳辐射两因素各自的单独作用。太阳辐射减弱20%,一定程度上增加了对聚合物类的分解。O3熏气条件下太阳辐射减弱,糖类、胺类代谢变异度较高,受环境影响较大。 Abstract:Enhanced ozone concentration and depressed solar irradiation were simulated by using open-top chambers (OTCs) method and shading net techniques at 100 nL/L ozone fumigation assembling with three different levels of depressed solar irradiance. The effect of enhanced O3 combination with depressed solar irradiance was also studied. Two experiments were performed over two years. The combination of three OTCs with six shaded chambers was set up. Each OTC fed with 100 nL/L ozone. In the shaded chambers, solar irradiance was reduced to different levels of 20%, 40%, 60% respectively. Combined actions of O3 and depressed solar irradiance were tested by shading net above OTCs. Using unshaded OTC and unfed with O3 as controls. OTC fed with 100 nL/L ozone only, and shaded chamber solar irradiance reduced 20% only were applied too. Each chamber was equivalent and repeated three times. Winter wheat was grown to all life stage in OTCs, shading net and their combine chambers. From reviving to mature stages, in OTCs the plants were treated for 8 h (8:00-16:00) every sunny day with O3, in shading chambers covered net all life stage. The ability of winter wheat (Triticumaestivum)rhizosphere microbial to use different carbon sources were measured by applying BIOLOG ECO MicroPlate and Average WelL-Color Development (AWCD). Microbial diversity index and Principal Component Analysis (PCA) were calculated on the utilization of different carbon sources. Each treatment was assayed in triplicate. The data were initially compared by analysis of variance and differences between means were detected using the Duncans Multiple Range Tests. Values of P < 0.05 indicated significance. Quite similar results were obtained during the two years' experiments. The results suggesting that under ozone fumigation and reduced solar irradiance, AWCD was reduced, catabolic ability of single carbon source was declined too. No obvious influence of O3 combined with shading on soil microbial diversity was found. Principal Component Analysis suggested that different forms of carbon source have different sensitivity. The variation degree of carbohydrates' is higher than others. Under ozone fumigation combined with reduced solar irradiance, AWCD and catabolic ability of single carbon sources were lower than enhanced O3 or lower solar irradiance single acting. For soil microbial, two years' results showed that combination effects of ozone fumigation and reduced solar irradiation reduced both rate and total utilization of carbon sources except polymers. However, there was no direct impact on the diversity of soil microbial. For Inhibitory effect on the degradation of carbon, combined effect of enhanced ozone concentration and reduced solar irradiation was greater than each factor functioning alone. 20% reduction of solar radiation increased the decomposition of polymers to some extent. On the conditions of combined O3 fumigation and solar radiation weakened, that makes the metabolism of carbohydrates and amines highly variable, as they are largely affected by the environment. Enhanced O3 and lower solar irradiation have a cooperative action. Reduced solar irradiance is benefit for winter wheat absorbing O3, resulting in a serious injury. 参考文献 相似文献 引证文献

Response of Birch and Alder Root Endophytes as Well as Rhizosphere and Bulk Soil Microorganisms to Heavy Metal Pollution

Research on soil microorganisms associated with plant roots (endophytes) and their outside habitats (rhizosphere, soil) under exposure to high concentrations of heavy metals in the environment may contribute to an increased knowledge about the effects of unfavorable pollutants in the natural ecosystem and improve the efficiency of remediation processes of degraded soils. The main goal of our study was to evaluate properties of microbial populations inhabiting different but spatially closed habitats: interior of the tree roots — endophytes (Betula pendula L. and Alnus glutinosa L.), rhizosphere and soil not influenced by plant roots at two heavy metal polluted areas in southern Poland where the content of cadmium, lead and zinc ranged 9.2–14.9, 26.2–75.1 and 1080–1559 mg-kg-1 of dried soil, respectively. In our experiment, we analyzed their density as well as determined the total metabolic activity and ability for utilization of different carbon sources. The density of endophytes (5.76–7.16 log10 c.f.u. × g dw_1) was higher than the density of bacteria inhabiting outside habitats — the rhizosphere and soil (5.43–5.91 and 5.08–5.57 log10 c.f.u. × g dw-1, respectively) and was not affected by heavy metal content. However, the total metabolic activity of endophytic populations was strongly influenced by the physicochemical properties of the soil and was significantly lower at more contaminated site. In general, the metabolic activity of endophytes was ∼15 times lower than the activity of rhizobacteria and at the same level or lower than the activity of soil microorganisms. Discriminant analysis revealed a higher utilization of a-Cyclodextrin and D-Xylose by microorganisms isolated from more polluted test site. The use of an artificial neural network (ANN) followed by principal component analysis (PCA) allowed the distinguishing of preferences in the utilization of carbon sources by microorganisms due to tree species but not the zone of isolation — endophytes, rhizosphere, soil.Our study revealed no significant impact of the metal concentrations present in the soil on the density of microorganisms (bacteria and fungi) inhabiting three analyzed zones (interior of the roots, rhziosphere, soil); however, their total metabolic activity was decreased in more contaminated site. Since the density of endophytes was higher compared to the number of bacteria present in the outside habitats (rhizosphere and soil), and their total metabolic activity was in general lower, we suggest a high specialization of microorganisms associated with the cellular spaces of plant roots compared to other microbial populations.

Bioaugmentation of polyethylene succinate-contaminated soil with Pseudomonas sp. AKS2 results in increased microbial activity and better polymer degradation

Pseudomonas sp. AKS2 isolated from soil degrades polyethylene succinate (PES) efficiently in the laboratory. However, this organism may not be able to degrade PES with similar efficiency in a natural habitat. Since in situ remediation is preferred for the effective removal of recalcitrant materials like plastic, in the current study, bioaugmentation potential of this organism was investigated. To investigate the potential of the AKS2 strain to bioaugment the PES-contaminated soil, a microcosm-based study was carried out wherein naturally attenuated, biostimulated, and AKS2-inoculated (bioaugmented) soil samples were examined for their ability to degrade PES. The results showed better degradation of PES by bioaugmented soil than other microcosms. Consistent with it, a higher number of PES-degrading organisms were found in the bioaugmented microcosm. The bioaugmented microcosm also exhibited a higher level of average well color development in BiOLOG ECO plate assay than the other two. The corresponding Shannon-Weaver index and Gini coefficient revealed a higher soil microbial diversity of bioaugmented microcosm than the others. This was further supported by community-level physiological profile of three different microcosms wherein we have observed better utilization of different carbon sources by bioaugmented microcosms. Collectively, these results demonstrate that bioaugmentation of PES-contaminated soil with AKS2 not only enhances polymer degradation but also increases microbial diversity. Bioaugmentation of soil with AKS2 enhances PES degradation without causing damage to soil ecology. Thus, Pseudomonas sp. AKS2 has the potential to be implemented as a useful tool for in situ bioremediation of PES.

Crude Oil-Degradation and Plasmid Profile of Nitrifying Bacteria Isolated from Oil-Impacted Mangrove Sediment in the Niger Delta of Nigeria

The crude oil degradability and plasmid profile of autotrophic nitrifying bacteria, Nitrosomonas and Nitrobacter species, isolated from mangrove sediment in the Niger Delta of Nigeria were studied. The effects of temperature, pH and optical density on the utilization of different carbon sources by the bacteria were also investigated. Results showed that nitrifying bacteria could utilize kerosene, diesel oil, jet fuel and engine oil as carbon sources. None utilized hexane and xylene but moderate growth was observed in benzene, phenol and toluene. However, their ability to utilized crude oil varied both in rates of utilization and in growth profiles. Mixed culture of the isolates degrades 52 % of crude oil introduced into the medium followed by Nitrosomonas sp. with 40 % degradation. The least was Nitrobacter sp. with 20 % degradation. The ability of the autotrophs to degrade crude oil was found to be plasmid-mediated through curing experiment and electrophoresis. The size of the plasmid involved was estimated to be 23 kb. The high crude oil utilization of the mixed culture implies that nitrifying bacteria isolated from contaminated ecosystem are excellent crude oil degraders and can be harnessed for bioremediation purposes.

Metabolic symbiosis in cancer: refocusing the Warburg lens.

Using relatively primitive tools in the 1920s, Otto Warburg demonstrated that tumor cells show an increased dependence on glycolysis to meet their energy needs, regardless of whether they were well-oxygenated or not. High rates of glucose uptake, fueling glycolysis, are now used clinically to identify cancer cells. However, the Warburg effect does not account for the metabolic diversity that has been observed amongst cancer cells nor the influences that might direct such diversity. Modern tools have shown that the oncogenes, variable hypoxia levels, and the utilization of different carbon sources affect tumor evolution. These influences may produce metabolic symbiosis, in which lactate from a hypoxic, glycolytic tumor cell population fuels ATP production in the oxygenated region of a tumor. Lactate, once considered a waste product of glycolysis, is an important metabolite for oxidative phosphorylation in many tissues. While much is known about how muscle and the brain use lactate in oxidative phosphorylation, the contribution of lactate in tumor bioenergetics is less defined. A refocused perspective of cancer metabolism that recognizes metabolic diversity within a tumor offers novel therapeutic targets by which cancer cells may be starved from their fuel sources, and thereby become more sensitive to traditional cancer treatments.

Construction and elementary mode analysis of a metabolic model for Shewanella oneidensis MR-1

A stoichiometric model describing the central metabolism of Shewanella oneidensis MR-1 wild-type and derivative strains was developed and used in elementary mode analysis (EMA). Shewanella oneidensis MR-1 can anaerobically respire a diverse pool of electron acceptors, and may be applied in several biotechnology settings, including bioremediation of toxic metals, electricity generation in microbial fuel cells, and whole-cell biocatalysis. The metabolic model presented here was adapted and verified by comparing the growth phenotypes of 13 single- and 1 double-knockout strains, while considering respiration via aerobic, anaerobic fumarate, and anaerobic metal reduction (Mtr) pathways, and utilizing acetate, n-acetylglucosamine (NAG), or lactate as carbon sources. The gene ppc, which encodes phosphoenolpyruvate carboxylase (Ppc), was determined to be necessary for aerobic growth on NAG and lactate, while not essential for growth on acetate. This suggests that Ppc is the only active anaplerotic enzyme when cultivated on lactate and NAG. The application of regulatory and substrate limitations to EMA has enabled creation of metabolic models that better reflect biological conditions, and significantly reduce the solution space for each condition, facilitating rapid strain optimization. This wild-type model can be easily adapted to include utilization of different carbon sources or secretion of different metabolic products, and allows the prediction of single- and multiple-knockout strains that are expected to operate under defined conditions with increased efficiency when compared to wild type cells.

Effect of transgenic alfalfa plants with introduced gene for Alfalfa Mosaic Virus coat protein on rhizosphere microbial community composition and physiological profile

The aim of this study was to evaluate the effect of transgenic alfalfa (Medicago sativa L.) plants, in comparison to their non-transgenic counterpart, on the density and physiological profiles of aerobic bacteria in the rhizosphere. Plants of transgenic alfalfa expressing the AMVcp-s gene coding for Alfalfa Mosaic Virus coat protein were cultivated in a climatic chamber. Two methods were used to determine the microbial diversity in rhizospheres of transgenic plants. First, the cultivation-dependent plating method, based on the determination of the density of colony-forming bacteria, and second, a biochemical method using the Biolog™ system, based on the utilization of different carbon sources by soil microorganisms. Statistically significant differences in densities of rhizospheric bacteria between transgenic and non-transgenic alfalfa clones were observed in ammonifying bacteria (GTL4/404-1), cellulolytic bacteria (GTL4/404-1, GTL4/402-2, A5-3-3), rhizobial bacteria (GTL4/402-2), denitrifying bacteria (A5-3-3) and Azotobacter spp. (GTL4/402-2). The highest values of substrate utilization by microbial communities and average respiration of C-sources were determined in non-transgenic alfalfa plants of the isogenic line SE/22-GT2. Carbohydrates, carboxylic acids and amino-acids were the most utilized carbon substrates by both Gram-negative and Gram-positive bacteria. Both, the community metabolic diversity and the utilization of C-sources increased in all alfalfa lines with culture time and regardless of transgenic or non-transgenic nature of lines.

Influence of intermittent estuary outflow on coastal sediments of adjacent sandy beaches

Outflows from estuaries potentially contribute to the productivity of adjacent coastal waters, although most previous work has been on estuaries with considerable river discharge. We investigated the influence of estuary outflow on aspects of coastal sediments adjacent to two seasonally intermittent estuaries, the Curdies and Anglesea Rivers, in southwest Victoria, Australia. For each estuary, we measured sediment organic matter, microphytobenthic chlorophyll a and microbial utilization of carbon sources at three locations associated with each estuary: (1) inside estuary mouth, (2) estuary swash and (3) control swash (an open beach distant from any estuarine influences). Sampling occurred one week before and at one and nine weeks after both an artificial mouth opening and a separate natural flood at both estuaries. Significant temporal changes were detected for all three variables at the estuary mouth and estuary swash but the direction of change was inconsistent across the two estuaries and between the artificial mouth opening and natural flood. Organic matter in both estuaries showed no difference after the artificial mouth openings. Only Anglesea showed an increase in organic matter in the estuary mouth and estuary swash after the floods. Microphytobenthic chlorophyll a concentrations were highest when the estuary mouths were closed. Concentrations decreased at all locations at Curdies after the mouth was artificially opened. The estuary mouth at Anglesea sustained high chlorophyll concentrations and the estuary swash increased one week post artificial opening. The flood event resulted in an increase in chlorophyll a at the estuary mouth and swash at both estuaries, one week post flood. At Curdies, the microbial utilization of different carbon sources changed after both mouth events; estuary mouth and estuary swash showed similar patterns at one and nine weeks post opening. At Anglesea, the bacteria utilized different carbon sources between locations and the only significant interaction between location and time was post flood with change in carbon sources utilized by bacteria in the estuary mouth and estuary swash for one and nine weeks post flood. The southern coastline of Australia is characterized by estuaries with small catchments. This study highlights the spatial and temporal variability in the effects of the output of relatively small, intermittent estuaries on coastal sediment of adjacent beaches, particularly during prolonged periods of drought.

Patterns of utilization of different carbon sources by Chytridiomycota

A phylogenetically diverse set of seventeen isolates of Chytridiomycota were selected for a study of the utilization of common carbohydrates as sole carbon sources in synthetic media. Rhizophlyctis rosea AUS 13 is capable of the digestion of crystalline cellulose in the form of lens paper, filter paper and powdered filter paper and grows well with noncrystaline carboxymethyl cellulose or cellobiose, but cannot use starch or maltose as sole carbon sources in liquid and on solid media. None of the other sixteen isolates tested can digest crystalline cellulose, but all grow well on starch and maltose and several can also use cellobiose and/or sucrose as a sole carbon source. Four of the other sixteen isolates could also digest carboxymethyl cellulose slowly. Glucose is an excellent sole source of carbon in synthetic media for all seventeen isolates in the present study. In general, these data suggest variability in the ability of zoosporic true fungi to use carbohydrates other than glucose as sole sources of carbon. Four patterns of carbohydrate utilization emerged from this study of seventeen isolates. R. rosea degrades cellulose over a relatively wide pH range which suggests that the cellulase enzymes are stable over a wide pH range.

A new chemically defined medium for wine lactic acid bacteria

Growth and activity of lactic acid bacteria is crucial for the production and quality of grape wines but studying their metabolism is difficult in wines or complex laboratory media because of the undefined substrate pools. This work presents a new chemically defined medium that meets the fastidious nutritional requirements of wine lactic acid bacteria and yields rapid and strong growth. The new medium is composed of 44 constituents and a precise protocol is provided for its preparation. Maximum specific growth rates and growth yields of the wine strains studied were comparable to those obtained in common laboratory media, and the new medium allows for various modifications, such as changing the medium pH to the wine range, addition of L-malic acid or utilization of different carbon sources while maintaining growth of wine lactic acid bacteria. The medium was successfully tested with 22 wine strains of the genera Oenococcus, Lactobacillus and Pediococcus. It is suggested that this chemically defined medium be considered for the investigation of the nutritional requirements and metabolism of wine lactic acid bacteria.

Selective utilization of different carbon sources by microorganism during fermentation

Selective utilization of different carbon sources by microorganism during fermentation

Relationships between sulfide-oxidizing bacterial mats and their carbon sources in northern Gulf of Mexico cold seeps

Chemical and isotopic characterization of microbial mats collected from methane and petroleum seeps in the Gulf of Mexico suggest microbial mat color is related to carbon utilization. A survey of white and orange-colored microbial mats collected in the northern Gulf of Mexico from the Brine Pool NR-1 (BP) and a hydrate mound site in Green Canyon 234 (GC 234) during Johnson Sea-Link submersible dives was conducted to explore the bacterial utilization of different carbon sources. Sedimentary organic matter at BP is predominantly derived from biogenic methane whereas organic material available in sediments at GC 234 originates from a mixture of methane and non-methane hydrocarbons. Interstitial sulfide concentrations were significantly elevated in porewater fluids below white mats collected from BP (1.2 ± 0.2 mM) and below orange mats at GC 234 (6.1 ± 0.7 mM). Sulfate reduction rates, ranging from 0.4 to 3.8 μmol SO 4 cm −3 d −1, indicate rapid sulfate consumption below GC 234 orange mats. A model based on carbon isotopes was used to delineate possible inorganic and organic carbon sources to BP white mats and GC 234 orange mats. The results suggest the white mats are chemoautotrophic and that the orange mats may employ either heterotrophy or autotrophy.

The yeast CPC2/ASC1 gene is regulated by the transcription factors Fhl1p and Ifh1p

CPC2/ASC1 is one of the most abundantly transcribed genes in Saccharomyces cerevisiae. It encodes a ribosome-associated Gbeta-like WD protein, which is highly conserved from yeast to man. Here, we show that CPC2 transcription depends on the carbon source and is induced during utilization of the sugar glucose. CPC2 promoter deletion and insertion analyses identified two upstream activation sequence elements for CPC2, which are required for basal expression and regulation. One of these upstream activation sequence elements has an ATGTACGGATGT motif, which has previously been described as a putative binding site for the forkhead-like transcription factor Fhl1p. Deletion of FHL1 reduces CPC2 transcription significantly in presence of glucose, but has no effect when the non-fermentable carbon source ethanol is provided. Increased amounts of the Fhl1p co-regulator Ifh1p induce CPC2 transcription even when ethanol is utilized. These data suggest that the interaction between Fhl1p and Ifh1p is critical for the regulation of CPC2 transcription during utilization of different carbon sources.

Diversity of nif gene location and nitrogen fixation among root-associated Enterobacter and Klebsiella strains

Our previous work showed that strains of dinitrogen fixing enterobacter and Klebsiella were found associated with the roots of uncultivated grasses in Finland more commonly than other species of diazotrophic bacteria. In this paper we compare E. agglomerans strains to K. pneumoniae and K. terrigena strains, and show that the E. agglomerans strains fall into two biogroups. The groups differ not only in the utilization of different carbon sources and other physiological characteristics such as the production of indole, but also in the physiology and genetics of nitrogenase activity. Biotype 1 (isolated from Achillea millefolium, Calamagrostis arundinacea, and Phleum pratense) showed active nitrogenase in atmospheric oxygen, whereas biotype 2 (from Phalaris arundinacea) resembled K. pneumoniae in that it was active at reduced oxygen pressure (pO2<-0.002) only. DNA of all strains showed positive hybridization with K. pneumoniae nifHDK genes (pSA30) but differed in the location of the genes. Biotype 1 strains of E. agglomerans carried nifHDK genes on large (105–125 Mdal) plasmids, whereas no plasmid was detected in biotype 2 or in the K. pneumoniae strains isolated from Agrostis stolonifera and Poa pratensis and K. terrigena strain isolated from Carex pallescens. The one K. terrigena strain (isolated from Ph. arundinacea) that was found to contain an indigenous plasmid (80 Mdal) did not carry nifHDK genes on this plasmid.

Characterization of indigenous rhizobia from wild legumes

Abstract Rhizobia isolated from root nodules of wild legumes (Macroptilium lathyroides (L.) Urb, Phaseolus atropurpureus Moc ⇐p; Sesse DC, Clitoria ternatea L., and Crotalaria verrucosa L.) were examined for cultural, biochemical, serological and symbiotic characters. The strains were characterized by their colony morphology, growth rate, alkali production, tolerance to acid or alkali, type of flagella, temperature sensitivity, resistance to antibiotics, utilization of different carbon sources, serological relatedness and ability to nodulate other host species. All of the strains had cultural characters consistent with the slow growing rhizobia of the cowpea group. Serological relatedness examined by the enzyme-linked immunosorbent assay (ELISA) technique showed that all of the 4 strains have antigenic homology to an isolate from a wild Arachis sp. and varying degrees of relatedness to cowpea rhizobia. All strains produced effective nodules on cowpeas and pigeonpeas but not on peanuts and kidney beans.

Characterization of indigenous rhizobia from wild legumes

Rhizobia isolated from root nodules of wild legumes (Macroptilium lathyroides (L.) Urb, Phaseolus atropurpureus Moc & Sesse DC, Clitoria ternatea L., and Crotalaria verrucosa L.) were examined for cultural, biochemical, serological and symbiotic characters. The strains were characterized by their colony morphology, growth rate, alkali production, tolerance to acid or alkali, type of flagella, temperature sensitivity, resistance to antibiotics, utilization of different carbon sources, serological relatedness and ability to nodulate other host species. All of the strains had cultural characters consistent with the slow growing rhizobia of the cowpea group. Serological relatedness examined by the enzyme-linked immunosorbent assay (ELISA) technique showed that all of the 4 strains have antigenic homology to an isolate from a wild Arachis sp. and varying degrees of relatedness to cowpea rhizobia. All strains produced effective nodules on cowpeas and pigeonpeas but not on peanuts and kidney beans.