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Sample records for acid-tolerant heterotrophic microorganisms

  1. Organic acid-tolerant microorganisms and uses thereof for producing organic acids

    DOEpatents

    Pfleger, Brian Frederick; Begemann, Matthew Brett

    2014-05-06

    Organic acid-tolerant microorganisms and methods of using same. The organic acid-tolerant microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid (3HP), acrylic acid, and propionic acid. Further modifications to the microorganisms such as increasing expression of malonyl-CoA reductase and/or acetyl-CoA carboxylase provide or increase the ability of the microorganisms to produce 3HP. Methods of generating an organic acid with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers include replacing acsA or homologs thereof in cells with genes of interest and selecting for the cells comprising the genes of interest with amounts of organic acids effective to inhibit growth of cells harboring acsA or the homologs.

  2. DENTINE CARIES: ACID-TOLERANT MICROORGANISMS AND ASPECTS ON COLLAGEN DEGRADATION.

    PubMed

    Lager, Anders Hedenbjörk

    2014-01-01

    Dental caries is a common disease all over the world, despite the fact that it can be both effectively prevented and treated. It is driven by acids produced by oral microorganisms as a consequence of their metabolism of dietary carbohydrates. Given enough acid challenge, eventually the tooth enamel barrier will be broken down, and the carious lesion will extend into underlying hard tissue, forming a macroscopic cavity in the dentine. In comparison to biofilm on enamel, a dentine carious lesion provides a vastly different environment for the residing microorganisms. The environment influences the types and numbers of microorganisms that can colonize the dentine caries lesion. The overall aims for this thesis are to enumerate and further study microorganisms found in established dentine caries lesions and also to illuminate how host-derived proteolytic enzymes might contribute to this degradation, not only to better understand the caries process in dentine but also to find incitements for new methods to influence the natural progression of caries lesions. In Paper I, the numbers of remaining viable microorganisms after completed excavation using two excavation methods were investigated. Samples of carious dentine tissue were collected before and after excavation and cultivated on different agar media in different atmospheres. Analysis was performed by counting the number of colony-forming units (CFUs). Key findings: The number of remaining microorganisms after excavation was low for both methods, but some microorganisms always remained in the cavity floors even when the cavities were judged as caries free using normal clinical criteria. In Paper II, the acid tolerant microbiota in established dentine caries lesions was investigated. Samples were taken as in Paper I, but on three levels (superficial, center of lesion, floor of lesion after completed excavation). The samples were cultivated in anaerobic conditions on solid pH-selective agar media of different acidity

  3. 14C-most-probable-number method for enumeration of active heterotrophic microorganisms in natural waters.

    PubMed Central

    Lehmicke, L G; Williams, R T; Crawford, R L

    1979-01-01

    A most-probable-number method using 14C-labeled substrates is described for the enumeration of aquatic populations of heterotrophic microorganisms. Natural populations of microorganisms are inoculated into dilution replicates prepared from the natural water from which the organisms originated. The natural water is supplemented with a 14C-labeled compound added so as to approximate a true environmental concentration. 14CO2 evolved by individual replicates is trapped in NaOH and counted by liquid scintillation techniques for use in scoring replicates as positive or negative. Positives (14CO2 evolution) are easily distinguished from negatives (no 14CO2 evolution). The results from a variety of environments using the 14CO2 procedure agreed well with previously described methods, in most instances. The 14C-most-probable-number method described here reduces handling procedures over previously described most-probable-number procedures using 14C-labeled substrates. It also appears to have advantages over other enumeration methods in its attempt to approximate natural conditions more closely. PMID:120133

  4. Interactions of the metal tolerant heterotrophic microorganisms and iron oxidizing autotrophic bacteria from sulphidic mine environment during bioleaching experiments.

    PubMed

    Jeremic, Sanja; Beškoski, Vladimir P; Djokic, Lidija; Vasiljevic, Branka; Vrvić, Miroslav M; Avdalović, Jelena; Gojgić Cvijović, Gordana; Beškoski, Latinka Slavković; Nikodinovic-Runic, Jasmina

    2016-05-01

    Iron and sulfur oxidizing chemolithoautotrophic acidophilic bacteria, such as Acidithiobacillus species, hold the dominant role in mine environments characterized by low pH values and high concentrations of reduced sulfur and iron compounds, such as ores, rocks and acid drainage waters from mines. On the other hand, heterotrophic microorganisms, especially their biofilms, from these specific niches are receiving increased attention, but their potential eco-physiological roles have not been fully understood. Biofilms are considered a threat to human health, but biofilms also have beneficial properties as they are deployed in waste recycling and bioremediation systems. We have analyzed interactions of the metal tolerant heterotrophic microorganisms in biofilms with iron oxidizing autotrophic bacteria both from the sulphidic mine environment (copper mine Bor, Serbia). High tolerance to Cu(2+), Cd(2+) and Cr(6+) and the presence of genetic determinants for the respective metal tolerance and biofilm-forming ability was shown for indigenous heterotrophic bacteria that included strains of Staphylococcus and Rhodococcus. Two well characterized bacteria- Pseudomonas aeruginosa PAO1 (known biofilm former) and Cupriavidus metallidurans CH34 (known metal resistant representative) were also included in the study. The interaction and survivability of autotrophic iron oxidizing Acidithiobacillus bacteria and biofilms of heterotrophic bacteria during co-cultivation was revealed. Finally, the effect of heterotrophic biofilms on bioleaching process with indigenous iron oxidizing Acidithiobacillus species was shown not to be inhibitory under in vitro conditions. PMID:26942859

  5. Interactions of the metal tolerant heterotrophic microorganisms and iron oxidizing autotrophic bacteria from sulphidic mine environment during bioleaching experiments.

    PubMed

    Jeremic, Sanja; Beškoski, Vladimir P; Djokic, Lidija; Vasiljevic, Branka; Vrvić, Miroslav M; Avdalović, Jelena; Gojgić Cvijović, Gordana; Beškoski, Latinka Slavković; Nikodinovic-Runic, Jasmina

    2016-05-01

    Iron and sulfur oxidizing chemolithoautotrophic acidophilic bacteria, such as Acidithiobacillus species, hold the dominant role in mine environments characterized by low pH values and high concentrations of reduced sulfur and iron compounds, such as ores, rocks and acid drainage waters from mines. On the other hand, heterotrophic microorganisms, especially their biofilms, from these specific niches are receiving increased attention, but their potential eco-physiological roles have not been fully understood. Biofilms are considered a threat to human health, but biofilms also have beneficial properties as they are deployed in waste recycling and bioremediation systems. We have analyzed interactions of the metal tolerant heterotrophic microorganisms in biofilms with iron oxidizing autotrophic bacteria both from the sulphidic mine environment (copper mine Bor, Serbia). High tolerance to Cu(2+), Cd(2+) and Cr(6+) and the presence of genetic determinants for the respective metal tolerance and biofilm-forming ability was shown for indigenous heterotrophic bacteria that included strains of Staphylococcus and Rhodococcus. Two well characterized bacteria- Pseudomonas aeruginosa PAO1 (known biofilm former) and Cupriavidus metallidurans CH34 (known metal resistant representative) were also included in the study. The interaction and survivability of autotrophic iron oxidizing Acidithiobacillus bacteria and biofilms of heterotrophic bacteria during co-cultivation was revealed. Finally, the effect of heterotrophic biofilms on bioleaching process with indigenous iron oxidizing Acidithiobacillus species was shown not to be inhibitory under in vitro conditions.

  6. Comparison of the effect of salinity on the D/H ratio of fatty acids of heterotrophic and photoautotrophic microorganisms.

    PubMed

    Heinzelmann, Sandra M; Chivall, David; M'Boule, Daniela; Sinke-Schoen, Danielle; Villanueva, Laura; Damsté, Jaap S Sinninghe; Schouten, Stefan; van der Meer, Marcel T J

    2015-05-01

    The core metabolism of microorganisms has a major influence on the hydrogen isotopic composition of their fatty acids. Heterotrophic microorganisms produce fatty acids with a deuterium to hydrogen (D/H) ratio either slightly depleted or enriched in D compared to the growth water, while photo- and chemoautotrophic microorganisms produce fatty acids which are heavily depleted in D. However, besides metabolism other biochemical and environmental factors (i.e. biosynthetic pathways, growth phase and temperature) have been shown to affect the D/H ratio of fatty acids, and it is necessary to evaluate the magnitude of these effects compared to that of metabolism. Here, we show that the effect of salinity on the D/H ratio of fatty acids depends on the core metabolism of the microorganism. While fatty acids of the photoautotroph Isochrysis galbana become more enriched in D with increasing salinity (enrichment of 30-40‰ over a range of 25 salinity units), no effect of salinity on the D/H ratio of fatty acids of the heterotrophic Pseudomonas str. LFY10 was observed ((ε)lipid/water of the C16:0 fatty acid of ~120‰ over a range of 10 salinity units). This can likely be explained by the relative contributions of different H and nicotinamide adenine dinucleotide phosphate sources during fatty acid biosynthesis. PMID:25883110

  7. Comparison of the effect of salinity on the D/H ratio of fatty acids of heterotrophic and photoautotrophic microorganisms.

    PubMed

    Heinzelmann, Sandra M; Chivall, David; M'Boule, Daniela; Sinke-Schoen, Danielle; Villanueva, Laura; Damsté, Jaap S Sinninghe; Schouten, Stefan; van der Meer, Marcel T J

    2015-05-01

    The core metabolism of microorganisms has a major influence on the hydrogen isotopic composition of their fatty acids. Heterotrophic microorganisms produce fatty acids with a deuterium to hydrogen (D/H) ratio either slightly depleted or enriched in D compared to the growth water, while photo- and chemoautotrophic microorganisms produce fatty acids which are heavily depleted in D. However, besides metabolism other biochemical and environmental factors (i.e. biosynthetic pathways, growth phase and temperature) have been shown to affect the D/H ratio of fatty acids, and it is necessary to evaluate the magnitude of these effects compared to that of metabolism. Here, we show that the effect of salinity on the D/H ratio of fatty acids depends on the core metabolism of the microorganism. While fatty acids of the photoautotroph Isochrysis galbana become more enriched in D with increasing salinity (enrichment of 30-40‰ over a range of 25 salinity units), no effect of salinity on the D/H ratio of fatty acids of the heterotrophic Pseudomonas str. LFY10 was observed ((ε)lipid/water of the C16:0 fatty acid of ~120‰ over a range of 10 salinity units). This can likely be explained by the relative contributions of different H and nicotinamide adenine dinucleotide phosphate sources during fatty acid biosynthesis.

  8. Acid tolerance in amphibians

    SciTech Connect

    Pierce, B.A.

    1985-04-01

    Studies of amphibian acid tolerance provide information about the potential effects of acid deposition on amphibian communities. Amphibians as a group appear to be relatively acid tolerant, with many species suffering increased mortality only below pH 4. However, amphibians exhibit much intraspecific variation in acid tolerance, and some species are sensitive to even low levels of acidity. Furthermore, nonlethal effects, including depression of growth rates and increases in developmental abnormalities, can occur at higher pH.

  9. Self-sustained phototrophic microbial fuel cells based on the synergistic cooperation between photosynthetic microorganisms and heterotrophic bacteria.

    PubMed

    He, Zhen; Kan, Jinjun; Mansfeld, Florian; Angenent, Largus T; Nealson, Kenneth H

    2009-03-01

    A sediment-type self-sustained phototrophic microbial fuel cell (MFC) was developed to generate electricity through the synergistic interaction between photosynthetic microorganisms and heterotrophic bacteria. Under illumination, the MFC continuously produced electricity without the external input of exogenous organics or nutrients. The current increased in the dark and decreased with the light on, possibly because of the negative effect of the oxygen produced via photosynthesis. Continuous illumination inhibited the current production while the continuous dark period stimulated the current production. Extended darkness resulted in a decrease of current, probably because of the consumption of the organics accumulated during the light phase. Using color filters or increasing the thickness of the sediment resulted in a reduction of the oxygen-induced inhibition. Molecular taxonomic analysis revealed that photosynthetic microorganisms including cyanobacteria and microalgae predominated in the water phase, adjacent to the cathode and on the surface of the sediment. In contrast, the sediments were dominated by heterotrophic bacteria, becoming less diverse with increasing depth. In addition, results from the air-cathode phototrophic MFC confirmed the light-induced current production while the test with the two-chamber MFC (in the dark) indicated the presence of electricigenic bacteria in the sediment.

  10. [Advances in functional genomics studies underlying acetic acid tolerance of Saccharomyces cerevisiae].

    PubMed

    Zhao, Xinqing; Zhang, Mingming; Xu, Guihong; Xu, Jianren; Bai, Fengwu

    2014-03-01

    Industrial microorganisms are subject to various stress conditions, including products and substrates inhibitions. Therefore, improvement of stress tolerance is of great importance for industrial microbial production. Acetic acid is one of the major inhibitors in the cellulosic hydrolysates, which affects seriously on cell growth and metabolism of Saccharomyces cerevisiae. Studies on the molecular mechanisms underlying adaptive response and tolerance of acetic acid of S. cerevisiae benefit breeding of robust strains of industrial yeast for more efficient production. In recent years, more insights into the molecular mechanisms underlying acetic acid tolerance have been revealed through analysis of global gene expression and metabolomics analysis, as well as phenomics analysis by single gene deletion libraries. Novel genes related to response to acetic acid and improvement of acetic acid tolerance have been identified, and novel strains with improved acetic acid tolerance were constructed by modifying key genes. Metal ions including potassium and zinc play important roles in acetic acid tolerance in S. cerevisiae, and the effect of zinc was first discovered in our previous studies on flocculating yeast. Genes involved in cell wall remodeling, membrane transport, energy metabolism, amino acid biosynthesis and transport, as well as global transcription regulation were discussed. Exploration and modification of the molecular mechanisms of yeast acetic acid tolerance will be done further on levels such as post-translational modifications and synthetic biology and engineering; and the knowledge obtained will pave the way for breeding robust strains for more efficient bioconversion of cellulosic materials to produce biofuels and bio-based chemicals.

  11. Acid tolerance mechanisms utilized by Streptococcus mutans

    PubMed Central

    Matsui, Robert; Cvitkovitch, Dennis

    2010-01-01

    Since its discovery in 1924 by J Clarke, Streptococcus mutans has been the focus of rigorous research efforts due to its involvement in caries initiation and progression. Its ability to ferment a range of dietary carbohydrates can rapidly drop the external environmental pH, thereby making dental plaque inhabitable to many competing species and can ultimately lead to tooth decay. Acid production by this oral pathogen would prove suicidal if not for its remarkable ability to withstand the acid onslaught by utilizing a wide variety of highly evolved acid-tolerance mechanisms. The elucidation of these mechanisms will be discussed, serving as the focus of this review. PMID:20210551

  12. Genetic dissection of acetic acid tolerance in Saccharomyces cerevisiae.

    PubMed

    Geng, Peng; Xiao, Yin; Hu, Yun; Sun, Haiye; Xue, Wei; Zhang, Liang; Shi, Gui-Yang

    2016-09-01

    Dissection of the hereditary architecture underlying Saccharomyces cerevisiae tolerance to acetic acid is essential for ethanol fermentation. In this work, a genomics approach was used to dissect hereditary variations in acetic acid tolerance between two phenotypically different strains. A total of 160 segregants derived from these two strains were obtained. Phenotypic analysis indicated that the acetic acid tolerance displayed a normal distribution in these segregants, and suggested that the acetic acid tolerant traits were controlled by multiple quantitative trait loci (QTLs). Thus, 220 SSR markers covering the whole genome were used to detect QTLs of acetic acid tolerant traits. As a result, three QTLs were located on chromosomes 9, 12, and 16, respectively, which explained 38.8-65.9 % of the range of phenotypic variation. Furthermore, twelve genes of the candidates fell into the three QTL regions by integrating the QTL analysis with candidates of acetic acid tolerant genes. These results provided a novel avenue to obtain more robust strains.

  13. Genetic dissection of acetic acid tolerance in Saccharomyces cerevisiae.

    PubMed

    Geng, Peng; Xiao, Yin; Hu, Yun; Sun, Haiye; Xue, Wei; Zhang, Liang; Shi, Gui-Yang

    2016-09-01

    Dissection of the hereditary architecture underlying Saccharomyces cerevisiae tolerance to acetic acid is essential for ethanol fermentation. In this work, a genomics approach was used to dissect hereditary variations in acetic acid tolerance between two phenotypically different strains. A total of 160 segregants derived from these two strains were obtained. Phenotypic analysis indicated that the acetic acid tolerance displayed a normal distribution in these segregants, and suggested that the acetic acid tolerant traits were controlled by multiple quantitative trait loci (QTLs). Thus, 220 SSR markers covering the whole genome were used to detect QTLs of acetic acid tolerant traits. As a result, three QTLs were located on chromosomes 9, 12, and 16, respectively, which explained 38.8-65.9 % of the range of phenotypic variation. Furthermore, twelve genes of the candidates fell into the three QTL regions by integrating the QTL analysis with candidates of acetic acid tolerant genes. These results provided a novel avenue to obtain more robust strains. PMID:27430512

  14. Differential soil acidity tolerance of dry bean genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil acidity is a major yield limiting factors for bean production in the tropical regions. Using soil acidity tolerant genotypes is an important strategy in improving bean yields and reducing cost of production. A greenhouse experiment was conducted with the objective of evaluating 20 dry bean geno...

  15. The more, the merrier: heterotroph richness stimulates methanotrophic activity.

    PubMed

    Ho, Adrian; de Roy, Karen; Thas, Olivier; De Neve, Jan; Hoefman, Sven; Vandamme, Peter; Heylen, Kim; Boon, Nico

    2014-09-01

    Although microorganisms coexist in the same environment, it is still unclear how their interaction regulates ecosystem functioning. Using a methanotroph as a model microorganism, we determined how methane oxidation responds to heterotroph diversity. Artificial communities comprising of a methanotroph and increasing heterotroph richness, while holding equal starting cell numbers were assembled. We considered methane oxidation rate as a functional response variable. Our results showed a significant increase of methane oxidation with increasing heterotroph richness, suggesting a complex interaction in the cocultures leading to a stimulation of methanotrophic activity. Therefore, not only is the methanotroph diversity directly correlated to methanotrophic activity for some methanotroph groups as shown before, but also the richness of heterotroph interacting partners is relevant to enhance methane oxidation too. In this unprecedented study, we provide direct evidence showing how heterotroph richness exerts a response in methanotroph-heterotroph interaction, resulting in increased methanotrophic activity. Our study has broad implications in how methanotroph and heterotroph interact to regulate methane oxidation, and is particularly relevant in methane-driven ecosystems.

  16. Intracellular pH of acid-tolerant ruminal bacteria.

    PubMed Central

    Russell, J B

    1991-01-01

    Acid-tolerant ruminal bacteria (Bacteroides ruminicola B1(4), Selenomonas ruminantium HD4, Streptococcus bovis JB1, Megasphaera elsdenii B159, and strain F) allowed their intracellular pH to decline as a function of extracellular pH and did not generate a large pH gradient across the cell membrane until the extracellular pH was low (less than 5.2). This decline in intracellular pH prevented an accumulation of volatile fatty acid anions inside the cells. PMID:1781695

  17. Usnic acid controls the acidity tolerance of lichens.

    PubMed

    Hauck, Markus; Jürgens, Sascha-René

    2008-11-01

    The hypotheses were tested that, firstly, lichens producing the dibenzofuran usnic acid colonize substrates characterized by specific pH ranges, secondly, this preferred pH is in a range where soluble usnic acid and its corresponding anion occur in similar concentrations, and thirdly, usnic acid makes lichens vulnerable to acidity. Lichens with usnic acid prefer an ambient pH range between 3.5 and 5.5 with an optimum between 4.0 and 4.5. This optimum is close to the pK(a1) value of usnic acid of 4.4. Below this optimum pH, dissolved SO(2) reduces the chlorophyll fluorescence yield more in lichens with than without their natural content of usnic acid. This suggests that usnic acid influences the acidity tolerance of lichens. The putative mechanism of the limited acidity tolerance of usnic acid-containing lichens is the acidification of the cytosol by molecules of protonated usnic acid shuttling protons through the plasma membrane at an apoplastic pH

  18. Acid tolerance, proton permeabilities, and membrane ATPases of oral streptococci.

    PubMed Central

    Bender, G R; Sutton, S V; Marquis, R E

    1986-01-01

    Differences in acid tolerance among representative oral streptococci were found to be related more closely to the dynamic permeabilities of the bacteria to protons than to differences in the sensitivities of cell membranes to gross damage caused by environmental acidification. For Streptococcus mutans GS-5, Streptococcus sanguis NCTC 10904, and Streptococcus salivarius ATCC 13419, gross membrane damage, indicated by the release of magnesium from whole cells, occurred at pH values below about 4 and was rapid and extensive at pH values of about 3 or less. A more aciduric, lactic acid bacterium, Lactobacillus casei ATCC 4646, was more resistant to environmental acidification, and gross membrane damage was evident only at pH values below 3. Assessments of the movements of protons into S. mutans cells after an acid pulse at various pH values indicated that permeability to protons was minimal at a pH value of about 5, at which the average half time for pH equilibration across the cell membrane was about 12 min. The corresponding values for the less aciduric organism S. sanguis were pH 7 and 8.2 min, and the values for the intermediate organism S. salivarius were pH 6 and 6.6 min. The ATPase inhibitor dicyclohexylcarbodiimide acted to increase markedly the permeability of each organism to protons, and this action indicated that permeability involved not only the passive inflow of protons but also active outflow through the proton-translocating membrane ATPase. Membranes were isolated from each of the bacteria, and pH profiles for ATPase activities indicated pH optima of about 7.5, 7.0, 6.0, and 5.0 for S. sanguis, S. salivarius, S. mutans, and L. casei, respectively. Thus, the pH profiles for the enzymes reflected the acid tolerances of the bacteria and the permeabilities of whole cells to protons. PMID:3015800

  19. 40 CFR 180.318 - 4-(2-Methyl-4-chlorophenoxy) butyric acid; tolerance for residues.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...)butanoic acid, and its metabolite MCPA, (4-chloro-2-methylphenoxy)acetic acid, in or on the following food... acid; tolerance for residues. 180.318 Section 180.318 Protection of Environment ENVIRONMENTAL... FOOD Specific Tolerances § 180.318 4-(2-Methyl-4-chlorophenoxy) butyric acid; tolerance for...

  20. 40 CFR 180.318 - 4-(2-Methyl-4-chlorophenoxy) butyric acid; tolerance for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...)butanoic acid, and its metabolite MCPA, (4-chloro-2-methylphenoxy)acetic acid, in or on the following food... acid; tolerance for residues. 180.318 Section 180.318 Protection of Environment ENVIRONMENTAL... FOOD Specific Tolerances § 180.318 4-(2-Methyl-4-chlorophenoxy) butyric acid; tolerance for...

  1. 40 CFR 180.318 - 4-(2-Methyl-4-chlorophenoxy) butyric acid; tolerance for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...)butanoic acid, and its metabolite MCPA, (4-chloro-2-methylphenoxy)acetic acid, in or on the following food... acid; tolerance for residues. 180.318 Section 180.318 Protection of Environment ENVIRONMENTAL... FOOD Specific Tolerances § 180.318 4-(2-Methyl-4-chlorophenoxy) butyric acid; tolerance for...

  2. Iron Transformations Induced by an Acid-Tolerant Desulfosporosinus Species

    PubMed Central

    Bertel, Doug; Peck, John; Quick, Thomas J.

    2012-01-01

    The mineralogical transformations of Fe phases induced by an acid-tolerant, Fe(III)- and sulfate-reducing bacterium, Desulfosporosinus sp. strain GBSRB4.2 were evaluated under geochemical conditions associated with acid mine drainage-impacted systems (i.e., low pH and high Fe concentrations). X-ray powder diffractometry coupled with magnetic analysis by first-order reversal curve diagrams were used to evaluate mineral phases produced by GBSRB4.2 in media containing different ratios of Fe(II) and Fe(III). In medium containing Fe predominately in the +II oxidation state, ferrimagnetic, single-domain greigite (Fe3S4) was formed, but the addition of Fe(III) inhibited greigite formation. In media that contained abundant Fe(III) [as schwertmannite; Fe8O8(OH)6SO4 · nH2O], the activities of strain GBSRB4.2 enhanced the transformation of schwertmannite to goethite (α-FeOOH), due to the increased pH and Fe(II) concentrations that resulted from the activities of GBSRB4.2. PMID:22038606

  3. Iron transformations induced by an acid-tolerant Desulfosporosinus species.

    PubMed

    Bertel, Doug; Peck, John; Quick, Thomas J; Senko, John M

    2012-01-01

    The mineralogical transformations of Fe phases induced by an acid-tolerant, Fe(III)- and sulfate-reducing bacterium, Desulfosporosinus sp. strain GBSRB4.2 were evaluated under geochemical conditions associated with acid mine drainage-impacted systems (i.e., low pH and high Fe concentrations). X-ray powder diffractometry coupled with magnetic analysis by first-order reversal curve diagrams were used to evaluate mineral phases produced by GBSRB4.2 in media containing different ratios of Fe(II) and Fe(III). In medium containing Fe predominately in the +II oxidation state, ferrimagnetic, single-domain greigite (Fe₃S₄) was formed, but the addition of Fe(III) inhibited greigite formation. In media that contained abundant Fe(III) [as schwertmannite; Fe₈O₈(OH)₆SO₄ · nH₂O], the activities of strain GBSRB4.2 enhanced the transformation of schwertmannite to goethite (α-FeOOH), due to the increased pH and Fe(II) concentrations that resulted from the activities of GBSRB4.2. PMID:22038606

  4. Thermal acclimation in widespread heterotrophic soil microbes.

    PubMed

    Crowther, Thomas W; Bradford, Mark A

    2013-04-01

    Respiration by plants and microorganisms is primarily responsible for mediating carbon exchanges between the biosphere and atmosphere. Climate warming has the potential to influence the activity of these organisms, regulating exchanges between carbon pools. Physiological 'down-regulation' of warm-adapted species (acclimation) could ameliorate the predicted respiratory losses of soil carbon under climate change scenarios, but unlike plants and symbiotic microbes, the existence of this phenomenon in heterotrophic soil microbes remains controversial. Previous studies using complex soil microbial communities are unable to distinguish physiological acclimation from other community-scale adjustments. We explored the temperature-sensitivity of individual saprotrophic basidiomycete fungi growing in agar, showing definitively that these widespread heterotrophic fungi can acclimate to temperature. In almost all cases, the warm-acclimated individuals had lower growth and respiration rates at intermediate temperatures than cold-acclimated isolates. Inclusion of such microbial physiological responses to warming is essential to enhance the robustness of global climate-ecosystem carbon models. PMID:23331708

  5. Acid tolerance response of Bordetella bronchiseptica in avirulent phase.

    PubMed

    Fingermann, M; Hozbor, D

    2015-12-01

    Bordetella bronchiseptica is a Gram-negative bacterium responsible for respiratory diseases in many mammalian hosts, including humans. This pathogen has been shown as able to persist inside the host cells, even in the phagosomes that are acidified to pH 4.5-5.0 after bacterial infection. Here we evaluated the resistance of B. bronchiseptica to survive under acidic conditions. In particular we analyzed the bacterial capacity to develop the mechanism known as acid tolerance response (ATR). Our studies were mainly focused on the avirulent phase of the bacteria since this phenotypic phase was reported to be more resistant to environmental stress conditions than the virulent phase. Results from B. bronchiseptica in virulent phase were also included for comparison purposes. In fact, for B. bronchiseptica 9.73 bacteria in virulent phase we observed that the viability of bacteria does not decrease significantly when grown at pH as low as 4.5, but it is affected when the pH of the medium was equal to or less than 4.0. After acid-adaptation at pH 5.5 for several hours, the survival rate of B. bronchiseptica 9.73 at lethal pH 4.0 for 6h was increased. Interestingly, the avirulent phase mediated by the two-component BvgAS system conferred further resistance to lethal acid challenge and a marked increase in the magnitude of the expressed ATR. The ATR for this avirulent phase seems to be associated with changes in LPS and surface protein profiles. 2D-gel electrophoresis revealed at least 25 polypeptides differentially expressed, 17 of which were only expressed or over-expressed under acid conditions. Using MALDI-TOF mass spectrometry, 10 of these differentially expressed polypeptides were identified. PMID:26640052

  6. Acid tolerance response of Bordetella bronchiseptica in avirulent phase.

    PubMed

    Fingermann, M; Hozbor, D

    2015-12-01

    Bordetella bronchiseptica is a Gram-negative bacterium responsible for respiratory diseases in many mammalian hosts, including humans. This pathogen has been shown as able to persist inside the host cells, even in the phagosomes that are acidified to pH 4.5-5.0 after bacterial infection. Here we evaluated the resistance of B. bronchiseptica to survive under acidic conditions. In particular we analyzed the bacterial capacity to develop the mechanism known as acid tolerance response (ATR). Our studies were mainly focused on the avirulent phase of the bacteria since this phenotypic phase was reported to be more resistant to environmental stress conditions than the virulent phase. Results from B. bronchiseptica in virulent phase were also included for comparison purposes. In fact, for B. bronchiseptica 9.73 bacteria in virulent phase we observed that the viability of bacteria does not decrease significantly when grown at pH as low as 4.5, but it is affected when the pH of the medium was equal to or less than 4.0. After acid-adaptation at pH 5.5 for several hours, the survival rate of B. bronchiseptica 9.73 at lethal pH 4.0 for 6h was increased. Interestingly, the avirulent phase mediated by the two-component BvgAS system conferred further resistance to lethal acid challenge and a marked increase in the magnitude of the expressed ATR. The ATR for this avirulent phase seems to be associated with changes in LPS and surface protein profiles. 2D-gel electrophoresis revealed at least 25 polypeptides differentially expressed, 17 of which were only expressed or over-expressed under acid conditions. Using MALDI-TOF mass spectrometry, 10 of these differentially expressed polypeptides were identified.

  7. Solid and liquid media for isolating and cultivating acidophilic and acid-tolerant sulfate-reducing bacteria.

    PubMed

    Ňancucheo, Ivan; Rowe, Owen F; Hedrich, Sabrina; Johnson, D Barrie

    2016-05-01

    Growth media have been developed to facilitate the enrichment and isolation of acidophilic and acid-tolerant sulfate-reducing bacteria (aSRB) from environmental and industrial samples, and to allow their cultivation in vitro The main features of the 'standard' solid and liquid devised media are as follows: (i) use of glycerol rather than an aliphatic acid as electron donor; (ii) inclusion of stoichiometric concentrations of zinc ions to both buffer pH and to convert potentially harmful hydrogen sulphide produced by the aSRB to insoluble zinc sulphide; (iii) inclusion of Acidocella aromatica (an heterotrophic acidophile that does not metabolize glycerol or yeast extract) in the gel underlayer of double layered (overlay) solid media, to remove acetic acid produced by aSRB that incompletely oxidize glycerol and also aliphatic acids (mostly pyruvic) released by acid hydrolysis of the gelling agent used (agarose). Colonies of aSRB are readily distinguished from those of other anaerobes due to their deposition and accumulation of metal sulphide precipitates. Data presented illustrate the effectiveness of the overlay solid media described for isolating aSRB from acidic anaerobic sediments and low pH sulfidogenic bioreactors.

  8. Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates

    PubMed Central

    Rawlings, Douglas E

    2005-01-01

    Microorganisms are used in large-scale heap or tank aeration processes for the commercial extraction of a variety of metals from their ores or concentrates. These include copper, cobalt, gold and, in the past, uranium. The metal solubilization processes are considered to be largely chemical with the microorganisms providing the chemicals and the space (exopolysaccharide layer) where the mineral dissolution reactions occur. Temperatures at which these processes are carried out can vary from ambient to 80°C and the types of organisms present depends to a large extent on the process temperature used. Irrespective of the operation temperature, biomining microbes have several characteristics in common. One shared characteristic is their ability to produce the ferric iron and sulfuric acid required to degrade the mineral and facilitate metal recovery. Other characteristics are their ability to grow autotrophically, their acid-tolerance and their inherent metal resistance or ability to acquire metal resistance. Although the microorganisms that drive the process have the above properties in common, biomining microbes usually occur in consortia in which cross-feeding may occur such that a combination of microbes including some with heterotrophic tendencies may contribute to the efficiency of the process. The remarkable adaptability of these organisms is assisted by several of the processes being continuous-flow systems that enable the continual selection of microorganisms that are more efficient at mineral degradation. Adaptability is also assisted by the processes being open and non-sterile thereby permitting new organisms to enter. This openness allows for the possibility of new genes that improve cell fitness to be selected from the horizontal gene pool. Characteristics that biomining microorganisms have in common and examples of their remarkable adaptability are described. PMID:15877814

  9. Microorganism immobilization

    DOEpatents

    Compere, Alicia L.; Griffith, William L.

    1981-01-01

    Live metabolically active microorganisms are immobilized on a solid support by contacting particles of aggregate material with a water dispersible polyelectrolyte such as gelatin, crosslinking the polyelectrolyte by reacting it with a crosslinking agent such as glutaraldehyde to provide a crosslinked coating on the particles of aggregate material, contacting the coated particles with live microorganisms and incubating the microorganisms in contact with the crosslinked coating to provide a coating of metabolically active microorganisms. The immobilized microorganisms have continued growth and reproduction functions.

  10. Improvement of acetic acid tolerance of Saccharomyces cerevisiae using a zinc-finger-based artificial transcription factor and identification of novel genes involved in acetic acid tolerance.

    PubMed

    Ma, Cui; Wei, Xiaowen; Sun, Cuihuan; Zhang, Fei; Xu, Jianren; Zhao, Xinqing; Bai, Fengwu

    2015-03-01

    Acetic acid is present in cellulosic hydrolysate as a potent inhibitor, and the superior acetic acid tolerance of Saccharomyces cerevisiae ensures good cell viability and efficient ethanol production when cellulosic raw materials are used as substrates. In this study, a mutant strain of S. cerevisiae ATCC4126 (Sc4126-M01) with improved acetic acid tolerance was obtained through screening strains transformed with an artificial zinc finger protein transcription factor (ZFP-TF) library. Further analysis indicated that improved acetic acid tolerance was associated with improved catalase (CAT) activity. The ZFP coding sequence associated with the improved phenotype was identified, and real-time RT-PCR analysis revealed that three of the possible genes involved in the enhanced acetic acid tolerance regulated by this ZFP-TF, namely YFL040W, QDR3, and IKS1, showed decreased transcription levels in Sc4126-M01 in the presence of acetic acid, compared to those in the control strain. Sc4126-M01 mutants having QDR3 and IKS1 deletion (ΔQDR3 and ΔIKS1) exhibited higher acetic acid tolerance than the wild-type strain under acetic acid treatment. Glucose consumption rate and ethanol productivity in the presence of 5 g/L acetic acid were improved in the ΔQDR3 mutant compared to the wild-type strain. Our studies demonstrated that the synthetic ZFP-TF library can be used to improve acetic acid tolerance of S. cerevisiae and that the employment of an artificial transcription factor can facilitate the exploration of novel functional genes involved in stress tolerance of S. cerevisiae.

  11. Improvement of acetic acid tolerance of Saccharomyces cerevisiae using a zinc-finger-based artificial transcription factor and identification of novel genes involved in acetic acid tolerance.

    PubMed

    Ma, Cui; Wei, Xiaowen; Sun, Cuihuan; Zhang, Fei; Xu, Jianren; Zhao, Xinqing; Bai, Fengwu

    2015-03-01

    Acetic acid is present in cellulosic hydrolysate as a potent inhibitor, and the superior acetic acid tolerance of Saccharomyces cerevisiae ensures good cell viability and efficient ethanol production when cellulosic raw materials are used as substrates. In this study, a mutant strain of S. cerevisiae ATCC4126 (Sc4126-M01) with improved acetic acid tolerance was obtained through screening strains transformed with an artificial zinc finger protein transcription factor (ZFP-TF) library. Further analysis indicated that improved acetic acid tolerance was associated with improved catalase (CAT) activity. The ZFP coding sequence associated with the improved phenotype was identified, and real-time RT-PCR analysis revealed that three of the possible genes involved in the enhanced acetic acid tolerance regulated by this ZFP-TF, namely YFL040W, QDR3, and IKS1, showed decreased transcription levels in Sc4126-M01 in the presence of acetic acid, compared to those in the control strain. Sc4126-M01 mutants having QDR3 and IKS1 deletion (ΔQDR3 and ΔIKS1) exhibited higher acetic acid tolerance than the wild-type strain under acetic acid treatment. Glucose consumption rate and ethanol productivity in the presence of 5 g/L acetic acid were improved in the ΔQDR3 mutant compared to the wild-type strain. Our studies demonstrated that the synthetic ZFP-TF library can be used to improve acetic acid tolerance of S. cerevisiae and that the employment of an artificial transcription factor can facilitate the exploration of novel functional genes involved in stress tolerance of S. cerevisiae. PMID:25698512

  12. Most acid-tolerant chickpea mesorhizobia show induction of major chaperone genes upon acid shock.

    PubMed

    Brígido, Clarisse; Oliveira, Solange

    2013-01-01

    Our goals were to evaluate the tolerance of mesorhizobia to acid and alkaline conditions as well as to investigate whether acid tolerance is related to the species or the origin site of the isolates. In addition, to investigate the molecular basis of acid tolerance, the expression of chaperone genes groEL and dnaKJ was analyzed using acid-tolerant and sensitive mesorhizobia. Tolerance to pH 5 and 9 was evaluated in liquid medium for 98 Portuguese chickpea mesorhizobia belonging to four species clusters. All isolates showed high sensitivity to pH 9. In contrast, mesorhizobia revealed high diversity in terms of tolerance to acid stress: 35 % of the isolates were acid sensitive and 45 % were highly tolerant to pH 5 or moderately acidophilic. An association between mesorhizobia tolerance to acid conditions and the origin soil pH was found. Furthermore, significant differences between species clusters regarding tolerance to acidity were obtained. Ten isolates were used to investigate the expression levels of the chaperone genes by northern hybridization. Interestingly, most acid-tolerant isolates displayed induction of the dnaK and groESL genes upon acid shock while the sensitive ones showed repression. This study suggests that acid tolerance in mesorhizobia is related to the pH of the origin soil and to the species cluster of the isolates. Additionally, the transcriptional analysis suggests a relationship between induction of major chaperone genes and higher tolerance to acid pH in mesorhizobia. This is the first report on transcriptional analysis of the major chaperones genes in mesorhizobia under acidity, contributing to a better understanding of the molecular mechanisms of rhizobia acidity tolerance.

  13. [Lipid synthesis by an acidic acid tolerant Rhodotorula glutinis].

    PubMed

    Lin, Zhangnan; Liu, Hongjuan; Zhang, Jian'an; Wang, Gehua

    2016-03-01

    Acetic acid, as a main by-product generated in the pretreatment process of lignocellulose hydrolysis, significantly affects cell growth and lipid synthesis of oleaginous microorganisms. Therefore, we studied the tolerance of Rhodotorula glutinis to acetic acid and its lipid synthesis from substrate containing acetic acid. In the mixed sugar medium containing 6 g/L glucose and 44 g/L xylose, and supplemented with acetic acid, the cell growth was not:inhibited when the acetic acid concentration was below 10 g/L. Compared with the control, the biomass, lipid concentration and lipid content of R. glutinis increased 21.5%, 171% and 122% respectively when acetic acid concentration was 10 g/L. Furthermore, R. glutinis could accumulate lipid with acetate as the sole carbon source. Lipid concentration and lipid yield reached 3.20 g/L and 13% respectively with the initial acetic acid concentration of 25 g/L. The lipid composition was analyzed by gas chromatograph. The main composition of lipid produced with acetic acid was palmitic acid, stearic acid, oleic acid, linoleic acid and linolenic acid, including 40.9% saturated fatty acids and 59.1% unsaturated fatty acids. The lipid composition was similar to that of plant oil, indicating that lipid from oleaginous yeast R. glutinis had potential as the feedstock of biodiesel production. These results demonstrated that a certain concentration of acetic acid need not to be removed in the detoxification process when using lignocelluloses hydrolysate to produce microbial lipid by R. glutinis. PMID:27349116

  14. 40 CFR 180.155 - 1-Naphthaleneacetic acid; tolerances for residues.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false 1-Naphthaleneacetic acid; tolerances for residues. 180.155 Section 180.155 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances § 180.155 1-Naphthaleneacetic...

  15. 40 CFR 180.155 - 1-Naphthaleneacetic acid; tolerances for residues.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false 1-Naphthaleneacetic acid; tolerances for residues. 180.155 Section 180.155 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances § 180.155 1-Naphthaleneacetic...

  16. 40 CFR 180.155 - 1-Naphthaleneacetic acid; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Tolerances § 180.155 1-Naphthaleneacetic acid; tolerances for residues. (a) General. Tolerances are established for the combined residues of the plant growth regulator 1-naphthaleneacetic acid and its... 40 Protection of Environment 23 2010-07-01 2010-07-01 false 1-Naphthaleneacetic acid;...

  17. Point mutation of H3/H4 histones affects acetic acid tolerance in Saccharomyces cerevisiae.

    PubMed

    Liu, Xiangyong; Zhang, Xiaohua; Zhang, Zhaojie

    2014-10-10

    The molecular mechanism of acetic acid tolerance in yeast remains unclear despite of its importance for efficient cellulosic ethanol production. In this study, we examined the effects of histone H3/H4 point mutations on yeast acetic acid tolerance by comprehensively screening a histone H3/H4 mutant library. A total of 24 histone H3/H4 mutants (six acetic acid resistant and 18 sensitive) were identified. Compared to the wild-type strain, the histone acetic acid-resistant mutants exhibited improved ethanol fermentation performance under acetic acid stress. Genome-wide transcriptome analysis revealed that changes in the gene expression in the acetic acid-resistant mutants H3 K37A and H4 K16Q were mainly related to energy production, antioxidative stress. Our results provide novel insights into yeast acetic acid tolerance on the basis of histone, and suggest a novel approach to improve ethanol production by altering the histone H3/H4 sequences.

  18. Engineering Clostridium beijerinckii with the Cbei_4693 gene knockout for enhanced ferulic acid tolerance.

    PubMed

    Liu, Jun; Guo, Ting; Shen, Xiaoning; Xu, Jiahui; Wang, Junzhi; Wang, Yanyan; Liu, Dong; Niu, Huanqing; Liang, Lei; Ying, Hanjie

    2016-07-10

    A mutant strain of Clostridium beijerinckii NCIMB 8052, C. beijerinckii M11, which exhibited ferulic acid tolerance up to 0.9g/L, was generated using atmospheric pressure glow discharge and high-throughput screening. Comparative genomic analysis revealed that this strain harbored a mutation of the Cbei_4693 gene, which encodes a hypothetical protein suspected to be an NADPH-dependent FMN reductase. After disrupting the Cbei_4693 gene in C. beijerinckii NCIMB 8052 using the ClosTron group II intron-based gene inactivation system, we obtained the Cbei_4693 gene inactivated mutant strain, C. beijerinckii 4693::int. Compared with C. beijerinckii NCIMB 8052, 6.23g/L of butanol was produced in P2 medium containing 0.5g/L of ferulic acid by 4693::int, and the ferulic acid tolerance was also significantly increased up to 0.8g/L. These data showed, for the first time, that the Cbei_4693 gene plays an important role in regulating ferulic acid tolerance in ABE fermentation by C. beijerinckii. PMID:27164255

  19. The Interaction between Heterotrophic Bacteria and Coliform, Fecal Coliform, Fecal Streptococci Bacteria in the Water Supply Networks

    PubMed Central

    AMANIDAZ, Nazak; ZAFARZADEH, Ali; MAHVI, Amir Hossein

    2015-01-01

    Background: This study investigated the interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in water supply networks. Methods: This study was conducted during 2013 on water supply distribution network in Aq Qala City, Golestan Province, Northern Iran and standard methods were applied for microbiological analysis. The surface method was applied to test the heterotrophic bacteria and MPN method was used for coliform, fecal coliform and fecal streptococci bacteria measurements. Results: In 114 samples, heterotrophic bacteria count were over 500 CFU/ml, which the amount of fecal coliform, coliform, and fecal streptococci were 8, 32, and 20 CFU/100 ml, respectively. However, in the other 242 samples, with heterotrophic bacteria count being less than 500 CFU/ml, the amount of fecal coliform, coliform, and fecal streptococci was 7, 23, and 11 CFU/100ml, respectively. The relationship between heterotrophic bacteria, coliforms and fecal streptococci was highly significant (P<0.05). We observed the concentration of coliforms, fecal streptococci bacteria being high, whenever the concentration of heterotrophic bacteria in the water network systems was high. Conclusion: Interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in the Aq Qala City water supply networks was not notable. It can be due to high concentrations of organic carbon, bio-films and nutrients, which are necessary for growth, and survival of all microorganisms. PMID:26811820

  20. Classifying Microorganisms.

    ERIC Educational Resources Information Center

    Baker, William P.; Leyva, Kathryn J.; Lang, Michael; Goodmanis, Ben

    2002-01-01

    Focuses on an activity in which students sample air at school and generate ideas about how to classify the microorganisms they observe. The results are used to compare air quality among schools via the Internet. Supports the development of scientific inquiry and technology skills. (DDR)

  1. Acidocella aromatica sp. nov.: an acidophilic heterotrophic alphaproteobacterium with unusual phenotypic traits.

    PubMed

    Jones, Rose M; Hedrich, Sabrina; Johnson, D Barrie

    2013-09-01

    Three obligately heterotrophic bacterial isolates were identified as strains of a proposed novel species of extremely acidophilic, mesophilic Alphaproteobacteria, Acidocella aromatica. They utilized a restricted range of organic substrates, which included fructose (but none of the other monosaccharides tested), acetate and several aromatic compounds (benzoate, benzyl alcohol and phenol). No growth was obtained on complex organic substrates, such as yeast extract and tryptone. Tolerance of the proposed type strain of the species (PFBC) to acetic acid was much greater than that typically reported for acidophiles. The bacteria grew aerobically, and catalyzed the dissimilatory reductive dissolution of the ferric iron mineral schwertmannite under both micro-aerobic and anaerobic conditions. Strain PFBC did not grow anaerobically via ferric iron respiration, though it has been reported to grow in co-culture with acid-tolerant sulfidogenic bacteria under strictly anoxic conditions. Tolerance of strains of Acidocella aromatica to nickel were about two orders of magnitude greater than those of other Acidocella spp., though similar levels of tolerance to other metals tested was observed. The use of this novel acidophile in solid media designed to promote the isolation and growth of other (aerobic and anaerobic) acidophilic heterotrophs is discussed.

  2. Enhance nisin yield via improving acid-tolerant capability of Lactococcus lactis F44

    PubMed Central

    Zhang, Jian; Caiyin, Qinggele; Feng, Wenjing; Zhao, Xiuli; Qiao, Bin; Zhao, Guangrong; Qiao, Jianjun

    2016-01-01

    Traditionally, nisin was produced industrially by using Lactococcus lactis in the neutral fermentation process. However, nisin showed higher activity in the acidic environment. How to balance the pH value for bacterial normal growth and nisin activity might be the key problem. In this study, 17 acid-tolerant genes and 6 lactic acid synthetic genes were introduced in L. lactis F44, respectively. Comparing to the 2810 IU/mL nisin yield of the original strain F44, the nisin titer of the engineered strains over-expressing hdeAB, ldh and murG, increased to 3850, 3979 and 4377 IU/mL, respectively. These engineered strains showed more stable intracellular pH value during the fermentation process. Improvement of lactate production could partly provide the extra energy for the expression of acid tolerance genes during growth. Co-overexpression of hdeAB, murG, and ldh(Z) in strain F44 resulted in the nisin titer of 4913 IU/mL. The engineered strain (ABGL) could grow on plates with pH 4.2, comparing to the surviving pH 4.6 of strain F44. The fed-batch fermentation showed nisin titer of the co-expression L. lactis strain could reach 5563 IU/mL with lower pH condition and longer cultivation time. This work provides a novel strategy of constructing robust strains for use in industry process. PMID:27306587

  3. Mini-review: Inhibition of biofouling by marine microorganisms.

    PubMed

    Dobretsov, Sergey; Abed, Raeid M M; Teplitski, Max

    2013-01-01

    Any natural or artificial substratum exposed to seawater is quickly fouled by marine microorganisms and later by macrofouling species. Microfouling organisms on the surface of a substratum form heterogenic biofilms, which are composed of multiple species of heterotrophic bacteria, cyanobacteria, diatoms, protozoa and fungi. Biofilms on artificial structures create serious problems for industries worldwide, with effects including an increase in drag force and metal corrosion as well as a reduction in heat transfer efficiency. Additionally, microorganisms produce chemical compounds that may induce or inhibit settlement and growth of other fouling organisms. Since the last review by the first author on inhibition of biofouling by marine microbes in 2006, significant progress has been made in the field. Several antimicrobial, antialgal and antilarval compounds have been isolated from heterotrophic marine bacteria, cyanobacteria and fungi. Some of these compounds have multiple bioactivities. Microorganisms are able to disrupt biofilms by inhibition of bacterial signalling and production of enzymes that degrade bacterial signals and polymers. Epibiotic microorganisms associated with marine algae and invertebrates have a high antifouling (AF) potential, which can be used to solve biofouling problems in industry. However, more information about the production of AF compounds by marine microorganisms in situ and their mechanisms of action needs to be obtained. This review focuses on the AF activity of marine heterotrophic bacteria, cyanobacteria and fungi and covers publications from 2006 up to the end of 2012.

  4. POLYPEPTIDE AND POLYSACCHARIDE PROCESSING IN HYPERTHERMOPHILIC MICROORGANISMS

    SciTech Connect

    KELLY, ROBERT M.

    2008-12-22

    This project focused on the microbial physiology and biochemistry of heterotrophic hyperthermophiles with respect to mechanisms by which these organisms process polypeptides and polysaccharides under normal and stressed conditions. Emphasis is on two model organisms, for which completed genome sequences are available: Pyrococcus furiosus (growth Topt of 98°C), an archaeon, and Thermotoga maritima (growth Topt of 80°C), a bacterium. Both organisms are obligately anaerobic heterotrophs that reduce sulfur facultatively. Whole genome cDNA spotted microarrays were used to follow transcriptional response to a variety of environmental conditions in order to identify genes encoding proteins involved in the acquisition, synthesis, processing and utilization of polypeptides and polysaccharides. This project provided new insights into the physiological aspects of hyperthermophiles as these relate to microbial biochemistry and biological function in high temperature habitats. The capacity of these microorganisms to produce biohydrogen from renewable feedstocks makes them important for future efforts to develop biofuels.

  5. Acid tolerance response (ATR) of microbial communities during the enhanced biohydrogen process via cascade acid stress.

    PubMed

    Lin, Xiaoqin; Xia, Yan; Yan, Qun; Shen, Wei; Zhao, Mingxing

    2014-03-01

    Enhanced biohydrogen production via cascade acid stress on microbial communities, structure patterns of the microbial communities revealed by PLFAs, and the succession of biohydrogen related species against cascade acid stress were all investigated. It was found that hydrogen production could be improved from 48.7 to 79.4mL/gVS after cascade acid stress. In addition, the Gram negative (G(-)) bacteria were found to be more tolerant to organic acids than those of the Gram positive (G(+)) bacteria, regardless of the dominance of G(+) bacteria within the microbial communities. Moreover, Clostridium butyricum, Clostridium aciditolerans and Azospira oryzae, were proved to be enriched, and then might play indispensable roles for the enhanced biohydrogen production after cascade acid stress, as which were responsible for the biohydrogen accumulation, acid tolerance and nitrogen removal, respectively.

  6. High cell density propionic acid fermentation with an acid tolerant strain of Propionibacterium acidipropionici.

    PubMed

    Wang, Zhongqiang; Jin, Ying; Yang, Shang-Tian

    2015-03-01

    Propionic acid is an important chemical with wide applications and its production via fermentation is of great interest. However, economic production of bio-based propionic acid requires high product titer, yield, and productivity in the fermentation. A highly efficient and stable high cell density (HCD) fermentation process with cell recycle by centrifugation was developed for propionic acid production from glucose using an acid-tolerant strain of Propionibacterium acidipropionici, which had a higher specific growth rate, productivity, and acid tolerance compared to the wild type ATCC 4875. The sequential batch HCD fermentation at pH 6.5 produced propionic acid at a high titer of ∼40 g/L and productivity of 2.98 g/L h, with a yield of ∼0.44 g/g. The product yield increased to 0.53-0.62 g/g at a lower pH of 5.0-5.5, which, however, decreased the productivity to 1.28 g/L h. A higher final propionic acid titer of >55 g/L with a productivity of 2.23 g/L h was obtained in fed-batch HCD fermentation at pH 6.5. A 3-stage simulated fed-batch process in serum bottles produced 49.2 g/L propionic acid with a yield of 0.53 g/g and productivity of 0.66 g/L h. These productivities, yields and propionic acid titers were among the highest ever obtained in free-cell propionic acid fermentation.

  7. Identification of novel factors involved in colonization and acid tolerance of Vibrio cholerae.

    PubMed

    Merrell, D Scott; Hava, David L; Camilli, Andrew

    2002-03-01

    Despite over 100 years of study, the intestinal pathogen Vibrio cholerae still causes epidemic disease in areas of the world where there is poor sanitation. While cholera toxin and the toxin-coregulated pilus (TCP) are known to be essential for full virulence, the role that other factors play has remained ill-defined. Herein, we describe a large-scale signature-tagged mutagenesis (STM) screen utilizing 100 pools of 96 mutants each to identify factors involved in colonization of the infant mouse small intestine. A total of 164 mutants representing transposition events into 95 different open reading frames were shown to be recovered at greatly reduced numbers from the infant mouse model. Analysis of the sites of insertion revealed multiple independent mutations within the rfb gene cluster, needed for synthesis of lipopolysaccharide (LPS), and the tcp gene cluster, needed for synthesis of the TCP. More importantly, in addition to these previously known colonization factors, we identified many genes whose activity in colonization was not previously appreciated. These can be divided into a number of functional groups, which include production of factors involved in metabolic activities, regulation of cellular processes, transport, adaptation to stress and unknown functions. In addition, we describe the reiterative use of STM, whereby colonization-defective mutants were assembled into virulence-attenuated pools (VAPs), which were used to begin to reveal roles that the identified virulence factors play in the infection process. Nine new factors were shown to be crucial for the V. cholerae acid tolerance response, which has previously been hypothesized to be important for epidemic spread of cholera. Competition assays of these nine acid tolerance response (ATR)-defective mutants revealed that mutations in gshB, hepA and recO result in a 1000-fold reduction in colonization. PMID:11952899

  8. Are heterotrophic and silica-rich eukaryotic microbes an important part of the lichen symbiosis?

    PubMed Central

    Wilkinson, David M.; Creevy, Angela L.; Kalu, Chiamaka L.; Schwartzman, David W.

    2015-01-01

    We speculate that heterotrophic and/or silica-rich eukaryotic microorganisms maybe an important part of the lichen symbiosis. None of the very few studies of heterotrophic protists associated with lichens have considered the possibility that they may be of functional significance in the lichen symbiosis. Here we start to develop, currently speculative, theoretical ideas about their potential significance. For example, all the protist taxa identified in lichens we sampled in Ohio USA depend on silica for growth and construction of their cell walls, this could suggest that silica-rich lichen symbionts may be significant in the biogeochemistry of the lichen symbiosis. We also present arguments suggesting a role for protists in nitrogen cycling within lichen thalli and a potential role in controlling bacterial populations associated with lichens. In this necessarily speculative paper we highlight areas for future research and how newer technologies may be useful for understanding the full suite of organisms involved in the lichen symbiosis. PMID:26000198

  9. The LysR-type regulator LeuO regulates the acid tolerance response in Vibrio cholerae.

    PubMed

    Ante, Vanessa M; Bina, X Renee; Bina, James E

    2015-12-01

    Vibrio cholerae is a neutrophilic enteric pathogen that is extremely sensitive to acid. As V. cholerae passages through the host gastrointestinal tract it is exposed to a variety of environmental stresses including low pH and volatile fatty acids. Exposure to acidic environments induces expression of the V. cholerae acid tolerance response. A key component of the acid tolerance response is the cad system, which is encoded by cadC and the cadBA operon. CadB is a lysine/cadaverine antiporter and CadA is a lysine decarboxylase and these function together to counter low intracellular and extracellular pH. CadC is a membrane-associated transcription factor that activates cadBA expression in response to acidic conditions. Herein we investigated the role of the LysR-type transcriptional regulator LeuO in the V. cholerae acid tolerance response. Transcriptional reporter assays revealed that leuO expression repressed cadC transcription, indicating that LeuO was a cadC repressor. Consistent with this, leuO expression was inversely linked to lysine decarboxylase production and leuO overexpression resulted in increased sensitivity to organic acids. Overexpression of leuO in a cadA mutant potentiated killing by organic acids, suggesting that the function of leuO in the acid tolerance response extended beyond its regulation of the cad system. Collectively, these studies have identified a new physiological role for LeuO in V. cholerae acid tolerance.

  10. Ecology of planktonic heterotrophic flagellates. A review.

    PubMed

    Mariottini, Gian Luigi; Pane, Luigi

    2003-01-01

    In aquatic environments heterotrophic flagellates are an important component within the microbial loop and the food web, owing to their involvement in the energy transfer and flux and as an intermediate link between bacteria and primary producers, and greater organisms, such as other protists and metazoan consumers. In the microbial loop heterotrophic flagellates highly contribute to fast biomass and nutrient recycling and to the production in aquatic environments. In fact, these protists consume efficiently viruses, bacteria, cyanobacteria and picophytoplankton, and are grazed mainly by other protists, rotifers and small crustaceans. In this paper the knowledge about these unicellular organisms is reviewed, taking into particular account their ecological relationships and trophic role within the plankton community of marine and freshwater environments.

  11. Fumarate Production by Torulopsis glabrata: Engineering Heterologous Fumarase Expression and Improving Acid Tolerance

    PubMed Central

    Chen, Xiulai; Song, Wei; Gao, Cong; Qin, Wen; Luo, Qiuling; Liu, Jia; Liu, Liming

    2016-01-01

    Fumarate is a well-known biomass building block compound. However, the poor catalytic efficiency of fumarase is one of the major factors preventing its widespread production. To address this issue, we selected residues 159HPND162 of fumarase from Rhizopus oryzae as targets for site-directed mutagenesis based on molecular docking analysis. Twelve mutants were generated and characterized in detail. Kinetic studies showed that the Km values of the P160A, P160T, P160H, N161E, and D162W mutants were decreased, whereas Km values of H159Y, H159V, H159S, N161R, N161F, D162K, and D162M mutants were increased. In addition, all mutants displayed decreased catalytic efficiency except for the P160A mutant, whose kcat/Km was increased by 33.2%. Moreover, by overexpressing the P160A mutant, the engineered strain T.G-PMS-P160A was able to produce 5.2 g/L fumarate. To further enhance fumarate production, the acid tolerance of T.G-PMS-P160A was improved by deleting ade12, a component of the purine nucleotide cycle, and the resulting strain T.G(△ade12)-PMS-P160A produced 9.2 g/L fumarate. The strategy generated in this study opens up new avenues for pathway optimization and efficient production of natural products. PMID:27711153

  12. Investigation of Growth Phase-Dependent Acid Tolerance in Bifidobacteria longum BBMN68.

    PubMed

    Jin, Junhua; Song, Jingyi; Ren, Fazheng; Zhang, Hongxing; Xie, Yuanhong; Ma, Jingsheng; Li, Xue

    2016-11-01

    The underlying mechanisms imparting the growth phase-dependent acid tolerance have not been extensively investigated. In this study, we compared the acid resistance of the Bifidobacterium longum strain BBMN68 from different growth phases at lethal pH values (pH 2.5, 3.0, and 3.5), and analyzed the activity of H(+)-ATPase, the composition of fatty acids, and the mRNA abundance of ffh, uvrA, recA, lexA, groES, and dnaK in cells from different growth phases. The results indicated that the survival rates of cells from early stationary (ES) and late stationary (LS) growth phases at lethal pH values were significantly higher than those of exponential growth phase cells. Our findings indicated that by inducing a continuously auto-acidizing environment during cell growth, the acid resistance of ES and LS cells was strengthened. The higher activity of H(+)-ATPase, the decrease in unsaturated fatty acids, and the increased expression of genes involved in DNA repair and protein protection in the cells in stationary growth phase were all implicated in the significantly increased acid resistance of ES and LS cells compared with exponential growth phase cells of the B. longum strain BBMN68.

  13. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations.

    PubMed

    Stopnisek, Nejc; Bodenhausen, Natacha; Frey, Beat; Fierer, Noah; Eberl, Leo; Weisskopf, Laure

    2014-06-01

    Bacteria belonging to the genus Burkholderia are highly versatile with respect to their ecological niches and lifestyles, ranging from nodulating tropical plants to causing melioidosis and fatal infections in cystic fibrosis patients. Despite the clinical importance and agronomical relevance of Burkholderia species, information about the factors influencing their occurrence, abundance and diversity in the environment is scarce. Recent findings have demonstrated that pH is the main predictor of soil bacterial diversity and community structure, with the highest diversity observed in neutral pH soils. As many Burkholderia species have been isolated from low pH environments, we hypothesized that acid tolerance may be a general feature of this genus, and pH a good predictor of their occurrence in soils. Using a combination of environmental surveys at trans-continental and local scales, as well as in vitro assays, we show that, unlike most bacteria, Burkholderia species have a competitive advantage in acidic soils, but are outcompeted in alkaline soils. Physiological assays and diversity analysis based on 16S rRNA clone libraries demonstrate that pH tolerance is a general phenotypic trait of the genus Burkholderia. Our results provide a basis for building a predictive understanding of the biogeographical patterns exhibited by Burkholderia sp.

  14. Heterotrophic bacteria in soils of Larsemann Oasis of East Antarctica

    NASA Astrophysics Data System (ADS)

    Churilin, Nikita; Soina, Vera

    2015-04-01

    The study of diversity and functional state of microorganisms in subsurface rocks layers, their participation in the biochemical weathering and formation of organic horizons of soils is important for understanding ecology and microorganisms in Antarctic soils. The study of cultured forms of microorganisms and their potential viability is still relevant to characterize the physiological state, biological activity and resilience of microorganisms involved in the initial soil formation. Improvement of isolation techniques of viable bacteria from the extreme habitats has a particular importance for rising the efficiency of environmental monitoring. The aim of the study was to investigate the viable heterotrophic bacteria involved in the formation of soils from wet valleys Larsemann Oasis, which is one of the warmest ice-free space of East Antarctica. Soil samples were taken from the intermountain humid valleys, where silt-gravelly substrates formed moss, algae, lichen cover. We used nutrient solutions (trypticase soy, R2A and glucose-peptone) to isolate cultured bacteria and study their morphological types in the light microscope. The total number of microorganisms was determined by fluorescent microscopy with acridine orange. SEM was used for morphological studies of bacterial communities in situ. To activate the growth processes we added into nutrient solutions various regulatory metabolites that have dose-dependence and operate at the community level. Physiological and functional conditions were determined by the duration of the lag phase and specific growth rate of bacterial communities in nutrient solutions containing various organic substrates. Soils form under protection of «stone pavement» and organisms leave the surface, so the forming organo-mineral horizon occurs inside of rock, thus the microprofile can form on both sides of the organic horizons. UV radiation, lack of moisture and strong wind are main limiting factors for microorganisms' growth in

  15. Heterotrophic potential of Atribacteria from deep marine Antarctic sediment

    NASA Astrophysics Data System (ADS)

    Carr, S. A.; Orcutt, B.; Mandernack, K. W.; Spear, J. R.

    2015-12-01

    Bacteria belonging to the newly classified candidate phylum "Atribacteria" (formerly referred to as "OP9" and "JS1") are common in anoxic methane-rich sediments. However, the metabolic functions and biogeochemical role of these microorganisms in the subsurface remains unrealized due to the lack of pure culture representatives. This study observed a steady increase of Atribacteria-related sequences with increasing sediment depth throughout the methane-rich zone of the Adélie Basin, Antarctica (according to a 16S rRNA gene survey). To explore the functional potential of Atribacteria in this basin, samples from various depths (14, 25 and 97 meters below seafloor), were subjected to metagenomic sequencing. Additionally, individual cells were separated from frozen, unpreserved sediment for whole genome amplification. The successful isolation and sequencing of a single-amplified Atribacteria genome from these unpreserved sediments demonstrates a future use of single cell techniques with previously collected and frozen sediments. Our resulting single-cell amplified genome, combined with metagenomic interpretations, provides our first insights to the functional potential of Atribacteria in deep subsurface settings. As observed for non-marine Atribacteria, genomic analyses suggest a heterotrophic metabolism, with Atribacteria potentially producing fermentation products such as acetate, ethanol and CO2. These products may in turn support methanogens within the sediment microbial community and explain the frequent occurrence of Atribacteria in anoxic methane-rich sediments.

  16. Hydrogen transfer between methanogens and fermentative heterotrophs in hyperthermophilic cocultures

    SciTech Connect

    Muralidharan, V.; Hirsh, I.S.; Bouwer, E.J.; Rinker, K.D.; Kelly, R.M.

    1997-11-05

    Interactions involving hydrogen transfer were studied in a coculture of two hyperthermophilic microorganisms: Thermotoga maritima, an anaerobic heterotroph, and Methanococcus jannaschii, a hydrogenotrophic methanogen. Cell densities of T. maritima increased 10-fold when cocultured with M. jannaschii at 85 C, and the methanogen was able to grow in the absence of externally supplied H{sub 2} and CO{sub 2}. The coculture could not be established if the two organisms were physically separated by a dialysis membrane, suggesting the importance of spatial proximity. The significance of spatial proximity was also supported by cell cytometry, where the methanogen was only found in cell sorts at or above 4.5 {micro}m in samples of the coculture in exponential phase. An unstructured mathematical model was used to compare the influence of hydrogen transport and metabolic properties on mesophilic and hyperthermophilic cocultures. Calculations suggest the increases in methanogenesis rates with temperature result from greater interactions between the methanogenic and fermentative organisms, as evidenced by the sharp decline in H{sub 2} concentration in the proximity of a hyperthermophilic methanogen. The experimental and modeling results presented here illustrate the need to consider the interactions within hyperthermophilic consortia when choosing isolation strategies and evaluating biotransformations at elevated temperatures.

  17. System-level understanding of the potential acid-tolerance components of Acidithiobacillus thiooxidans ZJJN-3 under extreme acid stress.

    PubMed

    Feng, Shoushuai; Yang, Hailin; Wang, Wu

    2015-09-01

    In previous study, two extremely acidophilic strains Acidithiobacillus thiooxidans ZJJN-3 (collection site: bioleaching leachate) and ZJJN-5 (collection site: bioleaching wastewater) were isolated from a typical industrial bio-heap in China. Here, we unraveled the potential acid-tolerance components of ZJJN-3 by comparing the physiological differences with ZJJN-5 under different acid stresses. The parameters used for comparison included intracellular pH (pHin), capsule morphology, fatty acid composition of cell membrane, transcription of key molecular chaperones, H(+)-ATPase activities and NAD(+)/NADH ratio. It was indicated that the acid-tolerance of A. thiooxidans ZJJN-3 was systematically regulated. Capsule first thickened and then shed off along with increased acid stress. Cell membrane maintained the intracellular stability by up-regulating the proportion of unsaturated fatty acid and cyclopropane fatty acids. Meanwhile, the transcription of key repair molecular chaperones (GrpE-DnaK-DnaJ) was up-regulated by 2.2-3.5 folds for ensuring the proper folding of peptide. Moreover, low pHin promoted ZJJN-3 to biosynthesize more H(+)-ATPase for pumping H(+) out of cells. Furthermore, the NAD(+)/NADH ratio increased due to the decreased H(+) concentration. Based on the above physiological analysis, the potential acid-tolerance components of A. thiooxidans ZJJN-3 were first proposed and it would be useful for better understanding how these extremophiles responded to the high acid stress.

  18. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps.

    PubMed

    Islam, Tajul; Torsvik, Vigdis; Larsen, Øivind; Bodrossy, Levente; Øvreås, Lise; Birkeland, Nils-Kåre

    2016-01-01

    Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2-7.5 (optimal 5.5-6.0) and at a temperature range of 30-60°C (optimal 51-55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1-94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems. PMID:27379029

  19. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps

    PubMed Central

    Islam, Tajul; Torsvik, Vigdis; Larsen, Øivind; Bodrossy, Levente; Øvreås, Lise; Birkeland, Nils-Kåre

    2016-01-01

    Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0) and at a temperature range of 30–60°C (optimal 51–55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems. PMID:27379029

  20. Easy visualization of the protist Oxyrrhis marina grazing on a live fluorescently labelled heterotrophic nanoflagellate.

    PubMed

    Martín-Cereceda, Mercedes; Williams, Richard A J; Novarino, Gianfranco

    2008-07-01

    Planktonic heterotrophic flagellates are ubiquitous eukaryotic microorganisms that play a crucial role in carbon and nutrient fluxes through pelagic food webs. Here we illustrate for the first time a grazing model of planktonic dinoflagellate, Oxyrrhis marina, on the heterotrophic nanoflagellate Goniomonas amphinema, using the DNA-binding fluorescent dye Hoechst 33342. A solution of 1 microg/mL of the fluorochrome allowed viability of the prey for at least 48 hours, provided low fluorescence quenching, and labelled the flagellate without masking the cytoplasm. After 2 hours of contact between the fluorescent prey and the predator, O. marina population had preyed on live G. amphinema at an ingestion rate of 2.2 prey Oxyrrhis (-1) h(-1). Results show that this model is a time-effective and inexpensive approach for the direct observation of heterotrophic flagellate grazing. The fact that prey remain alive while predation occurs, as well as the low rate of quenching, could be of help in studying the fate of real-time trophic interactions between protists in microbial webs.

  1. Crash of a population of the marine heterotrophic flagellate Cafeteria roenbergensis by viral infection.

    PubMed

    Massana, Ramon; del Campo, Javier; Dinter, Christian; Sommaruga, Ruben

    2007-11-01

    Viruses are known as important mortality agents of marine microorganisms. Most studies focus on bacterial and algal viruses, and few reports exist on viruses infecting marine heterotrophic protists. Here we show results from several incubations initiated with a microbial assemblage from the central Indian Ocean and amended with different amounts of organic matter. Heterotrophic flagellates developed up to 30,000 cells ml(-1) in the most enriched incubation. A 18S rDNA clone library and fluorescent in situ hybridization counts with newly designed probes indicated that the peak was formed by Cafeteria roenbergensis and Caecitellus paraparvulus (90% and 10% of the cells respectively). Both taxa were below detection in the original sample, indicating a strong positive selective bias during the enrichment. During the peak, C. roenbergensis cells were observed with virus-like particles in the cytoplasm, and 4 days later this taxa could not be detected. Transmission electron microscopy confirmed the viral nature of these particles, which were large (280 nm), had double-stranded DNA, and were produced with a burst size of approximately 70. This virus was specific of C. roenbergensis as neither C. paraparvulus that was never seen infected, nor other flagellate taxa that developed in later stages of the incubation, appeared attacked. This is one of the few reports on a heterotrophic flagellate virus and the implications of this finding in the Indian Ocean are discussed.

  2. Interactions of Nitrifying Bacteria and Heterotrophs: Identification of a Micavibrio-Like Putative Predator of Nitrospira spp.

    PubMed Central

    Dolinšek, Jan; Lagkouvardos, Ilias; Wanek, Wolfgang; Wagner, Michael

    2013-01-01

    Chemolithoautotrophic nitrifying bacteria release soluble organic compounds, which can be substrates for heterotrophic microorganisms. The identities of these heterotrophs and the specificities of their interactions with nitrifiers are largely unknown. In this study, we incubated nitrifying activated sludge with 13C-labeled bicarbonate and used stable isotope probing of 16S rRNA to monitor the flow of carbon from uncultured nitrifiers to heterotrophs. To facilitate the identification of heterotrophs, the abundant 16S rRNA molecules from nitrifiers were depleted by catalytic oligonucleotides containing locked nucleic acids (LNAzymes), which specifically cut the 16S rRNA of defined target organisms. Among the 13C-labeled heterotrophs were organisms remotely related to Micavibrio, a microbial predator of Gram-negative bacteria. Fluorescence in situ hybridization revealed a close spatial association of these organisms with microcolonies of nitrite-oxidizing sublineage I Nitrospira in sludge flocs. The high specificity of this interaction was confirmed by confocal microscopy and a novel image analysis method to quantify the localization patterns of biofilm microorganisms in three-dimensional (3-D) space. Other isotope-labeled bacteria, which were affiliated with Thermomonas, colocalized less frequently with nitrifiers and thus were commensals or saprophytes rather than specific symbionts or predators. These results suggest that Nitrospira spp. are subject to bacterial predation, which may influence the abundance and diversity of these nitrite oxidizers and the stability of nitrification in engineered and natural ecosystems. In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage. PMID:23335755

  3. Light scattering by marine heterotrophic bacteria

    NASA Technical Reports Server (NTRS)

    Ulloa, Osvaldo; Sathyendranath, Shubha; Platt, Trevor; Quinones, Renato A.

    1992-01-01

    Mie theory is applied to estimate scattering by polydispersions of marine heterotrophic bacteria, and a simple expression is derived for the bacterial scattering coefficient. The error incurred in deriving bacterial optical properties by use of the van de Hulst approximations is computed. The scattering properties of natural bacterial assemblages in three marine environments, Georges Bank, Northeast Channel, and Sargasso Sea, are assessed by applying Mie theory to field data on bacterial size and abundance. Results are used to examine the potential contribution of bacteria to the scattering properties of seawater. The utility of using pigment data to predict the magnitude of scattering by bacteria is discussed.

  4. Autotrophic and heterotrophic denitrification for simultaneous removal of nitrogen, sulfur and organic matter.

    PubMed

    Guerrero, Lorna; Aguirre, Juan P; Muñoz, Maria A; Barahona, Andrea; Huiliñir, Cesar; Montalvo, Silvio; Borja, Rafael

    2016-07-01

    The aim of this investigation was to assess the startup and operation of a laboratory-scale hybrid UASB-Anaerobic Filter Reactor (UASFB) of 1 L volume, kept at 30°C, in order to carry out a simultaneous autotrophic and heterotrophic denitrification process. First, the heterotrophic and autotrophic populations were separately enriched, with specific cultures and subsequently the UASFB was inoculated with 2 g L(-1) of volatile suspended solids (VSS), with a ratio of 1.5:1 (autotrophs: heterotrophs). The influent or synthetic wastewater used was composed of: Na2S2O3·5H2O, CH3COOK, NaNO3, NaHCO3, K2HPO4, NH4Cl and saline solution. The concentrations varied depending on the organic loading rate (OLR), nitrogen loading rate (NLR) and sulfur loading rate (SLR) applied. In the UASFB reactor, two experimental conditions were tested and assessed: (i) COD/N ratio of 3.6 and SLR of 0.75 kg S m(-3) d(-1); and (ii) COD/N ratio of 5.8 and SLR of 0.25 kg S m(-3) d(-1). The results obtained demonstrated that an inoculum coming from an anaerobic reactor was able to carry out the process, obtaining a maximum nitrate removal of 85.3% in the first stage of operation and 99.5% in the second stage. The recovery of sulfur in form of sulfate in the effluent did not present a tendency to stabilize during the measured time, with a maximum thiosulfate removal of 32.5%, when the SLR was lowered to 0.25 kg S m(-3) d(-1). The maximum organic matter elimination, measured as COD, was 75.8%, which indicates the relatively good performance and behavior of the heterotrophic microorganisms. PMID:27093220

  5. Autotrophic and heterotrophic denitrification for simultaneous removal of nitrogen, sulfur and organic matter.

    PubMed

    Guerrero, Lorna; Aguirre, Juan P; Muñoz, Maria A; Barahona, Andrea; Huiliñir, Cesar; Montalvo, Silvio; Borja, Rafael

    2016-07-01

    The aim of this investigation was to assess the startup and operation of a laboratory-scale hybrid UASB-Anaerobic Filter Reactor (UASFB) of 1 L volume, kept at 30°C, in order to carry out a simultaneous autotrophic and heterotrophic denitrification process. First, the heterotrophic and autotrophic populations were separately enriched, with specific cultures and subsequently the UASFB was inoculated with 2 g L(-1) of volatile suspended solids (VSS), with a ratio of 1.5:1 (autotrophs: heterotrophs). The influent or synthetic wastewater used was composed of: Na2S2O3·5H2O, CH3COOK, NaNO3, NaHCO3, K2HPO4, NH4Cl and saline solution. The concentrations varied depending on the organic loading rate (OLR), nitrogen loading rate (NLR) and sulfur loading rate (SLR) applied. In the UASFB reactor, two experimental conditions were tested and assessed: (i) COD/N ratio of 3.6 and SLR of 0.75 kg S m(-3) d(-1); and (ii) COD/N ratio of 5.8 and SLR of 0.25 kg S m(-3) d(-1). The results obtained demonstrated that an inoculum coming from an anaerobic reactor was able to carry out the process, obtaining a maximum nitrate removal of 85.3% in the first stage of operation and 99.5% in the second stage. The recovery of sulfur in form of sulfate in the effluent did not present a tendency to stabilize during the measured time, with a maximum thiosulfate removal of 32.5%, when the SLR was lowered to 0.25 kg S m(-3) d(-1). The maximum organic matter elimination, measured as COD, was 75.8%, which indicates the relatively good performance and behavior of the heterotrophic microorganisms.

  6. Heterotrophic communities supplied by ancient organic carbon predominate in deep fennoscandian bedrock fluids.

    PubMed

    Purkamo, Lotta; Bomberg, Malin; Nyyssönen, Mari; Kukkonen, Ilmo; Ahonen, Lasse; Itävaara, Merja

    2015-02-01

    The deep subsurface hosts diverse life, but the mechanisms that sustain this diversity remain elusive. Here, we studied microbial communities involved in carbon cycling in deep, dark biosphere and identified anaerobic microbial energy production mechanisms from groundwater of Fennoscandian crystalline bedrock sampled from a deep drill hole in Outokumpu, Finland, by using molecular biological analyses. Carbon cycling pathways, such as carbon assimilation, methane production and methane consumption, were studied with cbbM, rbcL, acsB, accC, mcrA and pmoA marker genes, respectively. Energy sources, i.e. the terminal electron accepting processes of sulphate-reducing and nitrate-reducing communities, were assessed with detection of marker genes dsrB and narG, respectively. While organic carbon is scarce in deep subsurface, the main carbon source for microbes has been hypothesized to be inorganic carbon dioxide. However, our results demonstrate that carbon assimilation is performed throughout the Outokumpu deep scientific drill hole water column by mainly heterotrophic microorganisms such as Clostridia. The source of carbon for the heterotrophic microbial metabolism is likely the Outokumpu bedrock, mainly composed of serpentinites and metasediments with black schist interlayers. In addition to organotrophic metabolism, nitrate and sulphate are other possible energy sources. Methanogenic and methanotrophic microorganisms are scarce, but our analyses suggest that the Outokumpu deep biosphere provides niches for these organisms; however, they are not very abundant. PMID:25260922

  7. Deep subsurface life from North Pond: Enrichment, isolation, characterization and genomes of heterotrophic bacteria

    DOE PAGES

    Russell, Joseph A.; Leon-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F.

    2016-05-10

    Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic watercolumn west of the Mid-Atlantic Ridge at 22° N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sedimentmore » column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. Furthermore, the cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface.« less

  8. Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria

    PubMed Central

    Russell, Joseph A.; León-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F.

    2016-01-01

    Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface. PMID:27242705

  9. Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria.

    PubMed

    Russell, Joseph A; León-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F

    2016-01-01

    Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface. PMID:27242705

  10. Heterotrophic activity and biodegradation of labile and refractory compounds by groundwater and stream microbial populations.

    PubMed Central

    Ladd, T I; Ventullo, R M; Wallis, P M; Costerton, J W

    1982-01-01

    The bacteriology and heterotrophic activity of a stream and of nearby groundwater in Marmot Basin, Alberta, Canada, were studied. Acridine orange direct counts indicated that bacterial populations in the groundwater were greater than in the stream. Bacteria that were isolated from the groundwater were similar to species associated with soils. Utilization of labile dissolved organic material as measured by the heterotrophic potential technique with glutamic acid, phenylalanine, and glycolic acid as substrates was generally greater in the groundwater. In addition, specific activity indices for the populations suggested greater metabolic activity per bacterium in the groundwater. 14C-labeled lignocellulose, preferentially labeled in the lignin fraction by feeding Picea engelmannii [14C]phenylalanine, was mineralized by microorganisms in both the groundwater and the stream, but no more than 4% of the added radioactivity was lost as 14CO2 within 960 h. Up to 20% of [3'-14C]cinnamic acid was mineralized by microorganisms in both environments within 500 h. Both microbial populations appear to influence the levels of labile and recalcitrant dissolved organic material in mountain streams. PMID:7125651

  11. Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria.

    PubMed

    Russell, Joseph A; León-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F

    2016-01-01

    Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface.

  12. Slr2019, lipid A transporter homolog, is essential for acidic tolerance in Synechocystis sp. PCC6803.

    PubMed

    Matsuhashi, Ayumi; Tahara, Hiroko; Ito, Yutaro; Uchiyama, Junji; Ogawa, Satoru; Ohta, Hisataka

    2015-08-01

    Living organisms must defend themselves against various environmental stresses. Extracellular polysaccharide-producing cells exhibit enhanced tolerance toward adverse environmental stress. In Synechocystis sp. PCC6803 (Synechocystis), lipopolysaccharide (LPS) may play a role in this protection. To examine the relationship between stress tolerance of Synechocystis and LPS, we focused on Slr2019 because Slr2019 is homologous to MsbA in Escherichia coli, which is related to LPS synthesis. First, to obtain a defective mutant of LPS, we constructed the slr2019 insertion mutant (slr2019) strain. Sodium deoxycholate-polyacrylamide gel electrophoresis indicated that slr2019 strain did not synthesize normal LPS. Second, to clarify the participation of LPS in acid tolerance, wild type (WT) and slr2019 strain were grown under acid stress; slr2019 strain growth was significantly weaker than WT growth. Third, to examine influences on stress tolerance, slr2019 strain was grown under various stresses. Under salinity and temperature stress, slr2019 strain grew significantly slower than WT. To confirm cell morphology, cell shape and envelope of slr2019 strain were observed by transmission electron microscopy; slr2019 cells contained more electron-transparent bodies than WT cells. Finally, to confirm whether electron-transparent bodies are poly-3-hydroxybutyrate (PHB), slr2019 strain was stained with Nile Blue A, a PHB detector, and observed by fluorescence microscopy. The PHB granule content ratio of WT and slr2019 strain grown at BG-11 pH 8.0 was each 7.18 and 8.41 %. At pH 6.0, the PHB granule content ratio of WT and slr2019 strain was 2.99 and 2.60 %. However, the PHB granule content ratio of WT and slr2019 strain grown at BG-11N-reduced was 10.82 and 0.56 %. Because slr2019 strain significantly decreased PHB under BG-11N-reduced compared with WT, LPS synthesis may be related to PHB under particular conditions. These results indicated that Slr2019 is necessary for

  13. Characterization of the sat Operon in Streptococcus mutans: Evidence for a Role of Ffh in Acid Tolerance

    PubMed Central

    Kremer, Bas H. A.; van der Kraan, Marieke; Crowley, Paula J.; Hamilton, Ian R.; Brady, L. Jeannine; Bleiweis, Arnold S.

    2001-01-01

    An essential protein translocation pathway in Escherichia coli and Bacillus subtilis involves the signal recognition particle (SRP), of which the 54-kDa homolog (Ffh) is an essential component. In a previous study, we found that a transposon insertion in the ylxM-ffh intergenic region of the designated secretion and acid tolerance (sat) operon of Streptococcus mutans resulted in an acid-sensitive phenotype. In the present study, we further characterized this genomic region in S. mutans after construction of bonafide sat operon mutants and confirmed the role of the SRP pathway in acid resistance. Northern blot and primer extension analyses identified an acid-inducible promoter upstream of ylxM that was responsible for upregulating the coordinate expression of all five genes of the sat operon when cells were grown at acid pH. Two constitutive promoters, one immediately upstream of satD and one just 3′ to the acid-inducible promoter, were also identified. Except for Ffh, the functions of the sat operon gene products are unknown. SatC, SatD, and SatE have no homology to proteins with known functions, although YlxM may function as a transcriptional regulator linked to genes encoding SRP pathway proteins. Nonpolar mutations created in each of the five genes of the sat locus resulted in viable mutants. Most striking, however, was the finding that a mutation in ffh did not result in loss of cell viability, as is the case in all other microbial species in which this pathway has been described. This mutant also lacked immunologically detectable Ffh and was severely affected in resistance to acid. Complementation of the mutation resulted in restoration of acid tolerance and reappearance of cytoplasmic Ffh. These data provide evidence that the SRP pathway plays an important role in acid tolerance in S. mutans. PMID:11274114

  14. Acid-tolerant microaerophilic Fe(II)-oxidizing bacteria promote Fe(III)-accumulation in a fen.

    PubMed

    Lüdecke, Claudia; Reiche, Marco; Eusterhues, Karin; Nietzsche, Sandor; Küsel, Kirsten

    2010-10-01

    The ecological importance of Fe(II)-oxidizing bacteria (FeOB) at circumneutral pH is often masked in the presence of O(2) where rapid chemical oxidation of Fe(II) predominates. This study addresses the abundance, diversity and activity of microaerophilic FeOB in an acidic fen (pH ∼ 5) located in northern Bavaria, Germany. Mean O(2) penetration depth reached 16 cm where the highest dissolved Fe(II) concentrations (up to 140 µM) were present in soil water. Acid-tolerant FeOB cultivated in gradient tubes were most abundant (10(6) cells g(-1) peat) at the 10-20 cm depth interval. A stable enrichment culture was active at up to 29% O(2) saturation and Fe(III) accumulated 1.6 times faster than in abiotic controls. An acid-tolerant, microaerophilic isolate (strain CL21) was obtained which was closely related to the neutrophilic, lithoautotrophic FeOB Sideroxydans lithotrophicus strain LD-1. CL21 oxidized Fe(II) between pH 4 and 6.0, and produced nanoscale-goethites with a clearly lower mean coherence length (7 nm) perpendicular to the (110) plane than those formed abiotically (10 nm). Our results suggest that an acid-tolerant population of FeOB is thriving at redox interfaces formed by diffusion-limited O(2) transport in acidic peatlands. Furthermore, this well-adapted population is successfully competing with chemical oxidation and thereby playing an important role in the microbial iron cycle.

  15. The Cytosolic pH of Individual Saccharomyces cerevisiae Cells Is a Key Factor in Acetic Acid Tolerance.

    PubMed

    Fernández-Niño, Miguel; Marquina, Maribel; Swinnen, Steve; Rodríguez-Porrata, Boris; Nevoigt, Elke; Ariño, Joaquín

    2015-11-01

    It was shown recently that individual cells of an isogenic Saccharomyces cerevisiae population show variability in acetic acid tolerance, and this variability affects the quantitative manifestation of the trait at the population level. In the current study, we investigated whether cell-to-cell variability in acetic acid tolerance could be explained by the observed differences in the cytosolic pHs of individual cells immediately before exposure to the acid. Results obtained with cells of the strain CEN.PK113-7D in synthetic medium containing 96 mM acetic acid (pH 4.5) showed a direct correlation between the initial cytosolic pH and the cytosolic pH drop after exposure to the acid. Moreover, only cells with a low initial cytosolic pH, which experienced a less severe drop in cytosolic pH, were able to proliferate. A similar correlation between initial cytosolic pH and cytosolic pH drop was also observed in the more acid-tolerant strain MUCL 11987-9. Interestingly, a fraction of cells in the MUCL 11987-9 population showed initial cytosolic pH values below the minimal cytosolic pH detected in cells of the strain CEN.PK113-7D; consequently, these cells experienced less severe drops in cytosolic pH. Although this might explain in part the difference between the two strains with regard to the number of cells that resumed proliferation, it was observed that all cells from strain MUCL 11987-9 were able to proliferate, independently of their initial cytosolic pH. Therefore, other factors must also be involved in the greater ability of MUCL 11987-9 cells to endure strong drops in cytosolic pH.

  16. Acidophilic, heterotrophic bacteria of acidic mine waters

    SciTech Connect

    Wichlacz, P.L.; Unz, R.F.

    1981-05-01

    Obligately acidophilic, heterotrophic bacteria were isolated both from enrichment cultures developed with acidic mine water and from natural mine drainage. The bacteria were grouped by the ability to utilize a number of organic acids as sole carbon sources. None of the strains were capable of chemolithotrophic growth on inorganic reduced iron and sulfur compounds. All bacteria were rod shaped, gram negative, nonencapsulated, motile, capable of growth at pH 2.6 but not at pH 6.0, catalase and oxidase positive, strictly aerobic, and capable of growth on citric acid. The bacteria were cultivatable on solid nutrient media only if agarose was employed as the hardening agent. Bacterial densities in natural mine waters ranged from approximately 20 to 250 cells per ml, depending upon source and culture medium.

  17. Biomining: metal recovery from ores with microorganisms.

    PubMed

    Schippers, Axel; Hedrich, Sabrina; Vasters, Jürgen; Drobe, Malte; Sand, Wolfgang; Willscher, Sabine

    2014-01-01

    Biomining is an increasingly applied biotechnological procedure for processing of ores in the mining industry (biohydrometallurgy). Nowadays the production of copper from low-grade ores is the most important industrial application and a significant part of world copper production already originates from heap or dump/stockpile bioleaching. Conceptual differences exist between the industrial processes of bioleaching and biooxidation. Bioleaching is a conversion of an insoluble valuable metal into a soluble form by means of microorganisms. In biooxidation, on the other hand, gold is predominantly unlocked from refractory ores in large-scale stirred-tank biooxidation arrangements for further processing steps. In addition to copper and gold production, biomining is also used to produce cobalt, nickel, zinc, and uranium. Up to now, biomining has merely been used as a procedure in the processing of sulfide ores and uranium ore, but laboratory and pilot procedures already exist for the processing of silicate and oxide ores (e.g., laterites), for leaching of processing residues or mine waste dumps (mine tailings), as well as for the extraction of metals from industrial residues and waste (recycling). This chapter estimates the world production of copper, gold, and other metals by means of biomining and chemical leaching (bio-/hydrometallurgy) compared with metal production by pyrometallurgical procedures, and describes new developments in biomining. In addition, an overview is given about metal sulfide oxidizing microorganisms, fundamentals of biomining including bioleaching mechanisms and interface processes, as well as anaerobic bioleaching and bioleaching with heterotrophic microorganisms.

  18. Biomining: metal recovery from ores with microorganisms.

    PubMed

    Schippers, Axel; Hedrich, Sabrina; Vasters, Jürgen; Drobe, Malte; Sand, Wolfgang; Willscher, Sabine

    2014-01-01

    Biomining is an increasingly applied biotechnological procedure for processing of ores in the mining industry (biohydrometallurgy). Nowadays the production of copper from low-grade ores is the most important industrial application and a significant part of world copper production already originates from heap or dump/stockpile bioleaching. Conceptual differences exist between the industrial processes of bioleaching and biooxidation. Bioleaching is a conversion of an insoluble valuable metal into a soluble form by means of microorganisms. In biooxidation, on the other hand, gold is predominantly unlocked from refractory ores in large-scale stirred-tank biooxidation arrangements for further processing steps. In addition to copper and gold production, biomining is also used to produce cobalt, nickel, zinc, and uranium. Up to now, biomining has merely been used as a procedure in the processing of sulfide ores and uranium ore, but laboratory and pilot procedures already exist for the processing of silicate and oxide ores (e.g., laterites), for leaching of processing residues or mine waste dumps (mine tailings), as well as for the extraction of metals from industrial residues and waste (recycling). This chapter estimates the world production of copper, gold, and other metals by means of biomining and chemical leaching (bio-/hydrometallurgy) compared with metal production by pyrometallurgical procedures, and describes new developments in biomining. In addition, an overview is given about metal sulfide oxidizing microorganisms, fundamentals of biomining including bioleaching mechanisms and interface processes, as well as anaerobic bioleaching and bioleaching with heterotrophic microorganisms. PMID:23793914

  19. Antagonistic interactions between filamentous heterotrophs and the cyanobacterium Nostoc muscorum

    PubMed Central

    2011-01-01

    Background Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2) and Fibrisoma limi (BUZ 3) with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82) were studied in mixed cultures under nutrient rich (carbon source present in medium) and poor (carbon source absent in medium) conditions. Findings F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc. The growth and survival of tested heterotrophs was enhanced by the presence of Nostoc or its metabolites, suggesting that the heterotrophs could utilize the autotrophs and its products as a nutrient source. However, the autotroph could withstand and out-compete the heterotrophs under nutrient poor conditions. Conclusions Our results suggest that the nutrients in cultivation media, which boost or reduce the number of heterotrophs, were the important factor influencing the outcome of the interplay between filamentous heterotrophs and autotrophs. For better understanding of these interactions, additional research is needed. In particular, it is necessary to elucidate the mode of action for lysis by heterotrophs, and the possible defense mechanisms of the autotrophs. PMID:21914201

  20. Heterotrophic nitrogen removal by a newly-isolated alkalitolerant microorganism, Serratia marcescens W5.

    PubMed

    Wang, Teng; Dang, Qifeng; Liu, Chengsheng; Yan, Jingquan; Fan, Bing; Cha, Dongsu; Yin, Yanyan; Zhang, Yubei

    2016-07-01

    A new microbe, Serratia marcescens W5 was successfully isolated. Its feasibility in purification of excessively nitrogen-containing wastewater was evaluated using inorganic nitrogen media. Single factor tests showed that W5 exhibited high ammonium removal rates (above 80%) under different culture conditions (pH 7-10, C/N ratios of 6-20, 15-35°C, 0-2.5% of salinity, respectively). Besides various organic carbon sources, W5 was able to utilize calcium carbonate with 28.05% of ammonium removed. Further experiments indicated that W5 was capable of resisting high-strength ammonium (1200mg/L) with the maximum removal rate of 514.13mgL(-1)d(-1). The nitrogen removal pathway of W5 was also tested, showing that both nitrite and nitrate were efficiently removed only in the presence of ammonium, with hydroxylamine as intermediate, which was different from the conventional nitrogen removal pathway. All the results verified that W5 was a good candidate for the purification of excessively nitrogenous wastewater.

  1. Heterotrophic nitrogen removal by a newly-isolated alkalitolerant microorganism, Serratia marcescens W5.

    PubMed

    Wang, Teng; Dang, Qifeng; Liu, Chengsheng; Yan, Jingquan; Fan, Bing; Cha, Dongsu; Yin, Yanyan; Zhang, Yubei

    2016-07-01

    A new microbe, Serratia marcescens W5 was successfully isolated. Its feasibility in purification of excessively nitrogen-containing wastewater was evaluated using inorganic nitrogen media. Single factor tests showed that W5 exhibited high ammonium removal rates (above 80%) under different culture conditions (pH 7-10, C/N ratios of 6-20, 15-35°C, 0-2.5% of salinity, respectively). Besides various organic carbon sources, W5 was able to utilize calcium carbonate with 28.05% of ammonium removed. Further experiments indicated that W5 was capable of resisting high-strength ammonium (1200mg/L) with the maximum removal rate of 514.13mgL(-1)d(-1). The nitrogen removal pathway of W5 was also tested, showing that both nitrite and nitrate were efficiently removed only in the presence of ammonium, with hydroxylamine as intermediate, which was different from the conventional nitrogen removal pathway. All the results verified that W5 was a good candidate for the purification of excessively nitrogenous wastewater. PMID:27043057

  2. Withania somnifera attenuates acid production, acid tolerance and extra-cellular polysaccharide formation of Streptococcus mutans biofilms.

    PubMed

    Pandit, Santosh; Song, Kwang-Yeob; Jeon, Jae-Gyu

    2014-01-01

    Withania somnifera (Ashwagandha) is a plant of the Solanaceae family. It has been widely used as a remedy for a variety of ailments in India and Nepal. The plant has also been used as a controlling agent for dental diseases. The aim of the present study was to evaluate the activity of the methanol extract of W. somnifera against the physiological ability of cariogenic biofilms and to identify the components of the extract. To determine the activity of the extract, assays for sucrose-dependent bacterial adherence, glycolytic acid production, acid tolerance, and extracellular polysaccharide formation were performed using Streptococcus mutans biofilms. The viability change of S. mutans biofilms cells was also determined. A phytochemical analysis of the extract was performed using TLC and LC/MS/MS. The extract showed inhibitory effects on sucrose-dependent bacterial adherence (≥ 100 μg/ml), glycolytic acid production (≥ 300 μg/ml), acid tolerance (≥ 300 μg/ml), and extracellular polysaccharide formation (≥ 300 μg/ml) of S. mutans biofilms. However, the extract did not alter the viability of S. mutans biofilms cells in all concentrations tested. Based on the phytochemical analysis, the activity of the extract may be related to the presence of alkaloids, anthrones, coumarines, anthraquinones, terpenoids, flavonoids, and steroid lactones (withanolide A, withaferin A, withanolide B, withanoside IV, and 12-deoxy withastramonolide). These data indicate that W. somnifera may be a potential agent for restraining the physiological ability of cariogenic biofilms.

  3. Separating Autotrophic and Heterotrophic Contributions to Soil Respiration in Maize-Based Agroecosystems Using Stable Carbon Isotope Ratio Mass Spectrometry.

    NASA Astrophysics Data System (ADS)

    Amos, B.; Walters, D. T.; Madhavan, S.; Arkebauer, T. J.; Scoby, D. L.

    2005-12-01

    Any effort to establish a carbon budget for a growing crop by means of a thorough accounting of all C sources and sinks will require the ability to discriminate between autotrophic and heterotrophic contributions to soil surface CO2 flux. Autotrophic soil respiration (Ra) is defined as combined root respiration and the respiration of soil microorganisms residing in the rhizosphere and using root-derived carbohydrates as an energy source, while heterotrophic respiration (Rh) is defined as the respiration of soil microorganisms and macroorganisms not directly under the influence of the live root system and using SOM as an energy source. We partition soil surface CO2 flux into its autotrophic and heterotrophic components by combining root exclusion with stable carbon isotope techniques in production scale (~65 ha) maize-based agroecosystems. After flux measurements, small chambers are placed on collars in both root excluded shields and in non-root excluded soil, ambient headspace CO2 is removed using a soda lime trap, and soil-respired C is allowed to collect in the chambers. Soil respiration samples are then collected in 12mL evacuated exetainers and analyzed for δ13C by means of a Finnigan Delta-S isotope ratio mass spectrometer interfaced with a Thermo Finnigan GasBench II and a cryogenic trap to increase CO2 concentration. These δ13C measurements were made throughout the 2005 growing season in maize fields representing three agroecosystems: irrigated continuous maize, irrigated maize-soybean rotation, and rainfed maize soybean rotation. Estimates of autotrophic and heterotrophic soil respiration along with other results of this study will be presented.

  4. Mechanisms of acid tolerance in bacteria and prospects in biotechnology and bioremediation.

    PubMed

    Liu, Yuping; Tang, Hongzhi; Lin, Zhanglin; Xu, Ping

    2015-11-15

    Acidogenic and aciduric bacteria have developed several survival systems in various acidic environments to prevent cell damage due to acid stress such as that on the human gastric surface and in the fermentation medium used for industrial production of acidic products. Common mechanisms for acid resistance in bacteria are proton pumping by F1-F0-ATPase, the glutamate decarboxylase system, formation of a protective cloud of ammonia, high cytoplasmic urease activity, repair or protection of macromolecules, and biofilm formation. The field of synthetic biology has rapidly advanced and generated an ever-increasing assortment of genetic devices and biological modules for applications in biofuel and novel biomaterial productions. Better understanding of aspects such as overproduction of general shock proteins, molecular mechanisms, and responses to cell density adopted by microorganisms for survival in low pH conditions will prove useful in synthetic biology for potential industrial and environmental applications.

  5. Heterotrophic plasticity and resilience in bleached corals.

    PubMed

    Grottoli, Andréa G; Rodrigues, Lisa J; Palardy, James E

    2006-04-27

    Mass coral bleaching events caused by elevated seawater temperatures have resulted in extensive coral mortality throughout the tropics over the past few decades. With continued global warming, bleaching events are predicted to increase in frequency and severity, causing up to 60% coral mortality globally within the next few decades. Although some corals are able to recover and to survive bleaching, the mechanisms underlying such resilience are poorly understood. Here we show that the coral host has a significant role in recovery and resilience. Bleached and recovering Montipora capitata (branching) corals met more than 100% of their daily metabolic energy requirements by markedly increasing their feeding rates and CHAR (per cent contribution of heterotrophically acquired carbon to daily animal respiration), whereas Porites compressa (branching) and Porites lobata (mounding) corals did not. These findings suggest that coral species with high-CHAR capability during bleaching and recovery, irrespective of morphology, will be more resilient to bleaching events over the long term, could become the dominant coral species on reefs, and may help to safeguard affected reefs from potential local and global extinction.

  6. Microorganisms and Chemical Pollution

    ERIC Educational Resources Information Center

    Alexander, M.

    1973-01-01

    Discusses the importance of microorganisms in chemical pollution and pollution abatement. Selected chemical pollutants are chosen to illustrate that microorganisms synthesize hazardous substances from reasonably innocuous precursors, while others act as excellent environmental decontaminating agents by removing undesirable natural and synthetic…

  7. Biotransformation of pharmaceuticals under nitrification, nitratation and heterotrophic conditions.

    PubMed

    Fernandez-Fontaina, E; Gomes, I B; Aga, D S; Omil, F; Lema, J M; Carballa, M

    2016-01-15

    The effect of nitrification, nitratation and heterotrophic conditions on the biotransformation of several pharmaceuticals in a highly enriched nitrifying activated sludge was evaluated in this study by selective activation of ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and heterotrophic bacteria. Nitrifiers displayed a noticeable capacity to process ibuprofen due to hydroxylation by ammonia monooxygenase (AMO) to produce 2-hydroxy-ibuprofen. Naproxen was also biotransformed under nitrifying conditions. On the other hand, heterotrophic bacteria present in the nitrifying activated sludge (NAS) biotransformed sulfamethoxazole. In contrast, both nitrifying and heterotrophic activities were ineffective against diclofenac, diazepam, carbamazepine and trimethoprim. Similar biotransformation rates of erythromycin, roxithromycin and fluoxetine were observed under all conditions tested. Overall, results from this study give more evidence on the role of the different microbial communities present in activated sludge reactors on the biological removal of pharmaceuticals. PMID:26479917

  8. Heterotrophic denitrification of aquaculture effluent using fluidized sand biofilters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ability to consistently and cost-effectively reduce nitrate-nitrogen loads in effluent from recirculating aquaculture systems would enhance the industry's environmental stewardship and allow improved facility proximity to large markets in sensitive watersheds. Heterotrophic denitrification techn...

  9. OCCURRENCE OF HETEROTROPHIC BACTERIA WITH VIRULENCE CHARACTERISTICS IN POTABLE WATER

    EPA Science Inventory

    Treated potable water contains a variety of heterotrophic bacteria that survive current treatment processes. There is evidence that these bacteria are not hazardous to the healthy population, however, the possibility exists that some of them may be opportunistic pathogens capabl...

  10. VIRULENCE CHARACTERISTICS OF HETEROTROPHIC BACTERIA COMMONLY ISOLATED FROM POTABLE WATER

    EPA Science Inventory

    Heterotrophic bacteria isolated from drinking water distribution systems were examined to determine if they possessed putative virulence factors such as hemolysins, proteases, or cytotoxins. Representative samples of colonies from several different distribution systems indicated ...

  11. Biotransformation of pharmaceuticals under nitrification, nitratation and heterotrophic conditions.

    PubMed

    Fernandez-Fontaina, E; Gomes, I B; Aga, D S; Omil, F; Lema, J M; Carballa, M

    2016-01-15

    The effect of nitrification, nitratation and heterotrophic conditions on the biotransformation of several pharmaceuticals in a highly enriched nitrifying activated sludge was evaluated in this study by selective activation of ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and heterotrophic bacteria. Nitrifiers displayed a noticeable capacity to process ibuprofen due to hydroxylation by ammonia monooxygenase (AMO) to produce 2-hydroxy-ibuprofen. Naproxen was also biotransformed under nitrifying conditions. On the other hand, heterotrophic bacteria present in the nitrifying activated sludge (NAS) biotransformed sulfamethoxazole. In contrast, both nitrifying and heterotrophic activities were ineffective against diclofenac, diazepam, carbamazepine and trimethoprim. Similar biotransformation rates of erythromycin, roxithromycin and fluoxetine were observed under all conditions tested. Overall, results from this study give more evidence on the role of the different microbial communities present in activated sludge reactors on the biological removal of pharmaceuticals.

  12. Pseudomonas aeruginosa and Heterotrophic Bacteria Count in Bottled Waters in Iran

    PubMed Central

    MOHAMMADI KOUCHESFAHANI, Matin; ALIMOHAMMADI, Mahmood; NABIZADEH NODEHI, Ramin; ASLANI, Hassan; REZAIE, Sassan; ASADIAN, Samieh

    2015-01-01

    Background: Nowadays, due to increased public awareness about water pollution and water borne diseases as well as water network deficiencies, bottled water consumers have increased dramatically worldwide, including Iran. Pseudomonas aeruginosa is an opportunistic human pathogen capable of causing widespread infections in burn and immune-compromised patients. The aim of this study was to investigate, P. aeruginosa in bottled waters selling in Iranian markets. Methods: One hundred and twenty samples of five unknown (not famous) domestic bottled water brands were purchased from Tehran retailers during 2013. The samples were evaluated for the presence of P. aeruginosa. In addition, heterotrophic plate counts were determined by incubation at 37 °C for 24 h. Results: P. aeruginosa was detected in 36.7% (44 samples) of all samples examined. In addition, heterotrophic bacteria in 32.5% (39 samples) of the samples were higher than 100 CFU/mL, while in 7.5% (9 samples) of the samples HPC relied between 20 and 100 CFU/ml. Conclusion: In contrast to public believe, bottled waters are not free of microorganisms, and it is suggested that authorities should provide stricter monitoring and control plan for water resources and plants. Concerning HPC and P. aeruginosa brands B and D were not suitable for drinking. PMID:26744709

  13. Antimicrobial Activity of Heterotrophic Bacterial Communities from the Marine Sponge Erylus discophorus (Astrophorida, Geodiidae)

    PubMed Central

    Graça, Ana Patrícia; Bondoso, Joana; Gaspar, Helena; Xavier, Joana R.; Monteiro, Maria Cândida; de la Cruz, Mercedes; Oves-Costales, Daniel; Vicente, Francisca; Lage, Olga Maria

    2013-01-01

    Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA), Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus), fish pathogen (Aliivibrio fischeri) and environmentally relevant bacteria (Vibrio harveyi). The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%), Vibrio (22.7%) and Bacillus (7.6%). Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I) and nonribosomal peptide synthetases (NRPSs) genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds. PMID:24236081

  14. Abundance and diversity of heterotrophic bacterial cells assimilating phosphate in the subtropical North Atlantic Ocean.

    PubMed

    Longnecker, Krista; Lomas, Michael W; Van Mooy, Benjamin A S

    2010-10-01

    Microorganisms play key roles in the cycles of carbon and nutrients in the ocean, and identifying the extent to which specific taxa contribute to these cycles will establish their ecological function. We examined the use of (33)P-phosphate to identify heterotrophic bacteria actively involved in the cycling of phosphate, an essential inorganic nutrient. Seawater from the sub-tropical North Atlantic Ocean was incubated with (33)P-phosphate and analysed by microautoradiography to determine the proportion and diversity of the bacterial community-assimilating phosphate. Complementary incubations using (3)H-leucine and (3)H-thymidine were also conducted. We found that a higher proportion of total heterotrophic bacterial cells in surface water samples assimilated phosphate compared with leucine or thymidine. Bacteria from all of the phylogenetic groups we identified by CARD-FISH were able to assimilate phosphate, although the abundances of cells within each group did not scale directly with the number found to assimilate phosphate. Furthermore, a significantly higher proportion of Alphaproteobacteria, Gammaproteobacteria and Cytophaga-like cells assimilated phosphate compared with leucine or thymidine. Our results suggest that a greater proportion of bacterial cells in surface waters are actively participating in the biogeochemical cycling of phosphorus, and possibly other elements, than is currently estimated through the use of (3)H-leucine or (3)H-thymidine.

  15. Heterotrophic euglenids from marine sediments of cape tribulation, tropical australia

    NASA Astrophysics Data System (ADS)

    Je Lee, Won

    2006-06-01

    This paper presents new data on free-living heterotrophic euglenids (Euglenozoa, Protista) that occurred in the marine sediments at Cape Tribulation, Queensland, Australia. Twenty-nine species from 9 genera are described with uninterpreted records based on light microscopy, including one new taxon: Notosolenus capetribulationi n. sp. There was little evidence for endemism because the majority of heterotrophic euglenid species encountered here have been reported or were found from other habitats.

  16. Unexpected diversity of heterotrophic prokaryotes living at the highest salt concentrations

    NASA Astrophysics Data System (ADS)

    Oren, Aharon

    2002-11-01

    Halophilic Archaea (family Halobacteriaceae) were until recently the only heterotrophic microorganisms known to grow optimally at near-saturating salt concentrations. It now appears that Salinibacter ruber, an extremely halophilic bacterium related to the Flavobacterium-Cytophaga group, may occur in large numbers in saltern crystallizer ponds. The organism is red, and harbors a novel carotenoid pigment. There is a surprising similarity between the physiology of Salinibacter and the Halobacteriaceae. In both cases the cells contain molar concentrations of KCl, and organic compatible solutes contribute little to osmotic adaptation. The proteins of Salinibacter contain a large excess of acidic amino acids and are depleted in hydrophobic amino acids. Its cytoplasmic enzymes function at high salt. The discovery of Salinibacter and the elucidation of its properties show that similar modes of adaptation to life at high salt concentrations and low water adaptation to life at high salt concentrations and low water activities may have evolved indpenednetly in phylogenetically distant groups.

  17. Phenotypic and genotypic adaptation of aerobic heterotrophic sediment bacterial communities to mercury stress.

    PubMed Central

    Barkay, T; Olson, B H

    1986-01-01

    The effects of mercury contamination of lake sediments on the phenotypic and genotypic mercury resistance of the indigenous heterotrophic aerobic bacterial communities were investigated. Strong positive correlations between mercury sediment concentration and the frequency of the gene coding for mercury volatilization (mer) (r = 0.96) or the phenotypic mercury resistance (r = 0.86) of the studied communities suggested that the inheritance via selection or genetic exchange of the mer gene had promoted bacterial adaptation to mercury. Failure to detect the mer gene in one mercury-contaminated sediment where phenotypic expression was low suggested that other mechanisms of resistance may partially determine the presence of mercury-resistant organisms in mercury-contaminated sediment or that the mercury in this particular sediment was very chemically limited in its availability to the microorganisms. PMID:3753001

  18. Heterotrophic respiration in disturbed forests: A review with examples from North America

    SciTech Connect

    Harmon, Mark; Bond-Lamberty, Benjamin; Tang, Jianwu; Vargas, Rodrigo

    2011-05-17

    Heterotrophic respiration (RH), the oxidation of organic matter to carbon dioxide by free-living microorganisms, is one of three major processes releasing carbon to the atmosphere, the other two being autotrophic respiration (RA) and combustion. Over long times and large spatial extents these three fluxes roughly equal the amount of carbon being fixed by photosynthesis, at least in upland ecosystems (Frey and Smith 2005). Over short period of time or within small areas changes in the strength of these fluxes can determine when and where an ecosystem is a source or sink of carbon relative to the atmosphere (reference from Hurtt disturbance paper). Thus, the understanding of the biophysical factors that regulate the strength of these fluxes is a current topic of research.

  19. Oceanic heterotrophic dinoflagellates: distribution, abundance, and role as microzooplankton

    SciTech Connect

    Lessard, E.J.

    1984-01-01

    The primary objectives of this thesis were to determine the distribution and abundance of heterotrophic dinoflagellates across the Gulf Stream system off Cape Hatteras and to assess the potential grazing impact of these microheterotrophs in plankton communities. A list of species encountered in this study and their trophic status based on epifluorescence is presented, as well as observations on the presence of external or internal symbionts. The abundance of heterotrophic dinoflagellates across the Gulf Stream region off Cape Hatteras was determined from bimonthly net tow samples over a year and from whole water samples in March. Their average abundance was twice that of net ciliates in the net plankton and ten times that of ciliates in the nanoplankton. An isotope technique was developed to measure grazing rates of individual dinoflaggellates and other microzooplankton which cannot be separated in natural populations on the basis of size. /sup 3/H-thymidine and /sup 14/C-bicarbonate were used to label natural heterotrophic (bacteria and bacterivores) and autotrophic (phytoplankton and herbivores) food, respectively. Estimates of the grazing impact of heterotrophic kinoflagellates relative to other groups of heterotrophs on phytoplankton and bacteria were made by combining abundance data and clearance rates. Such calculations suggested that heterotrophic dinoflagellates may be an important group of grazers in oceanic waters.

  20. Deficiency of PdxR in Streptococcus mutans affects vitamin B6 metabolism, acid tolerance response and biofilm formation.

    PubMed

    Liao, S; Bitoun, J P; Nguyen, A H; Bozner, D; Yao, X; Wen, Z T

    2015-08-01

    Streptococcus mutans, a key etiological agent of the human dental caries, lives primarily on the tooth surface in tenacious biofilms. The SMU864 locus, designated pdxR, is predicted to encode a member of the novel MocR/GabR family proteins, which are featured with a winged helix DNA-binding N-terminal domain and a C-terminal domain highly homologous to the pyridoxal phosphate-dependent aspartate aminotransferases. A pdxR-deficient mutant, TW296, was constructed using allelic exchange. PdxR deficiency in S. mutans had little effect on cell morphology and growth when grown in brain heart infusion. However, when compared with its parent strain, UA159, the PdxR-deficient mutant displayed major defects in acid tolerance response and formed significantly fewer biofilms (P < 0.01). When analyzed by real-time polymerase chain reaction, PdxR deficiency was found to drastically reduce expression of an apparent operon encoding a pyridoxal kinase (SMU865) and a pyridoxal permease (SMU866) of the salvage pathway of vitamin B6 biosynthesis. In addition, PdxR deficiency also altered the expression of genes for ClpL protease, glucosyltransferase B and adhesin SpaP, which are known to play important roles in stress tolerance and biofilm formation. Consistently, PdxR-deficiency affected the growth of the deficient mutant when grown in defined medium with and without vitamin B6 . Further studies revealed that although S. mutans is known to require vitamin B6 to grow in defined medium, B6 vitamers, especially pyridoxal, were strongly inhibitory at millimolar concentrations, against S. mutans growth and biofilm formation. Our results suggest that PdxR in S. mutans plays an important role in regulation of vitamin B6 metabolism, acid tolerance response and biofilm formation. PMID:25421565

  1. Deficiency of PdxR in Streptococcus mutans affects vitamin B6 metabolism, acid tolerance response and biofilm formation.

    PubMed

    Liao, S; Bitoun, J P; Nguyen, A H; Bozner, D; Yao, X; Wen, Z T

    2015-08-01

    Streptococcus mutans, a key etiological agent of the human dental caries, lives primarily on the tooth surface in tenacious biofilms. The SMU864 locus, designated pdxR, is predicted to encode a member of the novel MocR/GabR family proteins, which are featured with a winged helix DNA-binding N-terminal domain and a C-terminal domain highly homologous to the pyridoxal phosphate-dependent aspartate aminotransferases. A pdxR-deficient mutant, TW296, was constructed using allelic exchange. PdxR deficiency in S. mutans had little effect on cell morphology and growth when grown in brain heart infusion. However, when compared with its parent strain, UA159, the PdxR-deficient mutant displayed major defects in acid tolerance response and formed significantly fewer biofilms (P < 0.01). When analyzed by real-time polymerase chain reaction, PdxR deficiency was found to drastically reduce expression of an apparent operon encoding a pyridoxal kinase (SMU865) and a pyridoxal permease (SMU866) of the salvage pathway of vitamin B6 biosynthesis. In addition, PdxR deficiency also altered the expression of genes for ClpL protease, glucosyltransferase B and adhesin SpaP, which are known to play important roles in stress tolerance and biofilm formation. Consistently, PdxR-deficiency affected the growth of the deficient mutant when grown in defined medium with and without vitamin B6 . Further studies revealed that although S. mutans is known to require vitamin B6 to grow in defined medium, B6 vitamers, especially pyridoxal, were strongly inhibitory at millimolar concentrations, against S. mutans growth and biofilm formation. Our results suggest that PdxR in S. mutans plays an important role in regulation of vitamin B6 metabolism, acid tolerance response and biofilm formation.

  2. Spatial distribution of microorganisms and measurements of oxygen uptake rate and ammonia uptake rate activity in a drinking water biofilter.

    PubMed

    Madoni, P; Davoli, D; Fontani, N; Cucchi, A; Rossi, F

    2001-04-01

    The biofilm characteristics (population dynamics and biofilm composition) in a biological filter for the removal of iron, manganese and ammonium were studied in a drinking water treatment plant. The objective was to examine the spatial distribution and biological composition of active biomass that grows in a biological filter and to verify the effect of the backwashing on the quantity of fixed biomass and on the density and activity of the biological population. Heterotrophic microorganisms activity was higher in the upper layer of the filter. Nitrifying microorganisms colonized the biofilter in a stratified manner and their activity was higher in the second layer of the filter. A total of 14 species of ciliated protozoa and 7 species of filamentous microorganisms were found in the biofilters. Ciliates were concentrated in the filterbed layer in which the heterotrophic activity was higher. The grazing activity of ciliates on heterotrophic bacteria reduced the competition pressure on nitrifying microorganisms, supporting their growth and thus raising the ammonium removal efficiency. In general, filamentous microorganisms appeared to be indifferent to operating changes in the plant such as backwashing and filtering cycles. Crenothrix was the prevalent filamentous microorganism in terms of both frequency and abundance; it was found prevalently in the first layer where the oxidisation of iron and manganese occurred.

  3. Micro-Organ Device

    NASA Technical Reports Server (NTRS)

    Gonda, Steve R. (Inventor); Chang, Robert C. (Inventor); Starly, Binil (Inventor); Culbertson, Christopher (Inventor); Holtorf, Heidi L. (Inventor); Sun, Wei (Inventor); Leslie, Julia (Inventor)

    2013-01-01

    A method for fabricating a micro-organ device comprises providing a microscale support having one or more microfluidic channels and one or more micro-chambers for housing a micro-organ and printing a micro-organ on the microscale support using a cell suspension in a syringe controlled by a computer-aided tissue engineering system, wherein the cell suspension comprises cells suspended in a solution containing a material that functions as a three-dimensional scaffold. The printing is performed with the computer-aided tissue engineering system according to a particular pattern. The micro-organ device comprises at least one micro-chamber each housing a micro-organ; and at least one microfluidic channel connected to the micro-chamber, wherein the micro-organ comprises cells arranged in a configuration that includes microscale spacing between portions of the cells to facilitate diffusion exchange between the cells and a medium supplied from the at least one microfluidic channel.

  4. Micro-organ device

    NASA Technical Reports Server (NTRS)

    Gonda, Steve R. (Inventor); von Gustedt-Gonda, legal representative, Iris (Inventor); Chang, Robert C. (Inventor); Starly, Binil (Inventor); Culbertson, Christopher (Inventor); Holtorf, Heidi L. (Inventor); Sun, Wei (Inventor); Leslie, Julia (Inventor)

    2013-01-01

    A method for fabricating a micro-organ device comprises providing a microscale support having one or more microfluidic channels and one or more micro-chambers for housing a micro-organ and printing a micro-organ on the microscale support using a cell suspension in a syringe controlled by a computer-aided tissue engineering system, wherein the cell suspension comprises cells suspended in a solution containing a material that functions as a three-dimensional scaffold. The printing is performed with the computer-aided tissue engineering system according to a particular pattern. The micro-organ device comprises at least one micro-chamber each housing a micro-organ; and at least one microfluidic channel connected to the micro-chamber, wherein the micro-organ comprises cells arranged in a configuration that includes microscale spacing between portions of the cells to facilitate diffusion exchange between the cells and a medium supplied from the at least one microfluidic channel.

  5. Biofouling of contaminated ground-water recovery wells: Characterization of microorganisms

    SciTech Connect

    Taylor, S.W.; Lange, C.R.; Lesold, E.A.

    1997-11-01

    The taxonomy and physiology of microorganisms isolated from contaminated ground-water recovery wells prone to biofouling are characterized for an industrial site in Rochester, New York. Principal aquifer contaminants include acetone, cyclohexane, dichloroethane, dichloromethane, 1,4-dioxane, isopropanol, methanol, and toluene. These contaminants represent a significant fraction (up to 95%) of the total organic carbon in the ground water. Ground-water samples from 12 recovery wells were used to isolate, quantify, and identify aerobic and anaerobic bacterial populations. Samples from selected wells were also characterized geochemically to assess redox conditions and availability of essential and trace nutrients. Dominant bacteria, listed in order of descending numbers, including sulfate-reducers (Desulfovibrio desulfuricans), anaerobic heterotrophs (Actinomyces, Bacteriodes, Bacillus, Agrobacterium), aerobic heterotrophs (Pseudomonas, Flavobacterium, Nocardia, Citrobacter), iron-oxidizers (Gallionella ferruginea, Crenothrix polyspora), iron-reducers (Shewanella), and sulfur-oxidizers (Thiobacillus ferrooxidans). Fungi were also recovered in low numbers. Both aerobic and anaerobic heterotrophs were able to utilize all principal contaminants as sole carbon and energy sources except 1,4-dioxane. The prevalence of heterotrophic bacteria and their ability to use the available anthropogenic carbon suggests that aerobic and anaerobic heterotrophs contribute to the biofouling of wells at this site, in addition to the often cited fouling due to iron-oxidizing bacteria and sulfate-reducing bacteria.

  6. Acid-Tolerant Sulfate-Reducing Bacteria Play a Major Role in Iron Cycling in Acidic Iron Rich Sediments

    NASA Astrophysics Data System (ADS)

    Enright, K. A.; Moreau, J. W.

    2008-12-01

    Climate change drives drying and acidification of many rivers and lakes. Abundant sedimentary iron in these systems oxidizes chemically and biologically to form iron-ox(yhydrox)ide crusts and "hardpans". Given generally high sulfate concentrations, the mobilization and cycling of iron in these environments can be strongly influenced by bacterial sulfate reduction. Sulfate-reducing bacteria (SRB) induce reductive dissolution of oxidized iron phases by producing the reductant bisulfide as a metabolic product. These environmentally ubiquitous microbes also recycle much of the fixed carbon in sediment-hosted microbial mat communities. With prevalent drying, the buffering capacity for protons liberated from iron oxidation is exceeded, and the activity of sulfate-reducers is restricted to those species capable of tolerating low pH (and generally highly saline, i.e. sulfate-rich) conditions. These species will sustain the recycling of iron from more crystalline phases to more bioavailable species, as well as act as the only source of bisulfide for photosynthesizing microbial communities. The phylogeny and physiology of acid-tolerant SRB is therefore important to Fe, S and C cycling in iron-rich sedimentary environments, particularly those on a geochemical trajectory towards acidification. Previous studies have shown that these SRB species tend to be highly novel. We studied two distinct environments along a geochemical continuum towards acidification. In both settings, iron redox transformations exert a major, if not controlling, influence on reduction potential. An acidified, iron- rich tidal marsh receiving acid-mine drainage (San Francisco Bay, CA, USA) contained abundant textural evidence for reductive dissolution of Fe(III) in sediments with pH values varying from 2.4 - 3.8. From these sediments, full-length novel dsrAB gene sequences from acid-tolerant SRB were recovered, and sulfur isotope profiles reflected biological fractionation of sulfur under even the most

  7. Fossil Microorganisms in Archaean

    NASA Technical Reports Server (NTRS)

    Astafleva, Marina; Hoover, Richard; Rozanov, Alexei; Vrevskiy, A.

    2006-01-01

    Ancient Archean and Proterozoic rocks are the model objects for investigation of rocks comprising astromaterials. The first of Archean fossil microorganisms from Baltic shield have been reported at the last SPIE Conference in 2005. Since this confeence biomorphic structures have been revealed in Archean rocks of Karelia. It was determined that there are 3 types of such bion structures: 1. structures found in situ, in other words microorganisms even-aged with rock matrix, that is real Archean fossils biomorphic structures, that is to say forms inhabited early formed rocks, and 3. younger than Archean-Protherozoic minerali microorganisms, that is later contamination. We made attempt to differentiate these 3 types of findings and tried to understand of burial of microorganisms. The structures belongs (from our point of view) to the first type, or real Archean, forms were under examination. Practical investigation of ancient microorganisms from Green-Stone-Belt of Northern Karelia turns to be very perspective. It shows that even in such ancient time as Archean ancient diverse world existed. Moreover probably such relatively highly organized cyanobacteria and perhaps eukaryotic formes existed in Archean world.

  8. Application of molecular techniques on heterotrophic hydrogen production research.

    PubMed

    Li, R Y; Zhang, T; Fang, H H P

    2011-09-01

    This paper reviews the application of molecular techniques in heterotrophic hydrogen production studies. Commonly used molecular techniques are introduced briefly first, including cloning-sequencing after polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), terminal-restriction fragment length polymorphism (T-RFLP), fluorescence in situ hybridization (FISH) and quantitative real-time PCR. Application of the molecular techniques in heterotrophic hydrogen production studies are discussed in details, focusing on identification of new isolates for hydrogen production, characterization of microbial compositions in bioreactors, monitoring microbial diversity variation, visualization of microbial distribution in hydrogen-producing granular sludge, and quantification of various microbial populations. Some significant findings in recent hydrogen production studies with the application of molecular techniques are discussed, followed by a research outlook of the heterotrophic biohydrogen field.

  9. Micro-Organ Devices

    NASA Technical Reports Server (NTRS)

    Gonda, Steven R.; Leslie, Julia; Chang, Robert C.; Starly, Binil; Sun, Wei; Culbertson, Christopher; Holtorf, Heidi

    2009-01-01

    Micro-organ devices (MODs) are being developed to satisfy an emerging need for small, lightweight, reproducible, biological-experimentati on apparatuses that are amenable to automated operation and that imp ose minimal demands for resources (principally, power and fluids). I n simplest terms, a MOD is a microfluidic device containing a variety of microstructures and assemblies of cells, all designed to mimic a complex in vivo microenvironment by replicating one or more in vivo micro-organ structures, the architectures and composition of the extr acellular matrices in the organs of interest, and the in vivo fluid flows. In addition to microscopic flow channels, a MOD contains one or more micro-organ wells containing cells residing in microscopic e xtracellular matrices and/or scaffolds, the shapes and compositions o f which enable replication of the corresponding in vivo cell assembl ies and flows.

  10. Open fermentative production of fuel ethanol from food waste by an acid-tolerant mutant strain of Zymomonas mobilis.

    PubMed

    Ma, Kedong; Ruan, Zhiyong; Shui, Zongxia; Wang, Yanwei; Hu, Guoquan; He, Mingxiong

    2016-03-01

    The aim of present study was to develop a process for open ethanol fermentation from food waste using an acid-tolerant mutant of Zymomonas mobilis (ZMA7-2). The mutant showed strong tolerance to acid condition of food waste hydrolysate and high ethanol production performance. By optimizing fermentation parameters, ethanol fermentation with initial glucose concentration of 200 g/L, pH value around 4.0, inoculum size of 10% and without nutrient addition was considered as best conditions. Moreover, the potential of bench scales fermentation and cell reusability was also examined. The fermentation in bench scales (44 h) was faster than flask scale (48 h), and the maximum ethanol concentration and ethanol yield (99.78 g/L, 0.50 g/g) higher than that of flask scale (98.31 g/L, 0.49 g/g). In addition, the stable cell growth and ethanol production profile in five cycles successive fermentation was observed, indicating the mutant was suitable for industrial ethanol production.

  11. The synergistic preservative effects of the essential oils of sweet basil (Ocimum basilicum L.) against acid-tolerant food microflora.

    PubMed

    Lachowicz, K J; Jones, G P; Briggs, D R; Bienvenu, F E; Wan, J; Wilcock, A; Coventry, M J

    1998-03-01

    Essential oils extracted by hydrodistillation from five different varieties of Ocimum basilicum L. plants (Anise, Bush, Cinnamon, Dark Opal and a commercial sample of dried basil) were examined for antimicrobial activity against a wide range of foodborne Gram-positive and -negative bacteria, yeasts and moulds by an agar well diffusion method. All five essential oils of basil showed antimicrobial activity against most of the organisms tested with the exception of Flavimonas oryzihabitans and Pseudomonas species. The inhibitory effect of Anise oil, in comparison with mixtures of the predominant components of pure linalool and methyl chavicol, against the acid-tolerant organisms, Lactobacillus curvatus and Saccharomyces cerevisiae, was examined in broth by an indirect impedance method. Synergistic effects between Anise oil, low pH (pH 4.2) and salt (5% NaCl) were determined. The antimicrobial effect of Anise oil was also assessed in a tomato juice medium by direct viable count, showing that the growth of Lact. curvatus and S. cerevisiae was completely inhibited by 0.1% and 1% Anise oil, respectively. The results of the current study indicate the need for further investigations to understand the antimicrobial effects of basil oils in the presence of other food ingredients and preservation parameters.

  12. Comparative study of aluminum and copper transport and toxicity in an acid-tolerant freshwater green alga

    SciTech Connect

    Folsom, B.R.; Popescu, N.A.; Wood, J.M.

    1986-06-01

    A comparative study of the transport and toxicity of one nonessential metal (aluminum), and one essential metal (copper), has been performed with the acid-tolerant green alga Chlorella saccarophila. This organism was isolated from a naturally acidified lake and grows well in laboratory cultures at pH 3.0. Our results show that the fast-exchange ions Ca/sup 2 +/, Mg/sup 2 +/, and Na/sup +/ offer some protection against both Al/sup 3 +/ and Cu/sup 2 +/ toxicity whereas K/sup +/ protects against Al/sup 3 +/ toxicity but enhances Cu/sup 2 +/ toxicity. Plasma emission spectroscopy shows that complexation of Al/sup 3 +/ and Fe/sup 3 +/ to cell surfaces is important in preventing toxic cytoplasmic levels of these metals, both in culture media and in acid mine water. The aqueous ion chemistry for toxic metal uptake is simplified considerably in acidic conditions, where competing hydrolysis and precipitation reactions are eliminated. Therefore, simple competitive experiments can be performed quantitatively. 12 references, 7 figures, 1 table.

  13. Multiple-unit tablet of probiotic bacteria for improved storage stability, acid tolerability, and in vivo intestinal protective effect

    PubMed Central

    Park, Hee Jun; Lee, Ga Hyeon; Jun, Joonho; Son, Miwon; Kang, Myung Joo

    2016-01-01

    The aim of this study was to formulate probiotics-loaded pellets in a tablet form to improve storage stability, acid tolerability, and in vivo intestinal protective effect. Bacteria-loaded pellets primarily prepared with hydroxypropyl methylcellulose acetate succinate were compressed into tablets with highly compressible excipients and optimized for flow properties, hardness, and disintegration time. The optimized probiotic tablet consisted of enteric-coated pellets (335 mg), microcrystalline cellulose (Avicel PH102, 37.5 mg), and porous calcium silicate (25 mg) and allowed whole survival of living bacteria during the compaction process with sufficient tablet hardness (13 kp) and disintegration time (14 minutes). The multiple-unit tablet showed remarkably higher storage stability under ambient conditions (25°C/60% relative humidity) over 6 months and resistance to acidic medium compared to uncoated strains or pellets. Repeated intake of this multiple-unit tablet significantly lowered plasma level of endotoxin, a pathogenic material, compared to repeated intake of bare probiotics or marketed products in rats. These results, therefore, suggest that the multiple-unit tablet is advantageous to better bacterial viability and gain the beneficial effects on the gut flora, including the improvement of intestinal barrier function. PMID:27103789

  14. Absence of Rtt109p, a fungal-specific histone acetyltransferase, results in improved acetic acid tolerance of Saccharomyces cerevisiae.

    PubMed

    Cheng, Cheng; Zhao, Xinqing; Zhang, Mingming; Bai, Fengwu

    2016-03-01

    RTT109 is a histone acetyltransferase for the acetylation of histone H3. It is still not clear whether RTT109 plays a role in regulation of gene expression under environmental stresses. In this study, the involvement of RTT109 in acetic acid stress tolerance of Saccharomyces cerevisiae was investigated. It was revealed that the absence of RTT109 enhanced resistance to 5.5 g L(-1) acetic acid, which was indicated by improved growth of RTT109Δ mutant compared with that of the wild-type BY4741 strain. Meanwhile, the lag phase was shortened for 48 h and glucose consumption completed 36 h in advance for RTT109Δ mutant compared to the wild-type strain, with ethanol production rate increased from 0.39 to 0.60 g L(-1) h(-1). Significantly, elevated transcription levels of HSP12, CTT1 and GSH1, as well as increased activities of antioxidant enzymes were observed in RTT109Δ under acetic acid stress. Improved flocculation of RTT109Δ compared to that of the control strain BY4741 under the acetic acid stress was also observed. These results suggest that the absence of RTT109 not only activates transcription of stress responsive genes, but also improves resistance to oxidative stress, which ultimately contributes to improved acetic acid tolerance in S. cerevisiae.

  15. Absence of Rtt109p, a fungal-specific histone acetyltransferase, results in improved acetic acid tolerance of Saccharomyces cerevisiae.

    PubMed

    Cheng, Cheng; Zhao, Xinqing; Zhang, Mingming; Bai, Fengwu

    2016-03-01

    RTT109 is a histone acetyltransferase for the acetylation of histone H3. It is still not clear whether RTT109 plays a role in regulation of gene expression under environmental stresses. In this study, the involvement of RTT109 in acetic acid stress tolerance of Saccharomyces cerevisiae was investigated. It was revealed that the absence of RTT109 enhanced resistance to 5.5 g L(-1) acetic acid, which was indicated by improved growth of RTT109Δ mutant compared with that of the wild-type BY4741 strain. Meanwhile, the lag phase was shortened for 48 h and glucose consumption completed 36 h in advance for RTT109Δ mutant compared to the wild-type strain, with ethanol production rate increased from 0.39 to 0.60 g L(-1) h(-1). Significantly, elevated transcription levels of HSP12, CTT1 and GSH1, as well as increased activities of antioxidant enzymes were observed in RTT109Δ under acetic acid stress. Improved flocculation of RTT109Δ compared to that of the control strain BY4741 under the acetic acid stress was also observed. These results suggest that the absence of RTT109 not only activates transcription of stress responsive genes, but also improves resistance to oxidative stress, which ultimately contributes to improved acetic acid tolerance in S. cerevisiae. PMID:26851403

  16. The synergistic preservative effects of the essential oils of sweet basil (Ocimum basilicum L.) against acid-tolerant food microflora.

    PubMed

    Lachowicz, K J; Jones, G P; Briggs, D R; Bienvenu, F E; Wan, J; Wilcock, A; Coventry, M J

    1998-03-01

    Essential oils extracted by hydrodistillation from five different varieties of Ocimum basilicum L. plants (Anise, Bush, Cinnamon, Dark Opal and a commercial sample of dried basil) were examined for antimicrobial activity against a wide range of foodborne Gram-positive and -negative bacteria, yeasts and moulds by an agar well diffusion method. All five essential oils of basil showed antimicrobial activity against most of the organisms tested with the exception of Flavimonas oryzihabitans and Pseudomonas species. The inhibitory effect of Anise oil, in comparison with mixtures of the predominant components of pure linalool and methyl chavicol, against the acid-tolerant organisms, Lactobacillus curvatus and Saccharomyces cerevisiae, was examined in broth by an indirect impedance method. Synergistic effects between Anise oil, low pH (pH 4.2) and salt (5% NaCl) were determined. The antimicrobial effect of Anise oil was also assessed in a tomato juice medium by direct viable count, showing that the growth of Lact. curvatus and S. cerevisiae was completely inhibited by 0.1% and 1% Anise oil, respectively. The results of the current study indicate the need for further investigations to understand the antimicrobial effects of basil oils in the presence of other food ingredients and preservation parameters. PMID:9569711

  17. Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia

    PubMed Central

    Walker, Robert; Watkin, Elizabeth; Tian, Rui; Bräu, Lambert; O’Hara, Graham; Goodwin, Lynne; Han, James; Reddy, Tatiparthi; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

    2013-01-01

    Burkholderia sp. strain WSM2232 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod that was trapped in 2001 from acidic soil collected from Karijini National Park (Australia) using Gastrolobium capitatum as a host. WSM2232 was effective in nitrogen fixation with G. capitatum but subsequently lost symbiotic competence during long-term storage. Here we describe the features of Burkholderia sp. strain WSM2232, together with genome sequence information and its annotation. The 7,208,311 bp standard-draft genome is arranged into 72 scaffolds of 72 contigs containing 6,322 protein-coding genes and 61 RNA-only encoding genes. The loss of symbiotic capability can now be attributed to the loss of nodulation and nitrogen fixation genes from the genome. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. PMID:25197442

  18. YfdW and YfdU are required for oxalate-induced acid tolerance in Escherichia coli K-12.

    PubMed

    Fontenot, Elise M; Ezelle, Karen E; Gabreski, Lauren N; Giglio, Eleanor R; McAfee, John M; Mills, Alexandria C; Qureshi, Maryam N; Salmon, Kristin M; Toyota, Cory G

    2013-04-01

    Escherichia coli has several mechanisms for surviving low-pH stress. We report that oxalic acid, a small-chain organic acid (SCOA), induces a moderate acid tolerance response (ATR) in two ways. Adaptation of E. coli K-12 at pH 5.5 with 50 mM oxalate and inclusion of 25 mM oxalate in pH 3.0 minimal challenge medium separately conferred protection, with 67% ± 7% and 87% ± 17% survival after 2 h, respectively. The combination of oxalate adaptation and oxalate supplementation in the challenge medium resulted in increased survival over adaptation or oxalate in the challenge medium alone. The enzymes YfdW, a formyl coenzyme A (CoA) transferase, and YfdU, an oxalyl-CoA decarboxylase, are required for the adaptation effect but not during challenge. Unlike other SCOAs, this oxalate ATR is not a part of the RpoS regulon but appears to be linked to the signal protein GadE. We theorize that this oxalate ATR could enhance the pathogenesis of virulent E. coli consumed with oxalate-containing foods like spinach.

  19. Multiple-unit tablet of probiotic bacteria for improved storage stability, acid tolerability, and in vivo intestinal protective effect.

    PubMed

    Park, Hee Jun; Lee, Ga Hyeon; Jun, Joonho; Son, Miwon; Kang, Myung Joo

    2016-01-01

    The aim of this study was to formulate probiotics-loaded pellets in a tablet form to improve storage stability, acid tolerability, and in vivo intestinal protective effect. Bacteria-loaded pellets primarily prepared with hydroxypropyl methylcellulose acetate succinate were compressed into tablets with highly compressible excipients and optimized for flow properties, hardness, and disintegration time. The optimized probiotic tablet consisted of enteric-coated pellets (335 mg), microcrystalline cellulose (Avicel PH102, 37.5 mg), and porous calcium silicate (25 mg) and allowed whole survival of living bacteria during the compaction process with sufficient tablet hardness (13 kp) and disintegration time (14 minutes). The multiple-unit tablet showed remarkably higher storage stability under ambient conditions (25°C/60% relative humidity) over 6 months and resistance to acidic medium compared to uncoated strains or pellets. Repeated intake of this multiple-unit tablet significantly lowered plasma level of endotoxin, a pathogenic material, compared to repeated intake of bare probiotics or marketed products in rats. These results, therefore, suggest that the multiple-unit tablet is advantageous to better bacterial viability and gain the beneficial effects on the gut flora, including the improvement of intestinal barrier function. PMID:27103789

  20. YfdW and YfdU Are Required for Oxalate-Induced Acid Tolerance in Escherichia coli K-12

    PubMed Central

    Fontenot, Elise M.; Ezelle, Karen E.; Gabreski, Lauren N.; Giglio, Eleanor R.; McAfee, John M.; Mills, Alexandria C.; Qureshi, Maryam N.; Salmon, Kristin M.

    2013-01-01

    Escherichia coli has several mechanisms for surviving low-pH stress. We report that oxalic acid, a small-chain organic acid (SCOA), induces a moderate acid tolerance response (ATR) in two ways. Adaptation of E. coli K-12 at pH 5.5 with 50 mM oxalate and inclusion of 25 mM oxalate in pH 3.0 minimal challenge medium separately conferred protection, with 67% ± 7% and 87% ± 17% survival after 2 h, respectively. The combination of oxalate adaptation and oxalate supplementation in the challenge medium resulted in increased survival over adaptation or oxalate in the challenge medium alone. The enzymes YfdW, a formyl coenzyme A (CoA) transferase, and YfdU, an oxalyl-CoA decarboxylase, are required for the adaptation effect but not during challenge. Unlike other SCOAs, this oxalate ATR is not a part of the RpoS regulon but appears to be linked to the signal protein GadE. We theorize that this oxalate ATR could enhance the pathogenesis of virulent E. coli consumed with oxalate-containing foods like spinach. PMID:23335415

  1. Microorganisms and Man.

    ERIC Educational Resources Information Center

    Noble, W. C.

    1983-01-01

    Provides information to update Institute of Biology's Studies in Biology No. 111, "Microorganisms and Man," by W. C. Noble and Jay Naidoo (Edward Arnold, 1979). Topics include: (1) food poisoning; (2) airborn infections in man; (3) infection in animals and plants; and (4) biodegradation and biosynthesis. (JN)

  2. [Biotechnology using modified microorganisms].

    PubMed

    Deshayes, A F

    1992-11-01

    Few microorganisms, as compare to their high diversity, are used for human needs. They can produce molecules of interest, process fermentation, protect crops, treat wastes or clean environment. Molecular technics and genetic engineering are new tools offer to geneticists which breed microorganisms for years. Using them, it is now possible, theoretically, to introduce any gene in any organism. Some examples are given concerning genetic modifications in yeasts and lactic acid bacteria to optimize agrofood processes and to improve nutritive and flavour characteristics of fermented products like bread, beer, wine, cheese, meat, vegetable juices... In spite of scientific and industrial interest of the new technologies, limiting factors can explain that genetically modified microorganisms are not routinely used in agrofood yet. First, risks assessment on human health and environment are still in debate, but their is a consensus, within the scientific community, to consider that new characteristics of improved microorganisms are more important than the technics used for their construction. Second, regulations turn out to impose constraints susceptible to discourage technological innovations. At least, the public perception about the new technologies appears, actually, as the major factor to limit their development.

  3. A MEMBRANE FILTER PROCEDURE FOR ASSAYING CYTOTOXIC ACTIVITY IN HETEROTROPHIC BACTERIA ISOLATED FROM DRINKING WATER

    EPA Science Inventory

    Cytotoxic activity assays of Gram-negative, heterotrophic bacteria are often laborious and time consuming. The objective of this study was to develop in situ procedures for testing potential cytotoxic activities of heterotrophic bacteria isolated from drinking water systems. Wate...

  4. Diversification of myco-heterotrophic angiosperms: Evidence from Burmanniaceae

    PubMed Central

    2008-01-01

    Background Myco-heterotrophy evolved independently several times during angiosperm evolution. Although many species of myco-heterotrophic plants are highly endemic and long-distance dispersal seems unlikely, some genera are widely dispersed and have pantropical distributions, often with large disjunctions. Traditionally this has been interpreted as evidence for an old age of these taxa. However, due to their scarcity and highly reduced plastid genomes our understanding about the evolutionary histories of the angiosperm myco-heterotrophic groups is poor. Results We provide a hypothesis for the diversification of the myco-heterotrophic family Burmanniaceae. Phylogenetic inference, combined with biogeographical analyses, molecular divergence time estimates, and diversification analyses suggest that Burmanniaceae originated in West Gondwana and started to diversify during the Late Cretaceous. Diversification and migration of the species-rich pantropical genera Burmannia and Gymnosiphon display congruent patterns. Diversification began during the Eocene, when global temperatures peaked and tropical forests occurred at low latitudes. Simultaneous migration from the New to the Old World in Burmannia and Gymnosiphon occurred via boreotropical migration routes. Subsequent Oligocene cooling and breakup of boreotropical flora ended New-Old World migration and caused a gradual decrease in diversification rate in Burmanniaceae. Conclusion Our results indicate that extant diversity and pantropical distribution of myco-heterotrophic Burmanniaceae is the result of diversification and boreotropical migration during the Eocene when tropical rain forest expanded dramatically. PMID:18573195

  5. Capturing diversity of marine heterotrophic protists: one cell at a time.

    PubMed

    Heywood, Jane L; Sieracki, Michael E; Bellows, Wendy; Poulton, Nicole J; Stepanauskas, Ramunas

    2011-04-01

    Recent applications of culture-independent, molecular methods have revealed unexpectedly high diversity in a variety of functional and phylogenetic groups of microorganisms in the ocean. However, none of the existing research tools are free from significant limitations, such as PCR and cloning biases, low phylogenetic resolution and others. Here, we employed novel, single-cell sequencing techniques to assess the composition of small (<10 μm diameter), heterotrophic protists from the Gulf of Maine. Single cells were isolated by flow cytometry, their genomes amplified, and 18S rRNA marker genes were amplified and sequenced. We compared the results to traditional environmental PCR cloning of sorted cells. The diversity of heterotrophic protists was significantly higher in the library of single amplified genomes (SAGs) than in environmental PCR clone libraries of the 18S rRNA gene, obtained from the same coastal sample. Libraries of SAGs, but not clones contained several recently discovered, uncultured groups, including picobiliphytes and novel marine stramenopiles. Clone, but not SAG, libraries contained several large clusters of identical and nearly identical sequences of Dinophyceae, Cercozoa and Stramenopiles. Similar results were obtained using two alternative primer sets, suggesting that PCR biases may not be the only explanation for the observed patterns. Instead, differences in the number of 18S rRNA gene copies among the various protist taxa probably had a significant role in determining the PCR clone composition. These results show that single-cell sequencing has the potential to more accurately assess protistan community composition than previously established methods. In addition, the creation of SAG libraries opens opportunities for the analysis of multiple genes or entire genomes of the uncultured protist groups.

  6. Transcriptome analysis of acetic-acid-treated yeast cells identifies a large set of genes whose overexpression or deletion enhances acetic acid tolerance.

    PubMed

    Lee, Yeji; Nasution, Olviyani; Choi, Eunyong; Choi, In-Geol; Kim, Wankee; Choi, Wonja

    2015-08-01

    Acetic acid inhibits the metabolic activities of Saccharomyces cerevisiae. Therefore, a better understanding of how S. cerevisiae cells acquire the tolerance to acetic acid is of importance to develop robust yeast strains to be used in industry. To do this, we examined the transcriptional changes that occur at 12 h post-exposure to acetic acid, revealing that 56 and 58 genes were upregulated and downregulated, respectively. Functional categorization of them revealed that 22 protein synthesis genes and 14 stress response genes constituted the largest portion of the upregulated and downregulated genes, respectively. To evaluate the association of the regulated genes with acetic acid tolerance, 3 upregulated genes (DBP2, ASC1, and GND1) were selected among 34 non-protein synthesis genes, and 54 viable mutants individually deleted for the downregulated genes were retrieved from the non-essential haploid deletion library. Strains overexpressing ASC1 and GND1 displayed enhanced tolerance to acetic acid, whereas a strain overexpressing DBP2 was sensitive. Fifty of 54 deletion mutants displayed enhanced acetic acid tolerance. Three chosen deletion mutants (hsps82Δ, ato2Δ, and ssa3Δ) were also tolerant to benzoic acid but not propionic and sorbic acids. Moreover, all those five (two overexpressing and three deleted) strains were more efficient in proton efflux and lower in membrane permeability and internal hydrogen peroxide content than controls. Individually or in combination, those physiological changes are likely to contribute at least in part to enhanced acetic acid tolerance. Overall, information of our transcriptional profile was very useful to identify molecular factors associated with acetic acid tolerance.

  7. Signatures of Autotrophic and Heterotrophic Metabolic Activity in Enrichment Cultures from a Sulphur Oxidizing Acid Mine Site

    NASA Astrophysics Data System (ADS)

    Slater, G. F.; Bernier, L.; Cowie, B. R.; Warren, L. A.

    2006-12-01

    Delineating the role of microorganisms in geochemical processes of interest in natural environments requires the development of tools that provide the ability to distinguish amongst microbial activity associated with different metabolic guilds. The gap between phylogenetic characterization and phenotypic understanding remains, underscoring the need to consider alternative methods. Compound specific analysis of cellular components has the potential to differentiate between active metabolic processes supporting microbial communities and may be especially useful in extreme environments. The goal of this study was to determine whether the phospholipids fatty acid (PLFA) distribution and isotopic signatures associated with autotrophs and heterotrophs enriched from an acid mine drainage (AMD) system differed, and further whether natural consortial autotrophic isolates showed similar signatures to autotrophic pure strains of Acidithiobacillus ferrooxidans and A. thiooxidans. Two distinct initial enrichments with tetrathionate and CO2 yielded primarily autotrophic (95%) Acidithiobaccillus spp. sulphur oxidizing communities. The remaining microbial members of theses enrichments (<5%) were morphologically distinct and heterotrophic, as subculture of the consortial isolates in a medium amended with glucose but without tetrathionate selectively resulted in their visible growth. PLFA profiles and δ13C signatures from autotrophic (1) natural enrichments, pure cultures of (2) A. ferrooxidans and (3) A. thiooxidans were similar, but collectively differed from those of the natural heterotrophic enrichment cultures. The PLFA profiles for the heterotrophic communities were made up of primarily (88-99%) C16:0 and two isomers of C18:1. In contrast, the autotrophic communities had high proportions of C16:1 (up to 18%) as well as cyclo C17 and cyclo C19 PLFA that combined comprised 18 to 58% of the observed PLFA. The δ13C signatures of the PLFA also differed strongly between the two

  8. Clostridium aciditolerans sp. nov., an acid-tolerant spore-forming anaerobic bacterium from constructed wetland sediment.

    PubMed

    Lee, Yong-Jin; Romanek, Christopher S; Wiegel, Juergen

    2007-02-01

    An obligately anaerobic, spore-forming, moderately acid-tolerant bacterium, strain JW/YJL-B3T, was isolated from a sediment sample from a constructed wetland system receiving acid sulfate water. Based on 16S rRNA gene sequence analysis, the isolate belonged to the Firmicutes branch with Clostridium drakei SL1T (96.2 % gene sequence similarity) as its closest relative. The G+C content of the genomic DNA was 30.8 mol% (HPLC). Cells were straight to curved rods, 0.5-1.0 microm in diameter and 3.0-9.0 microm in length. The temperature range for growth was 20-45 degrees C, with an optimum around 35 degrees C. Growth was not detected below 18 degrees C or above 47 degrees C. The pH range for growth was broad, pH(25 degrees C) 3.8-8.9, with an optimum at 7.0-7.5. However at pH 4.5, the strain grew at 52 % of the optimal growth rate. The salinity range was 0-1.5 % NaCl (w/v). Strain JW/YJL-B3T utilized beef extract, Casamino acids, peptone, tryptone, arabinose, cellobiose, fructose, galactose, glucose, lactose, maltose, mannose, raffinose, ribose, sucrose, xylose, pyruvate, glutamate and inulin as a carbon and energy source. There were no indications of growth under aerobic or autotrophic conditions. The isolate produced acetate, butyrate and ethanol as fermentation end products from glucose. Based on these characteristics and other physiological properties, the isolate is placed into the novel taxon, Clostridium aciditolerans sp. nov., with strain JW/YJL-B3T (=DSM 17425T=ATCC BAA-1220T) as the type strain.

  9. Amino acids improve acid tolerance and internal pH maintenance in Bacillus cereus ATCC14579 strain.

    PubMed

    Senouci-Rezkallah, Khadidja; Schmitt, Philippe; Jobin, Michel P

    2011-05-01

    This study investigated the involvement of glutamate-, arginine- and lysine-dependent systems in the Acid Tolerance Response (ATR) of Bacillus cereus ATCC14579 strain. Cells were grown in a chemostat at external pH (pH(e)) 7.0 and 5.5. Population reduction after acid shock at pH 4.0 was strongly limited in cells grown at pH 5.5 (acid-adapted) compared with cells grown at pH 7.0 (unadapted), indicating that B. cereus cells grown at low pH(e) were able to induce a marked ATR. Glutamate, arginine and lysine enhanced the resistance of unadapted cells to pH 4.0 acid shock of 1-log or 2-log populations, respectively. Amino acids had no detectable effect on acid resistance in acid-adapted cells. An acid shock at pH 4.0 resulted in a marked drop in internal pH (pH(i)) in unadapted cells compared with acid-adapted cells. When acid shock was achieved in the presence of glutamate, arginine or lysine, pH(i) was maintained at higher values (6.31, 6.69 or 6.99, respectively) compared with pH(i) in the absence of amino acids (4.88). Acid-adapted cells maintained their pH(i) at around 6.4 whatever the condition. Agmatine (a competitive inhibitor of arginine decarboxylase) had a negative effect on the ability of B. cereus cells to survive and maintain their pH(i) during acid shock. Our data demonstrate that B. cereus is able to induce an ATR during growth at low pH. This adaptation depends on pH(i) homeostasis and is enhanced in the presence of glutamate, arginine and lysine. Hence evaluations of the pathogenicity of B. cereus must take into account its ability to adapt to acid stress.

  10. Methylomonas paludis sp. nov., the first acid-tolerant member of the genus Methylomonas, from an acidic wetland.

    PubMed

    Danilova, Olga V; Kulichevskaya, Irina S; Rozova, Olga N; Detkova, Ekaterina N; Bodelier, Paul L E; Trotsenko, Yuri A; Dedysh, Svetlana N

    2013-06-01

    An aerobic methanotrophic bacterium was isolated from an acidic (pH 3.9) Sphagnum peat bog in north-eastern Russia and designated strain MG30(T). Cells of this strain were Gram-negative, pale pink-pigmented, non-motile, thick rods that were covered by large polysaccharide capsules and contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme (pMMO) and utilized only methane and methanol. Carbon was assimilated via the ribulose-monophosphate pathway; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strain MG30(T) was able to grow at a pH range of 3.8-7.3 (optimum pH 5.8-6.4) and at temperatures between 8 and 30 °C (optimum 20-25 °C). The major cellular fatty acids were C16:1ω5t, C16:1ω8c, C16:1ω7c and C14:0; the DNA G+C content was 48.5 mol%. The isolate belongs to the family Methylococcaceae of the class Gammaproteobacteria and displayed 94.7-96.9% 16S rRNA gene sequence similarity to members of the genus Methylomonas. However, strain MG30(T) differed from all taxonomically characterized members of this genus by the absence of motility, the ability to grow in acidic conditions and low DNA G+C content. Therefore, we propose to classify this strain as representing a novel, acid-tolerant species of the genus Methylomonas, Methylomonas paludis sp. nov. Strain MG30(T) (=DSM 24973(T)=VKM B-2745(T)) is the type strain. PMID:23159751

  11. Inactivation of Microorganisms

    NASA Astrophysics Data System (ADS)

    Alzamora, Stella Maris; Guerrero, Sandra N.; Schenk, Marcela; Raffellini, Silvia; López-Malo, Aurelio

    Minimal processing techniques for food preservation allow better retention of product flavor, texture, color, and nutrient content than comparable conventional treatments. A wide range of novel alternative physical factors have been intensely investigated in the last two decades. These physical factors can cause inactivation of microorganisms at ambient or sublethal temperatures (e.g., high hydrostatic pressure, pulsed electric fields, ultrasound, pulsed light, and ultraviolet light). These technologies have been reported to reduce microorganism population in foods while avoiding the deleterious effects of severe heating on quality. Among technologies, high-energy ultrasound (i.e., intensities higher than 1 W/cm2, frequencies between 18 and 100 kHz) has attracted considerable interest for food preservation applications (Mason et al., 1996; Povey and Mason, 1998).

  12. Harmonic 'signatures' of microorganisms.

    PubMed

    Blake-Coleman, B C; Hutchings, M J; Silley, P

    1994-01-01

    The frequency/amplitude effect of various microorganisms exposed to periodic (time varying) electric fields, when proximate to immersed electrodes, has been studied using a novel analytical instrument. The harmonic distribution, in complex signals caused by cells exposed to harmonic free waveforms and occupying part of the electrode/suspension interface volume, was shown to be almost entirely due to the change in the standing interfacial transfer function by the (dielectrically nonlinear) presence of cells. Thus, the characteristic interfacial non-linearity is viewed as variable, being uniquely modulated by the presence of particular cells in the interfacial region. Little can be attributed to bulk (far field) effects. The tendency for subtle (characteristic) signal distortion to occur as a function of particulate (cell or molecular) occupancy of the near electrode interfacial region under controlled current conditions leads to the method of sample characterisation by harmonic (Fourier) analysis. We report here, as a sequel to our original studies (Hutchings et al., 1993; Hutchings and Blake-Coleman, 1993), preliminary results of the harmonic analysis of microbial suspensions under controlled signal conditions using a three-electrode configuration. These data provide three-dimensional graphical representations producing harmonic 'surfaces' for various microorganisms. Thus, cell type differences are characterised by their 'harmonic signature'. The visual distinction provided by these 'surface' forming three-dimensional plots is striking and gives a convincing impression of the ability to identify and enumerate specific microorganisms by acquisition of cell-modulated electrode interfacial Fourier spectra. PMID:8060593

  13. Detecting the presence of microorganisms

    NASA Technical Reports Server (NTRS)

    Wilkins, Judd R. (Inventor); Stoner, Glenn E. (Inventor)

    1977-01-01

    The presence of microorganisms in a sample is determined by culturing microorganisms in a growth medium which is in contact with a measuring electrode and a reference electrode and detecting a change in potential between the electrodes caused by the presence of the microorganisms in the medium with a high impedance potentiometer.

  14. Microorganisms for producing organic acids

    DOEpatents

    Pfleger, Brian Frederick; Begemann, Matthew Brett

    2014-09-30

    Organic acid-producing microorganisms and methods of using same. The organic acid-producing microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid, acrylic acid, propionic acid, lactic acid, and others. Further modifications to the microorganisms increase production of such organic acids as 3-hydroxypropionic acid, lactate, and others. Methods of producing such organic acids as 3-hydroxypropionic acid, lactate, and others with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers are also provided.

  15. Seasonal relationships between planktonic microorganisms and dissolved organic material in an alpine stream

    USGS Publications Warehouse

    McKnight, Diane M.; Smith, R.L.; Harnish, R.A.; Miller, C.L.; Bencala, K.E.

    1993-01-01

    The relationships between the abundance and activity of planktonic, heterotrophic microorganisms and the quantity and characteristics of dissolved organic carbon (DOC) in a Rocky Mountain stream were evaluated. Peak values of glucose uptake, 2.1 nmol L-1 hr-1, and glucose concentration, 333 nM, occurred during spring snowmelt when the water temperature was 4.0??C and the DOC concentration was greatest. The turnover time of the in situ glucose pool ranged seasonally from 40-1110 hours, with a mean of 272 hr. Seasonal uptake of3H-glucose, particulate ATP concentrations, and direct counts of microbial biomass were independent of temperature, but were positively correlated with DOC concentrations and negatively correlated with stream discharge. Heterotrophic activity in melted snow was generally low, but patchy. In the summer, planktonic heterotrophic activity and microbial biomass exhibited small-scale diel cycles which did not appear to be related to fluctuations in discharge or DOC, but could be related to the activity of benthic invertebrates. Leaf-packs placed under the snow progressively lost weight and leachable organic material during the winter, indicating that the annual litterfall in the watershed may be one source of the spring flush of DOC. These results indicate that the availability of labile DOC to the stream ecosystem is the primary control on seasonal variation in heterotrophic activity of planktonic microbial populations. ?? 1993 Kluwer Academic Publishers.

  16. Carbon dynamics in highly heterotrophic subarctic thaw ponds

    NASA Astrophysics Data System (ADS)

    Roiha, T.; Laurion, I.; Rautio, M.

    2015-12-01

    Global warming has accelerated the formation of permafrost thaw ponds in several subarctic and arctic regions. These ponds are net heterotrophic as evidenced by their greenhouse gas (GHG) supersaturation levels (CO2 and CH4), and generally receive large terrestrial carbon inputs from the thawing and eroding permafrost. We measured seasonal and vertical variations in the concentration and type of dissolved organic matter (DOM) in five subarctic thaw (thermokarst) ponds in northern Quebec, and explored how environmental gradients influenced heterotrophic and phototrophic biomass and productivity. Late winter DOM had low aromaticity indicating reduced inputs of terrestrial carbon, while the high concentration of dissolved organic carbon (DOC) suggests that some production of non-chromophoric dissolved compounds by the microbial food web took place under the ice cover. Summer DOM had a strong terrestrial signature, but was also characterized with significant inputs of algal-derived carbon, especially at the pond surface. During late winter, bacterial production was low (maximum of 0.8 mg C m-3 d-1) and was largely based on free-living bacterioplankton (58 %). Bacterial production in summer was high (up to 58 mg C m-3 d-1), dominated by particle-attached bacteria (67 %), and strongly correlated with the amount of terrestrial carbon. Primary production was restricted to summer surface waters due to strong light limitation deeper in the water column or in winter. The phototrophic biomass was equal to the heterotrophic biomass, but as the algae were mostly composed of mixotrophic species, most probably they used bacteria rather than solar energy in such shaded ponds. Our results point to a strong heterotrophic energy pathway in these thaw pond ecosystems, where bacterioplankton dominates the production of new carbon biomass in both summer and winter.

  17. Carbon dynamics in highly heterotrophic subarctic thaw ponds

    NASA Astrophysics Data System (ADS)

    Roiha, T.; Laurion, I.; Rautio, M.

    2015-07-01

    Global warming has accelerated the formation of permafrost thaw ponds in several subarctic and arctic regions. These ponds are net heterotrophic as evidenced by their greenhouse gas (GHG) supersaturation levels (CO2 and CH4), and generally receive large terrestrial carbon inputs from the thawing and eroding permafrost. We measured seasonal and vertical variations in the concentration and type of dissolved organic matter (DOM) in five subarctic thaw (thermokarst) ponds in northern Quebec, and explored how environmental gradients influenced heterotrophic and phototrophic biomass and productivity. Late winter DOM had low aromaticity indicating reduced inputs of terrestrial carbon, while the high concentration of dissolved organic carbon (DOC) suggests that some production of non-chromophoric dissolved compounds by the microbial food web took place under the ice cover. Summer DOM had a strong terrestrial signature, but was also characterized with significant inputs of algal-derived carbon, especially at the pond surface. During late winter, bacterial production was low (maximum of 0.8 mg C m-3 d-1) and was largely based on free-living bacterioplankton (58 %). Bacterial production in summer was high (up to 58 mg C m-3 d-1), dominated by particle-attached bacteria (67 %), and strongly correlated to the amount of terrestrial carbon. Primary production was restricted to summer surface waters due to strong light limitation deeper in the water column or in winter. The phototrophic biomass was equal to the heterotrophic biomass, but as the algae were mostly composed of mixotrophic species, most probably they used bacteria rather than solar energy in such shaded ponds. According to the δ13C analyses, non-algal carbon supported 51 % of winter and 37 % of summer biomass of the phantom midge larvae, Chaoborus sp., that are at the top of the trophic chain. Our results point to a strong heterotrophic energy pathway in these thaw pond ecosystems, where bacterioplankton dominates

  18. Anaerobic ferrous oxidation by heterotrophic denitrifying enriched culture.

    PubMed

    Wang, Ru; Zheng, Ping; Xing, Ya-Juan; Zhang, Meng; Ghulam, Abbas; Zhao, Zhi-Qing; Li, Wei; Wang, Lan

    2014-05-01

    Heterotrophic denitrifying enriched culture (DEC) from a lab-scale high-rate denitrifying reactor was discovered to perform nitrate-dependent anaerobic ferrous oxidation (NAFO). The DEC was systematically investigated to reveal their denitrification activity, their NAFO activity, and the predominant microbial population. The DEC was capable of heterotrophic denitrification with methanol as the electron donor, and autotrophic denitrification with ferrous salt as the electron donor named NAFO. The conversion ratios of ferrous-Fe and nitrate-N were 87.41 and 98.74 %, and the consumption Fe/N ratio was 2.3:1 (mol/mol). The maximum reaction velocity and half saturation constant of Fe were 412.54 mg/(l h) and 8,276.44 mg/l, and the counterparts of N were 20.87 mg/(l h) and 322.58 mg/l, respectively. The predominant bacteria were Hyphomicrobium, Thauera, and Flavobacterium, and the predominant archaea were Methanomethylovorans, Methanohalophilus, and Methanolobus. The discovery of NAFO by heterotrophic DEC is significant for the development of wastewater treatment and the biogeochemical iron cycle and nitrogen cycle. PMID:24619339

  19. Nutrient and media recycling in heterotrophic microalgae cultures.

    PubMed

    Lowrey, Joshua; Armenta, Roberto E; Brooks, Marianne S

    2016-02-01

    In order for microalgae-based processes to reach commercial production for biofuels and high-value products such as omega-3 fatty acids, it is necessary that economic feasibility be demonstrated at the industrial scale. Therefore, process optimization is critical to ensure that the maximum yield can be achieved from the most efficient use of resources. This is particularly true for processes involving heterotrophic microalgae, which have not been studied as extensively as phototrophic microalgae. An area that has received significant conceptual praise, but little experimental validation, is that of nutrient recycling, where the waste materials from prior cultures and post-lipid extraction are reused for secondary fermentations. While the concept is very simple and could result in significant economic and environmental benefits, there are some underlying challenges that must be overcome before adoption of nutrient recycling is viable at commercial scale. Even more, adapting nutrient recycling for optimized heterotrophic cultures presents some added challenges that must be identified and addressed that have been largely unexplored to date. These challenges center on carbon and nitrogen recycling and the implications of using waste materials in conjunction with virgin nutrients for secondary cultures. The aim of this review is to provide a foundation for further understanding of nutrient recycling for microalgae cultivation. As such, we outline the current state of technology and practical challenges associated with nutrient recycling for heterotrophic microalgae on an industrial scale and give recommendations for future work.

  20. Alkylphenol polyethoxylate removal in a pilot-scale reed bed and phenotypic characterization of the aerobic heterotrophic community.

    PubMed

    Sacco, Cristiana; Pizzo, Anna Maria; Tiscione, Emilia; Burrini, Daniela; Messeri, Luca; Lepri, Luciano; Del Bubba, Massimo

    2006-07-01

    The removal of the non-ionic surfactant Triton X-100, dosed at 30 and 300 mg/L in a pilot-scale subsurface horizontal flow reed bed, and the aerobic heterotrophic cultivable community associated with the roots and with the substrate gravel in both absence and presence of Triton X-100 were investigated. t-Octylphenol (OP) and its mono-, di- and tri-ethoxyl derivatives, among others, were found in the outlet. A mass balance allowed us to calculate that approximately 40% of the Triton X-100 metabolites OP and octylphenol polyethoxylate derivatives flowed out of the reed bed during the dosage and postdosage experiments. More aerobic heterotrophic microorganisms adhered to the roots than to the gravel. The appearance of new strains (Aeromonas, Flavobacterium, and Aquaspirillum) and the increased presence of others (Pseudomonas) during the dosage of Triton may be linked to the capacity of these bacteria to adapt to the presence of the surfactant or to use it as a nourishment. PMID:16929647

  1. Adaptation and Acclimation of Photosynthetic Microorganisms to Permanently Cold Environments

    PubMed Central

    Morgan-Kiss, Rachael M.; Priscu, John C.; Pocock, Tessa; Gudynaite-Savitch, Loreta; Huner, Norman P. A.

    2006-01-01

    Persistently cold environments constitute one of our world's largest ecosystems, and microorganisms dominate the biomass and metabolic activity in these extreme environments. The stress of low temperatures on life is exacerbated in organisms that rely on photoautrophic production of organic carbon and energy sources. Phototrophic organisms must coordinate temperature-independent reactions of light absorption and photochemistry with temperature-dependent processes of electron transport and utilization of energy sources through growth and metabolism. Despite this conundrum, phototrophic microorganisms thrive in all cold ecosystems described and (together with chemoautrophs) provide the base of autotrophic production in low-temperature food webs. Psychrophilic (organisms with a requirement for low growth temperatures) and psychrotolerant (organisms tolerant of low growth temperatures) photoautotrophs rely on low-temperature acclimative and adaptive strategies that have been described for other low-temperature-adapted heterotrophic organisms, such as cold-active proteins and maintenance of membrane fluidity. In addition, photoautrophic organisms possess other strategies to balance the absorption of light and the transduction of light energy to stored chemical energy products (NADPH and ATP) with downstream consumption of photosynthetically derived energy products at low temperatures. Lastly, differential adaptive and acclimative mechanisms exist in phototrophic microorganisms residing in low-temperature environments that are exposed to constant low-light environments versus high-light- and high-UV-exposed phototrophic assemblages. PMID:16524924

  2. Use of Stable Isotopes in Forensic Analysis of Microorganisms

    SciTech Connect

    Kreuzer-Martin, Helen W.; Hegg, Eric L.

    2012-01-18

    The use of isotopic signatures for forensic analysis of biological materials is well-established, and the same general principles that apply to interpretation of stable isotope content of C, N, O, and H apply to the analysis of microorganisms. Heterotrophic microorganisms derive their isotopic content from their growth substrates, which are largely plant and animal products, and the water in their culture medium. Thus the isotope signatures of microbes are tied to their growth environment. The C, N, O, and H isotope ratios of spores have been demonstrated to constitute highly discriminating signatures for sample matching. They can rule out specific samples of media and/or water as possible production media, and can predict isotope ratio ranges of the culture media and water used to produce a given sample. These applications have been developed and tested through analyses of approximately 250 samples of Bacillus subtilis spores and over 500 samples of culture media, providing a strong statistical basis for data interpretation. A Bayesian statistical framework for integrating stable isotope data with other types of signatures derived from microorganisms has been able to characterize the culture medium used to produce spores of various Bacillus species, leveraging isotopic differences in different medium types and demonstrating the power of data integration for forensic investigations.

  3. Growth rate characteristics of acidophilic heterotrophic organisms from mine waste rock piles

    NASA Astrophysics Data System (ADS)

    Yacob, T. W.; Silverstein, J.; Jenkins, J.; Andre, B. J.; Rajaram, H.

    2010-12-01

    Autotrophic iron oxidizing bacteria play a key role in pyrite oxidation and generation of acid mine drainage AMD. Scarcity of organic substrates in many disturbed sites insures that IOB have sufficient oxygen and other nutrients for growth. It is proposed that addition of organic carbon substrate to waste rock piles will result in enrichment of heterotrophic microorganisms limiting the role of IOB in AMD generation. Previous researchers have used the acidophilic heterotroph Acidiphilium cryptum as a model to study the effects of organic substrate addition on the pyrite oxidation/AMD cycle. In order to develop a quantitative model of effects such as competition for oxygen, it is necessary to use growth and substrate consumption rate expressions, and one approach is to choose a model strain such as A. cryptum for kinetic studies. However we have found that the growth rate characteristics of A. cryptum may not provide an accurate model of the remediation effects of organic addition to subsurface mined sites. Fluorescent in-situ hybridization (FISH) assays of extracts of mine waste rock enriched with glucose and yeast extract did not produce countable numbers of cells in the Acidiphilium genus, with a detection limit of3 x 104 cells/gram rock, despite evidence of the presence of well established heterotrophic organisms. However, an MPN enrichment produced heterotrophic population estimates of 1x107 and 1x109 cells/gram rock. Growth rate studies of A. cryptum showed that cultures took 120 hours to degrade 50% of an initial glucose concentration of 2,000 mg/L. However a mixed culture enriched from mine waste rock consumed 100% of the same amount of glucose in 24 hours. Substrate consumption data for the mixed culture were fit to a Monod growth model: {dS}/{dt} = μ_{max}S {( {X_0}/{Y} + S_0 -S )}/{(K_s +S)} Kinetic parameters were estimated utilizing a non linear regression method coupled with an ODE solver. The maximum specific growth rate of the mixed population with

  4. Microorganisms in bioaerosol emissions from wastewater treatment plants during summer at a Mediterranean site.

    PubMed

    Karra, Styliani; Katsivela, Eleftheria

    2007-03-01

    Measurements were conducted at a Mediterranean site (latitude 35 degrees 31' north and longitude 24 degrees 03' east) during summer, to study the concentration of microorganisms emitted from a wastewater treatment plant under intensive solar radiation (520-840 W/m2) and at elevated air temperatures (25-31 degrees C). Air samples were taken with the Air Sampler MAS 100 (Merck) at each stage of an activated-sludge wastewater treatment (pretreatment, primary settling tanks, aeration tanks, secondary settling tanks, chlorination, and sludge processors). Cultivation methods based on the viable counts of mesophilic heterotrophic bacteria, as well as of indicator microorganisms of faecal contamination (total and faecal coliforms and enterococci), and fungi were performed. During air sampling, temperature, solar radiation, relative humidity and wind speed were measured. The highest concentrations of airborne microorganisms were observed at the aerated grit removal of wastewater at the pretreatment stage. A gradual decrease of bioaerosol emissions was observed during the advanced wastewater treatment from the pretreatment to the primary, secondary and tertiary treatment (97.4% decrease of mesophilic heterotrophic bacteria, and 100% decrease of total coliforms, faecal coliforms and enterococci), 95.8% decrease of fungi. The concentration of the airborne microorganisms at the secondary and tertiary treatment of the wastewater was lower than in the outdoor control. At the same time, the reduction of the microbial load at the waste sludge processors was 19.7% for the mesophilic heterotrophic bacteria, 99.4% for the total coliforms, and 100% for the faecal coliforms and the enterococci, 84.2% for the fungi. The current study concludes that the intensive solar radiation, together with high ambient temperatures, as well as optimal wastewater treatment are the most important factors for low numbers of microbes in the air.

  5. Microcultural Study of Bacterial Size Changes and Microcolony and Ultramicrocolony Formation by Heterotrophic Bacteria in Seawater †

    PubMed Central

    Torrella, Francisco; Morita, Richard Y.

    1981-01-01

    With a microculture technique and time-lapse, phase-contrast photomicrography, it was possible to follow the division of individual cells and the development of microcolonies of bacteria in freshly collected marine water samples. A certain number of marine bacteria, upon inoculation onto a nutrient rich agar surface, displayed an increase in size as well as a high growth rate. Other bacteria were identified as very small marine bacteria (ultramicrobacteria). These had a very slow growth rate when inoculated onto a nutrient-rich agar surface. These latter cells formed very small microcolonies (ultramicrocolonies), and cell size did not increase significantly. These two types of marine heterotrophs could be described in terms of zymogenous and autochthonous bacteria, a concept used by Winogradsky for describing soil microorganisms. Images PMID:16345721

  6. Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming.

    PubMed

    Wu, Stephen Gang; Wang, Yuxuan; Jiang, Wu; Oyetunde, Tolutola; Yao, Ruilian; Zhang, Xuehong; Shimizu, Kazuyuki; Tang, Yinjie J; Bao, Forrest Sheng

    2016-04-01

    13C metabolic flux analysis (13C-MFA) has been widely used to measure in vivo enzyme reaction rates (i.e., metabolic flux) in microorganisms. Mining the relationship between environmental and genetic factors and metabolic fluxes hidden in existing fluxomic data will lead to predictive models that can significantly accelerate flux quantification. In this paper, we present a web-based platform MFlux (http://mflux.org) that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms. Three machine learning methods, namely Support Vector Machine (SVM), k-Nearest Neighbors (k-NN), and Decision Tree, were employed to study the sophisticated relationship between influential factors and metabolic fluxes. We performed a grid search of the best parameter set for each algorithm and verified their performance through 10-fold cross validations. SVM yields the highest accuracy among all three algorithms. Further, we employed quadratic programming to adjust flux profiles to satisfy stoichiometric constraints. Multiple case studies have shown that MFlux can reasonably predict fluxomes as a function of bacterial species, substrate types, growth rate, oxygen conditions, and cultivation methods. Due to the interest of studying model organism under particular carbon sources, bias of fluxome in the dataset may limit the applicability of machine learning models. This problem can be resolved after more papers on 13C-MFA are published for non-model species.

  7. Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming.

    PubMed

    Wu, Stephen Gang; Wang, Yuxuan; Jiang, Wu; Oyetunde, Tolutola; Yao, Ruilian; Zhang, Xuehong; Shimizu, Kazuyuki; Tang, Yinjie J; Bao, Forrest Sheng

    2016-04-01

    13C metabolic flux analysis (13C-MFA) has been widely used to measure in vivo enzyme reaction rates (i.e., metabolic flux) in microorganisms. Mining the relationship between environmental and genetic factors and metabolic fluxes hidden in existing fluxomic data will lead to predictive models that can significantly accelerate flux quantification. In this paper, we present a web-based platform MFlux (http://mflux.org) that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms. Three machine learning methods, namely Support Vector Machine (SVM), k-Nearest Neighbors (k-NN), and Decision Tree, were employed to study the sophisticated relationship between influential factors and metabolic fluxes. We performed a grid search of the best parameter set for each algorithm and verified their performance through 10-fold cross validations. SVM yields the highest accuracy among all three algorithms. Further, we employed quadratic programming to adjust flux profiles to satisfy stoichiometric constraints. Multiple case studies have shown that MFlux can reasonably predict fluxomes as a function of bacterial species, substrate types, growth rate, oxygen conditions, and cultivation methods. Due to the interest of studying model organism under particular carbon sources, bias of fluxome in the dataset may limit the applicability of machine learning models. This problem can be resolved after more papers on 13C-MFA are published for non-model species. PMID:27092947

  8. Automated measurement and quantification of heterotrophic bacteria in water samples based on the MPN method.

    PubMed

    Fuchsluger, C; Preims, M; Fritz, I

    2011-01-01

    Quantification of heterotrophic bacteria is a widely used measure for water analysis. Especially in terms of drinking water analysis, testing for microorganisms is strictly regulated by the European Drinking Water Directive, including quality criteria and detection limits. The quantification procedure presented in this study is based on the most probable number (MPN) method, which was adapted to comply with the need for a quick and easy screening tool for different kinds of water samples as well as varying microbial loads. Replacing tubes with 24-well titer plates for cultivation of bacteria drastically reduces the amount of culture media and also simplifies incubation. Automated photometric measurement of turbidity instead of visual evaluation of bacterial growth avoids misinterpretation by operators. Definition of a threshold ensures definite and user-independent determination of microbial growth. Calculation of the MPN itself is done using a program provided by the US Food and Drug Administration (FDA). For evaluation of the method, real water samples of different origins as well as pure cultures of bacteria were analyzed in parallel with the conventional plating methods. Thus, the procedure described requires less preparation time, reduces costs and ensures both stable and reliable results for water samples. PMID:20835882

  9. Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming

    PubMed Central

    Wu, Stephen Gang; Wang, Yuxuan; Jiang, Wu; Oyetunde, Tolutola; Yao, Ruilian; Zhang, Xuehong; Shimizu, Kazuyuki; Tang, Yinjie J.; Bao, Forrest Sheng

    2016-01-01

    13C metabolic flux analysis (13C-MFA) has been widely used to measure in vivo enzyme reaction rates (i.e., metabolic flux) in microorganisms. Mining the relationship between environmental and genetic factors and metabolic fluxes hidden in existing fluxomic data will lead to predictive models that can significantly accelerate flux quantification. In this paper, we present a web-based platform MFlux (http://mflux.org) that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms. Three machine learning methods, namely Support Vector Machine (SVM), k-Nearest Neighbors (k-NN), and Decision Tree, were employed to study the sophisticated relationship between influential factors and metabolic fluxes. We performed a grid search of the best parameter set for each algorithm and verified their performance through 10-fold cross validations. SVM yields the highest accuracy among all three algorithms. Further, we employed quadratic programming to adjust flux profiles to satisfy stoichiometric constraints. Multiple case studies have shown that MFlux can reasonably predict fluxomes as a function of bacterial species, substrate types, growth rate, oxygen conditions, and cultivation methods. Due to the interest of studying model organism under particular carbon sources, bias of fluxome in the dataset may limit the applicability of machine learning models. This problem can be resolved after more papers on 13C-MFA are published for non-model species. PMID:27092947

  10. Chemical and structural status of copper associated with oxygenic and anoxygenic phototrophs and heterotrophs: possible evolutionary consequences.

    PubMed

    Pokrovsky, O S; Pokrovski, G S; Shirokova, L S; Gonzalez, A G; Emnova, E E; Feurtet-Mazel, A

    2012-03-01

    Copper adsorption on the surface and intracellular uptake inside the cells of four representative taxons of soil and aquatic micro-organisms: aerobic rhizospheric heterotrophs (Pseudomonas aureofaciens), anoxygenic (Rhodovulum steppense) and oxygenic (cyanobacteria Gloeocapsa sp. and freshwater diatoms Navicula minima) phototrophs were studied in a wide range of pH, copper concentration, and time of exposure. Chemical status of adsorbed and assimilated Cu was investigated using in situ X-ray absorption spectroscopy. In case of adsorbed copper, XANES spectra demonstrated significant fractions of Cu(I) likely in the form of tri-coordinate complexes with O/N and/or S ligands. Upon short-term reversible adsorption at all four studied micro-organisms' cell surface, Cu(II) is coordinated by 4.0 ± 0.5 planar oxygens at an average distance of 1.97 ± 0.02 Å, which is tentatively assigned to the carboxylate groups. The atomic environment of copper incorporated into diatoms and cyanobacteria during long-term growth is similar to that of the adsorbed metal with slightly shorter distances to the first O/N neighbor (1.95 Å). In contrast to the common view of Cu status in phototrophic micro-organisms, XAFS failed to detect sulfur in the nearest atomic environment of Cu assimilated by freshwater plankton (cyanobacteria) and periphyton (diatoms). The appearance of S in Cu 1st coordination shell at 2.27-2.32 Å was revealed only after long-term interaction of Cu with anoxygenic phototrophs (and Cu uptake by soil heterotrophs), suggesting Cu scavenging in the form of sulfhydryl, histidine/carboxyl or a mixture of carboxylate and sulfhydryl complexes. These new structural constraints suggest that adsorbed Cu(II) is partially reduced to Cu(I) already at the cell surface, where as intracellular Cu uptake and storage occur in the form of both Cu(I)-S linked proteins and Cu(II) carboxylates. Obtained results allow to better understand how, in the course of biological evolution, micro-organisms

  11. Gravitaxis in unicellular microorganisms

    NASA Astrophysics Data System (ADS)

    Häder, D.-P.

    1999-01-01

    Orientation of organisms with respect to the gravitational field of the Earth has been studied for more than 100 years in a number of unicellular microorganisms including flagellates and ciliates. Several hypotheses have been developed how the weak stimulus is perceived. Intracellular statoliths have been found to be involved in gravitaxis of Loxodes, while no specialized organelles have been detected in other ciliates, e.g. Paramecium. Also in the slime mold Physarum no specialized gravireceptors have been identified yet. In the flagellate Euglena gracilis the whole cell body, which is denser than the surrounding medium, seems to act as a statolith pressing onto the lower membrane where it activates mechanosensitive ion channels. Similar results were obtained for the ciliate Paramecium. In contrast to the flagellate Euglena, several ciliates have been found to show gravikinesis, which is defined as a dependence of the swimming velocity on the direction of movement in the gravity field.

  12. Proteolysis in hyperthermophilic microorganisms

    DOE PAGES

    Ward, Donald E.; Shockley, Keith R.; Chang, Lara S.; Levy, Ryan D.; Michel, Joshua K.; Conners, Shannon B.; Kelly, Robert M.

    2002-01-01

    Proteases are found in every cell, where they recognize and break down unneeded or abnormal polypeptides or peptide-based nutrients within or outside the cell. Genome sequence data can be used to compare proteolytic enzyme inventories of different organisms as they relate to physiological needs for protein modification and hydrolysis. In this review, we exploit genome sequence data to compare hyperthermophilic microorganisms from the euryarchaeotal genus Pyrococcus , the crenarchaeote Sulfolobus solfataricus , and the bacterium Thermotoga maritima . An overview of the proteases in these organisms is given based on those proteases that have been characterized and on putativemore » proteases that have been identified from genomic sequences, but have yet to be characterized. The analysis revealed both similarities and differences in the mechanisms utilized for proteolysis by each of these hyperthermophiles and indicated how these mechanisms relate to proteolysis in less thermophilic cells and organisms.« less

  13. Thermal inactivation of microorganisms.

    PubMed

    Smelt, J P P M; Brul, S

    2014-01-01

    This paper serves as an overview of various aspects of thermal processing. Heat processing of foods has a long history and is still one of the most important preservation methods. To guarantee microbiological safety and stability, large safety margins are often applied in traditional heat processes. Because of the need for more fresh like foods, there is a need for milder preservation methods without compromising on safety and stability. The review deals with heat resistance data and mathematical models that describe heat inactivation. The effects of food composition are not yet fully clear and more knowledge of the cell physiology of the target microorganism could be of help in predicting the effects of food constituents. Finally, special attention has been paid to biological time temperature indicators to enable proper process calculations.

  14. Thermophilic microorganisms in biomining.

    PubMed

    Donati, Edgardo Rubén; Castro, Camila; Urbieta, María Sofía

    2016-11-01

    Biomining is an applied biotechnology for mineral processing and metal extraction from ores and concentrates. This alternative technology for recovering metals involves the hydrometallurgical processes known as bioleaching and biooxidation where the metal is directly solubilized or released from the matrix for further solubilization, respectively. Several commercial applications of biomining can be found around the world to recover mainly copper and gold but also other metals; most of them are operating at temperatures below 40-50 °C using mesophilic and moderate thermophilic microorganisms. Although biomining offers an economically viable and cleaner option, its share of the world´s production of metals has not grown as much as it was expected, mainly considering that due to environmental restrictions in many countries smelting and roasting technologies are being eliminated. The slow rate of biomining processes is for sure the main reason of their poor implementation. In this scenario the use of thermophiles could be advantageous because higher operational temperature would increase the rate of the process and in addition it would eliminate the energy input for cooling the system (bioleaching reactions are exothermic causing a serious temperature increase in bioreactors and inside heaps that adversely affects most of the mesophilic microorganisms) and it would decrease the passivation of mineral surfaces. In the last few years many thermophilic bacteria and archaea have been isolated, characterized, and even used for extracting metals. This paper reviews the current status of biomining using thermophiles, describes the main characteristics of thermophilic biominers and discusses the future for this biotechnology.

  15. Thermophilic microorganisms in biomining.

    PubMed

    Donati, Edgardo Rubén; Castro, Camila; Urbieta, María Sofía

    2016-11-01

    Biomining is an applied biotechnology for mineral processing and metal extraction from ores and concentrates. This alternative technology for recovering metals involves the hydrometallurgical processes known as bioleaching and biooxidation where the metal is directly solubilized or released from the matrix for further solubilization, respectively. Several commercial applications of biomining can be found around the world to recover mainly copper and gold but also other metals; most of them are operating at temperatures below 40-50 °C using mesophilic and moderate thermophilic microorganisms. Although biomining offers an economically viable and cleaner option, its share of the world´s production of metals has not grown as much as it was expected, mainly considering that due to environmental restrictions in many countries smelting and roasting technologies are being eliminated. The slow rate of biomining processes is for sure the main reason of their poor implementation. In this scenario the use of thermophiles could be advantageous because higher operational temperature would increase the rate of the process and in addition it would eliminate the energy input for cooling the system (bioleaching reactions are exothermic causing a serious temperature increase in bioreactors and inside heaps that adversely affects most of the mesophilic microorganisms) and it would decrease the passivation of mineral surfaces. In the last few years many thermophilic bacteria and archaea have been isolated, characterized, and even used for extracting metals. This paper reviews the current status of biomining using thermophiles, describes the main characteristics of thermophilic biominers and discusses the future for this biotechnology. PMID:27628339

  16. Genetically engineered acidophilic heterotrophic bacteria by bacteriophage transduction

    SciTech Connect

    Ward, T.E.; Bruhn, D.F.; Bulmer, D.F.

    1989-05-10

    A bacteriophage capable of infecting acidophilic heterotrophic bacteria and processes for genetically engineering acidophilic bacteria for biomining or sulfur removal from coal are disclosed. The bacteriophage is capable of growth in cells existing at pH at or below 3.0. Lytic forms of the phage introduced into areas experiencing acid drainage kill the bacteria causing such drainage. Lysogenic forms of the phage having genes for selective removal of metallic or nonmetallic elements can be introduced into acidophilic bacteria to effect removal of the desired element from ore or coal. 1 fig., 1 tab.

  17. Temporal dynamics of phytoplankton and heterotrophic protists at station ALOHA

    NASA Astrophysics Data System (ADS)

    Pasulka, Alexis L.; Landry, Michael R.; Taniguchi, Darcy A. A.; Taylor, Andrew G.; Church, Matthew J.

    2013-09-01

    Pico- and nano-sized autotrophic and heterotrophic unicellular eukaryotes (protists) are an important component of open-ocean food webs. To date, however, no direct measurements of cell abundance and biomass of these organisms have been incorporated into our understanding of temporal variability in the North Pacific Subtropical Gyre (NPSG). Based primarily on epifluoresence microscopy augmented with flow cytometry, we assessed the abundance and biomass of autotrophs and heterotrophic protists at Station ALOHA between June 2004 and January 2009. Autotrophic eukaryotes (A-EUKS) were more abundant in both the upper euphotic zone and deep chlorophyll maximum layer (DCML) during winter months, driven mostly by small flagellates. A higher ratio of A-EUKS to heterotrophic protists (A:H ratio) and a structural shift in A-EUKS to smaller cells during the winter suggests a seasonal minimum in grazing pressure. Although Prochlococcus spp. comprised between 30% and 50% of autotrophic biomass in both the upper and lower euphotic zone for most of the year, the community structure and seasonality of nano- and micro-phytoplankon differed between the two layers. In the upper layer, Trichodesmium spp. was an important contributor to total biomass (20-50%) in the late summer and early fall. Among A-EUKS, prymnesiophytes and other small flagellates were the dominant contributors to total biomass in both layers regardless of season (10-20% and 13-39%, respectively). Based on our biomass estimates, community composition was less seasonally variable in the DCML relative to the upper euphotic zone. In surface waters, mean estimates of C:Chl a varied with season—highest in the summer and lowest in the winter (means=156±157 and 89±32, respectively); however, there was little seasonal variability of C:Chl a in the DCML (100 m mean=29.9±9.8). Biomass of heterotrophic protists peaked in the summer and generally declined monotonically with depth without a deep maximum. Anomalous patterns

  18. The fraction of cells that resume growth after acetic acid addition is a strain-dependent parameter of acetic acid tolerance in Saccharomyces cerevisiae.

    PubMed

    Swinnen, Steve; Fernández-Niño, Miguel; González-Ramos, Daniel; van Maris, Antonius J A; Nevoigt, Elke

    2014-06-01

    High acetic acid tolerance of Saccharomyces cerevisiae is a relevant phenotype in industrial biotechnology when using lignocellulosic hydrolysates as feedstock. A screening of 38 S. cerevisiae strains for tolerance to acetic acid revealed considerable differences, particularly with regard to the duration of the latency phase. To understand how this phenotype is quantitatively manifested, four strains exhibiting significant differences were studied in more detail. Our data show that the duration of the latency phase is primarily determined by the fraction of cells within the population that resume growth. Only this fraction contributed to the exponential growth observed after the latency phase, while all other cells persisted in a viable but non-proliferating state. A remarkable variation in the size of the fraction was observed among the tested strains differing by several orders of magnitude. In fact, only 11 out of 10(7)  cells of the industrial bioethanol production strain Ethanol Red resumed growth after exposure to 157 mM acetic acid at pH 4.5, while this fraction was 3.6 × 10(6) (out of 10(7)  cells) in the highly acetic acid tolerant isolate ATCC 96581. These strain-specific differences are genetically determined and represent a valuable starting point to identify genetic targets for future strain improvement.

  19. Heterotrophic microbial colonization of the interior of impact-shocked rocks from Haughton impact structure, Devon Island, Nunavut, Canadian High Arctic

    NASA Astrophysics Data System (ADS)

    Fike, David A.; Cockell, Charles; Pearce, David; Lee, Pascal

    2002-10-01

    The polar desert is one of the most extreme environments on Earth. Endolithic organisms can escape or mitigate the hazards of the polar desert by using the resources available in the interior of rocks. We examined endolithic communities within crystalline rocks that have undergone shock metamorphism as a result of an asteroid or comet impact. Specifically, we present a characterization of the heterotrophic endolithic community and its environment in the interior of impact-shocked gneisses and their host polymict breccia from the Haughton impact structure on Devon Island, Nunavut, Canadian High Arctic. Microbiological colonization of impact-shocked rocks is facilitated by impact-induced fissures and cavities, which occur throughout the samples, the walls of which are lined with high abundances of biologically important elements owing to the partial volatilization of minerals within the rock during the impact. 27 heterotrophic bacteria were isolated from these shocked rocks and were identified by 16S rDNA sequencing. The isolates from the shocked gneiss and the host breccia are similar to each other, and to other heterotrophic communities isolated from polar environments, suggesting that the interiors of the rocks are colonized by microorganisms from the surrounding country rocks and soils. Inductively coupled plasma atomic emission spectroscopy (ICP-AES), scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) analysis were used to identify the chemical composition of the shocked materials and to document the in situ growth of microbes in their interiors. The identification of these heterotrophic communities within impact-shocked crystalline rocks extends our knowledge of the habitable biosphere on Earth. The colonization of the interiors of these samples has astrobiological applications both for considering terrestrial, microbiological contamination of meteorites from the Antarctic ice sheet and for investigating possible habitats for microbial

  20. Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria

    PubMed Central

    Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi

    2015-01-01

    Methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and CO2, the two most important greenhouse gases. This review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. Some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. Methanol-utilizing methylotrophs in the genus Methylobacterium are abundant in the phyllosphere and have the ability to promote the growth of some plants. Methanotrophs also inhabit the phyllosphere, and methanotrophs with high methane oxidation activities have been found on aquatic plants. Both plant and environmental factors are involved in shaping the methylotroph community on plants. Methanotrophic activity can be enhanced by heterotrophic bacteria that provide growth factors (e.g., cobalamin). Information regarding the biological interaction of methylotrophs with other organisms will facilitate a better understanding of the carbon cycle that is driven by methylotrophs. PMID:27682083

  1. Distribution, Diversity, and Activities of Sulfur Dioxygenases in Heterotrophic Bacteria

    PubMed Central

    Liu, Honglei; Xin, Yufeng

    2014-01-01

    Sulfur oxidation by chemolithotrophic bacteria is well known; however, sulfur oxidation by heterotrophic bacteria is often ignored. Sulfur dioxygenases (SDOs) (EC 1.13.11.18) were originally found in the cell extracts of some chemolithotrophic bacteria as glutathione (GSH)-dependent sulfur dioxygenases. GSH spontaneously reacts with elemental sulfur to generate glutathione persulfide (GSSH), and SDOs oxidize GSSH to sulfite and GSH. However, SDOs have not been characterized for bacteria, including chemolithotrophs. The gene coding for human SDO (human ETHE1 [hETHE1]) in mitochondria was discovered because its mutations lead to a hereditary human disease, ethylmalonic encephalopathy. Using sequence analysis and activity assays, we discovered three subgroups of bacterial SDOs in the proteobacteria and cyanobacteria. Ten selected SDO genes were cloned and expressed in Escherichia coli, and the recombinant proteins were purified. The SDOs used Fe2+ for catalysis and displayed considerable variations in specific activities. The wide distribution of SDO genes reveals the likely source of the hETHE1 gene and highlights the potential of sulfur oxidation by heterotrophic bacteria. PMID:24389926

  2. Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria

    PubMed Central

    Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi

    2015-01-01

    Methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and CO2, the two most important greenhouse gases. This review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. Some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. Methanol-utilizing methylotrophs in the genus Methylobacterium are abundant in the phyllosphere and have the ability to promote the growth of some plants. Methanotrophs also inhabit the phyllosphere, and methanotrophs with high methane oxidation activities have been found on aquatic plants. Both plant and environmental factors are involved in shaping the methylotroph community on plants. Methanotrophic activity can be enhanced by heterotrophic bacteria that provide growth factors (e.g., cobalamin). Information regarding the biological interaction of methylotrophs with other organisms will facilitate a better understanding of the carbon cycle that is driven by methylotrophs.

  3. Modeling of heterotrophic bacteria counts in a water distribution system.

    PubMed

    Francisque, Alex; Rodriguez, Manuel J; Miranda-Moreno, Luis F; Sadiq, Rehan; Proulx, François

    2009-03-01

    Heterotrophic plate count (HPC) constitutes a common indicator for monitoring of microbiological water quality in distribution systems (DS). This paper aims to identify factors explaining the spatiotemporal distribution of heterotrophic bacteria and model their occurrence in the distribution system. The case under study is the DS of Quebec City, Canada. The study is based on a robust database resulting from a sampling campaign carried out in about 50 DS locations, monitored bi-weekly over a three-year period. Models for explaining and predicting HPC levels were based on both one-level and multi-level Poisson regression techniques. The latter take into account the nested structure of data, the possible spatiotemporal correlation among HPC observations and the fact that sampling points, months and/or distribution sub-systems may represent clusters. Models show that the best predictors for spatiotemporal occurrence of HPC in the DS are: free residual chlorine that has an inverse relation with the HPC levels, water temperature and water ultraviolet absorbance, both having a positive impact on HPC levels. A sensitivity analysis based on the best performing model (two-level model) allowed for the identification of seasonal-based strategies to reduce HPC levels.

  4. Photoresponse in the heterotrophic marine dinoflagellate Oxyrrhis marina.

    PubMed

    Hartz, Aaron J; Sherr, Barry F; Sherr, Evelyn B

    2011-01-01

    Expressed rhodopsins were detected by proteomic analysis in an investigation of potential signal receptors in the cell membrane of the marine heterotrophic dinoflagellate Oxyrrhis marina (CCMP604). We inferred these to be sensory rhodopsins, a type of G-protein-coupled receptor trans-membrane signaling molecule. Because phototactic behavior based on sensory rhodopsins has been reported in other protists, we investigated the photosensory response of O. marina. This dinoflagellate exhibited strongest positive phototaxis at low levels (2-3 μE/m(2)/s) of white light when the cells were previously light adapted and well fed. Positive phototaxis was also found for blue (450 nm), green (525 nm), and red (680 nm) wavelengths. In a further test, O. marina showed significantly greater phototaxis toward concentrated algal food illuminated by blue light to stimulate red chlorophyll-a autofluorescence in the prey, compared with using bleached algae as prey. Concentration of a cytoplasmic downstream messenger molecule, cyclic adenosine monophosphate, a component of the signaling pathway of G-protein-coupled receptor molecules, rapidly increased in O. marina cells after exposure to white light. In addition, treatment with hydroxylamine, a rhodopsin signaling inhibitor, significantly decreased their phototactic response. Our results demonstrate that a heterotrophic marine dinoflagellate can orient to light based on rhodopsins present in the outer cell membrane and may be able to use photosensory response to detect algal prey based on chlorophyll autofluorescence.

  5. Modeling heterotrophic bacteria in plumbing system of drinking water.

    PubMed

    Chowdhury, Shakhawat; Al-Zahrani, Muhammad

    2014-06-01

    This study investigated occurrences of heterotrophic (HPC) bacteria and developed predictive models for HPC bacteria in plumbing pipes (PP) and hot water tanks (HWT) of two houses in Dhahran (Saudi Arabia). Heterotrophic bacteria in PP and HWT were observed to be 2.4 to 5.3 and 0.4 to 5.9 times the HPC bacteria in water distribution system (WDS), respectively. Three linear, one nonlinear, and one neural network models were investigated to predict HPC bacteria in PP and HWT. Significant factors for bacteria regrowth in PP and HWT were identified through numerical and graphical techniques. The R2 values of the models varied between 0.57 and 0.96, indicating moderate to excellent predictive ability for HPC bacteria in PP and HWT. The models were found to be statistically significant, which were also validated using additional data. These models can be used to predict HPC bacteria regrowth from WDS to PP and HWT, and could help to predict exposure and risks. PMID:25109196

  6. Carbon Limited Heterotrophic Activity in an Urban Stream

    NASA Astrophysics Data System (ADS)

    Hassett, B.; Bernhardt, E.; Palmer, M.

    2005-05-01

    Urban streams are characterized by flashy hydrographs, heavily incised channels, and scoured bed materials. Because of frequent scour, benthic organic matter in urban streams tends to be extremely low relative to nonurban streams. Recent research has related low organic matter availability to low rates of nitrogen uptake. We hypothesized that urban streams are carbon limited, and tested this hypothesis by adding a pulse of labile carbon (as potassium acetate) to the Stewart April tributary of Paint Branch, which drains a heavily urbanized watershed 73% impervious cover) in the suburbs of Washington, D.C. We predicted that the magnitude of the carbon effect on stream metabolism and N processing would be reduced as a result of litter inputs, and compared the stream response before and after peak litterfall. Adding labile dissolved organic carbon to the stream immediately increased metabolism in the stream channel during both additions, but this increase in heterotrophic activity did not lead to reductions in dissolved inorganic nitrogen concentrations. This indicates that while heterotrophs in this stream are carbon limited, the microbial community was not able to respond quickly enough to the pulse addition to appreciably reduce DIN concentrations in this eutrophic stream.

  7. Recovery and diversity of heterotrophic bacteria from chlorinated drinking waters.

    PubMed Central

    Maki, J S; LaCroix, S J; Hopkins, B S; Staley, J T

    1986-01-01

    Heterotrophic bacteria were enumerated from the Seattle drinking water catchment basins and distribution system. The highest bacterial recoveries were obtained by using a very dilute medium containing 0.01% peptone as the primary carbon source. Other factors favoring high recovery were the use of incubation temperatures close to that of the habitat and an extended incubation (28 days or longer provided the highest counts). Total bacterial counts were determined by using acridine orange staining. With one exception, all acridine orange counts in chlorinated samples were lower than those in prechlorinated reservoir water, indicating that chlorination often reduces the number of acridine orange-detectable bacteria. Source waters had higher diversity index values than did samples examined following chlorination and storage in reservoirs. Shannon index values based upon colony morphology were in excess of 4.0 for prechlorinated source waters, whereas the values for final chlorinated tap waters were lower than 2.9. It is not known whether the reduction in diversity was due solely to chlorination or in part to other factors in the water treatment and distribution system. Based upon the results of this investigation, we provide a list of recommendations for changes in the procedures used for the enumeration of heterotrophic bacteria from drinking waters. Images PMID:3524453

  8. Distribution of biomass of heterotrophic bacterioplankton in the Bohai Sea

    NASA Astrophysics Data System (ADS)

    Bai, Jie; Li, Kuiran; Zhang, Jing; Li, Zhengyan; Gao, Huiwang; Zhang, Haofei

    2005-12-01

    Distribution, variation and impact factors of biomass of bacterioplankton from April to May 1999 in Bohai Sea were studied in DAPI method with epifluorescence microscopy. The biomass in surface waters showed a small day-night variation, varying from 0.13 to 2.51 μg/dm3 with an average of 0.84 μg/dm3. The biomass in bottom waters showed, however, a large variation, changing from 0.15 to 4.18 μg/dm3 with an average of 1.36 μg/dm3. The peak values occurred at 5 and 11 a.m. The bottom water biomass showed a significant correlation with particulate organic carbon ( r=0.639, P<0.05). Heterotrophic bacterioplankton biomass was high in nearshore waters and low in offshore areas with a high biomass zone around Huanghe (Yellow) River mouth, showing the same distribution of nutrients. In vertical distribution, heterotrophic bacteria biomass in bottom waters was higher than that in surface water.

  9. 40 CFR 725.420 - Recipient microorganisms.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Recipient microorganisms. 725.420... CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS General Exemptions for New Microorganisms § 725.420 Recipient microorganisms. The following recipient microorganisms are eligible for...

  10. 40 CFR 725.420 - Recipient microorganisms.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Recipient microorganisms. 725.420... CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS General Exemptions for New Microorganisms § 725.420 Recipient microorganisms. The following recipient microorganisms are eligible for...

  11. 40 CFR 725.420 - Recipient microorganisms.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Recipient microorganisms. 725.420... CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS General Exemptions for New Microorganisms § 725.420 Recipient microorganisms. The following recipient microorganisms are eligible for...

  12. 40 CFR 725.420 - Recipient microorganisms.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Recipient microorganisms. 725.420... CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS General Exemptions for New Microorganisms § 725.420 Recipient microorganisms. The following recipient microorganisms are eligible for...

  13. Light scattering by microorganisms in the open ocean

    NASA Astrophysics Data System (ADS)

    Stramski, Dariusz; Kiefer, Dale A.

    Recent enumeration and identification of marine particles that are less than 2μm in diameter, suggests that they may be the major source of light scattering in the open ocean. The living components of these small particles include viruses, heterotrophic and photoautotrophic bacteria and the smallest eucaryotic cells. In order to examine the relative contribution by these (and other) microorganisms to scattering, we have calculated a budget for both the total scattering and backscattering coefficients (at 550nm) of suspended particles. This budget is determined by calculating the product of the numerical concentration of particles of a given category and the scattering cross-section of that category. Values for this product are then compared to values for the particulate scattering coefficients predicted by the models of GORDON and MOREL (1983) and MOREL (1988). In order to make such a comparison, we have estimated both the total scattering and backscattering cross-section of various microbial components that include viruses, heterotrophic bacteria, prochlorophytes, cyanobacteria, ultrananoplankton (2-8μm), larger nanoplankton (8-20μm) and microplankton (>20 μm). Such determinations are based upon Mie scattering calculations and measurements of the cell size distribution and the absorption and scattering coefficients of microbial cultures. In addition, we have gathered published information on the numerical concentration of living and detrial marine particles in the size range from 0.03 to 100μm. The results of such a study are summarized as follows. The size distribution of microorganisms in the ocean roughly obeys an inverse 4th power law over three orders of magnitude in cell diameter, from 0.2 to 100μm. Thus, the size distribution of living organisms is similar to that for total particulate matter as determined by electronic particle counters. For representative values of refractive index, it appears that most of the scattering in the sea comes from

  14. RELATIONSHIPS BETWEEN LEVELS OF HETEROTROPHIC BACTERIA AND WATER QUALITY PARAMETERS IN A DRINKING WATER DISTRIBUTION SYSTEM

    EPA Science Inventory

    Conventional plating methods were used to quantify heterotrophic bacteria from a drinking water distribution system. Three media, plate count agar (PCA), R2A agar and sheep blood agar (TSA-SB) were used to determine heterotrophic plate count (HPC) levels. Grab samples were collec...

  15. Sensor arrays for detecting microorganisms

    NASA Technical Reports Server (NTRS)

    Lewis, Nathan S. (Inventor); Freund, Michael S. (Inventor)

    2000-01-01

    A sensor array for detecting a microorganism comprising first and second sensors electrically connected to an electrical measuring apparatus, wherein the sensors comprise a region of nonconducting organic material and a region of conducting material compositionally that is different than the nonconducting organic material and an electrical path through the regions of nonconducting organic material and the conducting material. A system for identifying microorganisms using the sensor array, a computer and a pattern recognition algorithm, such as a neural net are also disclosed.

  16. Food waste as nutrient source in heterotrophic microalgae cultivation.

    PubMed

    Pleissner, Daniel; Lam, Wan Chi; Sun, Zheng; Lin, Carol Sze Ki

    2013-06-01

    Glucose, free amino nitrogen (FAN), and phosphate were recovered from food waste by fungal hydrolysis using Aspergillus awamori and Aspergillus oryzae. Using 100g food waste (dry weight), 31.9 g glucose, 0.28 g FAN, and 0.38 g phosphate were recovered after 24h of hydrolysis. The pure hydrolysate has then been used as culture medium and nutrient source for the two heterotrophic microalgae Schizochytrium mangrovei and Chlorella pyrenoidosa, S. mangrovei and C. pyrenoidosa grew well on the complex food waste hydrolysate by utilizing the nutrients recovered. At the end of fermentation 10-20 g biomass were produced rich in carbohydrates, lipids, proteins, and saturated and polyunsaturated fatty acids. Results of this study revealed the potential of food waste hydrolysate as culture medium and nutrient source in microalgae cultivation.

  17. Modeling pure culture heterotrophic production of polyhydroxybutyrate (PHB).

    PubMed

    Mozumder, Md Salatul Islam; Goormachtigh, Laurens; Garcia-Gonzalez, Linsey; De Wever, Heleen; Volcke, Eveline I P

    2014-03-01

    In this contribution a mechanistic model describing the production of polyhydroxybutyrate (PHB) through pure-culture fermentation was developed, calibrated and validated for two different substrates, namely glucose and waste glycerol. In both cases, non-growth-associated PHB production was triggered by applying nitrogen limitation. The occurrence of some growth-associated PHB production besides non-growth-associated PHB production was demonstrated, although it is inhibited in the presence of nitrogen. Other phenomena observed experimentally and described by the model included biomass growth on PHB and non-linear product inhibition of PHB production. The accumulated impurities from the waste substrate negatively affected the obtained maximum PHB content. Overall, the developed mathematical model provided an accurate prediction of the dynamic behavior of heterotrophic biomass growth and PHB production in a two-phase pure culture system. PMID:24457311

  18. Textiles for protection against microorganism

    NASA Astrophysics Data System (ADS)

    Sauperl, O.

    2016-04-01

    Concerning micro-organisms such as bacteria, viruses and fungi, there is a huge progress in the development of textile materials and procedures which should effectively protect against these various pathogens. In this sense there is especially problematic hospital environment, where it is necessary to take into account properly designed textile material which, when good selected and composed, act as a good barrier against transfer of micro-organisms through material mainly in its wet state. Respect to this it is necessary to be familiar with the rules regarding selection of the input material, the choice of proper yarn construction, the choice of the proper weaving mode, the rules regarding selection of antimicrobial-active compound suitable for (eco-friendly) treatment, and the choice of the most appropriate test method by which it is possible objectively to conclude on the reduction of selected microorganism. As is well known, fabrics are three-dimensional structures with void and non-void areas. Therefore, the physical-chemical properties of the textile material/fabric, the surface characteristics together with the shape of microorganism, and the carriers' characteristics contribute to control the transfer of microorganism through textile material. Therefore, careful planning of textile materials and treatment procedure with the compound which is able to reduce micro-organism satisfactory is particularly important, especially due to the fact that in hospital environment population with impaired immune system is mainly presented.

  19. Heterotrophic Activity of Deep-Sea Sediment Bacteria

    PubMed Central

    Schwarz, J. R.; Colwell, R. R.

    1975-01-01

    Sediment samples, containing mixed microbial populations that were decompressed during retrieval from 7,750 and 8,130 m in the Puerto Rican Trench, were recompressed and incubated at the approximate in situ temperature (3 C) and pressure (775 or 815 atm) in the presence of 14C-labeled amino acids. Heterotrophic activity (total uptake, CO2 respiration, and cellular assimilation) and cellular-associated “pool” concentrations were measured. Compared with atmospheric controls held at 3 C, the total uptake at elevated pressure at 3 C was reduced, on an average, 55 times, CO2 respiration was reduced 45 times, and cellular assimilation was reduced 69 times. Rate of total uptake at elevated pressure was found to range from 4.0 × 10-11 μg/cell per h for leucine to 2.61 × 10-10 μg/cell per h for an amino acid mixture. Also, the percentage of total uptake at elevated pressures, respired as CO2, increased at the expense of cellular assimilation (ca. 22% increase). Two cellular-associated amino acid pools were detected, a large, loosely bound, outer pool and a small, tightly bound internal pool. The loosely bound outer pool was removed by a change in the pH of the incubation medium. Even though heterotrophic uptake and the outer, cellular-associated pool were markedly reduced at an elevated pressure, the percentage of total uptake calculated for the unincorporated, tightly bound, intracellular pool was 2 to 19 times that obtained for cultures held at 1 atm. The results were interpreted as indicating that bacterial metabolism and biosynthesis in the deep sea are markedly reduced, with a greater proportion of metabolic activity devoted to cellular maintenance. PMID:1190762

  20. Diversity and distribution of pigmented heterotrophic bacteria in marine environments.

    PubMed

    Du, Hailian; Jiao, Nianzhi; Hu, Yaohua; Zeng, Yonghui

    2006-07-01

    A systematic investigation of marine pigmented heterotrophic bacteria (PHB) based on the cultivation method and sequencing analysis of 16S rRNA genes was conducted in Chinese coastal and shelf waters and the Pacific Ocean. Both the abundance of PHB and the ratio of PHB to CFU decreased along trophic gradients from coastal to oceanic waters, with the highest values of 9.9 x 10(3) cell mL(-1) and 39.6%, respectively, in the Yangtze River Estuary. In contrast to the total heterotrophic bacteria (TB) and CFU, which were present in the whole water column, PHB were primarily confined to the euphotic zone, with the highest abundance of PHB and ratio of PHB to CFU occurring in surface water. In total, 247 pigmented isolates were obtained during this study, and the phylogenetic analysis showed a wide genetic diversity covering 25 genera of six phylogenetic classes: Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacilli, Flavobacteria and Sphingobacteria. PHB belonging to Alphaproteobacteria, Flavobacteria and Sphingobacteria were obtained mainly from the South China Sea and East China Sea; PHB from the Pacific Ocean water were predominantly affiliated with Gammaproteobacteria, and most isolates from the Yangtze River Estuary fell into the classes Actinobacteria and Bacilli. The isolates exhibited various colours (e.g. golden, yellow, red, pink and orange), with genus or species specificity. Furthermore, the pigment of PHB cells absorbed light mainly in the wavelength range between 450 and 550 nm. In conclusion, our work has revealed that PHB with broad genetic diversity are widely distributed in the marine environment, and may account for up to 39.6% of culturable bacteria, equivalent to 1.4% of the total microbial community. This value might even be underestimated because it is probable that not all pigmented bacteria were isolated. Their abundance and genetic distribution are heavily influenced by environmental properties, such as light and nutrition

  1. Genetic and metabolic variability in autotrophic and heterotrophic bacteria

    NASA Technical Reports Server (NTRS)

    Decicco, B. T.

    1972-01-01

    The studies to evaluate an organism's ability to maintain normal physiological activities over a long period of time in a bioregenerative system are presented. Studies reviewed include: heat tolerant mutants of Pseudomonas fluoresceins, virulence factors of the Staphylococci, and the effect of mutations on the virulence for man in common and ubiquitous microorganisms.

  2. Microorganism dynamics during a rising tide: Disentangling effects of resuspension and mixing with offshore waters above an intertidal mudflat

    NASA Astrophysics Data System (ADS)

    Guizien, Katell; Dupuy, Christine; Ory, Pascaline; Montanié, Hélène; Hartmann, Hans; Chatelain, Mathieu; Karpytchev, Mikhaïl

    2014-01-01

    Resuspension of microphytobenthic biomass that builds up during low tide has been acknowledged as a major driver of the highly productive food web of intertidal mudflats. Yet, little is known about the contribution to pelagic food web of the resuspension of other microorganisms such as viruses, picoeukaryotes, cyanobacteria, bacteria, nanoflagellates, and ciliates, living in biofilms associated with microphytobenthos and surficial sediment. In the present study, a novel approach that involves simultaneous Lagrangian and Eulerian surveys enabled to disentangle the effects of resuspension and mixing with offshore waters on the dynamics of water column microorganisms during a rising tide in the presence of waves. Temporal changes in the concentration of microorganisms present in the water column were recorded along a 3 km cross-shore transect and at a fixed subtidal location. In both surveys, physical and biological processes were separated by comparing the time-evolution of sedimentary particles and microorganism concentrations. During a rising tide, sediment erosion under wave action occurred over the lower and upper parts of the mudflat, where erodibility was highest. Although erosion was expected to enrich the water column with the most abundant benthic microorganisms, such as diatoms, bacteria and viruses, enrichment was only observed for nanoflagellates and ciliates. Grazing probably overwhelmed erosion transfer for diatoms and bacteria, while adsorption on clayed particles may have masked the expected water column enrichment in free viruses due to resuspension. Ciliate enrichment could not be attributed to resuspension as those organisms were absent from the sediment. Wave agitation during the water flow on the mudflat likely dispersed gregarious ciliates over the entire water column. During the rising tide, offshore waters imported more autotrophic, mainly cyanobacteria genus Synechococcus sp. than heterotrophic microorganisms, but this import was also heavily

  3. Potential and limits of Raman spectroscopy for carotenoid detection in microorganisms: implications for astrobiology.

    PubMed

    Jehlička, Jan; Edwards, Howell G M; Osterrothová, Kateřina; Novotná, Julie; Nedbalová, Linda; Kopecký, Jiří; Němec, Ivan; Oren, Aharon

    2014-12-13

    In this paper, it is demonstrated how Raman spectroscopy can be used to detect different carotenoids as possible biomarkers in various groups of microorganisms. The question which arose from previous studies concerns the level of unambiguity of discriminating carotenoids using common Raman microspectrometers. A series of laboratory-grown microorganisms of different taxonomic affiliation was investigated, such as halophilic heterotrophic bacteria, cyanobacteria, the anoxygenic phototrophs, the non-halophilic heterotrophs as well as eukaryotes (Ochrophyta, Rhodophyta and Chlorophyta). The data presented show that Raman spectroscopy is a suitable tool to assess the presence of carotenoids of these organisms in cultures. Comparison is made with the high-performance liquid chromatography approach of analysing pigments in extracts. Direct measurements on cultures provide fast and reliable identification of the pigments. Some of the carotenoids studied are proposed as tracers for halophiles, in contrast with others which can be considered as biomarkers of other genera. The limits of application of Raman spectroscopy are discussed for a few cases where the current Raman spectroscopic approach does not allow discriminating structurally very similar carotenoids. The database reported can be used for applications in geobiology and exobiology for the detection of pigment signals in natural settings.

  4. Potential and limits of Raman spectroscopy for carotenoid detection in microorganisms: implications for astrobiology

    PubMed Central

    Jehlička, Jan; Edwards, Howell G. M.; Osterrothová, Kateřina; Novotná, Julie; Nedbalová, Linda; Kopecký, Jiří; Němec, Ivan; Oren, Aharon

    2014-01-01

    In this paper, it is demonstrated how Raman spectroscopy can be used to detect different carotenoids as possible biomarkers in various groups of microorganisms. The question which arose from previous studies concerns the level of unambiguity of discriminating carotenoids using common Raman microspectrometers. A series of laboratory-grown microorganisms of different taxonomic affiliation was investigated, such as halophilic heterotrophic bacteria, cyanobacteria, the anoxygenic phototrophs, the non-halophilic heterotrophs as well as eukaryotes (Ochrophyta, Rhodophyta and Chlorophyta). The data presented show that Raman spectroscopy is a suitable tool to assess the presence of carotenoids of these organisms in cultures. Comparison is made with the high-performance liquid chromatography approach of analysing pigments in extracts. Direct measurements on cultures provide fast and reliable identification of the pigments. Some of the carotenoids studied are proposed as tracers for halophiles, in contrast with others which can be considered as biomarkers of other genera. The limits of application of Raman spectroscopy are discussed for a few cases where the current Raman spectroscopic approach does not allow discriminating structurally very similar carotenoids. The database reported can be used for applications in geobiology and exobiology for the detection of pigment signals in natural settings. PMID:25368348

  5. C isotope fractionation during heterotrophic activity driven carbonate precipitation

    NASA Astrophysics Data System (ADS)

    Balci, Nurgul; Demirel, Cansu

    2016-04-01

    Stable carbon isotopic fractionation during carbonate precipitation induced by environmentally enriched heterotrophic halophilic microorganims was experimentally investigated under various salinity (% 4.5, %8, %15) conditions at 30 °C. Halophilic heterotrophic microorganims were enriched from a hypersaline Lake Acigöl located in SW Turkey (Balci et al.,2015) and later used for the precipitation experiments (solid and liquid medium). The carbonate precipitates had relatively high δ13C values (-4.3 to -16.9 ‰) compared to the δ13C values of the organic compounds that ranged from -27.5 to -25.4 ‰. At salinity of 4.5 % δ13C values of carbonate ranged from -4.9 ‰ to -10.9 ‰ with a 13C-enrichment factor of +20 to +16 ‰ higher than the δ13C values of the associated DOC (-27.5) . At salinity 8 % δ13C values of carbonate ranged from -16.3 ‰ to -11.7 ‰ with a 13C-enrichment factor of+11.3 to+15.9 ‰ higher than the δ13C values of the associated DOC. The respected values for 15 % salinity ranged from -12.3 ‰ to -9.7 ‰ with a 13C-enrichment factor of +15.2 to+16.8 ‰ higher than the δ13C values of the associated DOC. The carbonate precipitates produced in the solid medium are more enriched in 13C relative to liquid culture experiments. These results suggest that the carbon in the solid was derived from both the bacterial oxidation of organic compounds in the medium and from the atmospheric CO2. A solid medium used in the experiments may have suppressed convective and advective mass transport favouring diffusion-controlled system. This determination suggests that the rate and equilibration of CO2 exchange with the atmosphere is the major control on C isotope composition of carbonate minerals precipitated in the experiments. Key words: Lake Acıgöl, halophilic bacteria, carbonate biomineralization, C isotopes References Nurgul Balci, Meryem Menekşe, Nevin Gül Karagüler, M. Şeref Sönmez,Patrick Meister 2015.Reproducing authigenic carbonate

  6. C isotope fractionation during heterotrophic activity driven carbonate precipitation

    NASA Astrophysics Data System (ADS)

    Balci, Nurgul; Demirel, Cansu

    2016-04-01

    Stable carbon isotopic fractionation during carbonate precipitation induced by environmentally enriched heterotrophic halophilic microorganims was experimentally investigated under various salinity (% 4.5, %8, %15) conditions at 30 °C. Halophilic heterotrophic microorganims were enriched from a hypersaline Lake Acigöl located in SW Turkey (Balci et al.,2015) and later used for the precipitation experiments (solid and liquid medium). The carbonate precipitates had relatively high δ13C values (‑4.3 to ‑16.9 ‰) compared to the δ13C values of the organic compounds that ranged from ‑27.5 to ‑25.4 ‰. At salinity of 4.5 % δ13C values of carbonate ranged from -4.9 ‰ to -10.9 ‰ with a 13C-enrichment factor of +20 to +16 ‰ higher than the δ13C values of the associated DOC (-27.5) . At salinity 8 % δ13C values of carbonate ranged from -16.3 ‰ to -11.7 ‰ with a 13C-enrichment factor of+11.3 to+15.9 ‰ higher than the δ13C values of the associated DOC. The respected values for 15 % salinity ranged from -12.3 ‰ to -9.7 ‰ with a 13C-enrichment factor of +15.2 to+16.8 ‰ higher than the δ13C values of the associated DOC. The carbonate precipitates produced in the solid medium are more enriched in 13C relative to liquid culture experiments. These results suggest that the carbon in the solid was derived from both the bacterial oxidation of organic compounds in the medium and from the atmospheric CO2. A solid medium used in the experiments may have suppressed convective and advective mass transport favouring diffusion-controlled system. This determination suggests that the rate and equilibration of CO2 exchange with the atmosphere is the major control on C isotope composition of carbonate minerals precipitated in the experiments. Key words: Lake Acıgöl, halophilic bacteria, carbonate biomineralization, C isotopes References Nurgul Balci, Meryem Menekşe, Nevin Gül Karagüler, M. Şeref Sönmez,Patrick Meister 2015.Reproducing authigenic

  7. PCB breakdown by anaerobic microorganisms

    SciTech Connect

    Not Available

    1989-03-01

    Recently, altered PCB cogener distribution patterns observed in anaerobic sediment samples from the upper Hudson River are being attributed to biologically mediated reductive dechlorination. The authors report their successful demonstration of biologically mediated reductive dechlorination of an Aroclor mixture. In their investigation, they assessed the ability of microorganisms from PCB-contaminated Hudson River sediments (60-562 ppm PCBs) to dechlorinate Aroclor 1242 under anaerobic conditions by eluting microorganisms from the PCB- contaminated sediments and transferring them to a slurry of reduced anaerobic mineral medium and PCB-free sediments in tightly stoppered bottles. They observed dechlorination to be the most rapid at the highest PCB concentration tried by them.

  8. Evaluation of aquatic sediment microcosms and their use in assessing possible effects of introduced microorganisms on ecosystem parameters.

    PubMed Central

    Wagner-Döbler, I; Pipke, R; Timmis, K N; Dwyer, D F

    1992-01-01

    In this paper we describe a sediment microcosm system consisting of 20 undisturbed, layered sediment cores with overlying site water which are incubated under identical conditions of temperature, light, stirring rate of overlying water, and water exchange rate. Ecosystem parameters (nutrient level, photosynthetic potential, community structure of heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients) of the laboratory microcosms and the source ecosystem were compared and shown to be indistinguishable for the first 2 weeks. In weeks 3 and 4, small differences were detectable in the nutrient level, community structure of heterotrophic bacteria, and thymidine incorporation rate. However, the photosynthetic potential, depth profiles of heterotrophic bacterial community structure, and oxygen microgradients were maintained throughout the incubation period and did not differ between laboratory microcosms and the source ecosystem. The microcosm system described here would thus appear to be a valid model of aquatic sediments for up to 4 weeks; the actual period would depend on the sediment source and incubation temperature. The validated systems were used with Rhine river sediment to assess possible effects on ecosystem parameters of Pseudomonas sp. strain B13 FR1(pFRC20P), a genetically engineered microorganism (GEM) that had been constructed to degrade mixtures of halo- and alkylbenzoates and -phenols. The GEM survived in the surface sediment at densities of 5 x 10(4) to 5 x 10(5)/g (dry weight) for 4 weeks and degraded added chloro- and methylaromatics. The GEM did not measurably influence ecosystem parameters such as photosynthesis, densities of selected heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients. Thus, the microcosm system described here would seem to be useful for the study of the ecology of biodegradation and the fate and effect of microorganisms introduced into the environment. PMID:1599244

  9. Global net primary production and heterotrophic respiration for 1987

    SciTech Connect

    Hunt, R.E. Jr.; Piper, S.C.; Nemani, R. |

    1995-06-01

    An ecosystem process model, BIOME-BGC, was parameterized and used to simulate the actual net primary production and heterotrophic respiration using daily climatic data, land cover type, leaf area index gridded to 1{degree} latitude by 1{degree} longitude grid cells for the year 1987. Global net primary production was 52 Pg C. These estimates were validated directly by two different methods. First, the grid cells were aggregated and used as inputs to a 3D atmospheric transport model, to compare CO{sub 2} station data with predictions. We simulated the intra-annual variation of atmospheric CO{sub 2} well for the northern hemisphere, but not for the southern hemisphere. Second, we calculated the net {sup 13}C uptake of vegetation, which is a function of water use efficiency. The {sup 13}C/{sup 12}C ratios agreed with measured data, indicating a strong limitation of global primary processes by the hydrologic cycle, especially precipitation. These are different from other global carbon models as we can simulate the year-to-year variation of climate, including El Nino, on the global carbon cycle.

  10. Trimethylamine N-oxide metabolism by abundant marine heterotrophic bacteria

    PubMed Central

    Lidbury, Ian; Murrell, J. Colin; Chen, Yin

    2014-01-01

    Trimethylamine N-oxide (TMAO) is a common osmolyte found in a variety of marine biota and has been detected at nanomolar concentrations in oceanic surface waters. TMAO can serve as an important nutrient for ecologically important marine heterotrophic bacteria, particularly the SAR11 clade and marine Roseobacter clade (MRC). However, the enzymes responsible for TMAO catabolism and the membrane transporter required for TMAO uptake into microbial cells have yet to be identified. We show here that the enzyme TMAO demethylase (Tdm) catalyzes the first step in TMAO degradation. This enzyme represents a large group of proteins with an uncharacterized domain (DUF1989). The function of TMAO demethylase in a representative from the SAR11 clade (strain HIMB59) and in a representative of the MRC (Ruegeria pomeroyi DSS-3) was confirmed by heterologous expression of tdm (the gene encoding Tdm) in Escherichia coli. In R. pomeroyi, mutagenesis experiments confirmed that tdm is essential for growth on TMAO. We also identified a unique ATP-binding cassette transporter (TmoXWV) found in a variety of marine bacteria and experimentally confirmed its specificity for TMAO through marker exchange mutagenesis and lacZ reporter assays of the promoter for genes encoding this transporter. Both Tdm and TmoXWV are particularly abundant in natural seawater assemblages and actively expressed, as indicated by a number of recent metatranscriptomic and metaproteomic studies. These data suggest that TMAO represents a significant, yet overlooked, nutrient for marine bacteria. PMID:24550299

  11. Polyhydroxyalkanoate production potential of heterotrophic bacteria in activated sludge.

    PubMed

    Inoue, Daisuke; Suzuki, Yuta; Uchida, Takahiro; Morohoshi, Jota; Sei, Kazunari

    2016-01-01

    This study was conducted to evaluate the polyhydroxyalkanoate (PHA) production potential of cultivable heterotrophic bacteria in activated sludge by genotypic and phenotypic characterizations. A total of 114 bacterial strains were isolated from four activated sludge samples taken from a lab-scale sequencing batch reactor and three wastewater treatment processes of two municipal wastewater treatment plants. PCR detection of the phaC genes encoding class I and II PHA synthase revealed that 15% of the total isolates possessed phaC genes, all of which had the closest similarities to known phaC genes of α- and β-Proteobacteria and Actinobacteria. PHA production experiments under aerobic and nitrogen-limited conditions showed that 68% of the total isolates were capable of producing PHA from at least one of the six substrates used (acetate, propionate, lactate, butyrate, glucose and glycerol). Genotypic and phenotypic characterizations revealed that 75% of the activated sludge bacteria had PHA production potential. Our results also indicated that short-chain fatty acids would be the preferable substrates for PHA production by activated sludge bacteria, and that there might be a variety of unidentified phaC genes in activated sludge.

  12. Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures.

    PubMed

    Beier, Sara; Rivers, Adam R; Moran, Mary Ann; Obernosterer, Ingrid

    2015-05-01

    Phenotypic plasticity (PP) is the development of alternate phenotypes of a given taxon as an adaptation to environmental conditions. Methodological limitations have restricted the quantification of PP to the measurement of a few traits in single organisms. We used metatranscriptomic libraries to overcome these challenges and estimate PP using the expressed genes of multiple heterotrophic organisms as a proxy for traits in a microbial community. The metatranscriptomes captured the expression response of natural marine bacterial communities grown on differing carbon resource regimes in continuous cultures. We found that taxa with different magnitudes of PP coexisted in the same cultures, and that members of the order Rhodobacterales had the highest levels of PP. In agreement with previous studies, our results suggest that continuous culturing may have specifically selected for taxa featuring a rather high range of PP. On average, PP and abundance changes within a taxon contributed equally to the organism's change in functional gene abundance, implying that both PP and abundance mediated observed differences in community function. However, not all functional changes due to PP were directly reflected in the bulk community functional response: gene expression changes in individual taxa due to PP were partly masked by counterbalanced expression of the same gene in other taxa. This observation demonstrates that PP had a stabilizing effect on a community's functional response to environmental change.

  13. Global abundance of planktonic heterotrophic protists in the deep ocean.

    PubMed

    Pernice, Massimo C; Forn, Irene; Gomes, Ana; Lara, Elena; Alonso-Sáez, Laura; Arrieta, Jesus M; del Carmen Garcia, Francisca; Hernando-Morales, Victor; MacKenzie, Roy; Mestre, Mireia; Sintes, Eva; Teira, Eva; Valencia, Joaquin; Varela, Marta M; Vaqué, Dolors; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

    2015-03-01

    The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72±19 cells ml(-1) in mesopelagic waters down to 11±1 cells ml(-1) in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml(-1). The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web.

  14. Diversity of Heterotrophic Protists from Extremely Hypersaline Habitats.

    PubMed

    Park, Jong Soo; Simpson, Alastair G B

    2015-09-01

    Heterotrophic protists (protozoa) are a diverse but understudied component of the biota of extremely hypersaline environments, with few data on molecular diversity within halophile 'species', and almost nothing known of their biogeographic distribution. We have garnered SSU rRNA gene sequences for several clades of halophilic protozoa from enrichments from waters of >12.5% salinity from Australia, North America, and Europe (6 geographic sites, 25 distinct samples). The small stramenopile Halocafeteria was found at all sites, but phylogenies did not show clear geographic clustering. The ciliate Trimyema was recorded from 6 non-European samples. Phylogenies confirmed a monophyletic halophilic Trimyema group that included possible south-eastern Australian, Western Australian and North American clusters. Several halophilic Heterolobosea were detected, demonstrating that Pleurostomum contains at least three relatively distinct clades, and increasing known continental ranges for Tulamoeba peronaphora and Euplaesiobystra hypersalinica. The unclassified flagellate Palustrimonas, found in one Australian sample, proves to be a novel deep-branching alveolate. These results are consistent with a global distribution of halophilic protozoa groups (∼ morphospecies), but the Trimyema case suggests that is worth testing whether larger forms exhibit biogeographic phylogenetic substructure. The molecular detection/characterization of halophilic protozoa is still far from complete at the clade level, let alone the 'species level'.

  15. Diversity of chemotactic heterotrophic bacteria associated with arctic cyanobacteria.

    PubMed

    Prasad, Sathish; Pratibha, Mambatta Shankaranarayanan; Manasa, Poorna; Buddhi, Sailaja; Begum, Zareena; Shivaji, Sisinthy

    2013-01-01

    The abundance and diversity of chemotactic heterotrophic bacteria associated with Arctic cyanobacteria was determined. The viable numbers ranged between 10(4) and 10(6) cell g(-1) cyanobacterial biomass. A total of 112 morphotypes, representing 22 phylotypes based on their 16S rRNA sequence similarity were isolated from the samples. All the phylotypes were Gram-negative with affiliation to the proteobacterial and bacteroidetes divisions. Among the 22 phylotypes, 14 were chemotactic to glucose. Majority of the phylotypes were psychrotolerant showing growth up to 30 °C. Representatives of Alphaproteobacteria, the genus Flavobacterium and the gammaproteobacterial Alcanivorax sp, were psychrophilic with growth at or below 18 °C. A significant percentage of phylotypes were pigmented (~68 %), rich in unsaturated membrane fatty acids and tolerated pH values and NaCl concentrations between 5.0-8.0 and 0.15-1.0 M, respectively. The percentages of phylotypes producing extracellular cold-active enzymes at 4 °C were amylase (18.18 %), lipase and urease (45.45 %), caseinase (59.09 %) and gelatinase (31.8 %). PMID:23053490

  16. Heterotrophic bacteria in drinking water distribution system: a review.

    PubMed

    Chowdhury, Shakhawat

    2012-10-01

    The microbiological quality of drinking water in municipal water distribution systems (WDS) depends on several factors. Free residual chlorine and/or chloramines are typically used to minimize bacterial recontamination and/or regrowth in WDS. Despite such preventive measures, regrowth of heterotrophic (HPC) and opportunistic bacteria in bulk water and biofilms has yet to be controlled completely. No approach has shown complete success in eliminating biofilms or HPC bacteria from bulk water and pipe surfaces. Biofilms can provide shelter for pathogenic bacteria and protect these bacteria from disinfectants. Some HPC bacteria may be associated with aesthetic and non-life threatening diseases. Research to date has achieved important success in understanding occurrence and regrowth of bacteria in bulk water and biofilms in WDS. To achieve comprehensive understanding and to provide efficient control against bacteria regrowth, future research on bacteria regrowth dynamics and their implications is warranted. In this study, a review was performed on the literature published in this area. The findings and limitations of these papers are summarized. Occurrences of bacteria in WDS, factors affecting bacteria regrowth in bulk water and biofilms, bacteria control strategies, sources of nutrients, human health risks from bacterial exposure, modelling of bacteria regrowth and methods of bacteria sampling and detection and quantification are investigated. Advances to date are noted, and future research needs are identified. Finally, research directions are proposed to effectively control HPC and opportunistic bacteria in bulk water and biofilms in WDS.

  17. Global abundance of planktonic heterotrophic protists in the deep ocean.

    PubMed

    Pernice, Massimo C; Forn, Irene; Gomes, Ana; Lara, Elena; Alonso-Sáez, Laura; Arrieta, Jesus M; del Carmen Garcia, Francisca; Hernando-Morales, Victor; MacKenzie, Roy; Mestre, Mireia; Sintes, Eva; Teira, Eva; Valencia, Joaquin; Varela, Marta M; Vaqué, Dolors; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

    2015-03-01

    The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72±19 cells ml(-1) in mesopelagic waters down to 11±1 cells ml(-1) in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml(-1). The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web. PMID:25290506

  18. Influence of the Natural Microbial Flora on the Acid Tolerance Response of Listeria monocytogenes in a Model System of Fresh Meat Decontamination Fluids

    PubMed Central

    Samelis, John; Sofos, John N.; Kendall, Patricia A.; Smith, Gary C.

    2001-01-01

    Depending on its composition and metabolic activity, the natural flora that may be established in a meat plant environment can affect the survival, growth, and acid tolerance response (ATR) of bacterial pathogens present in the same niche. To investigate this hypothesis, changes in populations and ATR of inoculated (105 CFU/ml) Listeria monocytogenes were evaluated at 35°C in water (10 or 85°C) or acidic (2% lactic or acetic acid) washings of beef with or without prior filter sterilization. The model experiments were performed at 35°C rather than lower (≤15°C) temperatures to maximize the response of inoculated L. monocytogenes in the washings with or without competitive flora. Acid solution washings were free (<1.0 log CFU/ml) of natural flora before inoculation (day 0), and no microbial growth occurred during storage (35°C, 8 days). Inoculated L. monocytogenes died off (negative enrichment) in acid washings within 24 h. In nonacid (water) washings, the pathogen increased (approximately 1.0 to 2.0 log CFU/ml), irrespective of natural flora, which, when present, predominated (>8.0 log CFU/ml) by day 1. The pH of inoculated water washings decreased or increased depending on absence or presence of natural flora, respectively. These microbial and pH changes modulated the ATR of L. monocytogenes at 35°C. In filter-sterilized water washings, inoculated L. monocytogenes increased its ATR by at least 1.0 log CFU/ml from days 1 to 8, while in unfiltered water washings the pathogen was acid tolerant at day 1 (0.3 to 1.4 log CFU/ml reduction) and became acid sensitive (3.0 to >5.0 log CFU/ml reduction) at day 8. These results suggest that the predominant gram-negative flora of an aerobic fresh meat plant environment may sensitize bacterial pathogens to acid. PMID:11375145

  19. Smaller Fleas: Viruses of Microorganisms

    PubMed Central

    Hyman, Paul; Abedon, Stephen T.

    2012-01-01

    Life forms can be roughly differentiated into those that are microscopic versus those that are not as well as those that are multicellular and those that, instead, are unicellular. Cellular organisms seem generally able to host viruses, and this propensity carries over to those that are both microscopic and less than truly multicellular. These viruses of microorganisms, or VoMs, in fact exist as the world's most abundant somewhat autonomous genetic entities and include the viruses of domain Bacteria (bacteriophages), the viruses of domain Archaea (archaeal viruses), the viruses of protists, the viruses of microscopic fungi such as yeasts (mycoviruses), and even the viruses of other viruses (satellite viruses). In this paper we provide an introduction to the concept of viruses of microorganisms, a.k.a., viruses of microbes. We provide broad discussion particularly of VoM diversity. VoM diversity currently spans, in total, at least three-dozen virus families. This is roughly ten families per category—bacterial, archaeal, fungal, and protist—with some virus families infecting more than one of these microorganism major taxa. Such estimations, however, will vary with further discovery and taxon assignment and also are dependent upon what forms of life one includes among microorganisms. PMID:24278736

  20. Automated microorganism Sample Collection Module

    NASA Technical Reports Server (NTRS)

    Gall, L. S.; Graham, M. D.; Umbreit, W.

    1969-01-01

    Modified Gelman Sampler obtains representative sample of microorganism population. Proposed Sample Collection Module is based on direct inoculation of selected solid growth media encased in a cartridge at all times except during inoculation. Cartridge can be handled with no danger of contamination to sample or operator.

  1. Smaller fleas: viruses of microorganisms.

    PubMed

    Hyman, Paul; Abedon, Stephen T

    2012-01-01

    Life forms can be roughly differentiated into those that are microscopic versus those that are not as well as those that are multicellular and those that, instead, are unicellular. Cellular organisms seem generally able to host viruses, and this propensity carries over to those that are both microscopic and less than truly multicellular. These viruses of microorganisms, or VoMs, in fact exist as the world's most abundant somewhat autonomous genetic entities and include the viruses of domain Bacteria (bacteriophages), the viruses of domain Archaea (archaeal viruses), the viruses of protists, the viruses of microscopic fungi such as yeasts (mycoviruses), and even the viruses of other viruses (satellite viruses). In this paper we provide an introduction to the concept of viruses of microorganisms, a.k.a., viruses of microbes. We provide broad discussion particularly of VoM diversity. VoM diversity currently spans, in total, at least three-dozen virus families. This is roughly ten families per category-bacterial, archaeal, fungal, and protist-with some virus families infecting more than one of these microorganism major taxa. Such estimations, however, will vary with further discovery and taxon assignment and also are dependent upon what forms of life one includes among microorganisms.

  2. Screening, growth medium optimisation and heterotrophic cultivation of microalgae for biodiesel production.

    PubMed

    Jia, Zongchao; Liu, Ying; Daroch, Maurycy; Geng, Shu; Cheng, Jay J

    2014-08-01

    This article presents a study on screening of microalgal strains from the Peking University Algae Collection and heterotrophic cultivation for biodiesel production of a selected microalgal strain. Among 89 strains, only five were capable of growing under heterotrophic conditions in liquid cultures and Chlorella sp. PKUAC 102 was found the best for the production of heterotrophic algal biodiesel. Composition of the growth medium was optimised using response surface methodology and optimised growth conditions were successfully used for cultivation of the strain in a fermentor. Conversion of algal lipids to fatty acid methyl esters (FAMEs) showed that the lipid profile of the heterotrophically cultivated Chlorella sp. PKUAC 102 contains fatty acids suitable for biodiesel production.

  3. Heterotrophic bacterial activities and treatment performance of surface flow constructed wetlands receiving woodwaste leachate.

    PubMed

    Tao, Wendong; Hall, Ken J; Duff, Sheldon J B

    2006-07-01

    Heterotrophic activities were investigated by measuring 3H-leucine incorporation to bacterial protein and 14C-glucose turnover in surface flow constructed wetlands receiving woodwaste leachate. No significant longitudinal variation was found in heterotrophic activities of bacterioplankton. An open wetland, a vegetated wetland, and a fertilized vegetated wetland were used to examine the effects of vegetation and ammonium nitrate amendment. There was not a significant difference in treatment performance among the three wetlands, except for a significant pH increase and more efficient volatile fatty acids removal in the fertilized wetland. The fertilized wetland had the highest leucine incorporation rate and shortest glucose turnover time accompanied by the lowest glucose mineralization percentage, followed by the open wetland, then the vegetated wetland. Planktonic and sedimentary bacteria contributed to the majority of the total heterotrophic activities; epiphytic bacteria played a minor role. Heterotrophic activities were influenced by the availability of nutrient, electron acceptor, and organic substrate.

  4. RARE OCCURRENCE OF HETEROTROPHIC BACTERIA WITH PATHOGENIC POTENTIAL IN POTABLE WATER

    EPA Science Inventory

    Since the discovery of Legionella pneumophila, an opportunistic pathogen that is indigenous to water, microbiologists have speculated that there may be other opportunistic pathogens among the numerous heterotrophic bacteria found in potable water. The USEPA developed a series of...

  5. Effect of UV radiation on the bacterivory of a heterotrophic nanoflagellate

    SciTech Connect

    Sommaruga, R.; Oberleiter, A.; Psenner, R.

    1996-12-01

    Heterotrophic nanoflagellates can function as consumers of picoplankton biomass in different types of aquatic systems. However no study has looked at the effects of UV-B on the trophic interaction between HNF and bacteria. This study presents results from experiments designed to investigate the effect of solar and artificial UV radiation on the heterotrophic nonoflagellate Bodo saltans (Kinetoplastida). 33 refs., 6 figs., 1 tab.

  6. The effect of acidophilic heterotrophic bacteria on the leaching of cobalt by Thiobacillus ferrooxidans

    SciTech Connect

    Wichlacz, P.L.; Thompson, D.L.

    1987-01-01

    Experiments were conducted to determine if acidophilic heterotrophic bacteria influence the ability of T. ferrooxidans to solubilize cobalt. Short term (7 day) flask leaching studies were conducted wherein 28 strains of T. ferrooxidans were each incubated with one of three different cobalt sulfides (CoS, cobaltite flotation concentrate, or cobaltite ore), with and without ferrous iron and/or heterotrophic bacteria. Growth of T. ferrooxidans was determined by comparing cobalt solubilization and ferrous iron oxidation for inoculated and uninoculated control flasks. Under all conditions tested, except one, the addition of acidophilic heterotrophs was found to enhance the extent of cobalt leaching. Longer term (28 day) studies were conducted which included the addition of glucose as a controlled variable. The presence of heterotrophs enhanced the leaching of CoS by T. ferrooxidans under all conditions. Cobalt leaching from concentrate and high grade ore by T. ferrooxidans was enhanced by the addition of heterotrophs in all cases except when ferrous iron or glucose were absent from the leaching medium. The present studies indicate that cobalt solubilization is substrate and strain dependent and, in most cases, is increased when acidophilic heterotrophic bacteria are present. 13 refs., 3 tabs.

  7. Growth, feeding and ecological roles of the mixotrophic and heterotrophic dinoflagellates in marine planktonic food webs

    NASA Astrophysics Data System (ADS)

    Jeong, Hae Jin; Yoo, Yeong Du; Kim, Jae Seong; Seong, Kyeong Ah; Kang, Nam Seon; Kim, Tae Hoon

    2010-06-01

    Planktonic mixotrophic and heterotrophic dinoflagellates are ubiquitous protists and often abundant in marine environments. Recently many phototrophic dinoflagellate species have been revealed to be mixotrophic organisms and also it is suggested that most dinoflagellates may be mixotrophic or heterotrophic protists. The mixotrophic and heterotrophic dinoflagellates are able to feed on diverse prey items including bacteria, picoeukaryotes, nanoflagellates, diatoms, other dinoflagellates, heterotrophic protists, and metazoans due to their diverse feeding mechanisms. In turn they are ingested by many kinds of predators. Thus, the roles of the dinoflagellates in marine planktonic food webs are very diverse. The present paper reviewed the kind of prey which mixotrophic and heterotrophic dinoflagellates are able to feed on, feeding mechanisms, growth and ingestion rates of dinoflagellates, grazing impact by dinoflagellate predators on natural prey populations, predators on dinoflagellates, and red tides dominated by dinoflagellates. Based on this information, we suggested a new marine planktonic food web focusing on mixotrophic and heterotrophic dinoflagellates and provided an insight on the roles of dinoflagellates in the food web.

  8. Functional role of pyruvate kinase from Lactobacillus bulgaricus in acid tolerance and identification of its transcription factor by bacterial one-hybrid

    PubMed Central

    Zhai, Zhengyuan; An, Haoran; Wang, Guohong; Luo, Yunbo; Hao, Yanling

    2015-01-01

    Lactobacillus delbrueckii subsp. bulgaricus develops acid tolerance response when subjected to acid stress conditions, such as the induction of enzymes associated with carbohydrate metabolism. In this study, pyk gene encoding pyruvate kinase was over-expressed in heterologous host Lactococcus lactis NZ9000, and SDS-PAGE analysis revealed the successful expression of this gene in NZ9000. The survival rate of Pyk-overproducing strain was 45-fold higher than the control under acid stress condition (pH 4.0). In order to determine the transcription factor (TF) which regulates the expression of pyk by bacterial one-hybrid, we constructed a TF library including 65 TFs of L. bulgaricus. Western blotting indicated that TFs in this library could be successfully expressed in host strains. Subsequently, the promoter of pfk-pyk operon in L. bulgaricus was identified by 5′-RACE PCR. The bait plasmid pH3U3-p01 carrying the deletion fragment of pfk-pyk promoter captured catabolite control protein A (CcpA) which could regulate the expression of pyk by binding to a putative catabolite-responsive element (5′-TGTAAGCCCTAACA-3′) upstream the -35 region. Real-time qPCR analysis revealed the transcription of pyk was positively regulated by CcpA. This is the first report about identifying the TF of pyk in L. bulgaricus, which will provide new insight into the regulatory network. PMID:26581248

  9. [Improvement of acetic acid tolerance and fermentation performance of industrial Saccharomyces cerevisiae by overexpression of flocculent gene FLO1 and FLO1c].

    PubMed

    Du, Zhaoli; Cheng, Yanfei; Zhu, Hui; He, Xiuping; Zhang, Borun

    2015-02-01

    Flocculent gene FLO1 and its truncated form FLO1c with complete deletion of repeat unit C were expressed in a non-flocculent industrial strain Saccharomyces cerevisiae CE6 to generate recombinant flocculent strains 6-AF1 and 6-AF1c respectively. Both strains of 6-AF1 and 6-AF1c displayed strong flocculation and better cell growth than the control strain CE6-V carrying the empty vector under acetic acid stress. Moreover, the flocculent strains converted glucose to ethanol at much higher rates than the control strain CE6-V under acetic acid stress. In the presence of 0.6% (V/V) acetic acid, the average ethanol production rates of 6-AF1 and 6-AF1c were 1.56 and 1.62 times of that of strain CE6-V, while the ethanol production rates of 6-AF1 and 6-AF1c were 1.21 and 1.78 times of that of strain CE6-V under 1.0% acetic acid stress. Results in this study indicate that acetic acid tolerance and fermentation performance of industrial S. cerevisiae under acetic acid stress can be improved largely by flocculation endowed by expression of flocculent genes, especially FLO1c.

  10. Functional role of pyruvate kinase from Lactobacillus bulgaricus in acid tolerance and identification of its transcription factor by bacterial one-hybrid.

    PubMed

    Zhai, Zhengyuan; An, Haoran; Wang, Guohong; Luo, Yunbo; Hao, Yanling

    2015-11-19

    Lactobacillus delbrueckii subsp. bulgaricus develops acid tolerance response when subjected to acid stress conditions, such as the induction of enzymes associated with carbohydrate metabolism. In this study, pyk gene encoding pyruvate kinase was over-expressed in heterologous host Lactococcus lactis NZ9000, and SDS-PAGE analysis revealed the successful expression of this gene in NZ9000. The survival rate of Pyk-overproducing strain was 45-fold higher than the control under acid stress condition (pH 4.0). In order to determine the transcription factor (TF) which regulates the expression of pyk by bacterial one-hybrid, we constructed a TF library including 65 TFs of L. bulgaricus. Western blotting indicated that TFs in this library could be successfully expressed in host strains. Subsequently, the promoter of pfk-pyk operon in L. bulgaricus was identified by 5'-RACE PCR. The bait plasmid pH3U3-p01 carrying the deletion fragment of pfk-pyk promoter captured catabolite control protein A (CcpA) which could regulate the expression of pyk by binding to a putative catabolite-responsive element (5'-TGTAAGCCCTAACA-3') upstream the -35 region. Real-time qPCR analysis revealed the transcription of pyk was positively regulated by CcpA. This is the first report about identifying the TF of pyk in L. bulgaricus, which will provide new insight into the regulatory network.

  11. Cellular fatty acid profile and H(+)-ATPase activity to assess acid tolerance of Bacillus sp. for potential probiotic functional attributes.

    PubMed

    Shobharani, P; Halami, Prakash M

    2014-11-01

    The present study has been focused widely on comparative account of probiotic qualities of Bacillus spp. for safer usage. Initially, 170 heat resistant flora were isolated and selected for non-pathogenic cultures devoid of cytK, hblD, and nhe1 virulence genes. Subsequently, through biochemical tests along with 16S rRNA gene sequencing and fatty acid profiling, the cultures were identified as Bacillus megaterium (AR-S4), Bacillus subtilis (HR-S1), Bacillus licheniformis (Csm1-1a and HN-S1), and Bacillus flexus (CDM4-3c and CDM3-1). The selected cultures showed 70-80 % survival under simulated gastrointestinal condition which was also confirmed through H(+)-ATPase production. The amount of H(+)-ATPase increased by more than 2-fold when grown at pH 2 which support for the acid tolerance ability of Bacillus isolates. The study also examined the influence of acidic pH on cellular fatty acid composition of Bacillus spp. A remarkable shift in the fatty acid profile was observed at acidic pH through an increased amount of even numbered fatty acid (C16 and C18) in comparison with odd numbered (C15 and C17). Additionally, the cultures exhibited various probiotic functional properties. Overall, the study increases our understanding of Bacillus spp. and will allow both industries and consumers to choose for well-defined probiotic with possible health benefits. PMID:25125040

  12. Real-time ArcGIS and heterotrophic plate count based chloramine disinfectant control in water distribution system.

    PubMed

    Bai, Xiaohui; Zhi, Xinghua; Zhu, Huifeng; Meng, Mingqun; Zhang, Mingde

    2015-01-01

    This study investigates the effect of chloramine residual on bacteria growth and regrowth and the relationship between heterotrophic plate counts (HPCs) and the concentration of chloramine residual in the Shanghai drinking water distribution system (DWDS). In this study, models to control HPCs in the water distribution system and consumer taps are also developed. Real-time ArcGIS was applied to show the distribution and changed results of the chloramine residual concentration in the pipe system by using these models. Residual regression analysis was used to get a reasonable range of the threshold values that allows the chloramine residual to efficiently inhibit bacteria growth in the Shanghai DWDS; the threshold values should be between 0.45 and 0.5 mg/L in pipe water and 0.2 and 0.25 mg/L in tap water. The low residual chloramine value (0.05 mg/L) of the Chinese drinking water quality standard may pose a potential health risk for microorganisms that should be improved. Disinfection by-products (DBPs) were detected, but no health risk was identified.

  13. Characterization of anaerobic heterotrophic bacteria isolated from freshwater lake sediments.

    PubMed

    Molongoski, J J; Klug, M J

    1976-01-01

    Strict anaerobic culture techniques were used to quantitatively and qualitatively evaluate the anaerobic heterotrophic bacteria present at the sediment-water interface of hyperutrophic Wintergreen Lake (Augusta, Mich.). Anaerobic plate counts remained constant from March through December, 1973, ranging from 2.4 X 10(6) to 5.7 X 10(6) organisms/g (dry weight) of sediment. The isolatable bacteria represented a small percentage of the total microbial community, which was shown by direct microscopic counts to be 2.0 X 10'' organisms/g (dry weight) of sediment during June and July. Bacteria of the genus Clostridium dominated the isolates obtained, accounting for 71.8% of the 960 isolates examined. A single species, Clostridium bifermentens, comprised 47.7% of the total. Additional bacterial groups and the percentage in which they were isolated included: Streptococcus sp. (10.8%), unidentified curved rods (9.5%y, gram-positive nonsporing rods (5.6%), and motile gram-negative rods (1.9%). Temperature growth studies demonstrated the ability of all the isolates to grow at in situ sediment temperatures. Gas-liqid radiochromatography was used to determine the soluble metabolic end products from [U-14C]glucose and a U-14C-labeled amino acid mixture by representative sedimentary clostridial isolates and by natural sediment microbial communities. At in situ temperatures the natural sediment microflora produced soluble fermentative end products characteristic of those elaborated by the clostridial isolates tested. These results are considered strong presumptive evidence that clostridia are actively metabolizing in the sediments of Wintergreen Lake.

  14. Heterotrophic utilisation of biochemical compounds in Antarctic waters

    NASA Astrophysics Data System (ADS)

    Bölter, M.; Dawson, R.

    The heterotrophic utilisation of amino acids and carbohydrates (mono- and disaccharides) was investigated November-December 1980 on water samples taken from the Falkland Islands to the ice-edge of the Weddell Sea and Bransfield Strait. The uptake of 14C-labelled compounds and their respiration was measured with consideration of the natural concentration of the substrates which were measured directly by high performance liquid chromatography with fluoresencent detection. All incubations were carried out at in situ temperatures with trace amounts of labelled compounds without kinetic approach. The results show wide variations in microbial activity and actual substrate concentration which may be related to the physiological state and biomass of phytoplankton standing stock, dominated by Phaeocystis sp. and Thalassiosira sp. Microbial activities and biomass production were found to be comparable with others areas, e.g. the Baltic Sea. The composition of the dissolved and particulate matter in terms of amino acids, proteins, sugars and polysaccharides show many differences to other ecosystems. High levels of bound amino acids (dissolved proteins) often exceeding mg levels were found, particularly in waters with high chlorophyll contents (up to 30 μg·1 -1) where the plankton populations' physiological state was poor. Analysis of filtered particulate matter after water extraction and exhaustive hydrolysis showed that healthy plankton cells produced large quantities of high energy nitrogen compounds centred around glutamine and its degradation products. These products could be found in the free-pool of amino acids, only traces following the breakdown of planktonic organisms. A storage of proteinaceous matter seems to be characteristics feature of the Antarctic ecosystem.

  15. Pathogenic Leptospira interrogans exoproteins are primarily involved in heterotrophic processes.

    PubMed

    Eshghi, Azad; Pappalardo, Elisa; Hester, Svenja; Thomas, Benjamin; Pretre, Gabriela; Picardeau, Mathieu

    2015-08-01

    Leptospirosis is a life-threatening and emerging zoonotic disease with a worldwide annual occurrence of more than 1 million cases. Leptospirosis is caused by spirochetes belonging to the genus Leptospira. The mechanisms of disease manifestation in the host remain elusive, and the roles of leptospiral exoproteins in these processes have yet to be determined. Our aim in this study was to assess the composition and quantity of exoproteins of pathogenic Leptospira interrogans and to construe how these proteins contribute to disease pathogenesis. Label-free quantitative mass spectrometry of proteins obtained from Leptospira spirochetes cultured in vitro under conditions mimicking infection identified 325 exoproteins. The majority of these proteins are conserved in the nonpathogenic species Leptospira biflexa, and proteins involved in metabolism and energy-generating functions were overrepresented and displayed the highest relative abundance in culture supernatants. Conversely, proteins of unknown function, which represent the majority of pathogen-specific proteins (presumably involved in virulence mechanisms), were underrepresented. Characterization of various L. interrogans exoprotein mutants in the animal infection model revealed host mortality rates similar to those of hosts infected with wild-type L. interrogans. Collectively, these results indicate that pathogenic Leptospira exoproteins primarily function in heterotrophic processes (the processes by which organisms utilize organic substances as nutrient sources) to maintain the saprophytic lifestyle rather than the virulence of the bacteria. The underrepresentation of proteins homologous to known virulence factors, such as toxins and effectors in the exoproteome, also suggests that disease manifesting from Leptospira infection is likely caused by a combination of the primary and potentially moonlight functioning of exoproteins.

  16. Pathogenic Leptospira interrogans Exoproteins Are Primarily Involved in Heterotrophic Processes

    PubMed Central

    Eshghi, Azad; Pappalardo, Elisa; Hester, Svenja; Thomas, Benjamin; Pretre, Gabriela

    2015-01-01

    Leptospirosis is a life-threatening and emerging zoonotic disease with a worldwide annual occurrence of more than 1 million cases. Leptospirosis is caused by spirochetes belonging to the genus Leptospira. The mechanisms of disease manifestation in the host remain elusive, and the roles of leptospiral exoproteins in these processes have yet to be determined. Our aim in this study was to assess the composition and quantity of exoproteins of pathogenic Leptospira interrogans and to construe how these proteins contribute to disease pathogenesis. Label-free quantitative mass spectrometry of proteins obtained from Leptospira spirochetes cultured in vitro under conditions mimicking infection identified 325 exoproteins. The majority of these proteins are conserved in the nonpathogenic species Leptospira biflexa, and proteins involved in metabolism and energy-generating functions were overrepresented and displayed the highest relative abundance in culture supernatants. Conversely, proteins of unknown function, which represent the majority of pathogen-specific proteins (presumably involved in virulence mechanisms), were underrepresented. Characterization of various L. interrogans exoprotein mutants in the animal infection model revealed host mortality rates similar to those of hosts infected with wild-type L. interrogans. Collectively, these results indicate that pathogenic Leptospira exoproteins primarily function in heterotrophic processes (the processes by which organisms utilize organic substances as nutrient sources) to maintain the saprophytic lifestyle rather than the virulence of the bacteria. The underrepresentation of proteins homologous to known virulence factors, such as toxins and effectors in the exoproteome, also suggests that disease manifesting from Leptospira infection is likely caused by a combination of the primary and potentially moonlight functioning of exoproteins. PMID:25987703

  17. Bacterial Diversity in a Nonsaline Alkaline Environment: Heterotrophic Aerobic Populations

    PubMed Central

    Tiago, Igor; Chung, Ana Paula; Veríssimo, António

    2004-01-01

    Heterotrophic populations were isolated and characterized from an alkaline groundwater environment generated by active serpentinization, which results in a Ca(OH)2-enriched, extremely diluted groundwater with pH 11.4. One hundred eighty-five strains were isolated in different media at different pH values during two sampling periods. To assess the degree of diversity present in the environment and to select representative strains for further characterization of the populations, we screened the isolates by using random amplified polymorphic DNA-PCR profiles and grouped them based on similarities determined by fatty acid methyl ester analysis. Phenotypic characterization, determinations of G+C content, phylogenetic analyses by direct sequencing of 16S rRNA genes, and determinations of pH tolerance were performed with the selected isolates. Although 38 different populations were identified and characterized, the vast majority of the isolates were gram positive with high G+C contents and were affiliated with three distinct groups, namely, strains closely related to the species Dietzia natrolimnae (32% of the isolates), to Frigoribacterium/Clavibacter lineages (29% of the isolates), and to the type strain of Microbacterium kitamiense (20% of the isolates). Other isolates were phylogenetically related to strains of the genera Agrococcus, Leifsonia, Kytococcus, Janibacter, Kocuria, Rothia, Nesterenkonia, Citrococcus, Micrococcus, Actinomyces, Rhodococcus, Bacillus, and Staphylococcus. Only five isolates were gram negative: one was related to the Sphingobacteria lineage and the other four were related to the α-Proteobacteria lineage. Despite the pH of the environment, the vast majority of the populations were alkali tolerant, and only two strains were able to grow at pH 11. PMID:15574939

  18. Grazing rates and functional diversity of uncultured heterotrophic flagellates.

    PubMed

    Massana, Ramon; Unrein, Fernando; Rodríguez-Martínez, Raquel; Forn, Irene; Lefort, Thomas; Pinhassi, Jarone; Not, Fabrice

    2009-05-01

    Aquatic assemblages of heterotrophic protists are very diverse and formed primarily by organisms that remain uncultured. Thus, a critical issue is assigning a functional role to this unknown biota. Here we measured grazing rates of uncultured protists in natural assemblages (detected by fluorescent in situ hybridization (FISH)), and investigated their prey preference over several bacterial tracers in short-term ingestion experiments. These included fluorescently labeled bacteria (FLB) and two strains of the Roseobacter lineage and the family Flavobacteriaceae, of various cell sizes, which were offered alive and detected by catalyzed reporter deposition-FISH after the ingestion. We obtained grazing rates of the globally distributed and uncultured marine stramenopiles groups 4 and 1 (MAST-4 and MAST-1C) flagellates. Using FLB, the grazing rate of MAST-4 was somewhat lower than whole community rates, consistent with its small size. MAST-4 preferred live bacteria, and clearance rates with these tracers were up to 2 nl per predator per h. On the other hand, grazing rates of MAST-1C differed strongly depending on the tracer prey used, and these differences could not be explained by cell viability. Highest rates were obtained using FLB whereas the flavobacteria strain was hardly ingested. Possible explanations would be that the small flavobacteria cells were outside the effective size range of edible prey, or that MAST-1C selects against this particular strain. Our original dual FISH protocol applied to grazing experiments reveals important functional differences between distinct uncultured protists and offers the possibility to disentangle the complexity of microbial food webs.

  19. Microorganisms in subterranean acidic waters within Europe's deepest metal mine.

    PubMed

    Kay, Catherine M; Haanela, Anu; Johnson, D Barrie

    2014-11-01

    The Pyhäsalmi mine, central Finland, has operated as a deep metal mine since 1967. It currently reaches a depth of almost 1500 m, making it the deepest mining operation in Europe. Around 900,000 m(3) of metal-rich, extremely acidic water are pumped out of the mine each year. The near constant air temperature of ∼ 24 °C together with exposure of sulfidic rock surfaces to air and water, have created an environment that is highly suitable for colonization by acidophilic mineral-oxidizing microorganisms. Using a combined cultivation-dependent and molecular approach, indigenous bacteria in waters at two depths within the mine, and of an acid streamer sample were identified and isolated. Iron-oxidizing chemolithotrophs (Acidithiobacillus and Leptospirillum spp., and "Ferrovum myxofaciens" were the most abundant bacteria in mine water samples, whereas the acid streamer community contained a greater proportion of heterotrophic acidophiles (Ferrimicrobium acidiphilum and a gammaproteobacterium related to Metallibacterium scheffleri). The most abundant isolates obtained from both water and streamer samples were all strains of Acidithiobacillus Group IV, a proposed separate species of iron-oxidizing acidithiobacilli that has not yet been classified as such. Archaea were also detected in water and streamer samples using molecular methods, but most were not identified and no isolates were obtained.

  20. Stable Isotope Ratios and the Forensic Analysis of Microorganisms

    SciTech Connect

    Kreuzer-Martin, Helen W.; Jarman, Kristin H.

    2007-06-01

    In the aftermath of the anthrax letters of 2001, researchers have been exploring various analytical signatures for the purpose of characterizing the production environment of microorganisms. One such signature is stable isotope ratios, which in heterotrophs are a function of nutrient and water sources. Here we discuss the use of stable isotope ratios in microbe forensics, using as a database the carbon, nitrogen, oxygen and hydrogen stable isotope ratios of 247 separate cultures of B. subtilis 6051 spores produced on a total of 32 different culture media. In the context of using stable isotope ratios as a signature for sample matching, we present an analysis of variation between individual samples, between cultures produced in tandem, and between cultures produced in the same medium but at different times. Additionally, we correlate the stable isotope ratios of carbon, nitrogen, oxygen, and hydrogen for growth medium nutrients or water with those of spores and show examples of how these relationships can be used to exclude nutrient or water samples as possible growth substrates for specific cultures.

  1. Biochemical Effects of Technetium-99-Pertechnetate on Microorganisms 1

    PubMed Central

    Gearing, Patrick; Van Baalen, Chase; Parker, Patrick L.

    1975-01-01

    The biochemical effects of technetium-99 as pertechnetate (TcO4−) were investigated in a variety of microorganisms (a nonsulfur purple bacterium, five blue-green algae, a protozoan, a diatom, two heterotrophic bacteria, a red alga and two green algae). Sensitivity to pertechnetate as measured by growth ranged from marked inhibition at 1 μg Tc/ml (nonsulfur purple bacterium) to no effect at 600 μg Tc ml (both green algae). No correlation between organism type and growth susceptibility to pertechnetate was apparent. The blue-green alga, Agmenellum quadruplicatum strain PR-6, bound technetium-99 to a level of 3 μg/mg dry weight cells (from medium containing 1.5 mm pertechnetate) in the light, but little or none in the dark; cell death occurred only with uptake. Addition of TcO4− to the medium caused a rapid but temporary increase in ATP levels of PR-6 (in the light only) and Tetrahymena pyriformis strain WH14. Respiration of organisms WH14 and Bacillus subtilis and photosynthesis of organism PR-6 were immediately slowed by the introduction of pertechnetate. Technetium as pertechnetate has a possible biochemical effect on cells, unrelated to its radioactivity or to a general oxidation effect. PMID:16659059

  2. Drug resistance in eukaryotic microorganisms.

    PubMed

    Fairlamb, Alan H; Gow, Neil A R; Matthews, Keith R; Waters, Andrew P

    2016-06-24

    Eukaryotic microbial pathogens are major contributors to illness and death globally. Although much of their impact can be controlled by drug therapy as with prokaryotic microorganisms, the emergence of drug resistance has threatened these treatment efforts. Here, we discuss the challenges posed by eukaryotic microbial pathogens and how these are similar to, or differ from, the challenges of prokaryotic antibiotic resistance. The therapies used for several major eukaryotic microorganisms are then detailed, and the mechanisms that they have evolved to overcome these therapies are described. The rapid emergence of resistance and the restricted pipeline of new drug therapies pose considerable risks to global health and are particularly acute in the developing world. Nonetheless, we detail how the integration of new technology, biological understanding, epidemiology and evolutionary analysis can help sustain existing therapies, anticipate the emergence of resistance or optimize the deployment of new therapies.

  3. Drug resistance in eukaryotic microorganisms.

    PubMed

    Fairlamb, Alan H; Gow, Neil A R; Matthews, Keith R; Waters, Andrew P

    2016-01-01

    Eukaryotic microbial pathogens are major contributors to illness and death globally. Although much of their impact can be controlled by drug therapy as with prokaryotic microorganisms, the emergence of drug resistance has threatened these treatment efforts. Here, we discuss the challenges posed by eukaryotic microbial pathogens and how these are similar to, or differ from, the challenges of prokaryotic antibiotic resistance. The therapies used for several major eukaryotic microorganisms are then detailed, and the mechanisms that they have evolved to overcome these therapies are described. The rapid emergence of resistance and the restricted pipeline of new drug therapies pose considerable risks to global health and are particularly acute in the developing world. Nonetheless, we detail how the integration of new technology, biological understanding, epidemiology and evolutionary analysis can help sustain existing therapies, anticipate the emergence of resistance or optimize the deployment of new therapies. PMID:27572976

  4. Phosphate Biomineralization of Cambrian Microorganisms

    NASA Technical Reports Server (NTRS)

    McKay, David S.; Rozanov, Alexei Yu.; Hoover, Richard B.; Westall, Frances

    1998-01-01

    As part of a long term study of biological markers (biomarkers), we are documenting a variety of features which reflect the previous presence of living organisms. As we study meteorites and samples returned from Mars, our main clue to recognizing possible microbial material may be the presence of biomarkers rather than the organisms themselves. One class of biomarkers consists of biominerals which have either been precipitated directly by microorganisms, or whose precipitation has been influenced by the organisms. Such microbe-mediated mineral formation may include important clues to the size, shape, and environment of the microorganisms. The process of fossilization or mineralization can cause major changes in morphologies and textures of the original organisms. The study of fossilized terrestrial organisms can help provide insight into the interpretation of mineral biomarkers. This paper describes the results of investigations of microfossils in Cambrian phosphate-rich rocks (phosphorites) that were found in Khubsugul, Northern Mongolia.

  5. [Redox-sensors of microorganisms].

    PubMed

    Lushchak, V I

    2008-01-01

    This review summarizes available literature data on the existence and operation of redox sensors of microorganisms. It is partially focused on the activation by hyrdrogen peroxide OxyR protein and by superoxide anion SoxR protein in bacteria Escherichia coli and the activation by hyrdrogen peroxide and superoxide anion of Orp1-Yap1 protein system in yeast Saccharomyces cerevisiae. The similarities and peculiarities of redox signal sensing in pro- and eukaryotes have been discussed. PMID:19140447

  6. Phylogenetic relationships among subsurface microorganisms

    SciTech Connect

    Nierzwicki-Bauer, S.A.

    1991-01-01

    This report summarizes the progress made from 6/90--3/91 toward completion of our project, Phylogenetic Relationships among subsurface microorganisms. 16S rRNA was sequenced, and based on the sequence the SMCC isolates were assigned to preliminary groups. Microorganisms were obtained at various depths at the Savannah River Site, including the Surface (0 m), Congaree (91 m), and Middendorf (244 m, 259 m, 265 m). Sequence data from four isolates from the Congaree formation indicate these microorganisms can be divided into Pseudomonas spp. or Acinetobacter spp. Three 16S rRNA probes were synthesized based on sequence data. The synthesized probes were tested through in situ hybridization. Optimal conditions for in situ hybridization were determined. Because stability of RNA-DNA hybrids is dependent on hybridization stringency, related organisms can be differentiated using a single probe under different strigencies. The results of these hybridizations agree with results obtained by Balkwill and Reeves using restriction fragment length polymorphism analysis. The RNA content of a cell reflects its metabolic state. Cells which are starved for four days are not detectable with the homologous 16S rRNA probe. However, within 15 minutes of refeeding, detectable rRNA appeared. This suggests that organisms which are undetectable in environmental samples due to starvation may be detectable after addition of nutrients. Stepwise addition of specific nutrients could indicate which nutrients are rate limiting for growth. Preliminary experiments with soil samples from the Hanford Site indicate indigenous microorganisms can be detected by oligionucleotide probes. Further, using multiple probes based on universal sequences increases the number of organisms detected. Double label experiments, using a rhodamine-labelled oligionucleotide probe with free coumarin succinimidyl ester will allow simultaneous detection of total bacteria and specific 16S rRNA containing bacteria. 4 tabs. (MHB)

  7. Microorganism Utilization for Synthetic Milk

    NASA Technical Reports Server (NTRS)

    Morford, Megan A.; Khodadad, Christina L.; Caro, Janicce I.; Spencer, LaShelle E.; Richards, Jeffery T.; Strayer, Richard F.; Birmele, Michele N.; Wheeler, Raymond M.

    2014-01-01

    A desired architecture for long duration spaceflight, like aboard the International Space Station or for future missions to Mars, is to provide a supply of fresh food crops for the astronauts. However, some crops can create a high proportion of inedible plant waste. The main goal of the Synthetic Biology project, Cow in a Column, was to produce the components of milk (sugar, lipid, protein) from inedible plant waste by utilizing microorganisms (fungi, yeast, bacteria). Of particular interest was utilizing the valuable polysaccharide, cellulose, found in plant waste, to naturally fuel-through microorganism cellular metabolism- the creation of sugar (glucose), lipid (milk fat), and protein (casein) in order to produce a synthetic edible food product. Environmental conditions such as pH, temperature, carbon source, aeration, and choice microorganisms were optimized in the laboratory and the desired end-products, sugars and lipids, were analyzed. Trichoderma reesei, a known cellulolytic fungus, was utilized to drive the production of glucose, with the intent that the produced glucose would serve as the carbon source for milk fat production and be a substitute for the milk sugar lactose. Lipid production would be carried out by Rhodosporidium toruloides, yeast known to accumulate those lipids that are typically found in milk fat. Results showed that glucose and total lipid content were below what was expected during this phase of experimentation. In addition, individual analysis of six fatty acids revealed that the percentage of each fatty acid was lower than naturally produced bovine milk. Overall, this research indicates that microorganisms could be utilized to breakdown inedible solid waste to produce useable products. For future work, the production of the casein protein for milk would require the development of a genetically modified organism, which was beyond the scope of the original project. Additional trials would be needed to further refine the required

  8. Planetary protection Approaching uncultivable microorganisms

    NASA Astrophysics Data System (ADS)

    Nellen, J.; Rettberg, P.; Horneck, G.; Streit, W. R.

    2006-01-01

    With ESA's MiDiv project [ Rettberg, P., Fritze, D., Verbarg, S., Nellen, J., Horneck, G., Stackebrandt, E., Kminek, G. Final report ESA project MiDiv, ESA contract number 17538/03/NL/VS] the exobiology group at the German Aerospace Centre (DLR) in Cologne started to investigate the microbial diversity found on spacecrafts and in assembly halls used by Europe [ Rettberg, P., Nellen, J., Horneck, G., Fritze, D., Verbarg, S., Stackebrandt, E., Kminek, G. Determination of the microbial diversity of spacecraft assembly facilities: first results of the ESA project MiDiv. Adv. Space Res., 2005]. So far this examination was limited to cultivable microorganisms, probably excluding the majority of organisms present. To approach the microbial diversity of uncultivable microorganisms, new methods, have to be implemented into the analysing process. Therefore, we describe in this paper the adaptation of an existing protocol (surface sampling with swabs) to be used with a method based on the detection of DNA-fragments by polymerase chain reaction (PCR). Our data indicate that it is feasible to adapt the standardized sample taking process to be used with the PCR-method. While using a classical swabbing/cultivation approach for the detection of microorganisms on a surface, two impairing factors have to be accounted for. First, not all bacteria present on a surface will be taken up by the swab and second, not all the bacteria taken up will be released again from the swab. This will lead to a diminished overall estimation of the microorganisms present on a surface. Our studies further suggested that the estimated data had to be corrected by a factor of 2-3 to correspond with the actual numbers of spores spotted.

  9. Enhanced lipid accumulation of photoautotrophic microalgae by high-dose CO2 mimics a heterotrophic characterization.

    PubMed

    Sun, Zhilan; Dou, Xiao; Wu, Jun; He, Bing; Wang, Yuancong; Chen, Yi-Feng

    2016-01-01

    Microalgae possess higher photosynthetic efficiency and accumulate more neutral lipids when supplied with high-dose CO2. However, the nature of lipid accumulation under conditions of elevated CO2 has not been fully elucidated so far. We now revealed that the enhanced lipid accumulation of Chlorella in high-dose CO2 was as efficient as under heterotrophic conditions and this may be attributed to the driving of enlarged carbon source. Both photoautotrophic and heterotrophic cultures were established by using Chlorella sorokiniana CS-1. A series of changes in the carbon fixation, lipid accumulation, energy conversion, and carbon-lipid conversion under high-dose CO2 (1-10%) treatment were characterized subsequently. The daily carbon fixation rate of C. sorokiniana LS-2 in 10% CO2 aeration was significantly increased compared with air CO2. Correspondingly, double oil content (28%) was observed in 10% CO2 aeration, close to 32.3% produced under heterotrophic conditions. In addition, with 10% CO2 aeration, the overall energy yield (Ψ) in Chlorella reached 12.4 from 7.3% (with air aeration) because of the enhanced daily carbon fixation rates. This treatment also improved the energetic lipid yield (Ylipid/Es) with 4.7-fold, tending to the heterotrophic parameters. More significantly, 2.2 times of carbon-lipid conversion efficiency (ηClipid/Ctotal, 42.4%) was observed in 10% CO2 aeration, towards to 53.7% in heterotrophic cultures, suggesting that more fixed carbon might flow into lipid synthesis under both 10% CO2 aeration and heterotrophic conditions. Taken together, all our evidence showed that 10% CO2 may push photoautotrophic Chlorella to display heterotrophic-like efficiency at least in lipid production. It might bring us an efficient model of lipid production based on microalgal cells with high-dose CO2, which is essential to sustain biodiesel production at large scales. PMID:26712624

  10. Predatory Microorganisms Would Help Reclaim Water

    NASA Technical Reports Server (NTRS)

    Benjaminson, Morris A.; Lehrer, Stanley

    1995-01-01

    Wastewater-reclamation systems of proposed type use predatory, nonpathogenic microorganisms to consume pathogenic microorganisms. Unlike some other wastewater-reclamation systems, these systems do not require use of toxic chemicals, intense heat, or ionizing radiation (conductivity rays or ultraviolet) to destroy microorganisms.

  11. 40 CFR 725.420 - Recipient microorganisms.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Recipient microorganisms. 725.420 Section 725.420 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS General Exemptions for New Microorganisms § 725.420 Recipient...

  12. 40 CFR 725.85 - Microorganism identity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Microorganism identity. 725.85 Section... to Information § 725.85 Microorganism identity. (a) Claims applicable to the period prior to... specific microorganism identity at the time of submission of the information. This claim will apply only...

  13. 40 CFR 725.85 - Microorganism identity.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Microorganism identity. 725.85 Section... to Information § 725.85 Microorganism identity. (a) Claims applicable to the period prior to... specific microorganism identity at the time of submission of the information. This claim will apply only...

  14. 40 CFR 725.85 - Microorganism identity.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Microorganism identity. 725.85 Section... to Information § 725.85 Microorganism identity. (a) Claims applicable to the period prior to... specific microorganism identity at the time of submission of the information. This claim will apply only...

  15. 40 CFR 725.85 - Microorganism identity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Microorganism identity. 725.85 Section... ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS Confidentiality and Public Access to Information § 725.85 Microorganism identity. (a) Claims applicable to the period prior...

  16. Heterotrophic plate count methodology in the United States.

    PubMed

    Reasoner, Donald J

    2004-05-01

    In the United States (US), the history of bacterial plate counting (BPC) methods used for water can be traced largely through Standard Methods for the Examination of Water and Wastewater (Standard Methods). The bacterial count method has evolved from the original Standard Methods (1st edition, 1905) plate count which used nutrient gelatin and incubation at 20 degrees C for 48 h, to the HPC method options in the latest edition of Standard Methods that provide greater flexibility of application, depending on the data needs of the water analyst. The use of agar-agar as a gelling agent, replacing gelatin, allowed the use of higher incubation temperatures and resulted in the "body temperature count" (37 degrees C) found in the 3rd through the 8th edition of Standard Methods. The change from 37 degrees C incubation to 35+/-0.5 degrees C accommodated laboratories that did both milk and water analyses. By using a single temperature, fewer incubators were needed. The term "standard plate count" (SPC) first appeared in 1960 (11th edition) along with plate count agar. Incubation at 20 degrees C for the plate count was dropped from the 13th to 15th editions and few changes were made in the SPC method from the 11th edition through the 13th editions. Plate count analysis of bottled waters was included in the 14th edition (1975), calling for incubation at 35+/-0.5 degrees C for 72+/-4 h. Perhaps the most significant changes in plate count methods occurred with the 16th edition (1985). The term heterotrophic plate count replaced the standard plate count, and the spread plate (SP) and membrane filter (MF) methods were added along with new media for pour and spread plates (R2A agar and NWRI agar, both low nutrient) and for the membrane filter method (mHPC medium). The use of low nutrient media, lower incubation temperature, and longer incubation times, results in higher plate count results for most water samples. The options currently available, including low and high nutrient media

  17. A combined physiological and proteomic approach to reveal lactic-acid-induced alterations in Lactobacillus casei Zhang and its mutant with enhanced lactic acid tolerance.

    PubMed

    Wu, Chongde; Zhang, Juan; Chen, Wei; Wang, Miao; Du, Guocheng; Chen, Jian

    2012-01-01

    Lactobacillus casei has traditionally been recognized as a probiotic and frequently used as an adjunct culture in fermented dairy products, where acid stress is an environmental condition commonly encountered. In the present study, we carried out a comparative physiological and proteomic study to investigate lactic-acid-induced alterations in Lactobacillus casei Zhang (WT) and its acid-resistant mutant. Analysis of the physiological data showed that the mutant exhibited 33.8% higher glucose phosphoenolpyruvate:sugar phosphotransferase system activity and lower glycolytic pH compared with the WT under acidic conditions. In addition, significant differences were detected in both cells during acid stress between intracellular physiological state, including intracellular pH, H(+)-ATPase activity, and intracellular ATP pool. Comparison of the proteomic data based on 2D-DIGE and i-TRAQ indicated that acid stress invoked a global change in both strains. The mutant protected the cells against acid damage by regulating the expression of key proteins involved in cellular metabolism, DNA replication, RNA synthesis, translation, and some chaperones. Proteome results were validated by Lactobacillus casei displaying higher intracellular aspartate and arginine levels, and the survival at pH 3.3 was improved 1.36- and 2.10-fold by the addition of 50-mM aspartate and arginine, respectively. To our knowledge, this is the first demonstration that aspartate may be involved in acid tolerance in Lactobacillus casei. Results presented here may help us understand acid resistance mechanisms and help formulate new strategies to enhance the industrial applications of this species. PMID:22159611

  18. Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms.

    PubMed

    Silva-Bedoya, Lina Marcela; Sánchez-Pinzón, María Solange; Cadavid-Restrepo, Gloria Ester; Moreno-Herrera, Claudia Ximena

    2016-11-01

    The operation of wastewater treatment technologies depends on a combination of physical, chemical and biological factors. Microorganisms present in wastewater treatment plants play essential roles in the degradation and removal of organic waste and xenobiotic pollutants. Several microorganisms have been used in complementary treatments to process effluents rich in fats and oils. Microbial lipases have received significant industrial attention because of their stability, broad substrate specificity, high yields, and regular supply, as well as the fact that the microorganisms producing them grow rapidly on inexpensive media. In Colombia, bacterial community studies have focused on populations of cultivable nitrifying, heterotrophic and nitrogen-fixing bacteria present in constructed wetlands. In this study, culture-dependent methods, culture-independent methods (TTGE, RISA) and enzymatic methods were used to estimate bacterial diversity, to monitor temporal and spatial changes in bacterial communities, and to screen microorganisms that presented lipolytic activity. The dominant microorganisms in the Wastewater Treatment Plant (WWTP) examined in this study belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. The enzymatic studies performed indicated that five bacterial isolates and three fungal isolates possessed the ability to degrade lipids; additionally, the Serratia, Kosakonia and Mucor genera presented lipase-mediated transesterification activity. The implications of these findings in regard to possible applications are discussed later in this paper. Our results indicate that there is a wide diversity of aerobic Gram-negative bacteria inhabiting the different sections of the WWTP, which could indicate its ecological condition, functioning and general efficiency.

  19. Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms.

    PubMed

    Silva-Bedoya, Lina Marcela; Sánchez-Pinzón, María Solange; Cadavid-Restrepo, Gloria Ester; Moreno-Herrera, Claudia Ximena

    2016-11-01

    The operation of wastewater treatment technologies depends on a combination of physical, chemical and biological factors. Microorganisms present in wastewater treatment plants play essential roles in the degradation and removal of organic waste and xenobiotic pollutants. Several microorganisms have been used in complementary treatments to process effluents rich in fats and oils. Microbial lipases have received significant industrial attention because of their stability, broad substrate specificity, high yields, and regular supply, as well as the fact that the microorganisms producing them grow rapidly on inexpensive media. In Colombia, bacterial community studies have focused on populations of cultivable nitrifying, heterotrophic and nitrogen-fixing bacteria present in constructed wetlands. In this study, culture-dependent methods, culture-independent methods (TTGE, RISA) and enzymatic methods were used to estimate bacterial diversity, to monitor temporal and spatial changes in bacterial communities, and to screen microorganisms that presented lipolytic activity. The dominant microorganisms in the Wastewater Treatment Plant (WWTP) examined in this study belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. The enzymatic studies performed indicated that five bacterial isolates and three fungal isolates possessed the ability to degrade lipids; additionally, the Serratia, Kosakonia and Mucor genera presented lipase-mediated transesterification activity. The implications of these findings in regard to possible applications are discussed later in this paper. Our results indicate that there is a wide diversity of aerobic Gram-negative bacteria inhabiting the different sections of the WWTP, which could indicate its ecological condition, functioning and general efficiency. PMID:27664750

  20. Heterotrophic flagellates in the littoral and sublittoral zones of the southeast part of the Pechora Sea

    NASA Astrophysics Data System (ADS)

    Mazei, Yu. A.; Tikhonenkov, D. V.

    2006-05-01

    For the first time, data on the heterotrophic flagellate fauna in the littoral and the sublittoral zones of the southeastern part of the Pechora Sea were obtained. Sixty-six heterotrophic flagellate species were found in the study region: 48 and 42 species were found on the shelf and in the intertidal zone, respectively. The most common species were Cafeteria roenbergensis, Paraphysomonas sp., Ancyromonas sigmoides, Cafeteria minuta, Actinomonas mirabilis, and Spumella sp. The littoral fauna of the heterotrophic flagellates was more peculiar than the sublittoral fauna and equally rich. In the region studied, the community can be divided into two types: (a) the predominantly littoral community characterized by a special composition of the dominant species and by high similarity between its local varieties and (b) the heterogeneous predominantly sublittoral community characterized by a lack of a complex of particular species. The local diversity of the heterotrophic flagellate community was low (on the average, 4.5 species per one sample 1 cm3 in volume). The overall distribution pattern of the flagellates was extremely heterogeneous. The large amount of species that were encountered only once causes a great variability in the species structure from one station to another. The total number of the species monotonously increased with the growth in the number of samples and no manifested saturation of the cumulative curve was reached. This indicates the potentially greater diversity of the heterotrophic flagellate species in the region studied.

  1. Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Dual Energy-Limited Chemostats

    PubMed Central

    Verhagen, Frank J. M.; Laanbroek, Hendrikus J.

    1991-01-01

    The absence of nitrification in soils rich in organic matter has often been reported. Therefore, competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis was studied in the presence of Nitrobacter winogradskyi in continuous cultures at dilution rates of 0.004 and 0.01 h−1. Ammonium limitation of A. globiformis was achieved by increasing the glucose concentration in the reservoir stepwise from 0 to 5 mM while maintaining the ammonium concentration at 2 mM. The numbers of N. europaea and N. winogradskyi cells decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations for both dilution rates. Critical carbon-to-nitrogen ratios of 11.6 and 9.6 were determined for the dilution rates of 0.004 and 0.01 h−1, respectively. Below these critical values, coexistence of the competing species was found in steady-state situations. Although the numbers were strongly reduced, the nitrifying bacteria were not fully outcompeted by the heterotrophic bacteria above the critical carbon-to-nitrogen ratios. Nitrifying bacteria could probably maintain themselves in the system above the critical carbon-to-nitrogen ratios because they are attached to the glass wall of the culture vessels. The numbers of N. europaea decreased more than did those of N. winogradskyi. This was assumed to be due to heterotrophic growth of the latter species on organic substrates excreted by the heterotrophic bacteria. PMID:16348588

  2. Investigation of mixotrophic, heterotrophic, and autotrophic growth of Chlorella vulgaris under agricultural waste medium.

    PubMed

    Mohammad Mirzaie, M A; Kalbasi, M; Mousavi, S M; Ghobadian, B

    2016-01-01

    Growth of Chlorella vulgaris and its lipid production were investigated under autotrophic, heterotrophic, and mixotrophic conditions. Cheap agricultural waste molasses and corn steep liquor from industries were used as carbon and nitrogen sources, respectively. Chlorella vulgaris grew remarkably under this agricultural waste medium, which resulted in a reduction in the final cost of the biodiesel production. Maximum dry weight of 2.62 g L(-1) was obtained in mixotrophic growth with the highest lipid concentration of 0.86 g L(-1). These biomass and lipid concentrations were, respectively, 140% and 170% higher than autotrophic growth and 300% and 1200% higher than heterotrophic growth. In mixotrophic growth, independent or simultaneous occurrence of autotrophic and heterotrophic metabolisms was investigated. The growth of the microalgae was observed to take place first heterotrophically to a minimum substrate concentration with a little fraction in growth under autotrophic metabolism, and then the cells grew more autotrophically. It was found that mixotrophic growth was not a simple combination of heterotrophic and autotrophic growth.

  3. Heterotrophic plate count monitoring of treated drinking water in the UK: a useful operational tool.

    PubMed

    Sartory, David P

    2004-05-01

    The count of general or heterotrophic bacterial populations in treated drinking water in the UK has been undertaken since the 1880s. Counts of heterotrophic bacteria at 22 and 37 degrees C are used widely as part of an overall assessment of treated drinking water quality. There were no legislated standards for water quality in the UK until adoption of the first EU Directive in 1989. The UK has, however, never stipulated numerical standards or guidelines for heterotrophic bacteria, although their enumeration has long been part of the assessment of 'wholesome' water, on which advice regarding microbiological quality was given in a series of documents known as 'Report 71'. The current regulations stipulate only that there should be 'no abnormal change' in numbers normally associated with a given supply. This paper reviews the historical context regarding the enumeration, and interpretation of results, of heterotrophic bacteria from treated drinking water, and information regarding current practices by UK water suppliers. The appropriateness of using heterotrophic bacteria counts as an operational tool or as a health parameter is briefly discussed in the light of the UK experience.

  4. Investigation of mixotrophic, heterotrophic, and autotrophic growth of Chlorella vulgaris under agricultural waste medium.

    PubMed

    Mohammad Mirzaie, M A; Kalbasi, M; Mousavi, S M; Ghobadian, B

    2016-01-01

    Growth of Chlorella vulgaris and its lipid production were investigated under autotrophic, heterotrophic, and mixotrophic conditions. Cheap agricultural waste molasses and corn steep liquor from industries were used as carbon and nitrogen sources, respectively. Chlorella vulgaris grew remarkably under this agricultural waste medium, which resulted in a reduction in the final cost of the biodiesel production. Maximum dry weight of 2.62 g L(-1) was obtained in mixotrophic growth with the highest lipid concentration of 0.86 g L(-1). These biomass and lipid concentrations were, respectively, 140% and 170% higher than autotrophic growth and 300% and 1200% higher than heterotrophic growth. In mixotrophic growth, independent or simultaneous occurrence of autotrophic and heterotrophic metabolisms was investigated. The growth of the microalgae was observed to take place first heterotrophically to a minimum substrate concentration with a little fraction in growth under autotrophic metabolism, and then the cells grew more autotrophically. It was found that mixotrophic growth was not a simple combination of heterotrophic and autotrophic growth. PMID:25807048

  5. Overestimation of heterotrophic bacteria in the Sargasso Sea: direct evidence by flow and imaging cytometry

    NASA Astrophysics Data System (ADS)

    Sieracki, Michael E.; Haugen, Elin M.; Cucci, Terry L.

    1995-08-01

    Accurate measurements of bacterial biomass in the ocean are needed for modeling marine microbial food webs and global biogeochemical cycling. We present direct evidence that previous estimates of heterotrophic bacteria biomass in the oligotrophic ocean are confounded by the presence of the abundant photosynthetic procaryote, Prochlorococcus. The chlorophyll autofluorescence of these photosynthetic bacterial cells is very faint and fades rapidly under epifluorescence microscopy. Detection and enumeration of these cells thus far has almost exclusively been by flow cytometry. Using a cooled, charge-coupled device (CCD) camera we were able to image these cells for direct biovolume measurements. A double-exposed image of DAPI-stained Prochlorococcus cells shows that they are indistinguishable from heterotrophic bacteria in standard slide preparations. At two Sargasso Sea stations Prochlorococcus could cause an overestimation of surface (top 150 m) integrated heterotrophic bacterial biovolume (biomass) of 18 and 22% determined by standard microscope methods. At the subsurface chlorophyll maximum Prochlorococcus was 33 and 43% of the heterotrophic bacterial biovolume (biomass) at these stations. Prochlorococcus cell size increased from 0.05 μm 3 in the surface mixed layer to about 0.2 μm 3 below 100 m, confirming previous interpretations of flow cytometric light scatter measurements. Shifting biomass from the heterotrophic bacteria pool to the primary producer compartment has significant implications for ecosystem structure and trophic transfer in marine food webs.

  6. Incidence of Legionella and heterotrophic bacteria in household rainwater tanks in Azumino, Nagano prefecture, Japan.

    PubMed

    Kobayashi, Michiko; Oana, Kozue; Kawakami, Yoshiyuki

    2014-01-01

    Many administrative agencies in Japan are encouraging installation of household rainwater-storage tanks for more effective use of natural rainwater. Water samples were collected periodically from 43 rainwater tanks from 40 households and tested for the presence of Legionella species and the extent of heterotrophic bacteria in Azumino city, Nagano prefecture, Japan. PCR assays indicated the presence of Legionella spp. in 12 (30%) of the 43 tank water samples. Attempts were made to identify correlations between PCR positive samples, topography, pH, chemical oxygen demand (COD), atmospheric temperature and the numbers of heterotrophic bacteria. Between June and October, 2012, the numbers of heterotrophic bacteria in rainwater tanks and the values of COD positively correlated with the presence of Legionella species. In most of the Legionella-positive cases, heterotrophic bacterial cell counts were >10(4) CFU/mL. Moreover, Legionella species were less frequently detected when the COD value was >5 mg KMnO(4)/L. Therefore, at least in Azumino, Japan between June and October 2012, both heterotrophic bacterial counts and COD values may be considered index parameters for the presence of Legionella cells in rainwater tanks. Much more accumulation of such data is needed to verify the accuracy of these findings.

  7. Phylogenetic constraints on elemental stoichiometry and resource allocation in heterotrophic marine bacteria.

    PubMed

    Zimmerman, Amy E; Allison, Steven D; Martiny, Adam C

    2014-05-01

    The objective of this study was to evaluate the contribution of evolutionary history to variation in the biomass stoichiometry and underlying biochemical allocation patterns of heterotrophic marine bacteria. We hypothesized that phylogeny significantly constrains biochemical allocation strategy and elemental composition among taxa of heterotrophic marine bacteria. Using a 'common-garden' experimental design, we detected significant interspecific variation in stoichiometry, macromolecule allocation and growth rate among 13 strains of marine Proteobacteria. However, this variation was not well explained by 16S rRNA phylogenetic relationships or differences in growth rate. Heterotrophic bacteria likely experience C-limitation when consuming resources in Redfield proportions, which consequently decouples growth rate from allocation to rRNA and biomass P content. Accordingly, overall bacterial C : nutrient ratios (C : P = 77, C : N = 4.9) were lower than Redfield proportions, whereas the average N : P ratio of 17 was consistent with the Redfield ratio. Our results suggest that strain-level diversity is an important driver of variation in the C : N : P ratios of heterotrophic bacterial biomass and that the potential importance of non-nucleic acid pools of P warrants further investigation. Continued work clarifying the range and controls on the stoichiometry of heterotrophic marine bacteria will help improve understanding and predictions of global ocean C, N and P dynamics.

  8. Assessment of Heterotrophic Growth Supported by Soluble Microbial Products in Anammox Biofilm using Multidimensional Modeling

    PubMed Central

    Liu, Yiwen; Sun, Jing; Peng, Lai; Wang, Dongbo; Dai, Xiaohu; Ni, Bing-Jie

    2016-01-01

    Anaerobic ammonium oxidation (anammox) is known to autotrophically convert ammonium to dinitrogen gas with nitrite as the electron acceptor, but little is known about their released microbial products and how these are relative to heterotrophic growth in anammox system. In this work, we applied a mathematical model to assess the heterotrophic growth supported by three key microbial products produced by bacteria in anammox biofilm (utilization associated products (UAP), biomass associated products (BAP), and decay released substrate). Both One-dimensional and two-dimensional numerical biofilm models were developed to describe the development of anammox biofilm as a function of the multiple bacteria–substrate interactions. Model simulations show that UAP of anammox is the main organic carbon source for heterotrophs. Heterotrophs are mainly dominant at the surface of the anammox biofilm with small fraction inside the biofilm. 1-D model is sufficient to describe the main substrate concentrations/fluxes within the anammox biofilm, while the 2-D model can give a more detailed biomass distribution. The heterotrophic growth on UAP is mainly present at the outside of anammox biofilm, their growth on BAP (HetB) are present throughout the biofilm, while the growth on decay released substrate (HetD) is mainly located in the inner layers of the biofilm. PMID:27273460

  9. Assessment of Heterotrophic Growth Supported by Soluble Microbial Products in Anammox Biofilm using Multidimensional Modeling.

    PubMed

    Liu, Yiwen; Sun, Jing; Peng, Lai; Wang, Dongbo; Dai, Xiaohu; Ni, Bing-Jie

    2016-01-01

    Anaerobic ammonium oxidation (anammox) is known to autotrophically convert ammonium to dinitrogen gas with nitrite as the electron acceptor, but little is known about their released microbial products and how these are relative to heterotrophic growth in anammox system. In this work, we applied a mathematical model to assess the heterotrophic growth supported by three key microbial products produced by bacteria in anammox biofilm (utilization associated products (UAP), biomass associated products (BAP), and decay released substrate). Both One-dimensional and two-dimensional numerical biofilm models were developed to describe the development of anammox biofilm as a function of the multiple bacteria-substrate interactions. Model simulations show that UAP of anammox is the main organic carbon source for heterotrophs. Heterotrophs are mainly dominant at the surface of the anammox biofilm with small fraction inside the biofilm. 1-D model is sufficient to describe the main substrate concentrations/fluxes within the anammox biofilm, while the 2-D model can give a more detailed biomass distribution. The heterotrophic growth on UAP is mainly present at the outside of anammox biofilm, their growth on BAP (HetB) are present throughout the biofilm, while the growth on decay released substrate (HetD) is mainly located in the inner layers of the biofilm. PMID:27273460

  10. Purple Sulfur Bacteria Control the Growth of Aerobic Heterotrophic Bacterioplankton in a Meromictic Salt Lake

    PubMed Central

    Overmann, J.; Beatty, J. T.; Hall, K. J.

    1996-01-01

    In meromictic Mahoney Lake, British Columbia, Canada, the heterotrophic bacterial production in the mixolimnion exceeded concomitant primary production by a factor of 7. Bacterial growth rates were correlated neither to primary production nor to the amount of chlorophyll a. Both results indicate an uncoupling of bacteria and phytoplankton. In the chemocline of the lake, an extremely dense population of the purple sulfur bacterium Amoebobacter purpureus is present year round. We investigated whether anoxygenic phototrophs are significant for the growth of aerobic bacterioplankton in the overlaying water. Bacterial growth rates in the mixolimnion were limited by inorganic phosphorus or nitrogen most of the time, and the biomass of heterotrophic bacteria did not increase until, in autumn, 86% of the cells of A. purpureus appeared in the mixolimnion because of their reduced buoyant density. The increase in heterotrophic bacterial biomass, soluble phosphorus concentrations below the detection limit, and an extraordinarily high activity of alkaline phosphatase in the mixolimnion indicate a rapid liberation of organically bound phosphorus from A. purpureus cells accompanied by a simultaneous incorporation into heterotrophic bacterioplankton. High concentrations of allochthonously derived dissolved organic carbon (mean, 60 mg of C(middot)liter(sup-1)) were measured in the lake water. In Mahoney Lake, liberation of phosphorus from upwelling purple sulfur bacteria and degradation of allochthonous dissolved organic carbon as an additional carbon source render heterotrophic bacterial production largely independent of the photosynthesis of phytoplankton. A recycling of inorganic nutrients via phototrophic bacteria also appears to be relevant in other lakes with anoxic bottom waters. PMID:16535399

  11. Heterotrophic free-living and particle-bound bacterial cell size in the river Cauvery and its downstream tributaries.

    PubMed

    Harsha, T S; Yamakanamardi, Sadanand M; Mahadevaswamy, M

    2007-03-01

    This is the first comprehensive study on planktonic heterotrophic bacterial cell size in the river Cauvery and its important tributaries in Karnataka State, India. The initial hypothesis that the mean cell size of planktonic heterotrophic bacteria in the four tributaries are markedly different from each other and also from that in the main river Cauvery was rejected, because all five watercourses showed similar planktonic heterotrophic bacterial cell size. Examination of the correlation between mean heterotrophic bacterial cell size and environmental variables showed four correlations in the river Arkavathy and two in the river Shimsha. Regression analysis revealed that 18%of the variation in mean heterotrophic free-living bacterial cell size was due to biological oxygen demand (BOD)in the river Arkavathy, 11% due to surface water velocity (SWV)in the river Cauvery and 11% due to temperature in the river Kapila. Heterotrophic particle-bound bacterial cell size variation was 28% due to chloride and BOD in the river Arkavathy, 11% due to conductivity in the river Kapila and 8% due to calcium in the river Cauvery. This type of relationship between heterotrophic bacterial cell size and environmental variables suggests that,though the mean heterotrophic bacterial cell size was similar in all the five water courses, different sets of environmental variables apparently control the heterotrophic bacterial cell size in the various water bodies studied in this investigation. The possible cause for this environmental (bottom -up) control is discussed. PMID:17435327

  12. Ocean microbes. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages.

    PubMed

    Ottesen, Elizabeth A; Young, Curtis R; Gifford, Scott M; Eppley, John M; Marin, Roman; Schuster, Stephan C; Scholin, Christopher A; DeLong, Edward F

    2014-07-11

    Oscillating diurnal rhythms of gene transcription, metabolic activity, and behavior are found in all three domains of life. However, diel cycles in naturally occurring heterotrophic bacteria and archaea have rarely been observed. Here, we report time-resolved whole-genome transcriptome profiles of multiple, naturally occurring oceanic bacterial populations sampled in situ over 3 days. As anticipated, the cyanobacterial transcriptome exhibited pronounced diel periodicity. Unexpectedly, several different heterotrophic bacterioplankton groups also displayed diel cycling in many of their gene transcripts. Furthermore, diel oscillations in different heterotrophic bacterial groups suggested population-specific timing of peak transcript expression in a variety of metabolic gene suites. These staggered multispecies waves of diel gene transcription may influence both the tempo and the mode of matter and energy transformation in the sea.

  13. Negative consequences of glacial turbidity for the survival of freshwater planktonic heterotrophic flagellates.

    PubMed

    Sommaruga, Ruben; Kandolf, Georg

    2014-02-17

    Heterotrophic (phagotrophic) flagellates are key components of planktonic food webs in freshwater and marine ecosystems because they are the main consumers of bacteria. Although they are ubiquitous in aquatic ecosystems, they were numerically undetectable in turbid glacier-fed lakes. Here we show that glacial particles had negative effects on the survival and growth of heterotrophic flagellates. The effect of glacial particles was concentration-dependent and was caused by their interference with bacterial uptake rather than by physical damage. These results are the first to reveal why establishment of heterotrophic flagellates populations is hindered in very turbid glacial lakes. Because glaciers are vanishing around the world, recently formed turbid meltwater lakes represent an excellent opportunity to understand the environmental conditions that probably shaped the establishment of lake communities at the end of the last glaciation.

  14. Cellulolytic Microorganisms from Thermal Environments

    SciTech Connect

    Vishnivetskaya, Tatiana A; Raman, Babu; Phelps, Tommy Joe; Podar, Mircea; Elkins, James G

    2012-01-01

    Thermal, anaerobic environments rich in decaying plant material are a potential source of novel cellulolytic bacteria. Samples collected from geothermal aquifers in the Yellowstone National Park (YNP) were used to select for cellulolytic thermophiles. Laboratory enrichments on dilute-acid pretreated plant biomass (switchgrass, Populus), and crystalline cellulose (Avicel) resulted in the isolation of 247 environmental clones. The majority of individual clones were affiliated with the cellulolytic bacteria of phylum Firmicutes, followed by xylanolytic and saccharolytic members of the phylum Dictyoglomi. Among the Firmicutes, the clones were affiliated with the genera Caldicellulosiruptor (54.4%), Caloramator (11.5%), Thermoanaerobacter (8.8%), Thermovenabulum (4.1%), and Clostridium (2.0%). From established anaerobic thermophilic enrichments a total of 81 single strains of the genera Caldicellulosiruptor (57%) and Thermoanaerobacter (43%) were isolated. With continuous flow enrichment on Avicel, increases in the relative abundance of Caloramator sp. was observed over clones detected from the Caldicellulosiruptor. Complex communities of interacting microorganisms bring about cellulose decomposition in nature, therefore using up-to-date approaches may yield novel cellulolytic microorganisms with high activity and a rapid rate of biomass conversion to biofuels.

  15. Start-up and microbial communities of a simultaneous nitrogen removal system for high salinity and high nitrogen organic wastewater via heterotrophic nitrification.

    PubMed

    Chen, Jiahao; Han, Yi; Wang, Yingmu; Gong, Benzhou; Zhou, Jian; Qing, Xiaoxia

    2016-09-01

    In this study, a simultaneous nitrogen removal system for high salinity and high nitrogen organic wastewater was developed in a pressurized biofilm reactor. The result showed that under the air supply rate of 200Lh(-1), salinity of 3.0±0.2%, organic load of 10kgCODm(-3)d(-1) and nitrogen loading of 0.185kgm(-3)d(-1), the reactor started up rapidly and performed stably after 30days operation. Meanwhile, a simultaneous COD and nitrogen removal was achieved in the single-stage reactor, with COD, NH4(+)-N and TN removal efficiency of 97%, 99% and 98%, respectively. Denaturing gradient gel electrophoresis profile demonstrated that simultaneous nitrogen removal could be achieved through heterotrophic nitrification-aerobic denitrification, and the pivotal microorganisms were Flavobacterium phragmitis and Paracoccus denitrificans. The microbial community of salt-tolerant halophilic microorganisms was developed successfully. This study can provide a more efficient and feasible solution to treat high salinity organic wastewater. PMID:27240235

  16. Growth of non-phototrophic microorganisms using solar energy through mineral photocatalysis.

    PubMed

    Lu, Anhuai; Li, Yan; Jin, Song; Wang, Xin; Wu, Xiao-Lei; Zeng, Cuiping; Li, Yan; Ding, Hongrui; Hao, Ruixia; Lv, Ming; Wang, Changqiu; Tang, Yueqin; Dong, Hailiang

    2012-01-01

    Phototrophy and chemotrophy are two dominant modes of microbial metabolism. To date, non-phototrophic microorganisms have been excluded from the solar light-centered phototrophic metabolism. Here we report a pathway that demonstrates a role of light in non-phototrophic microbial activity. In lab simulations, visible light-excited photoelectrons from metal oxide, metal sulfide, and iron oxide stimulated the growth of chemoautotrophic and heterotrophic bacteria. The measured bacterial growth was dependent on light wavelength and intensity, and the growth pattern matched the light absorption spectra of the minerals. The photon-to-biomass conversion efficiency was in the range of 0.13-1.90‰. Similar observations were obtained in a natural soil sample containing both bacteria and semiconducting minerals. Results from this study provide evidence for a newly identified, but possibly long-existing pathway, in which the metabolisms and growth of non-phototrophic bacteria can be stimulated by solar light through photocatalysis of semiconducting minerals.

  17. Effects of biocidal treatments to inhibit the growth of legionellae and other microorganisms in cooling towers.

    PubMed

    Yamamoto, H; Ezaki, T; Ikedo, M; Yabuuchi, E

    1991-01-01

    The effects of biocidal treatments for cooling towers were examined through the use of chemicals and ultraviolet irradiation to inhibit the growth of legionellae and other microorganisms. In the water of cooling towers without continuous biocidal treatments, heterotrophic bacteria and bacterivorous protozoan first appeared, and then legionellae increased up to 10(4) CFU/100 ml. When a UV sterilizer was connected to the cooling tower, the legionellae count was 1/10 or 1/100 of that in the nontreated tower water. In the water of towers supplemented continuously with the biocidal chemicals, legionellae were not found during a 4-month period. The biocidal treatments tested were proved to suppress the increase of legionellae in cooling-tower water, and thus are useful in preventing the outbreak of legionellosis due to inhalation of contaminated aerosol from the cooling tower system.

  18. The effectiveness of a multi-spark electric discharge system in the destruction of microorganisms in domestic and industrial wastewaters.

    PubMed

    Anpilov, A M; Barkhudarov, E M; Christofi, N; Kop'ev, V A; Kossyi, I A; Taktakishvili, M I; Zadiraka, Yu V

    2004-12-01

    The aim of this work was to investigate the effectiveness of a high voltage multi-spark electric discharge, with pulse energy of 1 Joule, in killing microorganisms in wastewater. Wastewater from primary treated effluent arising from domestic and industrial sources was abstracted for continuous pulsed discharge disinfection. The wastewater contained a large mixed population of microorganisms (approximately 10(7) CFU ml(-1) [10(9) CFU 100 ml(-1)] total aerobic heterotrophic bacteria) including vegetative cells and spores. The electrical conductivity of the wastewater ranged from 900-1400 microS cm(-1) and it was shown that a specific energy of 1.25-1.5 J cm(-3) was required to achieve 1 log reduction in bacterial (faecal coliforms/total aerobic heterotrophs) content. This is higher than that previously shown to reduce the population of E. coli in tap water of low conductivity, demonstrating the role of total wastewater constituents, including dissolved and particulate substances, water colour and the presence of microbial spores, in effective disinfection. The system can be engineered to eradicate microbial populations to levels governed by legislation by increasing treatment time or energy input.

  19. Evaluation of aquatic sediment microcosms and their use in assessing possible effects of introduced microorganisms on ecosystem parameters

    SciTech Connect

    Wagner-Doebler, I.; Pipke, R.; Timmis, K.N.; Dwyer, D.F. )

    1992-04-01

    In this paper the authors describe a sediment microcosm system consisting of 20 undisturbed, layered sediment cores with overlying site water which are incubated under identical conditions of temperature, light stirring rate of overlying water, and water exchange rate. Ecosystem parameters (nutrient level, photosynthetic potential, community structure of heterotrophic bacterium thymidine incorporation rate, and oxygen microgradients) of the laboratory microcosms and the source ecosystem were compared and shown to be indistinguishable for the first 2 weeks. The microcosm system described here would thus appear to be a valid model of aquatic sediments for up to 4 weeks; the actual period would depend on the sediment source and incubation temperature. The validated systems were used with Rhine river sediment to assess possible effects on ecosystem parameters of Pseudomonas sp. strain B13 FR1(pFRC20P), a genetically engineered microorganism (GEM) survived in the surface sediment at densities of 5 {times} 10{sup 4} to 5 {times} 10{sup 5}/g (dry weight) for 4 weeks and degraded added chloro- and methylaromatics. The GEM did not measurably influence ecosystem parameters such as photosynthesis, densities of selected heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients. Thus, the microcosm system described here would seem to be useful for the study of the ecology of biodegradation and the fate and effect of microorganisms introduced into the environment.

  20. The remote sensing of microorganisms

    NASA Astrophysics Data System (ADS)

    Bramall, Nathan Earl

    An approach for detecting microbial life in extreme environments, including glacial ice and deep water, using autofluorescence is described. The emission spectra for a variety of microorganisms and common minerals were measured for excitation at 224 nm and it is shown that exciting autofluorescence at 224 nm provides adequate separation between mineral and microbial emission spectra to detect a single microorganism in the glacial ice of Antarctica or on mineral surfaces. The different generations of borehole-logging instruments, dubbed 'biospectral loggers' (BSLs), were designed, built and deployed. The first BSL is a prototype that uses ˜375 nm excitation from UV LEDS and was deployed in the ˜1,000 m deep Siple Dome borehole (January, 2002) and in oligotrophic Lake Tahoe (October, 2002), where microbial NADH, chlorophyll, and dissolved organic matter (DOM) fluorescence was measured. The fluorescence red-shifted with depth, suggesting an increase in of terrestrially-derived DOM with depth, perhaps indicating a benthic source and little recent vertical mixing. The second BSL uses a similar optical geometry as the first, but employs a 224 nm HeAg laser to excite protein fluorescence and was deployed at the SPRESO borehole at the South Pole (January; 2004). It recorded a strong microbial signal corresponding to the time period spanning 1,200 B.P. and 900 B.P., which roughly correlates with major desiccation events in both Patagonia and the Antarctic Dry Valleys, suggesting they may have been aeolian sources of aquatic microorganisms for the South Pole. The third BSL, dubbed the mini-BSL, also uses a 224 nm laser for excitation of protein fluorescence, but its novel optical layout enabled its diameter to be reduced to less than 5.1 cm, allowing it to operate in a borehole produced by a modified JPL 'Gopher' drill[16]. High sensitivity was not sacrificed in the miniaturization process as the mBSL is capable of detecting a single B. megatcrium on a background of iron

  1. Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria

    PubMed Central

    da Silva, Fábio Daniel Florêncio; Lima, Alex Ranieri Jerônimo; Moraes, Pablo Henrique Gonçalves; Siqueira, Andrei Santos; Dall’Agnol, Leonardo Teixeira; Baraúna, Anna Rafaella Ferreira; Martins, Luisa Carício; Oliveira, Karol Guimarães; de Lima, Clayton Pereira Silva; Nunes, Márcio Roberto Teixeira; Vianez-Júnior, João Lídio Silva Gonçalves

    2016-01-01

    Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known. To improve the genomic studies of heterotrophic bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus sp. (cyanobacteria), is presented here. PMID:27198027

  2. Swimming of a Ciliated Microorganism

    NASA Astrophysics Data System (ADS)

    Guo, Hanliang; Kanso, Eva

    2013-11-01

    We propose a 2D model to consider the locomotion of a ciliated microorganism in a viscous fluid. The model consists of a circular body whose boundary is covered by a finite number of cilia. Stokes paradox does not hold due to the self-propelling nature of the organism. Using a regularized Stokeslet method, we determine numerically the time-dependent swimming motion for prescribed kinematics (undulatory beat) of the individual cilium. Phase differences between neighboring cilia result in metachronal waves characteristic of biological cilia. We compare our results based on the discrete cilia approach with the envelope model proposed by JR Blake. We then study the net locomotion as function of the metachronal wave. We find that, for a given geometry and cilia density, there is an optimal wave number (phase difference) for locomotion in terms of velocity of propulsion and efficiency.

  3. Functional Basis of Microorganism Classification

    PubMed Central

    Zhu, Chengsheng; Delmont, Tom O.; Vogel, Timothy M.; Bromberg, Yana

    2015-01-01

    Correctly identifying nearest “neighbors” of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned

  4. Functional Basis of Microorganism Classification.

    PubMed

    Zhu, Chengsheng; Delmont, Tom O; Vogel, Timothy M; Bromberg, Yana

    2015-08-01

    Correctly identifying nearest "neighbors" of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with

  5. Biocorrosion produced by Thiobacillus-like microorganisms.

    PubMed

    López, A I; Marín, I; Amils, R

    1994-01-01

    Biocorrosion can be produced by many different microorganisms through diverse mechanisms. The biocorrosion produced by acidophilic microorganisms of the genus Thiobacillus is based on the production of sulfuric acid and ferric ion from pyrites or related mineral structures, as a result of the chemolithotrophic metabolism of these microorganisms. The products of this aerobic respiration are also powerful oxidant elements, which can produce chemical oxidations of other metallic structures. The Tinto River, a very unusual extremophilic habitat (pH around 2, and high concentration of ferric ion), product of the growth of strict chemolithotrophic microorganisms, is discussed as a model case. PMID:7946115

  6. Biocorrosion produced by Thiobacillus-like microorganisms.

    PubMed

    López, A I; Marín, I; Amils, R

    1994-01-01

    Biocorrosion can be produced by many different microorganisms through diverse mechanisms. The biocorrosion produced by acidophilic microorganisms of the genus Thiobacillus is based on the production of sulfuric acid and ferric ion from pyrites or related mineral structures, as a result of the chemolithotrophic metabolism of these microorganisms. The products of this aerobic respiration are also powerful oxidant elements, which can produce chemical oxidations of other metallic structures. The Tinto River, a very unusual extremophilic habitat (pH around 2, and high concentration of ferric ion), product of the growth of strict chemolithotrophic microorganisms, is discussed as a model case.

  7. Heterotrophic bacteria from an extremely phosphate-poor lake have conditionally reduced phosphorus demand and utilize diverse sources of phosphorus.

    PubMed

    Yao, Mengyin; Elling, Felix J; Jones, CarriAyne; Nomosatryo, Sulung; Long, Christopher P; Crowe, Sean A; Antoniewicz, Maciek R; Hinrichs, Kai-Uwe; Maresca, Julia A

    2016-02-01

    Heterotrophic Proteobacteria and Actinobacteria were isolated from Lake Matano, Indonesia, a stratified, ferruginous (iron-rich), ultra-oligotrophic lake with phosphate concentrations below 50 nM. Here, we describe the growth of eight strains of heterotrophic bacteria on a variety of soluble and insoluble sources of phosphorus. When transferred to medium without added phosphorus (P), the isolates grow slowly, their RNA content falls to as low as 1% of cellular dry weight, and 86-100% of the membrane lipids are replaced with amino- or glycolipids. Similar changes in lipid composition have been observed in marine photoautotrophs and soil heterotrophs, and similar flexibility in phosphorus sources has been demonstrated in marine and soil-dwelling heterotrophs. Our results demonstrate that heterotrophs isolated from this unusual environment alter their macromolecular composition, which allows the organisms to grow efficiently even in their extremely phosphorus-limited environment. PMID:26415900

  8. Genomic Analysis Unravels Reduced Inorganic Sulfur Compound Oxidation of Heterotrophic Acidophilic Acidicaldus sp. Strain DX-1

    PubMed Central

    Liu, Yuanyuan; Yang, Hongying; Zhang, Xian; Xiao, Yunhua; Guo, Xue; Liu, Xueduan

    2016-01-01

    Although reduced inorganic sulfur compound (RISC) oxidation in many chemolithoautotrophic sulfur oxidizers has been investigated in recent years, there is little information about RISC oxidation in heterotrophic acidophiles. In this study, Acidicaldus sp. strain DX-1, a heterotrophic sulfur-oxidizing acidophile, was isolated. Its genome was sequenced and then used for comparative genomics. Furthermore, real-time quantitative PCR was performed to identify the expression of genes involved in the RISC oxidation. Gene encoding thiosulfate: quinone oxidoreductase was present in Acidicaldus sp. strain DX-1, while no candidate genes with significant similarity to tetrathionate hydrolase were found. Additionally, there were genes encoding heterodisulfide reductase complex, which was proposed to play a crucial role in oxidizing cytoplasmic sulfur. Like many heterotrophic sulfur oxidizers, Acidicaldus sp. strain DX-1 had no genes encoding enzymes essential for the direct oxidation of sulfite. An indirect oxidation of sulfite via adenosine-5′-phosphosulfate was proposed in Acidicaldus strain DX-1. However, compared to other closely related bacteria Acidiphilium cryptum and Acidiphilium multivorum, which harbored the genes encoding Sox system, almost all of these genes were not detected in Acidicaldus sp. strain DX-1. This study might provide some references for the future study of RISC oxidation in heterotrophic sulfur-oxidizing acidophiles. PMID:27239474

  9. HETEROTROPHIC PLATE COUNT BACTERIA - WHAT IS THEIR SIGNIFICANCE IN DRINKING WATER?

    EPA Science Inventory

    The possible health significance of heterotrophic plate count (HPC) bacteria, also know in earlier terminology as standard plate count (SPC) bacteria, in drinking water has been debated for decades. While the literature documents the universal occurrence of HPC bacteria in soil, ...

  10. Warming and Acidification Effects on Planktonic Heterotrophic Pico- and Nanoflagellates in a Mesocosm Experiment.

    PubMed

    Moustaka-Gouni, Maria; Kormas, Konstantinos A; Scotti, Marco; Vardaka, Elisabeth; Sommer, Ulrich

    2016-08-01

    We studied the response of the heterotrophic flagellate (HF) community to the combined impact of warming and ocean acidification in a mesocosm experiment with a plankton community from the western Baltic Sea. We performed a quantitative analysis of the response at the level of total biomass and size classes and a semi-quantitative one at the level of individual taxa. Total biomass of HF was significantly lower under higher temperatures while there was no significant effect of CO2. The mean biomass of the picoflagellates did not respond to temperature while the three nanoflagellate size classes (class limits 3, 5, 8, 15μm) responded negatively to warming while not responding to CO2. The taxon-level results indicate that heterotrophic flagellates do not form a homogenous trophic guild, as often assumed in pelagic food web studies. Instead, the heterotrophic flagellates formed a "food web within the food web". There was a pronounced succession of flagellates leading from a dominance of bacterivores and colloidal matter feeders before the phytoplankton bloom to omnivorous feeders preying upon phytoplankton and heterotrophic flagellates during and after the bloom. This complex intraguild predation patterns probably dampened the response to experimental treatments. PMID:27472657

  11. Free-Living Heterotrophic Nitrogen-Fixing Bacteria Isolated from Fuel-Contaminated Antarctic Soils

    PubMed Central

    Eckford, Ruth; Cook, Fred D.; Saul, David; Aislabie, Jackie; Foght, Julia

    2002-01-01

    Five bacterial isolates enriched from fuel-contaminated Antarctic soils fixed nitrogen in the dark heterotrophically and nonsymbiotically. Two isolates utilized jet fuel vapors and volatile hydrocarbons for growth but not in N-deficient medium. Bacteria such as these may contribute to in situ biodegradation of hydrocarbons in Antarctic soils. PMID:12324373

  12. Heterotrophic Bacteria Show Weak Competition for Nitrogen in Mediterranean Coastal Waters (Thau Lagoon) in Autumn.

    PubMed

    Trottet, Aurore; Leboulanger, Christophe; Vidussi, Francesca; Pete, Romain; Bouvy, Marc; Fouilland, Eric

    2016-02-01

    The importance of heterotrophic bacteria relative to phytoplankton in the uptake of ammonium and nitrate was studied in Mediterranean coastal waters (Thau Lagoon) during autumn, when the Mediterranean Sea received the greatest allochthonous nutrient loads. Specific inhibitors and size-fractionation methods were used in combination with isotopic (15)N tracers. NO3 (-) and NH4 (+) uptake was dominated by phytoplankton (60 % on average) during the study period, which included a flood event. Despite lower biomass specific NH4 (+) and NO3 uptake rates, free-living heterotrophic bacteria contributed significantly (>30 %) to total microbial NH4 (+) and NO3 (-) uptake rates in low chlorophyll waters. Under these conditions, heterotrophic bacteria may be responsible for more than 50 % of primary production, using very little freshly produced phytoplankton exudates. In low chlorophyll coastal waters as reported during the present 3-month study, the heterotrophic bacteria seemed to depend to a greater extent on allochthonous N and C substrates than on autochthonous substrates derived from phytoplankton.

  13. The Relationship between Cognitive Functioning Level and Understanding of the Heterotroph Hypothesis.

    ERIC Educational Resources Information Center

    Glass, Lynn W.

    1981-01-01

    Reports results supporting the theoretical rationale that there are certain cognitive skills, including data interpretation, identification of assumptions and hypotheses, and controlling of variables, that appear to be necessary for successful understanding of the heterotroph hypothesis, as presented in the BSCS Blue Version. Implications for…

  14. Impact of Sulfur Starvation in Autotrophic and Heterotrophic Cultures of the Extremophilic Microalga Galdieria phlegrea (Cyanidiophyceae).

    PubMed

    Carfagna, Simona; Bottone, Claudia; Cataletto, Pia Rosa; Petriccione, Milena; Pinto, Gabriele; Salbitani, Giovanna; Vona, Vincenza; Pollio, Antonino; Ciniglia, Claudia

    2016-09-01

    In plants and algae, sulfate assimilation and cysteine synthesis are regulated by sulfur (S) accessibility from the environment. This study reports the effects of S deprivation in autotrophic and heterotrophic cultures of Galdieria phlegrea (Cyanidiophyceae), a unicellular red alga isolated in the Solfatara crater located in Campi Flegrei (Naples, Italy), where H2S is the prevalent form of gaseous S in the fumarolic fluids and S is widespread in the soils near the fumaroles. This is the first report on the effects of S deprivation on a sulfurous microalga that is also able to grow heterotrophically in the dark. The removal of S from the culture medium of illuminated cells caused a decrease in the soluble protein content and a significant decrease in the intracellular levels of glutathione. Cells from heterotrophic cultures of G. phlegrea exhibited high levels of internal proteins and high glutathione content, which did not diminish during S starvation, but rather glutathione significantly increased. The activity of O-acetylserine(thiol)lyase (OASTL), the enzyme synthesizing cysteine, was enhanced under S deprivation in a time-dependent manner in autotrophic but not in heterotrophic cells. Analysis of the transcript abundance of the OASTL gene supports the OASTL activity increase in autotrophic cultures under S deprivation. PMID:27388343

  15. Dissolved Organic Nitrogen Hydrolysis Rates in Axenic Cultures of Aureococcus anophagefferens (Pelagophyceae): Comparison with Heterotrophic Bacteria

    PubMed Central

    Berg, Gry Mine; Repeta, Daniel J.; Laroche, Julie

    2002-01-01

    The marine autotroph Aureococcus anophagefferens (Pelagophyceae) was rendered axenic in order to investigate hydrolysis rates of peptides, chitobiose, acetamide, and urea as indicators of the ability to support growth on dissolved organic nitrogen. Specific rates of hydrolysis varied between 8 and 700% of rates observed in associated heterotrophic marine bacteria. PMID:11772651

  16. Genomic Analysis Unravels Reduced Inorganic Sulfur Compound Oxidation of Heterotrophic Acidophilic Acidicaldus sp. Strain DX-1.

    PubMed

    Liu, Yuanyuan; Yang, Hongying; Zhang, Xian; Xiao, Yunhua; Guo, Xue; Liu, Xueduan

    2016-01-01

    Although reduced inorganic sulfur compound (RISC) oxidation in many chemolithoautotrophic sulfur oxidizers has been investigated in recent years, there is little information about RISC oxidation in heterotrophic acidophiles. In this study, Acidicaldus sp. strain DX-1, a heterotrophic sulfur-oxidizing acidophile, was isolated. Its genome was sequenced and then used for comparative genomics. Furthermore, real-time quantitative PCR was performed to identify the expression of genes involved in the RISC oxidation. Gene encoding thiosulfate: quinone oxidoreductase was present in Acidicaldus sp. strain DX-1, while no candidate genes with significant similarity to tetrathionate hydrolase were found. Additionally, there were genes encoding heterodisulfide reductase complex, which was proposed to play a crucial role in oxidizing cytoplasmic sulfur. Like many heterotrophic sulfur oxidizers, Acidicaldus sp. strain DX-1 had no genes encoding enzymes essential for the direct oxidation of sulfite. An indirect oxidation of sulfite via adenosine-5'-phosphosulfate was proposed in Acidicaldus strain DX-1. However, compared to other closely related bacteria Acidiphilium cryptum and Acidiphilium multivorum, which harbored the genes encoding Sox system, almost all of these genes were not detected in Acidicaldus sp. strain DX-1. This study might provide some references for the future study of RISC oxidation in heterotrophic sulfur-oxidizing acidophiles. PMID:27239474

  17. Enrichment and activity of methanotrophic microorganisms from municipal wastewater sludge.

    PubMed

    Siniscalchi, Luciene Alves Batista; Vale, Isabel Campante; Dell'Isola, Jéssica; Chernicharo, Carlos Augusto; Calabria Araujo, Juliana

    2015-01-01

    In this study, methanotrophic microorganisms were enriched from a municipal wastewater sludge taken from an Upflow Anaerobic Sludge Blanket reactor. The enrichment was performed in a sequencing batch reactor (SBR) with an autotrophic medium containing nitrite and nitrate. The microbial community composition of the inoculum and of the enrichment culture after 100 days of SBR operation was investigated and compared with the help of data obtained from 454 pyrosequencing analyses. The nitrite and nitrate removal efficiencies were 68% and 53%, respectively, probably due to heterotrophic denitrification. Archaeal cells of the anaerobic methanotrophic Archaic (ANME)-I and ANME-II groups were detected by polymerase chain reaction throughout the whole cultivation period. Pyrosequencing analysis showed that community composition was different among the two samples analysed. The dominant phyla found in the inoculum were Synergistestes, Firmicutes and Euryarchaeota, while Planctomycetes, Verrucomicrobia, Chloroflexi and Proteobacteria prevailed in the enriched biomass. The cultivation conditions decreased Methanobacterium abundance from 8% to 1%, and enriched for methanotrophic bacteria such as Methylocaldum, Methylocistis and Methylosinus. Sequences of Methylocaldum sp. accounted for 2.5% of the total reads. The presence and high predominance of Verrucomicrobia in the enriched biomass suggested that other unknown methanotrophic species related to that phylum might also have occurred in the reactor. Anaerobic methane oxidation activity was measured for both samples, and showed that the activity of the enrichment culture was nearly three times higher than the activity of the inoculum. Taken together, these results showed that the inoculum type and cultivation conditions were properly suited for methanotrophic enrichment.

  18. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils.

    PubMed

    Pajares, Silvia; Bohannan, Brendan J M

    2016-01-01

    Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research. PMID:27468277

  19. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils

    PubMed Central

    Pajares, Silvia; Bohannan, Brendan J. M.

    2016-01-01

    Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research. PMID:27468277

  20. Isolation of Phyllosilicate–Iron Redox Cycling Microorganisms from an Illite–Smectite Rich Hydromorphic Soil

    PubMed Central

    Shelobolina, Evgenya; Konishi, Hiromi; Xu, Huifang; Benzine, Jason; Xiong, Mai Yia; Wu, Tao; Blöthe, Marco; Roden, Eric

    2012-01-01

    The biogeochemistry of phyllosilicate–Fe redox cycling was studied in a Phalaris arundinacea (reed canary grass) dominated redoximorphic soil from Shovelers Sink, a small glacial depression near Madison, WI. The clay size fraction of Shovelers Sink soil accounts for 16% of the dry weight of the soil, yet contributes 74% of total Fe. The dominant mineral in the clay size fraction is mixed layer illite–smectite, and in contrast to many other soils and sediments, Fe(III) oxides are present in low abundance. We examined the Fe biogeochemistry of Shovelers Sink soils, estimated the abundance of Fe redox cycling microorganisms, and isolated in pure culture representative phyllosilicate–Fe oxidizing and reducing organisms. The abundance of phyllosilicate–Fe reducing and oxidizing organisms was low compared to culturable aerobic heterotrophs. Both direct isolation and dilution-to-extinction approaches using structural Fe(II) in Bancroft biotite as a Fe(II) source, and O2 as the electron acceptor, resulted in recovery of common rhizosphere organisms including Bradyrhizobium spp. and strains of Cupriavidus necator and Ralstonia solanacearum. In addition to oxidizing biotite and soluble Fe(II) with O2, each of these isolates was able to oxidize Fe(II) in reduced NAu-2 smectite with NO3- as the electron acceptor. Oxidized NAu-2 smectite or amorphous Fe(III) oxide served as electron acceptors for enrichment and isolation of Fe(III)-reducing microorganisms, resulting in recovery of a strain related to Geobacter toluenoxydans. The ability of the recovered microorganisms to cycle phyllosilicate–Fe was verified in an experiment with native Shovelers Sink clay. This study confirms that Fe in the native Shovelers Sink clay is readily available for microbial redox transformation and can be cycled by the Fe(III)-reducing and Fe(II)-oxidizing microorganisms recovered from the soil. PMID:22493596

  1. Source Bioaerosol Concentration and rRNA Gene-Based Identification of Microorganisms Aerosolized at a Flood Irrigation Wastewater Reuse Site

    PubMed Central

    Paez-Rubio, Tania; Viau, Emily; Romero-Hernandez, Socorro; Peccia, Jordan

    2005-01-01

    Reuse of partially treated domestic wastewater for agricultural irrigation is a growing practice in arid regions throughout the world. A field sampling campaign to determine bioaerosol concentration, culturability, and identity at various wind speeds was conducted at a flooded wastewater irrigation site in Mexicali, Baja California, Mexico. Direct fluorescent microscopy measurements for total microorganisms, culture-based assays for heterotrophs and gram-negative enteric bacteria, and small-subunit rRNA gene-based cloning were used for microbial characterizations of aerosols and effluent wastewater samples. Bioaerosol results were divided into two wind speed regimens: (i) below 1.9 m/s, average speed 0.5 m/s, and (ii) above 1.9 m/s, average speed 4.5 m/s. Average air-borne concentration of total microorganisms, culturable heterotrophs, and gram-negative enteric bacteria were, respectively, 1.1, 4.2, and 6.2 orders of magnitude greater during the high-wind-speed regimen. Small-subunit rRNA gene clone libraries processed from samples from air and the irrigation effluent wastewater during a high-wind sampling event indicate that the majority of air clone sequences were more than 98% similar to clone sequences retrieved from the effluent wastewater sample. Overall results indicate that wind is a potential aerosolization mechanism of viable wastewater microorganisms at flood irrigation sites. PMID:15691934

  2. Photosynthetic microorganisms in cold environments

    NASA Astrophysics Data System (ADS)

    Kviderova, Jana; Hajek, Josef; Elster, Josef; Bartak, Milos; Vaczi, Peter; Nedbalova, Linda

    The polar regions are considered as a model of extraterrestrial ecosystems. Depending on the average temperature, temperature variation and water availability, these conditions could be used as a model of Mars or Europa (e.g. (Elster and Benson, 2004). Two cases are presented: 1) Stable temperature and water availability The environment of cryosestic communities, i.e. organisms living in snow, is characterized by very stable temperature; the diurnal variations do not exceed 1 -2 ° C (Kváderová, 2010) and a are not usually exposed to freeze/thaw. Water is not usually limiting since the water content could reach up to 54 % (Nedbalová et al., 2008). The windblown sediments are important a source of nutrient and could provide protection against the excess of radiation. The nutrient concentrations in the snow are low are depleted rapidly when massive algal blooms forms. Such environment could be found near Mars polar caps or in Europa ice cover. The snow algae are the most important primary producers in snow. Their adaptation strategy is dependent on the developmental stages; the motile stages avoid the harsh conditions (e.g. high light) and sessile stages acclimatize to actual conditions. The main genera Chlamydomonas and Chloromonas (both Chlorophyta) are psychrophilic. Their growth optimum temperature is lower than 15 ° C and their growth is inhibited at temperatures above 20 ° C. 2) Unstable temperature and water availability The deglaciated surfaces, inhabited by lichen communities, are typical by variation in temper-ature and moisture. The temperature could range several tens ° C within a short time and the water availability is usually very limited. Due to temperature variation, the lichens are subjected to many freeze/thaw cycles. Such environments could be found in Martian deserts. The lichens are symbotic organisms composed of a mycobiont (heterotrophic fungi) and photo-bionts (algae and/or cyanobacteria). Majority of lichens are dehydrated in the field

  3. Microorganisms detected by enzyme-catalyzed reaction

    NASA Technical Reports Server (NTRS)

    Vango, S. P.; Weetall, H. H.; Weliky, N.

    1966-01-01

    Enzymes detect the presence of microorganisms in soils. The enzyme lysozymi is used to release the enzyme catalase from the microorganisms in a soil sample. The catalase catalyzes the decomposition of added hydrogen peroxide to produce oxygen which is detected manometrically. The partial pressure of the oxygen serves as an index of the samples bacteria content.

  4. Biofouling of marbles by oxygenic photosynthetic microorganisms.

    PubMed

    Karaca, Zeki; Öztürk, Ayten; Çolak, Emel

    2015-08-01

    Phototrophic microorganisms disfigure the surfaces of different types of stone. Stone structure is damaged by the activity of photoautotrophic and other microorganisms. However, to date few, investigations have been undertaken into the relationship between microorganisms and the properties of different types of marble. In this study, biological activity of photoautotrophic microorganisms on three types of marble (Yatagan White, Giallo Anticato and Afyon White) was investigated under laboratory conditions over a short period of time. The three types of marble supported the growth of phototrophic microbial communities on their outer and inner layers, turning their original colour from white to a yellowish green colour. The porosity of the marble types facilitated filamentous microbial growth in the presence of water. Scanning electron microscope analysis revealed the accumulation of aggregates such as small spherical, fibrillar, calcified globular bodies on the inner surfaces of the marbles. This suggests that the microscopic characteristics of particular marble types may stimulate the growth of certain types of microorganisms.

  5. Systems Biology of Industrial Microorganisms

    NASA Astrophysics Data System (ADS)

    Papini, Marta; Salazar, Margarita; Nielsen, Jens

    The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

  6. Hydrogen production by photosynthetic microorganisms

    SciTech Connect

    Akano, T.; Fukatsu, K.; Miyasaka, H. |

    1996-12-31

    Hydrogen is a clean energy alternative to the fossil fuels, the main source of greenhouse gas emissions. We developed a stable system for the conversion of solar energy into hydrogen using photosynthetic microorganisms. Our system consists of the following three stages: (1) Photosynthetic starch accumulation in green microalgae (400 L x2); (2) Dark anaerobic fermentation of the algal starch biomass to produce hydrogen and organic compounds (155 L x2); and (3) Further conversion of the organic compounds to produce hydrogen using photosynthetic bacteria (three types of reactors, parallel plate, raceway, and tubular). We constructed a test plant of this process at Nankoh power plant of Kansai Electric Power Company in Osaka, Japan, and carried out a series of tests using CO{sub 2} obtained from a chemical absorption pilot-plant. The photobiological hydrogen production process used a combination of a marine alga, Chlamydomonas sp. MGA 161 and marine photosynthetic bacterium, Rhodopseudomonas sp. W-1S. The dark anaerobic fermentation of algal starch biomass was also investigated. Sustained and stable starch accumulation, starch degradation in the algal cell, and hydrogen production from algal fermentation and photosynthetic bacteria in the light were demonstrated during several experiments. 3 refs., 12 figs., 1 tab.

  7. [Genome editing of industrial microorganism].

    PubMed

    Zhu, Linjiang; Li, Qi

    2015-03-01

    Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.

  8. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms.

    PubMed

    Barrett, Craig F; Freudenstein, John V; Li, Jeff; Mayfield-Jones, Dustin R; Perez, Leticia; Pires, J Chris; Santos, Cristian

    2014-12-01

    Parasitic organisms exemplify morphological and genomic reduction. Some heterotrophic, parasitic plants harbor drastically reduced and degraded plastid genomes resulting from relaxed selective pressure on photosynthetic function. However, few studies have addressed the initial stages of plastome degradation in groups containing both photosynthetic and nonphotosynthetic species. Corallorhiza is a genus of leafless, heterotrophic orchids that contains both green, photosynthetic species and nongreen, putatively nonphotosynthetic species, and represents an ideal system in which to assess the beginning of the transition to a "minimal plastome." Complete plastomes were generated for nine taxa of Corallorhiza using Illumina paired-end sequencing of genomic DNA to assess the degree of degradation among taxa, and for comparison with a general model of degradation among angiosperms. Quantification of total chlorophyll suggests that nongreen Corallorhiza still produce chlorophyll, but at 10-fold lower concentrations than green congeners. Complete plastomes and partial nuclear rDNA cistrons yielded a fully resolved tree for Corallorhiza, with at least two independent losses of photosynthesis, evidenced by gene deletions and pseudogenes in Co. striata and nongreen Co. maculata. All Corallorhiza show some evidence of degradation in genes of the NAD(P)H dehydrogenase complex. Among genes with open reading frames, photosynthesis-related genes displayed evidence of neutral evolution in nongreen Corallorhiza, whereas genes of the ATP synthase complex displayed some evidence of positive selection in these same groups, though for reasons unknown. Corallorhiza spans the early stages of a general model of plastome degradation and has added critical insight for understanding the process of plastome evolution in heterotrophic angiosperms.

  9. [Molecular karyotyping of eukaryotic microorganisms].

    PubMed

    Nasonova, E S

    2012-01-01

    In many fungi and protists small size and weak morphological differentiation of chromosomes embarrass the study of karyotypes using microscopical tools. Molecular karyotyping based on the fractionation of intact chromosomal DNAs by pulsed field gel electrophoresis (PFGE) provides an alternative approach to the analysis of chromosomal sets in such organisms. To assign the bands observed in PFGE gel to the individual chromosomes the following methods of chromosome identification are applied: densitometric analysis of the bands; Southern hybridization with chromosome- and telomere-specific probes, which often is combined with comparative karyotyping of a series of strains with pronounced size polymorphism of chromosomes; comparison of the patterns of restriction fragments of chromosomal DNAs fractioned by KARD 2-D PFGE; comparison with the strains with well-studied interchromosomal rearrangements. Besides estimation of the number and the size of chromosomes, molecular karyotyping allows assessment of haploid genome size and ploidy level, study of genome dynamics, identification of chromosomal rearrangements and associated chromosomal polymorphism. The analysis of karyotype and dynamics of the genomes is important for the study of intra- and interspecial variability, investigation of the chromosome evolution in closely related species and elaboration of the models of speciation. The comparison of molecular karyotypes among isolates of different origin is of great practical importance for clinical diagnostics and for agricultural microbiology. In this review we discuss: 1) the methods of karyotyping and their application to the analysis of chromosomal sets in eukaryotic microorganisms; 2) the specificity of the methods used for extraction and fractionation of intact chromosomal DNAs; 3) the reasons for difficulties in interpretation of molecular karyotypes and the ways of their overcoming; 4) fields of application of molecular karyotyping; 5) the definition of

  10. Heterotrophic bacterial production and metabolic balance during the VAHINE mesocosm experiment in the New Caledonia lagoon

    NASA Astrophysics Data System (ADS)

    Van Wambeke, France; Pfreundt, Ulrike; Barani, Aude; Berthelot, Hugo; Moutin, Thierry; Rodier, Martine; Hess, Wolfgang R.; Bonnet, Sophie

    2016-06-01

    Studies investigating the fate of diazotrophs through the microbial food web are lacking, although N2 fixation can fuel up to 50 % of new production in some oligotrophic oceans. In particular, the role played by heterotrophic prokaryotes in this transfer is largely unknown. In the frame of the VAHINE (VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific) experiment, three replicate large-volume (˜ 50 m3) mesocosms were deployed for 23 days in the new Caledonia lagoon and were intentionally fertilized on day 4 with dissolved inorganic phosphorus (DIP) to stimulate N2 fixation. We specifically examined relationships between heterotrophic bacterial production (BP) and N2 fixation or primary production, determined bacterial growth efficiency and established carbon budgets. BP was statistically higher during the second phase of the experiment (P2: days 15-23), when chlorophyll biomass started to increase compared to the first phase (P1: days 5-14). Phosphatase alkaline activity increased drastically during the second phase of the experiment, showing adaptations of microbial populations after utilization of the added DIP. Notably, among autotrophs, Synechococcus abundances increased during P2, possibly related to its capacity to assimilate leucine and to produce alkaline phosphatase. Bacterial growth efficiency based on the carbon budget (27-43 %), was notably higher than generally cited for oligotrophic environments and discussed in links with the presence of abundant species of bacteria expressing proteorhodopsin. The main fates of gross primary production (particulate + dissolved) were respiration (67 %) and export through sedimentation (17 %). BP was highly correlated with particulate primary production and chlorophyll biomass during both phases of the experiment but was slightly correlated, and only during P2 phase, with N2 fixation rates. Heterotrophic bacterial production was strongly stimulated after mineral N enrichment

  11. Heterotrophic microalgae cultivation to synergize biodiesel production with waste remediation: progress and perspectives.

    PubMed

    Venkata Mohan, S; Rohit, M V; Chiranjeevi, P; Chandra, Rashmi; Navaneeth, B

    2015-05-01

    Microalgae are inexhaustible feedstock for synthesis of biodiesel rich in polyunsaturated fatty acids (PUFA) and valuable bioactive compounds. Their cultivation is critical in sustaining the global economy in terms of human consumption of food and fuel. When compared to autotrophic cultivation, heterotrophic systems are more suitable for producing high cell densities of microalgae for accumulation of large quantities of lipids (triacylglycerols) which can be converted into biodiesel. Consorted efforts are made in this communication to converge recent literature on heterotrophic cultivation systems with simultaneous wastewater treatment and algal oil production. Challenges faced during large scale production and limiting factors which hinder the microalgae growth are enumerated. A strategic deployment of integrated closed loop biorefinery concept with multi-product recovery is proposed to exploit the full potential of algal systems. Sustainable algae cultivation is essential to produce biofuels leading to green future.

  12. Dynamics of planktonic bacteria and heterotrophic microflagellates in the Parker Estuary, northern Massachusetts

    NASA Astrophysics Data System (ADS)

    Wright, Richard T.; Coffin, Richard B.; Lebo, Martin E.

    1987-11-01

    The temporal and spatial abundance and activities of members of the planktonic microbial food web in a salt marsh estuary were analysed over the course of a year. Analysis of the data was focused on the factors that control the density and productivity of the heterotrophic bacteria. Temperature exercises a long-term influence on substrate sources, but short-term control is a function of the interaction of grazing and substrate supply. A model has been developed to give a framework for understanding how the microbial food web may work under steady-state assumptions. The model assumptions and predictions appear to be supported by the field data. Equations were generated for estimating substrate flux through the bacteria and estimating bacterial density as a result of grazing and substrate input. The results give some insights into the question of whether the heterotrophic bacteria function as a link to higher organisms or as an energy sink.

  13. Gases generated from simulated thermal degradation of autotrophic and heterotrophic chlorella

    SciTech Connect

    Qingyu Wu )

    1992-01-01

    The content of crude lipid in the cells of heterotrophic Chlorella protothecoides is 4.4 times as high as in the autotrophic algal cells. The gases thermally degraded from autotrophic cells at 200-300[degrees]C contain mainly CO[sub 2], while the heterotrophic algal cells produce hydrocarbon gas at a much higher rate than autotraophic algal cells. With the rise in temperature, both kinds of cells display a rapid drop in the acid/alkane ratio of the gas components and the ratio of ethane to ethylene increases regularly. Their ratio of normal and isomeric alkanes are all above 1. The study reveals that the actual potential of microplanktonic algae in producing oil and natural gas should be much greater than what people have recognized before.

  14. Formalising a mechanistic linkage between heterotrophic feeding and thermal bleaching resistance

    NASA Astrophysics Data System (ADS)

    Wooldridge, Scott A.

    2014-12-01

    In this paper, I utilise the CO2 (sink) limitation model of coral bleaching to propose a new biochemical framework that explains how certain (well-adapted) coral species can utilise heterotrophic carbon acquisition to combat the damaging algal photoinhibition response sequence that underpins thermal bleaching, thereby increasing thermal bleaching resistance. This mechanistic linkage helps to clarify a number of previously challenging experimental responses arising from feeding (versus starved) temperature stress experiments, and isotope labelling (tracer) experiments with heterotrophic carbon sources (e.g., zooplankton). In an era of rapidly warming surface ocean temperatures, the conferred fitness benefits arising from such a mechanistic linkage are considerable. Yet, various ecological constraints are outlined which caution against the ultimate benefit of the mechanism for raising bleaching thresholds at the coral community (reef) scale. Future experiments are suggested that can strengthen these proposed arguments.

  15. Molecular Comparisons of Freshwater and Marine Isolates of the Same Morphospecies of Heterotrophic Flagellates

    PubMed Central

    Scheckenbach, Frank; Wylezich, Claudia; Mylnikov, Alexander P.; Weitere, Markus; Arndt, Hartmut

    2006-01-01

    Heterotrophic flagellates are key components of all ecosystems. Understanding the patterns of biodiversity of these organisms is thus particularly important. Here we analyzed the intraspecific diversity of 10 morphospecies of heterotrophic flagellates comprising representatives of the Apusozoa (2 morphospecies) and Kinetoplastea (8 morphospecies), all belonging to the most common flagellates with worldwide distribution. Most morphospecies showed a mixing of lineages isolated from diverse habitats, indicating that some lineages of these morphospecies had been able to colonize different habitats several times. Furthermore, our results revealed remarkable levels of genetic divergence within most of the morphospecies studied, underlining the difficulty of correctly determining species by means of morphology alone. Many cryptic or pseudocryptic species seem to occur. Our results revealed clear divergence between marine and freshwater lineages of the morphospecies Ancyromonas sigmoides, showing that freshwater lineages have not been able to colonize marine environments and marine lineages have not been able to colonize freshwater environments for a long time. PMID:17021215

  16. Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium

    PubMed Central

    Chan, Leong-Keat; Newton, Ryan J.; Sharma, Shalabh; Smith, Christa B.; Rayapati, Pratibha; Limardo, Alexander J.; Meile, Christof; Moran, Mary Ann

    2012-01-01

    Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC), a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ∼50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium Ruegeria pomeroyi (a member of the Roseobacter clade) under four element limitation regimes (C, N, P, and S). Microarray analysis indicated that the bacterium scavenged for alternate sources of the scarce element when cells were C-, N-, or P-limited; reworked the ratios of biomolecules when C- and P- limited; and exerted tighter control over import/export and cytoplasmic pools when N-limited. Under S limitation, a scenario not existing naturally for surface ocean microbes, stress responses dominated transcriptional changes. Resource-driven changes in C:N ratios of up to 2.5-fold and in C:P ratios of up to sixfold were measured in R. pomeroyi biomass. These changes were best explained if the C and P content of the cells was flexible in the face of shifting resources but N content was not, achieved through the net balance of different transcriptional strategies. The cellular-level metabolic trade-offs that govern biomass stoichiometry in R. pomeroyi may have implications for global carbon cycling if extendable to other heterotrophic bacteria. Strong homeostatic responses to N limitation by marine bacteria would intensify competition with autotrophs. Modification of cellular inventories in C- and P-limited heterotrophs would vary the elemental ratio of particulate organic matter sequestered in the deep ocean. PMID:22783226

  17. Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Continuously Percolated Soil Columns

    PubMed Central

    Verhagen, Frank J. M.; Duyts, Hendrik; Laanbroek, Hendrikus J.

    1992-01-01

    Although the absence of nitrate formation in grassland soils rich in organic matter has often been reported, low numbers of nitrifying bacteria are still found in these soils. To obtain more insight into these observations, we studied the competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis in the presence of Nitrobacter winogradskyi with soil columns containing calcareous sandy soil. The soil columns were percolated continuously at a dilution rate of 0.007 h-1, based on liquid volumes, with medium containing 5 mM ammonium and different amounts of glucose ranging from 0 to 12 mM.A. globiformis was the most competitive organism for limiting amounts of ammonium. The numbers of N. europaea and N. winogradskyi cells were lower at higher glucose concentrations, and the potential ammonium-oxidizing activities in the uppermost 3 cm of the soil columns were nonexistent when at least 10 mM glucose was present in the reservoir, although 107 nitrifying cells per g of dry soil were still present. This result demonstrated that there was no correlation between the numbers of nitrifying bacteria and their activities. The numbers and activities of N. winogradskyi cells decreased less than those of N. europaea cells in all layers of the soil columns, probably because of heterotrophic growth of the nitrite-oxidizing bacteria on organic substrates excreted by the heterotrophic bacteria or because of nitrate reduction at reduced oxygen concentrations by the nitrite-oxidizing bacteria. Our conclusion was that the nitrifying bacteria were less competitive than the heterotrophic bacteria for ammonium in soil columns but that they survived as viable inactive cells. Inactive nitrifying bacteria may also be found in the rhizosphere of grassland plants, which is rich in organic carbon. They are possibly reactivated during periods of net mineralization. PMID:16348787

  18. Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination.

    PubMed

    Lu, Huijie; Xue, Zheng; Saikaly, Pascal; Nunes, Suzana P; Bluver, Ted R; Liu, Wen-Tso

    2016-01-01

    Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles. PMID:26512812

  19. Oxidation of hydrogen sulfide by mixed cultures of Thiobacillus denitrificans and heterotrophs

    SciTech Connect

    Sublette, K.L.; Sylvester, N.D.

    1987-04-01

    A process for the microbial desulfurization of natural gas based on the oxidation of H/sub 2/S(g) by Thiobacillus denitrificans has been previously proposed. The proposed process could be greatly simplified if aseptic operation of the reactor was not required. Accordingly, the authors report here a study of the effects of heterotrophic contaminants on H/sub 2/S(g) oxidation by T. denitrificans.

  20. [Spatial structure of communities of heterotrophic flagellates from a sphagnum bog].

    PubMed

    Tikhonenkov, D V; Mazeĭ, Iu A

    2009-01-01

    Spatial distribution pattern of heterotrophic flagellates within a macroscopically homogenous sphagnum parcel of a transitional bog in the southern taiga was studied. Under investigation was horizontal pattern at different scales (1 cm, 10 cm, 1 m, 10 m) and the vertical heterogeneity of the community in the sphagnum quagmire. 105 species and forms of heterotrophic flagellates were revealed. Predominating were euglenids, less abundant are kynetoplastids and cercomonads. The most numerous appeared to be Cryptomonas sp., Heteromita minima, Goniomonas truncata, Protaspis simplex, Bodo designis, B. saltans, Phyllomitus apiculatus, Paraphysomonas sp., Petalomonas minuta. More abundant species were characterized by less patchy distribution than less abundant. At a smaller scale, the community was formed by the species with different degree of patchiness while at larger scales, all the species possess nearly the same distribution pattern. The same number of samples of equal sizes revealed nearly the same species numbers independently of distances between the sample sites, as the samples at each scale differ from each other nearly at the same magnitude. An averaged size of the species aggregations in the community is as large as several centimeters. Such a scale is probably a characteristic size (minimum area) of the community of the sphagnum dwelling heterotrophic flagellates. Rather low environmental heterogeneity within the sphagnum quagmire leads to significant homogeneity of the community at larger scales. Vertical differentiation of the heterotrophic flagellate community within that quagmire appeared to be very unstable with the time. The same species are characterized by different preferences to the depths at different spatial-temporal loci. Specific vertical distributions and community patterns are formed under different local conditions.

  1. Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination.

    PubMed

    Lu, Huijie; Xue, Zheng; Saikaly, Pascal; Nunes, Suzana P; Bluver, Ted R; Liu, Wen-Tso

    2016-01-01

    Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles.

  2. PARTICLE-ASSOCIATED MICROORGANISMS IN STORMWATER RUNOFF

    EPA Science Inventory

    This research investigated the effects of blending and chemical addition before analysis of the concentration of microorganisms in stormwater runoff to determine whether clumped or particle-associated organisms play a significant role. All organisms, except for Escherichia coli, ...

  3. Detection of microorganisms using terahertz metamaterials.

    PubMed

    Park, S J; Hong, J T; Choi, S J; Kim, H S; Park, W K; Han, S T; Park, J Y; Lee, S; Kim, D S; Ahn, Y H

    2014-05-16

    Microorganisms such as fungi and bacteria cause many human diseases and therefore rapid and accurate identification of these substances is essential for effective treatment and prevention of further infections. In particular, contemporary microbial detection technique is limited by the low detection speed which usually extends over a couple of days. Here we demonstrate that metamaterials operating in the terahertz frequency range shows promising potential for use in fabricating the highly sensitive and selective microbial sensors that are capable of high-speed on-site detection of microorganisms in both ambient and aqueous environments. We were able to detect extremely small amounts of the microorganisms, because their sizes are on the same scale as the micro-gaps of the terahertz metamaterials. The resonant frequency shift of the metamaterials was investigated in terms of the number density and the dielectric constants of the microorganisms, which was successfully interpreted by the change in the effective dielectric constant of a gap area.

  4. Detection of microorganisms using terahertz metamaterials

    NASA Astrophysics Data System (ADS)

    Park, S. J.; Hong, J. T.; Choi, S. J.; Kim, H. S.; Park, W. K.; Han, S. T.; Park, J. Y.; Lee, S.; Kim, D. S.; Ahn, Y. H.

    2014-05-01

    Microorganisms such as fungi and bacteria cause many human diseases and therefore rapid and accurate identification of these substances is essential for effective treatment and prevention of further infections. In particular, contemporary microbial detection technique is limited by the low detection speed which usually extends over a couple of days. Here we demonstrate that metamaterials operating in the terahertz frequency range shows promising potential for use in fabricating the highly sensitive and selective microbial sensors that are capable of high-speed on-site detection of microorganisms in both ambient and aqueous environments. We were able to detect extremely small amounts of the microorganisms, because their sizes are on the same scale as the micro-gaps of the terahertz metamaterials. The resonant frequency shift of the metamaterials was investigated in terms of the number density and the dielectric constants of the microorganisms, which was successfully interpreted by the change in the effective dielectric constant of a gap area.

  5. Detection of microorganisms using terahertz metamaterials

    PubMed Central

    Park, S. J.; Hong, J. T.; Choi, S. J.; Kim, H. S.; Park, W. K.; Han, S. T.; Park, J. Y.; Lee, S.; Kim, D. S.; Ahn, Y. H.

    2014-01-01

    Microorganisms such as fungi and bacteria cause many human diseases and therefore rapid and accurate identification of these substances is essential for effective treatment and prevention of further infections. In particular, contemporary microbial detection technique is limited by the low detection speed which usually extends over a couple of days. Here we demonstrate that metamaterials operating in the terahertz frequency range shows promising potential for use in fabricating the highly sensitive and selective microbial sensors that are capable of high-speed on-site detection of microorganisms in both ambient and aqueous environments. We were able to detect extremely small amounts of the microorganisms, because their sizes are on the same scale as the micro-gaps of the terahertz metamaterials. The resonant frequency shift of the metamaterials was investigated in terms of the number density and the dielectric constants of the microorganisms, which was successfully interpreted by the change in the effective dielectric constant of a gap area. PMID:24832607

  6. Roots affect the response of heterotrophic soil respiration to temperature in tussock grass microcosms

    PubMed Central

    Graham, Scott L.; Millard, Peter; Hunt, John E.; Rogers, Graeme N. D.; Whitehead, David

    2012-01-01

    Aims and Background While the temperature response of soil respiration (RS) has been well studied, the partitioning of heterotrophic respiration (RH) by soil microbes from autotrophic respiration (RA) by roots, known to have distinct temperature sensitivities, has been problematic. Further complexity stems from the presence of roots affecting RH, the rhizosphere priming effect. In this study the short-term temperature responses of RA and RH in relation to rhizosphere priming are investigated. Methods Temperature responses of RA, RH and rhizosphere priming were assessed in microcosms of Poa cita using a natural abundance δ13C discrimination approach. Results The temperature response of RS was found to be regulated primarily by RA, which accounted for 70 % of total soil respiration. Heterotrophic respiration was less sensitive to temperature in the presence of plant roots, resulting in negative priming effects with increasing temperature. Conclusions The results emphasize the importance of roots in regulating the temperature response of RS, and a framework is presented for further investigation into temperature effects on heterotrophic respiration and rhizosphere priming, which could be applied to other soil and vegetation types to improve models of soil carbon turnover. PMID:22492330

  7. Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency

    PubMed Central

    Sebastián, Marta; Smith, Alastair F; González, José M; Fredricks, Helen F; Van Mooy, Benjamin; Koblížek, Michal; Brandsma, Joost; Koster, Grielof; Mestre, Mireia; Mostajir, Behzad; Pitta, Paraskevi; Postle, Anthony D; Sánchez, Pablo; Gasol, Josep M; Scanlan, David J; Chen, Yin

    2016-01-01

    Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean. PMID:26565724

  8. Acidophilic algae isolated from mine-impacted environments and their roles in sustaining heterotrophic acidophiles.

    PubMed

    Nancucheo, Ivan; Barrie Johnson, D

    2012-01-01

    Two acidophilic algae, identified as strains of Chlorella protothecoides var. acidicola and Euglena mutabilis, were isolated in pure culture from abandoned copper mines in Spain and Wales and grown in pH- and temperature-controlled bioreactors. The Chlorella isolate grew optimally at pH 2.5 and 30°C, with a corresponding culture doubling time of 9 h. The isolates displayed similar tolerance (10-50 mM) to four transition metals tested. Growth of the algae in liquid media was paralleled with increasing concentrations of dissolved organic carbon (DOC). Glycolic acid was identified as a significant component (12-14%) of total DOC. Protracted incubation resulted in concentrations of glycolic acid declining in both cases, and glycolic acid added to a culture of Chlorella incubated in the dark was taken up by the alga (~100% within 3 days). Two monosaccharides were identified in cell-free liquors of each algal isolate: fructose and glucose (Chlorella), and mannitol and glucose (Euglena). These were rapidly metabolized by acidophilic heterotrophic bacteria (Acidiphilium and Acidobacterium spp.) though only fructose was utilized by the more fastidious heterotroph "Acidocella aromatica." The significance of algae in promoting the growth of iron- (and sulfate-) reducing heterotrophic acidophiles that are important in remediating mine-impacted waters (MIWs) is discussed.

  9. Risk assessment of heterotrophic bacteria from bottled drinking water sold in Indian markets.

    PubMed

    Jeena, M I; Deepa, P; Mujeeb Rahiman, K M; Shanthi, R T; Hatha, A A M

    2006-03-01

    One hundred and five samples of bottled drinking water belonging to 30 different brands, collected from six different states of India have been analysed for total heterotrophic bacterial (THB) load and coliforms. Almost all bottlers used multiple treatment procedures such as microfiltration, reverse osmosis and ozonization to treat the water. Around 40% of the samples exceeded the limit of 100 cfu/ml set by the department of health as well as Bureau of Indian Standards (BIS), Government of India. Fourteen percent and 44% of the samples with THB loads between 100 and 1000 cfu/ml or 1000 cfu/ml tested positive for coliforms indicating a linear relationship between THB and coliform bacteria. Gram-positive genera such as Kurthia and Corynebacterium were found to be dominant genera, while members of the family enterobacteriaceae contributed to 7%. Risk assessment of the heterotrophic bacteria revealed that the majority of the strains acquired resistance against ampicillin, nalidixic acid, novobiocin and oxytetracycline. As bottled drinking water is a ready to drink commodity, the high load of heterotrophic bacteria with multiple drug resistance poses significant health hazards to the consumers, especially to immunocompromised individuals.

  10. The characteristics of a novel heterotrophic nitrification-aerobic denitrification bacterium, Bacillus methylotrophicus strain L7.

    PubMed

    Zhang, Qing-Ling; Liu, Ying; Ai, Guo-Min; Miao, Li-Li; Zheng, Hai-Yan; Liu, Zhi-Pei

    2012-03-01

    Bacillus methylotrophicus strain L7, exhibited efficient heterotrophic nitrification-aerobic denitrification ability, with maximum NH(4)(+)-N and NO(2)(-)-N removal rate of 51.58 mg/L/d and 5.81 mg/L/d, respectively. Strain L7 showed different gaseous emitting patterns from those strains ever described. When (15)NH(4)Cl, or Na(15)NO(2), or K(15)NO(3) was used, results of GC-MS indicated that N(2)O was emitted as the intermediate of heterotrophic nitrification or aerobic denitrification, while GC-IRMS results showed that N(2) was produced as end product when nitrite was used. Single factor experiments suggested that the optimal conditions for heterotrophic nitrification were sodium succinate as carbon source, C/N 6, pH 7-8, 0 g/L NaCl, 37 °C and a wide range of NH(4)(+)-N from 80 to 1000 mg/L. Orthogonal tests showed that the optimal conditions for aerobic denitrification were C/N 20, pH 7-8, 10 g/L NaCl and DO 4.82 mg/L (shaking speed 50 r/min) when nitrite was served as substrate.

  11. Weak Coupling between Heterotrophic Nanoflagellates and Bacteria in a Eutrophic Freshwater Environment.

    PubMed

    Wieltschnig, C.; Kirschner, A.K.T.; Steitz, A.; Velimirov, B.

    2001-08-01

    In a study on the dynamics and trophic role of the heterotrophic nanoflagellate (HNAN) assemblage in the microbial food web of a eutrophic oxbow lake abundances, biomass, and production rates of HNAN and their potential prey organisms, namely heterotrophic bacteria and autotrophic picoplankton, were monitored for a period of 2 years. No coupling between HNAN abundance and biomass and the abundance and biomass of their picoplanktonic prey was observed for the investigation period. The ratio of heterotrophic bacterial to HNAN abundance ranged from 2.2 x 103 to 8.6 x 103 (mean: 4.2 x 103 +/- 1.8 x 103). HNAN carbon consumption could account for only 10% to 40% of bacterial secondary production. The lack of coupling between HNAN and their potential prey and the low HNAN abundance relative to bacterial abundance suggested (a) that HNAN grazing was an insignificant factor in the regulation of bacterial abundance and (b) that HNAN abundance was regulated by predation rather than by prey abundance. This hypothesis was supported by the fact that HNAN growth rates were high (in the range of 0.45 d-1 to 1.00 d-1 during spring and summer, yearly mean: 0.52 d-1), and only weakly correlated with prey abundance and biomass. The results indicated strong top-down control of HNAN and consequently a weak coupling of HNAN and picoplankton in the investigated eutrophic freshwater environment. PMID:12024278

  12. Contribution of mono and polysaccharides to heterotrophic N2 fixation at the eastern Mediterranean coastline.

    PubMed

    Rahav, E; Giannetto, M J; Bar-Zeev, E

    2016-01-01

    N2 fixation should be a critical process in the nitrogen-poor surface water of the eastern Mediterranean Sea. Despite favorable conditions, diazotroph abundance and N2 fixation rates remains low for reasons yet explained. The main goal of this study was to investigate the limiting nutrients for diazotrophy in this oligotrophic environment. Hence, we conducted dedicated bottle-microcosms with eastern Mediterranean Sea water that were supplemented with mono and polysaccharides as well as inorganic nitrogen and phosphorous. Our results indicate that the diazotrophic community expressing nifH was primarily represented by heterotrophic Proteobacteria. N2 fixation and heterotrophic bacterial activity increased up-to tenfold following two days of dark incubations, once seawater was supplemented with organic carbon substrate in the form of glucose (monosaccharides) or gum-xanthan (polysaccharide surrogate). Furthermore, our results point that carbon-rich polysaccharides, such as transparent exopolymer particles, enhance heterotrophic N2 fixation, by forming microenvironments of intense metabolic activity, high carbon: nitrogen ratio, and possibly low O2 levels. The conclusions of this study indicate that diazotrophs in the eastern Mediterranean coast are primarily limited by organic carbon substrates, as possibly in many other marine regions.

  13. [Heterotrophic Nitrification and Aerobic Denitrification of the Hypothermia Aerobic Denitrification Bacterium: Arthrobacter arilaitensis].

    PubMed

    He, Teng-xia; Ni, Jiu-pai; Li, Zhen-lun; Sun, Quan; Ye Qing; Xu, Yi

    2016-03-15

    High concentrations of ammonium, nitrate and nitrite nitrogen were employed to clarify the abilities of heterotrophic nitrification and aerobic denitrification of Arthrobacter arilaitensis strain Y-10. Meanwhile, by means of inoculating the strain suspension into the mixed ammonium and nitrate, ammonium and nitrite nitrogen simulated wastewater, we studied the simultaneous nitrification and denitrification ability of Arthrobacter arilaitensis strain Y-10. In addition, cell optical density was assayed in each nitrogen removal process to analyze the relationship of cell growth and nitrogen removal efficiency. The results showed that the hypothermia denitrification strain Arthrobacter arilaitensis Y-10 exhibited high nitrogen removal efficiency during heterotrophic nitrification and aerobic denitrification. The ammonium, nitrate and nitrite removal rates were 65.0%, 100% and 61.2% respectively when strain Y-10 was cultivated for 4 d at 15°C with initial ammonium, nitrate and nitrite nitrogen concentrations of 208.43 mg · L⁻¹, 201.16 mg · L⁻¹ and 194.33 mg · L⁻¹ and initial pH of 7.2. Nitrite nitrogen could only be accumulated in the medium containing nitrate nitrogen during heterotrophic nitrification and aerobic denitrification process. Additionally, the ammonium nitrogen was mainly removed in the inorganic nitrogen mixed synthetic wastewater. In short, Arthrobacter arilaitensis Y-10 could conduct nitrification and denitrification effectively under aerobic condition and the ammonium nitrogen removal rate was more than 80.0% in the inorganic nitrogen mixed synthetic wastewater. PMID:27337904

  14. Nitrogen, carbon, and sulfur isotopic change during heterotrophic (Pseudomonas aureofaciens) and autotrophic (Thiobacillus denitrificans) denitrification reactions.

    PubMed

    Hosono, Takahiro; Alvarez, Kelly; Lin, In-Tian; Shimada, Jun

    2015-12-01

    In batch culture experiments, we examined the isotopic change of nitrogen in nitrate (δ(15)NNO3), carbon in dissolved inorganic carbon (δ(13)CDIC), and sulfur in sulfate (δ(34)SSO4) during heterotrophic and autotrophic denitrification of two bacterial strains (Pseudomonas aureofaciens and Thiobacillus denitrificans). Heterotrophic denitrification (HD) experiments were conducted with trisodium citrate as electron donor, and autotrophic denitrification (AD) experiments were carried out with iron disulfide (FeS2) as electron donor. For heterotrophic denitrification experiments, a complete nitrate reduction was accomplished, however bacterial denitrification with T. denitrificans is a slow process in which, after seventy days nitrate was reduced to 40% of the initial concentration by denitrification. In the HD experiment, systematic change of δ(13)CDIC (from -7.7‰ to -12.2‰) with increase of DIC was observed during denitrification (enrichment factor εN was -4.7‰), suggesting the contribution of C of trisodium citrate (δ(13)C=-12.4‰). No SO4(2-) and δ(34)SSO4 changes were observed. In the AD experiment, clear fractionation of δ(13)CDIC during DIC consumption (εC=-7.8‰) and δ(34)SSO4 during sulfur use of FeS2-S (around 2‰), were confirmed through denitrification (εN=-12.5‰). Different pattern in isotopic change between HD and AD obtained on laboratory-scale are useful to recognize the type of denitrification occurring in the field. PMID:26529303

  15. Nitrogen, carbon, and sulfur isotopic change during heterotrophic (Pseudomonas aureofaciens) and autotrophic (Thiobacillus denitrificans) denitrification reactions

    NASA Astrophysics Data System (ADS)

    Hosono, Takahiro; Alvarez, Kelly; Lin, In-Tian; Shimada, Jun

    2015-12-01

    In batch culture experiments, we examined the isotopic change of nitrogen in nitrate (δ15NNO3), carbon in dissolved inorganic carbon (δ13CDIC), and sulfur in sulfate (δ34SSO4) during heterotrophic and autotrophic denitrification of two bacterial strains (Pseudomonas aureofaciens and Thiobacillus denitrificans). Heterotrophic denitrification (HD) experiments were conducted with trisodium citrate as electron donor, and autotrophic denitrification (AD) experiments were carried out with iron disulfide (FeS2) as electron donor. For heterotrophic denitrification experiments, a complete nitrate reduction was accomplished, however bacterial denitrification with T. denitrificans is a slow process in which, after seventy days nitrate was reduced to 40% of the initial concentration by denitrification. In the HD experiment, systematic change of δ13CDIC (from - 7.7‰ to - 12.2‰) with increase of DIC was observed during denitrification (enrichment factor εN was - 4.7‰), suggesting the contribution of C of trisodium citrate (δ13C = - 12.4‰). No SO42 - and δ34SSO4 changes were observed. In the AD experiment, clear fractionation of δ13CDIC during DIC consumption (εC = - 7.8‰) and δ34SSO4 during sulfur use of FeS2-S (around 2‰), were confirmed through denitrification (εN = - 12.5‰). Different pattern in isotopic change between HD and AD obtained on laboratory-scale are useful to recognize the type of denitrification occurring in the field.

  16. Soil respiration under climate warming: differential response of heterotrophic and autotrophic respiration.

    PubMed

    Wang, Xin; Liu, Lingli; Piao, Shilong; Janssens, Ivan A; Tang, Jianwu; Liu, Weixing; Chi, Yonggang; Wang, Jing; Xu, Shan

    2014-10-01

    Despite decades of research, how climate warming alters the global flux of soil respiration is still poorly characterized. Here, we use meta-analysis to synthesize 202 soil respiration datasets from 50 ecosystem warming experiments across multiple terrestrial ecosystems. We found that, on average, warming by 2 °C increased soil respiration by 12% during the early warming years, but warming-induced drought partially offset this effect. More significantly, the two components of soil respiration, heterotrophic respiration and autotrophic respiration showed distinct responses. The warming effect on autotrophic respiration was not statistically detectable during the early warming years, but nonetheless decreased with treatment duration. In contrast, warming by 2 °C increased heterotrophic respiration by an average of 21%, and this stimulation remained stable over the warming duration. This result challenged the assumption that microbial activity would acclimate to the rising temperature. Together, our findings demonstrate that distinguishing heterotrophic respiration and autotrophic respiration would allow us better understand and predict the long-term response of soil respiration to warming. The dependence of soil respiration on soil moisture condition also underscores the importance of incorporating warming-induced soil hydrological changes when modeling soil respiration under climate change.

  17. A pH-control model for heterotrophic and hydrogen-based autotrophic denitrification.

    PubMed

    Tang, Youneng; Zhou, Chen; Ziv-El, Michal; Rittmann, Bruce E

    2011-01-01

    This work presents a model to predict the alkalinity, pH, and Langelier Saturation Index (LSI) in heterotrophic and H(2)-based autotrophic denitrification systems. The model can also be used to estimate the amount of acid, e.g. HCl, added to the influent (method 1) or the pH set point in the reactor (method 2: pH can be maintained stable by CO(2)-sparge using a pH-control loop) to prevent the pH from exceeding the optimal range for denitrification and to prevent precipitation from occurring. The model was tested with two pilot plants carrying out denitrification of groundwater with high hardness: a heterotrophic system using ethanol as the electron donor and an H(2)-based autotrophic system. The measured alkalinity, pH, and LSI were consistent with the model for both systems. This work also quantifies: (1) how the alkalinity and pH in Stage-1 significantly differ from those in Stage-2; (2) how the pH and LSI differ significantly in the two denitrification systems while the alkalinity increase is about the same; and (3) why CO(2) addition is the preferred method for autotrophic system, while HCl addition is the preferred method for the heterotrophic system.

  18. Nitrogen, carbon, and sulfur isotopic change during heterotrophic (Pseudomonas aureofaciens) and autotrophic (Thiobacillus denitrificans) denitrification reactions.

    PubMed

    Hosono, Takahiro; Alvarez, Kelly; Lin, In-Tian; Shimada, Jun

    2015-12-01

    In batch culture experiments, we examined the isotopic change of nitrogen in nitrate (δ(15)NNO3), carbon in dissolved inorganic carbon (δ(13)CDIC), and sulfur in sulfate (δ(34)SSO4) during heterotrophic and autotrophic denitrification of two bacterial strains (Pseudomonas aureofaciens and Thiobacillus denitrificans). Heterotrophic denitrification (HD) experiments were conducted with trisodium citrate as electron donor, and autotrophic denitrification (AD) experiments were carried out with iron disulfide (FeS2) as electron donor. For heterotrophic denitrification experiments, a complete nitrate reduction was accomplished, however bacterial denitrification with T. denitrificans is a slow process in which, after seventy days nitrate was reduced to 40% of the initial concentration by denitrification. In the HD experiment, systematic change of δ(13)CDIC (from -7.7‰ to -12.2‰) with increase of DIC was observed during denitrification (enrichment factor εN was -4.7‰), suggesting the contribution of C of trisodium citrate (δ(13)C=-12.4‰). No SO4(2-) and δ(34)SSO4 changes were observed. In the AD experiment, clear fractionation of δ(13)CDIC during DIC consumption (εC=-7.8‰) and δ(34)SSO4 during sulfur use of FeS2-S (around 2‰), were confirmed through denitrification (εN=-12.5‰). Different pattern in isotopic change between HD and AD obtained on laboratory-scale are useful to recognize the type of denitrification occurring in the field.

  19. A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus.

    PubMed

    Lyu, Xueliang; Shen, Cuicui; Xie, Jiatao; Fu, Yanping; Jiang, Daohong; Hu, Zijin; Tang, Lihua; Tang, Liguang; Ding, Feng; Li, Kunfei; Wu, Song; Hu, Yanping; Luo, Lilian; Li, Yuanhao; Wang, Qihua; Li, Guoqing; Cheng, Jiasen

    2015-01-01

    Carbon fixation pathway of plants (CFPP) in photosynthesis converts solar energy to biomass, bio-products and biofuel. Intriguingly, a large number of heterotrophic fungi also possess enzymes functionally associated with CFPP, raising the questions about their roles in fungal development and in evolution. Here, we report on the presence of 17 CFPP associated enzymes (ten in Calvin-Benson-Basham reductive pentose phosphate pathway and seven in C4-dicarboxylic acid cycle) in the genome of Sclerotinia sclerotiorum, a heterotrophic phytopathogenic fungus, and only two unique enzymes: ribulose-1, 5-bisphosphate carboxylase-oxygenase (Rubisco) and phosphoribulokinase (PRK) were absent. This data suggested an incomplete CFPP-like pathway (CLP) in fungi. Functional profile analysis demonstrated that the activity of the incomplete CLP was dramatically regulated during different developmental stages of S. sclerotiorum. Subsequent experiments confirmed that many of them were essential to the virulence and/or sclerotial formation. Most of the CLP associated genes are conserved in fungi. Phylogenetic analysis showed that many of them have undergone gene duplication, gene acquisition or loss and functional diversification in evolutionary history. These findings showed an evolutionary links in the carbon fixation processes of autotrophs and heterotrophs and implicated the functions of related genes were in course of continuous change in different organisms in evolution. PMID:26263551

  20. Significant N₂ fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries.

    PubMed

    Bentzon-Tilia, Mikkel; Traving, Sachia J; Mantikci, Mustafa; Knudsen-Leerbeck, Helle; Hansen, Jørgen L S; Markager, Stiig; Riemann, Lasse

    2015-02-01

    Nitrogen (N) fixation is fueling planktonic production in a multitude of aquatic environments. In meso- and poly-haline estuaries, however, the contribution of N by pelagic N₂ fixation is believed to be insignificant due to the high input of N from land and the presumed absence of active N₂-fixing organisms. Here we report N₂ fixation rates, nifH gene composition and nifH gene transcript abundance for key diazotrophic groups over 1 year in two contrasting, temperate, estuarine systems: Roskilde Fjord (RF) and the Great Belt (GB) strait. Annual pelagic N₂ fixation rates averaged 17 and 61 mmol N m(-2) per year at the two sites, respectively. In RF, N₂ fixation was mainly accompanied by transcripts related to heterotrophic (for example, Pseudomonas sp.) and photoheterotrophic bacteria (for example, unicellular diazotrophic cyanobacteria group A). In the GB, the first of two N₂ fixation peaks coincided with a similar nifH-expressing community as in RF, whereas the second peak was synchronous with increased nifH expression by an array of diazotrophs, including heterotrophic organisms as well as the heterocystous cyanobacterium Anabaena. Thus, we show for the first time that significant planktonic N₂ fixation takes place in mesohaline, temperate estuaries and that the importance of heterotrophic, photoheterotrophic and photosynthetic diazotrophs is clearly variable in space and time.

  1. Contribution of mono and polysaccharides to heterotrophic N2 fixation at the eastern Mediterranean coastline

    PubMed Central

    Rahav, E.; Giannetto, M. J.; Bar-Zeev, E.

    2016-01-01

    N2 fixation should be a critical process in the nitrogen-poor surface water of the eastern Mediterranean Sea. Despite favorable conditions, diazotroph abundance and N2 fixation rates remains low for reasons yet explained. The main goal of this study was to investigate the limiting nutrients for diazotrophy in this oligotrophic environment. Hence, we conducted dedicated bottle-microcosms with eastern Mediterranean Sea water that were supplemented with mono and polysaccharides as well as inorganic nitrogen and phosphorous. Our results indicate that the diazotrophic community expressing nifH was primarily represented by heterotrophic Proteobacteria. N2 fixation and heterotrophic bacterial activity increased up-to tenfold following two days of dark incubations, once seawater was supplemented with organic carbon substrate in the form of glucose (monosaccharides) or gum-xanthan (polysaccharide surrogate). Furthermore, our results point that carbon-rich polysaccharides, such as transparent exopolymer particles, enhance heterotrophic N2 fixation, by forming microenvironments of intense metabolic activity, high carbon: nitrogen ratio, and possibly low O2 levels. The conclusions of this study indicate that diazotrophs in the eastern Mediterranean coast are primarily limited by organic carbon substrates, as possibly in many other marine regions. PMID:27306501

  2. Acidophilic algae isolated from mine-impacted environments and their roles in sustaining heterotrophic acidophiles

    PubMed Central

    Ňancucheo, Ivan; Barrie Johnson, D.

    2012-01-01

    Two acidophilic algae, identified as strains of Chlorella protothecoides var. acidicola and Euglena mutabilis, were isolated in pure culture from abandoned copper mines in Spain and Wales and grown in pH- and temperature-controlled bioreactors. The Chlorella isolate grew optimally at pH 2.5 and 30°C, with a corresponding culture doubling time of 9 h. The isolates displayed similar tolerance (10–50 mM) to four transition metals tested. Growth of the algae in liquid media was paralleled with increasing concentrations of dissolved organic carbon (DOC). Glycolic acid was identified as a significant component (12–14%) of total DOC. Protracted incubation resulted in concentrations of glycolic acid declining in both cases, and glycolic acid added to a culture of Chlorella incubated in the dark was taken up by the alga (~100% within 3 days). Two monosaccharides were identified in cell-free liquors of each algal isolate: fructose and glucose (Chlorella), and mannitol and glucose (Euglena). These were rapidly metabolized by acidophilic heterotrophic bacteria (Acidiphilium and Acidobacterium spp.) though only fructose was utilized by the more fastidious heterotroph “Acidocella aromatica.” The significance of algae in promoting the growth of iron- (and sulfate-) reducing heterotrophic acidophiles that are important in remediating mine-impacted waters (MIWs) is discussed. PMID:22973267

  3. A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus.

    PubMed

    Lyu, Xueliang; Shen, Cuicui; Xie, Jiatao; Fu, Yanping; Jiang, Daohong; Hu, Zijin; Tang, Lihua; Tang, Liguang; Ding, Feng; Li, Kunfei; Wu, Song; Hu, Yanping; Luo, Lilian; Li, Yuanhao; Wang, Qihua; Li, Guoqing; Cheng, Jiasen

    2015-08-11

    Carbon fixation pathway of plants (CFPP) in photosynthesis converts solar energy to biomass, bio-products and biofuel. Intriguingly, a large number of heterotrophic fungi also possess enzymes functionally associated with CFPP, raising the questions about their roles in fungal development and in evolution. Here, we report on the presence of 17 CFPP associated enzymes (ten in Calvin-Benson-Basham reductive pentose phosphate pathway and seven in C4-dicarboxylic acid cycle) in the genome of Sclerotinia sclerotiorum, a heterotrophic phytopathogenic fungus, and only two unique enzymes: ribulose-1, 5-bisphosphate carboxylase-oxygenase (Rubisco) and phosphoribulokinase (PRK) were absent. This data suggested an incomplete CFPP-like pathway (CLP) in fungi. Functional profile analysis demonstrated that the activity of the incomplete CLP was dramatically regulated during different developmental stages of S. sclerotiorum. Subsequent experiments confirmed that many of them were essential to the virulence and/or sclerotial formation. Most of the CLP associated genes are conserved in fungi. Phylogenetic analysis showed that many of them have undergone gene duplication, gene acquisition or loss and functional diversification in evolutionary history. These findings showed an evolutionary links in the carbon fixation processes of autotrophs and heterotrophs and implicated the functions of related genes were in course of continuous change in different organisms in evolution.

  4. Distribution and abundance of uncultured heterotrophic flagellates in the world oceans.

    PubMed

    Massana, Ramon; Terrado, Ramon; Forn, Irene; Lovejoy, Connie; Pedrós-Alió, Carlos

    2006-09-01

    Heterotrophic flagellates play fundamental roles in marine ecosystems as picoplankton grazers. This recognized importance contrasts with our ignorance of the taxonomic composition of this functional group, which remains mostly unidentified by microscopical and culturing approaches. Recent molecular marine surveys based on 18S rDNA genes have retrieved many sequences unrelated to cultured organisms and marine stramenopiles were among the first reported uncultured eukaryotes. However, little is known about the organisms corresponding to these sequences. Here we determine the abundance of several marine stramenopile lineages in surface marine waters using molecular probes and fluorescent in situ hybridization. We show that these protists are free-living bacterivorous heterotrophic flagellates. They were widely distributed, occurring in the five world oceans, and accounted for a significant fraction (up to 35%) of heterotrophic flagellates in diverse geographic regions. A single group, MAST-4, represented 9% of cells within this functional assemblage, with the intriguing exception of polar waters where it was absent. MAST-4 cells likely contribute substantially to picoplankton grazing and nutrient re-mineralization in vast areas of the oceans and represent a key eukaryotic group in marine food webs.

  5. Simultaneous heterotrophic nitrification and aerobic denitrification by the marine origin bacterium Pseudomonas sp. ADN-42.

    PubMed

    Jin, Ruofei; Liu, Tianqi; Liu, Guangfei; Zhou, Jiti; Huang, Jianyu; Wang, Aijie

    2015-02-01

    Recent research has highlighted the existence of some bacteria that are capable of performing heterotrophic nitrification and have a phenomenal ability to denitrify their nitrification products under aerobic conditions. A high-salinity-tolerant strain ADN-42 was isolated from Hymeniacidon perleve and found to display high heterotrophic ammonium removal capability. This strain was identified as Pseudomonas sp. via 16S rRNA gene sequence analysis. Gene cloning and sequencing analysis indicated that the bacterial genome contains N2O reductase function (nosZ) gene. NH3-N removal rate of ADN-42 was very high. And the highest removal rate was 6.52 mg/L · h in the presence of 40 g/L NaCl. Under the condition of pure oxygen (DO >8 mg/L), NH3-N removal efficiency was 56.9 %. Moreover, 38.4 % of oxygen remained in the upper gas space during 72 h without greenhouse gas N2O production. Keeping continuous and low level of dissolved oxygen (DO <3 mg/L) was helpful for better denitrification performance. All these results indicated that the strain has heterotrophic nitrification and aerobic denitrification abilities, which guarantee future application in wastewater treatment.

  6. Contribution of mono and polysaccharides to heterotrophic N2 fixation at the eastern Mediterranean coastline.

    PubMed

    Rahav, E; Giannetto, M J; Bar-Zeev, E

    2016-01-01

    N2 fixation should be a critical process in the nitrogen-poor surface water of the eastern Mediterranean Sea. Despite favorable conditions, diazotroph abundance and N2 fixation rates remains low for reasons yet explained. The main goal of this study was to investigate the limiting nutrients for diazotrophy in this oligotrophic environment. Hence, we conducted dedicated bottle-microcosms with eastern Mediterranean Sea water that were supplemented with mono and polysaccharides as well as inorganic nitrogen and phosphorous. Our results indicate that the diazotrophic community expressing nifH was primarily represented by heterotrophic Proteobacteria. N2 fixation and heterotrophic bacterial activity increased up-to tenfold following two days of dark incubations, once seawater was supplemented with organic carbon substrate in the form of glucose (monosaccharides) or gum-xanthan (polysaccharide surrogate). Furthermore, our results point that carbon-rich polysaccharides, such as transparent exopolymer particles, enhance heterotrophic N2 fixation, by forming microenvironments of intense metabolic activity, high carbon: nitrogen ratio, and possibly low O2 levels. The conclusions of this study indicate that diazotrophs in the eastern Mediterranean coast are primarily limited by organic carbon substrates, as possibly in many other marine regions. PMID:27306501

  7. Simultaneous heterotrophic nitrification and aerobic denitrification by the marine origin bacterium Pseudomonas sp. ADN-42.

    PubMed

    Jin, Ruofei; Liu, Tianqi; Liu, Guangfei; Zhou, Jiti; Huang, Jianyu; Wang, Aijie

    2015-02-01

    Recent research has highlighted the existence of some bacteria that are capable of performing heterotrophic nitrification and have a phenomenal ability to denitrify their nitrification products under aerobic conditions. A high-salinity-tolerant strain ADN-42 was isolated from Hymeniacidon perleve and found to display high heterotrophic ammonium removal capability. This strain was identified as Pseudomonas sp. via 16S rRNA gene sequence analysis. Gene cloning and sequencing analysis indicated that the bacterial genome contains N2O reductase function (nosZ) gene. NH3-N removal rate of ADN-42 was very high. And the highest removal rate was 6.52 mg/L · h in the presence of 40 g/L NaCl. Under the condition of pure oxygen (DO >8 mg/L), NH3-N removal efficiency was 56.9 %. Moreover, 38.4 % of oxygen remained in the upper gas space during 72 h without greenhouse gas N2O production. Keeping continuous and low level of dissolved oxygen (DO <3 mg/L) was helpful for better denitrification performance. All these results indicated that the strain has heterotrophic nitrification and aerobic denitrification abilities, which guarantee future application in wastewater treatment. PMID:25432342

  8. Automated systems for identification of microorganisms.

    PubMed Central

    Stager, C E; Davis, J R

    1992-01-01

    Automated instruments for the identification of microorganisms were introduced into clinical microbiology laboratories in the 1970s. During the past two decades, the capabilities and performance characteristics of automated identification systems have steadily progressed and improved. This article explores the development of the various automated identification systems available in the United States and reviews their performance for identification of microorganisms. Observations regarding deficiencies and suggested improvements for these systems are provided. PMID:1498768

  9. Polyphasic approach to characterize heterotrophic bacteria of biofilms and patina on walls of the Suburban Bath of the Herculaneum's archaeological excavations in Italy

    NASA Astrophysics Data System (ADS)

    Ventorino, V.; Pepe, O.; Sannino, L.; Blaiotta, G.; Palomba, S.

    2012-04-01

    plates were purified in the same growth medium by streaking and differentiated by assessing their morphological (phase-contrast microscopy) and biochemical characteristics (Gram-stains KOH-lysis and catalase activity). Cultural-based method allow us to identify by 16S and 26S rRNA partial sequence analysis, heterotrophic bacteria belonging to different genera as Bacillus, Pseudomonas, Aeromonas and Microbacterium. By using this approach, Bacillus-related species (B. benzoevorans, B. megaterium and B. pumilis and B. megaterium/B. simplex group) as well as Aeromonas sobria/Aeromonas salmonicida/Aeromonas hydrophila group, Pseudomonas plecoglossicida and Microbacterium esteraromaticum were isolated in different sample points analysed. DGGE analysis of PCR amplified V3 region of rDNA from DNA directly recovered from samples of biofilms and patina, enabled identification of bacterial species not found using culturable technology, as those closest related to Aeromonas, Paenibacillus, Brevibacterium, Exiguobacterium, Microbacterium, Brevibacterium, Stenothophomonas and Streptomyces. Combination of culture-dependent and independent methods provide a better characterization of heterotrophic microbiota that colonize the surface of ancient decorated walls and can contribute to understand the potential of biodeterioration activity by heterotrophic microorganisms.

  10. Occurrence of heterotrophic and coliform bacteria in liquid hand soaps from bulk refillable dispensers in public facilities.

    PubMed

    Chattman, Marisa; Gerba, Sheri L; Maxwell, Charles P

    2011-03-01

    The goal of the study discussed in this article was to determine the occurrence of heterotrophic and coliform bacteria in liquid soap from bulk refillable dispensers, obtained from restrooms in a variety of public facilities. A total of 541 samples was collected from five U.S. cities. Liquid soap from dispensers in public areas was found to contain heterotrophic and coliform bacterial numbers averaging more than 106 CFU/mL in 24.8% of the dispensers.

  11. Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

    SciTech Connect

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-04-07

    Though microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, the diversity and complexity of natural systems and their intractability to in situ environmental manipulation makes elucidation of the principles governing these interactions challenging. Examination of primary succession during phototrophic biofilm assembly provides a robust means by which to elucidate the dynamics of such interactions and determine their influence upon recruitment and maintenance of phylogenetic and functional diversity in microbial communities. We isolated and characterized two unicyanobacterial consortia from the Hot Lake phototrophic mat, quantifying the structural and community composition of their assembling biofilms. The same heterotrophs were retained in both consortia and included members of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, taxa frequently reported as consorts of microbial photoautotrophs. Cyanobacteria led biofilm assembly, eventually giving way to a late heterotrophic bloom. The consortial biofilms exhibited similar patterns of assembly, with the relative abundances of members of Bacteroidetes and Alphaproteobacteria increasing and members of Gammaproteobacteria decreasing as colonization progressed. Despite similar trends in assembly at higher taxa, the consortia exhibited substantial differences in community structure at the species level. These similar patterns of assembly with divergent community structures suggest that, while similar niches are created by the metabolism of the cyanobacteria, the resultant webs of autotroph-heterotroph and heterotroph-heterotroph interactions driving metabolic exchange are specific to each primary producer. Altogether, our data support these Hot Lake unicyanobacterial consortia as generalizable model systems whose simplicity and tractability permit the deciphering of community assembly principles relevant to natural microbial communities.

  12. The Heterotrophic Bacterial Response During the Meso-scale Southern Ocean Iron Experiment (SOFeX)

    NASA Astrophysics Data System (ADS)

    Oliver, J. L.; Barber, R. T.; Ducklow, H. W.

    2002-12-01

    Previous meso-scale iron enrichments have demonstrated the stimulatory effect of iron on primary productivity and the accelerated flow of carbon into the surface ocean foodweb. In stratified waters, heterotrophic activity can work against carbon export by remineralizing POC and/or DOC back to CO2, effectively slowing the biological pump. To assess the response of heterotrophic activity to iron enrichment, we measured heterotrophic bacterial production and abundance during the Southern Ocean Iron Experiment (SOFeX). Heterotrophic bacterial processes primarily affect the latter of the two carbon export mechanisms, removal of DOC to the deep ocean. Heterotrophic bacterial production (BP), measured via tritiated thymidine (3H-TdR) and leucine (3H-Leu) incorporation, increased ~40% over the 18-d observation period in iron fertilized waters south of the Polar Front (South Patch). Also, South Patch BP was 61% higher than in the surrounding unfertilized waters. Abundance, measured by flow cytometry (FCM) and acridine orange direct counts (AODC), also increased in the South Patch from 3 to 5 x 108 cells liter-1, a 70% increase. Bacterial biomass increased from ~3.6 to 6.3 μg C liter-1, a clear indication that production rates exceeded removal rates (bactivory, viral lysis) over the course of 18 days. Biomass within the fertilized patch was 11% higher than in surrounding unfertilized waters reflecting a similar trend. This pattern is in contrast to SOIREE where no accumulation of biomass was observed. High DNA-containing (HDNA) cells detected by FCM also increased over time in iron fertilized waters from 20% to 46% relative to the total population suggesting an active subpopulation of cells that were growing faster than the removal rates. In iron fertilized waters north of the Polar Front (North Patch), BP and abundance were ~90% and 80% higher, respectively, than in unfertilized waters. Our results suggest an active bacterial population that responded to iron fertilization

  13. Unicellular cyanobacteria Synechocystis accommodate heterotrophic bacteria with varied enzymatic and metal resistance properties.

    PubMed

    Abdulaziz, Anas; Sageer, Saliha; Chekidhenkuzhiyil, Jasmin; Vijayan, Vijitha; Pavanan, Pratheesh; Athiyanathil, Sujith; Nair, Shanta

    2016-08-01

    The interactions between heterotrophic bacteria and primary producers have a profound impact on the functioning of marine ecosystem. We characterized the enzymatic and metal resistance properties of fourteen heterotrophic bacteria isolated from a unicellular cyanobacterium Synechocystis sp. that came from a heavy metal contaminated region of Cochin estuary, southwest coast of India. Based on 16S rRNA gene sequence similarities, the heterotrophic bacteria were grouped into three phyla: namely Actinobacteria, Firmicute, and Proteobacteria. Overall Proteobacteria showed a higher level of enzyme expression while Actinobacteria and Firmicutes showed higher tolerance to heavy metals. Among Proteobacteria, an isolate of Marinobacter hydrocarbonoclasticus (MMRF-584) showed highest activities of β-glucosidase (1.58 ± 0.2 μMml(-1)  min(-1) ) and laminarinase (1170.17 ± 95.4 μgml(-1)  min(-1) ), while other two isolates of M. hydrocarbonoclasticus, MMRF-578 and 581, showed highest phosphatase (44.71 ± 0.2 μMml(-1)  min(-1) ) and aminopeptidase (33.22 ± 0 μMml(-1)  min(-1) ) activities respectively. Among Firmicutes, the Virgibacillus sp. MMRF-571 showed exceptional resistance against the toxic heavy metals Cd (180 mM), Pb (150 mM), and Hg (0.5 mM). Bacillus cereus, MMRF-575, showed resistance to the highest concentrations of Co (250 mM), Cd (150 mM), Pb (180 mM), Hg (0.5 mM), Ni (280 mM), and Zn (250 mM) tested. Our results show that heterotrophic bacteria with varied enzymatic and metal resistance properties are associated with Synechocystis sp. Further studies to delineate the role of these heterotrophic bacteria in protecting primary producers from toxic effects of heavy metals and their potential application in bioremediation will be appreciated. PMID:27106264

  14. Antifungal and antibacterial activity of marine microorganisms.

    PubMed

    El Amraoui, B; El Amraoui, M; Cohen, N; Fassouane, A

    2014-03-01

    In order to explore marine microorganisms with pharmaceutical potential, marine bacteria, collected from different coastal areas of the Moroccan Atlantic Ocean, were previously isolated from seawater, sediment, marine invertebrates and seaweeds. The antimicrobial activities of these microorganisms were investigated against the pathogens involved in human pathologies. Whole cultures of 34 marine microorganisms were screened for antimicrobial activities using the method of agar diffusion against three Gram-positive bacteria, two Gram-negative bacteria, and against yeast. The results showed that among the 34 isolates studied, 28 (82%) strains have antimicrobial activity against at least one pathogen studied, 11 (32%) strains have antifungal activity and 24 (76%) strains are active against Gram-positive bacteria, while 21 (62%) strains are active against Gram-negative bacteria. Among isolates having antimicrobial activity, 14 were identified and were assigned to the genera Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Chromobacterium, Enterococcus, Pantoea and Pseudomonas. Due to a competitive role for space and nutrient, the marine microorganisms can produce antibiotic substance; therefore, these marine microorganisms were expected to be potential resources of natural antibiotic products.

  15. Microorganisms in the atmosphere over Antarctica.

    PubMed

    Pearce, David A; Bridge, Paul D; Hughes, Kevin A; Sattler, Birgit; Psenner, Roland; Russell, Nick J

    2009-08-01

    Antarctic microbial biodiversity is the result of a balance between evolution, extinction and colonization, and so it is not possible to gain a full understanding of the microbial biodiversity of a location, its biogeography, stability or evolutionary relationships without some understanding of the input of new biodiversity from the aerial environment. In addition, it is important to know whether the microorganisms already present are transient or resident - this is particularly true for the Antarctic environment, as selective pressures for survival in the air are similar to those that make microorganisms suitable for Antarctic colonization. The source of potential airborne colonists is widespread, as they may originate from plant surfaces, animals, water surfaces or soils and even from bacteria replicating within the clouds. On a global scale, transport of air masses from the well-mixed boundary layer to high-altitude sites has frequently been observed, particularly in the warm season, and these air masses contain microorganisms. Indeed, it has become evident that much of the microbial life within remote environments is transported by air currents. In this review, we examine the behaviour of microorganisms in the Antarctic aerial environment and the extent to which these microorganisms might influence Antarctic microbial biodiversity.

  16. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

    PubMed Central

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice C.; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-01-01

    Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities. PMID

  17. Soil moisture sensitivity of autotrophic and heterotrophic forest floor respiration in boreal xeric pine and mesic spruce forests

    NASA Astrophysics Data System (ADS)

    Ťupek, Boris; Launiainen, Samuli; Peltoniemi, Mikko; Heikkinen, Jukka; Lehtonen, Aleksi

    2016-04-01

    Litter decomposition rates of the most process based soil carbon models affected by environmental conditions are linked with soil heterotrophic CO2 emissions and serve for estimating soil carbon sequestration; thus due to the mass balance equation the variation in measured litter inputs and measured heterotrophic soil CO2 effluxes should indicate soil carbon stock changes, needed by soil carbon management for mitigation of anthropogenic CO2 emissions, if sensitivity functions of the applied model suit to the environmental conditions e.g. soil temperature and moisture. We evaluated the response forms of autotrophic and heterotrophic forest floor respiration to soil temperature and moisture in four boreal forest sites of the International Cooperative Programme on Assessment and Monitoring of Air Pollution Effects on Forests (ICP Forests) by a soil trenching experiment during year 2015 in southern Finland. As expected both autotrophic and heterotrophic forest floor respiration components were primarily controlled by soil temperature and exponential regression models generally explained more than 90% of the variance. Soil moisture regression models on average explained less than 10% of the variance and the response forms varied between Gaussian for the autotrophic forest floor respiration component and linear for the heterotrophic forest floor respiration component. Although the percentage of explained variance of soil heterotrophic respiration by the soil moisture was small, the observed reduction of CO2 emissions with higher moisture levels suggested that soil moisture response of soil carbon models not accounting for the reduction due to excessive moisture should be re-evaluated in order to estimate right levels of soil carbon stock changes. Our further study will include evaluation of process based soil carbon models by the annual heterotrophic respiration and soil carbon stocks.

  18. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions.

    PubMed

    Cole, Jessica K; Hutchison, Janine R; Renslow, Ryan S; Kim, Young-Mo; Chrisler, William B; Engelmann, Heather E; Dohnalkova, Alice C; Hu, Dehong; Metz, Thomas O; Fredrickson, Jim K; Lindemann, Stephen R

    2014-01-01

    Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities.

  19. Combating Antimicrobial Resistance in Foodborne Microorganisms.

    PubMed

    Lai, Edward P C; Iqbal, Zafar; Avis, Tyler J

    2016-02-01

    This review addresses an important public health hazard affecting food safety. Antimicrobial agents are used in foods to reduce or eliminate microorganisms that cause disease. Many traditional organic compounds, novel synthetic organic agents, natural products, peptides, and proteins have been extensively studied for their effectiveness as antimicrobial agents against foodborne Campylobacter spp., Escherichia coli, Listeria spp. and Salmonella. However, antimicrobial resistance can develop in microorganisms, enhancing their ability to withstand the inhibiting or killing action of antimicrobial agents. Knowledge gaps still exist with regard to the actual chemical and microbiological mechanisms that must be identified to facilitate the search for new antimicrobial agents. Technical implementation of antimicrobial active packing films and coatings against target microorganisms must also be improved for extended product shelf life. Recent advances in antimicrobial susceptibility testing can provide researchers with new momentum to pursue their quest for a resistance panacea.

  20. Microorganism Utilization for Synthetic Milk Production

    NASA Technical Reports Server (NTRS)

    Birmele, Michele; Morford, Megan; Khodadad, Christina; Spencer, Lashelle; Richards, Jeffrey; Strayer, Richard; Caro, Janicce; Hummerick, Mary; Wheeler, Ray

    2014-01-01

    A desired architecture for long duration spaceflight, such as aboard the International Space Station (ISS) or for future missions to Mars, is to provide a supply of fresh food crops for the astronauts. However, some crops can create a high proportion of inedible plant waste. The main goal of this project was to produce the components of milk (sugar, lipid, protein) from inedible plant waste by utilizing microorganisms (fungi, yeast, bacteria). Of particular interest was utilizing the valuable polysaccharide, cellulose, found in plant waste, to naturally fuel- through microorganism cellular metabolism- the creation of sugar (glucose), lipid (milk fat), and protein (casein) to produce a synthetic edible food product. Environmental conditions such as pH, temperature, carbon source, aeration, and choice microorganisms.

  1. Selective enumeration of probiotic microorganisms in cheese.

    PubMed

    Karimi, Reza; Mortazavian, Amir M; Amiri-Rigi, Atefeh

    2012-02-01

    Cheese is a dairy product which has a good potential for delivery of probiotic microorganisms into the human intestine. To be considered to offer probiotic health benefits, probiotics must remain viable in food products above a threshold level (e.g., 10(6) cfu g(-1)) until the time of consumption. In order to ensure that a minimal number of probiotic bacteria is present in the cheese, reliable methods for enumeration are required. The choice of culture medium for selective enumeration of probiotic strains in combination with starters depends on the product matrix, the target group and the taxonomic diversity of the bacterial background flora in the product. Enumeration protocol should be designed as a function of the target microorganism(s) to be quantified in the cheese. An overview of some series of culture media for selective enumeration of commercial probiotic cultures is presented in this review.

  2. Leaching of pyrite by acidophilic heterotrophic iron-oxidizing bacteria in pure and mixed cultures

    SciTech Connect

    Bacelar-Nicolau, P.; Johnson, D.B.

    1999-02-01

    Seven strains of heterotrophic iron-oxidizing acidophilic bacteria were examined to determine their abilities to promote oxidative dissolution of pyrite (FeS{sub 2}) when they were grown in pure cultures and in mixed cultures with sulfur-oxidizing Thiobacillus spp. Only one of the isolates (strain T-24) oxidized pyrite when it was grown in pyrite-basal salts medium. However, when pyrite-containing cultures were supplemented with 0.02% (wt/vol) yeast extract, most of the isolates oxidized pyrite, and one (strain T-24) promoted rates of mineral dissolution similar to the rates observed with the iron-oxidizing autotroph Thiobacillus ferroxidans. Pyrite oxidation by another isolate (strain T-21) occurred in cultures containing between 0.005 and 0.05% (wt/vol) yeast extract but was completely inhibited in cultures containing 0.5% yeast extract. Ferrous iron was also needed for mineral dissolution by the iron-oxidizing heterotrophs, indicating that these organisms oxidize pyrite via the indirect mechanism. Mixed cultures of three isolates (strains T-21, T-232, and T-24) and the sulfur-oxidizing autotroph Thiobacillus thiooxidans promoted pyrite dissolution; since neither strains T-21 and T-23 nor T. thiooxidans could oxidize this mineral in yeast extract-free media, this was a novel example of bacterial synergism. Mixed cultures of strains T-21 and T-23 and the sulfur-oxidizing mixotroph Thiobacillus acidophilus also oxidized pyrite but to a lesser extent than did mixed cultures containing T. thiooxidans. Pyrite leaching by strain T -23 grown in an organic compound-rich medium and incubated either shaken or unshaken was also assessed. The potential environmental significance of iron-oxidizing heterotrophs in accelerating pyrite oxidation is discussed.

  3. Stoichiometric flexibility in diverse aquatic heterotrophic bacteria is coupled to differences in cellular phosphorus quotas

    PubMed Central

    Godwin, Casey M.; Cotner, James B.

    2015-01-01

    It is frequently presumed that heterotrophic bacteria from aquatic environments have low carbon (C) content, high phosphorus (P) content, and maintain homeostasis at low C:P in their biomass. Dissolved and particulate organic matter from primary producers in terrestrial and aquatic environments typically has high C:P ratios, suggesting that heterotrophic bacteria consuming this resource experience stoichiometric imbalance in C and P. The strength of elemental homeostasis is important for understanding how heterotrophic bacteria couple C and P cycles in response to environmental change, yet these generalizations are based upon data from only a few species that might not represent the physiology of bacteria in freshwaters. However, recent research has indicated that some strains of bacteria isolated from freshwaters have flexible C:P stoichiometry and can acclimate to changes in resource C:P. Although it is apparent that strains differ in their biomass C:P and flexibility, the basis for these characteristics has not been explained. We evaluated biomass C:P homeostasis in 24 strains of bacteria isolated from temperate lakes using a uniform relative growth rate in chemostats. Overall, the strains exhibited a range of homeostatic regulation from strong homeostasis to highly flexible biomass stoichiometry, but strains that were isolated using P-rich media formulations were more homeostatic than strains isolated using P-poor media. Strains exhibiting homeostatic biomass C:P had high cellular C and P content and showed little morphological change between C and P limitation. In contrast, stoichiometrically flexible strains had low P quotas and increased their C quotas and cell size under P limitation. Because stoichiometric flexibility is closely coupled to absolute P content in bacteria, anthropogenic inputs of P could lead to prevalence of more homeostatic bacteria, reducing the ability of natural assemblages to buffer changes in the availability of P and organic C. PMID

  4. Fate of antibiotic resistant cultivable heterotrophic bacteria and antibiotic resistance genes in wastewater treatment processes.

    PubMed

    Zhang, Songhe; Han, Bing; Gu, Ju; Wang, Chao; Wang, Peifang; Ma, Yanyan; Cao, Jiashun; He, Zhenli

    2015-09-01

    Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are emerging contaminants of environmental concern. Heterotrophic bacteria in activated sludge have an important role in wastewater treatment plants (WWTPs). However, the fate of cultivable heterotrophic ARB and ARGs in WWPTs process remains unclear. In the present study, we investigated the antibiotic-resistant phenotypes of cultivable heterotrophic bacteria from influent and effluent water of three WWTPs and analysed thirteen ARGs in ARB and in activated sludge from anoxic, anaerobic and aerobic compartments. From each influent or effluent sample of the three plants, 200 isolates were randomly tested for susceptibility to 12 antibiotics. In these samples, between 5% and 64% isolates showed resistance to >9 antibiotics and the proportion of >9-drug-resistant bacteria was lower in isolates from effluent than from influent. Eighteen genera were identified in 188 isolates from influent (n=94) and effluent (n=94) of one WWTP. Six genera (Aeromonas, Bacillus, Lysinibacillus, Microbacterium, Providencia, and Staphylococcus) were detected in both influent and effluent samples. Gram-negative and -positive isolates dominated in influent and effluent, respectively. The 13 tetracycline-, sulphonamide-, streptomycin- and β-lactam-resistance genes were detected at a higher frequency in ARB from influent than from effluent, except for sulA and CTX-M, while in general, the abundances of ARGs in activated sludge from two of the three plants were higher in aerobic compartments than in anoxic ones, indicating abundant ARGs exit in the excess sledges and/or in uncultivable bacteria. These findings may be useful for elucidating the effect of WWTP on ARB and ARGs.

  5. Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing

    SciTech Connect

    Beliaev, Alex S.; Romine, Margaret F.; Serres, Margaret; Bernstein, Hans C.; Linggi, Bryan E.; Markillie, Lye Meng; Isern, Nancy G.; Chrisler, William B.; Kucek, Leo A.; Hill, Eric A.; Pinchuk, Grigoriy; Bryant, Donald A.; Wiley, H. S.; Fredrickson, Jim K.; Konopka, Allan

    2014-04-29

    We employed deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and the marine facultative aerobe Shewanella putrefaciens W3-18-1 to growth in a co-culture and infer the effect of carbon flux distributions on photoautotroph-heterotroph interactions. The overall transcriptome response of both organisms to co-cultivation was shaped by their respective physiologies and growth constraints. Carbon limitation resulted in the expansion of metabolic capacities which was manifested through the transcriptional upregulation of transport and catabolic pathways. While growth coupling occurred via lactate oxidation or secretion of photosynthetically fixed carbon, there was evidence of specific metabolic interactions between the two organisms. On one hand, the production and excretion of specific amino acids (methionine and alanine) by the cyanobacterium correlated with the putative downregulation of the corresponding biosynthetic machinery of Shewanella W3-18-1. On the other hand, the broad and consistent decrease of mRNA levels for many Fe-regulated Synechococcus 7002 genes during co-cultivation suggested increased Fe availability as well as more facile and energy-efficient mechanisms for Fe acquisition by the cyanobacterium. Furthermore, evidence pointed at potentially novel interactions between oxygenic photoautotrophs and heterotrophs related to the oxidative stress response as transcriptional patterns suggested that Synechococcus 7002 rather than Shewanella W3-18-1 provided scavenging functions for reactive oxygen species under co-culture conditions. This study provides an initial insight into the complexity of photoautotrophic-heterotrophic interactions and brings new perspectives of their role in the robustness and stability of the association.

  6. Effects of Forest Age on Soil Autotrophic and Heterotrophic Respiration Differ between Evergreen and Deciduous Forests

    PubMed Central

    Wang, Wei; Zeng, Wenjing; Chen, Weile; Yang, Yuanhe; Zeng, Hui

    2013-01-01

    We examined the effects of forest stand age on soil respiration (SR) including the heterotrophic respiration (HR) and autotrophic respiration (AR) of two forest types. We measured soil respiration and partitioned the HR and AR components across three age classes ∼15, ∼25, and ∼35-year-old Pinus sylvestris var. mongolica (Mongolia pine) and Larix principis-rupprechtii (larch) in a forest-steppe ecotone, northern China (June 2006 to October 2009). We analyzed the relationship between seasonal dynamics of SR, HR, AR and soil temperature (ST), soil water content (SWC) and normalized difference vegetation index (NDVI, a plant greenness and net primary productivity indicator). Our results showed that ST and SWC were driving factors for the seasonal dynamics of SR rather than plant greenness, irrespective of stand age and forest type. For ∼15-year-old stands, the seasonal dynamics of both AR and HR were dependent on ST. Higher Q10 of HR compared with AR occurred in larch. However, in Mongolia pine a similar Q10 occurred between HR and AR. With stand age, Q10 of both HR and AR increased in larch. For Mongolia pine, Q10 of HR increased with stand age, but AR showed no significant relationship with ST. As stand age increased, HR was correlated with SWC in Mongolia pine, but for larch AR correlated with SWC. The dependence of AR on NDVI occurred in ∼35-year-old Mongolia pine. Our study demonstrated the importance of separating autotrophic and heterotrophic respiration components of SR when stimulating the response of soil carbon efflux to environmental changes. When estimating the response of autotrophic and heterotrophic respiration to environmental changes, the effect of forest type on age-related trends is required. PMID:24282560

  7. Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water

    PubMed Central

    Bentzon-Tilia, Mikkel; Severin, Ina; Hansen, Lars H.

    2015-01-01

    ABSTRACT The ability to reduce atmospheric nitrogen (N2) to ammonia, known as N2 fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N2-fixing heterotrophic organisms are widespread in marine bacterioplankton, but their autecology and ecological significance are unknown. Here, we report genomic and ecophysiology data in relation to N2 fixation by three environmentally relevant heterotrophic bacteria isolated from Baltic Sea surface water: Pseudomonas stutzeri strain BAL361 and Raoultella ornithinolytica strain BAL286, which are gammaproteobacteria, and Rhodopseudomonas palustris strain BAL398, an alphaproteobacterium. Genome sequencing revealed that all were metabolically versatile and that the gene clusters encoding the N2 fixation complex varied in length and complexity between isolates. All three isolates could sustain growth by N2 fixation in the absence of reactive N, and this fixation was stimulated by low concentrations of oxygen in all three organisms (≈4 to 40 µmol O2 liter−1). P. stutzeri BAL361 did, however, fix N at up to 165 µmol O2 liter−1, presumably accommodated through aggregate formation. Glucose stimulated N2 fixation in general, and reactive N repressed N2 fixation, except that ammonium (NH4+) stimulated N2 fixation in R. palustris BAL398, indicating the use of nitrogenase as an electron sink. The lack of correlations between nitrogenase reductase gene expression and ethylene (C2H4) production indicated tight posttranscriptional-level control. The N2 fixation rates obtained suggested that, given the right conditions, these heterotrophic diazotrophs could contribute significantly to in situ rates. PMID:26152586

  8. Pollen performance before and during the autotrophic-heterotrophic transition of pollen tube growth.

    PubMed Central

    Stephenson, Andrew G; Travers, Steven E; Mena-Ali, Jorge I; Winsor, James A

    2003-01-01

    For species with bicellular pollen, the attrition of pollen tubes is often greatest where the style narrows at the transition between stigmatic tissue and the transmitting tissue of the style. In this region, the tubes switch from predominantly autotrophic to predominantly heterotrophic growth, the generative cell divides, the first callose plugs are produced, and, in species with RNase-type self-incompatibility (SI), incompatible tubes are arrested. We review the literature and present new findings concerning the genetic, environmental and stylar influences on the performance of pollen before and during the autotrophic-heterotrophic transition of pollen tube growth. We found that the ability of the paternal sporophyte to provision its pollen during development significantly influences pollen performance during the autotrophic growth phase. Consequently, under conditions of pollen competition, pollen selection during the autotrophic phase is acting on the phenotype of the paternal sporophyte. In a field experiment, using Cucurbita pepo, we found broad-sense heritable variation for herbivore-pathogen resistance, and that the most resistant families produced larger and better performing pollen when the paternal sporophytes were not protected by insecticides, indicating that selection during the autotrophic phase can act on traits that are not expressed by the microgametophyte. In a study of a weedy SI species, Solanum carolinense, we found that the ability of the styles to arrest self-pollen tubes at the autotrophic-heterotrophic transition changes with floral age and the presence of developing fruits. These findings have important implications for selection at the level of the microgametophyte and the evolution of mating systems of plants. PMID:12831466

  9. Heterotrophic bacterial production and metabolic balance during the VAHINE mesocosm experiment in the New Caledonia lagoon

    NASA Astrophysics Data System (ADS)

    Van Wambeke, F.; Pfreundt, U.; Barani, A.; Berthelot, H.; Moutin, T.; Rodier, M.; Hess, W. R.; Bonnet, S.

    2015-12-01

    N2 fixation fuels ~ 50 % of new primary production in the oligotrophic South Pacific Ocean. The VAHINE mesocosm experiment designed to track the fate of diazotroph derived nitrogen (DDN) in the New Caledonia lagoon. Here, we examined the temporal dynamics of heterotrophic bacterial production during this experiment. Three replicate large-volume (~ 50 m3) mesocosms were deployed and were intentionally fertilized with dissolved inorganic phosphorus (DIP) to stimulate N2 fixation. We specifically examined relationships between N2 fixation rates and primary production, determined bacterial growth efficiency and established carbon budgets of the system from the DIP fertilization to the end of the experiment (days 5-23). Heterotrophic bacterioplankton production (BP) and alkaline phosphatase activity (APA) were statistically higher during the second phase of the experiment (P2: days 15-23), when chlorophyll biomass started to increase compared to the first phase (P1: days 5-14). Among autotrophs, Synechococcus abundances increased during P2, possibly related to its capacity to assimilate leucine and to produce alkaline phosphatase. Bacterial growth efficiency based on the carbon budget was notably higher than generally cited for oligotrophic environments (27-43 %), possibly due to a high representation of proteorhodopsin-containing organisms within the picoplanctonic community. The carbon budget showed that the main fate of gross primary production (particulate + dissolved) was respiration (67 %), and export through sedimentation (17 %). BP was highly correlated with particulate primary production and chlorophyll biomass during both phases of the experiment but slightly correlated, and only during P2 phase, with N2 fixation rates. Our results suggest that most of the DDN reached the heterotrophic bacterial community through indirect processes, like mortality, lysis and grazing.

  10. Effects of forest age on soil autotrophic and heterotrophic respiration differ between evergreen and deciduous forests.

    PubMed

    Wang, Wei; Zeng, Wenjing; Chen, Weile; Yang, Yuanhe; Zeng, Hui

    2013-01-01

    We examined the effects of forest stand age on soil respiration (SR) including the heterotrophic respiration (HR) and autotrophic respiration (AR) of two forest types. We measured soil respiration and partitioned the HR and AR components across three age classes ~15, ~25, and ~35-year-old Pinus sylvestris var. mongolica (Mongolia pine) and Larix principis-rupprechtii (larch) in a forest-steppe ecotone, northern China (June 2006 to October 2009). We analyzed the relationship between seasonal dynamics of SR, HR, AR and soil temperature (ST), soil water content (SWC) and normalized difference vegetation index (NDVI, a plant greenness and net primary productivity indicator). Our results showed that ST and SWC were driving factors for the seasonal dynamics of SR rather than plant greenness, irrespective of stand age and forest type. For ~15-year-old stands, the seasonal dynamics of both AR and HR were dependent on ST. Higher Q10 of HR compared with AR occurred in larch. However, in Mongolia pine a similar Q10 occurred between HR and AR. With stand age, Q10 of both HR and AR increased in larch. For Mongolia pine, Q10 of HR increased with stand age, but AR showed no significant relationship with ST. As stand age increased, HR was correlated with SWC in Mongolia pine, but for larch AR correlated with SWC. The dependence of AR on NDVI occurred in ~35-year-old Mongolia pine. Our study demonstrated the importance of separating autotrophic and heterotrophic respiration components of SR when stimulating the response of soil carbon efflux to environmental changes. When estimating the response of autotrophic and heterotrophic respiration to environmental changes, the effect of forest type on age-related trends is required.

  11. Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

    PubMed Central

    Beliaev, Alexander S; Romine, Margie F; Serres, Margrethe; Bernstein, Hans C; Linggi, Bryan E; Markillie, Lye M; Isern, Nancy G; Chrisler, William B; Kucek, Leo A; Hill, Eric A; Pinchuk, Grigoriy E; Bryant, Donald A; Steven Wiley, H; Fredrickson, Jim K; Konopka, Allan

    2014-01-01

    We used deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and the marine facultative aerobe Shewanella putrefaciens W3-18-1 to growth in a co-culture and infer the effect of carbon flux distributions on photoautotroph–heterotroph interactions. The overall transcriptome response of both organisms to co-cultivation was shaped by their respective physiologies and growth constraints. Carbon limitation resulted in the expansion of metabolic capacities, which was manifested through the transcriptional upregulation of transport and catabolic pathways. Although growth coupling occurred via lactate oxidation or secretion of photosynthetically fixed carbon, there was evidence of specific metabolic interactions between the two organisms. These hypothesized interactions were inferred from the excretion of specific amino acids (for example, alanine and methionine) by the cyanobacterium, which correlated with the downregulation of the corresponding biosynthetic machinery in Shewanella W3-18-1. In addition, the broad and consistent decrease of mRNA levels for many Fe-regulated Synechococcus 7002 genes during co-cultivation may indicate increased Fe availability as well as more facile and energy-efficient mechanisms for Fe acquisition by the cyanobacterium. Furthermore, evidence pointed at potentially novel interactions between oxygenic photoautotrophs and heterotrophs related to the oxidative stress response as transcriptional patterns suggested that Synechococcus 7002 rather than Shewanella W3-18-1 provided scavenging functions for reactive oxygen species under co-culture conditions. This study provides an initial insight into the complexity of photoautotrophic–heterotrophic interactions and brings new perspectives of their role in the robustness and stability of the association. PMID:24781900

  12. Metabolic activity of microorganisms in evaporites

    NASA Technical Reports Server (NTRS)

    Rothschild, L. J.; Giver, L. J.; White, M. R.; Mancinelli, R. L.

    1994-01-01

    Crystalline salt is generally considered so hostile to most forms of life that it has been used for centuries as a preservative. Here, we present evidence that prokaryotes inhabiting a natural evaporite crust of halite and gypsum are metabolically active while inside the evaporite for at least 10 months. In situ measurements demonstrated that some of these "endoevaporitic" microorganisms (probably the cyanobacterium Synechococcus Nageli) fixed carbon and nitrogen. Denitrification was not observed. Our results quantified the slow microbial activity that can occur in salt crystals. Implications of this study include the possibility that microorganisms found in ancient evaporite deposits may have been part of an evaporite community.

  13. Physiologically anaerobic microorganisms of the deep subsurface

    SciTech Connect

    Stevens, S.E. Jr.; Chung, K.T.

    1991-06-01

    This study seeks to determine numbers, diversity, and morphology of anaerobic microorganisms in 15 samples of subsurface material from the Idaho National Engineering Laboratory, in 18 samples from the Hanford Reservation and in 1 rock sample from the Nevada Test Site; set up long term experiments on the chemical activities of anaerobic microorganisms based on these same samples; work to improve methods for the micro-scale determination of in situ anaerobic microbial activity;and to begin to isolate anaerobes from these samples into axenic culture with identification of the axenic isolates.

  14. Screening and Separation of Microorganisms Degrading PCBs.

    PubMed Central

    Bokvajova, A; Burkhard, J; Demnerova, K; Pazlarova, J

    1994-01-01

    We performed an assay to assess the polychlorinated biphenyl (PCB) degradative capability and congener specificity of aerobic microorganisms. Microbial strains were isolated and separated from different types of soils in the Czech Republic, and their PCB-degrading abilities were compared. An industrial mixture of PCB congeners ranging from dichloro- to hexachlorobiphenyl and representing various chlorination patterns was used throughout. The PCB degradative ability of microorganisms was determined by gas chromatography after 7 days of incubation. The degree of degradation was found to depend on the number of chlorine substituents. PMID:9679114

  15. Functional Properties of Microorganisms in Fermented Foods

    PubMed Central

    Tamang, Jyoti P.; Shin, Dong-Hwa; Jung, Su-Jin; Chae, Soo-Wan

    2016-01-01

    Fermented foods have unique functional properties imparting some health benefits to consumers due to presence of functional microorganisms, which possess probiotics properties, antimicrobial, antioxidant, peptide production, etc. Health benefits of some global fermented foods are synthesis of nutrients, prevention of cardiovascular disease, prevention of cancer, gastrointestinal disorders, allergic reactions, diabetes, among others. The present paper is aimed to review the information on some functional properties of the microorganisms associated with fermented foods and beverages, and their health-promoting benefits to consumers. PMID:27199913

  16. Effect of microwaves on microorganisms in foods

    SciTech Connect

    Fung, D.Y.C.; Cunningham, F.E.

    1980-08-01

    The microbial safety of foods cooked in microwave ovens was investigated. The mechanisms of microwave destruction of microorganisms were examined. Effects of time and temperature on microorganisms in different food systems were described. Studies showed that: microwave heating of food is more ''''food dependent'' than conventional heating; recommended microwave treatment time for some foods may not destroy high levels of bacteria; use of microwaves in combination with conventional heating methods results in more uniform heating of foods and destruction of bacteria; and microwaves exert different killing effects on individual bacterial species. (78 references, 2 tables)

  17. [Metagenomics in studying gastrointestinal tract microorganism].

    PubMed

    Xu, Bo; Yang, Yunjuan; Li, Junjun; Tang, Xianghua; Mu, Yuelin; Huang, Zunxi

    2013-12-01

    Animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host. The gut microbial community of humans and animals has received significant attention from researchers because of its association with health and disease. The application of metagenomics technology enables researchers to study not only the microbial composition but also the function of microbes in the gastrointestinal tract. In this paper, combined with our own findings, we summarized advances in studying gastrointestinal tract microorganism with metagenomics and the bioinformatics technology.

  18. Metabolic activity of microorganisms in evaporites.

    PubMed

    Rothschild, L J; Giver, L J; White, M R; Mancinelli, R L

    1994-06-01

    Crystalline salt is generally considered so hostile to most forms of life that it has been used for centuries as a preservative. Here, we present evidence that prokaryotes inhabiting a natural evaporite crust of halite and gypsum are metabolically active while inside the evaporite for at least 10 months. In situ measurements demonstrated that some of these "endoevaporitic" microorganisms (probably the cyanobacterium Synechococcus Nageli) fixed carbon and nitrogen. Denitrification was not observed. Our results quantified the slow microbial activity that can occur in salt crystals. Implications of this study include the possibility that microorganisms found in ancient evaporite deposits may have been part of an evaporite community. PMID:11539827

  19. Metabolic activity of microorganisms in evaporites.

    PubMed

    Rothschild, L J; Giver, L J; White, M R; Mancinelli, R L

    1994-06-01

    Crystalline salt is generally considered so hostile to most forms of life that it has been used for centuries as a preservative. Here, we present evidence that prokaryotes inhabiting a natural evaporite crust of halite and gypsum are metabolically active while inside the evaporite for at least 10 months. In situ measurements demonstrated that some of these "endoevaporitic" microorganisms (probably the cyanobacterium Synechococcus Nageli) fixed carbon and nitrogen. Denitrification was not observed. Our results quantified the slow microbial activity that can occur in salt crystals. Implications of this study include the possibility that microorganisms found in ancient evaporite deposits may have been part of an evaporite community.

  20. [Effect of electromagnetic fields on movement of microorganisms].

    PubMed

    Zel'nichenko, A T; Koval'chuk, V S; Posudin, Iu I

    1988-01-01

    Relationships between the motor activity and orientation of microorganisms and parameters of the electromagnetic field and of the microorganisms themselves were investigated. It has been shown that the type of microorganism and field amplitude produces the strongest influence on the behaviour of microorganisms in the fields. Theoretical relationships of the value of rotating moment and the field parameters, microorganism and environment were obtained. The results of the experiments well agree with the theory. PMID:3224110

  1. Factors regulating the use of dissolved organic matter by heterotrophic biofilm communities in boreal headwater streams

    NASA Astrophysics Data System (ADS)

    Franke, D.; Ziegler, S. E.

    2011-12-01

    Biofilm communities in headwater streams are the primary drivers of carbon and nutrient cycling, and are critical to our understanding of ecosystem processes and environmental change in boreal watersheds. In situ experiments were conducted using stream water and colonized tiles to assess how biofilm heterotrophic activity, e.g. use of dissolved organic matter (DOM), may be regulated by carbon and nutrient availability at sites within headwater streams of forest, wetland, and nutrient-impacted catchments. Community level respiration and dissolved organic carbon (DOC) uptake were measured and indicate highest microbial activity within wetland-dominated and pond-influenced sites congruent with both the elevated DOC concentrations and greater proportion of carbohydrate carbon in DOM sources in these watersheds. Further, trends of decreasing respiration rates downstream in the forest and wetland catchments followed decreases in DOM carbohydrate and aromatic relative to aliphatic content. These findings suggest that wetland and pond derived sources may increase the bioavailability of DOM relative to DOM derived from landscapes with lower contributions of these sources. To investigate this further, we conducted an additional set of short-term in situ experiments using additions of pond and bog derived DOM concentrates added as substrates to biofilms collected from sites that have exhibited significantly different levels of biofilm activity. Heterotrophic biofilm activity response to these changes in DOM source and composition did not vary significantly relative to the incubations without DOM additions, whether added within or outside the source area. This suggests that DOM lability and the microbial community developed to use this DOM are likely responsible for greater respiration rates and DOC uptake at pond and wetland-influenced locations. Furthermore, nutrient addition treatments in these experiments indicate heterotrophic activity within these catchments was co

  2. Novel insight into the role of heterotrophic dinoflagellates in the fate of crude oil in the sea.

    PubMed

    Almeda, Rodrigo; Connelly, Tara L; Buskey, Edward J

    2014-01-01

    Although planktonic protozoans are likely to interact with dispersed crude oil after a spill, protozoan-mediated processes affecting crude oil pollution in the sea are still not well known. Here, we present the first evidence of ingestion and defecation of physically or chemically dispersed crude oil droplets (1-86 μm in diameter) by heterotrophic dinoflagellates, major components of marine planktonic food webs. At a crude oil concentration commonly found after an oil spill (1 μL L(-1)), the heterotrophic dinoflagellates Noctiluca scintillans and Gyrodinium spirale grew and ingested ~0.37 μg-oil μg-C(dino)(-1) d(-1), which could represent ~17% to 100% of dispersed oil in surface waters when heterotrophic dinoflagellates are abundant or bloom. Egestion of faecal pellets containing crude oil by heterotrophic dinoflagellates could contribute to the sinking and flux of toxic petroleum hydrocarbons in coastal waters. Our study indicates that crude oil ingestion by heterotrophic dinoflagellates is a noteworthy route by which petroleum enters marine food webs and a previously overlooked biological process influencing the fate of crude oil in the sea after spills.

  3. Novel insight into the role of heterotrophic dinoflagellates in the fate of crude oil in the sea

    NASA Astrophysics Data System (ADS)

    Almeda, Rodrigo; Connelly, Tara L.; Buskey, Edward J.

    2014-12-01

    Although planktonic protozoans are likely to interact with dispersed crude oil after a spill, protozoan-mediated processes affecting crude oil pollution in the sea are still not well known. Here, we present the first evidence of ingestion and defecation of physically or chemically dispersed crude oil droplets (1-86 μm in diameter) by heterotrophic dinoflagellates, major components of marine planktonic food webs. At a crude oil concentration commonly found after an oil spill (1 μL L-1), the heterotrophic dinoflagellates Noctiluca scintillans and Gyrodinium spirale grew and ingested ~0.37 μg-oil μg-Cdino-1 d-1, which could represent ~17% to 100% of dispersed oil in surface waters when heterotrophic dinoflagellates are abundant or bloom. Egestion of faecal pellets containing crude oil by heterotrophic dinoflagellates could contribute to the sinking and flux of toxic petroleum hydrocarbons in coastal waters. Our study indicates that crude oil ingestion by heterotrophic dinoflagellates is a noteworthy route by which petroleum enters marine food webs and a previously overlooked biological process influencing the fate of crude oil in the sea after spills.

  4. Pyruvic Oxime Nitrification and Copper and Nickel Resistance by a Cupriavidus pauculus, an Active Heterotrophic Nitrifier-Denitrifier

    PubMed Central

    Linchangco, Richard

    2014-01-01

    Heterotrophic nitrifiers synthesize nitrogenous gasses when nitrifying ammonium ion. A Cupriavidus pauculus, previously thought an Alcaligenes sp. and noted as an active heterotrophic nitrifier-denitrifier, was examined for its ability to produce nitrogen gas (N2) and nitrous oxide (N2O) while heterotrophically nitrifying the organic substrate pyruvic oxime [CH3–C(NOH)–COOH]. Neither N2 nor N2O were produced. Nucleotide and phylogenetic analyses indicated that the organism is a member of a genus (Cupriavidus) known for its resistance to metals and its metabolism of xenobiotics. The microbe (a Cupriavidus pauculus designated as C. pauculus strain UM1) was examined for its ability to perform heterotrophic nitrification in the presence of Cu2+ and Ni2+ and to metabolize the xenobiotic phenol. The bacterium heterotrophically nitrified well when either 1 mM Cu2+ or 0.5 mM Ni2+ was present in either enriched or minimal medium. The organism also used phenol as a sole carbon source in either the presence or absence of 1 mM Cu2+ or 0.5 mM Ni2+. The ability of this isolate to perform a number of different metabolisms, its noteworthy resistance to copper and nickel, and its potential use as a bioremediation agent are discussed. PMID:25580463

  5. Novel insight into the role of heterotrophic dinoflagellates in the fate of crude oil in the sea.

    PubMed

    Almeda, Rodrigo; Connelly, Tara L; Buskey, Edward J

    2014-01-01

    Although planktonic protozoans are likely to interact with dispersed crude oil after a spill, protozoan-mediated processes affecting crude oil pollution in the sea are still not well known. Here, we present the first evidence of ingestion and defecation of physically or chemically dispersed crude oil droplets (1-86 μm in diameter) by heterotrophic dinoflagellates, major components of marine planktonic food webs. At a crude oil concentration commonly found after an oil spill (1 μL L(-1)), the heterotrophic dinoflagellates Noctiluca scintillans and Gyrodinium spirale grew and ingested ~0.37 μg-oil μg-C(dino)(-1) d(-1), which could represent ~17% to 100% of dispersed oil in surface waters when heterotrophic dinoflagellates are abundant or bloom. Egestion of faecal pellets containing crude oil by heterotrophic dinoflagellates could contribute to the sinking and flux of toxic petroleum hydrocarbons in coastal waters. Our study indicates that crude oil ingestion by heterotrophic dinoflagellates is a noteworthy route by which petroleum enters marine food webs and a previously overlooked biological process influencing the fate of crude oil in the sea after spills. PMID:25523528

  6. Novel insight into the role of heterotrophic dinoflagellates in the fate of crude oil in the sea

    PubMed Central

    Almeda, Rodrigo; Connelly, Tara L.; Buskey, Edward J.

    2014-01-01

    Although planktonic protozoans are likely to interact with dispersed crude oil after a spill, protozoan-mediated processes affecting crude oil pollution in the sea are still not well known. Here, we present the first evidence of ingestion and defecation of physically or chemically dispersed crude oil droplets (1–86 μm in diameter) by heterotrophic dinoflagellates, major components of marine planktonic food webs. At a crude oil concentration commonly found after an oil spill (1 μL L−1), the heterotrophic dinoflagellates Noctiluca scintillans and Gyrodinium spirale grew and ingested ~0.37 μg-oil μg-Cdino−1 d−1, which could represent ~17% to 100% of dispersed oil in surface waters when heterotrophic dinoflagellates are abundant or bloom. Egestion of faecal pellets containing crude oil by heterotrophic dinoflagellates could contribute to the sinking and flux of toxic petroleum hydrocarbons in coastal waters. Our study indicates that crude oil ingestion by heterotrophic dinoflagellates is a noteworthy route by which petroleum enters marine food webs and a previously overlooked biological process influencing the fate of crude oil in the sea after spills. PMID:25523528

  7. Measuring micro-organism gas production

    NASA Technical Reports Server (NTRS)

    Wilkins, J. R.; Pearson, A. O.; Mills, S. M.

    1973-01-01

    Transducer, which senses pressure buildup, is easy to assemble and use, and rate of gas produced can be measured automatically and accurately. Method can be used in research, in clinical laboratories, and for environmental pollution studies because of its ability to detect and quantify rapidly the number of gas-producing microorganisms in water, beverages, and clinical samples.

  8. Metagenomics: Application of Genomics to Uncultured Microorganisms

    PubMed Central

    Handelsman, Jo

    2004-01-01

    Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na+(Li+)/H+ antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies. PMID:15590779

  9. Engineered microorganisms having resistance to ionic liquids

    DOEpatents

    Ruegg, Thomas Lawrence; Thelen, Michael P.

    2016-03-22

    The present invention provides for a method of genetically modifying microorganisms to enhance resistance to ionic liquids, host cells genetically modified in accordance with the methods, and methods of using the host cells in a reaction comprising biomass that has been pretreated with ionic liquids.

  10. Microorganism lipid droplets and biofuel development.

    PubMed

    Liu, Yingmei; Zhang, Congyan; Shen, Xipeng; Zhang, Xuelin; Cichello, Simon; Guan, Hongbin; Liu, Pingsheng

    2013-12-01

    Lipid droplet (LD) is a cellular organelle that stores neutral lipids as a source of energy and carbon. However, recent research has emerged that the organelle is involved in lipid synthesis, transportation, and metabolism, as well as mediating cellular protein storage and degradation. With the exception of multi-cellular organisms, some unicellular microorganisms have been observed to contain LDs. The organelle has been isolated and characterized from numerous organisms. Triacylglycerol (TAG) accumulation in LDs can be in excess of 50% of the dry weight in some microorganisms, and a maximum of 87% in some instances. These microorganisms include eukaryotes such as yeast and green algae as well as prokaryotes such as bacteria. Some organisms obtain carbon from CO2 via photosynthesis, while the majority utilizes carbon from various types of biomass. Therefore, high TAG content generated by utilizing waste or cheap biomass, coupled with an efficient conversion rate, present these organisms as bio-tech 'factories' to produce biodiesel. This review summarizes LD research in these organisms and provides useful information for further LD biological research and microorganism biodiesel development.

  11. Microorganism lipid droplets and biofuel development

    PubMed Central

    Liu, Yingmei; Zhang, Congyan; Shen, Xipeng; Zhang, Xuelin; Cichello, Simon; Guan, Hongbin; Liu, Pingsheng

    2013-01-01

    Lipid droplet (LD) is a cellular organelle that stores neutral lipids as a source of energy and carbon. However, recent research has emerged that the organelle is involved in lipid synthesis, transportation, and metabolism, as well as mediating cellular protein storage and degradation. With the exception of multi-cellular organisms, some unicellular microorganisms have been observed to contain LDs. The organelle has been isolated and characterized from numerous organisms. Triacylglycerol (TAG) accumulation in LDs can be in excess of 50% of the dry weight in some microorganisms, and a maximum of 87% in some instances. These microorganisms include eukaryotes such as yeast and green algae as well as prokaryotes such as bacteria. Some organisms obtain carbon from CO2 via photosynthesis, while the majority utilizes carbon from various types of biomass. Therefore, high TAG content generated by utilizing waste or cheap biomass, coupled with an efficient conversion rate, present these organisms as bio-tech ‘factories’ to produce biodiesel. This review summarizes LD research in these organisms and provides useful information for further LD biological research and microorganism biodiesel development. [BMB Reports 2013; 46(12): 575-581] PMID:24355300

  12. 40 CFR 725.85 - Microorganism identity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    .... (iii) Upon receipt of a request described in § 725.15(b), EPA may require the submitter who originally...)(2) of this section, EPA will issue for publication in the Federal Register notice described in § 725... microorganism which is described by a generic name on the public Inventory may submit an inquiry to EPA...

  13. Ecophysiology of psychrophilic and psychrotolerant microorganisms.

    PubMed

    Bölter, M

    2004-07-01

    This review describes psychrophilic and psychrotolerant microorganisms, which are abundant in different kinds of environments. Their ecophysiological properties and strategies for survival are reviewed in relation to their occurrences in marine and terrestrial environments, with special reference to the deep-sea, the sea ice and the permafrost soils. PMID:15559973

  14. Mechanisms of nickel toxicity in microorganisms

    PubMed Central

    Macomber, Lee

    2014-01-01

    Summary Nickel has long been known to be an important human toxicant, including having the ability to form carcinomas, but until recently nickel was believed to be an issue only to microorganisms living in nickel-rich serpentine soils or areas contaminated by industrial pollution. This assumption was overturned by the discovery of a nickel defense system (RcnR/RcnA) found in microorganisms that live in a wide range of environmental niches, suggesting that nickel homeostasis is a general biological concern. To date, the mechanisms of nickel toxicity in microorganisms and higher eukaryotes are poorly understood. In this review, we summarize nickel homeostasis processes used by microorganisms and highlight in vivo and in vitro effects of exposure to elevated concentrations of nickel. On the basis of this evidence we propose four mechanisms of nickel toxicity: 1) nickel replaces the essential metal of metalloproteins, 2) nickel binds to catalytic residues of non-metalloenzymes; 3) nickel binds outside the catalytic site of an enzyme to inhibit allosterically, and 4) nickel indirectly causes oxidative stress. PMID:21799955

  15. Human recombinant lysosomal enzymes produced in microorganisms.

    PubMed

    Espejo-Mojica, Ángela J; Alméciga-Díaz, Carlos J; Rodríguez, Alexander; Mosquera, Ángela; Díaz, Dennis; Beltrán, Laura; Díaz, Sergio; Pimentel, Natalia; Moreno, Jefferson; Sánchez, Jhonnathan; Sánchez, Oscar F; Córdoba, Henry; Poutou-Piñales, Raúl A; Barrera, Luis A

    2015-01-01

    Lysosomal storage diseases (LSDs) are caused by accumulation of partially degraded substrates within the lysosome, as a result of a function loss of a lysosomal protein. Recombinant lysosomal proteins are usually produced in mammalian cells, based on their capacity to carry out post-translational modifications similar to those observed in human native proteins. However, during the last years, a growing number of studies have shown the possibility to produce active forms of lysosomal proteins in other expression systems, such as plants and microorganisms. In this paper, we review the production and characterization of human lysosomal proteins, deficient in several LSDs, which have been produced in microorganisms. For this purpose, Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, and Ogataea minuta have been used as expression systems. The recombinant lysosomal proteins expressed in these hosts have shown similar substrate specificities, and temperature and pH stability profiles to those produced in mammalian cells. In addition, pre-clinical results have shown that recombinant lysosomal enzymes produced in microorganisms can be taken-up by cells and reduce the substrate accumulated within the lysosome. Recently, metabolic engineering in yeasts has allowed the production of lysosomal enzymes with tailored N-glycosylations, while progresses in E. coli N-glycosylations offer a potential platform to improve the production of these recombinant lysosomal enzymes. In summary, microorganisms represent convenient platform for the production of recombinant lysosomal proteins for biochemical and physicochemical characterization, as well as for the development of ERT for LSD.

  16. Mass spectrometry for rapid characterization of microorganisms.

    PubMed

    Demirev, Plamen A; Fenselau, Catherine

    2008-01-01

    Advances in instrumentation, proteomics, and bioinformatics have contributed to the successful applications of mass spectrometry (MS) for detection, identification, and classification of microorganisms. These MS applications are based on the detection of organism-specific biomarker molecules, which allow differentiation between organisms to be made. Intact proteins, their proteolytic peptides, and nonribosomal peptides have been successfully utilized as biomarkers. Sequence-specific fragments for biomarkers are generated by tandem MS of intact proteins or proteolytic peptides, obtained after, for instance, microwave-assisted acid hydrolysis. In combination with proteome database searching, individual biomarker proteins are unambiguously identified from their tandem mass spectra, and from there the source microorganism is also identified. Such top-down or bottom-up proteomics approaches permit rapid, sensitive, and confident characterization of individual microorganisms in mixtures and are reviewed here. Examples of MS-based functional assays for detection of targeted microorganisms, e.g., Bacillus anthracis, in environmental or clinically relevant backgrounds are also reviewed. PMID:20636075

  17. Radiation sensitivity of hyperthermal composting microorganisms

    NASA Astrophysics Data System (ADS)

    Choi, Jong-Il; Yoon, Min-Chul; Kim, Jae-Hun; Yamashita, Masamichi; Kim, Geun Joong; Lee, Ju-Woon

    In the space station and vehicles designed for long human mission, high-temperature compost is a promising technology for decomposing organic waste and producing the fertilizers. In space, the microorganisms could have the changed biological activities or even be mutated by ionizing irradiation. Therefore, in this study, the effect of gamma irradiation on the sensitivity of bacteria in hyperthermal composting was investigated. The sequence analysis of the amplified 16s rDNA genes and amoA gene were used for the identification of composting microorganisms. Viability of microorganisms in compost soil after gamma irradiation was directly visualized with LIVE/DEAD Baclight viability kit. The dominant bacterial genera are Weissella cibaria and Leuconostoc sp. and fungus genera are Metschnikowia bicuspidate and Pichia guilliermondii, respectively. By the gamma irradiation up to the dose of 1 kGy, the microbial population was not changed. Also, the enzyme activities of amylase and cellulose were sustained by the gamma irradiation. These results show that these hyperthermia microorganisms might have the high resistance to gamma radiation and could be used for agriculture in the Space Station.

  18. Diversity of root associated microorganisms of selected medicinal plants and influence of rhizomicroorganisms on the antimicrobial property of Coriandrum sativum.

    PubMed

    Tamilarasi, S; Nanthakumar, K; Karthikeyan, K; Lakshmanaperumalsamy, P

    2008-01-01

    The total heterotrophic bacteria, actinomycetes and fungus were enumerated from the rhizosphere and non-rhizosphere soil of 50 selected locally available medicinal plants in and around Bharathiar University. In all the plants, population of microorganism were higher in the rhizosphere soil than in the non rhizosphere soil. Among the microorganisms, bacterial population was higher in number followed by fungus and actinomycetes. Of the medicinal plants, the maximum rhizosphere effect was observed in Annona squamosa and the minimum effect was seen in Eclipta alba and Cassia auriculata. Among the bacteria the dominant species was Bacillus followed by Pseudomonas, Enterobacter, Corynebacterium, Micrococcus and Serratia. The Streptomyces species was found to be dominant followed by Deuteromycetes and Frankia among the actinomycetes. Among the fungal isolates Rhizopus was found to be higher in number followed by Aspergillus, Penicillium, Mucor and Fusarium. About 70.96% of the bacterial isolates were found to be nitrate reducers and 90.60% of the bacteria solubilised phosphate. The rhizosphere bacterial isolates were also capable of hydrolyzing starch, cellulose, casein, urea and gelatin. The isolates of bacteria, actinomycetes and fungus were also able to produce phytohormone Indole-3-acetic acid (IAA). The maximum IAA production was recorded by Fusarium sp (5.8 mg/l). The rhizosphere bacterial isolates showed resistance to 14 commercially used antibiotics. In an attempt to check the influence of these plant growth promoting microorganisms on the antimicrobial property of Coriandrum sativum against Escherichia coli MTCC-443 and Aeromonas hydrophila MTCC-646, the results observed was not encouraging since the inoculants did not influence the antibacterial property. However extensive and in depth study is required to find out the influence of rhizomicroorganisms on the antibacterial property of medicinal plants. The other results clearly indicated that the rhizosphere

  19. Optimization of complex medium composition for heterotrophic cultivation of Euglena gracilis and paramylon production.

    PubMed

    Ivušić, Franjo; Šantek, Božidar

    2015-06-01

    Heterotrophic cultivation of Euglena gracilis was carried out on synthetic (Hutner medium) and complex cultivation media in order to optimize production of β-1,3-glucan (paramylon). For preparation of complex media, various industrial by-products (e.g., molasses, corn steep solid, yeast extract, and beef extract) were used with or without addition of pure compounds [glucose, galactose, fructose, lactose, maltose, sucrose, and (NH4)2HPO4]. Heterotrophic cultivation of E. gracilis was performed in Erlenmeyer flasks and additionally confirmed during research in the stirred tank bioreactor. The results clearly show that E. gracilis can easily metabolize glucose and fructose as carbon sources and corn steep solid as complex nitrogen and growth factors source for biomass growth and paramylon synthesis. Furthermore, it was also proved that addition of (NH4)2HPO4, beef extract, or gibberellic acid did not have positive effect on the biomass growth and paramylon synthesis. After optimization of complex medium composition and verification in the stirred tank bioreactor, it was concluded that medium composed of glucose (20 g/L) and corn steep solid (30 g/L) is the most suitable complex medium for industrial cultivation of E. gracilis and paramylon production.

  20. Ammonium removal by Agrobacterium sp. LAD9 capable of heterotrophic nitrification-aerobic denitrification.

    PubMed

    Chen, Qian; Ni, Jinren

    2012-05-01

    Characteristics of ammonium removal by a newly isolated heterotrophic nitrification-aerobic denitrification bacterium Agrobacterium sp. LAD9 were systematically investigated. Succinate and acetate were found to be the most favorable carbon sources for LAD9. Response surface methodology (RSM) analysis demonstrated that maximum removal of ammonium occurred under the conditions with an initial pH of 8.46, C/N ratio of 8.28, temperature of 27.9°C and shaking speed of 150rpm, where temperature and shaking speed produced the largest effect. Further nitrogen balance analysis revealed that 50.1% of nitrogen was removed as gas products and 40.8% was converted to the biomass. Moreover, the occurrence of aerobic denitrification was evidenced by the utilization of nitrite and nitrate as nitrogen sources, and the successful amplifications of membrane bound nitrate reductase and cytochrome cd(1) nitrite reductase genes from strain LAD9. Thus, the nitrogen removal in strain LAD9 was speculated to comply with the mechanism of heterotrophic nitrification coupled with aerobic denitrification (NH(4)(+)-NH(2)OH-NO(2)(-)-N(2)O-N(2)), in which also accompanied with the mutual transformation of nitrite and nitrate. The findings can help in applying appropriate controls over operational parameters in systems involving the use of this kind of strain.

  1. Diffusive fractionation complicates isotopic partitioning of autotrophic and heterotrophic sources of soil respiration.

    PubMed

    Moyes, Andrew B; Gaines, Sarah J; Siegwolf, Rolf T W; Bowling, David R

    2010-11-01

    Carbon isotope ratios (δ¹³C) of heterotrophic and rhizospheric sources of soil respiration under deciduous trees were evaluated over two growing seasons. Fluxes and δ¹³C of soil respiratory CO₂ on trenched and untrenched plots were calculated from closed chambers, profiles of soil CO₂ mole fraction and δ¹³C and continuous open chambers. δ¹³C of respired CO₂ and bulk carbon were measured from excised leaves and roots and sieved soil cores. Large diel variations (>5‰) in δ¹³C of soil respiration were observed when diel flux variability was large relative to average daily fluxes, independent of trenching. Soil gas transport modelling supported the conclusion that diel surface flux δ¹³C variation was driven by non-steady state gas transport effects. Active roots were associated with high summertime soil respiration rates and around 1‰ enrichment in the daily average δ¹³C of the soil surface CO₂ flux. Seasonal δ¹³C variability of about 4‰ (most enriched in summer) was observed on all plots and attributed to the heterotrophic CO₂ source. PMID:20545887

  2. Away from darkness: a review on the effects of solar radiation on heterotrophic bacterioplankton activity

    PubMed Central

    Ruiz-González, Clara; Simó, Rafel; Sommaruga, Ruben; Gasol, Josep M.

    2013-01-01

    Heterotrophic bacterioplankton are main consumers of dissolved organic matter (OM) in aquatic ecosystems, including the sunlit upper layers of the ocean and freshwater bodies. Their well-known sensitivity to ultraviolet radiation (UVR), together with some recently discovered mechanisms bacteria have evolved to benefit from photosynthetically available radiation (PAR), suggest that natural sunlight plays a relevant, yet difficult to predict role in modulating bacterial biogeochemical functions in aquatic ecosystems. Three decades of experimental work assessing the effects of sunlight on natural bacterial heterotrophic activity reveal responses ranging from high stimulation to total inhibition. In this review, we compile the existing studies on the topic and discuss the potential causes underlying these contrasting results, with special emphasis on the largely overlooked influences of the community composition and the previous light exposure conditions, as well as the different temporal and spatial scales at which exposure to solar radiation fluctuates. These intricate sunlight-bacteria interactions have implications for our understanding of carbon fluxes in aquatic systems, yet further research is necessary before we can accurately evaluate or predict the consequences of increasing surface UVR levels associated with global change. PMID:23734148

  3. Transcriptionally active heterotrophic diazotrophs are widespread in the upper water column of the Arabian Sea.

    PubMed

    Bird, Clare; Wyman, Michael

    2013-04-01

    Pelagic nitrogen fixation makes an important contribution to the fixed nitrogen budget of the world's oceans. Filamentous and unicellular cyanobacteria are significant players in this process but less is known of the potential activity of heterotrophic diazotrophs, although they are present and can be quite numerous in the nitrogen-deplete surface waters of the tropical and sub-tropical oceans. In this study we focused on the potential activity of several clades of heterotrophic nitrogen-fixers identified by phylogenetic analysis of 44 non-Trichodesmium-related, nifH (encoding the Fe-subunit of nitrogenase) clones from the Arabian Sea. Specific Northern slot blot protocols were developed to quantify nifH mRNAs from each clade and showed that two groups of Gammaproteobacteria, including the previously characterized UMB clade, and a third, novel phylotype affiliated with cluster III anaerobes, were actively expressing nitrogenase in the equatorial waters of this region. Transcripts (nifH mRNAs) from the latter clade were particularly abundant and were also detected in the suboxic waters of the oxygen minimum zone further north. Like the gammaproteobacterial groups, nifH expression by these organisms appeared to be insensitive to combined nitrogen concentrations and was readily detected in the nutrient-replete waters below the upper mixed layer as well as at shallower depths.

  4. Halotolerant aerobic heterotrophic bacteria from the Great Salt Plains of Oklahoma.

    PubMed

    Caton, T M; Witte, L R; Ngyuen, H D; Buchheim, J A; Buchheim, M A; Schneegurt, M A

    2004-11-01

    The Salt Plains National Wildlife Refuge (SPNWR) near Cherokee, Oklahoma, contains a barren salt flat where Permian brine rises to the surface and evaporates under dry conditions to leave a crust of white salt. Rainfall events dissolve the salt crust and create ephemeral streams and ponds. The rapidly changing salinity and high surface temperatures, salinity, and UV exposure make this an extreme environment. The Salt Plains Microbial Observatory (SPMO) examined the soil microbial community of this habitat using classic enrichment and isolation techniques and phylogenetic rDNA studies. Rich growth media have been emphasized that differ in total salt concentration and composition. Aerobic heterotrophic enrichments were performed under a variety of conditions. Heterotrophic enrichments and dilution plates have generated 105 bacterial isolates, representing 46 phylotypes. The bacterial isolates have been characterized phenotypically and subjected to rDNA sequencing and phylogenetic analyses. Fast-growing isolates obtained from enrichments with 10% salt are predominantly from the gamma subgroup of the Proteobacteria and from the low GC Gram-positive cluster. Several different areas on the salt flats have yielded a variety of isolates from the Gram-negative genera Halomonas, Idiomarina, Salinivibrio, and Bacteroidetes. Gram-positive bacteria are well represented in the culture collection including members of the Bacillus, Salibacillus, Oceanobacillus, and Halobacillus. PMID:15696379

  5. Coupling Between Heterotrophic Nanoflagellates and Bacteria in Fresh Waters: Does Latitude Make a Difference?

    PubMed

    Segovia, Bianca T; Domingues, Carolina D; Meira, Bianca R; Lansac-Toha, Fernando M; Fermani, Paulina; Unrein, Fernando; Lobão, Lúcia M; Roland, Fabio; Velho, Luiz F M; Sarmento, Hugo

    2016-01-01

    Recent studies reported comparatively lower heterotrophic bacteria (HB) abundances in tropical regions, indicating that factors involved in bacterial losses could be more relevant in the tropics. Heterotrophic nanoflagellates (HNF) are considered the main predators of HB in aquatic ecosystems, and one should expect higher abundances in the tropics because of differences in the food web configuration (absence of large daphnids). However, there are no comprehensive studies comparing HB and HNF abundances in a latitudinal gradient. We hypothesized that HB abundance would be lower in the tropics because HNF abundance would be higher, resulting in a tighter HNF-HB coupling. To test this hypothesis, we compiled a large dataset of HB and HNF abundances from tropical and temperate freshwater environments. We found that both HB and HNF abundances were lower in the tropical region, and that HNF-HB coupling does not differ between temperate and tropical regions. The lower HNF abundance and lack of coupling may be explained by a strong top-down control on HNF and/or their herbivory preference. Besides, no relationship was found between bacterial specific growth rate and either chlorophyll-a and HB abundance, indicating that bacterial losses may have an important role in tropical freshwaters. Thus, we found that HNF is likely not the main controllers of HB abundance, and that grazing by ciliates and cladocerans, together with the physiological effects of higher temperatures, may explain the high bacterial loss rates in the tropics.

  6. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge.

    PubMed

    Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Bajic, Vladimir; Qian, Pei-Yuan

    2014-11-01

    Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body.

  7. Electricity-driven metabolic shift through direct electron uptake by electroactive heterotroph Clostridium pasteurianum

    PubMed Central

    Choi, Okkyoung; Kim, Taeyeon; Woo, Han Min; Um, Youngsoon

    2014-01-01

    Although microbes directly accepting electrons from a cathode have been applied for CO2 reduction to produce multicarbon-compounds, a high electron demand and low product concentration are critical limitations. Alternatively, the utilization of electrons as a co-reducing power during fermentation has been attempted, but there must be exogenous mediators due to the lack of an electroactive heterotroph. Here, we show that Clostridium pasteurianum DSM 525 simultaneously utilizes both cathode and substrate as electron donors through direct electron transfer. In a cathode compartment poised at +0.045 V vs. SHE, a metabolic shift in C. pasteurianum occurs toward NADH-consuming metabolite production such as butanol from glucose (20% shift in terms of NADH consumption) and 1,3-propandiol from glycerol (21% shift in terms of NADH consumption). Notably, a small amount of electron uptake significantly induces NADH-consuming pathways over the stoichiometric contribution of the electrons as reducing equivalents. Our results demonstrate a previously unknown electroactivity and metabolic shift in the biochemical-producing heterotroph, opening up the possibility of efficient and enhanced production of electron-dense metabolites using electricity. PMID:25376371

  8. Optimization of complex medium composition for heterotrophic cultivation of Euglena gracilis and paramylon production.

    PubMed

    Ivušić, Franjo; Šantek, Božidar

    2015-06-01

    Heterotrophic cultivation of Euglena gracilis was carried out on synthetic (Hutner medium) and complex cultivation media in order to optimize production of β-1,3-glucan (paramylon). For preparation of complex media, various industrial by-products (e.g., molasses, corn steep solid, yeast extract, and beef extract) were used with or without addition of pure compounds [glucose, galactose, fructose, lactose, maltose, sucrose, and (NH4)2HPO4]. Heterotrophic cultivation of E. gracilis was performed in Erlenmeyer flasks and additionally confirmed during research in the stirred tank bioreactor. The results clearly show that E. gracilis can easily metabolize glucose and fructose as carbon sources and corn steep solid as complex nitrogen and growth factors source for biomass growth and paramylon synthesis. Furthermore, it was also proved that addition of (NH4)2HPO4, beef extract, or gibberellic acid did not have positive effect on the biomass growth and paramylon synthesis. After optimization of complex medium composition and verification in the stirred tank bioreactor, it was concluded that medium composed of glucose (20 g/L) and corn steep solid (30 g/L) is the most suitable complex medium for industrial cultivation of E. gracilis and paramylon production. PMID:25601569

  9. Long-term changes in heterotrophic prokaryotes abundance and growth characteristics in the northern Adriatic Sea

    NASA Astrophysics Data System (ADS)

    Ivančić, Ingrid; Fuks, Dragica; Najdek, Mirjana; Blažina, Maria; Devescovi, Massimo; Šilović, Tina; Paliaga, Paolo; Orlić, Sandi

    2010-09-01

    During the 1990-2008 period heterotrophic prokaryotes abundance (HP) in the northern Adriatic showed a substantial decrease after 2003. Before 2003 the HP annual cycle was characterized by minimal values during winter (100-134 · 10 7 cell l - 1 , on average) and a gradual increase toward summer (up to 212 · 10 7 cell l - 1 , on average). After 2003 HP was low during the most part of the year (27-63 · 10 7 cell l - 1 , on average), with somewhat higher values only at the end of summer and in April (up to 80 · 10 7 cell l - 1 in average). The overall higher Leu/TdR ratio after 2003 showed that prokaryotes were increasing their cellular biomass but more slowly dividing than before. There were indications that changed hydrographic conditions, reduced substrate supply and quality changes might be the most responsible factors for the observed HP decrease and change in their growth characteristics. As a consequence of lower HP heterotrophic flagellates abundance (HF) after 2003 (average 0.57 · 10 6 cell l - 1 ) generally decreased by about three times. Weakened coupling between HP and HF confirmed the minor role of grazing pressure in controlling HP after 2003. This study shows the direct response of the microbial community to meteorological and subsequent hydrographical condition changes that occurred in the northern Adriatic.

  10. Heterotrophic feeding as a newly identified survival strategy of the dinoflagellate Symbiodinium

    NASA Astrophysics Data System (ADS)

    Jeong, Hae Jin; Du Yoo, Yeong; Kang, Nam Seon; Lim, An Suk; Seong, Kyeong Ah; Lee, Sung Yeon; Lee, Moo Joon; Lee, Kyung Ha; Kim, Hyung Seop; Shin, Woongghi; Nam, Seung Won; Yih, Wonho; Lee, Kitack

    2012-07-01

    Survival of free-living and symbiotic dinoflagellates (Symbiodinium spp.) in coral reefs is critical to the maintenance of a healthy coral community. Most coral reefs exist in oligotrophic waters, and their survival strategy in such nutrient-depleted waters remains largely unknown. In this study, we found that two strains of Symbiodinium spp. cultured from the environment and acquired from the tissues of the coral Alveopora japonica had the ability to feed heterotrophically. Symbiodinium spp. fed on heterotrophic bacteria, cyanobacteria (Synechococcus spp.), and small microalgae in both nutrient-replete and nutrient-depleted conditions. Cultured free-living Symbiodinium spp. displayed no autotrophic growth under nitrogen-depleted conditions, but grew when provided with prey. Our results indicate that Symbiodinium spp.'s mixotrophic activity greatly increases their chance of survival and their population growth under nitrogen-depleted conditions, which tend to prevail in coral habitats. In particular, free-living Symbiodinium cells acquired considerable nitrogen from algal prey, comparable to or greater than the direct uptake of ammonium, nitrate, nitrite, or urea. In addition, free-living Symbiodinium spp. can be a sink for planktonic cyanobacteria (Synechococcus spp.) and remove substantial portions of Synechococcus populations from coral reef waters. Our discovery of Symbiodinium's feeding alters our conventional views of the survival strategies of photosynthetic Symbiodinium and corals.

  11. Flow cytometric detection and quantification of heterotrophic nanoflagellates in enriched seawater and cultures.

    PubMed

    Guindulain Rifà, Teresa; Latatu, Ainhoa; Ayo, Begoña; Iriberri, Juan; Comas-Riu, Jaume; Vives-Rego, Josep

    2002-04-01

    A flow cytometric protocol to detect and enumerate heterotrophic nanoflagellates (HNF) in enriched waters is reported. At present, the cytometric protocols that allow accurate quantification of bacterioplankton cannot be used to quantify protozoa for the following reasons: i) the background produced by the bacterial acquisitions does not allow the discrimination of protozoa at low abundance, ii) since the final protozoan fluorescence is much higher than the bacterioplankton fluorescence (more than 35 fold) the protozoa acquisitions lie outside the range. With an increase in the fluorescence threshold and a reduction of the fluorescence detector voltage, low fluorescence particles (bacteria) are beneath the detection limits and only higher fluorescence particles (most of them heterotrophic nanoflagellates) are detected. The main limitation for the application of the cytometric protocol developed is that a ratio of bacteria/HNF below 1000 is needed. At higher ratios, the background of larger cells of bacterioplankton makes it difficult to discriminate protozoa. The proposed protocol has been validated by epifluorescence microscopy analyzing both a mixed community and two single species of HFN: Rhynchomonas nasuta and Jakoba libera. Taking into account the required bacteria/HNF ratio cited above, the results provide evidence that the flow cytometric protocol reported here is valid for counting mixed communities of HNF in enriched seawater and in experimental micro or mesocosms. In the case of single species of HNF previous knowledge of the biological characteristics of the protist and how they can affect the effectiveness of the flow cytometric count is necessary. PMID:12086176

  12. Direct Effects of UV-B Radiation on the Freshwater Heterotrophic Nanoflagellate Paraphysomonas sp.▿

    PubMed Central

    Macaluso, Amy L.; Mitchell, David L.; Sanders, Robert W.

    2009-01-01

    The formation of DNA photoproducts in organisms exposed to ambient levels of UV-B radiation can lead to death and/or reduced population growth in aquatic systems. Dependence on photoenzymatic repair to reverse DNA damage caused by UV-B radiation is demonstrated for Paraphysomonas sp., a member of a widely distributed genus of heterotrophic nanoflagellates. At 20°C, Paraphysomonas sp. was exposed to a range of UV-B intensities encountered in natural systems. Populations of the flagellate survived and grew in a dose-dependent manner, but only when simultaneously exposed to photorepair radiation (PRR). In contrast, flagellates exposed to UV-B at 15°C suffered 100% mortality except at the lowest UV-B level (with PRR) tested, which suggested a photorepair temperature optimum above 15°C. After acute UV-B exposures, DNA damage (measured as the formation of pyrimidine dimers) was reduced only in organisms that underwent subsequent exposure to PRR. Populations kept in the dark after UV-B exposure maintained the initial levels of pyrimidine dimers. These results are the first to demonstrate the reliance of a heterotrophic flagellate on photoenzymatic DNA repair for survival from UV-B exposure. PMID:19429560

  13. Bacterial pollution, activity and heterotrophic diversity of the northern part of the Aegean Sea, Turkey.

    PubMed

    Çiftçi Türetken, Pelin S; Altuğ, Gülşen

    2016-02-01

    Isolation and characterization studies of marine heterotrophic bacteria are important to describe and understand eco-metobolism of the marine environments. In this study, diversity and community structures of the culturable heterotrophic bacteria, metabollicaly active bacteria and bacterial pollution in the coastal and offshore areas of Gökçeada Island, in the Northern Aegean Sea, Turkey were investigated from March 2012 to November 2013. The primary hydrographic parameters were recorded in situ. The frequency of the metabolically active bacteria was determined by using a modified staining technique. The indicator bacteria were determined by using membrane filtration technique; 126 bacteria isolates, 24 of them first records for this region, were identified using an automated micro-identification system, VITEK2 Compact30. The results showed that detected bacterial community profiles were significantly different when compared with previous studies conducted in polluted marine areas of Turkey. High frequency of faecal bacteria detected at station 2 indicated that increasing human activities and terrestrial pollution sources are shaping factors for possible risks, regarding recreational uses of this region, in the summer seasons.

  14. Coupling Between Heterotrophic Nanoflagellates and Bacteria in Fresh Waters: Does Latitude Make a Difference?

    PubMed Central

    Segovia, Bianca T.; Domingues, Carolina D.; Meira, Bianca R.; Lansac-Toha, Fernando M.; Fermani, Paulina; Unrein, Fernando; Lobão, Lúcia M.; Roland, Fabio; Velho, Luiz F. M.; Sarmento, Hugo

    2016-01-01

    Recent studies reported comparatively lower heterotrophic bacteria (HB) abundances in tropical regions, indicating that factors involved in bacterial losses could be more relevant in the tropics. Heterotrophic nanoflagellates (HNF) are considered the main predators of HB in aquatic ecosystems, and one should expect higher abundances in the tropics because of differences in the food web configuration (absence of large daphnids). However, there are no comprehensive studies comparing HB and HNF abundances in a latitudinal gradient. We hypothesized that HB abundance would be lower in the tropics because HNF abundance would be higher, resulting in a tighter HNF–HB coupling. To test this hypothesis, we compiled a large dataset of HB and HNF abundances from tropical and temperate freshwater environments. We found that both HB and HNF abundances were lower in the tropical region, and that HNF-HB coupling does not differ between temperate and tropical regions. The lower HNF abundance and lack of coupling may be explained by a strong top-down control on HNF and/or their herbivory preference. Besides, no relationship was found between bacterial specific growth rate and either chlorophyll-a and HB abundance, indicating that bacterial losses may have an important role in tropical freshwaters. Thus, we found that HNF is likely not the main controllers of HB abundance, and that grazing by ciliates and cladocerans, together with the physiological effects of higher temperatures, may explain the high bacterial loss rates in the tropics. PMID:26903993

  15. Particle handling during interception feeding by four species of heterotrophic nanoflagellates.

    PubMed

    Boenigk, J; Arndt, H

    2000-01-01

    High resolution video-microscopy was used to observe grazing patterns of the heterotrophic nanoflagellates Cafeteria roenbergensis, Bodo saltans, Spumella sp., and Ochromonas sp. Spumella and Ochromonas enclose food particles with pseudopodia while Cafeteria and Bodo engulf particles by invagination of the cell surface. The following parameters of the feeding process were quantified: frequency of flagellar beating, speed of particles in different positions of the feeding current, food size selection, feeding rate, and the time budget for the handling of particles. The mean handling times differed between 94 s for Cafeteria and 4 s for Ochromonas for ingested particles. Handling times for ingested particles were significantly longer than for non-captured particles. Long handling times were calculated to be disadvantageous only for flagellates which propel a high water volume per hour (esp. Ochromonas) or live in a bacteria-rich environment. Our model calculations may provide a reasonable theoretical explanation for a concentration-dependent behavioural variability of the feeding strategy of different heterotrophic nanoflagellates (HNF) species.

  16. Population of aerobic heterotrophic nitrogen-fixing bacteria associated with wetland and dryland rice

    SciTech Connect

    Barraquio, W.L.; De Guzman, M.R.; Barrion, M.; Watanahe, I.

    1982-01-01

    Nitrogen-fixing activity and populations of nitrogen-fixing bacteria associated with two varieties of rice grown in dryland and wetland conditions were measured at various growth stages during the dry season. Acetylene reduction activities were measured both in the field and for the hydroponically grown rice, which was transferred from the field to water culture 1 day before assay. The activities measured by both methods were higher in wetland than in dryland rice. The population of nitrogen-fixing heterotrophic bacteria associated with rhizosphere soil, root, and basal shoots was determined by the most probable number method with semisolid glucose-yeast extract and semisolid malate-yeast extract media. The number of nitrogen-fixing bacteria was higher in wetland conditions than in dryland conditions. The difference between two conditions was most pronounced in the population associated with the basal shoot. The glucose medium gave higher counts than did the malate medium. Colonies were picked from tryptic soy agar plates, and their nitrogen-fixing activity was tested on a semisolid glucose-yeast extract medium. The incidence of nitrogen-fixing bacteria among aerobic heterotrophic bacteria in association with rhizosphere soil, root, and basal shoots was much lower in dryland rice than in wetland rice. (Refs. 11).

  17. Electricity-driven metabolic shift through direct electron uptake by electroactive heterotroph Clostridium pasteurianum.

    PubMed

    Choi, Okkyoung; Kim, Taeyeon; Woo, Han Min; Um, Youngsoon

    2014-11-07

    Although microbes directly accepting electrons from a cathode have been applied for CO2 reduction to produce multicarbon-compounds, a high electron demand and low product concentration are critical limitations. Alternatively, the utilization of electrons as a co-reducing power during fermentation has been attempted, but there must be exogenous mediators due to the lack of an electroactive heterotroph. Here, we show that Clostridium pasteurianum DSM 525 simultaneously utilizes both cathode and substrate as electron donors through direct electron transfer. In a cathode compartment poised at +0.045 V vs. SHE, a metabolic shift in C. pasteurianum occurs toward NADH-consuming metabolite production such as butanol from glucose (20% shift in terms of NADH consumption) and 1,3-propandiol from glycerol (21% shift in terms of NADH consumption). Notably, a small amount of electron uptake significantly induces NADH-consuming pathways over the stoichiometric contribution of the electrons as reducing equivalents. Our results demonstrate a previously unknown electroactivity and metabolic shift in the biochemical-producing heterotroph, opening up the possibility of efficient and enhanced production of electron-dense metabolites using electricity.

  18. Halotolerant aerobic heterotrophic bacteria from the Great Salt Plains of Oklahoma.

    PubMed

    Caton, T M; Witte, L R; Ngyuen, H D; Buchheim, J A; Buchheim, M A; Schneegurt, M A

    2004-11-01

    The Salt Plains National Wildlife Refuge (SPNWR) near Cherokee, Oklahoma, contains a barren salt flat where Permian brine rises to the surface and evaporates under dry conditions to leave a crust of white salt. Rainfall events dissolve the salt crust and create ephemeral streams and ponds. The rapidly changing salinity and high surface temperatures, salinity, and UV exposure make this an extreme environment. The Salt Plains Microbial Observatory (SPMO) examined the soil microbial community of this habitat using classic enrichment and isolation techniques and phylogenetic rDNA studies. Rich growth media have been emphasized that differ in total salt concentration and composition. Aerobic heterotrophic enrichments were performed under a variety of conditions. Heterotrophic enrichments and dilution plates have generated 105 bacterial isolates, representing 46 phylotypes. The bacterial isolates have been characterized phenotypically and subjected to rDNA sequencing and phylogenetic analyses. Fast-growing isolates obtained from enrichments with 10% salt are predominantly from the gamma subgroup of the Proteobacteria and from the low GC Gram-positive cluster. Several different areas on the salt flats have yielded a variety of isolates from the Gram-negative genera Halomonas, Idiomarina, Salinivibrio, and Bacteroidetes. Gram-positive bacteria are well represented in the culture collection including members of the Bacillus, Salibacillus, Oceanobacillus, and Halobacillus.

  19. Are Freshwater Mixotrophic Ciliates Less Sensitive to Solar Ultraviolet Radiation than Heterotrophic Ones?1

    PubMed Central

    SONNTAG, BETTINA; SUMMERER, MONIKA; SOMMARUGA, RUBEN

    2011-01-01

    We tested whether mixotrophic ciliates are more resistant to solar ultraviolet radiation (UVR) than heterotrophic ones because symbiotic algae can provide self-shading by cell matter absorption and eventually by direct UV screening from mycosporine-like amino acids (MAAs). Sensitivity of a natural assemblage to solar radiation was tested in experiments in the original lake and in a more UV transparent alpine lake after transplantation of the ciliates. In both lakes, the assemblage was exposed either to full sunlight, to photosynthetically active radiation only, or kept in the dark. In each lake, exposure was for 5 h at the surface and at the depth corresponding to the 10% attenuation depth at 320 nm. Overall, when the assemblage was exposed to surface UVR, only one out of four dominant mixotrophic ciliates, Vorticella chlorellata, was more resistant than heterotrophic species. The higher UV resistance in V. chlorellata was related to the presence of MAAs and the high percentage of ciliate volume occupied by algal symbionts. Our results indicate that effects of UVR were species-specific and depended on efficient screening of these wavelengths, but also on the depth preference of the ciliates and thus, on their previous exposure history to UVR. PMID:21414057

  20. Heterotrophic feeding as a newly identified survival strategy of the dinoflagellate Symbiodinium

    PubMed Central

    Jeong, Hae Jin; Yoo, Yeong Du; Kang, Nam Seon; Lim, An Suk; Seong, Kyeong Ah; Lee, Sung Yeon; Lee, Moo Joon; Lee, Kyung Ha; Kim, Hyung Seop; Shin, Woongghi; Nam, Seung Won; Yih, Wonho; Lee, Kitack

    2012-01-01

    Survival of free-living and symbiotic dinoflagellates (Symbiodinium spp.) in coral reefs is critical to the maintenance of a healthy coral community. Most coral reefs exist in oligotrophic waters, and their survival strategy in such nutrient-depleted waters remains largely unknown. In this study, we found that two strains of Symbiodinium spp. cultured from the environment and acquired from the tissues of the coral Alveopora japonica had the ability to feed heterotrophically. Symbiodinium spp. fed on heterotrophic bacteria, cyanobacteria (Synechococcus spp.), and small microalgae in both nutrient-replete and nutrient-depleted conditions. Cultured free-living Symbiodinium spp. displayed no autotrophic growth under nitrogen-depleted conditions, but grew when provided with prey. Our results indicate that Symbiodinium spp.’s mixotrophic activity greatly increases their chance of survival and their population growth under nitrogen-depleted conditions, which tend to prevail in coral habitats. In particular, free-living Symbiodinium cells acquired considerable nitrogen from algal prey, comparable to or greater than the direct uptake of ammonium, nitrate, nitrite, or urea. In addition, free-living Symbiodinium spp. can be a sink for planktonic cyanobacteria (Synechococcus spp.) and remove substantial portions of Synechococcus populations from coral reef waters. Our discovery of Symbiodinium’s feeding alters our conventional views of the survival strategies of photosynthetic Symbiodinium and corals. PMID:22814379

  1. Influence of river discharge on abundance and dissemination of heterotrophic, indicator and pathogenic bacteria along the East Coast of India.

    PubMed

    Prasad, V R; Srinivas, T N R; Sarma, V V S S

    2015-06-15

    In order to examine the influence of discharge from different rivers from peninsular India and urban sewage on intensity and dissemination of heterotrophic, indicator and pathogenic bacteria, a study was carried out during peak discharge period along coastal Bay of Bengal. The coastal Bay received freshwater inputs from the river Ganges while Godavari and Krishna contributed to the south. Contrasting difference in salinity, temperature, nutrients and organic matter was observed between north and south east coast of India. The highest heterotrophic, indicator and pathogenic bacterial abundance was observed in the central coastal Bay that received urban sewage from the major city. Intensity and dissemination of heterotrophic, indicator and pathogenic bacteria displayed linear relation with magnitude of discharge. The coliform load was observed up to 100km from the coast suggesting that marine waters were polluted during the monsoon season and its impact on the ecosystem needs further studies. PMID:25934433

  2. Dynamic Responses of Root, Mycorrhizal and Soil Heterotrophic Respiration to Temperature Increases in an Arid System of Southeast Spain.

    NASA Astrophysics Data System (ADS)

    Estruch, C.; Pugnaire, F. I.

    2014-12-01

    Mycorrhizal and heterotrophic respiration may represent up to 80% of total soil respiration in temperate environments; however little is known about arid environments where the dynamics of carbon cycling is less known. To improve models of CO2 efflux to the atmosphere in these environments it is necessary to quantify the contribution of soil components (roots, mycorrhizas and heterotrophic respiration) to soil respiration and their response to temperature increases. We settled up a soil partitioning experiment in December 2013 to address this topic. Using a mesh-collar design we quantified soil respiration of the tree main components (roots, mycorrhiza and heterotrophic respiration) in a Mediterranean arid location dominated by the shrub Rethama sphaerocarpa under two temperature regimes, an increased air temperature using open-top chambers (OTC) and a control. For the firths 6 months of measurements, we recorded a decrease in annual species cover with increased temperature; total soil respiration varied between treatments, being higher in the control treatment while, contrary to our expectations, mycorrhizal and soil heterotrophic respiration did not vary between treatments. When looking at the relative contribution of the different soil components, the treatment enclosing both mycorrhizal and soil heterotrophic respiration represented more than half the total soil respiration. These results show that temperature affects total soil respiration and that, in our case, mycorrhizal and soil heterotrophic community were not major drivers of soil respiration responses to temperature. However, these data correspond to an abnormal dry period and data to be collected during the wet season would help us to better understand the contribution of the different soil components to temperature increases in arid environments.

  3. Comparison of lysogeny (prophage induction) in heterotrophic bacterial and Synechococcus populations in the Gulf of Mexico and Mississippi River plume.

    PubMed

    Long, Amy; McDaniel, Lauren D; Mobberley, Jennifer; Paul, John H

    2008-02-01

    Lysogeny has been documented as a fundamental process occurring in natural marine communities of heterotrophic and autotrophic bacteria. Prophage induction has been observed to be prevalent during conditions of low host abundance, but factors controlling the process are poorly understood. A research cruise was undertaken to the Gulf of Mexico during July 2005 to explore environmental factors associated with lysogeny. Ambient physical and microbial parameters were measured and prophage induction experiments were performed in contrasting oligotrophic Gulf and eutrophic Mississippi plume areas. Three of 11 prophage induction experiments in heterotrophic bacteria (27%) demonstrated significant induction in response to Mitomycin C. In contrast, there was significant Synechococcus cyanophage induction in seven of nine experiments (77.8%). A strong negative correlation was observed between lysogeny and log-transformed activity measurements for both heterotrophic and autotrophic populations (r=-0.876, P=0.002 and r=-0.815, P=0.025, respectively), indicating that bacterioplankton with low host growth favor lysogeny. Multivariate statistical analyses indicated that ambient level of viral abundance and productivity were inversely related to heterotrophic prophage induction and both factors combined were most predictive of lysogeny (rho=0.899, P=0.001). For Synechococcus, low ambient cyanophage abundance was most predictive of lysogeny (rho=0.862, P=0.005). Abundance and productivity of heterotrophic bacteria was strongly inversely correlated with salinity, while Synechococcus was not. This indicated that heterotrophic bacterial populations were well adapted to the river plume environments, thus providing a possible explanation for differences in prevalence of lysogeny observed between the two populations. PMID:18049460

  4. Decadal warming causes a consistent and persistent shift from heterotrophic to autotrophic respiration in contrasting permafrost ecosystems.

    PubMed

    Hicks Pries, Caitlin E; van Logtestijn, Richard S P; Schuur, Edward A G; Natali, Susan M; Cornelissen, Johannes H C; Aerts, Rien; Dorrepaal, Ellen

    2015-12-01

    Soil carbon in permafrost ecosystems has the potential to become a major positive feedback to climate change if permafrost thaw increases heterotrophic decomposition. However, warming can also stimulate autotrophic production leading to increased ecosystem carbon storage-a negative climate change feedback. Few studies partitioning ecosystem respiration examine decadal warming effects or compare responses among ecosystems. Here, we first examined how 11 years of warming during different seasons affected autotrophic and heterotrophic respiration in a bryophyte-dominated peatland in Abisko, Sweden. We used natural abundance radiocarbon to partition ecosystem respiration into autotrophic respiration, associated with production, and heterotrophic decomposition. Summertime warming decreased the age of carbon respired by the ecosystem due to increased proportional contributions from autotrophic and young soil respiration and decreased proportional contributions from old soil. Summertime warming's large effect was due to not only warmer air temperatures during the growing season, but also to warmer deep soils year-round. Second, we compared ecosystem respiration responses between two contrasting ecosystems, the Abisko peatland and a tussock-dominated tundra in Healy, Alaska. Each ecosystem had two different timescales of warming (<5 years and over a decade). Despite the Abisko peatland having greater ecosystem respiration and larger contributions from heterotrophic respiration than the Healy tundra, both systems responded consistently to short- and long-term warming with increased respiration, increased autotrophic contributions to ecosystem respiration, and increased ratios of autotrophic to heterotrophic respiration. We did not detect an increase in old soil carbon losses with warming at either site. If increased autotrophic respiration is balanced by increased primary production, as is the case in the Healy tundra, warming will not cause these ecosystems to become

  5. Recombinant microorganisms for increased production of organic acids

    DOEpatents

    Yi, Jian; Kleff, Susanne; Guettler, Michael V

    2013-04-30

    Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

  6. Recombinant microorganisms for increased production of organic acids

    DOEpatents

    Yi, Jian; Kleff, Susanne; Guettler, Michael V.

    2012-02-21

    Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

  7. Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park.

    PubMed

    Vishnivetskaya, Tatiana A; Hamilton-Brehm, Scott D; Podar, Mircea; Mosher, Jennifer J; Palumbo, Anthony V; Phelps, Tommy J; Keller, Martin; Elkins, James G

    2015-02-01

    The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this study, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55-85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.

  8. Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park.

    PubMed

    Vishnivetskaya, Tatiana A; Hamilton-Brehm, Scott D; Podar, Mircea; Mosher, Jennifer J; Palumbo, Anthony V; Phelps, Tommy J; Keller, Martin; Elkins, James G

    2015-02-01

    The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this study, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55-85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures. PMID:25319238

  9. Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park

    DOE PAGES

    Vishnivetskaya, Tatiana A.; Hamilton-Brehm, Scott D.; Podar, Mircea; Mosher, Jennifer J.; Palumbo, Anthony V.; Phelps, Tommy J.; Keller, Martin; Elkins, James G.

    2014-10-16

    The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this paper, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversitymore » in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55–85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Finally, independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.« less

  10. Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park

    SciTech Connect

    Vishnivetskaya, Tatiana A.; Hamilton-Brehm, Scott D.; Podar, Mircea; Mosher, Jennifer J.; Palumbo, Anthony V.; Phelps, Tommy J.; Keller, Martin; Elkins, James G.

    2014-10-16

    The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this paper, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55–85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Finally, independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.

  11. Abundance of potentially pathogenic micro-organisms in Penaeus monodon larvae rearing systems in India.

    PubMed

    Vaseeharan, Baskaralingam; Ramasamy, Palaniappan

    2003-01-01

    Monodon baculovirls (MBV), external fouling organisms (EFO) and bacteria (especially Vibrio species) were monitored during 1996-1997 at nine different Penaeus monodon rearing hatcheries in India. Total cultivable heterotrophic bacteria, Vibrio-like-bacteria, presumptive Vibrio harveyi, Vibrio anguillarum, Vibrio vulnificus counts were determined from shrimp eggs, post larvae, rearing tank water, source sea water, feed (Artemia nauplii and microencapsulated feed). The MBV infected post larvae and their environment showed higher Vibrio-like-bacteria than uninfected post larvae. An overwhelming predominance of presumptive Vibrio harveyi and Vibrio anguillarum was observed in post larval rearing tank water, MBV infected and uninfected post larvae. Vibrio-like-bacteria in Artemia nauplii clearly showed the possible source of these pathogenic bacteria in the hatchery environments. Quantitative analysis of Vibrio-like-bacteria in hatcheries revealed that when the Vibrio-like-bacteria increases to 2 x 10(2) CFU mortality of the post larvae occurs. Abundance of these micro-organisms in hatchery samples indicated that they are opportunistic pathogens which can invade the shrimp tissue, subsequently cause disease when the post larvae were under stressful conditions.

  12. New microorganisms and processes for MEOR. Quarterly report ending, December 31, 1992

    SciTech Connect

    Sperl, P.L.; Sperl, G.T.

    1992-12-31

    We have been successful in isolating and characterizing sulfate reducing bacteria and denitrifying Thiobacillus sp. from oil field waters which can use volatile fatty acids and dissolve carbonates found in these waters and formations. We have shown that these cultures can feed each other in sequential cultures and survive in mixed culture as long as sterile conditions are maintained. When nonsterile conditions are present both organism types are only successful to a limited degree, and, instead, an additional microflora develop belonging to the heterotrophic denitrifying bacteria. These microorganisms appear to be potentially useful in new MEOR processes through the production of pressure forming gases, viscosifying agents and the removal and prevention of de novo synthesis of hydrogen sulfide and are currently being pursued. They are capable of producing large amounts of gas, predominantly nitrogen and carbon dioxide and also form viscosifying agents under conditions which we believe we can easily maintain in an oil reservoir. In this report we show that they are also potent agents for the control of SRB growth, development and production of sulfide.

  13. Local climatic adaptation in a widespread microorganism.

    PubMed

    Leducq, Jean-Baptiste; Charron, Guillaume; Samani, Pedram; Dubé, Alexandre K; Sylvester, Kayla; James, Brielle; Almeida, Pedro; Sampaio, José Paulo; Hittinger, Chris Todd; Bell, Graham; Landry, Christian R

    2014-02-22

    Exploring the ability of organisms to locally adapt is critical for determining the outcome of rapid climate changes, yet few studies have addressed this question in microorganisms. We investigated the role of a heterogeneous climate on adaptation of North American populations of the wild yeast Saccharomyces paradoxus. We found abundant among-strain variation for fitness components across a range of temperatures, but this variation was only partially explained by climatic variation in the distribution area. Most of fitness variation was explained by the divergence of genetically distinct groups, distributed along a north-south cline, suggesting that these groups have adapted to distinct climatic conditions. Within-group fitness components were correlated with climatic conditions, illustrating that even ubiquitous microorganisms locally adapt and harbour standing genetic variation for climate-related traits. Our results suggest that global climatic changes could lead to adaptation to new conditions within groups, or changes in their geographical distributions.

  14. Characterization of Microorganisms by MALDI Mass Spectrometry

    SciTech Connect

    Petersen, Catherine E.; Valentine, Nancy B.; Wahl, Karen L.

    2008-10-02

    Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for characterization and analysis of microorganisms, specifically bacteria, is described here as a rapid screening tool. The objective of this technique is not comprehensive protein analysis of a microorganism but rather a rapid screening of the organism and the accessible protein pattern for characterization and distinction. This method is based on the ionization of the readily accessible and easily ionizable portion of the protein profile of an organism that is often characteristic of different bacterial species. The utility of this screening approach is yet to reach its full potential but could be applied to food safety, disease outbreak monitoring in hospitals, culture stock integrity and verification, microbial forensics or homeland security applications.

  15. Microorganisms detection on substrates using QCL spectroscopy

    NASA Astrophysics Data System (ADS)

    Padilla-Jiménez, Amira C.; Ortiz-Rivera, William; Castro-Suarez, John R.; Ríos-Velázquez, Carlos; Vázquez-Ayala, Iris; Hernández-Rivera, Samuel P.

    2013-05-01

    Recent investigations have focused on the improvement of rapid and accurate methods to develop spectroscopic markers of compounds constituting microorganisms that are considered biological threats. Quantum cascade lasers (QCL) systems have revolutionized many areas of research and development in defense and security applications, including his area of research. Infrared spectroscopy detection based on QCL was employed to acquire mid infrared (MIR) spectral signatures of Bacillus thuringiensis (Bt), Escherichia coli (Ec) and Staphylococcus epidermidis (Se), which were used as biological agent simulants of biothreats. The experiments were carried out in reflection mode on various substrates such as cardboard, glass, travel baggage, wood and stainless steel. Chemometrics statistical routines such as principal component analysis (PCA) regression and partial least squares-discriminant analysis (PLS-DA) were applied to the recorded MIR spectra. The results show that the infrared vibrational techniques investigated are useful for classification/detection of the target microorganisms on the types of substrates studied.

  16. UV inactivation of pathogenic and indicator microorganisms

    SciTech Connect

    Chang, J.C.; Ossoff, S.F.; Lobe, D.C.; Dorfman, M.H.; Dumais, C.M.; Qualls, R.G.; Johnson, J.D.

    1985-06-01

    Survival was measured as a function of the dose of germicidal UV light for the bacteria Escherichia coli, Salmonella typhi, Shigella sonnei, Streptococcus faecalis, Staphylococcus aureus, and Bacillus subtilis spores, the enteric viruses poliovirus type 1 and simian rotavirus SA11, the cysts of the protozoan Acanthamoeba castellanii, as well as for total coliforms and standard plate count microorganisms from secondary effluent. The doses of UV light necessary for a 99.9% inactivation of the cultured vegetative bacteria, total coliforms, and standard plate count microorganisms were comparable. However, the viruses, the bacterial spores, and the amoebic cysts required about 3 to 4 times, 9 times, and 15 times, respectively, the dose required for E. coli. These ratios covered a narrower relative dose range than that previously reported for chlorine disinfection of E. coli, viruses, spores, and cysts.

  17. How could haloalkaliphilic microorganisms contribute to biotechnology?

    PubMed

    Zhao, Baisuo; Yan, Yanchun; Chen, Shulin

    2014-11-01

    Haloalkaliphiles are microorganisms requiring Na(+) concentrations of at least 0.5 mol·L(-1) and an alkaline pH of 9 for optimal growth. Their unique features enable them to make significant contributions to a wide array of biotechnological applications. Organic compatible solutes produced by haloalkaliphiles, such as ectoine and glycine betaine, are correlated with osmoadaptation and may serve as stabilizers of intracellular proteins, salt antagonists, osmoprotectants, and dermatological moisturizers. Haloalkaliphiles are an important source of secondary metabolites like rhodopsin, polyhydroxyalkanoates, and exopolysaccharides that play essential roles in biogeocycling organic compounds. These microorganisms also can secrete unique exoenzymes, including proteases, amylases, and cellulases, that are highly active and stable in extreme haloalkaline conditions and can be used for the production of laundry detergent. Furthermore, the unique metabolic pathways of haloalkaliphiles can be applied in the biodegradation and (or) biotransformation of a broad range of toxic industrial pollutants and heavy metals, in wastewater treatment, and in the biofuel industry.

  18. Assessment of microorganisms from Indonesian Oil Fields

    SciTech Connect

    Kadarwati, S.; Udiharto, M.; Rahman, M.; Jasjfi, E.; Legowo, E.H.

    1995-12-31

    Petroleum resources have been the mainstay of the national development in Indonesia. However, resources are being depleted after over a century of exploitation, while the demand continues to grow with the rapid economic development of the country. In facing the problem, EOR has been applied in Indonesia, such as the steamflooding project in Duri field, but a more energy efficient technology would be preferable. Therefore, MEOR has been recommended as a promising solution. Our study, aimed at finding indigenous microorganisms which can be developed for application in MEOR, has isolated microbes from some oil fields of Indonesia. These microorganisms have been identified, their activities studied, and the effects of their metabolisms examined. This paper describes the research carried out by LEMIGAS in this respect, giving details on the methods of sampling, incubation, identification, and activation of the microbes as well as tests on the effects of their metabolites, with particular attention to those with potential for application in MEOR.

  19. Local climatic adaptation in a widespread microorganism

    PubMed Central

    Leducq, Jean-Baptiste; Charron, Guillaume; Samani, Pedram; Dubé, Alexandre K.; Sylvester, Kayla; James, Brielle; Almeida, Pedro; Sampaio, José Paulo; Hittinger, Chris Todd; Bell, Graham; Landry, Christian R.

    2014-01-01

    Exploring the ability of organisms to locally adapt is critical for determining the outcome of rapid climate changes, yet few studies have addressed this question in microorganisms. We investigated the role of a heterogeneous climate on adaptation of North American populations of the wild yeast Saccharomyces paradoxus. We found abundant among-strain variation for fitness components across a range of temperatures, but this variation was only partially explained by climatic variation in the distribution area. Most of fitness variation was explained by the divergence of genetically distinct groups, distributed along a north–south cline, suggesting that these groups have adapted to distinct climatic conditions. Within-group fitness components were correlated with climatic conditions, illustrating that even ubiquitous microorganisms locally adapt and harbour standing genetic variation for climate-related traits. Our results suggest that global climatic changes could lead to adaptation to new conditions within groups, or changes in their geographical distributions. PMID:24403328

  20. UV inactivation of pathogenic and indicator microorganisms.

    PubMed Central

    Chang, J C; Ossoff, S F; Lobe, D C; Dorfman, M H; Dumais, C M; Qualls, R G; Johnson, J D

    1985-01-01

    Survival was measured as a function of the dose of germicidal UV light for the bacteria Escherichia coli, Salmonella typhi, Shigella sonnei, Streptococcus faecalis, Staphylococcus aureus, and Bacillus subtilis spores, the enteric viruses poliovirus type 1 and simian rotavirus SA11, the cysts of the protozoan Acanthamoeba castellanii, as well as for total coliforms and standard plate count microorganisms from secondary effluent. The doses of UV light necessary for a 99.9% inactivation of the cultured vegetative bacteria, total coliforms, and standard plate count microorganisms were comparable. However, the viruses, the bacterial spores, and the amoebic cysts required about 3 to 4 times, 9 times, and 15 times, respectively, the dose required for E. coli. These ratios covered a narrower relative dose range than that previously reported for chlorine disinfection of E. coli, viruses, spores, and cysts. PMID:2990336

  1. Consolidated bioprocessing method using thermophilic microorganisms

    DOEpatents

    Mielenz, Jonathan Richard

    2016-02-02

    The present invention is directed to a method of converting biomass to biofuel, and particularly to a consolidated bioprocessing method using a co-culture of thermophilic and extremely thermophilic microorganisms which collectively can ferment the hexose and pentose sugars produced by degradation of cellulose and hemicelluloses at high substrate conversion rates. A culture medium therefor is also provided as well as use of the methods to produce and recover cellulosic ethanol.

  2. The transfer of viable microorganisms between planets.

    PubMed

    Davies, P C

    1996-01-01

    There is increasing acceptance that catastrophic cosmic impacts have played an important role in shaping the history of terrestrial life. Large asteroid and cometary impacts are also capable of displacing substantial quantities of planetary surface material into space. The discovery of Martian rocks on Earth suggests that viable microorganisms within such ejecta could be exchanged between planets. If this conjecture is correct, it will have profound implications for the origin and evolution of life in the solar system.

  3. Microorganism Utilization for Synthetic Milk Production

    NASA Technical Reports Server (NTRS)

    Morford, Megan A.; Khodadad, Christina L.; Mccoy, LaShelle E.; Richards, Jeffrey T.; Strayer, Richard F.; Caro, Janicce L.; Hummerick, Mary E.; Birmele, Michele N.; Wheeler, Raymond M.

    2014-01-01

    A desired architecture for long duration spaceflight, such as aboard the International Space Station (ISS) or for future missions to Mars, is to provide a supply of fresh food crops for the astronauts. However, some crops can create a high proportion of inedible plant waste. The main goal of this project was to produce the components of milk (sugar, lipid, protein) from inedible plant waste by utilizing microorganisms (fungi, yeast, bacteria). Of particular interest was utilizing the valuable polysaccharide, cellulose, found in plant waste, to naturally fuel- through microorganism cellular metabolism- the creation of sugar (glucose), lipid (milk fat), and protein (casein) to produce a synthetic edible food product. Environmental conditions such as pH, temperature, carbon source, aeration, and choice microorganisms were optimized in the laboratory and the desired end-products, sugars and lipids, were analyzed. Trichoderma reesei, a known cellulolytic fungus, was utilized to drive the production of glucose, with the intent that the produced glucose would serve as the carbon source for milk fat production and be a substitute for the milk sugar lactose. Lipid production would be carried out by Rhodosporidium toruloides, yeast known to accumulate those lipids that are typically found in milk fat. Results showed that glucose and total lipid content were below what was expected during this phase of experimentation. In addition, individual analysis of six fatty acids revealed that the percentage of each fatty acid was lower than naturally produced bovine milk. Overall, this research indicates that microorganisms could be utilized to breakdown inedible solid waste to produce useable products.

  4. Mass Spectrometer for Airborne Micro-Organisms

    NASA Technical Reports Server (NTRS)

    Sinha, M. P.; Friedlander, S. K.

    1986-01-01

    Bacteria and other micro-organisms identified continously with aid of new technique for producing samples for mass spectrometer. Technique generates aerosol of organisms and feeds to spectrometer. Given species of organism produces characteristic set of peaks in mass spectrum and thereby identified. Technique useful for monitoring bacterial makeup in environmental studies and in places where cleanliness is essential, such as hospital operating rooms, breweries, and pharmaceutical plants.

  5. Control of microorganisms in flowing nutrient solutions.

    PubMed

    Evans, R D

    1994-11-01

    Controlling microorganisms in flowing nutrient solutions involves different techniques when targeting the nutrient solution, hardware surfaces in contact with the solution, or the active root zone. This review presents basic principles and applications of a number of treatment techniques, including disinfection by chemicals, ultrafiltration, ultrasonics, and heat treatment, with emphasis on UV irradiation and ozone treatment. Procedures for control of specific pathogens by nutrient solution conditioning also are reviewed.

  6. MICROORGANISMS DIE-OFF RATES IN URBAN STORMWATER RUNOFF 2007

    EPA Science Inventory

    Stormwater best management practices (BMPs) are often considered effective tools to mitigate the effects of stormwater pollutants before they are discharged to receiving waters. However, BMP performance for microorganisms removal is not well documented. Microorganisms die-off in...

  7. MICROORGANISMS DIE-OFF RATES IN URBAN STORMWATER RUNOFF 2007

    EPA Science Inventory

    Stormwater best management practices (BMPs) are often considered effective tools to mitigate the effects of stormwater pollutants before they are discharged to receiving waters. However, BMP performance for microorganisms removal is not well documented. Microorganisms die-off in ...

  8. MODELING THE FATE OF MICROORGANISMS IN WATER, WASTEWATER, AND SOIL

    EPA Science Inventory

    The natural environment is filled with microorganisms, most of which are natural residents and colonize various ecological niches. These microorganisms either live independently within the environment, or live in association with various host organisms. There also are places and ...

  9. Investigation to identify paint coatings resistive to microorganism growth

    NASA Technical Reports Server (NTRS)

    Cooper, C. W.; Kemp, H. T.

    1971-01-01

    All selected coatings contain nutrients that support microbial growth and survival. Incorporation of microbiocidal agents into coatings more susceptible to attack is recommended for improved inhibition of microorganism growth and for increased protection against deterioration of coatings by microorganisms.

  10. Protein Languages Differ Depending on Microorganism Lifestyle

    PubMed Central

    Grzymski, Joseph J.; Marsh, Adam G.

    2014-01-01

    Few quantitative measures of genome architecture or organization exist to support assumptions of differences between microorganisms that are broadly defined as being free-living or pathogenic. General principles about complete proteomes exist for codon usage, amino acid biases and essential or core genes. Genome-wide shifts in amino acid usage between free-living and pathogenic microorganisms result in fundamental differences in the complexity of their respective proteomes that are size and gene content independent. These differences are evident across broad phylogenetic groups–a result of environmental factors and population genetic forces rather than phylogenetic distance. A novel comparative analysis of amino acid usage–utilizing linguistic analyses of word frequency in language and text–identified a global pattern of higher peptide word repetition in 376 free-living versus 421 pathogen genomes across broad ranges of genome size, G+C content and phylogenetic ancestry. This imprint of repetitive word usage indicates free-living microorganisms have a bias for repetitive sequence usage compared to pathogens. These findings quantify fundamental differences in microbial genomes relative to life-history function. PMID:24828817

  11. Prokaryotic silicon utilizing microorganisms in the biosphere

    NASA Astrophysics Data System (ADS)

    Gupta, D.; Das, S.

    2012-12-01

    Although a little study has been done to determine the silicon utilizing prokaryotes, our previous experiments indicated that almost all Gram-positive bacteria are silicon utilizing; one of them, Streptococci survived exposure on the lunar surface for a long period in experiment done by others. Our initial experiments with these Gram positive microorganisms showed that there were limited growths of these microorganisms on carbon free silicate medium probably with the help of some carry over carbon and nitrogen during cultivation procedures. However, increase in growth rate after repeated subcultures could not be explained at present. The main groups of prokaryotes which were found silicon utilizing microorganisms were Mycobacterium, Bacillus, Nocardia, Streptomyces, Staphylococcus, Streptococcus, Lactobacillus, and Clostridium. In a another previous study by us when silicon level was studied in such grown up cells on carbon "free" silicate medium by electron prove microanalyser, it was found that silicon in cells grown on carbon "free" silicate medium was much higher (24.9%) than those grown on conventional carbon based medium (0.84%). However, these initial findings are encouraging for our future application of this group of organisms on extraterrestrial surfaces for artificial micro-ecosystem formation. It was found that when electropositive elements are less in extraterrestrial situation, then polymerization of silicon-oxygen profusion may occur easily, particularly in carbon and nitrogen paucity in the rocky worlds of the Universe.

  12. Role of microorganisms in emission of nitrous oxide and methane in pulse cultivated soil under laboratory incubation condition.

    PubMed

    Jena, Jyotsnarani; Ray, Sanak; Srichandan, Haragobinda; Das, Anuradha; Das, Trupti

    2013-03-01

    Soil from a pulse cultivated farmers land of Odisha, India, have been subjected to incubation studies for 40 consecutive days, to establish the impact of various nitrogenous fertilizers and water filled pore space (WFPS) on green house gas emission (N2O & CH4). C2H2 inhibition technique was followed to have a comprehensive understanding about the individual contribution of nitrifiers and denitrifiers towards the emission of N2O. Nevertheless, low concentration of C2H2 (5 ml: flow rate 0.1 kg/cm(2)) is hypothesized to partially impede the metabolic pathways of denitrifying bacterial population, thus reducing the overall N2O emission rate. Different soil parameters of the experimental soil such as moisture, total organic carbon, ammonium content and nitrate-nitrogen contents were measured at regular intervals. Application of external N-sources under different WFPS conditions revealed the diverse role played by the indigenous soil microorganism towards green house gas emission. Isolation of heterotrophic microorganisms (Pseudomonas) from the soil samples, further supported the fact that denitrification might be prevailing during specific conditions thus contributing to N2O emission. Statistical analysis showed that WFPS was the most influential parameter affecting N2O formation in soil in absence of an inhibitor like C2H2.

  13. Microbiological assessment of house and imported bottled water by comparison of bacterial endotoxin concentration, heterotrophic plate count, and fecal coliform count.

    PubMed

    Reyes, Mayra I; Pérez, Cynthia M; Negrón, Edna L

    2008-03-01

    Consumers increasingly use bottled water and home water treatment systems to avoid direct tap water. According to the International Bottled Water Association (IBWA), an industry trade group, 5 billion gallons of bottled water were consumed by North Americans in 2001. The principal aim of this study was to assess the microbial quality of in-house and imported bottled water for human consumption, by measurement and comparison of the concentration of bacterial endotoxin and standard cultivable methods of indicator microorganisms, specifically, heterotrophic and fecal coliform plate counts. A total of 21 brands of commercial bottled water, consisting of 10 imported and 11 in-house brands, selected at random from 96 brands that are consumed in Puerto Rico, were tested at three different time intervals. The Standard Limulus Amebocyte Lysate test, gel clot method, was used to measure the endotoxin concentrations. The minimum endotoxin concentration in 63 water samples was less than 0.0625 EU/mL, while the maximum was 32 EU/mL. The minimum bacterial count showed no growth, while the maximum was 7,500 CFU/mL. Bacterial isolates like P. fluorescens, Corynebacterium sp. J-K, S. paucimobilis, P. versicularis, A. baumannii, P. chlororaphis, F. indologenes, A. faecalis and P. cepacia were identified. Repeated measures analysis of variance demonstrated that endotoxin concentration did not change over time, while there was a statistically significant (p < 0.05) decrease in bacterial count over time. In addition, multiple linear regression analysis demonstrated that a unit change in the concentration of endotoxin across time was associated with a significant (p < 0.05) reduction in the bacteriological cell count. This analysis evidenced a significant time effect in the average log bacteriological cell count. Although bacterial growth was not detected in some water samples, endotoxin was present. Measurement of Gram-negative bacterial endotoxins is one of the methods that have been

  14. Effects of UV-A (320 to 399 Nanometers) on Grazing Pressure of a Marine Heterotrophic Nanoflagellate on Strains of the Unicellular Cyanobacteria Synechococcus spp.

    PubMed Central

    Ochs, Clifford A.; Eddy, Laura P.

    1998-01-01

    In the open ocean, where turbidity is very low, UV radiation may be an important factor regulating interactions among planktonic microorganisms. The effect of exposure to UV radiation on grazing by a commonly isolated marine heterotrophic nanoflagellate, Paraphysomonas bandaiensis, on two strains of the cyanobacteria Synechococcus spp. was investigated. Laboratory cultures were exposed to a range of irradiances of artificially produced UV-B (290 to 319 nm) and UV-A (320 to 399 nm) for up to 10 h. At a UV-B irradiance of 0.19 W m−2, but not 0.12 W m−2, grazing mortality of Synechococcus spp. and nanoflagellate-specific grazing rates were reduced compared to mortality and grazing rates with UV-A treatment. Within 6 h of exposure, UV-A alone suppressed grazing mortality at irradiances as low as 3.02 W m−2. The extent to which grazing mortality and nanoflagellate-specific grazing rates were suppressed by UV-A increased with both irradiance and duration of exposure. Over a 6-h exposure period, differences in grazing mortality were largely attributable to differential survival of nanoflagellates. Over a longer period of exposure, there was impairment by UV-A alone of nanoflagellate-specific grazing rates. Rates of primary productivity of Synechococcus spp. were also reduced by UV-A. The extent to which Synechococcus productivity was reduced, compared to the reduction in Synechococcus grazing mortality, depended on the duration of UV-A exposure. These results support the hypothesis that UV-A alone influences the composition and biomass of marine microbial communities by affecting predator-prey interactions and primary production. PMID:16349489

  15. Health concerns of heterotrophic plate count (HPC) bacteria in dental equipment water lines.

    PubMed

    Allen, Martin J; Edberg, Stephen C

    2016-06-01

    There is an unsubstantiated concern as to the health relevance of HPC (heterotrophic plate count) bacteria in dental equipment waterlines. The American Dental Association (ADA) web site includes guidelines for controlling HPC populations and implies that HPC populations >500 CFU/mL as a "health" benchmark. The world-wide published literature including the United Nations fully examined this situation and concluded that HPC bacteria are not a health risk, but merely a general water quality parameter for all waters including dental water lines. This review provides documentation that the standard measurement of HPC bacteria in waters alone do not pose a health risk and the ADA already provides appropriate practices to minimize HPC bacteria in dental equipment water. PMID:27505988

  16. Kinetic modeling of growth and lipid body induction in Chlorella pyrenoidosa under heterotrophic conditions.

    PubMed

    Sachdeva, Neha; Kumar, G Dinesh; Gupta, Ravi Prakash; Mathur, Anshu Shankar; Manikandan, B; Basu, Biswajit; Tuli, Deepak Kumar

    2016-10-01

    The aim of the present work was to develop a mathematical model to describe the biomass and (total) lipid productivity of Chlorella pyrenoidosa NCIM 2738 under heterotrophic conditions. Biomass growth rate was predicted by Droop's cell quota model, while changes observed in cell quota (utilization) under carbon excess conditions were used for the modeling and predicting the lipid accumulation rate. The model was simulated under non-limiting (excess) carbon and limiting nitrate concentration and validated with experimental data for the culture grown in batch (flask) mode under different nitrate concentrations. The present model incorporated two modes (growth and stressed) for the prediction of endogenous lipid synthesis/induction and aimed to predict the effect and response of the microalgae under nutrient starvation (stressed) conditions. MATLAB and Genetic Algorithm were employed for the prediction and validation of the model parameters. PMID:27450124

  17. 'Prepackaged symbioses': propagules on roots of the myco-heterotrophic plant Arachnitis uniflora.

    PubMed

    Domínguez, Laura; Sérsic, Alicia; Melville, Lewis; Peterson, R Larry

    2006-01-01

    Arachnitis uniflora, a myco-heterotrophic plant species, has fleshy tuberous roots colonized by the arbuscular mycorrhizal fungal genus Glomus (Phylum Glomeromycota). These roots produce apical and lateral propagules, both reported here for the first time. The objective of the study was to characterize the ontogeny and structure of the propagules, and to determine their function. Scanning electron microscopy, laser scanning confocal microscopy and light microscopy were used to study the ontogeny and structure of the propagules. Propagules developed either from cortical parenchyma cells or from cells immediately beneath the root cap; they developed a shoot meristem and cells in the basal region which were colonized by various fungal structures including hyphae and vesicles. These propagules may detach from the roots, establishing new plants.

  18. Activity and growth efficiency of heterotrophic bacteria in a salt marsh (Ria de Aveiro, Portugal).

    PubMed

    Cunha, M A; Pedro, R; Almeida, M A; Silva, M H

    2005-01-01

    Bacterial utilization of monomers is recognized as an important step in the biogeochemical cycling of organic matter. In this study we have compared the heterotrophic activity of bacterial communities from different micro-habitats within a salt marsh environment (Ria de Aveiro, Portugal) in order to establish spatial patterns of bacterial abundance, monomer turnover rates (Tr) and bacterial growth efficiency (BGE). Differences in bacterial abundance and activity could be found between distinct plant rhizospheres. BGE tended to be lower at Halimione portulacoides banks, when compared to Sarcocornia perennis subsp. perennis banks which, on the contrary, showed the highest bacterial densities. Experiments of amendment of natural samples with organic and inorganic supplements indicated that salt marsh bacteria are not strongly regulated by salinity but the increased availability of labile organic matter causes a significant metabolic shift towards mineralization.

  19. Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Chemostats

    PubMed Central

    Verhagen, Frank J. M.; Laanbroek, Hendrikus J.

    1992-01-01

    The enhanced mineralization of organic nitrogen by bacteriophagous protozoa is thought to favor the nitrification process in soils, in which nitrifying bacteria have to compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the bacteriovorous flagellate Adriamonas peritocrescens on the competition for limiting amounts of ammonium between the ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis was studied in the presence of Nitrobacter winogradskyi in continuous cultures at dilution rates of 0.004 and 0.01 h-1. The ammonium concentration in the reservoir was maintained at 2 mM, whereas the glucose concentration was increased stepwise from 0 to 7 mM. A. globiformis won the competition for limiting amounts of ammonium when the glucose concentration in the reservoirs increased, in agreement with previously described experiments in which the flagellates were not included. The numbers of nitrifying bacteria decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations. Critical C/N ratios, i.e., ratios between glucose and ammonium in the reservoirs at which no nitrate was found in the culture vessels, of 12.5 and 10.5 were determined at dilution rates of 0.004 and 0.01 h-1, respectively. Below these critical values, coexistence of the competing species was found. The numbers of nitrifying bacteria decreased more in the presence of flagellates than in their absence, presumably by selective predation on the nitrifying bacteria, either in the liquid culture or on the glass wall of the culture vessels. Despite this, the rate of nitrate production did not decrease more in the presence of flagellates than in their absence. This demonstrates that no correlation has to be expected between numbers of nitrifying bacteria and their activity and that a constant nitrification rate per cell cannot be assumed for nitrifying

  20. Health concerns of heterotrophic plate count (HPC) bacteria in dental equipment water lines.

    PubMed

    Allen, Martin J; Edberg, Stephen C

    2016-06-01

    There is an unsubstantiated concern as to the health relevance of HPC (heterotrophic plate count) bacteria in dental equipment waterlines. The American Dental Association (ADA) web site includes guidelines for controlling HPC populations and implies that HPC populations >500 CFU/mL as a "health" benchmark. The world-wide published literature including the United Nations fully examined this situation and concluded that HPC bacteria are not a health risk, but merely a general water quality parameter for all waters including dental water lines. This review provides documentation that the standard measurement of HPC bacteria in waters alone do not pose a health risk and the ADA already provides appropriate practices to minimize HPC bacteria in dental equipment water.

  1. Effect of sodium accumulation on heterotrophic growth and polyhydroxybutyrate (PHB) production by Cupriavidus necator.

    PubMed

    Mozumder, Md Salatul Islam; Garcia-Gonzalez, Linsey; De Wever, Heleen; Volcke, Eveline I P

    2015-09-01

    This study evaluates the effect of sodium (Na(+)) concentration on the growth and PHB production by Cupriavidus necator. Both biomass growth and PHB production were inhibited by Na(+): biomass growth became zero at 8.9 g/L Na(+) concentration while PHB production was completely stopped at 10.5 g/L Na(+). A mathematical model for pure culture heterotrophic PHB production was set up to describe the Na(+) inhibition effect. The parameters related to Na(+) inhibition were estimated based on shake flask experiments. The accumulated Na(+) showed non-linear inhibition effect on biomass growth but linear inhibition effect on PHB production kinetics. Fed-batch experiments revealed that a high accumulation of Na(+) due to a prolonged growth phase, using NaOH for pH control, decreased the subsequent PHB production. The model was validated based on independent experimental data sets, showing a good agreement between experimental data and simulation results.

  2. Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine sponge Arenosclera brasiliensis

    PubMed Central

    Rua, Cintia P.J.; Trindade-Silva, Amaro E.; Appolinario, Luciana R.; Venas, Tainá M.; Garcia, Gizele D.; Carvalho, Lucas S.; Lima, Alinne; Kruger, Ricardo; Pereira, Renato C.; Berlinck, Roberto G.S.; Valle, Rogério A.B.; Thompson, Cristiane C.

    2014-01-01

    Marine sponges are the oldest Metazoa, very often presenting a complex microbial consortium. Such is the case of the marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro State, Brazil. In this investigation we characterized the diversity of some of the culturable heterotrophic bacteria living in association with A. brasiliensis and determined their antimicrobial activity. The genera Endozoicomonas (N = 32), Bacillus (N = 26), Shewanella (N = 17), Pseudovibrio (N = 12), and Ruegeria (N = 8) were dominant among the recovered isolates, corresponding to 97% of all isolates. Approximately one third of the isolates living in association with A. brasiliensis produced antibiotics that inhibited the growth of Bacillus subtilis, suggesting that bacteria associated with this sponge play a role in its health. PMID:25024903

  3. Effect of sodium accumulation on heterotrophic growth and polyhydroxybutyrate (PHB) production by Cupriavidus necator.

    PubMed

    Mozumder, Md Salatul Islam; Garcia-Gonzalez, Linsey; De Wever, Heleen; Volcke, Eveline I P

    2015-09-01

    This study evaluates the effect of sodium (Na(+)) concentration on the growth and PHB production by Cupriavidus necator. Both biomass growth and PHB production were inhibited by Na(+): biomass growth became zero at 8.9 g/L Na(+) concentration while PHB production was completely stopped at 10.5 g/L Na(+). A mathematical model for pure culture heterotrophic PHB production was set up to describe the Na(+) inhibition effect. The parameters related to Na(+) inhibition were estimated based on shake flask experiments. The accumulated Na(+) showed non-linear inhibition effect on biomass growth but linear inhibition effect on PHB production kinetics. Fed-batch experiments revealed that a high accumulation of Na(+) due to a prolonged growth phase, using NaOH for pH control, decreased the subsequent PHB production. The model was validated based on independent experimental data sets, showing a good agreement between experimental data and simulation results. PMID:25997010

  4. The effects of freshwater flushing on marine heterotrophic protists--implications for ballast water management.

    PubMed

    Hülsmann, N; Galil, B S

    2001-11-01

    Survivorship of ballast-entrained marine heterotrophic protists was examined following freshwater flushing. The recovered taxa, including typical marine rhizopods such as Platyamoeba murchelanoi, Labyrinthula spp, Pontifex maximus, Thecamoeba orbis, and the ciliate Condylostoma arenarium, were reared in waters of various salinities. After 2 months, the original salinity subsample retained five protist taxa, the freshwater six, including the amoeba Cochliopodium bilimbosum, the brackish water 22 taxa, and the seawater 19 taxa. Since protists form a major component of marine microbial food webs, their survival may be instrumental in supporting complex ballast-entrained food webs. Our study raises questions as to the reliability of open-ocean exchange (OOE) or freshwater flushing as effective control measures.

  5. Microbial activity and phosphorus uptake on decomposing leaf detritus in a heterotrophic stream

    SciTech Connect

    Elwood, J.W.; Mulholland, P.J.; Newbold, J.D.

    1987-01-01

    This paper reports results of experiments to determine the influence of microbes associated with decomposing leaf detritus on the uptake length and retention of phosphorus in a heterotrophic stream. The purposes were to (1) determine the relationship between the biomass and activity of microbes associated with decomposing leaf detritus and the uptake length of PO/sub 4/-P in a stream; (2) compare the temporal pattern in the uptake rate of phosphorus among species of leaves that have been shown to differ in their rate of decomposition as a function of time in a stream; and (3) examine the temporal patterns in the net accumulation, leaching, and transformations of phosphorus in flow-through systems containing decomposing leaf detritus.

  6. 40 CFR 725.88 - Uses of a microorganism.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Uses of a microorganism. 725.88... CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS Confidentiality and Public Access to Information § 725.88 Uses of a microorganism. (a) Assertion of claim. A person who...

  7. 40 CFR 725.88 - Uses of a microorganism.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Uses of a microorganism. 725.88... CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS Confidentiality and Public Access to Information § 725.88 Uses of a microorganism. (a) Assertion of claim. A person who...

  8. 40 CFR 725.88 - Uses of a microorganism.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Uses of a microorganism. 725.88... CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS Confidentiality and Public Access to Information § 725.88 Uses of a microorganism. (a) Assertion of claim. A person who...

  9. 40 CFR 725.88 - Uses of a microorganism.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Uses of a microorganism. 725.88... CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS Confidentiality and Public Access to Information § 725.88 Uses of a microorganism. (a) Assertion of claim. A person who...

  10. 40 CFR 725.88 - Uses of a microorganism.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Uses of a microorganism. 725.88... CONTROL ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS Confidentiality and Public Access to Information § 725.88 Uses of a microorganism. (a) Assertion of claim. A person who...

  11. Ultraviolet reduction of erythromycin and tetracycline resistant heterotrophic bacteria and their resistance genes in municipal wastewater.

    PubMed

    Guo, Mei-Ting; Yuan, Qing-Bin; Yang, Jian

    2013-11-01

    Antibiotic resistance in wastewater is becoming a major public health concern, but poorly understood about impact of disinfection on antibiotic resistant bacteria and antibiotic resistance genes. The UV disinfection of antibiotic resistant heterotrophic bacteria and their relevant genes in the wastewater of a municipal wastewater treatment plant has been evaluated. Two commonly used antibiotics, erythromycin and tetracycline were selected because of their wide occurrences in regard to the antibiotic resistance problem. After UV treatment at a fluence of 5mJcm(-2), the log reductions of heterotrophic bacteria resistant to erythromycin and tetracycline in the wastewater were found to be 1.4±0.1 and 1.1±0.1, respectively. The proportion of tetracycline-resistant bacteria (5%) was nearly double of that before UV disinfection (3%). Tetracycline-resistant bacteria exhibited more tolerance to UV irradiation compared to the erythromycin-resistant bacteria (p<0.05). Gene copy numbers were quantified via qPCR and normalized to the volume of original sample. The total concentrations of erythromycin- and tetracycline-resistance genes were (3.6±0.2)×10(5) and (2.5±0.1)×10(5) copies L(-1), respectively. UV treatment at a fluence of 5mJcm(-2) removed the total erythromycin- and tetracycline-resistance genes by 3.0±0.1 log and 1.9±0.1 log, respectively. UV treatment was effective in reducing antibiotic resistance in the wastewater.

  12. Heterotrophic plate count and consumer's health under special consideration of water softeners.

    PubMed

    Hambsch, Beate; Sacré, Clara; Wagner, Ivo

    2004-05-01

    The phenomenon of bacterial growth in water softeners is well known since years. To upgrade the hygienic safety of water softeners, the German DIN Standard 19636 was developed, to assure that the distribution system could not be contaminated by these devices and that the drinking water to be used in the household still meets the microbiological standards according to the German drinking water guidelines, i.e. among others heterotrophic plate count (HPC) below 100 CFU/ml. Moreover, the standard for the water softeners includes a test for contamination with Pseudomonas aeruginosa which has to be disinfected during the regeneration phase. This is possible by sanitizing the resin bed during regeneration by producing chlorine. The results of the last 10 years of tests of water softeners according to DIN 19636 showed that it is possible to produce water softeners that comply with that standard. Approximately 60% of the tested models were accepted. P. aeruginosa is used as an indicator for potentially pathogenic bacteria being able to grow also in low nutrient conditions which normally prevail in drinking water. Like other heterotrophs, the numbers of P. aeruginosa increase rapidly as stagnation occurs. Normally P. aeruginosa is not present in the distributed drinking water. However, under certain conditions, P. aeruginosa can be introduced into the drinking water distribution system, for instance, during construction work. The occurrence of P. aeruginosa is shown in different cases in treatment plants, public drinking water systems and in-house installations. The compliance with DIN 19636 provides assurance that a water softener will not be a constant source of contamination, even if it is once inoculated with a potentially pathogenic bacterium like P. aeruginosa.

  13. Position-specific measurement of oxygen isotope ratios in cellulose: Isotopic exchange during heterotrophic cellulose synthesis

    NASA Astrophysics Data System (ADS)

    Waterhouse, John S.; Cheng, Shuying; Juchelka, Dieter; Loader, Neil J.; McCarroll, Danny; Switsur, V. Roy; Gautam, Lata

    2013-07-01

    We describe the first reported method for the measurement of oxygen isotope ratios at each position in the glucose units of the cellulose molecule. The overall process comprises a series of synthetic organic sequences, by which α-cellulose is hydrolysed to glucose, and oxygen atoms at specific positions in the glucose molecule are removed in samples of benzoic acid for measurement of δ18O. Values of δ18O at specific positions in cellulose are calculated from these δ18O values and the overall δ18O value of the cellulose. We apply the method to determine the degree to which oxygen atoms at each position undergo isotopic exchange with water during heterotrophic cellulose synthesis, such as occurs in the cambium of trees. To do this we extract α-cellulose from wheat seedlings germinated in the dark in aqueous media of differing oxygen isotope ratios. Results indicate that oxygen atoms at positions 5 and 6 (O-5 and O-6 respectively) undergo around 80% exchange with medium water, O-3 undergoes around 50% exchange, and O-2 and O-4 do not undergo isotopic exchange. The results have important implications for extracting palaeoclimatic records from oxygen isotope time series obtained from tree ring cellulose. As O-5 and O-6 undergo significant exchange with medium water during heterotrophic cellulose synthesis, oxygen isotopes at these positions in tree ring cellulose should carry a predominantly trunk (source) water signal. On the other hand, O-2 and O-4 should retain the isotopic signature of leaf water in tree ring cellulose. Our method therefore potentially enables the separate reconstruction of past temperature and humidity data from oxygen isotope ratios of tree ring cellulose - something that has hitherto not been possible. The measured degrees of isotopic exchange are to some extent unexpected and cannot be fully explained using current biochemical mechanisms, suggesting that knowledge of these processes is incomplete.

  14. Effects of soil moisture on the temperature sensitivity of soil heterotrophic respiration: a laboratory incubation study.

    PubMed

    Zhou, Weiping; Hui, Dafeng; Shen, Weijun

    2014-01-01

    The temperature sensitivity (Q10) of soil heterotrophic respiration (Rh) is an important ecological model parameter and may vary with temperature and moisture. While Q10 generally decreases with increasing temperature, the moisture effects on Q10 have been controversial. To address this, we conducted a 90-day laboratory incubation experiment using a subtropical forest soil with a full factorial combination of five moisture levels (20%, 40%, 60%, 80%, and 100% water holding capacity--WHC) and five temperature levels (10, 17, 24, 31, and 38°C). Under each moisture treatment, Rh was measured several times for each temperature treatment to derive Q10 based on the exponential relationships between Rh and temperature. Microbial biomass carbon (MBC), microbial community structure and soil nutrients were also measured several times to detect their potential contributions to the moisture-induced Q10 variation. We found that Q10 was significantly lower at lower moisture levels (60%, 40% and 20% WHC) than at higher moisture level (80% WHC) during the early stage of the incubation, but became significantly higher at 20%WHC than at 60% WHC and not significantly different from the other three moisture levels during the late stage of incubation. In contrast, soil Rh had the highest value at 60% WHC and the lowest at 20% WHC throughout the whole incubation period. Variations of Q10 were significantly associated with MBC during the early stages of incubation, but with the fungi-to-bacteria ratio during the later stages, suggesting that changes in microbial biomass and community structure are related to the moisture-induced Q10 changes. This study implies that global warming's impacts on soil CO2 emission may depend upon soil moisture conditions. With the same temperature rise, wetter soils may emit more CO2 into the atmosphere via heterotrophic respiration. PMID:24647610

  15. Soil heterotrophic respiration responses to meteorology, soil types and cropping systems in a temperate agricultural watershed.

    NASA Astrophysics Data System (ADS)

    Buysse, Pauline; Viaud, Valérie; Fléchard, Chris

    2015-04-01

    Within the context of Climate Change, a better understanding of soil organic matter dynamics is of considerable importance in agro-ecosystems, due to their large mitigation potential. This study aims at better understanding the process of soil heterotrophic respiration at the annual scale and at the watershed scale, with these temporal and spatial scales allowing an integration of the most important drivers: cropping systems and management, topography, soil types, soil organic carbon content and meteorological conditions. Twenty-four soil CO2 flux measurement sites - comprising three PVC collars each - were spread over the Naizin-Kervidy catchment (ORE AgrHys, 4.9 km², W. France) in March 2014. These sites were selected in order to represent most of the diversity in drainage classes, soil types and cropping systems. Soil CO2 flux measurements were performed about every ten to fifteen days at each site, starting from 20 March 2014, using the dynamic closed chamber system Li-COR 8100. Soil temperature and soil moisture content down to 5 cm depth were measured simultaneously. An empirical model taking the influence of meteorological drivers (soil temperature and soil water content) on soil CO2 fluxes was applied to each site and the different responses were analyzed with regard to site characteristics (topography, soil organic carbon content, soil microbial biomass, crop type, crop management,…) in order to determine the most important driving variables of soil heterotrophic respiration. The modeling objective is then to scale the fluxes measured at all sites up to the full watershed scale.

  16. Relationships between meiofaunal biodiversity and prokaryotic heterotrophic production in different tropical habitats and oceanic regions.

    PubMed

    Pusceddu, Antonio; Gambi, Cristina; Corinaldesi, Cinzia; Scopa, Mariaspina; Danovaro, Roberto

    2014-01-01

    Tropical marine ecosystems are among the most diverse of the world oceans, so that assessing the linkages between biodiversity and ecosystem functions (BEF) is a crucial step to predict consequences of biodiversity loss. Most BEF studies in marine ecosystems have been carried out on macrobenthic diversity, whereas the influence of the meiofauna on ecosystem functioning has received much less attention. We compared meiofaunal and nematode biodiversity and prokaryotic heterotrophic production across seagrass, mangrove and reef sediments in the Caribbean, Celebes and Red Seas. For all variables we report the presence of differences among habitats within the same region, and among regions within the same habitat. In all regions, the richness of meiofaunal taxa in reef and seagrass sediments is higher than in mangrove sediments. The sediments of the Celebes Sea show the highest meiofaunal biodiversity. The composition of meiofaunal assemblages varies significantly among habitats in the same region. The nematode beta diversity among habitats within the same region is higher than the beta diversity among regions. Although one site per habitat was considered in each region, these results suggest that the composition of meiofaunal assemblages varies primarily among biogeographic regions, whereas the composition of nematode assemblages varies more considerably among habitats. Meiofauna and nematode biodiversity and prokaryotic heterotrophic production, even after the removal of covariate effects linked with longitude and the quantity and nutritional quality of organic matter, are positively and linearly linked both across regions and within each habitat type. Our results confirm that meiofauna and nematode biodiversity may influence benthic prokaryotic activity, which, in turn, implies that diversity loss could have negative impacts on ecosystem functioning in these systems.

  17. The antimicrobial activity of heterotrophic bacteria isolated from the marine sponge Erylus deficiens (Astrophorida, Geodiidae)

    PubMed Central

    Graça, Ana Patrícia; Viana, Flávia; Bondoso, Joana; Correia, Maria Inês; Gomes, Luis; Humanes, Madalena; Reis, Alberto; Xavier, Joana R.; Gaspar, Helena; Lage, Olga M.

    2015-01-01

    Interest in the study of marine sponges and their associated microbiome has increased both for ecological reasons and for their great biotechnological potential. In this work, heterotrophic bacteria associated with three specimens of the marine sponge Erylus deficiens, were isolated in pure culture, phylogenetically identified and screened for antimicrobial activity. The isolation of bacteria after an enrichment treatment in heterotrophic medium revealed diversity in bacterial composition with only Pseudoalteromonas being shared by two specimens. Of the 83 selected isolates, 58% belong to Proteobacteria, 23% to Actinobacteria and 19% to Firmicutes. Diffusion agar assays for bioactivity screening against four bacterial strains and one yeast, revealed that a high number of the isolated bacteria (68.7%) were active, particularly against Candida albicans and Vibrio anguillarum. Pseudoalteromonas, Microbacterium, and Proteus were the most bioactive genera. After this preliminary screening, the bioactive strains were further evaluated in liquid assays against C. albicans, Bacillus subtilis and Escherichia coli. Filtered culture medium and acetone extracts from three and 5 days-old cultures were assayed. High antifungal activity against C. albicans in both aqueous and acetone extracts as well as absence of activity against B. subtilis were confirmed. Higher levels of activity were obtained with the aqueous extracts when compared to the acetone extracts and differences were also observed between the 3 and 5 day-old extracts. Furthermore, a low number of active strains was observed against E. coli. Potential presence of type-I polyketide synthases (PKS-I) and non-ribosomal peptide synthetases (NRPSs) genes were detected in 17 and 30 isolates, respectively. The high levels of bioactivity and the likely presence of associated genes suggest that Erylus deficiens bacteria are potential sources of novel marine bioactive compounds. PMID:25999928

  18. Relationships between meiofaunal biodiversity and prokaryotic heterotrophic production in different tropical habitats and oceanic regions.

    PubMed

    Pusceddu, Antonio; Gambi, Cristina; Corinaldesi, Cinzia; Scopa, Mariaspina; Danovaro, Roberto

    2014-01-01

    Tropical marine ecosystems are among the most diverse of the world oceans, so that assessing the linkages between biodiversity and ecosystem functions (BEF) is a crucial step to predict consequences of biodiversity loss. Most BEF studies in marine ecosystems have been carried out on macrobenthic diversity, whereas the influence of the meiofauna on ecosystem functioning has received much less attention. We compared meiofaunal and nematode biodiversity and prokaryotic heterotrophic production across seagrass, mangrove and reef sediments in the Caribbean, Celebes and Red Seas. For all variables we report the presence of differences among habitats within the same region, and among regions within the same habitat. In all regions, the richness of meiofaunal taxa in reef and seagrass sediments is higher than in mangrove sediments. The sediments of the Celebes Sea show the highest meiofaunal biodiversity. The composition of meiofaunal assemblages varies significantly among habitats in the same region. The nematode beta diversity among habitats within the same region is higher than the beta diversity among regions. Although one site per habitat was considered in each region, these results suggest that the composition of meiofaunal assemblages varies primarily among biogeographic regions, whereas the composition of nematode assemblages varies more considerably among habitats. Meiofauna and nematode biodiversity and prokaryotic heterotrophic production, even after the removal of covariate effects linked with longitude and the quantity and nutritional quality of organic matter, are positively and linearly linked both across regions and within each habitat type. Our results confirm that meiofauna and nematode biodiversity may influence benthic prokaryotic activity, which, in turn, implies that diversity loss could have negative impacts on ecosystem functioning in these systems. PMID:24603709

  19. Massive regime shifts and high activity of heterotrophic bacteria in an ice-covered lake.

    PubMed

    Bižić-Ionescu, Mina; Amann, Rudolf; Grossart, Hans-Peter

    2014-01-01

    In winter 2009/10, a sudden under-ice bloom of heterotrophic bacteria occurred in the seasonally ice-covered, temperate, deep, oligotrophic Lake Stechlin (Germany). Extraordinarily high bacterial abundance and biomass were fueled by the breakdown of a massive bloom of Aphanizomenon flos-aquae after ice formation. A reduction in light resulting from snow coverage exerted a pronounced physiological stress on the cyanobacteria. Consequently, these were rapidly colonized, leading to a sudden proliferation of attached and subsequently of free-living heterotrophic bacteria. Total bacterial protein production reached 201 µg C L(-1) d(-1), ca. five times higher than spring-peak values that year. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis at high temporal resolution showed pronounced changes in bacterial community structure coinciding with changes in the physiology of the cyanobacteria. Pyrosequencing of 16S rRNA genes revealed that during breakdown of the cyanobacterial population, the diversity of attached and free-living bacterial communities were reduced to a few dominant families. Some of these were not detectable during the early stages of the cyanobacterial bloom indicating that only specific, well adapted bacterial communities can colonize senescent cyanobacteria. Our study suggests that in winter, unlike commonly postulated, carbon rather than temperature is the limiting factor for bacterial growth. Frequent phytoplankton blooms in ice-covered systems highlight the need for year-round studies of aquatic ecosystems including the winter season to correctly understand element and energy cycling through aquatic food webs, particularly the microbial loop. On a global scale, such knowledge is required to determine climate change induced alterations in carbon budgets in polar and temperate aquatic systems.

  20. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota

    SciTech Connect

    Anderson, Iain; Lakshmi, Lakshmi Dharmarajan; Rodriquez, Jason; Hooper, Sean; Porat, I.; Ulrich, Luke; Mavromatis, K; Sun, Hui; Land, Miriam L; Lapidus, Alla L.; Lucas, Susan; Barry, Kerrie; Huber, Harald; Zhulin, Igor B; Whitman, W. B.; Mukhopadhyay, Biswarup; Woese, Carl; Bristow, James; Kyrpides, Nikos C

    2009-01-01

    Background Staphylothermus marinus is an anaerobic, sulfur-reducing peptide fermenter of the archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes. Results The 1.57 Mbp genome of the hyperthermophilic crenarchaeote Staphylothermus marinus has been completely sequenced. The main energy generating pathways likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. S. marinus possesses several enzymes not present in other crenarchaeotes including a sodium ion-translocating decarboxylase likely to be involved in amino acid degradation. S. marinus lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that have been sequenced Thermofilum pendens and Hyperthermus butylicus. Instead it has three operons similar to the mbh and mbx operons of Pyrococcus furiosus, which may play a role in sulfur reduction and/or hydrogen production. The two marine organisms, S. marinus and H. butylicus, possess more sodium-dependent transporters than T. pendens and use symporters for potassium uptake while T. pendens uses an ATP-dependent potassium transporter. T. pendens has adapted to a nutrient-rich environment while H. butylicus is adapted to a nutrient-poor environment, and S. marinus lies between these two extremes. Conclusion The three heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs. marine, via their transporter content, and they have also adapted to environments with differing levels of nutrients. Despite the fact that they all use sulfur as an electron acceptor, they are likely to have different pathways for sulfur reduction.

  1. N2 fixation in marine heterotrophic bacteria: dynamics of environmental and molecular regulation.

    PubMed Central

    Coyer, J A; Cabello-Pasini, A; Swift, H; Alberte, R S

    1996-01-01

    Molecular and immunological techniques were used to examine N2 fixation in a ubiquitous heterotrophic marine bacterium, the facultative anaerobic Vibrio natriegens. When batch cultures were shifted from aerobic N-replete to anaerobic N-deplete conditions, transcriptional and post-translational regulation of N2 fixation was observed. Levels of nifHDK mRNA encoding the nitrogenase enzyme were highest at 140 min postshift and undetectable between 6 and 9 h later. Immunologically determined levels of nitrogenase enzyme (Fe protein) were highest between 6 and 15 h postshift, and nitrogenase activity peaked between 6 and 9 h postshift, declining by a factor of 2 after 12-15 h. Unlike their regulation in cyanobacteria, Fe protein and nitrogenase activity were present when nifHDK mRNA was absent in V. natriegens, indicating that nitrogenase is stored and stable under anaerobic conditions. Both nifHDK mRNA and Fe protein disappeared within 40 min after cultures were shifted from N2-fixing conditions (anaerobic, N-deplete) to non- N2-fixing conditions (aerobic, N-enriched) but reappeared when shifted to conditions favoring N2 fixation. Thus, unlike other N2-fixing heterotrophic bacteria, nitrogenase must be resynthesized after aerobic exposure in V. natriegens. Immunological detection based on immunoblot (Western) analysis and immunogold labeling correlated positively with nitrogenase activity; no localization of nitrogenase was observed. Because V. natriegens continues to fix N2 for many hours after anaerobic induction, this species may play an important role in providing "new" nitrogen in marine ecosystems. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:11607653

  2. The antimicrobial activity of heterotrophic bacteria isolated from the marine sponge Erylus deficiens (Astrophorida, Geodiidae).

    PubMed

    Graça, Ana Patrícia; Viana, Flávia; Bondoso, Joana; Correia, Maria Inês; Gomes, Luis; Humanes, Madalena; Reis, Alberto; Xavier, Joana R; Gaspar, Helena; Lage, Olga M

    2015-01-01

    Interest in the study of marine sponges and their associated microbiome has increased both for ecological reasons and for their great biotechnological potential. In this work, heterotrophic bacteria associated with three specimens of the marine sponge Erylus deficiens, were isolated in pure culture, phylogenetically identified and screened for antimicrobial activity. The isolation of bacteria after an enrichment treatment in heterotrophic medium revealed diversity in bacterial composition with only Pseudoalteromonas being shared by two specimens. Of the 83 selected isolates, 58% belong to Proteobacteria, 23% to Actinobacteria and 19% to Firmicutes. Diffusion agar assays for bioactivity screening against four bacterial strains and one yeast, revealed that a high number of the isolated bacteria (68.7%) were active, particularly against Candida albicans and Vibrio anguillarum. Pseudoalteromonas, Microbacterium, and Proteus were the most bioactive genera. After this preliminary screening, the bioactive strains were further evaluated in liquid assays against C. albicans, Bacillus subtilis and Escherichia coli. Filtered culture medium and acetone extracts from three and 5 days-old cultures were assayed. High antifungal activity against C. albicans in both aqueous and acetone extracts as well as absence of activity against B. subtilis were confirmed. Higher levels of activity were obtained with the aqueous extracts when compared to the acetone extracts and differences were also observed between the 3 and 5 day-old extracts. Furthermore, a low number of active strains was observed against E. coli. Potential presence of type-I polyketide synthases (PKS-I) and non-ribosomal peptide synthetases (NRPSs) genes were detected in 17 and 30 isolates, respectively. The high levels of bioactivity and the likely presence of associated genes suggest that Erylus deficiens bacteria are potential sources of novel marine bioactive compounds.

  3. Coscinaraea marshae corals that have survived prolonged bleaching exhibit signs of increased heterotrophic feeding

    NASA Astrophysics Data System (ADS)

    Bessell-Browne, Pia; Stat, Michael; Thomson, Damian; Clode, Peta L.

    2014-09-01

    Colonies of Coscinaraea marshae corals from Rottnest Island, Western Australia have survived for more than 11 months in various bleached states following a severe heating event in the austral summer of 2011. These colonies are situated in a high-latitude, mesophotic environment, which has made their long-term survival of particular interest as such environments typically suffer from minimal thermal pressures. We have investigated corals that remain unbleached, moderately bleached, or severely bleached to better understand potential survival mechanisms utilised in response to thermal stress. Specifically, Symbiodinium (algal symbiont) density and genotype, chlorophyll- a concentrations, and δ13C and δ15N levels were compared between colonies in the three bleaching categories. Severely bleached colonies housed significantly fewer Symbiodinium cells ( p < 0.05) and significantly reduced chlorophyll- a concentrations ( p < 0.05), compared with unbleached colonies. Novel Symbiodinium clade associations were observed for this coral in both severely and moderately bleached colonies, with clade C and a mixed clade population detected. In unbleached colonies, only clade B was observed. Levels of δ15N indicate that severely bleached colonies are utilising heterotrophic feeding mechanisms to aid survival whilst bleached. Collectively, these results suggest that these C. marshae colonies can survive with low symbiont and chlorophyll densities, in response to prolonged thermal stress and extended bleaching, and increase heterotrophic feeding levels sufficiently to meet energy demands, thus enabling some colonies to survive and recover over long time frames. This is significant as it suggests that corals in mesophotic and high-latitude environments may possess considerable plasticity and an ability to tolerate and adapt to large environmental fluctuations, thereby improving their chances of survival as climate change impacts coral ecosystems worldwide.

  4. Effects of soil moisture on the temperature sensitivity of soil heterotrophic respiration: a laboratory incubation study.

    PubMed

    Zhou, Weiping; Hui, Dafeng; Shen, Weijun

    2014-01-01

    The temperature sensitivity (Q10) of soil heterotrophic respiration (Rh) is an important ecological model parameter and may vary with temperature and moisture. While Q10 generally decreases with increasing temperature, the moisture effects on Q10 have been controversial. To address this, we conducted a 90-day laboratory incubation experiment using a subtropical forest soil with a full factorial combination of five moisture levels (20%, 40%, 60%, 80%, and 100% water holding capacity--WHC) and five temperature levels (10, 17, 24, 31, and 38°C). Under each moisture treatment, Rh was measured several times for each temperature treatment to derive Q10 based on the exponential relationships between Rh and temperature. Microbial biomass carbon (MBC), microbial community structure and soil nutrients were also measured several times to detect their potential contributions to the moisture-induced Q10 variation. We found that Q10 was significantly lower at lower moisture levels (60%, 40% and 20% WHC) than at higher moisture level (80% WHC) during the early stage of the incubation, but became significantly higher at 20%WHC than at 60% WHC and not significantly different from the other three moisture levels during the late stage of incubation. In contrast, soil Rh had the highest value at 60% WHC and the lowest at 20% WHC throughout the whole incubation period. Variations of Q10 were significantly associated with MBC during the early stages of incubation, but with the fungi-to-bacteria ratio during the later stages, suggesting that changes in microbial biomass and community structure are related to the moisture-induced Q10 changes. This study implies that global warming's impacts on soil CO2 emission may depend upon soil moisture conditions. With the same temperature rise, wetter soils may emit more CO2 into the atmosphere via heterotrophic respiration.

  5. Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies

    PubMed Central

    Barbeau, Katherine A.

    2016-01-01

    Heterotrophic bacteria in the SAR11 and Roseobacter lineages shape the marine carbon, nitrogen, phosphorous, and sulfur cycles, yet they do so having adopted divergent ecological strategies. Currently, it is unknown whether these globally significant groups partition into specific niches with respect to micronutrients (e.g., trace metals) and how that may affect marine trace metal cycling. Here, we used comparative genomics to identify diverse iron, cobalt, nickel, copper, and zinc uptake capabilities in SAR11 and Roseobacter genomes and uncover surprising unevenness within and between lineages. The strongest predictors for the extent of the metal uptake gene content are the total number of transporters per genome, genome size, total metal transporters, and GC content, but numerous exceptions exist in both groups. Taken together, our results suggest that SAR11 have strongly minimized their trace metal uptake versatility, with high-affinity zinc uptake being a unique exception. The larger Roseobacter genomes have greater trace metal uptake versatility on average, but they also appear to have greater plasticity, resulting in phylogenetically similar genomes having largely different capabilities. Ultimately, phylogeny is predictive of the diversity and extent of 20 to 33% of all metal uptake systems, suggesting that specialization in metal utilization mostly occurred independently from overall lineage diversification in both SAR11 and Roseobacter. We interpret these results as reflecting relatively recent trace metal niche partitioning in both lineages, suggesting that concentrations and chemical forms of metals in the marine environment are important factors shaping the gene content of marine heterotrophic Alphaproteobacteria of the SAR11 and Roseobacter lineages. PMID:26729720

  6. Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies.

    PubMed

    Hogle, Shane L; Thrash, J Cameron; Dupont, Chris L; Barbeau, Katherine A

    2016-03-01

    Heterotrophic bacteria in the SAR11 and Roseobacter lineages shape the marine carbon, nitrogen, phosphorous, and sulfur cycles, yet they do so having adopted divergent ecological strategies. Currently, it is unknown whether these globally significant groups partition into specific niches with respect to micronutrients (e.g., trace metals) and how that may affect marine trace metal cycling. Here, we used comparative genomics to identify diverse iron, cobalt, nickel, copper, and zinc uptake capabilities in SAR11 and Roseobacter genomes and uncover surprising unevenness within and between lineages. The strongest predictors for the extent of the metal uptake gene content are the total number of transporters per genome, genome size, total metal transporters, and GC content, but numerous exceptions exist in both groups. Taken together, our results suggest that SAR11 have strongly minimized their trace metal uptake versatility, with high-affinity zinc uptake being a unique exception. The larger Roseobacter genomes have greater trace metal uptake versatility on average, but they also appear to have greater plasticity, resulting in phylogenetically similar genomes having largely different capabilities. Ultimately, phylogeny is predictive of the diversity and extent of 20 to 33% of all metal uptake systems, suggesting that specialization in metal utilization mostly occurred independently from overall lineage diversification in both SAR11 and Roseobacter. We interpret these results as reflecting relatively recent trace metal niche partitioning in both lineages, suggesting that concentrations and chemical forms of metals in the marine environment are important factors shaping the gene content of marine heterotrophic Alphaproteobacteria of the SAR11 and Roseobacter lineages. PMID:26729720

  7. De Novo Transcriptomes of a Mixotrophic and a Heterotrophic Ciliate from Marine Plankton

    PubMed Central

    Santoferrara, Luciana F.; Guida, Stephanie; Zhang, Huan; McManus, George B.

    2014-01-01

    Studying non-model organisms is crucial in the context of the current development of genomics and transcriptomics for both physiological experimentation and environmental characterization. We investigated the transcriptomes of two marine planktonic ciliates, the mixotrophic oligotrich Strombidium rassoulzadegani and the heterotrophic choreotrich Strombidinopsis sp., and their respective algal food using Illumina RNAseq. Our aim was to characterize the transcriptomes of these contrasting ciliates and to identify genes potentially involved in mixotrophy. We detected approximately 10,000 and 7,600 amino acid sequences for S. rassoulzadegani and Strombidinopsis sp., respectively. About half of these transcripts had significant BLASTP hits (E-value <10−6) against previously-characterized sequences, mostly from the model ciliate Oxytricha trifallax. Transcriptomes from both the mixotroph and the heterotroph species provided similar annotations for GO terms and KEGG pathways. Most of the identified genes were related to housekeeping activity and pathways such as the metabolism of carbohydrates, lipids, amino acids, nucleotides, and vitamins. Although S. rassoulzadegani can keep and use chloroplasts from its prey, we did not find genes clearly linked to chloroplast maintenance and functioning in the transcriptome of this ciliate. While chloroplasts are known sources of reactive oxygen species (ROS), we found the same complement of antioxidant pathways in both ciliates, except for one enzyme possibly linked to ascorbic acid recycling found exclusively in the mixotroph. Contrary to our expectations, we did not find qualitative differences in genes potentially related to mixotrophy. However, these transcriptomes will help to establish a basis for the evaluation of differential gene expression in oligotrichs and choreotrichs and experimental investigation of the costs and benefits of mixotrophy. PMID:24983246

  8. Biology of the Marine Heterotrophic Dinoflagellate Oxyrrhis marina: Current Status and Future Directions

    PubMed Central

    Guo, Zhiling; Zhang, Huan; Liu, Sheng; Lin, Senjie

    2013-01-01

    Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhis marina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of ecological, biogeographic, and evolutionary studies. Despite the increasing research effort on this species, there lacks a synthesis of the existing data and a coherent picture of this organism. Here we reviewed the literature to provide an overview of what is known regarding the biology of O. marina, and identify areas where further studies are needed. As an early branch of the dinoflagellate lineage, O. marina shares similarity with typical dinoflagellates in permanent condensed chromosomes, less abundant nucleosome proteins compared to other eukaryotes, multiple gene copies, the occurrence of trans-splicing in nucleus-encoded mRNAs, highly fragmented mitochondrial genome, and disuse of ATG as a start codon for mitochondrial genes. On the other hand, O. marina also exhibits some distinct cytological features (e.g., different flagellar structure, absence of girdle and sulcus or pustules, use of intranuclear spindle in mitosis, presence of nuclear plaque, and absence of birefringent periodic banded chromosomal structure) and genetic features (e.g., a single histone-like DNA-associated protein, cob-cox3 gene fusion, 5′ oligo-U cap in the mitochondrial transcripts of protein-coding genes, the absence of mRNA editing, the presence of stop codon in the fused cob-cox3 mRNA produced by post-transcriptional oligoadenylation, and vestigial plastid genes). The best-studied biology of this dinoflagellate is probably the prey and predators types, which include a wide range of organisms. On the other hand, the abundance of this species in the natural waters and its controlling factors, genome organization and gene expression regulation that underlie the unusual cytological and

  9. Effects of Soil Moisture on the Temperature Sensitivity of Soil Heterotrophic Respiration: A Laboratory Incubation Study

    PubMed Central

    Zhou, Weiping; Hui, Dafeng; Shen, Weijun

    2014-01-01

    The temperature sensitivity (Q10) of soil heterotrophic respiration (Rh) is an important ecological model parameter and may vary with temperature and moisture. While Q10 generally decreases with increasing temperature, the moisture effects on Q10 have been controversial. To address this, we conducted a 90-day laboratory incubation experiment using a subtropical forest soil with a full factorial combination of five moisture levels (20%, 40%, 60%, 80%, and 100% water holding capacity - WHC) and five temperature levels (10, 17, 24, 31, and 38°C). Under each moisture treatment, Rh was measured several times for each temperature treatment to derive Q10 based on the exponential relationships between Rh and temperature. Microbial biomass carbon (MBC), microbial community structure and soil nutrients were also measured several times to detect their potential contributions to the moisture-induced Q10 variation. We found that Q10 was significantly lower at lower moisture levels (60%, 40% and 20% WHC) than at higher moisture level (80% WHC) during the early stage of the incubation, but became significantly higher at 20%WHC than at 60% WHC and not significantly different from the other three moisture levels during the late stage of incubation. In contrast, soil Rh had the highest value at 60% WHC and the lowest at 20% WHC throughout the whole incubation period. Variations of Q10 were significantly associated with MBC during the early stages of incubation, but with the fungi-to-bacteria ratio during the later stages, suggesting that changes in microbial biomass and community structure are related to the moisture-induced Q10 changes. This study implies that global warming’s impacts on soil CO2 emission may depend upon soil moisture conditions. With the same temperature rise, wetter soils may emit more CO2 into the atmosphere via heterotrophic respiration. PMID:24647610

  10. Relationships between Meiofaunal Biodiversity and Prokaryotic Heterotrophic Production in Different Tropical Habitats and Oceanic Regions

    PubMed Central

    Pusceddu, Antonio; Gambi, Cristina; Corinaldesi, Cinzia; Scopa, Mariaspina; Danovaro, Roberto

    2014-01-01

    Tropical marine ecosystems are among the most diverse of the world oceans, so that assessing the linkages between biodiversity and ecosystem functions (BEF) is a crucial step to predict consequences of biodiversity loss. Most BEF studies in marine ecosystems have been carried out on macrobenthic diversity, whereas the influence of the meiofauna on ecosystem functioning has received much less attention. We compared meiofaunal and nematode biodiversity and prokaryotic heterotrophic production across seagrass, mangrove and reef sediments in the Caribbean, Celebes and Red Seas. For all variables we report the presence of differences among habitats within the same region, and among regions within the same habitat. In all regions, the richness of meiofaunal taxa in reef and seagrass sediments is higher than in mangrove sediments. The sediments of the Celebes Sea show the highest meiofaunal biodiversity. The composition of meiofaunal assemblages varies significantly among habitats in the same region. The nematode beta diversity among habitats within the same region is higher than the beta diversity among regions. Although one site per habitat was considered in each region, these results suggest that the composition of meiofaunal assemblages varies primarily among biogeographic regions, whereas the composition of nematode assemblages varies more considerably among habitats. Meiofauna and nematode biodiversity and prokaryotic heterotrophic production, even after the removal of covariate effects linked with longitude and the quantity and nutritional quality of organic matter, are positively and linearly linked both across regions and within each habitat type. Our results confirm that meiofauna and nematode biodiversity may influence benthic prokaryotic activity, which, in turn, implies that diversity loss could have negative impacts on ecosystem functioning in these systems. PMID:24603709

  11. [Characteristics of Nitrogen Removal by a Heterotrophic Nitrification-Aerobic Denitrification Bacterium YL].

    PubMed

    Liang, Xian; Ren, Yong-xiang; Yang, Lei; Zhao, Si-qi; Xia, Zhi-hong

    2015-05-01

    Traditional process of autotrophic nitrification-anaerobic denitrification usually has problems of long procedure and low efficiency. To overcome these problems, a heterotrophic nitrification-aerobic denitrification bacterium YL was isolated from a domesticated mature SBR reactor with efficient simultaneous nitrification and denitrification ability, and was identified as Pseudomonas aeruginosa YL. Meanwhile, the characteristics of the nitrogen removal of strain YL was investigated through single-factor experiments and an orthogonal experiment. The results showed that the preferred conditions were: succinate as the carbon source, C/N ratio of 10, pH of 7.0, temperature of 30°C, and the shaking speed of 160-200 r · min(-1), while the removal rate of ammonia oxidation was 5. 05 mg · (g · h)(-1), the transformation rate of TOC was 45.95 mg · (g · h)(-1), and the removal rates of nitrogen and TOC were 100% and 90.8%, respectively. Nitrite, nitrate and hydroxylamine could also be metabolized by strain YL, and the removal rates were 92.7%, 93.6% and 94.8%, respectively. The most important influencing factor on aerobic denitrification of strain YL was C/N ratio. Under the optimal conditions (C/N = 10, T = 30°C , r = 200 r · min(-1), pH = 7), the removal rates of nitrate and total nitrogen were 94.6% and 76.3%, respectively. Hence, strain YL could remove nitrogen by heterotrophic nitrification-aerobic denitrification independently, quickly, and effectively.

  12. Feeding by heterotrophic dinoflagellates and ciliates on the free-living dinoflagellate Symbiodinium sp. (Clade E).

    PubMed

    Jeong, Hae Jin; Lim, An Suk; Yoo, Yeong Du; Lee, Moo Joon; Lee, Kyung Ha; Jang, Tae Young; Lee, Kitack

    2014-01-01

    To investigate heterotrophic protists grazing on Symbiodinium sp., we tested whether the common heterotrophic dinoflagellates Gyrodinium dominans, Gyrodinium moestrupii, Gyrodinium spirale, Oblea rotundata, Oxyrrhis marina, and Polykrikos kofoidii and the ciliates Balanion sp. and Parastrombidinopsis sp. preyed on the free-living dinoflagellate Symbiodinium sp. (clade E). We measured the growth and ingestion rates of O. marina and G. dominans on Symbiodinium sp. as a function of prey concentration. Furthermore, we compared the results to those obtained for other algal prey species. In addition, we measured the growth and ingestion rates of other predators at single prey concentrations at which these rates of O. marina and G. dominans were saturated. All predators tested in the present study, except Balanion sp., preyed on Symbiodinium sp. The specific growth rates of O. marina and G. dominans on Symbiodinium sp. increased rapidly with increasing mean prey concentration < ca. 740-815 ng C/ml (7,400-8,150 cells/ml), but became saturated at higher concentrations. The maximum growth rates of O. marina and G. dominans on Symbiodinium sp. (0.87 and 0.61/d) were much higher than those of G. moestrupii and P. kofoidii (0.11 and 0.04/d). Symbiodinium sp. did not support positive growth of G. spirale, O. rotundata, and Parastrombidinopsis sp. However, the maximum ingestion rates of P. kofoidii and Parastrombidinopsis sp. (6.7-10.0 ng C/predator/d) were much higher than those of O. marina and G. dominans on Symbiodinium sp. (1.9-2.1 ng C/predator/d). The results of the present study suggest that Symbiodinium sp. may increase or maintain the populations of some predators.

  13. Absence of association between total heterotrophic and total coliform bacteria from a public water supply.

    PubMed Central

    Edberg, S; Smith, D B

    1989-01-01

    Heterotrophic plate counts (HPC) and total coliforms (TC) are two major microbial indicators that are used to monitor the potability of water. Although the presence of heterotrophs has been hypothesized to predict the presence of TC, there have been few documented reports. Intensive sampling of raw, treated effluent and distribution water from a public water supply serving 400,000 people provided an opportunity to study the relationship between these two indicator groups of bacteria. A total of 26,158 samples were analyzed, including 12,970 from 1986 and 13,188 from 1985. There were 13,429 samples from the distribution system, 5,524 from treatment effluents, and 7,205 from raw water. The associations between HPC and TC were made on both a hits-and-misses and numerical comparison (CFU per milliliter) basis. The periodicity of the two indicators was also analyzed to determine whether the presence of one group could predict the presence of the other. Atypical bacteria were also related to the presence of these two indicator bacteria. Venn diagrams and nonparametric statistics revealed the following correlation coefficients for HPC and TC for 1985 and 1986 combined: raw water r = 0.45, treated effluent r = 0.06, and distribution system r = 0.10. Atypical bacteria showed a similar relationship with HPC. There was no predictive periodicity for HPC and TC within +/- 10 days of isolation of each other. Therefore, in a 2-year survey of a public water supply, the presence of HPC had a low correlation coefficient with TC, as determined by hits-and-misses and numerical comparisons. The enumeration of one group was found to be independent of the other. PMID:2719479

  14. Biology of the Marine Heterotrophic Dinoflagellate Oxyrrhis marina: Current Status and Future Directions

    PubMed Central

    Guo, Zhiling; Zhang, Huan; Liu, Sheng; Lin, Senjie

    2013-01-01

    Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhis marina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of ecological, biogeographic, and evolutionary studies. Despite the increasing research effort on this species, there lacks a synthesis of the existing data and a coherent picture of this organism. Here we reviewed the literature to provide an overview of what is known regarding the biology of O. marina, and identify areas where further studies are needed. As an early branch of the dinoflagellate lineage, O. marina shares similarity with typical dinoflagellates in permanent condensed chromosomes, less abundant nucleosome proteins compared to other eukaryotes, multiple gene copies, the occurrence of trans-splicing in nucleus-encoded mRNAs, highly fragmented mitochondrial genome, and disuse of ATG as a start codon for mitochondrial genes. On the other hand, O. marina also exhibits some distinct cytological features (e.g., different flagellar structure, absence of girdle and sulcus or pustules, use of intranuclear spindle in mitosis, presence of nuclear plaque, and absence of birefringent periodic banded chromosomal structure) and genetic features (e.g., a single histone-like DNA-associated protein, cob-cox3 gene fusion, 5′ oligo-U cap in the mitochondrial transcripts of protein-coding genes, the absence of mRNA editing, the presence of stop codon in the fused cob-cox3 mRNA produced by post-transcriptional oligoadenylation, and vestigial plastid genes). The best-studied biology of this dinoflagellate is probably the prey and predators types, which include a wide range of organisms. On the other hand, the abundance of this species in the natural waters and its controlling factors, genome organization and gene expression regulation that underlie the unusual cytological and

  15. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota

    SciTech Connect

    Anderson, iain J.; Dharmarajan, Lakshmi; Rodriguez, Jason; Hooper, Sean; Porat, Iris; Ulrich, Luke E.; Elkins, James G.; Mavromatis, Kostas; Sun, Hui; Land, Miriam; Lapidus, Alla; Lucas, Susan; Barry, Kerrie; Huber, Harald; Zhulin, Igor B.; Whitman, William B.; Mukhopadhyay, Biswarup; Woese, Carl; Bristow, James; Kyrpides, Nikos

    2008-09-05

    Staphylothermus marinus is an anaerobic, sulfur-reducing peptide fermenter of the archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes. The 1.57 Mbp genome of the hyperthermophilic crenarchaeote Staphylothermus marinus has been completely sequenced. The main energy generating pathways likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. S. marinus possesses several enzymes not present in other crenarchaeotes including a sodium ion-translocating decarboxylase likely to be involved in amino acid degradation. S. marinus lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that have been sequenced - Thermofilum pendens and Hyperthermus butylicus. Instead it has three operons similar to the mbh and mbx operons of Pyrococcus furiosus, which may play a role in sulfur reduction and/or hydrogen production. The two marine organisms, S. marinus and H. butylicus, possess more sodium-dependent transporters than T. pendens and use symporters for potassium uptake while T. pendens uses an ATP-dependent potassium transporter. T. pendens has adapted to a nutrient-rich environment while H. butylicus is adapted to a nutrient-poor environment, and S. marinus lies between these two extremes. The three heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs. marine, via their transporter content, and they have also adapted to environments with differing levels of nutrients. Despite the fact that they all use sulfur as an electron acceptor, they are likely to have different pathways for sulfur reduction.

  16. Fast labile carbon turnover obscures sensitivity of heterotrophic respiration from soil to temperature: A model analysis

    NASA Astrophysics Data System (ADS)

    Gu, Lianhong; Post, Wilfred M.; King, Anthony W.

    2004-03-01

    Labile carbon, although often a small fraction of soil organic carbon (SOC), significantly affects heterotrophic respiration at short timescales because of its rapid decomposition. However, in the current literature, most soil respiration measurements are interpreted without simultaneous information on labile carbon pool dynamics. Sensitivity of soil respiration to temperature is routinely derived directly from field observations, and such relationships have been used to extrapolate effects of global change (e.g., warming) on carbon emission from SOC. Here we use a multipool SOC model to demonstrate the impacts of seasonal fluctuations of labile carbon pools on interpretation of soil respiration measurements. We find that labile carbon pool sizes vary widely in response to seasonal changes in representative plant material inputs and temperature even though the model is operating at equilibrium in terms of annual means. Convolution of the dynamics of fast turnover carbon pools and temporal progression in temperature lead to misrepresentation and misinterpretation of the heterotrophic respiration-temperature relationships estimated from bulk soil CO2 exchanges. Temperature sensitivity is overestimated when the variations of labile carbon pools and temperature are in phase and underestimated when they are out of phase. Furthermore, with normally used observation time windows (weeks to a year), temperature sensitivity is more likely to be underestimated. A distortion of temperature sensitivity (Q10) from 2 (actual, sensitive dependence on temperature) to nearly 1 (false, no dependence on temperature) is shown. Applying estimated temperature sensitivity parameter back into the model considerably overestimates soil carbon storage at equilibrium. Our findings indicate that caution must be taken when soil respiration-temperature relationships are evaluated based on bulk soil observations and when sensitivity of soil respiration to temperature estimated directly under field

  17. Heterotrophic bacterial production and extracellular enzymatic activity in sinking particulate matter in the western North Pacific Ocean.

    PubMed

    Yamada, Namiha; Fukuda, Hideki; Ogawa, Hiroshi; Saito, Hiroaki; Suzumura, Masahiro

    2012-01-01

    Heterotrophic activities on sinking particulate matter (SPM) play an important role in SPM fluxes in the ocean. To demonstrate regional differences in heterotrophic activities on SPM, we measured heterotrophic bacterial production (HBP) in seawater (HBP(SW)) and SPM (HBP(SPM)) as well as potential extracellular enzyme activity (EEA) in SPM on a transect along 155°E in the western North Pacific Ocean in the subarctic (44°N), the Kuroshio Extension area (35°N), and the subtropical gyre (20°N). Depth-integrated HBP(SW) from the surface to 500 m was comparable between the locations, whereas HBP(SPM) at 44°N was substantially lower than at the other sites. We found the highest particulate organic carbon (POC) export flux and export efficiency to bathypelagic depths, and the lowest water temperatures, at 44°N. We found significant correlations between leucine aminopeptidase (LAPase) activity, β-glucosidase (BGase) activity, POC flux and particulate organic nitrogen flux. LAPase activity was two orders of magnitude higher than BGase activity, with a BGase:LAPase activity ratio of 0.027. There were no significant correlations between HBP and EEA in SPM except for lipase, and lipase activity was significantly correlated with temperature. We propose that hydrographic conditions are an important factor controlling heterotrophic bacterial activity and export efficiency of organic carbon to the deep ocean, as are the sources and abundance of SPM produced in the euphotic zone via primary production. PMID:23109933

  18. NATURAL ABUNDANCE STABLE ISOTOPE RATIOS SUPPORT MYCO-HETEROTROPHIC NATURE AND HOST -SPECIFICITY OF CERTAIN ACHLOROPHYLLUS PLANTS

    EPA Science Inventory

    Over 400 species of achlorophyllous vascular plants are thought to obtain all carbon from symbiotic fungi. Consequently, they are termed ?myco-heterotrophic.' However, direct evidence of myco-heterotrophy in these plants is limited. During an investigation of the patterns of nitr...

  19. NITROGEN AND CARBON STABLE ISOTOPE ABUNDANCES SUPPORT THE MYCO-HETEROTROPHIC NATURE AND HOST-SPECIFICITY OF CERTAIN ACHLOROPHYLLOUS PLANTS

    EPA Science Inventory


    ? Over 400 species of achlorophyllous vascular plants are thought to obtain all carbon from symbiotic fungi. Consequently, they are termed ?myco-heterotrophic.' However, direct evidence of myco-heterotrophy in these plants is limited.
    ? During an investigation of the pat...

  20. Dual Label Stable Isotope Incubations Followed By Single Cell Nanosims Analyses To Investigate Microscale Phototroph-Heterotroph Interactions

    NASA Astrophysics Data System (ADS)

    Mayali, X.; Samo, T. J.; Nilson, D.; Arandia Gorostidi, N.; alonso Saez, L.; Moran, X. A.; Weber, P. K.

    2015-12-01

    In natural ecosystems such as lakes and oceans as well as human-engineered systems for sunlight-regulated biomass production (such as algal biofuel ponds), the interaction between autotrophic and heterotrophic processes are critical to determine whether such systems are net autotrophic or heterotrophic. Traditional methods to quantify autotrophy and heterotrophy include primary productivity and bacterial production measurements using radiolabeled substrates that quantify these processes on the bulk scale. To examine the microscale interactions between individual autotrophic and heterotrophic cells, we incubate mixed microbial assemblages with 13C-bicarbonate and 15N-leucine to label individual autotrophs and heterotrophs, respectively. We use nano imaging secondary ion mass spectrometry (with a Cameca NanoSIMS 50) to quantify the incorporation of the rare isotopes by single cells. We will present results from experiments examining the impact of warming on the exchange of C and N between algal and bacterial cells from the coastal Atlantic Ocean, which suggest that increased temperature may strengthen physical interactions and exchange. We will also present data from experiments examining the influence of attached bacteria on the cell-specific inorganic carbon fixation rates of biofuel-producing algal cultures which suggest that certain algal-attached bacterial groups grow faster than when free-living and influence algal growth. We conclude that the examination of individual cells uncover interactions that would be difficult, if not impossible, to investigate with bulk methods.

  1. Production of dissolved organic matter by phytoplankton and its uptake by heterotrophic prokaryotes in large tropical lakes

    NASA Astrophysics Data System (ADS)

    Morana, Cedric; Sarmento, Hugo; Descy, Jean-Pierre; Gasol, Josep M.; Borges, Alberto V.; Bouillon, Steven; Darchambeau, François

    2014-05-01

    In pelagic ecosystems, phytoplankton extracellular release (ER) can substantially subsidize the heterotrophic prokaryotic carbon demand. Factors influencing ER were never investigated in large tropical lakes. We performed time-course experiments to quantify the fraction of phytoplankton production released (PER) and the microbial uptake of freshly excreted compounds (DOCp) in 4 large tropical lakes: lakes Kivu, Edward, Victoria and Albert. In Lake Kivu, we also examined whether the major heterotrophic bacterial group were active in the uptake of freshly excreted compounds using MAR-FISH (microautoradiography coupled to fluorescent in situ hybridization). PER varied across a productivity gradient covering 2 orders of magnitude, with higher values at low productivity. Futhermore, PER was comparatively higher in oligotrophic tropical lakes than in their temperate counterparts and was positively related to the light:phosphate balance. Both observations suggest that environmental factors play a key role in the control of phytoplankton excretion. Furthermore, the standing stocks of DOCp were small and generally contributed less than 1 % to the total dissolved organic carbon as it was rapidly assimilated by prokaryotes, in other words we observed a tight coupling between the production and the heterotrophic consumption of DOCp. We found that none of the major phylogenetic bacterial groups investigated differed in their ability to take up DOCp, in contrast with earlier results reported for standard labelled single-molecule substrates (leucine, glucose, ATP). Overall, these results highlight the strong dependence of all heterotrophic prokaryotes on the labile pool of DOCp, and the importance of carbon transfer between phytoplankton and heterotrophic prokaryotes in large African lakes.

  2. Nitrogen control of 13C enrichment in heterotrophic organs relative to leaves in a landscape-building desert plant species

    DOE PAGES

    Zhang, J.; Gu, L.; Bao, F.; Cao, Y.; Hao, Y.; He, J.; Li, J.; Li, Y.; Ren, Y.; Wang, F.; et al

    2014-09-10

    A longstanding puzzle in isotope studies of C3 plant species is that heterotrophic plant organs (e.g., stems, roots, seeds, and fruits) tend to be enriched in 13C compared to the autotrophic organ (leaves) that provides them with photosynthate. Our inability to explain this puzzle suggests key deficiencies in understanding post-photosynthetic metabolic processes. It also limits the effectiveness of applications of stable carbon isotope analyses in a variety of scientific disciplines ranging from plant physiology to global carbon cycle studies. To gain insight into this puzzle, we excavated whole plant architectures of Nitraria tangutorum Bobrov, a C3 species that has anmore » exceptional capability of fixing sands and building sand dunes, in two deserts in northwestern China. We systematically and simultaneously measured carbon isotope ratios and nitrogen and phosphorous contents of different parts of the excavated plants. We also determined the seasonal variations in leaf carbon isotope ratios on nearby intact plants of N. tangutorum. We found, for the first time, that higher nitrogen contents in heterotrophic organs were significantly correlated with increased heterotrophic 13C enrichment compared to leaves. However, phosphorous contents had no effect on the enrichment. In addition, new leaves had carbon isotope ratios similar to roots but were progressively depleted in 13C as they matured. We concluded that a nitrogen-mediated process, probably the refixation of respiratory CO2 by phosphoenolpyruvate (PEP) carboxylase, was responsible for the differences in 13C enrichment among different heterotrophic organs while processes within leaves or during phloem loading may contribute to the overall autotrophic – heterotrophic difference in carbon isotope compositions.« less

  3. Heterotrophic denitrification plays an important role in N₂O production from nitritation reactors treating anaerobic sludge digestion liquor.

    PubMed

    Wang, Qilin; Jiang, Guangming; Ye, Liu; Pijuan, Maite; Yuan, Zhiguo

    2014-10-01

    Nitrous oxide (N2O) emissions from nitritation reactors receiving real anaerobic sludge digestion liquor have been reported to be substantially higher than those from reactors receiving synthetic digestion liquor. This study aims to identify the causes for the difference, and to develop strategies to reduce N2O emissions from reactors treating real digestion liquor. Two sequencing batch reactors (SBRs) performing nitritation, fed with real (SBR-R) and synthetic (SBR-S) digestion liquors, respectively, were employed. The N2O emission factors for SBR-R and SBR-S were determined to be 3.12% and 0.80% of the NH4(+)-N oxidized, respectively. Heterotrophic denitrification supported by the organic carbon present in the real digestion liquor was found to be the key contributor to the higher N2O emission from SBR-R. Heterotrophic nitrite reduction likely stopped at N2O (rather than N2), with a hypothesised cause being free nitrous acid inhibition. This implies that all nitrite reduced by heterotrophic bacteria was converted to and emitted as N2O. Increasing dissolved oxygen (DO) concentration from 0.5 to 1.0 mg/L, or above, decreased aerobic N2O production from 2.0% to 0.5% in SBR-R, whereas aerobic N2O production in SBR-S remained almost unchanged (at approximately 0.5%). We hypothesised that DO at 1 mg/L or above suppressed heterotrophic nitrite reduction thus reduced aerobic heterotrophic N2O production. We recommend that DO in a nitritation system receiving anaerobic sludge digestion liquor should be maintained at approximately 1 mg/L to minimise N2O emission.

  4. Heterotrophic Compensation: A Possible Mechanism for Resilience of Coral Reefs to Global Warming or a Sign of Prolonged Stress?

    PubMed Central

    Hughes, Adam D.; Grottoli, Andréa G.

    2013-01-01

    Thermally induced bleaching has caused a global decline in corals and the frequency of such bleaching events will increase. Thermal bleaching severely disrupts the trophic behaviour of the coral holobiont, reducing the photosynthetically derived energy available to the coral host. In the short term this reduction in energy transfer from endosymbiotic algae results in an energy deficit for the coral host. If the bleaching event is short-lived then the coral may survive this energy deficit by depleting its lipid reserves, or by increasing heterotrophic energy acquisition. We show for the first time that the coral animal is capable of increasing the amount of heterotrophic carbon incorporated into its tissues for almost a year following bleaching. This prolonged heterotrophic compensation could be a sign of resilience or prolonged stress. If the heterotrophic compensation is in fact an acclimatization response, then this physiological response could act as a buffer from future bleaching by providing sufficient heterotrophic energy to compensate for photoautotrophic energy losses during bleaching, and potentially minimizing the effect of subsequent elevated temperature stresses. However, if the elevated incorporation of zooplankton is a sign that the effects of bleaching continue to be stressful on the holobiont, even after 11 months of recovery, then this physiological response would indicate that complete coral recovery requires more than 11 months to achieve. If coral bleaching becomes an annual global phenomenon by mid-century, then present temporal refugia will not be sufficient to allow coral colonies to recover between bleaching events and coral reefs will become increasingly less resilient to future climate change. If, however, increasing their sequestration of zooplankton-derived nutrition into their tissues over prolonged periods of time is a compensating mechanism, the impacts of annual bleaching may be reduced. Thus, some coral species may be better

  5. Can heterotrophic uptake of dissolved organic carbon and zooplankton mitigate carbon budget deficits in annually bleached corals?

    NASA Astrophysics Data System (ADS)

    Levas, Stephen; Grottoli, Andréa G.; Schoepf, Verena; Aschaffenburg, Matthew; Baumann, Justin; Bauer, James E.; Warner, Mark E.

    2016-06-01

    Annual coral bleaching events due to increasing sea surface temperatures are predicted to occur globally by the mid-century and as early as 2025 in the Caribbean, and severely impact coral reefs. We hypothesize that heterotrophic carbon (C) in the form of zooplankton and dissolved organic carbon (DOC) is a significant source of C to bleached corals. Thus, the ability to utilize multiple pools of fixed carbon and/or increase the amount of fixed carbon acquired from one or more pools of fixed carbon (defined here as heterotrophic plasticity) could underlie coral acclimatization and persistence under future ocean-warming scenarios. Here, three species of Caribbean coral— Porites divaricata, P. astreoides, and Orbicella faveolata—were experimentally bleached for 2.5 weeks in two successive years and allowed to recover in the field. Zooplankton feeding was assessed after single and repeat bleaching, while DOC fluxes and the contribution of DOC to the total C budget were determined after single bleaching, 11 months on the reef, and repeat bleaching. Zooplankton was a large C source for P. astreoides, but only following single bleaching. DOC was a source of C for single-bleached corals and accounted for 11-36 % of daily metabolic demand (CHARDOC), but represented a net loss of C in repeat-bleached corals. In repeat-bleached corals, DOC loss exacerbated the negative C budgets in all three species. Thus, the capacity for heterotrophic plasticity in corals is compromised under annual bleaching, and heterotrophic uptake of DOC and zooplankton does not mitigate C budget deficits in annually bleached corals. Overall, these findings suggest that some Caribbean corals may be more susceptible to repeat bleaching than to single bleaching due to a lack of heterotrophic plasticity, and coral persistence under increasing bleaching frequency may ultimately depend on other factors such as energy reserves and symbiont shuffling.

  6. Nitrogen control of 13C enrichment in heterotrophic organs relative to leaves in a landscape-building desert plant species

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Gu, L.; Bao, F.; Cao, Y.; Hao, Y.; He, J.; Li, J.; Li, Y.; Ren, Y.; Wang, F.; Wu, R.; Yao, B.; Zhao, Y.; Lin, G.; Wu, B.; Lu, Q.; Meng, P.

    2015-01-01

    A longstanding puzzle in isotope studies of C3 plant species is that heterotrophic plant organs (e.g., stems, roots, seeds, and fruits) tend to be enriched in 13C compared to the autotrophic organ (leaves) that provides them with photosynthate. Our inability to explain this puzzle suggests key deficiencies in understanding post-photosynthetic metabolic processes. It also limits the effectiveness of applications of stable carbon isotope analyses in a variety of scientific disciplines ranging from plant physiology to global carbon cycle studies. To gain insight into this puzzle, we excavated whole plant architectures of Nitraria tangutorum Bobrov, a C3 species that has an exceptional capability of fixing sands and building sand dunes, in two deserts in northwestern China. We systematically and simultaneously measured carbon isotope ratios and nitrogen and phosphorous contents of different parts of the excavated plants. We also determined the seasonal variations in leaf carbon isotope ratios on nearby intact plants of N. tangutorum. We found, for the first time, that higher nitrogen contents in heterotrophic organs were significantly correlated with increased heterotrophic 13C enrichment compared to leaves. However, phosphorous contents had no effect on the enrichment. In addition, new leaves had carbon isotope ratios similar to roots but were progressively depleted in 13C as they matured. We concluded that a nitrogen-mediated process, hypothesized to be the refixation of respiratory CO2 by phosphoenolpyruvate (PEP) carboxylase, was responsible for the differences in 13C enrichment among different heterotrophic organs, while processes such as fractionating foliar metabolism and preferentially loading into phloem of 13C-enriched sugars may contribute to the overall autotrophic-heterotrophic difference in carbon isotope compositions.

  7. Extracellular electron transfer mechanisms between microorganisms and minerals.

    PubMed

    Shi, Liang; Dong, Hailiang; Reguera, Gemma; Beyenal, Haluk; Lu, Anhuai; Liu, Juan; Yu, Han-Qing; Fredrickson, James K

    2016-10-01

    Electrons can be transferred from microorganisms to multivalent metal ions that are associated with minerals and vice versa. As the microbial cell envelope is neither physically permeable to minerals nor electrically conductive, microorganisms have evolved strategies to exchange electrons with extracellular minerals. In this Review, we discuss the molecular mechanisms that underlie the ability of microorganisms to exchange electrons, such as c-type cytochromes and microbial nanowires, with extracellular minerals and with microorganisms of the same or different species. Microorganisms that have extracellular electron transfer capability can be used for biotechnological applications, including bioremediation, biomining and the production of biofuels and nanomaterials. PMID:27573579

  8. Extracellular electron transfer mechanisms between microorganisms and minerals.

    PubMed

    Shi, Liang; Dong, Hailiang; Reguera, Gemma; Beyenal, Haluk; Lu, Anhuai; Liu, Juan; Yu, Han-Qing; Fredrickson, James K

    2016-10-01

    Electrons can be transferred from microorganisms to multivalent metal ions that are associated with minerals and vice versa. As the microbial cell envelope is neither physically permeable to minerals nor electrically conductive, microorganisms have evolved strategies to exchange electrons with extracellular minerals. In this Review, we discuss the molecular mechanisms that underlie the ability of microorganisms to exchange electrons, such as c-type cytochromes and microbial nanowires, with extracellular minerals and with microorganisms of the same or different species. Microorganisms that have extracellular electron transfer capability can be used for biotechnological applications, including bioremediation, biomining and the production of biofuels and nanomaterials.

  9. Six Siderophore-Producing Microorganisms Identified in Biological Soil Crusts

    NASA Astrophysics Data System (ADS)

    Noonan, K.; Anbar, A. D.; Garcia-Pichel, F.; Poret-peterson, A. T.; Hartnett, H. E.

    2011-12-01

    Biological soil crusts (BSCs) are diverse microbial communities that colonize soils in arid and semi-arid environments. Cyanobacteria in BSCs are pioneer organisms that increase ecosystem habitability by providing fixed carbon (C) and nitrogen (N) as well as by reducing water run-off and increasing infiltration. Photosynthesis and N fixation, in particular, require a variety of metals in large quantities, and yet, metals are predominantly insoluble in the environments where BSCs thrive. Therefore, BSC organisms must have efficient strategies for extracting metals from soil minerals. We hypothesized that BSC microbes, particularly the cyanobacteria, produce siderophores to serve their metal-acquisition needs. Siderophores are small organic compounds that bind Fe with high affinity and are produced by a variety of microorganisms, including cyanobacteria. Most siderophores bind Fe, primarily; however, some can also bind Mo, V, and Cu. Soil siderophores are released by microbes to increase the solubility of metals from minerals and to facilitate microbial uptake. Thus, siderophores serve as chemical weathering agents and provide a direct link between soil microbes and minerals. Studying siderophore production in BSCs provides insight into how BSCs tackle the challenge of acquiring insoluble metals, and may help conservationists determine useful fertilizers for BSC growth by facilitating metal acquisition. Biological soil crusts were collected near Moab, UT. Soil slurries were prepared in deionized water and transferred to modified BG-11 agar plates. The O-CAS agar plate assay was used to screen organisms for siderophore production. Siderophore producing microbes were isolated and identified by16S rRNA gene sequencing. Cultures were then grown in 3 L batch cultures under metal limitation, and siderophore presence was monitored using the traditional liquid CAS assay. After siderophore detection, cells were removed by centrifugation, organic compounds were separated using

  10. How Many Microorganisms Are Present? Techniques for Enumerating Microorganisms in Oilfields

    NASA Astrophysics Data System (ADS)

    Sørensen, Ketil Bernt; Skovhus, Torben Lund; Larsen, Jan

    The different techniques that exist for enumerating microorganisms will often yield very different results when applied to oilfield samples. For example, enumeration of sulphate-reducing bacteria (SRB) by cultivation may fail to find any microorganisms in samples for which molecular microbiological methods (MMM) indicate levels of thousands or even millions per millilitre or gram. Therefore, it is important to realise the limitations and advantages of the different techniques available to the industry and to take them into account when interpreting data. In oil systems, the most widely used techniques for quantification are based either on culturing, epifluorescence microscopy, or quantitative PCR. In complex samples in which live, inactive, and dead cells are present together with cell material in various states of decomposition, each of these three methodologies enumerates a different subset of microorganisms (Fig. 10.1).

  11. Biofilms: Survival Mechanisms of Clinically Relevant Microorganisms

    PubMed Central

    Donlan, Rodney M.; Costerton, J. William

    2002-01-01

    Though biofilms were first described by Antonie van Leeuwenhoek, the theory describing the biofilm process was not developed until 1978. We now understand that biofilms are universal, occurring in aquatic and industrial water systems as well as a large number of environments and medical devices relevant for public health. Using tools such as the scanning electron microscope and, more recently, the confocal laser scanning microscope, biofilm researchers now understand that biofilms are not unstructured, homogeneous deposits of cells and accumulated slime, but complex communities of surface-associated cells enclosed in a polymer matrix containing open water channels. Further studies have shown that the biofilm phenotype can be described in terms of the genes expressed by biofilm-associated cells. Microorganisms growing in a biofilm are highly resistant to antimicrobial agents by one or more mechanisms. Biofilm-associated microorganisms have been shown to be associated with several human diseases, such as native valve endocarditis and cystic fibrosis, and to colonize a wide variety of medical devices. Though epidemiologic evidence points to biofilms as a source of several infectious diseases, the exact mechanisms by which biofilm-associated microorganisms elicit disease are poorly understood. Detachment of cells or cell aggregates, production of endotoxin, increased resistance to the host immune system, and provision of a niche for the generation of resistant organisms are all biofilm processes which could initiate the disease process. Effective strategies to prevent or control biofilms on medical devices must take into consideration the unique and tenacious nature of biofilms. Current intervention strategies are designed to prevent initial device colonization, minimize microbial cell attachment to the device, penetrate the biofilm matrix and kill the associated cells, or remove the device from the patient. In the future, treatments may be based on inhibition of genes

  12. Screening of biosurfactants from cloud microorganisms

    NASA Astrophysics Data System (ADS)

    Sancelme, Martine; Canet, Isabelle; Traikia, Mounir; Uhliarikova, Yveta; Capek, Peter; Matulova, Maria; Delort, Anne-Marie; Amato, Pierre

    2015-04-01

    The formation of cloud droplets from aerosol particles in the atmosphere is still not well understood and a main source of uncertainties in the climate budget today. One of the principal parameters in these processes is the surface tension of atmospheric particles, which can be strongly affected by trace compounds called surfactants. Within a project devoted to bring information on atmospheric surfactants and their effects on cloud droplet formation, we focused on surfactants produced by microorganisms present in atmospheric waters. From our unique collection of microorganisms, isolated from cloud water collected at the Puy-de-Dôme (France),1 we undertook a screening of this bank for biosurfactant producers. After extraction of the supernatants of the pure cultures, surface tension of crude extracts was determined by the hanging drop technique. Results showed that a wide variety of microorganisms are able to produce biosurfactants, some of them exhibiting strong surfactant properties as the resulting tension surface decreases to values less then 35 mN.m-1. Preliminary analytical characterization of biosurfactants, obtained after isolation from overproducing cultures of Rhodococcus sp. and Pseudomonas sp., allowed us to identify them as belonging to two main classes, namely glycolipids and glycopeptides. 1. Vaïtilingom, M.; Attard, E.; Gaiani, N.; Sancelme, M.; Deguillaume, L.; Flossmann, A. I.; Amato, P.; Delort, A. M. Long-term features of cloud microbiology at the puy de Dôme (France). Atmos. Environ. 2012, 56, 88-100. Acknowledgements: This work is supported by the French-USA ANR SONATA program and the French-Slovakia programs Stefanik and CNRS exchange.

  13. Phylogenetic conservatism of functional traits in microorganisms.

    PubMed

    Martiny, Adam C; Treseder, Kathleen; Pusch, Gordon

    2013-04-01

    A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and the presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we developed a new phylogenetic metric-consenTRAIT-to estimate the clade depth where organisms share a trait. We then analyzed the distribution of 89 functional traits across a broad range of Bacteria and Archaea using genotypic and phenotypic data. A total of 93% of the traits were significantly non-randomly distributed, which suggested that vertical inheritance was generally important for the phylogenetic dispersion of functional traits in microorganisms. Further, traits in microbes were associated with a continuum of trait depths (τD), ranging from a few deep to many shallow clades (average τD: 0.101-0.0011 rRNA sequence dissimilarity). Next, we demonstrated that the dispersion and the depth of clades that contain a trait is correlated with the trait's complexity. Specifically, complex traits encoded by many genes like photosynthesis and methanogenesis were found in a few deep clusters, whereas the ability to use simple carbon substrates was highly phylogenetically dispersed. On the basis of these results, we propose a framework for predicting the phylogenetic conservatism of functional traits depending on the complexity of the trait. This framework enables predicting how variation in microbial composition may affect microbially-mediated ecosystem processes as well as linking phylogenetic and trait-based patterns of biogeography.

  14. Complete nitrification by a single microorganism

    PubMed Central

    van Kessel, Maartje A.H.J.; Speth, Daan R.; Albertsen, Mads; Nielsen, Per H.; Op den Camp, Huub J.M.; Kartal, Boran; Jetten, Mike S.M.; Lücker, Sebastian

    2016-01-01

    Summary Nitrification is a two-step process where ammonia is considered to first be oxidized to nitrite by ammonia-oxidizing bacteria (AOB) and/or archaea (AOA), and subsequently to nitrate by nitrite-oxidizing bacteria (NOB). Described by Winogradsky already in 18901, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle2. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible and it was postulated that this process could occur under conditions selecting for species with lower growth-rates but higher growth-yields than canonical ammonia-oxidizing microorganisms3. Still, organisms catalysing this process have not yet been discovered. Here, we report the enrichment and initial characterization of two Nitrospira species that encode all enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding on the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle. PMID:26610025

  15. Synthetic biology expands chemical control of microorganisms.

    PubMed

    Ford, Tyler J; Silver, Pamela A

    2015-10-01

    The tools of synthetic biology allow researchers to change the ways engineered organisms respond to chemical stimuli. Decades of basic biology research and new efforts in computational protein and RNA design have led to the development of small molecule sensors that can be used to alter organism function. These new functions leap beyond the natural propensities of the engineered organisms. They can range from simple fluorescence or growth reporting to pathogen killing, and can involve metabolic coordination among multiple cells or organisms. Herein, we discuss how synthetic biology alters microorganisms' responses to chemical stimuli resulting in the development of microbes as toxicity sensors, disease treatments, and chemical factories.

  16. Microorganisms and biomolecules in space hard environment

    NASA Technical Reports Server (NTRS)

    Horneck, G.

    1981-01-01

    Microorganisms and biomolecules exposed to space vacuum and to different intensities of selected wavelengths of solar ultraviolet radiation is studied. The influence of these factors, applied singly or simultaneously, on the integrity of microbial systems and biomolecules is measured. Specifically, this experiment will study in Bacillus subtilis spores (1) disturbances in subsequent germination, outgrowth, and colony formation; (2) photochemical reactions of the DNA and protein in vivo and in vitro and their role in biological injury; and (3) the efficiency of repair processes in these events.

  17. Temperature response of Antarctic cryptoendolithic photosynthetic microorganisms

    NASA Technical Reports Server (NTRS)

    Ocampo-Friedmann, R.; Meyer, M. A.; Chen, M.; Friedmann, E. I.

    1988-01-01

    Growth responses to temperatures between 12.5 [degrees] C and 25 degrees C were determined for five photosynthetic microorganisms isolated from the Ross Desert cryptoendolithic community. Among eukaryotic algae, two strains of Trebouxia sp. have an upper temperature limit of 20 degrees C, and two strains of Hemichloris antarctica of 25 degrees C. The cyanobacterium Chroococcidiopsis sp., in contrast, grows at temperatures above 25 degrees C. These and earlier studies suggest that the eukaryotic algae of the Antarctic cryptoendolithic community have an upper temperature limit near 25 degrees C.

  18. Engineering photosynthesis in plants and synthetic microorganisms.

    PubMed

    Maurino, Veronica G; Weber, Andreas P M

    2013-01-01

    Photosynthetic organisms, such as cyanobacteria, algae, and plants, sustain life on earth by converting light energy, water, and CO(2) into chemical energy. However, due to global change and a growing human population, arable land is becoming scarce and resources, including water and fertilizers, are becoming exhausted. It will therefore be crucial to design innovative strategies for sustainable plant production to maintain the food and energy bases of human civilization. Several different strategies for engineering improved photosynthesis in crop plants and introducing novel photosynthetic capacity into microorganisms have been reviewed.

  19. Lead resistance in micro-organisms.

    PubMed

    Jarosławiecka, Anna; Piotrowska-Seget, Zofia

    2014-01-01

    Lead (Pb) is an element present in the environment that negatively affects all living organisms. To diminish its high toxicity, micro-organisms have developed several mechanisms that allow them to survive exposure to Pb(II). The main mechanisms of lead resistance involve adsorption by extracellular polysaccharides, cell exclusion, sequestration as insoluble phosphates, and ion efflux to the cell exterior. This review describes the various lead resistance mechanisms, and the regulation of their expression by lead binding regulatory proteins. Special attention is given to the Pbr system from Cupriavidus metallidurans CH34, which involves a unique mechanism combining efflux and lead precipitation.

  20. Temperature response of Antarctic cryptoendolithic photosynthetic microorganisms.

    PubMed

    Ocampo-Friedmann, R; Meyer, M A; Chen, M; Friedmann, E I

    1988-01-01

    Growth responses to temperatures between 12.5 [degrees] C and 25 degrees C were determined for five photosynthetic microorganisms isolated from the Ross Desert cryptoendolithic community. Among eukaryotic algae, two strains of Trebouxia sp. have an upper temperature limit of 20 degrees C, and two strains of Hemichloris antarctica of 25 degrees C. The cyanobacterium Chroococcidiopsis sp., in contrast, grows at temperatures above 25 degrees C. These and earlier studies suggest that the eukaryotic algae of the Antarctic cryptoendolithic community have an upper temperature limit near 25 degrees C.