Rapid evaluation of the antibiotic susceptibility of fuel ethanol contaminant biofilms

Bacterial contaminants from commercial fuel ethanol production facilities were previously shown to form biofilms as mixed cultures under laboratory conditions. In this study, a rapid assay was developed to simultaneously compare isolates for their ability to form biofilms as pure cultures. A total of 10 strains were isolated from a dry-grind fuel ethanol plant that routinely doses with virginiamycin. These were identified by sequence analysis as six strains of Lactobacillus fermentum, two strains of L. johnsonii, and one strain each of L. mucosae and L. amylovorus. Isolates exhibited a range of susceptibility to virginiamycin in a planktonic assay, with MIC's (minimum inhibitory concentration) of ≤0.5-16 μg/ml. Even though all strains were isolated from a mixed culture biofilm, they varied greatly in their ability to form biofilms as pure cultures. Surprisingly, growth as biofilms did not appear to provide resistance to virginiamycin, even if biofilms were grown for 144 h prior to antibiotic challenge.

Biofilm formation by strains of Leuconostoc citreum and L. mesenteroides

Although biofilms produced by various Leuconostoc sp. are economically important as contaminants of sugar processing plants, very few studies are available on these systems. Twelve strains of Leuconostoc citreum and L. mesenteroides that produce a variety of extracellular glucans were compared for their capacity to produce biofilms. 16s rRNA sequence analysis was used to confirm the species identity of these strains, which included four isolates of L. mesenteroides, five isolates of L. citreum, and three glucansucrase mutants of L. citreum strain NRRL B-1355. Strains identified as L. mesenteroides produce glucans that are generally similar to commercial dextran. Nevertheless, these strains differed widely in their capacity to form biofilms, with densities ranging from 2.7 to 6.1 log cfu/cm(2). L. citreum strains and their derivatives produce a variety of glucans. These strains exhibited biofilm densities ranging from 2.5 to 5.9 log cfu/cm(2). Thus, biofilm-forming capacity varied widely on a strain-specific basis in both species. The types of polysaccharides produced did not appear to affect the ability to form biofilms.

Detection of lignin peroxidase and xylanase by immunocytochemical labeling in wood decayed by basidiomycetes

The white rot fungi used in this study caused two different forms of degradation. Phanerochaete chrysosporium, strain BKM-F-1767, and Phellinus pini caused a preferential removal of lignin from birch wood, whereas Trametes (Coriolus) versicolor caused a nonselective attack of all cell wall components. Use of polyclonal antisera to H8 lignin peroxidase and monoclonal antisera to H2 lignin peroxidase followed by immunogold labeling with protein A-gold or protein G-gold, respectively, showed lignin peroxidase extra-and intracellularly to fungal hyphae and within the delignified cell walls after 12 weeks of laboratory decay. Lignin peroxidase was localized at sites within the cell wall where electron-dense areas of the lignified cell wall layers remained. In wood decayed by Trametes versicolor, lignin peroxidase was located primarily along the surface of eroded cell walls. No lignin peroxidase was evident in brown-rotted wood, but slight labeling occurred within hyphal cells. Use of polyclonal antisera to xylanase followed by immunogold labeling showed intense labeling on fungal hyphae and surrounding slime layers and within the woody cell wall, where evidence of degradation was apparent. Colloidal-gold-labeled xylanase was prevalent in wood decayed by all fungi used in this study. Areas of the wood with early stages of cell wall decay had the greatest concentration of gold particles, while little labeling occurred in cells in advanced stages of decay by brown or white rot fungi.

Multilocus phylogenetic analyses, pullulan production and xylanase activity of tropical isolates of Aureobasidium pullulans

Aureobasidium pullulans is the source of the commercially valuable polysaccharide pullulan and the enzyme xylanase. Isolates are typically off-white to pale pink or black on solid media, while some tropical isolates have been described as 'color variants' with bright pigments of red, yellow or purple. We sequenced 5 loci (internal transcribed spacer, intergenic spacer 1, translation elongation factor-1 alpha, beta tubulin, and RNA polymerase II) from 45 new isolates from Thailand. Based on the phylogenetic analyses, isolates were classified into 12 clades. Each clade showed different colors on different culture media including two clades with 'color variants' and some clades exhibited high levels of pullulan production or xylanase activity. Colony characteristics do not correlate perfectly with DNA sequence phylogeny or the physiological characters, but DNA sequence differences rapidly identify isolates with genetic novelty.

Modeling bacterial contamination of fuel ethanol fermentation

The emergence of antibiotic-resistant bacteria may limit the effectiveness of antibiotics to treat bacterial contamination in fuel ethanol plants, and therefore, new antibacterial intervention methods and tools to test their application are needed. Using shake-flask cultures of Saccharomyces cerevisiae grown on saccharified corn mash and strains of lactic acid bacteria isolated from a dry-grind ethanol facility, a simple model to simulate bacterial contamination and infection was developed. Challenging the model with 10(8) CFU/mL Lactobacillus fermentum decreased ethanol yield by 27% and increased residual glucose from 6.2 to 45.5 g/L. The magnitude of the effect was proportional to the initial bacterial load, with 10(5) CFU/mL L. fermentum still producing an 8% decrease in ethanol and a 3.2-fold increase in residual glucose. Infection was also dependent on the bacterial species used to challenge the fermentation, as neither L. delbrueckii ATCC 4797 nor L. amylovorus 0315-7B produced a significant decrease in ethanol when inoculated at a density of 10(8) CFU/mL. In the shake-flask model, treatment with 2 microg/mL virginiamycin mitigated the infection when challenged with a susceptible strain of L. fermentum (MIC for virginiamycin < or =2 ppm), but treatment was ineffective at treating infection by a resistant strain of L. fermentum (MIC = 16 ppm). The model may find application in developing new antibacterial agents and management practices for use in controlling contamination in the fuel ethanol industry.

Conversion of biomass hydrolysates and other substrates to ethanol and other chemicals by Lactobacillus buchneri*

AIMS

A Lactobacillus buchneri strain NRRL B-30929 can convert xylose and glucose into ethanol and chemicals. The aims of the study were to survey three strains (NRRL B-30929, NRRL 1837 and DSM 5987) for fermenting 17 single substrates and to exam NRRL B-30929 for fermenting mixed substrates from biomass hydrolysates.

METHODS AND RESULTS

Mixed acid fermentation was observed for all three L. buchneri strains using various carbohydrates; the only exception was uridine which yielded lactate, acetate and uracil. Only B-30929 is capable of utilizing cellobiose, a desired trait in a potential biocatalyst for biomass conversion. Flask fermentation indicated that the B-30929 strain can use all the sugars released from pretreated hydrolysates, and producing 1.98-2.35 g l(-1) ethanol from corn stover hydrolysates and 2.92-3.01 g l(-1) ethanol from wheat straw hydrolysates when supplemented with either 0.25x MRS plus 1% corn steep liquor or 0.5x MRS.

CONCLUSIONS

The L. buchneri NRRL B-30929 can utilize mixed sugars in corn stover and wheat straw hydrolysates for ethanol and other chemical production.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results are valuable for future research in engineering L. buchneri NRRL B-30929 for fermentative production of ethanol and chemicals from biomass.

Modification of alternan by dextranase

Alternan is a unique glucan with a backbone structure of alternating alpha-(1 --> 6) and alpha-(1 --> 3) linkages. Previously, we isolated strains of Penicillium sp. that modify native, high molecular weight alternan in a novel bioconversion process to a lower molecular weight form with solution viscosity properties similar to those of commercial gum arabic. The mechanism of this modification was unknown. Here, we report that these Penicillium sp. strains secrete dextranase during germination on alternan. Furthermore, alternan is modified in vitro by commercial dextranases, and dextranase-modified alternan appears to be identical to bioconversion-modified alternan. This is surprising, since alternan has long been considered to be resistant to dextranase. Results suggest that native alternan may have localized regions of consecutive alpha-(1 --> 6) linkages that serve as substrates for dextranase. Dextranase treatment of native alternan, particularly with GRAS enzymes, may have practical advantages for the production of modified alternan as a gum arabic substitute.

Lactobacillus buchneri strain NRRL B-30929 converts a concentrated mixture of xylose and glucose into ethanol and other products

Lactobacillus buchneri strain NRRL B-30929 was isolated from a fuel ethanol production facility. This heterofermentative, facultative anaerobe can utilize xylose as a sole carbon source and tolerates up to 12% ethanol. Carbohydrate utilization (API, Biomerieux) and Phenotype Microarrays (PM, Biolog) analyses indicated that the strain is able to metabolize a broad spectrum of carbon sources including various monosaccharides (C5 and C6), disaccharides and oligosaccharides, with better rates under anaerobic conditions. In pH-controlled bioreactors, the bacterium consumed xylose and glucose simultaneously at high concentrations (125 g L(-1), pH 6.0). The major fermentation products were lactate (52 g L(-1)), acetate (26 g L(-1)) and ethanol (12 g L(-1)). The strain ferments glucose alone (pH 4.0) into lactate and ethanol with a molar ratio of 1.03:1. This strain will be further explored via genetic engineering for potential applications in biomass conversion.

Antimicrobial susceptibility of Lactobacillus species isolated from commercial ethanol plants

Bacterial contamination of commercial fermentation cultures is a common and costly problem to the fuel ethanol industry. Antimicrobials such as virginiamycin (VIR) and penicillin (PEN) are frequently used to control contamination but there are little data available on the susceptibility of bacterial contaminants to these agents. A survey of bacterial contaminants from a wet-mill ethanol plant with no history of using antibiotics and a dry-grind facility that periodically doses with VIR found that the majority of contaminants were species of Lactobacillus. Thirty-seven isolates of Lactobacillus species from the wet-mill and 42 isolates from the dry-grind facility were tested for antimicrobial susceptibility using broth dilution and agar dilution methods. In general, the Lactobacillus isolates from the dry-grind plant had higher minimum inhibitory concentrations (MICs) for the tested agents than the isolates from the wet-mill facility. The MIC(90) for VIR was 4 microg/ml for the dry-grind isolates versus 0.25 microg/ml for the wet-mill isolates; and for PEN, the MIC(90)'s were >8 and 2 microg/ml for the dry-grind and wet-mill isolates, respectively. Sixteen Lactobacillus isolates from the dry-grind plant but none from the wet-mill possessed vatE, a gene that encodes a streptogramin acetyltransferase associated with resistance to virginiamycin. Despite decreased susceptibility to virginiamycin, most dry-grind isolates had MICs lower than the maximal recommended application rate of 6 ppm.

Biofilm formation by bacterial contaminants of fuel ethanol production

Commercial fuel ethanol production facilities were previously shown to have characteristic populations of bacterial contaminants which reduce product yield and are difficult to eradicate. Bacterial contaminants were found, for the first time, to form biofilms under laboratory conditions. Fermentor samples from a commercial fuel ethanol production facility were used to inoculate a biofilm reactor and purified bacterial isolates were identified. Biofilms were composed of many of the same species present in production samples, with lactic acid bacteria predominating.

Co-production of schizophyllan and arabinoxylan from corn fiber

Schizophyllum commune strain ATCC 38548 grew well on a medium containing alkaline H2O2 -pretreated corn fiber as a sole carbon source, and clarified the culture medium within 7 days. The strain preferentially utilized the starch component of corn fiber for growth and production of schizophyllan. Culture supernatants contained approx. 50 mg schizophyllan and 200 mg arabinoxylan per g corn fiber. These polysaccharides were recovered separately by differential precipitation with ethanol.

Pullulan production by tropical isolates of Aureobasidium pullulans

Tropical isolates of Aureobasidium pullulans previously isolated from distinct habitats in Thailand were characterized for their capacities to produce the valuable polysaccharide, pullulan. A. pullulans strain NRM2, the so-called "color variant" strain, was the best producer, yielding 25.1 g pullulan l(-1) after 7 days in sucrose medium with peptone as the nitrogen source. Pullulan from strain NRM2 was less pigmented than those from the other strains and was remarkably pure after a simple ethanol precipitation. The molecular weight of pullulan from all cultures dramatically decreased after 3 days growth, as analyzed by high performance size exclusion chromatography. Alpha-amylase with apparent activity against pullulan was expressed constitutively in sucrose-grown cultures and induced in starch-grown cultures. When the alpha-amylase inhibitor acarbose was added to the culture medium, pullulan of slightly higher molecular weight was obtained from late cultures, supporting the notion that alpha-amylase plays a role in the reduction of the molecular weight of pullulan during the production phase.

A method for surveying and classifying Leuconostoc spp. glucansucrases according to strain-dependent acceptor product patterns

A number of Leuconostoc spp. strains were screened for their ability to produce glucansucrases and carry out acceptor reactions with maltose. Acceptor products were analyzed by thin-layer chromatography (TLC) and it was discovered that they could be grouped into four distinct categories based on oligosaccharide product patterns. These patterns corresponded with structural features of the dextrans each strain is reported to produce. Strains that produced a typical dextran-characterized by a predominantly linear alpha(1-->6)-linked D: -glucan chain with a low to moderate degree of branching-produced a homologous series of isomaltooligosaccharides via acceptor reactions. Strains that produced dextrans with moderate to high levels of alpha(1-->2) branch points, exemplified by NRRL B-1299, synthesized the same isomaltodextrins as well as another series of oligosaccharides migrating slightly faster in our TLC system. Strains that produced dextrans with higher levels of alpha(1-->3)-branches, such as NRRL B-742, synthesized isomaltodextrins plus a series of oligosaccharides that migrated slightly more slowly on TLC. And finally, strains known to produce alternansucrase produced isomaltodextrins plus oligoalternans. Within a given type, variability exists in the relative proportions of each product. The data presented here may be useful in selecting strains for the production of specific types of oligosaccharides, for example as prebiotics.

Bacterial contaminants of fuel ethanol production

Bacterial contamination is an ongoing problem for commercial fuel ethanol production facilities. Both chronic and acute infections are of concern, due to the fact that bacteria compete with the ethanol-producing yeast for sugar substrates and micronutrients. Lactic acid levels often rise during bouts of contamination, suggesting that the most common contaminants are lactic acid bacteria. However, quantitative surveys of commercial corn-based fuel ethanol facilities are lacking. For this study, samples were collected from one wet mill and two dry grind fuel ethanol facilities over a 9 month period at strategic time points and locations along the production lines, and bacterial contaminants were isolated and identified. Contamination in the wet mill facility consistently reached 10(6) bacteria/ml. Titers from dry grind facilities were more variable but often reached 10(8)/ml. Antibiotics were not used in the wet mill operation. One dry grind facility added antibiotic to the yeast propagation tank only, while the second facility dosed the fermentation with antibiotic every 4 h. Neither dosing procedure appeared to reliably reduce overall contamination, although the second facility showed less diversity among contaminants. Lactobacillus species were the most abundant isolates from all three plants, averaging 51, 38, and 77% of total isolates from the wet mill and the first and second dry grind facilities, respectively. Although populations varied over time, individual facilities tended to exhibit characteristic bacterial profiles, suggesting the occurrence of persistent endemic infections.

Transformation of alternan-producing strains of Leuconostoc by electroporation

Alternan-producing Leuconostoc mesenteroides strain NRRL B-1355 and its glucansucrase-negative derivative NRRL B-21414 were transformed by electroporation using four Gram positive-Gram negative shuttle vectors. Optimal conditions were 400 Omega and 10 kV cm(-1), resulting in transformation efficiencies of up to 3.5 x 10(4) per microg DNA. Relatively low copy numbers and native plasmids made it difficult to visualize the introduced plasmids on ethidium bromide-stained gels and, in some cases, on blot hybridizations. However, PCR analysis indicated that 95% of putative transformants carried plasmid sequences. Direct colony PCR was shown to work well for this system and also for transformants of L. mesenteroides subsp. cremoris.

Enzymatic Saccharification of Defatted Corn Germ*

Commercial defatted germ from wet milled corn was efficiently saccharified by a crude enzyme preparation from Aureobasidium sp. with yields of up to 200 mg glucose, 140 mg xylose, and 130 mg arabinose per g germ. These yields exceeded sugar composition estimates based on trifluoroacetic acid digestion. Neither chemical nor mechanical pretreatments were necessary. Results from independent lots of defatted germ were similar. Enzymatically digested germ residues were enriched to 40% (w/v) protein. Defatted germ from dry milled corn contained approx. 50% more starch than wet milled germ and was saccharified to produce up to 315 mg glucose per g germ with reduced yields of pentose sugars.

Biotechnological production and applications of pullulan

Pullulan is a unique biopolymer with many useful traits and hundreds of patented applications. However, despite the fact that pullulan has been in commercial production for more than 25 years, few of these potential uses have been widely adopted. In large part this may be due to the relatively high price of pullulan. Nevertheless, the last few years have seen a resurgence in interest in pullulan, particularly for higher-value health and pharmaceutical applications.

Corn fiber hydrolysis by Thermobifida fusca extracellular enzymes

Thermobifida fusca was grown on cellulose (Solka-Floc), xylan or corn fiber and the supernatant extracellular enzymes were concentrated. SDS gels showed markedly different protein patterns for the three different carbon sources. Activity assays on a variety of synthetic and natural substrates showed major differences in the concentrated extracellular enzyme activities. These crude enzyme preparations were used to hydrolyze corn fiber, a low-value biomass byproduct of the wet milling of corn. Approximately 180 mg of reducing sugar were produced per gram of untreated corn fiber. When corn fiber was pretreated with alkaline hydrogen peroxide, up to 429 mg of reducing sugars were released per gram of corn fiber. Saccharification was enhanced by the addition of beta-glucosidase or by the addition of a crude xylanase preparation from Aureobasidium sp.

Bioconversions of maize residues to value-added coproducts using yeast-like fungi

Agricultural residues are abundant potential feedstocks for bioconversions to industrial fuels and chemicals. Every bushel of maize (approximately 25 kg) processed for sweeteners, oil, or ethanol generates nearly 7 kg of protein- and fiber-rich residues. Currently these materials are sold for very low returns as animal feed ingredients. Yeast-like fungi are promising biocatalysts for conversions of agricultural residues. Although corn fiber (pericarp) arabinoxylan is resistant to digestion by commercially available enzymes, a crude mixture of enzymes from the yeast-like fungus Aureobasidium partially saccharifies corn fiber without chemical pretreatment. Sugars derived from corn fiber can be converted to ethanol or other valuable products using a variety of naturally occurring or recombinant yeasts. Examples are presented of Pichia guilliermondii strains for the conversion of corn fiber hydrolysates to the alternative sweetener xylitol. Corn-based fuel ethanol production also generates enormous volumes of low-value stillage residues. These nutritionally rich materials are prospective substrates for numerous yeast fermentations. Strains of Aureobasidium and the red yeast Phaffia rhodozyma utilize stillage residues for production of the polysaccharide pullulan and the carotenoid astaxanthin, respectively.

Modification of alternan by novel Penicillium spp

Four strains identified as Penicillium spp. were isolated from soil samples based on their capacity to modify the unique polysaccharide, alternan. Spores from these isolates germinated in medium containing alternan and reduced the apparent molecular weight of alternan as determined by high-performance size exclusion chromatography and viscometry. However, the fungi exhibited limited growth on alternan and did not consume the substrate. The rheological properties of the modified alternan resembled those of commercial gum arabic. Thus, treatment of native alternan with spores from these Penicillium spp. strains constitutes a simple bioconversion method to quantitatively produce novel and potentially useful modified alternan.

Analysis of ethanol-glucose mixtures by two microbial sensors: application of chemometrics and artificial neural networks for data processing

Although biosensors based on whole microbial cells have many advantages in terms of convenience, cost and durability, a major limitation of these sensors is often their inability to distinguish between different substrates of interest. This paper demonstrates that it is possible to use sensors entirely based upon whole microbial cells to selectively measure ethanol and glucose in mixtures. Amperometric sensors were constructed using immobilized cells of either Gluconobacter oxydans or Pichia methanolica. The bacterial cells of G. oxydans were sensitive to both substrates, while the yeast cells of P. methanolica oxidized only ethanol. Using chemometric principles of polynomial approximation, data from both of these sensors were processed to provide accurate estimates of glucose and ethanol over a concentration range of 1.0-8.0 mM (coefficients of determination, R(2)=0.99 for ethanol and 0.98 for glucose). When data were processed using an artificial neural network, glucose and ethanol were accurately estimated over a range of 1.0-10.0 mM (R(2)=0.99 for both substrates). The described methodology extends the sphere of utility for microbial sensors.