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Sample records for beta-proteobacterium methylibium petroleiphilum

  1. Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8

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    Shi Yan

    2013-01-01

    Full Text Available Abstract Background Lignin materials are abundant and among the most important potential sources for biofuel production. Development of an efficient lignin degradation process has considerable potential for the production of a variety of chemicals, including bioethanol. However, lignin degradation using current methods is inefficient. Given their immense environmental adaptability and biochemical versatility, bacterial could be used as a valuable tool for the rapid degradation of lignin. Kraft lignin (KL is a polymer by-product of the pulp and paper industry resulting from alkaline sulfide treatment of lignocellulose, and it has been widely used for lignin-related studies. Results Beta-proteobacterium Cupriavidus basilensis B-8 isolated from erosive bamboo slips displayed substantial KL degradation capability. With initial concentrations of 0.5–6 g L-1, at least 31.3% KL could be degraded in 7 days. The maximum degradation rate was 44.4% at the initial concentration of 2 g L-1. The optimum pH and temperature for KL degradation were 7.0 and 30°C, respectively. Manganese peroxidase (MnP and laccase (Lac demonstrated their greatest level of activity, 1685.3 U L-1 and 815.6 U L-1, at the third and fourth days, respectively. Many small molecule intermediates were formed during the process of KL degradation, as determined using GC-MS analysis. In order to perform metabolic reconstruction of lignin degradation in this bacterium, a draft genome sequence for C. basilensis B-8 was generated. Genomic analysis focused on the catabolic potential of this bacterium against several lignin-derived compounds. These analyses together with sequence comparisons predicted the existence of three major metabolic pathways: β-ketoadipate, phenol degradation, and gentisate pathways. Conclusion These results confirmed the capability of C. basilensis B-8 to promote KL degradation. Whole genomic sequencing and systematic analysis of the C. basilensis B-8 genome

  2. Formation of alkenes via degradation of tert-alkyl ethers and alcohols by Aquincola tertiaricarbonis L108 and Methylibium spp.

    Science.gov (United States)

    Schäfer, Franziska; Muzica, Liudmila; Schuster, Judith; Treuter, Naemi; Rosell, Mònica; Harms, Hauke; Müller, Roland H; Rohwerder, Thore

    2011-09-01

    Bacterial degradation pathways of fuel oxygenates such as methyl tert-butyl and tert-amyl methyl ether (MTBE and TAME, respectively) have already been studied in some detail. However, many of the involved enzymes are still unknown, and possible side reactions have not yet been considered. In Aquincola tertiaricarbonis L108, Methylibium petroleiphilum PM1, and Methylibium sp. strain R8, we have now detected volatile hydrocarbons as by-products of the degradation of the tert-alkyl ether metabolites tert-butyl and tert-amyl alcohol (TBA and TAA, respectively). The alkene isobutene was formed only during TBA catabolism, while the beta and gamma isomers of isoamylene were produced only during TAA conversion. Both tert-alkyl alcohol degradation and alkene production were strictly oxygen dependent. However, the relative contribution of the dehydration reaction to total alcohol conversion increased with decreasing oxygen concentrations. In resting-cell experiments where the headspace oxygen content was adjusted to less than 2%, more than 50% of the TAA was converted to isoamylene. Isobutene formation from TBA was about 20-fold lower, reaching up to 4% alcohol turnover at low oxygen concentrations. It is likely that the putative tert-alkyl alcohol monooxygenase MdpJ, belonging to the Rieske nonheme mononuclear iron enzymes and found in all three strains tested, or an associated enzymatic step catalyzed the unusual elimination reaction. This was also supported by the detection of mdpJK genes in MTBE-degrading and isobutene-emitting enrichment cultures obtained from two treatment ponds operating at Leuna, Germany. The possible use of alkene formation as an easy-to-measure indicator of aerobic fuel oxygenate biodegradation in contaminated aquifers is discussed. PMID:21742915

  3. Cropping systems modulate the rate and magnitude of soil microbial autotrophic CO2 fixation in soil

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    Xiao Hong Wu

    2015-05-01

    Full Text Available The effect of different cropping systems on CO2 fixation by soil microorganisms was studied by comparing soils from three exemplary cropping systems: continuous cropping of paddy rice (rice-rice, rotation of paddy rice and rapeseed (rice-rapeseed, and rotated cropping of rapeseed and corn (rapeseed-corn. Soils from different cropping systems were continuously labeling with 14C-CO2 for 110 days. The CO2-fixing bacterial communities were investigated by analyzing the cbbL gene encoding ribulose-1,5-bisphosphate carboxylase oxygenase (RubisCO. Abundance, diversity and activity of cbbL-carrying bacteria were analyzed by quantitative PCR, cbbL clone libraries and enzyme assays. After 110 days incubation, substantial amounts of 14C-CO2 were incorporated into soil organic carbon (14C-SOC and microbial organic carbon (14C-MBC. Rice-rice rotated soil showed stronger incorporation rates when looking at 14C-SOC and 14C-MBC contents. These differences in incorporation rates were also reflected by RubisCO activities. 14C-MBC, cbbL gene abundances and RubisCO activity were found to correlate significantly with 14C-SOC, indicating cbbL-carrying bacteria to be key players for CO2 fixation in these soils. The analysis of clone libraries revealed distinct cbbL-carrying bacterial communities for the individual soils analyzed. Most of the identified operational taxonomic units (OTU were related to Nitrobacter hamburgensis, Methylibium petroleiphilum, Rhodoblastus acidophilus, Bradyrhizobium, Cupriavidus metallidurans, Rubrivivax, Burkholderia, stappia and Thiobacillus thiophilus. OTUs related to Rubrivivax gelatinosus were specific for rice-rice soil. OTUs linked to Methylibium petroleiphilum were exclusively found in rice-rapeseed soil. Observed differences could be linked to differences in soil parameters such as SOC. We conclude that the long-term application of cropping systems alters underlying soil parameters, which in turn selects for distinct autotrophic

  4. Genome of Methylobacillus flagellatus, Molecular Basis for Obligate Methylotrophy, and Polyphyletic Origin of Methylotrophy

    Energy Technology Data Exchange (ETDEWEB)

    Chistoserdova, L; Lapidus, A; Han, C; Godwin, L; Saunders, L; Brettin, T; Tapia, R; Gilna, P; Lucas, S; Richardson, P M; Lidstrom, M E

    2007-07-24

    Along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. The complete genome of a model obligate methanol and methylamine utilizer, Methylobacillus flagellatus (strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp, potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol and methylamine dehydrogenases and their specific electron transport chain components, the tetrahydromethanopterin-linked formaldehyde oxidation pathway and the assimilatory and dissimilatory ribulose monophosphate cycles, and by a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or nonidentical) copy. The obligate dependence on single-carbon compounds appears to be due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alpha-ketoglutarate, malate, or succinate dehydrogenases are identifiable. The genome of M. flagellatus was compared in terms of methylotrophy functions to the previously sequenced genomes of three methylotrophs, Methylobacterium extorquens (an alphaproteobacterium, 7 Mbp), Methylibium petroleiphilum (a betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (a gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, the methylotrophy functions in M. flagellatus were more similar to those in M. capsulatus and M. extorquens than to the ones in the more closely related M. petroleiphilum species, providing the first genomic evidence for the polyphyletic origin of methylotrophy in Betaproteobacteria.

  5. Internal loop photobiodegradation reactor (ILPBR) for accelerated degradation of sulfamethoxazole (SMX).

    Science.gov (United States)

    Yan, Ning; Xia, Siqing; Xu, Linke; Zhu, Jun; Zhang, Yongming; Rittmann, Bruce E

    2012-04-01

    The internal loop photobiodegradation reactor (ILPBR) was evaluated for the degradation of the pharmaceutical sulfamethoxazole (SMX) using batch experiments following three protocols: photolysis alone (P), biodegradation alone (B), and intimately coupled photolysis and biodegradation (P&B). SMX was removed more rapidly by P&B than by either P or B alone, and the corresponding dissolved organic carbon (DOC) removals by P&B also were higher. The faster SMX removal probably was due to a synergy between photolysis and the rapid biodegradation of SMX by the biofilm. The greater DOC removal was brought about by the presence of biofilm bacteria able to biodegrade photolysis products. Ammonium N released during photolysis of SMX gave more evidence for the formation of intermediates and was enough in P&B experiments to support bioactivity when no other N was supplied. Clone libraries performed on the biofilms before and after the P&B experiments showed profound changes in the microbial community. Whereas Rhodopirellula baltica and Methylibium petroleiphilum PM1 dominated the biofilm after the B experiments, they were replaced by Micrococcus luteus, Delftia acidovorans, and Oligotropha carboxidovorans after the P&B experiments. The changes in microbial community structure mirrored the change in function in the P&B experiments: SMX biodegradation (presumably the roles of R. baltica and M. petroleiphilum) was out-competed by SMX photolysis, but biodegradation of photolysis products (most likely by M. luteus and D. acidovorans) became important. The higher removal rates of SMX and DOC, as well as the changes in microbial community structure, confirm the value of intimately coupling photolysis with biodegradation in the ILPBR. PMID:22215070

  6. Successful treatment of an MTBE-impacted aquifer using a bioreactor self-colonized by native aquifer bacteria.

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    Hicks, Kristin A; Schmidt, Radomir; Nickelsen, Michael G; Boyle, Susan L; Baker, Jeffrey M; Tornatore, Paul M; Hristova, Krassimira R; Scow, Kate M

    2014-02-01

    A field-scale fixed bed bioreactor was used to successfully treat an MTBE-contaminated aquifer in North Hollywood, CA without requiring inoculation with introduced bacteria. Native bacteria from the MTBE-impacted aquifer rapidly colonized the bioreactor, entering the bioreactor in the contaminated groundwater pumped from the site, and biodegraded MTBE with greater than 99 % removal efficiency. DNA sequencing of the 16S rRNA gene identified MTBE-degrading bacteria Methylibium petroleiphilum in the bioreactor. Quantitative PCR showed M. petroleiphilum enriched by three orders of magnitude in the bioreactor above densities pre-existing in the groundwater. Because treatment was carried out by indigenous rather than introduced organisms, regulatory approval was obtained for implementation of a full-scale bioreactor to continue treatment of the aquifer. In addition, after confirmation of MTBE removal in the bioreactor to below maximum contaminant limit levels (MCL; MTBE = 5 μg L(-1)), treated water was approved for reinjection back into the aquifer rather than requiring discharge to a water treatment system. This is the first treatment system in California to be approved for reinjection of biologically treated effluent into a drinking water aquifer. This study demonstrated the potential for using native microbial communities already present in the aquifer as an inoculum for ex-situ bioreactors, circumventing the need to establish non-native, non-acclimated and potentially costly inoculants. Understanding and harnessing the metabolic potential of native organisms circumvents some of the issues associated with introducing non-native organisms into drinking water aquifers, and can provide a low-cost and efficient remediation technology that can streamline future bioremediation approval processes.

  7. Bacteriocinogenic Bacteria Isolated from Raw Goat Milk and Goat Cheese Produced in the Center of México.

    Science.gov (United States)

    Hernández-Saldaña, Oscar F; Valencia-Posadas, Mauricio; de la Fuente-Salcido, Norma M; Bideshi, Dennis K; Barboza-Corona, José E

    2016-09-01

    Currently, there are few reports on the isolation of microorganisms from goat milk and goat cheese that have antibacterial activity. In particular, there are no reports on the isolation of microorganisms with antibacterial activity from these products in central Mexico. Our objective was to isolate bacteria, from goat products, that synthesized antimicrobial peptides with activity against a variety of clinically significant bacteria. We isolated and identified Lactobacillus rhamnosus, L. plantarum, L. pentosus, L. helveticus and Enterococcus faecium from goat cheese, and Aquabacterium fontiphilum, Methylibium petroleiphilum, Piscinobacter aquaticus and Staphylococcus xylosus from goat milk. These bacteria isolated from goat cheese were able to inhibit Staphylococcus aureus, Bacillus cereus, Escherichia coli, Listeria monocytogenes, L. inoccua, Pseudomona aeruginosa, Shigella flexneri, Serratia marcescens, Enterobacter cloacae and Klebsiella pneumoniae. In addition, bacteria from goat milk showed inhibitory activity against B. cereus, L. lactis, E. coli, S. flexneri, E. cloacae and K. pneumonia; S. aureus, L. innocua, S. agalactiae and S. marcescens. The bacteriocins produced by these isolates were shown to be acid stable (pH 2-6) and thermotolerant (up to 100 °C), but were susceptible to proteinases. When screened by PCR for the presence of nisin, pediocin and enterocin A genes, none was found in isolates recovered from goat milk, and only the enterocin A gene was found in isolates from goat cheese. PMID:27407294

  8. Enhancement of methyl tert-butyl ether degradation by the addition of readily metabolizable organic substrates

    International Nuclear Information System (INIS)

    Supplements with readily metabolizable organic substrates were investigated to increase the biomass and enhance degradation of methyl tert-butyl ether (MTBE) due to the low biomass yield of MTBE which has been one of the factors for low-rate MTBE degradation. The influence of various organic substrates on the rate of aerobic degradation of methyl tert-butyl ether (MTBE) by Methylibium petroleiphilum PM1 was investigated, and only yeast extract (YE), beef extract and tryptone exhibited stimulatory effect. With the concentration of each substrate being 100 mg/L, the average MTBE removal rate could increase to 1.29, 1.20 and 1.04 mg/(L h), respectively, in comparison with 0.71 mg/(L h) when carried out in medium without addition. The stimulatory effects of YE addition, as well as induction period required by MTBE degradation, varied dramatically with the storage conditions, pre-culture medium and concentrations of the inoculums. The extent of stimulatory effects of YE might be closely related to the proportion of induction period in the total time of MTBE-degradation. The removal efficiency increased from about 50% to 90.5% with the addition of YE in a packed-bed reactor loaded with calcium alginate immobilized cells.

  9. Bacteriocinogenic Bacteria Isolated from Raw Goat Milk and Goat Cheese Produced in the Center of México.

    Science.gov (United States)

    Hernández-Saldaña, Oscar F; Valencia-Posadas, Mauricio; de la Fuente-Salcido, Norma M; Bideshi, Dennis K; Barboza-Corona, José E

    2016-09-01

    Currently, there are few reports on the isolation of microorganisms from goat milk and goat cheese that have antibacterial activity. In particular, there are no reports on the isolation of microorganisms with antibacterial activity from these products in central Mexico. Our objective was to isolate bacteria, from goat products, that synthesized antimicrobial peptides with activity against a variety of clinically significant bacteria. We isolated and identified Lactobacillus rhamnosus, L. plantarum, L. pentosus, L. helveticus and Enterococcus faecium from goat cheese, and Aquabacterium fontiphilum, Methylibium petroleiphilum, Piscinobacter aquaticus and Staphylococcus xylosus from goat milk. These bacteria isolated from goat cheese were able to inhibit Staphylococcus aureus, Bacillus cereus, Escherichia coli, Listeria monocytogenes, L. inoccua, Pseudomona aeruginosa, Shigella flexneri, Serratia marcescens, Enterobacter cloacae and Klebsiella pneumoniae. In addition, bacteria from goat milk showed inhibitory activity against B. cereus, L. lactis, E. coli, S. flexneri, E. cloacae and K. pneumonia; S. aureus, L. innocua, S. agalactiae and S. marcescens. The bacteriocins produced by these isolates were shown to be acid stable (pH 2-6) and thermotolerant (up to 100 °C), but were susceptible to proteinases. When screened by PCR for the presence of nisin, pediocin and enterocin A genes, none was found in isolates recovered from goat milk, and only the enterocin A gene was found in isolates from goat cheese.

  10. Deep RNA-Seq profile reveals biodiversity, plant-microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues.

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    Chakraborty, Sandeep; Britton, Monica; Martínez-García, P J; Dandekar, Abhaya M

    2016-03-01

    Deep RNA-Seq profiling, a revolutionary method used for quantifying transcriptional levels, often includes non-specific transcripts from other co-existing organisms in spite of stringent protocols. Using the recently published walnut genome sequence as a filter, we present a broad analysis of the RNA-Seq derived transcriptome profiles obtained from twenty different tissues to extract the biodiversity and possible plant-microbe interactions in the walnut ecosystem in California. Since the residual nature of the transcripts being analyzed does not provide sufficient information to identify the exact strain, inferences made are constrained to the genus level. The presence of the pathogenic oomycete Phytophthora was detected in the root through the presence of a glyceraldehyde-3-phosphate dehydrogenase. Cryptococcus, the causal agent of cryptococcosis, was found in the catkins and vegetative buds, corroborating previous work indicating that the plant surface supported the sexual cycle of this human pathogen. The RNA-Seq profile revealed several species of the endophytic nitrogen fixing Actinobacteria. Another bacterial species implicated in aerobic biodegradation of methyl tert-butyl ether (Methylibium petroleiphilum) is also found in the root. RNA encoding proteins from the pea aphid were found in the leaves and vegetative buds, while a serine protease from mosquito with significant homology to a female reproductive tract protease from Drosophila mojavensis in the vegetative bud suggests egg-laying activities. The comprehensive analysis of RNA-seq data present also unraveled detailed, tissue-specific information of ~400 transcripts encoded by the largest family of resistance (R) genes (NBS-LRR), which possibly rationalizes the resistance of the specific walnut plant to the pathogens detected. Thus, we elucidate the biodiversity and possible plant-microbe interactions in several walnut (Juglans regia) tissues in California using deep RNA-Seq profiling.

  11. Electrokinetic remediation and microbial community shift of β-cyclodextrin-dissolved petroleum hydrocarbon-contaminated soil.

    Science.gov (United States)

    Wan, Chunli; Du, Maoan; Lee, Duu-Jong; Yang, Xue; Ma, Wencheng; Zheng, Lina

    2011-03-01

    Electrokinetic (EK) migration of β-cyclodextrin (β-CD), which is inclusive of total petroleum hydrocarbon (TPH), is an economically beneficial and environmentally friendly remediation process for oil-contaminated soils. Remediation studies of oil-contaminated soils generally prepared samples using particular TPHs. This study investigates the removal of TPHs from, and electromigration of microbial cells in field samples via EK remediation. Both TPH content and soil respiration declined after the EK remediation process. The strains in the original soil sample included Bacillus sp., Sporosarcina sp., Beta proteobacterium, Streptomyces sp., Pontibacter sp., Azorhizobium sp., Taxeobacter sp., and Williamsia sp. Electromigration of microbial cells reduced the biodiversity of the microbial community in soil following EK remediation. At 200 V m(-1) for 10 days, 36% TPH was removed, with a small population of microbial cells flushed out, demonstrating that EK remediation is effective for the present oil-contaminated soils collected in field.

  12. Electrokinetic remediation and microbial community shift of β-cyclodextrin-dissolved petroleum hydrocarbon-contaminated soil.

    Science.gov (United States)

    Wan, Chunli; Du, Maoan; Lee, Duu-Jong; Yang, Xue; Ma, Wencheng; Zheng, Lina

    2011-03-01

    Electrokinetic (EK) migration of β-cyclodextrin (β-CD), which is inclusive of total petroleum hydrocarbon (TPH), is an economically beneficial and environmentally friendly remediation process for oil-contaminated soils. Remediation studies of oil-contaminated soils generally prepared samples using particular TPHs. This study investigates the removal of TPHs from, and electromigration of microbial cells in field samples via EK remediation. Both TPH content and soil respiration declined after the EK remediation process. The strains in the original soil sample included Bacillus sp., Sporosarcina sp., Beta proteobacterium, Streptomyces sp., Pontibacter sp., Azorhizobium sp., Taxeobacter sp., and Williamsia sp. Electromigration of microbial cells reduced the biodiversity of the microbial community in soil following EK remediation. At 200 V m(-1) for 10 days, 36% TPH was removed, with a small population of microbial cells flushed out, demonstrating that EK remediation is effective for the present oil-contaminated soils collected in field. PMID:21052991

  13. Electrokinetic remediation and microbial community shift of {beta}-cyclodextrin-dissolved petroleum hydrocarbon-contaminated soil

    Energy Technology Data Exchange (ETDEWEB)

    Wan, Chunli; Du, Maoan; Yang, Xue; Ma, Wencheng [Harbin Institute of Technology (China). School of Municipal and Environmental Engineering; Lee, Duu-Jong [National Taiwan Univ., Taipei (China). Dept. of Chemical Engineering; Zheng, Lina [Dalian Ocean Univ. (China). College of Marine Environmental Engineering

    2011-03-15

    Electrokinetic (EK) migration of {beta}-cyclodextrin ({beta}-CD), which is inclusive of total petroleum hydrocarbon (TPH), is an economically beneficial and environmentally friendly remediation process for oil-contaminated soils. Remediation studies of oil-contaminated soils generally prepared samples using particular TPHs. This study investigates the removal of TPHs from, and electromigration of microbial cells in field samples via EK remediation. Both TPH content and soil respiration declined after the EK remediation process. The strains in the original soil sample included Bacillus sp., Sporosarcina sp., Beta proteobacterium, Streptomyces sp., Pontibacter sp., Azorhizobium sp., Taxeobacter sp., and Williamsia sp. Electromigration of microbial cells reduced the biodiversity of the microbial community in soil following EK remediation. At 200 V m{sup -1} for 10 days, 36% TPH was removed, with a small population of microbial cells flushed out, demonstrating that EK remediation is effective for the present oil-contaminated soils collected in field. (orig.)

  14. Bacterial genomic adaptation and response to metals

    International Nuclear Information System (INIS)

    The beta-proteobacterium Cupriavidus metallidurans CH34 (formerly Ralstonia metallidurans) has been intensively studied since 1976 in SCK-CEN and VITO, for its adaptation capacity to survive in harsh (mostly industrial) environments, to overcome acute environmental stresses, for its resistance to a variety of heavy metals and for applications in environmental biotechnology. Recently, CH34 has become a model bacterium to study the effect of spaceflight conditions in several space flight experiments conducted by SCK-CEN (e.g. MESSAGE, BASE). Furthermore, Cupriavidus and Ralstonia species are isolated from the floor, air and surfaces of spacecraft assembly rooms; were found prior-to-flight on surfaces of space robots such as the Mars Odyssey Orbiter and even in-flight in ISS cooling water and Shuttle drinking water, vindicating its role as model bacterium in space research. In addition, Ralstonia species are also the causative agent of nosocomial infections and are among the unusual species recovered from cystic fibrosis (CF) patients. The genomic organization of Cuprivavidus metallidurans CH34 was studied in-depth to identify the genetic and regulatory structures involved in the resistance to heavy metals

  15. Cycle inhibiting factors (CIFs are a growing family of functional cyclomodulins present in invertebrate and mammal bacterial pathogens.

    Directory of Open Access Journals (Sweden)

    Grégory Jubelin

    Full Text Available The cycle inhibiting factor (Cif produced by enteropathogenic and enterohemorrhagic Escherichia coli was the first cyclomodulin to be identified that is injected into host cells via the type III secretion machinery. Cif provokes cytopathic effects characterized by G(1 and G(2 cell cycle arrests, accumulation of the cyclin-dependent kinase inhibitors (CKIs p21(waf1/cip1 and p27(kip1 and formation of actin stress fibres. The X-ray crystal structure of Cif revealed it to be a divergent member of a superfamily of enzymes including cysteine proteases and acetyltransferases that share a conserved catalytic triad. Here we report the discovery and characterization of four Cif homologs encoded by different pathogenic or symbiotic bacteria isolated from vertebrates or invertebrates. Cif homologs from the enterobacteria Yersinia pseudotuberculosis, Photorhabdus luminescens, Photorhabdus asymbiotica and the beta-proteobacterium Burkholderia pseudomallei all induce cytopathic effects identical to those observed with Cif from pathogenic E. coli. Although these Cif homologs are remarkably divergent in primary sequence, the catalytic triad is strictly conserved and was shown to be crucial for cell cycle arrest, cytoskeleton reorganization and CKIs accumulation. These results reveal that Cif proteins form a growing family of cyclomodulins in bacteria that interact with very distinct hosts including insects, nematodes and humans.

  16. The involvement of the nif-associated ferredoxin-like genes fdxA and fdxN of Herbaspirillum seropedicae in nitrogen fixation.

    Science.gov (United States)

    Souza, André L F; Invitti, Adriana L; Rego, Fabiane G M; Monteiro, Rose A; Klassen, Giseli; Souza, Emanuel M; Chubatsu, Leda S; Pedrosa, Fábio O; Rigo, Liu U

    2010-02-01

    The pathway of electron transport to nitrogenase in the endophytic beta-Proteobacterium Herbaspirillum seropedicae has not been characterized. We have generated mutants in two nif-associated genes encoding putative ferredoxins, fdxA and fdxN. The fdxA gene is part of the operon nifHDKENXorf1orf2fdxAnifQmodABC and is transcribed from the nifH promoter, as revealed by lacZ gene fusion. The fdxN gene is probably cotranscribed with the nifB gene. Mutational analysis suggests that the FdxA protein is essential for maximum nitrogenase activity, since the nitrogenase activity of the fdxA mutant strain was reduced to about 30% of that of the wild-type strain. In addition, the fdxA mutation had no effect on the nitrogenase switch-off in response to ammonium. Nitrogenase activity of a mutant strain lacking the fdxN gene was completely abolished. This phenotype was reverted by complementation with fdxN expressed under lacZ promoter control. The results suggest that the products of both the fdxA and fdxN genes are probably involved in electron transfer during nitrogen fixation.

  17. Extracellular polymeric substances, microbial activity and microbial community of biofilm and suspended sludge at different divalent cadmium concentrations.

    Science.gov (United States)

    Wang, Zichao; Gao, Mengchun; Wei, Junfeng; Ma, Kedong; Zhang, Jing; Yang, Yusuo; Yu, Shuping

    2016-04-01

    The differences between biofilm and suspended sludge (S-sludge) in extracellular polymeric substances (EPS), microbial activity, and microbial community in an anoxic-aerobic sequencing batch biofilm reactor (SBBR) at different concentrations of divalent cadmium (Cd(II)) were investigated. As the increase of Cd(II) concentration from 0 to 50mgL(-1), the specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR), and specific nitrate reduction rate (SNRR) of biofilm decreased from 4.85, 5.22 and 45mgNg(-1) VSSh(-1) to 1.54, 2.38 and 26mgNg(-1)VSSh(-1), respectively, and the SAOR, SNOR and SNRR of S-sludge decreased from 4.80, 5.02 and 34mgNg(-1)VSSh(-1) to 1.46, 2.20 and 17mgNg(-1)VSSh(-1), respectively. Biofilm had higher protein (PN) content in EPS than S-sludge. Contrast to S-sludge, biofilm could provide Nitrobacter vulgaris, beta proteobacterium INBAF015, and Pseudoxanthomonas mexicana with the favorable conditions of growth and reproduction. PMID:26829529

  18. Comparison of Ca{sup 2+} and Mg{sup 2+} enhancing aerobic granulation in SBR

    Energy Technology Data Exchange (ETDEWEB)

    Liu Lin [School of Forestry, Northeast Forestry University, Harbin 150040 (China); Gao Dawen, E-mail: dawengao@gmail.com [School of Forestry, Northeast Forestry University, Harbin 150040 (China); State Key Laboratory of Urban Water Resource and Environment, 73 Huanghe Rd., Harbin 150090 (China); Zhang Min [School of Forestry, Northeast Forestry University, Harbin 150040 (China); Fu Yuan [State Key Laboratory of Urban Water Resource and Environment, 73 Huanghe Rd., Harbin 150090 (China)

    2010-09-15

    Two sequencing batch reactors (SBRs) were operated to investigate the effect of Ca{sup 2+} and Mg{sup 2+} augmentation on aerobic granulation. Reactor R1 was augmented with Ca{sup 2+} at 40 mg/L, while Mg{sup 2+} was added to the reactor R2 with 40 mg/L. Results showed that the reactor R1 had a faster granulation process compared with R2, and the mature granules in R1 showed better physical characteristics. However, the mature granules in R2 had the higher production yield of polysaccharides and proteins, and aerobic granules in R2 experienced a faster substrate biodegradation. Microbial and genetic characteristics in mature granules were analyzed using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) techniques. The results revealed that Mg{sup 2+} addition led to higher microbial diversity in mature granules. In addition, an uncultured bacterium (AB447697) was major specie in R1, and {beta}-proteobacterium was dominant in R2. It can be concluded that Ca{sup 2+} had an important effect on physical properties of aerobic granules, while Mg{sup 2+} played a key role on biological properties during the sludge granulation.

  19. A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

    Directory of Open Access Journals (Sweden)

    Daniel Muller

    2007-04-01

    Full Text Available Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the beta-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.

  20. DNA repair in Chromobacterium violaceum.

    Science.gov (United States)

    Duarte, Fábio Teixeira; Carvalho, Fabíola Marques de; Bezerra e Silva, Uaska; Scortecci, Kátia Castanho; Blaha, Carlos Alfredo Galindo; Agnez-Lima, Lucymara Fassarella; Batistuzzo de Medeiros, Silvia Regina

    2004-03-31

    Chromobacterium violaceum is a Gram-negative beta-proteobacterium that inhabits a variety of ecosystems in tropical and subtropical regions, including the water and banks of the Negro River in the Brazilian Amazon. This bacterium has been the subject of extensive study over the last three decades, due to its biotechnological properties, including the characteristic violacein pigment, which has antimicrobial and anti-tumoral activities. C. violaceum promotes the solubilization of gold in a mercury-free process, and has been used in the synthesis of homopolyesters suitable for the production of biodegradable polymers. The complete genome sequence of this organism has been completed by the Brazilian National Genome Project Consortium. The aim of our group was to study the DNA repair genes in this organism, due to their importance in the maintenance of genomic integrity. We identified DNA repair genes involved in different pathways in C. violaceum through a similarity search against known sequences deposited in databases. The phylogenetic analyses were done using programs of the PHILYP package. This analysis revealed various metabolic pathways, including photoreactivation, base excision repair, nucleotide excision repair, mismatch repair, recombinational repair, and the SOS system. The similarity between the C. violaceum sequences and those of Neisserie miningitidis and Ralstonia solanacearum was greater than that between the C. violaceum and Escherichia coli sequences. The peculiarities found in the C. violaceum genome were the absence of LexA, some horizontal transfer events and a large number of repair genes involved with alkyl and oxidative DNA damage.

  1. Characterization of cycP gene expression in Achromobacter xylosoxidans NCIMB 11015 and high-level heterologous synthesis of cytochrome c' in Escherichia coli.

    Science.gov (United States)

    Harris, Roger L; Barbieri, Sonia; Paraskevopoulos, Kostas; Murphy, Loretta M; Eady, Robert R; Hasnain, S Samar; Sawers, R Gary

    2010-01-01

    The cycP gene encoding a periplasmic cytochrome c' from the denitrifying beta-proteobacterium Achromobacter xylosoxidans was characterized. The genes flanking cycP encode components of a mobile genetic element characteristic of the beta-proteobacteria, suggesting that cycP has inserted within a transposon or insertion element. The gene therefore does not form part of a denitrification operon or gene cluster. The level of expression of the cycP gene and the level of synthesis of its corresponding gene product were found to increase by maximally 3-fold anaerobically. Expression of cycP appears to occur mainly by non-specific read-through transcription from portions of the insertion element. Conditions were developed for high-level overproduction of cytochrome c' in Escherichia coli, which resulted in signal peptide cleavage concomitant with secretion of the protein into the periplasm. Using a single-step purification, 20-30 mg of pure protein were isolated from a 1-litre culture. Based on UV-visible spectrophotometry the dimeric protein was shown to have a full complement of haem and to be indistinguishable from the native protein purified from A. xylosoxidans. This system provides an excellent platform to facilitate biochemical and structural dissection of the mechanism underlying the novel specificity of NO binding to the proximal face of the haem.

  2. A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan

    Science.gov (United States)

    Pershina, E. V.; Ivanova, E. A.; Nagieva, A. G.; Zhiengaliev, A. T.; Chirak, E. L.; Andronov, E. E.; Sergaliev, N. Kh.

    2016-06-01

    The goal of this study was to determine the relationships between the structure of the soil microbiome and the agroecological state of soils by the example of natural undisturbed (steppe areas) and anthropogenically disturbed (pastures, croplands, fallows) areas in the territory of northwestern Kazakhstan. The highest abundance of proteobacteria was found in the anthropogenically disturbed of fallows and in undisturbed soils; in other cases, actinobacteria and representatives of the Firmicutes phylum predominated. Different kinds of anthropogenic impacts resulted in the decrease in the portions of bacteria from the Acidobacteria, Gemmatimonadetes, and Firmicutes phyla. In the disturbed soils, the portions of bacteria from the Erysipelothrix, Mycobacterium, Methylibium, Skermanella, Ralstonia, Lactococcus, Bdellovibrio, Candidatus nitrososphaera, Catellatospora, Cellulomonas, Stenotrophomonas, and Steroidobacter genera increased. Bacteria of the Erysipelothrix and Methylibium genera occurred only in the undisturbed soils. The anthropogenically disturbed and undisturbed soils differed significantly in the taxonomic structure of their microbiomes forming two separate clusters, which confirms the efficiency of using the data on the structure of soil microbiomes when assessing the agroecological status of soils.

  3. Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates.

    Science.gov (United States)

    Mao, Yuejian; Li, Xiangzhen; Smyth, Eoghan M; Yannarell, Anthony C; Mackie, Roderick I

    2014-06-01

    Identification of microbes that actively utilize root exudates is essential to understand plant-microbe interactions. To identify active root exudate-utilizing microorganisms associated with switchgrass - a potential bioenergy crop - plants were labelled in situ with (13) CO2 , and 16S and 18S rRNA genes in the (13) C-labelled rhizosphere DNA were pyrosequenced. Multi-pulse labelling for 5 days produced detectable (13) C-DNA, which was well separated from unlabelled DNA. Methylibium from the order Burkholderiales were the most heavily labelled bacteria. Pythium, Auricularia and Galerina were the most heavily labelled eukaryotic microbes. We also identified a Glomus intraradices-like species; Glomus members are arbuscular mycorrhizal fungi that are able to colonize the switchgrass root. All of these heavily labelled microorganisms were also among the most abundant species in the rhizosphere. Species belonging to Methylibium and Pythium were the most heavily labelled and the most abundant bacteria and eukaryotes in the rhizosphere of switchgrass. Our results revealed that nearly all of the dominant rhizosphere bacterial and eukaryotic microbes were able to utilize root exudates. The enrichment of microbial species in the rhizosphere is selective and mostly due to root exudation, which functions as a nutrition source, promoting the growth of these microbes.

  4. Variations in AOC and microbial diversity in an advanced water treatment plant

    Science.gov (United States)

    Yang, B. M.; Liu, J. K.; Chien, C. C.; Surampalli, R. Y.; Kao, C. M.

    2011-10-01

    SummaryThe objective of this study was to evaluate the variations in assimilable organic carbon (AOC) and microbial diversities in an advanced water treatment plant. The efficiency of biofiltration on AOC removal using anthracite and granular activated carbon (GAC) as the media was also evaluated through a pilot-scale column experiment. Effects of hydrological factors (seasonal effects and river flow) on AOC concentrations in raw water samples and hydraulic retention time (HRT) of biofiltration on AOC treatment were also evaluated. Results show that AOC concentrations in raw water and clear water of the plant were about 138 and 27 μg acetate-C/L, respectively. Higher AOC concentrations were observed in wet seasons probably due to the resuspension of organic-contained sediments and discharges of non-point source (NPS) pollutants from the upper catchment. This reveals that seasonal effect played an important role in the variations in influent AOC concentrations. Approximately 82% and 70% of AOC removal efficiencies were observed in GAC and anthracite columns, respectively. Results from column experiment reveal that the applied treatment processes in the plant and biofiltration system were able to remove AOC effectively. Microbial colonization on GAC and anthracite were detected via the observation of scanning electron microscopic (SEM) images. Results of polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and nucleotide sequence analysis reveal significant decrease in microbial diversities after the ozonation process. Higher HRT caused higher microbial contact time, and thus, more microbial colonies and higher microbial diversity were observed in the latter part of the biofilters. Some of the dominant microbial species in the biofiltration columns belonged to the beta- proteobacterium, which might contribute to the AOC degradation. Results of this study provide us insight into the variations in AOC and microbial diversity in the advanced

  5. The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

    Energy Technology Data Exchange (ETDEWEB)

    Lykidis, Athanasios; Perez-Pantoja, Danilo; Ledger, Thomas; Mavromatis, Kostantinos; Anderson, Iain J.; Ivanova, Natalia N.; Hooper, Sean D.; Lapidus, Alla; Lucas, Susan; Gonzalez, Bernardo; Kyrpides, Nikos C.

    2010-02-01

    Cupriavidus necator JMP134 (formerly Ralstonia eutropha JMP134) is a Gram-negative {beta}-proteobacterium able to degrade a variety of chloroaromatic compounds and chemically-related pollutants. It was originally isolated based on its ability to use 2,4 dichlorophenoxyacetic acid (2,4-D) as a sole carbon and energy source [1]. In addition to 2,4-D, this strain can also grow on a variety of aromatic substrates, such as 4-chloro-2-methylphenoxyacetate (MCPA), 3-chlorobenzoic acid (3-CB) [2], 2,4,6-trichlorophenol [3], and 4-fluorobenzoate [4]. The genes necessary for 2,4-D utilization have been identified. They are located in two clusters on plasmid pPJ4: tfd{sub I} and tfd{sub II} [5,6,7,8]. The sequence and analysis of plasmid pJP4 was reported and a congruent model for bacterial adaptation to chloroaromatic pollutants was proposed [9]. According to this model, catabolic gene clusters assemble in a modular manner into broad-host-range plasmid backbones by means of repeated chromosomal capture events. Cupriavidus and related Burkholderia genomes are typically multipartite, composed of two large replicons (chromosomes) accompanied by classical plasmids. Previous work with Burkholderia xenovorans LB400 revealed a differential gene distribution with core functions preferentially encoded by the larger chromosome and secondary functions by the smaller [10]. It has been proposed that the secondary chromosomes in many bacteria originated from ancestral plasmids which, in turn, had been the recipient of genes transferred earlier from ancestral primary chromosomes [11]. The existence of multiple Cupriavidus and Burkholderia genomes provides the opportunity for comparative studies that will lead to a better understanding of the evolutionary mechanisms for the formation of multipartite genomes and the relation with biodegradation abilities.

  6. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.

    Directory of Open Access Journals (Sweden)

    Athanasios Lykidis

    Full Text Available BACKGROUND: Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source. METHODOLOGY/PRINCIPAL FINDINGS: Its genome consists of four replicons (two chromosomes and two plasmids containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000. Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation seems to be shaped mostly by the acquisition of "specialized" plasmids. CONCLUSIONS/SIGNIFICANCE: The availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.

  7. Coordinated surface activities in Variovorax paradoxus EPS

    Directory of Open Access Journals (Sweden)

    Gregory Glenn A

    2009-06-01

    with methionine, arginine, or tyrosine. Large effects of mineral content on swarming were seen with tyrosine and methionine as nitrogen sources. Biofilms form readily under various culture circumstances, and show wide variance in structure under different conditions. The amount of biofilm as measured by crystal violet retention was dependent on carbon source, but not nitrogen source. Filamentous growth in the biofilm depends on shear stress, and is enhanced by continuous input of nutrients in chemostat culture. Conclusion Our studies have established that the beta-proteobacterium Variovorax paradoxus displays a number of distinct physiologies when grown on surfaces, indicative of a complex response to several growth parameters. We have identified a number of factors that drive sessile and motile surface phenotypes. This work forms a basis for future studies using this genetically tractable soil bacterium to study the regulation of microbial development on surfaces.

  8. Interplay between seven secondary metal uptake systems is required for full metal resistance of Cupriavidus metallidurans.

    Science.gov (United States)

    Herzberg, M; Bauer, L; Kirsten, A; Nies, D H

    2016-03-01

    The beta-proteobacterium Cupriavidus metallidurans is able to grow in metal-contaminated environments due to having sophisticated metal efflux systems. Here, the contribution of all seven known secondary metal uptake systems (ZupT, PitA, CorA1, CorA2, CorA3, ZntB, HoxN) to metal resistance is characterized. In a strategic deletion approach, all ten double deletion mutants, a variety of triple and quadruple mutants, and from the Δ4 mutant (ΔzupT ΔcorA1 ΔcorA2 ΔcorA3) the mutants Δ5 (=Δ4 ΔpitA), Δ6 (=Δ4 ΔpitA ΔzntB), and finally Δ7 (ΔzupT ΔcorA1 ΔcorA2 ΔcorA3 ΔpitA ΔzntB ΔhoxN) were constructed. Metal resistance, metal content, and regulation of expression of these genes were characterized in these mutants. The ΔzupT single deletion strain exhibited an extended lag phase in Tris-buffered liquid mineral salts medium (TMM) compared to its parent strain AE104, indicating a decreased fitness level. Further deletions up to Δ6 did not influence growth in TMM without added metals but fitness of the Δ7 strain dropped to a lower level compared to Δ6, Δ5 and ΔzupT. The cells of the Δ7 multiple deletion strain still contained all essential metals, demonstrating that additional metal import systems must exist in C. metallidurans. PitA was an important contributor of metal:phosphate complexes to C. metallidurans. Up to Δ5 no evidence was found for increased expression of the transporter genes to recruit substitutes for the deleted importers. Only the hoxN-lacZ reporter gene fusion displayed a changed expression pattern in the Δ6 strain, indicating recruitment of HoxN. Metal resistance of the deletion strains decreased along the deletion series although all strains still contained metal efflux systems: up to the Δ6 mutant the overall fitness was kept at the ΔzupT mutant strain level at the cost of a diminished competence to handle μM concentrations of transition metals. Together, these data demonstrated an important contribution of the seven

  9. 生防菌哈茨木霉T4对黄瓜根围土壤细菌群落的影响%Effects of the Introduction of Biocontrol Agent Trichoderma harzianum T4 on the Bacterial Community in Cucumber Rhizosphere

    Institute of Scientific and Technical Information of China (English)

    尹丹韩; 高观朋; 夏飞; 王伟

    2012-01-01

    [目的]评价生防菌哈茨木霉(Trichoderma harzianum)T4对根围土壤细菌群落的影响,为生防菌田间应用的生态安全提供依据.[方法]结合DGGE技术与T-RFLP方法,综合考察引入生防菌哈茨木霉T4后黄瓜根围土壤细菌群落变化,[结果]在引入生防菌的14-56 d内(黄瓜整个生育期),木霉对根围土壤细菌群落可产生显著影响,并持续一段的时间,随后逐渐减弱.表现为对蓝细菌、β-变形细菌、葡萄球菌、伯克霍尔德菌、沙雷氏菌、酸杆菌和一些不可培养细菌的有效抑制作用,对芽孢杆菌、土壤杆菌、芽单胞菌的明显促进作用.但到70d时,即收获后2周,检测不到木霉对细菌群落影响.[结论]DGGE和T-RFLP序列分析技术相结合研究生防菌对土壤细菌群落的影响,既能全面描述土壤细菌群落结构变化,还可以初步定性描述变化细菌的种类信息.生防菌哈茨木霉T4的引入对土壤细菌群落产生短期影响,不会长期对土壤细菌群落稳定构成威胁.%[ Objective ] The objective of this study is to analysis the impact of T. Harzianum T4 introduction on the indigenous bacterial community of rhizosphere soil, and to provide objective biosafety evaluations for the field application of biocontrol agents.[ Method 1 Comprised molecular tools DGGE and T-RFLP were used in this study to assess the modifications of the bacterial community in cucumber rhizosphere after inoculation with T. Harzianum T4. [Result] Introduction of T. Harzianum T4 in the soil resulted in significant variations of the bacterial community structures from 14 to 56 days post-inoculation. During this period the impact of T4 was sustainable and weakened gradually. T. Harzianum T4 could restrain effectively Cyanobacterium, Beta-proteobacterium, Staphylococcus, Burkholderia, Serratia, Acidobacterium and some kinds of soil uncultured bacterium, while it improved the growth of Bacillus, Agrobacterium and Gemmatimonadetes observably

  10. 水稻土氨氧化细菌多样性的RFLP分析%RFLP Analysis of Ammonia Oxidizing Bacteria Diversity in Paddy Soil

    Institute of Scientific and Technical Information of China (English)

    李惠民; 程林; 王保莉; 曲东

    2011-01-01

    Ammonia-oxidizing microbes play an important role in the biogeochemical cycle of N element and limit the rate of nitrification.The diversity and composition of the rhizosphere paddy soil and bulk paddy soil ammonia-oxidizing bacteria were analyzed through constructing its 16S rDNA gene clone library and by PCR-based Restriction Fragment Length Polymorphism analysis (RFLP).Total genome DNA of soil microorganism was extracted from the rhizosphere paddy soil(G) and bulk paddy soil(F).16S rDNAs of the extracted DNA were amplified using ammona oxidizing bacteria special primers (Eub338, Nso1225) and relevant clone libraries were constructed.110 and 105 restriction endonuclease types of these samples were detected based on restriction endonuclease Hha Ⅰ and Rsa Ⅰ using PCR-RFLP.The data were analyzed by diversity index and clustering of the dominated bacteria.The results showed that the ammonia-oxidizing bacteria community structure index H', Dg and Jgi of bulk paddy soil were slightly higher than rhizosphere paddy soil, which indicated that the population of ammonia-oxidizing bacteria in bulk paddy soil was slightly more than that in rhizosphere paddy soil; the index Hmax and dMax of rhizosphere paddy soil were higher than bulk paddy soil, which meant that the quantity of ammonia- oxidizing bacteria in rhizosphere paddy soil was more than in bulk paddy soil;Sequencing the dominate ammonia-oxidizing bacteria community in rhizosphere paddy soil showed that they mainly belong to Nitrosospira sp., Uncultured Nitrosomonadaceae bacterium, Uncultured Beta proteobacterium , and UncuLtured Alcaligenaceae bacterium.%提取苗期水稻根际土和非根际土土样微生物总DNA,采用氨氧化细菌特异性引物(Eub338,Nso1225)扩增16S rDNA基因片段,分别建立水稻根际土(G)和非根际土(F)氨氧化细菌克隆文库.用限制性内切酶HhaⅠ/RsaⅠ进行PCR-RFLP分型,分别得到110和105个酶切类型.多样性指数和优势细菌聚类比对

  11. The genome of Methylobacillus flagellatus, the molecular basis forobligate methylotrophy, and the polyphyletic origin ofmethylotrophy

    Energy Technology Data Exchange (ETDEWEB)

    Chistoserdova, Ludmila; Lapidus, Alla; Han, Cliff; Goodwin,Lynne; Saunders, Liz; Brettin, Tom; Tapia, Roxanne; Gilna, Paul; Lucas,Susan; Richardson, Paul M.; Lidstrom, Mary E.

    2007-01-08

    Along with methane, methanol and methylated amines representimportant biogenic atmospheric constituents, thus not only methanotrophs,but also non-methanotrophic methylotrophs play a significant role inglobal carbon cycling. The complete genome of a model obligate methanoland methylamine utilizer, Methylobacillus flagellatus (strain KT) wassequenced. The genome is represented by a single circular chromosome ofapproximately 3 Mb pairs, potentially encoding a total of 2,766 proteins.Based on genome analysis as well as the results from previous genetic andmutational analyses, methylotrophy is enabled by methanol- andmethylamine dehydrogenases, the tetrahydromethanopterin-linkedformaldehyde oxidation pathway, the assimilatory and dissimilatorybranches of the ribulose monophosphate cycle, and by formatedehydrogenases. Some of the methylotrophy genes are present in more thanone (identical or non-identical) copy. The obligate dependence on singlecarbon compounds appears to be due to the incomplete tricarboxylic acidcycle, as no genes potentially encoding alpha ketoglutarate, malate orsuccinate dehydrogenases are identifiable. The genome of M. flagellatuswas compared, in terms of methylotrophy functions, to the previouslysequenced genomes of three methylotrophs: Methylobacterium extorquens(Alphaproteobacterium, 7 Mbp), Methylibium petroleophilum(Betaproteobacterium, 4 Mbp), and Methylococcus capsulatus(Gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/orphylogenetically, methylotrophy functions in M. flagellatus were moresimilar to the ones in M. capsulatus and M. extorquens than to the onesin the more closely related M. petroleophilum, providing the firstgenomic evidence for the polyphyletic origin of methylotrophy inBetaproteobacteria.

  12. Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms

    Directory of Open Access Journals (Sweden)

    Heini eKutvonen

    2015-10-01

    Full Text Available We investigated the N-utilizing bacterial community in anoxic brackish groundwater of the low and intermediate level nuclear waste repository cave in Olkiluoto, Finland, at 100 m depth using 15N-based stable isotope probing (SIP and enrichment with 14/15N-ammonium or 14/15N-nitrate complemented with methane. 28 days of incubation at 12°C increased the concentration of bacterial 16S rRNA and nitrate reductase (narG gene copies in the substrate amended microcosms simultaneously with a radical drop in the overall bacterial diversity and OTU richness. Hydrogenophaga/Malikia were enriched in all substrate amended microcosms and Methylobacter in the ammonium and ammonium+methane supplemented microcosms. Sulfuricurvum was especially abundant in the nitrate+methane treatment and the unamended incubation control. Membrane-bound nitrate reductase genes (narG from Polarimonas sp. were detected in the original groundwater, while Burkholderia, Methylibium and Pseudomonas narG genes were enriched due to substrate supplements. Identified amoA genes belonged to Nitrosomonas sp. 15N-SIP revealed that Burkholderiales and Rhizobiales clades belonging to the minority groups in the original groundwater used 15N from ammonium and nitrate as N source indicating an important ecological function of these bacteria, despite their low number, in the groundwater N cycle in Olkiluoto bedrock system.

  13. Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms

    Science.gov (United States)

    Kutvonen, Heini; Rajala, Pauliina; Carpén, Leena; Bomberg, Malin

    2015-01-01

    We investigated the N-utilizing bacterial community in anoxic brackish groundwater of the low and intermediate level nuclear waste repository cave in Olkiluoto, Finland, at 100 m depth using 15N-based stable isotope probing (SIP) and enrichment with 14∕15N-ammonium or 14∕15N-nitrate complemented with methane. Twenty-eight days of incubation at 12°C increased the concentration of bacterial 16S rRNA and nitrate reductase (narG) gene copies in the substrate amended microcosms simultaneously with a radical drop in the overall bacterial diversity and OTU richness. Hydrogenophaga/Malikia were enriched in all substrate amended microcosms and Methylobacter in the ammonium and ammonium+methane supplemented microcosms. Sulfuricurvum was especially abundant in the nitrate+methane treatment and the unamended incubation control. Membrane-bound nitrate reductase genes (narG) from Polarimonas sp. were detected in the original groundwater, while Burkholderia, Methylibium, and Pseudomonas narG genes were enriched due to substrate supplements. Identified amoA genes belonged to Nitrosomonas sp. 15N-SIP revealed that Burkholderiales and Rhizobiales clades belonging to the minority groups in the original groundwater used 15N from ammonium and nitrate as N source indicating an important ecological function of these bacteria, despite their low number, in the groundwater N cycle in Olkiluoto bedrock system. PMID:26528251

  14. [Nitrate removal from recirculating aquaculture system using polyhydroxybutyrate-co-hydroxyvalerate as carbon source ].

    Science.gov (United States)

    Zhang, Lanhe; Liu, Lili; Qiu, Tianlei; Gao, Min; Han, Meilin; Yuan, Ding; Wang, Xuming

    2014-09-01

    [ OBJECTIVE] Polyhydroxybutyrate-co-hydroxyvalerate (PHBV) was used as solid carbon source and biofilm carrier to remove nitrate from recirculating aquaculture system (RAS). Dynamics of microbial community structure in biofilm coating on carbon source packed into denitrification reactor were investigated. [METHODS] Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the microbial community in biofilm from denitrifiation reactor. Bacteria degrading PHBV were isolated from the reactor using pure culture method. [RESULTS] Nitrate decreased remarkably in the RAS connected with dentrification reactor. In contrast, Nitrate increased continuously in the conventional RAS without dentrification reactor. According to the phylogenetic analysis, the microbes in the biofilm samples from denitrification reactor were divided into Proteobacteria ( p-proteobacteria, γ-proteobacteria and δ- proteobacteria) , Firmicutes and Bacteroidetes. The major advantageous populations were Acidovorax and Bacillus in the 40-day reactor. The advantageous populations in the 150-day reactor were in order of Clostridium, Desulfitobacterium, Dechloromonas, Pseudoxanthomonas and Flavobacterium. Pure cultures of bacteria degrading PHBV isolated from denitrification reactor were classified into Acidovorax, Methylibium, Pseudoxanthomonas and Dechloromonas. [CONCLUSION] Nitrate could be removed effectively from RAS using PHBV as carbon source. Advantageous bacteria and their dynamic changes were ascertained in biofilm from denitrification reactor packed with PHBV. PMID:25522594

  15. Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area

    Science.gov (United States)

    Wang, Neng Fei; Zhang, Tao; Yang, Xiao; Wang, Shuang; Yu, Yong; Dong, Long Long; Guo, Yu Dong; Ma, Yong Xing; Zang, Jia Ye

    2016-01-01

    This study assessed the diversity and composition of bacterial communities within soils and lake sediments from an Arctic lake area (London Island, Svalbard). A total of 2,987 operational taxonomic units were identified by high-throughput sequencing, targeting bacterial 16S rRNA gene. The samples from four sites (three samples in each site) were significantly different in geochemical properties and bacterial community composition. Proteobacteria and Acidobacteria were abundant phyla in the nine soil samples, whereas Proteobacteria and Bacteroidetes were abundant phyla in the three sediment samples. Furthermore, Actinobacteria, Chlorobi, Chloroflexi, Elusimicrobia, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria significantly varied in their abundance among the four sampling sites. Additionally, members of the dominant genera, such as Clostridium, Luteolibacter, Methylibium, Rhodococcus, and Rhodoplanes, were significantly different in their abundance among the four sampling sites. Besides, distance-based redundancy analysis revealed that pH (p soils and sediments from a lake area in the Arctic harbor a high diversity of bacterial communities, which are influenced by many geochemical factors of Arctic environments.

  16. Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils.

    Science.gov (United States)

    Leung, Hilary T C; Maas, Kendra R; Wilhelm, Roland C; Mohn, William W

    2016-02-01

    Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here, we investigated the effects of three timber-harvesting methods, varying in the degree of organic matter removal, on putatively hemicellulolytic bacterial and fungal populations 10 or more years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated (13)C from labeled hemicellulose, analyzing (13)C-enriched phospholipid fatty acids, bacterial 16 S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, whereas distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears