Journal articles: 'Microbial culture enrichment'

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Grosser, Robert J., Michael Friedrich, David M. Ward, and William P. Inskeep. "Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Different Enrichment Conditions Influence Bioavailability and Selection of Phenanthrene-Degrading Isolates." Applied and Environmental Microbiology 66, no. 7 (July 1, 2000): 2695–702. http://dx.doi.org/10.1128/aem.66.7.2695-2702.2000.

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ABSTRACT The sorption of organic contaminants by natural organic matter (NOM) often limits substrate bioavailability and is an important factor affecting microbial degradation rates in soils and sediments. We hypothesized that reduced substrate bioavailability might influence which microbial assemblages are responsible for contaminant degradation under enrichment culture conditions. Our primary goal was to characterize enrichments in which different model organic solid phases were used to establish a range of phenanthrene bioavailabilities for soil microorganisms. Phenanthrene sorption coefficients (expressed as log KD values) ranged from 3.0 liters kg−1 for Amberlite carboxylic acid cation-exchange resin (AMB) to 3.5 liters kg−1 for Biobeads polyacrylic resin (SM7) and 4.2 liters kg−1 for Biobeads divinyl benzene resin (SM2). Enrichment cultures were established for control (no sorptive phase), sand, AMB, SM7, and SM2 treatments by using two contaminated soils (from Dover, Ohio, and Libby, Mont.) as the initial inocula. The effects of sorption by model phases on the degradation of phenanthrene were evaluated for numerous transfers in order to obtain stable microbial assemblages representative of sorptive and nonsorptive enrichment cultures and to eliminate the effects of the NOM present in the initial inoculum. Phenanthrene degradation rates were similar for each soil inoculum and ranged from 4 to 5 μmol day−1 for control and sand treatments to approximately 0.4 μmol day−1 in the presence of the SM7 sorptive phase. The rates of phenanthrene degradation in the highly sorptive SM2 enrichment culture were insignificant; consequently, stable microbial populations could not be obtained. Bacterial isolates obtained from serial dilutions of enrichment culture samples exhibited significant differences in rates of phenanthrene degradation performed in the presence of SM7, suggesting that enrichments performed in the presence of a sorptive phase selected for different microbial assemblages than control treatments containing solid phase phenanthrene.

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Sousa, D. Z., M. A. Pereira, J. I. Alves, H. Smidt, A. J. M. Stams, and M. M. Alves. "Anaerobic microbial LCFA degradation in bioreactors." Water Science and Technology 57, no. 3 (February 1, 2008): 439–44. http://dx.doi.org/10.2166/wst.2008.090.

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This paper reviews recent results obtained on long-chain fatty acids (LCFA) anaerobic degradation. Two LCFA were used as model substrates: oleate, a mono-unsaturated LCFA, and palmitate, a saturated LCFA, both abundant in LCFA-rich wastewaters. 16S rRNA gene analysis of sludge samples submitted to continuous oleate- and palmitate-feeding followed by batch degradation of the accumulated LCFA demonstrated that bacterial communities were dominated by members of the Clostridiaceae and Syntrophomonadaceae families. Archaeal populations were mainly comprised of hydrogen-consuming microorganisms belonging to the genus Methanobacterium, and acetate-utilizers from the genera Methanosaeta and Methanosarcina. Enrichment cultures growing on oleate and palmitate, in the absence or presence of sulfate, gave more insight into the major players involved in the degradation of unsaturated and saturated LCFA. Syntrophomonas-related species were identified as predominant microorganisms in all the enrichment cultures. Microorganisms clustering within the family Syntrophobacteraceae were identified in the methanogenic and sulfate-reducing enrichments growing on palmitate. Distinct bacterial consortia were developed in oleate and palmitate enrichments, and observed differences might be related to the different degrees of saturation of these two LCFA. A new obligately syntrophic bacterium, Syntrophomonas zehnderi, was isolated from an oleate-degrading culture and its presence in oleate-degrading sludges detected by 16S rRNA gene cloning and sequencing.

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Sousa, Diana Z., M. Alcina Pereira, Alfons J. M. Stams, M. Madalena Alves, and Hauke Smidt. "Microbial Communities Involved in Anaerobic Degradation of Unsaturated or Saturated Long-Chain Fatty Acids." Applied and Environmental Microbiology 73, no. 4 (December 8, 2006): 1054–64. http://dx.doi.org/10.1128/aem.01723-06.

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ABSTRACTAnaerobic long-chain fatty acid (LCFA)-degrading bacteria were identified by combining selective enrichment studies with molecular approaches. Two distinct enrichment cultures growing on unsaturated and saturated LCFAs were obtained by successive transfers in medium containing oleate and palmitate, respectively, as the sole carbon and energy sources. Changes in the microbial composition during enrichment were analyzed by denaturing gradient gel electrophoresis (DGGE) profiling of PCR-amplified 16S rRNA gene fragments. Prominent DGGE bands of the enrichment cultures were identified by 16S rRNA gene sequencing. A significant part of the retrieved 16S rRNA gene sequences was most similar to those of uncultured bacteria. Bacteria corresponding to predominant DGGE bands in oleate and palmitate enrichment cultures clustered with fatty acid-oxidizing bacteria withinSyntrophomonadaceaeandSyntrophobacteraceaefamilies. A low methane yield, corresponding to 9 to 18% of the theoretical value, was observed in the oleate enrichment, and acetate, produced according to the expected stoichiometry, was not further converted to methane. In the palmitate enrichment culture, the acetate produced was completely mineralized and a methane yield of 48 to 70% was achieved from palmitate degradation. Furthermore, the oleate enrichment culture was able to use palmitate without detectable changes in the DGGE profile. However, the palmitate-specialized consortia degraded oleate only after a lag phase of 3 months, after which the DGGE profile had changed. Two predominant bands appeared, and sequence analysis showed affiliation with theSyntrophomonasgenus. These bands were also present in the oleate enrichment culture, suggesting that these bacteria are directly involved in oleate degradation, emphasizing possible differences between the degradation of unsaturated and saturated LCFAs.

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Nixon, Sophie L., Jon P. Telling, Jemma L. Wadham, and Charles S. Cockell. "Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments." Biogeosciences 14, no. 6 (March 21, 2017): 1445–55. http://dx.doi.org/10.5194/bg-14-1445-2017.

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Abstract. Subglacial environments are known to harbour metabolically diverse microbial communities. These microbial communities drive chemical weathering of underlying bedrock and influence the geochemistry of glacial meltwater. Despite its importance in weathering reactions, the microbial cycling of iron in subglacial environments, in particular the role of microbial iron reduction, is poorly understood. In this study we address the prevalence of viable iron-reducing microorganisms in subglacial sediments from five geographically isolated glaciers. Iron-reducing enrichment cultures were established with sediment from beneath Engabreen (Norway), Finsterwalderbreen (Svalbard), Leverett and Russell glaciers (Greenland), and Lower Wright Glacier (Antarctica). Rates of iron reduction were higher at 4 °C compared with 15 °C in all but one duplicated second-generation enrichment culture, indicative of cold-tolerant and perhaps cold-adapted iron reducers. Analysis of bacterial 16S rRNA genes indicates Desulfosporosinus were the dominant iron-reducing microorganisms in low-temperature Engabreen, Finsterwalderbreen and Lower Wright Glacier enrichments, and Geobacter dominated in Russell and Leverett enrichments. Results from this study suggest microbial iron reduction is widespread in subglacial environments and may have important implications for global biogeochemical iron cycling and export to marine ecosystems.

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Muenks, Carol E., Patrick G. Hogan, Carey-Ann D. Burnham, and Stephanie A. Fritz. "Comparing the Yield of Staphylococcus aureus Recovery with Static versus Agitated Broth Incubation." Journal of Pathogens 2018 (July 26, 2018): 1–3. http://dx.doi.org/10.1155/2018/1462671.

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Given the lack of standardization of methodologies for microbial recovery from built environments, we sought to compare the yield of Staphylococcus aureus with a broth enrichment method when incubated in agitated versus static conditions. Five unique strains of S. aureus at five different concentrations were cultured to compare direct plating, agitated broth enrichment, and static broth enrichment culture methods. All samples were incubated at 35° in ambient air. The lowest concentration recovered across three replicates and five strains did not differ between culture methods (Fisher’s exact test, p=0.50); notably, recovery of S. aureus was equivalent between static and agitated broth incubation. When broth enrichment was used (both static and agitated), the burden of S. aureus growth was higher (by semiquantitative assessment of 4-quadrant streaking) compared to the direct plating culture method. Optimizing strategies for microbial recovery is essential, particularly in areas of lower biomass, given the paucity of research concerning microbial communities of built environments. The results of this study, in conjunction with other experiments investigating microbiomes of built environments, can help inform protocols for standardizing culturing methods within built environments.

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Venkateswaran, Kasthuri, and Shigeaki Harayama. "Sequential enrichment of microbial populations exhibiting enhanced biodegradation of crude oil." Canadian Journal of Microbiology 41, no. 9 (September 1, 1995): 767–75. http://dx.doi.org/10.1139/m95-106.

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The distribution of oil-degrading bacteria in the coastal water and sediments of Hokkaido, Japan, was surveyed. The potential of mixed microbial populations to degrade weathered crude oil was not confined to any ecological components (water or sediment) nor to the sampling stations. One microbial culture that was stable during repeated subculturing degraded 45% of the saturates and 20% of the aromatics present in crude oil in 10 days during the initial screening. The residual hydrocarbons in this culture were extracted by chloroform and dispersed in a fresh seawater-based medium and subsequently inoculated with microorganisms from the first culture. After full growth of the second culture, the residual hydrocarbons were again extracted and dispersed in a fresh medium in which microorganisms from the second culture had been inoculated. This sequential process was carried out six times to enrich those microorganisms that grew on the recalcitrant components of crude oil. After repeated exposure of the residual crude oil to the enriched microorganisms, about 80% of the initially added crude oil was degraded. The cultures obtained after each enrichment cycle were kept, and the degradation of fresh crude oil by the enriched microorganisms was examined. The degradative activity of the enriched cultures increased as the number of enrichment cycles increased. A microbial population that had been selected six times on the residual crude oil could degrade 70% of the saturates and 30% of the aromatics of crude oil. Thus, growth of a microbial population on residual crude oil improved its ability to biodegrade crude oil.Key words: crude oil, biodegradation, sequential enrichment, saturated hydrocarbon, aromatic hydrocarbon.

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Nï¿½ Chadhain, Sinï¿½ad M., R. Sean Norman, Karen V. Pesce, Jerome J. Kukor, and Gerben J. Zylstra. "Microbial Dioxygenase Gene Population Shifts during Polycyclic Aromatic Hydrocarbon Biodegradation." Applied and Environmental Microbiology 72, no. 6 (June 2006): 4078–87. http://dx.doi.org/10.1128/aem.02969-05.

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ABSTRACT The degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria has been widely studied. While many pure cultures have been isolated and characterized for their ability to grow on PAHs, limited information is available on the diversity of microbes involved in PAH degradation in the environment. We have designed generic PCR primers targeting the gene fragment encoding the Rieske iron sulfur center common to all PAH dioxygenase enzymes. These Rieske primers were employed to track dioxygenase gene population shifts in soil enrichment cultures following exposure to naphthalene, phenanthrene, or pyrene. PAH degradation was monitored by gas chromatograph with flame ionization detection. DNA was extracted from the enrichment cultures following PAH degradation. 16S rRNA and Rieske gene fragments were PCR amplified from DNA extracted from each enrichment culture and an unamended treatment. The PCR products were cloned and sequenced. Molecular monitoring of the enrichment cultures before and after PAH degradation using denaturing gradient gel electrophoresis and 16S rRNA gene libraries suggests that specific phylotypes of bacteria were associated with the degradation of each PAH. Sequencing of the cloned Rieske gene fragments showed that different suites of genes were present in soil microbe populations under each enrichment culture condition. Many of the Rieske gene fragment sequences fell into clades which are distinct from the reference dioxygenase gene sequences used to design the PCR primers. The ability to profile not only the bacterial community but also the dioxygenases which they encode provides a powerful tool for both assessing bioremediation potential in the environment and for the discovery of novel dioxygenase genes.

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MURAKAMI, TAKU. "Filter-Based Pathogen Enrichment Technology for Detection of Multiple Viable Foodborne Pathogens in 1 Day." Journal of Food Protection 75, no. 9 (September 1, 2012): 1603–10. http://dx.doi.org/10.4315/0362-028x.jfp-12-039.

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Conventional foodborne pathogen assays currently used in the food industry often require long culture enrichments to increase pathogen levels so they can be detected. Even using sensitive real-time PCR assays, culture enrichment at least overnight is necessary especially for detection of pathogens with slow growth rates such as Listeria monocytogenes. To eliminate this cumbersome enrichment step and detect minute amounts of pathogens within 1 day, filter-based pathogen enrichment technology was developed utilizing a unique combination of glass fiber depth filter and porous filter aid materials to efficiently separate pathogens from food homogenates and avoid filter clogging by food particles. After pathogen immobilization in depth filters, only viable pathogens were selectively collected in a small volume of growth medium via microbial multiplication and migration; nonviable pathogens remained inside the filters. By assaying viable pathogens using real-time PCRs, multiple species of foodborne pathogens were detected, including L. monocytogenes, Salmonella enterica, and Escherichia coli O157:H7, at around 1 CFU/ml or 1 CFU/g in various food samples. This filter-based pathogen enrichment technology is a unique bacterial enrichment alternative to the conventional culture enrichment step and can significantly shorten the time necessary to obtain assay results.

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Yoochatchaval, W., S. Kumakura, D. Tanikawa, T. Yamaguchi, M. F. M. Yunus, S. S. Chen, K. Kubota, H. Harada, and K. Syutsubo. "Anaerobic degradation of palm oil mill effluent (POME)." Water Science and Technology 64, no. 10 (November 1, 2011): 2001–8. http://dx.doi.org/10.2166/wst.2011.782.

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The biodegradation characteristics of palm oil mill effluent (POME) and the related microbial community were studied in both actual sequential anaerobic ponds in Malaysia and enrichment cultures. The significant degradation of the POME was observed in the second pond, in which the temperature was 35–37 °C. In this pond, biodegradation of major long chain fatty acids (LCFA), such as palmitic acid (C16:0) and oleic acid (C18:1), was also confirmed. The enrichment culture experiment was conducted with different feeding substrates, i.e. POME, C16:0 and C18:1, at 35 °C. Good recovery of methane indicated biodegradation of feeds in the POME and C16:0 enrichments. The methane production rate of the C18:1 enrichment was slower than other substrates and inhibition of methanogenesis was frequently observed. Denaturing gradient gel electrophoresis (DGGE) analyses indicated the existence of LCFA-degrading bacteria, such as the genus Syntrophus and Syntorophomonas, in all enrichment cultures operated at 35 °C. Anaerobic degradation of the POME under mesophilic conditions was stably processed as compared with thermophilic conditions.

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Köpke, Beate, Reinhard Wilms, Bert Engelen, Heribert Cypionka, and Henrik Sass. "Microbial Diversity in Coastal Subsurface Sediments: a Cultivation Approach Using Various Electron Acceptors and Substrate Gradients." Applied and Environmental Microbiology 71, no. 12 (December 2005): 7819–30. http://dx.doi.org/10.1128/aem.71.12.7819-7830.2005.

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ABSTRACT Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria, “Bacteroidetes,” “Fusobacteria,” Actinobacteria, and “Firmicutes.” Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.

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Hirschler, Agnes, Jean-Francois Rontani, Danielle Raphel, Robert Matheron, and Jean-Claude Bertrand. "Anaerobic Degradation of Hexadecan-2-one by a Microbial Enrichment Culture under Sulfate-Reducing Conditions." Applied and Environmental Microbiology 64, no. 4 (April 1, 1998): 1576–79. http://dx.doi.org/10.1128/aem.64.4.1576-1579.1998.

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ABSTRACT A microbial enrichment culture from marine sediment was able to grow on hexadecan-2-one as the sole source of carbon and energy under sulfate-reducing conditions. Oxidation of the ketone involved carboxylation reactions and was coupled to sulfide production. This enrichment culture also grew on 6,10,14-trimethylpentadecan-2-one.

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Wang, Zhi Rong, Yan Ni Li, Xiao Yan Zhu, Wei Li Wang, and Jing Lan Wang. "Experimental Study on Oil-Degradation Microbial Consortium from Oil-Contaminated Soil by Different Enrichment and Domestication." Advanced Materials Research 779-780 (September 2013): 1304–8. http://dx.doi.org/10.4028/www.scientific.net/amr.779-780.1304.

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In order to increase the effectiveness of remediation on oil-contaminated soil, culture techniques and molecular biological methods were adopted to analyze community structure enriched and domesticated by different ways. The results showed that the bacterial concentration cultured in a medium of inorganic salts and oil was 1.30×1012cfu/ml, while the bacterial concentration cultured in a medium of LB and oil was 3.05×108cfu/ml; Within the perspective of structure, the microbial community cultured in a medium of inorganic salts and oil contained 11 kinds of bacterial, Meanwhile, the microbial community cultured in a medium of LB and oil was composed of 4 kinds of bacteria. Based on the results of this study, it can be inferred that the cultured medium has a significant influence on the composition of microbial communities. When domesticated oil-contaminated soil was cultured in a medium of inorganic salts and oil, the microbial concentrations and diversities were relatively higher than those cultured in LB and oil.

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Orphan, V. J., L. T. Taylor, D. Hafenbradl, and E. F. Delong. "Culture-Dependent and Culture-Independent Characterization of Microbial Assemblages Associated with High-Temperature Petroleum Reservoirs." Applied and Environmental Microbiology 66, no. 2 (February 1, 2000): 700–711. http://dx.doi.org/10.1128/aem.66.2.700-711.2000.

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ABSTRACT Recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. In this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in California. Enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90°C. Heterotrophic enrichments from all sites yielded sheathed rods (Thermotogales), pleomorphic rods resemblingThermoanaerobacter, and Thermococcus-like isolates. The predominant autotrophic microorganisms recovered from inorganic enrichments using H2, acetate, and CO2 as energy and carbon sources were methanogens, including isolates closely related to Methanobacterium,Methanococcus, and Methanoculleus species. Two 16S rRNA gene (rDNA) libraries were generated from total community DNA collected from production wellheads, using either archaeal or universal oligonucleotide primer sets. Sequence analysis of the universal library indicated that a large percentage of clones were highly similar to known bacterial and archaeal isolates recovered from similar habitats. Represented genera in rDNA clone libraries includedThermoanaerobacter, Thermococcus,Desulfothiovibrio, Aminobacterium,Acidaminococcus, Pseudomonas,Halomonas, Acinetobacter,Sphingomonas, Methylobacterium, andDesulfomicrobium. The archaeal library was dominated by methanogen-like rDNAs, with a lower percentage of clones belonging to the Thermococcales. Our results strongly support the hypothesis that sulfur-utilizing and methane-producing thermophilic microorganisms have a widespread distribution in oil reservoirs and the potential to actively participate in the biogeochemical transformation of carbon, hydrogen, and sulfur in situ.

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HUANG, Xiaoyu, Akiko MATSUMOTO, Akihiro OHNISHI, Masaru SAKAMOTO, Naoshi FUJIMOTO, and Masaharu SUZUKI. "Enrichment Culture of Hydrogen Fermentation Microorganisms and Analysis of Microbial Communities." Journal of Environmental Conservation Engineering 36, no. 7 (2007): 501–8. http://dx.doi.org/10.5956/jriet.36.501.

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Révész, Fruzsina, Perla Abigail Figueroa-Gonzalez, Alexander J. Probst, Balázs Kriszt, Sinchan Banerjee, Sándor Szoboszlay, Gergely Maróti, and András Táncsics. "Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures." Archives of Microbiology 202, no. 2 (October 29, 2019): 329–42. http://dx.doi.org/10.1007/s00203-019-01749-2.

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Abstract The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with high an abundance of Betaproteobacteriales (36.5%), followed by Alphaproteobacteria (8.7%), Actinobacteria (5.6%), and Candidatus Saccharibacteria (4.5%). The most abundant alkane monooxygenase (alkB) genotypes in this enrichment could be linked to members of the genus Rhodococcus and to a novel Gammaproteobacterium, for which we generated a high-quality draft genome using genome-resolved metagenomics of the enrichment culture. Contrarily, in the microaerobic enrichment, Gammaproteobacteria (99%) overwhelmingly dominated the microbial community with a high abundance of the genera Acinetobacter (66.3%), Pseudomonas (11%) and Acidovorax (11%). Under microaerobic conditions, the vast majority of alkB gene sequences could be linked to Pseudomonas veronii. Consequently, results shed light on the fact that the excellent aliphatic hydrocarbon degrading Rhodococcus species favour clear aerobic conditions, while oxygen-limited conditions can facilitate the high abundance of Acinetobacter species in aliphatic hydrocarbon-contaminated subsurface environments.

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Entcheva, Plamena, Wolfgang Liebl, Andre Johann, Thomas Hartsch, and Wolfgang R. Streit. "Direct Cloning from Enrichment Cultures, a Reliable Strategy for Isolation of Complete Operons and Genes from Microbial Consortia." Applied and Environmental Microbiology 67, no. 1 (January 1, 2001): 89–99. http://dx.doi.org/10.1128/aem.67.1.89-99.2001.

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ABSTRACT Enrichment cultures of microbial consortia enable the diverse metabolic and catabolic activities of these populations to be studied on a molecular level and to be explored as potential sources for biotechnology processes. We have used a combined approach of enrichment culture and direct cloning to construct cosmid libraries with large (>30-kb) inserts from microbial consortia. Enrichment cultures were inoculated with samples from five environments, and high amounts of avidin were added to the cultures to favor growth of biotin-producing microbes. DNA was extracted from three of these enrichment cultures and used to construct cosmid libraries; each library consisted of between 6,000 and 35,000 clones, with an average insert size of 30 to 40 kb. The inserts contained a diverse population of genomic DNA fragments isolated from the consortia organisms. These three libraries were used to complement the Escherichia coli biotin auxotrophic strain ATCC 33767 Δ(bio-uvrB). Initial screens resulted in the isolation of seven different complementing cosmid clones, carrying biotin biosynthesis operons. Biotin biosynthesis capabilities and growth under defined conditions of four of these clones were studied. Biotin measured in the different culture supernatants ranged from 42 to 3,800 pg/ml/optical density unit. Sequencing the identified biotin synthesis genes revealed high similarities to biooperons from gram-negative bacteria. In addition, random sequencing identified other interesting open reading frames, as well as two operons, the histidine utilization operon (hut), and the cluster of genes involved in biosynthesis of molybdopterin cofactors in bacteria (moaABCDE).

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Muniesa, Maite, Anicet R. Blanch, Francisco Lucena, and Juan Jofre. "Bacteriophages May Bias Outcome of Bacterial Enrichment Cultures." Applied and Environmental Microbiology 71, no. 8 (August 2005): 4269–75. http://dx.doi.org/10.1128/aem.71.8.4269-4275.2005.

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ABSTRACT Enrichment cultures are widely used for the isolation of bacteria in clinical, biotechnological, and environmental studies. However, competition, relative growth rates, or inhibitory effects may alter the outcome of enrichment cultures, causing the phenomenon known as enrichment bias. Bacteriophages are a major component in many microbial systems, and it abounds in natural settings. This abundance means that bacteriophages are likely to be present in many laboratory enrichment cultures. Our hypothesis was that bacteriophages present in the sample might bias the enriched subpopulation, since it can infect and lyse the target bacteria during the enrichment step once the bacteria reach a given density. Here we show that the presence of bacteriophages in Salmonella and Shigella enrichment cultures produced a significant reduction (more than 1 log unit) in the number of these bacteria compared with samples in which bacteriophages had been reduced by filtration through 0.45-μm non-protein-binding membranes. Furthermore, our data indicate that the Salmonella biotypes isolated after the enrichment culture change if bacteriophages are present, thus distorting the results of the analysis.

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Petrie, Lainie, Nadia N. North, Sherry L. Dollhopf, David L. Balkwill, and Joel E. Kostka. "Enumeration and Characterization of Iron(III)-Reducing Microbial Communities from Acidic Subsurface Sediments Contaminated with Uranium(VI)." Applied and Environmental Microbiology 69, no. 12 (December 2003): 7467–79. http://dx.doi.org/10.1128/aem.69.12.7467-7479.2003.

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ABSTRACT Iron(III)-reducing bacteria have been demonstrated to rapidly catalyze the reduction and immobilization of uranium(VI) from contaminated subsurface sediments. Thus, these organisms may aid in the development of bioremediation strategies for uranium contamination, which is prevalent in acidic subsurface sediments at U.S. government facilities. Iron(III)-reducing enrichment cultures were initiated from pristine and contaminated (high in uranium, nitrate; low pH) subsurface sediments at pH 7 and pH 4 to 5. Enumeration of Fe(III)-reducing bacteria yielded cell counts of up to 240 cells ml−1 for the contaminated and background sediments at both pHs with a range of different carbon sources (glycerol, acetate, lactate, and glucose). In enrichments where nitrate contamination was removed from the sediment by washing, MPN counts of Fe(III)-reducing bacteria increased substantially. Sediments of lower pH typically yielded lower counts of Fe(III)-reducing bacteria in lactate- and acetate-amended enrichments, but higher counts were observed when glucose was used as an electron donor in acidic enrichments. Phylogenetic analysis of 16S rRNA gene sequences extracted from the highest positive MPN dilutions revealed that the predominant members of Fe(III)-reducing consortia from background sediments were closely related to members of the Geobacteraceae family, whereas a recently characterized Fe(III) reducer (Anaeromyxobacter sp.) and organisms not previously shown to reduce Fe(III) (Paenibacillus and Brevibacillus spp.) predominated in the Fe(III)-reducing consortia of contaminated sediments. Analysis of enrichment cultures by terminal restriction fragment length polymorphism (T-RFLP) strongly supported the cloning and sequencing results. Dominant members of the Fe(III)-reducing consortia were observed to be stable over several enrichment culture transfers by T-RFLP in conjunction with measurements of Fe(III) reduction activity and carbon substrate utilization. Enrichment cultures from contaminated sites were also shown to rapidly reduce millimolar amounts of U(VI) in comparison to killed controls. With DNA extracted directly from subsurface sediments, quantitative analysis of 16S rRNA gene sequences with MPN-PCR indicated that Geobacteraceae sequences were more abundant in pristine compared to contaminated environments,whereas Anaeromyxobacter sequences were more abundant in contaminated sediments. Thus, results from a combination of cultivation-based and cultivation-independent approaches indicate that the abundance/community composition of Fe(III)-reducing consortia in subsurface sediments is dependent upon geochemical parameters (pH, nitrate concentration) and that microorganisms capable of producing spores (gram positive) or spore-like bodies (Anaeromyxobacter) were representative of acidic subsurface environments.

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Booker, R. "Microbial reductive dechlorination of hexachloro-1,3-butadiene in a methanogenic enrichment culture." Water Research 34, no. 18 (December 15, 2000): 4437–45. http://dx.doi.org/10.1016/s0043-1354(00)00214-1.

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Dai, Hongliang, Xiwu Lu, Lihong Peng, Xiang Li, and Zheqin Dai. "Enrichment culture of denitrifying phosphorus removal sludge and its microbial community analysis." Environmental Technology 38, no. 22 (January 17, 2017): 2800–2810. http://dx.doi.org/10.1080/09593330.2016.1278276.

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Sutton, Nora B., Siavash Atashgahi, Edoardo Saccenti, Tim Grotenhuis, Hauke Smidt, and Huub H. M. Rijnaarts. "Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation." PLOS ONE 10, no. 8 (August 5, 2015): e0134615. http://dx.doi.org/10.1371/journal.pone.0134615.

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Kocamemi, Bilge Alpaslan, Duygu Dityapak, Neslihan Semerci, Esra Keklik, Alper Akarsubası, Mert Kumru, and Halil Kurt. "Anammox start-up strategies: the use of local mixed activated sludge seed versus Anammox seed." Water Science and Technology 78, no. 9 (October 19, 2018): 1901–15. http://dx.doi.org/10.2166/wst.2018.431.

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Abstract The start-up period of Anammox systems is still a big challenge due to the unavailability of large volumes of slowly growing Anammox seed locally in most countries. This study aims to evaluate the effects of seeding strategy on the start-up and enrichment period of Anammox systems by monitoring both process performance and microbial population dynamics. Two different seeding strategies, the use of mixed activated sludge culture from a local STP and the use of enriched Anammox culture transported from abroad, were comparatively studied in SBR systems operated for 410 days. The enriched Anammox seed from abroad inhibited seriously during transportation. Anammox activity re-started after 195 days' recovery period. An active Anammox culture was successfully enriched within 95 days from a local activated sludge source without seeding any Anammox. The Anammox population reached levels of 1011 copies/ng at the end of 410 days' enrichment period. Based on FISH, Ca. Brocadia anammoxidans and Ca. Scalindua species were dominant in the enriched culture. The maximum TNRR was observed as 430 mg N/day. DGGE analyses revealed a drastic change in the microbial community (56%) with Anammox enrichment. Phylogenetic analysis demonstrated a significant decrease in phylotype Proteobacteria and increase in phylotypes Planctomycetes, Chloroflexi and Acidobacteria with enrichment.

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Zhang, Rui Yong, Sabrina Hedrich, and Axel Schippers. "Reduction of Iron(III) Ions at Elevated Pressure by Acidophilic Microorganisms." Solid State Phenomena 262 (August 2017): 88–92. http://dx.doi.org/10.4028/www.scientific.net/ssp.262.88.

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A composed mixed acidophilic, iron-oxidizing culture (FIGB) and a thermo-acidophilic enrichment culture (TK65) were used to evaluate microbial iron(III) reduction coupled to oxidation of reduced inorganic sulfur compounds (RISCs) under high pressure. Experiments were done in batch culture in high pressure vessels at 1 and 100 bar. Microbial abundance and activity were determined by measuring iron(II) concentration, direct cell counting, T-RFLP and quantitative real-time PCR. The data indicate that both cultures are able to reduce soluble iron(III) by oxidation of sulfur compounds under anaerobic conditions. At high pressure (100 bar) these acidophiles were capable of growing and microbial ferric iron reduction was only partially inhibited. These results indicate that acidophiles can be barotolerant and their activities are contributing to sulfur and iron cycling in anaerobic environments including deep ore deposits which is highly relevant for in situ leaching operations.

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Ziemer, Cherie J. "Newly Cultured Bacteria with Broad Diversity Isolated from Eight-Week Continuous Culture Enrichments of Cow Feces on Complex Polysaccharides." Applied and Environmental Microbiology 80, no. 2 (November 8, 2013): 574–85. http://dx.doi.org/10.1128/aem.03016-13.

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ABSTRACTOne of the functions of the mammalian large intestinal microbiota is the fermentation of plant cell wall components. In ruminant animals, the majority of their nutrients are obtained via pregastric fermentation; however, up to 20% can be recovered from microbial fermentation in the large intestine. Eight-week continuous culture enrichments of cattle feces with cellulose and xylan-pectin were used to isolate bacteria from this community. A total of 459 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented:Firmicutes(51.9%),Bacteroidetes(30.9%),Proteobacteria(11.1%),Actinobacteria(3.5%),Synergistetes(1.5%), andFusobacteria(1.1%). The majority of bacterial isolates had <98.5% identity to cultured bacteria with sequences in the Ribosomal Database Project and thus represent new species and/or genera. Within theFirmicutesisolates, most were classified in the familiesLachnospiraceae,Ruminococcaceae,Erysipelotrichaceae, andClostridiaceaeI. The majority of theBacteroideteswere most closely related toBacteroides thetaiotaomicron,B. ovatus, andB. xylanisolvensand members of thePorphyromonadaceaefamily. Many of theFirmicutesandBacteroidetesisolates were related to species demonstrated to possess enzymes which ferment plant cell wall components; the others were hypothesized to cross-feed these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 98% of the isolates not represented as previously cultured, there are new opportunities to study the genomic and metabolic capacities of these members of the complex intestinal microbiota.

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Pisco, Ana R., Simon Bengtsson, Alan Werker, Maria A. M. Reis, and Paulo C. Lemos. "Community Structure Evolution and Enrichment of Glycogen-Accumulating Organisms Producing Polyhydroxyalkanoates from Fermented Molasses." Applied and Environmental Microbiology 75, no. 14 (May 22, 2009): 4676–86. http://dx.doi.org/10.1128/aem.02486-08.

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ABSTRACT An open mixed culture was enriched with glycogen-accumulating organisms (GAOs) by using a sequencing batch reactor and treating an agroindustrial waste (sugar cane molasses) under cyclic anaerobic-aerobic conditions. Over a 1-year operating period, the culture exhibited a very stable GAO phenotype with an average polyhydroxyalkanoate (PHA) content of 17% total suspended solids. However, the GAO microbial community evolved over the course of operation to a culture exhibiting unusual characteristics in producing PHAs comprised of short-chain-length monomers, namely, 3-hydroxybutyrate, 3-hydroxy-2-methylbutyrate, 3-hydroxyvalerate, and 3-hydroxy-2-methylvalerate, and also, up to 31 mol% of the medium-chain-length (MCL) monomer 3-hydroxyhexanoate (3HHx). Microbial community analysis by fluorescence in situ hybridization revealed a concurrent long-term drift in the GAO community balance, from mainly “Candidatus Competibacter phosphatis” to mainly Defluviicoccus vanus-related organisms. The production of 3HHx was confirmed by 13C nuclear magnetic resonance (NMR) and appeared to be related to the increased presence of D. vanus-related GAOs. These results suggest a broadened spectrum of material, chemical, and mechanical properties that can be achieved for biopolymers produced by open mixed cultures from fermented waste. The increased spectrum of polymer properties brings a wider scope of potential applications.

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Manchester, Marie J., Laura A. Hug, Matt Zarek, Anna Zila, and Elizabeth A. Edwards. "Discovery of atrans-Dichloroethene-Respiring Dehalogenimonas Species in the 1,1,2,2-Tetrachloroethane-Dechlorinating WBC-2 Consortium." Applied and Environmental Microbiology 78, no. 15 (May 25, 2012): 5280–87. http://dx.doi.org/10.1128/aem.00384-12.

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ABSTRACTThe WBC-2 consortium is an organohalide-respiring anaerobic microbial enrichment culture capable of dechlorinating 1,1,2,2-tetrachloroethane (TeCA) to ethene. In the WBC-2 culture, TeCA is first transformed totrans-dichloroethene (tDCE) by dichloroelimination; tDCE is subsequently transformed to vinyl chloride (VC) and then to ethene by hydrogenolysis. Analysis of 16S rRNA gene clone libraries from culture DNA revealed sequences from three putative dechlorinating organisms belonging toDehalococcoides,Dehalobacter, andDehalogenimonasgenera. Quantitative PCR primers were designed for each of these sequences, and their abundance was quantified in enrichment cultures over time. These data revealed that complete dechlorination of TeCA to ethene involves all three organisms.Dehalobacterspp. grew during the dihaloelimination of TeCA to tDCE, whileDehalococcoidesandDehalogenimonasspp. grew during hydrogenolysis of tDCE to ethene. This is the first time a genus other thanDehalococcoideshas been implicated in dechlorination of tDCE to VC.

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Paungfoo, C., P. Prasertsan, N. Intrasungkha, L. L. Blackall, and R. Bhamidimarri. "Enrichment of nitrifying microbial communities from shrimp farms and commercial inocula." Water Science and Technology 48, no. 8 (November 1, 2003): 143–50. http://dx.doi.org/10.2166/wst.2003.0463.

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Nitrifying bacteria were selected from shrimp farm water and sediment (ÒnaturalÓ seed) in Thailand and from commercial seed cultures. The microbial consortia from each source giving the best ammonia removal during batch culture pre-enrichments were used as inocula for two sequencing batch reactors (SBRs). Nitrifiers were cultivated in the SBRs with 100 mg NH4-N/l and artificial wastewater containing 25 ppt salinity. The two SBRs were operated at a 7 d hydraulic retention time (HRT) for 77 d after which the HRT was reduced to 3.5 d. The amounts of ammonia removed from the influent by microorganisms sourced from the natural seed were 85% and 92% for the 7 d HRT and the 3.5 d HRT, respectively. The ammonia removals of microbial consortia from the commercial seed were 71% and 83% for these HRTs respectively. The quantity of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was determined in the SBRs using the most probable number (MPN) technique. Both AOB and NOB increased in number over the long-term operation of both SBRs. According to quantitative fluorescence in situ hybridisation (FISH) probing, AOB from the natural seed and commercial seed comprised 21 ± 2% and 30 ± 2%, respectively of all bacteria. NOB could not be detected with currently-reported FISH probes, suggesting that novel NOB were enriched from both sources. Taken collectively, the results from this study provide an indication that the nitrifiers from shrimp farm sources are more effective at ammonia removal than those from commercial seed cultures.

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Bentham, Richard, Nick McClure, and David Catcheside. "Biotreatment of an industrial waste oil condensate." Water Science and Technology 36, no. 10 (November 1, 1997): 125–29. http://dx.doi.org/10.2166/wst.1997.0374.

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The biotreatment of an industrial waste oil condensate has been investigated. The waste is an oily emulsion resulting from chemical processing and condensation of grease trap wastes and industrial waste oils. The oil consists of a complex mix of hydrocarbons with significant fuel oil and lube oil fractions. Currently this waste is disposed of by incineration. The feasibility of using a biological pretreatment process to remove a significant proportion of the hydrocarbons has been investigated. Enrichment cultures produced a stable bacterial consortium. Flask cultures of this enrichment culture were capable of rapid emulsification of the oil. Within 10 days, 40–50% of the oil waste was degraded. Degradation was monitored using gas chromatographic analysis with flame ionisation detector (GC-FID) and by assessment of microbial dehydrogenase activity using triphenyl tetrazolium chloride (TTC) dye reduction. The enrichment culture consisted of 9 component organisms, 7 Gram negative and one Gram positive organisms. Their degradative abilities in monoculture have been investigated. Degradation of the waste using monocultures was monitored using GC-FID analysis of the Pristane:C17 ratio in the waste. The degradation capability of each of the component organisms in pure culture was similar to that of the consortium.

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Visscher, Pieter T., Rachel F. Gritzer, and Edward R. Leadbetter. "Low-Molecular-Weight Sulfonates, a Major Substrate for Sulfate Reducers in Marine Microbial Mats." Applied and Environmental Microbiology 65, no. 8 (August 1, 1999): 3272–78. http://dx.doi.org/10.1128/aem.65.8.3272-3278.1999.

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ABSTRACT Several low-molecular-weight sulfonates were added to microbial mat slurries to investigate their effects on sulfate reduction. Instantaneous production of sulfide occurred after taurine and cysteate were added to all of the microbial mats tested. The rates of production in the presence of taurine and cysteate were 35 and 24 μM HS− h−1 in a stromatolite mat, 38 and 36 μM HS− h−1 in a salt pond mat, and 27 and 18 μM HS− h−1 in a salt marsh mat, respectively. The traditionally used substrates lactate and acetate stimulated the rate of sulfide production 3 to 10 times more than taurine and cysteate stimulated the rate of sulfide production in all mats, but when ethanol, glycolate, and glutamate were added to stromatolite mat slurries, the resulting increases were similar to the increases observed with taurine and cysteate. Isethionate, sulfosuccinate, and sulfobenzoate were tested only with the stromatolite mat slurry, and these compounds had much smaller effects on sulfide production. Addition of molybdate resulted in a greater inhibitory effect on acetate and lactate utilization than on sulfonate use, suggesting that different metabolic pathways were involved. In all of the mats tested taurine and cysteate were present in the pore water at nanomolar to micromolar concentrations. An enrichment culture from the stromatolite mat was obtained on cysteate in a medium lacking sulfate and incubated anaerobically. The rate of cysteate consumption by this enrichment culture was 1.6 pmol cell−1h−1. Compared to the results of slurry studies, this rate suggests that organisms with properties similar to the properties of this enrichment culture are a major constituent of the sulfidogenic population. In addition, taurine was consumed at some of highest dilutions obtained from most-probable-number enrichment cultures obtained from stromatolite samples. Based on our comparison of the sulfide production rates found in various mats, low-molecular-weight sulfonates are important sources of C and S in these ecosystems.

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Cutter, Leah, Kevin R. Sowers, and Harold D. May. "Microbial Dechlorination of 2,3,5,6-Tetrachlorobiphenyl under Anaerobic Conditions in the Absence of Soil or Sediment." Applied and Environmental Microbiology 64, no. 8 (August 1, 1998): 2966–69. http://dx.doi.org/10.1128/aem.64.8.2966-2969.1998.

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ABSTRACT Bacterial enrichment cultures developed with Baltimore Harbor (BH) sediments were found to reductively dechlorinate 2,3,5,6-tetrachlorobiphenyl (2,3,5,6-CB) when incubated in a minimal estuarine medium containing short-chain fatty acids under anaerobic conditions with and without the addition of sediment. Primary enrichment cultures formed both meta and orthodechlorination products from 2,3,5,6-CB. The lag time preceding dechlorination decreased from 30 to less than 20 days as the cultures were sequentially transferred into estuarine medium containing dried, sterile BH sediment. In addition, only ortho dechlorination was observed following transfer of the cultures. Sequential transfer into medium without added sediment also resulted in the development of a strict ortho-dechlorinating culture following a lag of more than 100 days. Upon further transfer into the minimal medium without sediment, the lag time decreased to less than 50 days. At this stage all cultures, regardless of the presence of sediment, would produce 2,3,5-CB and 3,5-CB from 2,3,5,6-CB. The strictortho-dechlorinating activity in the sediment-free cultures has remained stable for more than 1 year through several transfers. These results reveal that the classical microbial enrichment technique using a minimal medium with a single polychlorinated biphenyl (PCB) congener selected for ortho dechlorination of 2,3,5,6-CB. Furthermore, this is the first report of sustained anaerobic PCB dechlorination in the complete absence of soil or sediment.

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Susilawati, Rita, Paul N. Evans, Joan S. Esterle, Steven J. Robbins, Gene W. Tyson, Suzanne D. Golding, and Tennille E. Mares. "Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals." International Journal of Coal Geology 137 (January 2015): 66–76. http://dx.doi.org/10.1016/j.coal.2014.10.015.

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Sun, Hone L., Thomas J. Sheets, and Frederick T. Corbin. "Transformation of Alachlor by Microbial Communities." Weed Science 38, no. 4-5 (September 1990): 416–20. http://dx.doi.org/10.1017/s0043174500056770.

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A mixed microbial culture able to transform alachlor at a concentration of 50 μg ml-1was obtained from alachlor-treated soil after an enrichment period of 84 days. The microbial community was composed of seven strains of bacteria. No single isolate was able to utilize alachlor as a sole source of carbon. There was no alachlor left in the enriched culture after a 14-day incubation, but only 12% of the14C-ring-labeled alachlor was converted to14CO2through ring cleavage during 14 days in the basal medium amended with alachlor as a sole carbon source. The presence of sucrose as an alternative carbon source decreased the mineralization potential of the enriched culture, but sucrose increased the mineralizing ability of a three-member mixed culture. Thin-layer chromatographic analysis showed that there were four unidentified metabolites of alachlor produced by the enriched culture. Sucrose decreased the amount of two of the four metabolites. The absence of a noticeable decline in radioactivity beyond the initial 12% suggested that the side chain of alachlor was utilized as carbon source by the enriched culture. Little difference in radioactivity between growth medium and cell-free supernatant of the growth medium suggested that the carbon in the ring was not incorporated into the cells of the degrading microorganisms.

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Chaudhuri, B. K., and U. Wiesmann. "Enhanced anaerobic degradation of benzene by enrichment of mixed microbial culture and optimization of the culture medium." Applied Microbiology and Biotechnology 43, no. 1 (April 1, 1995): 178–87. http://dx.doi.org/10.1007/s002530050388.

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Chaudhuri, B. K., and U. Wiesmann. "Enhanced anaerobic degradation of benzene by enrichment of mixed microbial culture and optimization of the culture medium." Applied Microbiology and Biotechnology 43, no. 1 (April 1995): 178–87. http://dx.doi.org/10.1007/bf00170641.

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KANJANASOPA, Duangkhaetita, Benchamaporn PIMPA, Suraphon THITITHANAKUL, and Suwaluk WISUNTHORN. "Biodegradation of Polyvinyl Alcohol by Thai Indigenous Mixed Microbial Culture." Walailak Journal of Science and Technology (WJST) 17, no. 7 (July 1, 2020): 698–707. http://dx.doi.org/10.48048/wjst.2020.6158.

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PVA is biodegradable plastic and a water-soluble synthetic polymer that plays a significant role in industry. A large amount of PVA in wastewater causes heavy environmental pollution in terms of accumulation, disposal, and long-term degradation; therefore it must be removed from wastewater before the water is discharged. In this study, NS3 mixed microbial culture, capable of completely degrading 5 g.L-1 polyvinyl alcohol (PVA), was isolated from landfill soil using the enrichment culture method. It completely degraded PVA at an initial concentration in the range 1 - 5 g.L-1 over 5 - 20 days of incubation with continuous shaking at 30 °C. Moreover, mixed microbial cultures were found to remove PVA at a high range concentration of 10 - 25 g.L-1. Urea and glucose added to the medium inhibited PVA degradation by increasing the pH to a strongly alkaline level, which would cause cell viability and enzyme stability. The FT-IR spectra and SEM imaging revealed the mechanisms and the physical degradation of PVA films, respectively. PVA uptake in bacterial cells produced a dent in the cell surface, which represented the consumption of PVA by bacterial cell. The PVA-degrading mixed microbial culture is the first reported in Thailand and can be beneficial in PVA wastewater treatment.

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Qiu, Yan-Ling, Yuji Sekiguchi, Hiroyuki Imachi, Yoichi Kamagata, I.-Cheng Tseng, Sheng-Shung Cheng, Akiyoshi Ohashi, and Hideki Harada. "Identification and Isolation of Anaerobic, Syntrophic Phthalate Isomer-Degrading Microbes from Methanogenic Sludges Treating Wastewater from Terephthalate Manufacturing." Applied and Environmental Microbiology 70, no. 3 (March 2004): 1617–26. http://dx.doi.org/10.1128/aem.70.3.1617-1626.2004.

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ABSTRACT The microbial populations responsible for anaerobic degradation of phthalate isomers were investigated by enrichment and isolation of those microbes from anaerobic sludge treating wastewater from the manufacturing of terephthalic acid. Primary enrichments were made with each of three phthalate isomers (ortho-, iso-, and terephthalate) as the sole energy source at 37Ã¯Â¿Â½C with two sources of anaerobic sludge (both had been used to treat wastewater containing high concentrations of phthalate isomers) as the inoculum. Six methanogenic enrichment cultures were obtained which not only degraded the isomer used for the enrichment but also had the potential to degrade part of other phthalate isomers as well as benzoate with concomitant production of methane, presumably involving strictly syntrophic substrate degradation. Our 16S rRNA gene-cloning analysis combined with fluorescence in situ hybridization revealed that the predominant bacteria in the enrichment cultures were affiliated with a recently recognized non-sulfate-reducing subcluster (subcluster Ih) in the group ‘Desulfotomaculum lineage I' or a clone cluster (group TA) in the class delta-Proteobacteria. Several attempts were made to isolate these microbes, resulting in the isolation of a terephthalate-degrading bacterium, designated strain JT, in pure culture. A coculture of the strain with the hydrogenotrophic methanogen Methanospirillum hungatei converted terephthalate to acetate and methane within 3 months of incubation, whereas strain JT could not degrade terephthalate in pure culture. During the degradation of terephthalate, a small amount of benzoate was transiently accumulated as an intermediate, indicative of decarboxylation of terephthalate to benzoate as the initial step of the degradation. 16S rRNA gene sequence analysis revealed that the strain was a member of subcluster Ih of the group ‘Desulfotomaculum lineage I', but it was only distantly related to other known species.

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Wu, Qingzhong, Kevin R. Sowers, and Harold D. May. "Establishment of a Polychlorinated Biphenyl-Dechlorinating Microbial Consortium, Specific for Doubly Flanked Chlorines, in a Defined, Sediment-Free Medium." Applied and Environmental Microbiology 66, no. 1 (January 1, 2000): 49–53. http://dx.doi.org/10.1128/aem.66.1.49-53.2000.

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ABSTRACT Estuarine sediment from Charleston Harbor, South Carolina, was used as inoculum for the development of an anaerobic enrichment culture that specifically dechlorinates doubly flanked chlorines (i.e., chlorines bound to carbon that are flanked on both sides by other chlorine-carbon bonds) of polychlorinated biphenyls (PCBs). Dechlorination was restricted to the para chlorine in cultures enriched with 10 mM fumarate, 50 ppm (173 μM) 2,3,4,5-tetrachlorobiphenyl, and no sediment. Initially the rate of dechlorination decreased upon the removal of sediment from the medium. However, the dechlorinating activity was sustainable, and following sequential transfer in a defined, sediment-free estuarine medium, the activity increased to levels near that observed with sediment. The culture was nonmethanogenic, and molybdate, ampicillin, chloramphenicol, neomycin, and streptomycin inhibited dechlorination activity; bromoethanesulfonate and vancomycin did not. Addition of 17 PCB congeners indicated that the culture specifically removes double flanked chlorines, preferably in the para position, and does not attack ortho chlorines. This is the first microbial consortium shown to para or metadechlorinate a PCB congener in a defined sediment-free medium. It is the second PCB-dechlorinating enrichment culture to be sustained in the absence of sediment, but its dechlorinating capabilities are entirely different from those of the other sediment-free PCB-dechlorinating culture, an ortho-dechlorinating consortium, and do not match any previously published Aroclor-dechlorinating patterns.

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Guisnet, Aurélie, Malosree Maitra, Sreeparna Pradhan, and Michael Hendricks. "A three-dimensional habitat for C. elegans environmental enrichment." PLOS ONE 16, no. 1 (January 11, 2021): e0245139. http://dx.doi.org/10.1371/journal.pone.0245139.

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As we learn more about the importance of gene-environment interactions and the effects of environmental enrichment, it becomes evident that minimalistic laboratory conditions can affect gene expression patterns and behaviors of model organisms. In the laboratory, Caenorhabditis elegans is generally cultured on two-dimensional, homogeneous agar plates abundantly covered with axenic bacteria culture as a food source. However, in the wild, this nematode thrives in rotting fruits and plant stems feeding on bacteria and small eukaryotes. This contrast in habitat complexity suggests that studying C. elegans in enriched laboratory conditions can deepen our understanding of its fundamental traits and behaviors. Here, we developed a protocol to create three-dimensional habitable scaffolds for trans-generational culture of C. elegans in the laboratory. Using decellularization and sterilization of fruit tissue, we created an axenic environment that can be navigated throughout and where the microbial environment can be strictly controlled. C. elegans were maintained over generations on this habitat, and showed a clear behavioral bias for the enriched environment. As an initial assessment of behavioral variations, we found that dauer populations in scaffolds exhibit high-frequency, complex nictation behavior including group towering and jumping behavior.

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Pernthaler, Jakob, Thomas Posch, Karel S̆imek, Jaroslav Vrba, Annelie Pernthaler, Frank Oliver Glöckner, Ulrich Nübel, Roland Psenner, and Rudolf Amann. "Predator-Specific Enrichment of Actinobacteria from a Cosmopolitan Freshwater Clade in Mixed Continuous Culture." Applied and Environmental Microbiology 67, no. 5 (May 1, 2001): 2145–55. http://dx.doi.org/10.1128/aem.67.5.2145-2155.2001.

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ABSTRACT We investigated whether individual populations of freshwater bacteria in mixed experimental communities may exhibit specific responses to the presence of different bacterivorous protists. In two successive experiments, a two-stage continuous cultivation system was inoculated with nonaxenic batch cultures of the cryptophyteCryptomonas sp. Algal exudates provided the sole source of organic carbon for growth of the accompanying microflora. The dynamics of several 16S rRNA-defined bacterial populations were followed in the experimental communities. Although the composition and stability of the two microbial communities differed, numerous members of the first assemblage could again be detected during the second experiment. The introduction of a size-selectively feeding mixotrophic nanoflagellate (Ochromonas sp.) always resulted in an immediate bloom of a single phylotype population of members of the classActinobacteria (Ac1). These bacteria were phylogenetically affiliated with an uncultured lineage of gram-positive bacteria that have been found in freshwater habitats only. The Ac1 cells were close to the average size of freshwater bacterioplankton and significantly smaller than any of the other experimental community members. In contrast, no increase of the Ac1 population was observed in vessels exposed to the bacterivorous ciliate Cyclidium glaucoma. However, when the Ochromonas sp. was added after the establishment of C. glaucoma, the proportion of population Ac1 within the microbial community rapidly increased. Populations of a beta proteobacterial phylotype related to an Aquabacteriumsp. decreased relative to the total bacterial communities following the addition of either predator, albeit to different extents. The community structure of pelagic microbial assemblages can therefore be influenced by the taxonomic composition of the predator community.

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Rowe, Annette R., Brendan J. Lazar, Robert M. Morris, and Ruth E. Richardson. "Characterization of the Community Structure of a Dechlorinating Mixed Culture and Comparisons of Gene Expression in Planktonic and Biofloc-Associated “Dehalococcoides” and Methanospirillum Species." Applied and Environmental Microbiology 74, no. 21 (September 5, 2008): 6709–19. http://dx.doi.org/10.1128/aem.00445-08.

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ABSTRACT This study sought to characterize bacterial and archaeal populations in a perchloroethene- and butyrate-fed enrichment culture containing hydrogen-consuming “Dehalococcoides ethenogenes” strain 195 and a Methanospirillum hungatei strain. Phylogenetic characterization of this microbial community was done via 16S rRNA gene clone library and gradient gel electrophoresis analyses. Fluorescence in situ hybridization was used to quantify populations of “Dehalococcoides” and Archaea and to examine the colocalization of these two groups within culture bioflocs. A technique for enrichment of planktonic and biofloc-associated biomass was developed and used to assess differences in population distribution and gene expression patterns following provision of substrate. On a per-milliliter-of-culture basis, most D. ethenogenes genes (the hydrogenase gene hupL; the highly expressed gene for an oxidoreductase of unknown function, fdhA; the RNA polymerase subunit gene rpoB; and the 16S rRNA gene) showed no statistical difference in expression between planktonic and biofloc enrichments at either time point studied (1 to 2 and 6 h postfeeding). Normalization of transcripts to ribosome (16S rRNA) levels supported that planktonic and biofloc-associated D. ethenogenes had similar gene expression profiles, with one notable exception; planktonic D. ethenogenes showed higher expression of tceA relative to biofloc-associated cells at 6 h postfeeding. These trends were compared to those for the hydrogen-consuming methanogen in the culture, M. hungatei. The vast majority of M. hungatei cells, ribosomes (16S rRNA), and transcripts of the hydrogenase gene mvrD and the housekeeping gene rpoE were observed in the biofloc enrichments. This suggests that, unlike the comparable activity of D. ethenogenes from both enrichments, planktonic M. hungatei is responsible for only a small fraction of the hydrogenotrophic methanogenesis in this culture.

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Kharitonov, Sergey, Mikhail Semenov, Alexander Sabrekov, Oleg Kotsyurbenko, Alena Zhelezova, and Natalia Schegolkova. "Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology." Environments 8, no. 2 (February 22, 2021): 16. http://dx.doi.org/10.3390/environments8020016.

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The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.

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Sutherland, T. D., K. M. Weir, M. J. Lacey, I. Horne, R. J. Russell, and J. G. Oakeshott. "Enrichment of a microbial culture capable of degrading endosulphate, the toxic metabolite of endosulfan." Journal of Applied Microbiology 92, no. 3 (March 2002): 541–48. http://dx.doi.org/10.1046/j.1365-2672.2002.01559.x.

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Villemur, Richard, Silvia Cristina Cunha dos Santos, Julianne Ouellette, Pierre Juteau, François Lépine, and Eric Déziel. "Biodegradation of Endocrine Disruptors in Solid-Liquid Two-Phase Partitioning Systems by Enrichment Cultures." Applied and Environmental Microbiology 79, no. 15 (May 31, 2013): 4701–11. http://dx.doi.org/10.1128/aem.01239-13.

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ABSTRACTNaturally occurring and synthetic estrogens and other molecules from industrial sources strongly contribute to the endocrine disruption of urban wastewater. Because of the presence of these molecules in low but effective concentrations in wastewaters, these endocrine disruptors (EDs) are only partially removed after most wastewater treatments, reflecting the presence of these molecules in rivers in urban areas. The development of a two-phase partitioning bioreactor (TPPB) might be an effective strategy for the removal of EDs from wastewater plant effluents. Here, we describe the establishment of three ED-degrading microbial enrichment cultures adapted to a solid-liquid two-phase partitioning system using Hytrel as the immiscible water phase and loaded with estrone, estradiol, estriol, ethynylestradiol, nonylphenol, and bisphenol A. All molecules except ethynylestradiol were degraded in the enrichment cultures. The bacterial composition of the three enrichment cultures was determined using 16S rRNA gene sequencing and showed sequences affiliated with bacteria associated with the degradation of these compounds, such asSphingomonadales. OneRhodococcusisolate capable of degrading estrone, estradiol, and estriol was isolated from one enrichment culture. These results highlight the great potential for the development of TPPB for the degradation of highly diluted EDs in water effluents.

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Yin, Chao, Jia Lu, Xiao Hou Shao, Xin Yu Mao, Long Wang, Yong Min, and Mu Chen Shu. "Preliminary Study on Reaction Kinetics of Ammonia Nitrogen in Aqueous Samples Removed by Microbial Nano-Silica Ball." Advanced Materials Research 1010-1012 (August 2014): 528–31. http://dx.doi.org/10.4028/www.scientific.net/amr.1010-1012.528.

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EM enrichment culture liquid was immobilized on nano-silica carrier to form microbial nano ball, so as to investigate the reaction kinetics of ammonia nitrogen (NH4+-N) by microbial nano ball. The results showed that first order reaction kinetics model could describe NH4+-N removal by different diameter microbial nano-silica balls well. And the microbe could keep higher biological activity between 0-72h. Reaction kinetic equations of NH4+-N were: (1) when diameter was 10mm, (0-48h), (48-72h); (2) when diameter was 20mm, (0-48h), (48-72h); (3) (0-48h), (48-72h).

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Leonard, Susan R., Mark K. Mammel, David W. Lacher, and Christopher A. Elkins. "Application of Metagenomic Sequencing to Food Safety: Detection of Shiga Toxin-Producing Escherichia coli on Fresh Bagged Spinach." Applied and Environmental Microbiology 81, no. 23 (September 18, 2015): 8183–91. http://dx.doi.org/10.1128/aem.02601-15.

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ABSTRACTCulture-independent diagnostics reduce the reliance on traditional (and slower) culture-based methodologies. Here we capitalize on advances in next-generation sequencing (NGS) to apply this approach to food pathogen detection utilizing NGS as an analytical tool. In this study, spiking spinach with Shiga toxin-producingEscherichia coli(STEC) following an established FDA culture-based protocol was used in conjunction with shotgun metagenomic sequencing to determine the limits of detection, sensitivity, and specificity levels and to obtain information on the microbiology of the protocol. We show that an expected level of contamination (∼10 CFU/100 g) could be adequately detected (including key virulence determinants and strain-level specificity) within 8 h of enrichment at a sequencing depth of 10,000,000 reads. We also rationalize the relative benefit of static versus shaking culture conditions and the addition of selected antimicrobial agents, thereby validating the long-standing culture-based parameters behind such protocols. Moreover, the shotgun metagenomic approach was informative regarding the dynamics of microbial communities during the enrichment process, including initial surveys of the microbial loads associated with bagged spinach; the microbes found included key genera such asPseudomonas,Pantoea, andExiguobacterium. Collectively, our metagenomic study highlights and considers various parameters required for transitioning to such sequencing-based diagnostics for food safety and the potential to develop better enrichment processes in a high-throughput manner not previously possible. Future studies will investigate new species-specific DNA signature target regimens, rational design of medium components in concert with judicious use of additives, such as antibiotics, and alterations in the sample processing protocol to enhance detection.

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Kim, Byung-Hyuk, Kyung-Hwa Baek, Dae-Hyun Cho, Youlboong Sung, Sung-Cheol Koh, Chi-Yong Ahn, Hee-Mock Oh, and Hee-Sik Kim. "Complete reductive dechlorination of tetrachloroethene to ethene by anaerobic microbial enrichment culture developed from sediment." Biotechnology Letters 32, no. 12 (August 17, 2010): 1829–35. http://dx.doi.org/10.1007/s10529-010-0381-y.

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KOSTIĆ, TANJA, BEATRIX STESSL, MARTIN WAGNER, and ANGELA SESSITSCH. "Microarray Analysis Reveals the Actual Specificity of Enrichment Media Used for Food Safety Assessment." Journal of Food Protection 74, no. 6 (June 1, 2011): 1030–34. http://dx.doi.org/10.4315/0362-028x.jfp-10-388.

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Microbial diagnostic microarrays are tools for simultaneous detection and identification of microorganisms in food, clinical, and environmental samples. In comparison to classic methods, microarray-based systems have the potential for high throughput, parallelism, and miniaturization. High specificity and high sensitivity of detection have been demonstrated. A microbial diagnostic microarray for the detection of the most relevant bacterial food- and waterborne pathogens and indicator organisms was developed and thoroughly validated. The microarray platform based on sequence-specific end labeling of oligonucleotides and the phylogenetically robust gyrB marker gene allowed a highly specific (resolution on genus and/or species level) and sensitive (0.1% relative and 104 CFU absolute sensitivity) detection of the target pathogens. In initial challenge studies of the applicability of microarray-based food analysis, we obtained results demonstrating the questionable specificity of standardized culture-dependent microbiological detection methods. Taking into consideration the importance of reliable food safety assessment methods, comprehensive performance assessment is essential. Results demonstrate the potential of this new pathogen diagnostic microarray to evaluate culture-based standard methods in microbiological food analysis.

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Willis, Graciana, Sabrina Hedrich, Ivan Nancucheo, D. Barrie Johnson, and Edgardo R. Donati. "Microbial Diversity in Acidic Anaerobic Sediments at the Geothermal Caviahue-Copahue System, Argentina." Advanced Materials Research 825 (October 2013): 7–10. http://dx.doi.org/10.4028/www.scientific.net/amr.825.7.

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In this work we have examined the bacterial diversity from the hot spring sediment Agua del Limón (AL1) present at the geothermal Caviahue-Copahue system using a combination of molecular and cultivation techniques, with particular emphasis on indigenous anaerobic prokaryotes. Microorganisms involved in the iron (Acidithiobacillus ferrooxidansandLeptospirillumspp.) and sulphur (Acidithiobacillusspp., Thermotogales-like bacteria,Thiomonassp., andDesulfurellasp.) cycles were identified in the clone library. Although no obvious sulfate-reducing bacteria were detected by culture-independent techniques, several isolates related to the mesophilic, spore-forming sulfate-reducer"Desulfobacillus acidavidus"strain CL4 were isolated at 30°C and 40°C. The 16S rRNA gene of another isolate showed 94% similarity toDesulfotomaculum thermobenzoicum. Sulfate-reducing enrichment cultures of the Copahue samples were also dominated by"Dsb. acidavidus"CL4.

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Seychelles, Laurent H., Kim Doiron, Céline Audet, Réjean Tremblay, Fabrice Pernet, and Karine Lemarchand. "Impact of arachidonic acid enrichment of live rotifer prey on bacterial communities in rotifer and larval fish cultures." Canadian Journal of Microbiology 59, no. 3 (March 2013): 189–96. http://dx.doi.org/10.1139/cjm-2012-0564.

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Rotifers (Brachionus plicatilis), commonly used at first feeding in commercial fish hatcheries, carry a large bacteria load. Because they are relatively poor in essential fatty acids, it is common practice to enrich them with fatty acids, including arachidonic acid (AA). This study aims to determine whether prey enrichment with AA may act as a prebiotic and modify the microbial community composition either in AA-enriched rotifer cultures or in larval-rearing water using winter flounder (Pseudopleuronectes americanus) as a larval fish model. AA enrichment modified the bacterial community composition in both the rotifer culture tanks and the larval-rearing tanks. We observed an increase in the number of cultivable bacteria on TCBS (thiosulfate–citrate–bile salts–sucrose) agar, used as a proxy for the abundance of Vibrio sp. The results suggest that AA may also play an indirect role in larval health.

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Bulaev, Aleksander, Nikolay V. Pimenov, Denis A. Ivasenko, and Olga V. Karnachuk. "Enrichment and Isolation of Acidophilic Microorganisms from Sediments of Gold Mine Waste Leachate." Advanced Materials Research 1130 (November 2015): 581–84. http://dx.doi.org/10.4028/www.scientific.net/amr.1130.581.

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Microorganisms living in acidic environments associated with various types of mining wastes can be used for bioremediation of acid mine drainage (AMD) and related waste streams. We studied microbial diversity of the acidic sediments of a leachate puddle at the basement of a waste rock pile from gold mining in abandoned gold deposit in Martiga (Kemerovo region, West Siberia, Russia). The enrichments were established from four sediment samples with a pH ranging from 2.29 to 6.16. The enrichments cultures were set up at aerobic and anaerobic conditions. Pure cultures of bacteria involved in iron and sulfur oxidation were isolated. The isolated iron- and sulfur-oxidizing cultures were affiliated with Acidithiobacillus and Acidocella genera as was revealed by 16S rRNA gene sequencing. Strains of Desulfosporosinus-like spore-forming bacteria were isolated under anaerobic conditions. The pure culture isolates physiological and biochemical characterization is underway, which will provide new knowledge of AMD formation and natural processes of metal attenuation. The strains can also be prospective agents for use in bioleaching and bioremediation processes.

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Journal articles on the topic 'Microbial culture enrichment'

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