Conversion of ammonia-pretreated switchgrass to biofuel precursors by bacterial-fungal consortia under solid-state and submerged-state cultivation.

AIM: The aim of this study was to develop and evaluate bacterial-fungal communities to deconstruct switchgrass to biofuel precursors. METHODS AND RESULTS: Bacterial-fungal consortia, mesophilic (25°C) and thermophilic (50°C), were enriched from switchgrass bales from which enzyme mixtures were used to deconstruct delignified switchgrass (DSG). The bacterial-fungal consortia were able to produce enzymes including endoglucanase, exoglucanase, ß-glucosidase, xylanase, xylosidase and pectinase to convert DSG to soluble carbohydrates. 454 pyrosequencing revealed that Paenibacillus and Streptomyces were the dominant bacteria in the mesophilic and thermophilic consortia respectively. Penicillium and Acremonium were the dominant fungi in the mesophilic consortia, whereas Aspergillus and Penicillium were the dominant fungi present in the thermophilic consortia. CONCLUSIONS: The results show that the state of cultivation, solid-state or submerged-state, affects the community structure as well as enzyme activities produced by these bacterial-fungal consortia. The enzyme mixture produced by the bacterial-fungal consortia released a higher amount of xylose than glucose during saccharification of DSG. SIGNIFICANCE AND IMPACT OF THE STUDY: The study provides a novel approach to produce enzymes for conversion of lignocellulolytic feedstocks to soluble sugars which can be used to produce biofuel precursors.

Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli.

Escherichia coli mutants with temperature-sensitive (ts) mutations in dnaX and dnaY genes have been isolated. Based on transduction by phage P1, dnaX and Y have been mapped at minutes 10.4--10.5 and 12.1, respectively, in the sequence dnaX purE dnaY. Both dna Xts36 and Yts10 are recessive to wild-type alleles present on episomes. F13 carries both dnaX+ and Y+; the shorter F210 carries dnaY+, but not X+. Lambda tranducing phages that carry dnaX+ or Y+ have been isolated, and hybrid plasmids of Col E1 and E. coli DNA from the Clarke and Carbon (1976) collection also carry portions of the dnaX purE dnaY region. Results obtained with the lambda transducing phages and the hybrid plasmids suggest that dnaX is a different gene from the previously characterized dnaZ gene, which is also near minute 10.5--The dnaXts36 mutant, after a shift to 42 degrees, stopped DNA synthesis gradually, and the total amount of DNA increased two-fold. When this mutant was shifted to 44 degrees, the rate of DNA synthesis dropped immediately and the final increment of DNA was only 10% of the initial amount. Replicative DNA synthesis in toluene-treated cells was completely inhibited at 42 degrees and was partially inhibited even at 30 degrees.--When the dnaYts10 mutant was shifted to 42 degrees, DNA synthesis gradually stopped, and the amount of DNA increased 3.6-fold. At 44 degrees, residual DNA synthesis amounted to a two-fold increase. Replicative DNA synthesis in vitro in toluene-treated cells was inactivated after 20 minutes at 42 degrees or by "preincubation" of cells at 42 degrees before toluene treatment.--The dnaX and dnaY products probably function in polymerization of DNA, although participation also in initiation cannot be excluded.

Isolation and serological analyses of fungal melanins.

Melanins are notoriously difficult to work with because of their unique physical and chemical properties. The study of melanins is hampered by the scarcity of melanin-specific reagents and serological techniques. In this study we describe modifications to the standard method for the isolation of melanins from in vitro-melanized fungal cells and detail the optimization of serological techniques for the study of melanin compounds. The isolation procedure involves the digestion of melanized cells with a combination of proteolytic and glycolytic enzymes, denaturant, organic extractions, and boiling in 6.0 M HCl. Elemental quantitative analyses suggest that this procedure does not significantly affect the relative elemental composition of melanins. For the serological assays, our goal was to achieve a homogenous distribution of melanin particles on a solid support to maximize their recognition by melanin-binding antibodies. The results from enzyme-linked immunosorbent assays (ELISAs) demonstrate that melanins, in general, disperse more efficiently on, and adhere better to, medium-binding polystyrene surfaces, especially in the presence of trace amounts of salt. Blocking the melanin-coated ELISA plates with the commercially available SuperBlock((R)) Blocking Buffer for 4 h was more efficient at reducing non-specific binding of a negative control monoclonal antibody (mAb) compared to blocking with 2% bovine serum albumin (BSA) and 5% milk. Increasing the ionic strength of the antibody solutions reduced binding to the melanins, indicating that binding is in part mediated by electrostatic interactions. These conditions were also applied to immunofluorescence (IF) analyses of melanins, and the results were consistent with those obtained by ELISA.

Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms.

Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.

Heat shock-like polypeptides of the sporozoites and merozoites of Eimeria bovis.

Heat shock proteins (hsps) are a group of highly conserved polypeptides found in a wide variety of organisms. Polypeptides of sporozoites and merozoites of Eimeria bovis, blotted onto nitrocellulose, were probed with antibodies to artificially constructed peptides representing portions of the cDNA-generated fragment of pf75, the 75K hsp of merozoites of Plasmodium falciparum. Polypeptide antigens of sporozoites and merozoites of E. bovis with molecular weights of 46K, 71-72K, and 75K reacted with antibodies against pf75, indicating that they are hsp70 (the 70K family of hsps) or hsp70 cognates (noninducible proteins homologous to hsps). Radiolabeling with 125I and treatment with antibodies against pf75 detected a 71K antigen on the merozoite surface. Hsps in sporozoites of E. bovis are either constitutive or evoked by treatment at 37 C for in vitro excystation. If hsp70 is mandatory for parasite survival, it may prove to be an appropriate antigen for a vaccine against bovine coccidiosis.

Computerization and adaptive administration of the NEO PI-R.

This study asks, how well does an item response theory (IRT) based computerized adaptive NEO PI-R work? To explore this question, real-data simulations (N = 1,059) were used to evaluate a maximum information item selection computerized adaptive test (CAT) algorithm. Findings indicated satisfactory recovery of full-scale facet scores with the administration of around four items per facet scale. Thus, the NEO PI-R could be reduced in half with little loss in precision by CAT administration. However, results also indicated that the CAT algorithm was not necessary. We found that for many scales, administering the "best" four items per facet scale would have produced similar results. In the conclusion, we discuss the future of computerized personality assessment and describe the role IRT methods might play in such assessments.

Algal species and light microenvironment in a low-pH, geothermal microbial mat community.

Unicellular algae are the predominant microbial mat-forming phototrophs in the extreme environments of acidic geothermal springs. The ecology of these algae is not well known because concepts of species composition are inferred from cultivated isolates and microscopic observations, methods known to provide incomplete and inaccurate assessments of species in situ. We used sequence analysis of 18S rRNA genes PCR amplified from mat samples from different seasons and different temperatures along a thermal gradient to identify algae in an often-studied acidic (pH 2.7) geothermal creek in Yellowstone National Park. Fiber-optic microprobes were used to show that light for algal photosynthesis is attenuated to < 1% over the 1-mm surface interval of the mat. Three algal sequences were detected, and each was present year-round. A Cyanidioschyzon merolae sequence was predominant at temperatures of > or = 49 degrees C. A Chlorella protothecoides var. acidicola sequence and a Paradoxia multisita-like sequence were predominant at temperatures of < or = 39 degrees C.

DNA Probe for Identification of the Take-All Fungus, Gaeumannomyces graminis.

A 4.3-kilobase mitochondrial DNA fragment was cloned from Gaeumannomyces graminis var. tritici, the causative agent of take-all disease of wheat. Although this DNA fragment hybridized with all three varieties of G. graminis, it showed little homology with DNA from other fungi and thus should be useful for identification of Gaeumannomyces sp. recovered from infected plants.

Deletion of the terminus region (340 kilobase pairs of DNA) from the chromosome of Escherichia coli.

A strain of Escherichia coli with a 7-minute (340 kilobase pairs of DNA) deletion of the terminus region of the chromosome was isolated. This deletion was probably an IS10-promoted event and its extent was characterized by both genetic and DNA hybridization analyses. The most dramatic property of strains harboring this deletion was the absence of the sites that inhibit clockwise- and counterclockwise-traveling replication forks. These strains also grew slowly, produced many nonviable cells, were filamentous, and appeared to have an induced SOS system.

Isolation of a Butyrate-Utilizing Bacterium in Coculture with Methanobacterium thermoautotrophicum from a Thermophilic Digester.

Sludge from a thermophilic, 55 degrees C digester produced methane without a lag period when enriched with butyrate. The sludge was found by most-probable-number enumeration to have ca. 5 x 10 butyrate-utilizing bacteria per ml. A thermophilic butyrate-utilizing bacterium was isolated in coculture with Methanobacterium thermoautotrophicum. This bacterium was a gram-negative, slightly curved rod, occurred singly, was nonmotile, and did not appear to produce spores. When this coculture was incubated with Methanospirillum hungatei at 37 degrees C, the quantity of methane produced was less than 5% of the methane produced when the coculture was incubated at 55 degrees C, the routine incubation temperature. The coculture required clarified digester fluid. The addition of yeast extract to medium containing 5% clarified digester fluid stimulated methane production when a Methanosarcina sp. was present. Hydrogen in the gas phase prevented butyrate utilization. However, when the hydrogen was removed, butyrate utilization began. Penicillin G and d-cycloserine caused the complete inhibition of butyrate utilization by the coculture. The ability of various ecosystems to convert butyrate to methane was studied. Marine sediments enriched with butyrate required a 2-week incubation period before methanogenesis began. Hypersaline sediments did not produce methane after 3 months when enriched with butyrate.

Cloning and expression of the Escherichia coli K-12 sad gene.

The Escherichia coli K-12 sad gene, which encodes an NAD-dependent succinic semialdehyde dehydrogenase, was cloned into a high-copy-number vector. Minicells carrying a sad+ plasmid produced a 55,000-dalton peptide, the probable sad gene product.

Genetic analysis of acrA and lir mutations of Escherichia coli.

An analysis of acrA (acriflavine- and methylene blue-sensitive) and lir (lincomycin- and erythromycin-sensitive) mutants of Escherichia coli indicated that these mutations are probably within the same gene.

The use of transposon insertion zdc-235::Tn10 (min 32) to clone and delete DNA from the terminus region of Escherichia coli.

Transposon zdc-235::Tn10 is inserted at min 32 on the genetic map of Escherichia coli, and we have used this transposon to clone 14 kb of DNA that flanks this insertion. The site of insertion of the transposon, and the restriction map of the cloned DNA, correspond well with the predictions of the Bouché restriction map for the terminus region (Bouché 1982). The zdc-235::Tn10 insertion, along with the zdd-230::Tn9 insertion, was used to obtain deletions of the region that has been cloned. Strains lacking a minimum of 14 kb, and more likely a minimum of 40 kb of DNA, showed no alteration of growth or cell morphology.

Deletion of 60 kilobase pairs of DNA from the terC region of the chromosome of Escherichia coli.

The terminus of replication (terC) of the chromosome of Escherichia coli is located between the rac (min 30.0) and manA (min 35.7) loci, presumably close to the trg (min 31.4) locus. We have used a strain containing lambda reverse (min 30.0) and trg-2::Tn10 (min 31.4) to obtain deletions of the entire 60 kilobase pair region that separates these elements. Strains harboring these deletions possessed fusion fragments that contained DNA homologous to both lambda reverse and trg region DNA. In addition, chromosomal DNA normally present between min 30.0 and min 31.4 was absent in these strains. The strains had no readily apparent mutant phenotype, which demonstrates that this large region of DNA is not essential for normal growth.

Examination of thermophilic methane-producing digesters by analysis of bacterial lipids.

Thermophilic methane-producing digesters were examined by the analysis of lipids to determine the microbial biomass, community structure, and nutritional status of the microbes within the digesters. The digesters received a daily feedstock of cattle feed and Bermuda grass, with some digesters receiving additional supplements of propionate, butyrate, or nitrate. Microbial biomass, measured as total extractable lipid phosphate, was decreased in slurries from digesters receiving continuous addition of the fermentation intermediates propionate or butyrate as compared with slurries from control digesters receiving the feedstock alone. In slurries from digesters that received continuous addition of nitrate, the microbial biomass was higher than in the slurries from control digesters. The control digesters had ca. 2.5 x 10 bacteria per g (dry weight) as determined from total extractable lipid phosphate. Shifts in microbial community structure were observed by analysis of ester-linked phospholipid fatty acids. Statistical analysis of the patterns of phospholipid fatty acids indicated that the digesters receiving different supplements could be distinguished from the control digester and from each other. Poly-beta-hydroxybutyric acid, an indicator of metabolic stress, was detected in slurries from all the digesters. Slurries from the nitrate-amended digester had the highest concentration of poly-beta-hydroxybutyric acid, whereas slurries from the propionate-amended digester had the lowest concentration. These chemical analyses offer a quantitative means to correlate shifts in microbial biomass, community structure, and nutritional status in complex fermentation systems to the production of a specific end product.

Use of Polymerase Chain Reaction To Detect the Take-All Fungus, Gaeumannomyces graminis, in Infected Wheat Plants.

Gaeumannomyces graminis, the causative agent of take-all disease of wheat, barley, and oats, was detected in infected wheat seedlings by using the polymerase chain reaction to amplify Gaeumannomyces-specific DNA fragments. Nested primers and two rounds of amplification were used to amplify two fragments, approximately 287 and 188 bp in size, from G. graminis-infected wheat seedlings. The use of nested primers greatly decreased the number of nonspecific amplification products. Polymerase chain reaction products were not obtained with DNA from seedlings infected with several other phytopathogenic fungi or with DNA from uninfected seedlings. Amplified products were visualized on agarose gels, and their identities were confirmed by DNA hybridization. This method did not require culturing the fungus and has potential for detecting G. graminis in infested wheat, barley, or oat fields.

Isolation and characterization of plaque-forming lambdadnaZ+ transducing bacteriophages.

The Escherichia coli dnaZ gene, a deoxyribonucleic acid (DNA) polymerization gene, is located 1.2 min counterclockwise from purE, at approximately min 10.5 on the E. coli map. From a lysogen with lamdacI857 integrated at a secondary attachment site near purE, transducing phages (lambdadnaS+) that transduced a dnaZts (lambda+) recipient to temperature insensitivity (TS+) were discovered. Three different plaque-forming transducing phages were isolated from seven primary heterogenotes. Genetic tests and heteroduplex mapping were used to determine the length and position of E. coli DNA within the lambda DNA. Complementation tests demonstrated that the deletions in all three strains removed both att P and the int gene, i,e., DNA from both prophage ends. Heteroduplex mapping confirmed this result by demonstrating that all three strains had deletions of lambda DNA that covered the b2 to red region, thereby removing both prophage ends. Specifically, the deletions removed lambda DNA between the points 39.3 to 66.5% of lambda length (measured in percent length from the left and of lambda phage DNA) in all three strains. The three strains are distinct, however, because they had differing lengths of host DNA insertions. These phages must have been formed by an anomalous procedure, because standard lambda transducing phages are deleted for one prophage end only. In lambdagal and lambdabio strains, the deletions of lambda DNA begin at the union of prophage ends (i.e., position 57.3% of lambda length) and extend leftward or rightward, respectively (Davidson and Szybalski, in A, D. Hershey [ed.], The Bacteriophage Lambda, p. 45-82, 1971). Models for formation of the lambdadnaZ+ phages are discussed.

The Escherichia coli dnaW mutation is an allele of the adk gene.

A dnaW mutant, isolated on the basis of inability to effect conjugal DNA transfer at high temperature, has been shown by complementation and enzyme assay to be defective in the adk (adenylate kinase; EC 2.7.4.3) locus. The adk mutant, known to have reduced ATP concentration at the nonpermissive temperature (Cousin and Belaich 1966), was used to demonstrate a donor energy requirement for stable aggregate formation and for chromosome transfer in conjugation.

The isolation of fumB mutants of Escherichia coli.

Escherichia coli strains lacking the terminus region of the chromosome (min 29-36) due to an IS10-promoted deletion did not grow well in rich medium; they also did not grow on fumarate minimal medium because fumAC (min 35.7) is deleted. Strains with secondary mutations that partially suppress the deletion phenotype displayed healthier growth on rich medium and grew on minimal fumarate medium. These suppressor mutants had an IS10 insertion just upstream of the fumB structural gene (min 93.4). A strain with a Tn10 insertion at this location was constructed and used to delete nonessential fumB; fumB deletion mutants grew well on both rich and minimal fumarate media.