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Artykuły w czasopismach na temat "Bacterial communities"
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Tetz, V. V., V. P. Korobov, N. K. Artemenko, L. M. Lemkina, N. V. Panjkova i G. V. Tetz. "Extracellular phospholipids of isolated bacterial communities". Biofilms 1, nr 3 (lipiec 2004): 149–55. http://dx.doi.org/10.1017/s147905050400136x.
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We have made a comparative analysis of the extracellular phospholipid composition of biofilms of Gram-negative and Gram-positive bacteria. The surface film of a growing bacterial community contains small membrane vesicles and a bilipid layer covering the entire surface of that community. These supracommunity films containing the bilipid layer can cover the entire surface of a Petri dish and form a boundary between bacterial communities and the environment. A mixed bacterial lawn, formed by unrelated bacteria, also becomes covered with a single film containing a lipid bilayer. The phospholipid compositions of the bacterial cell and surface film bilipid layer reflect the nature of the bacterial strains forming the community, but have some specific differences.
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Karim, Md Abdul, i Mehedi Al Masum. "Characteristics and antibiogram of airborne bacterial communities". Bangladesh Journal of Botany 49, nr 4 (31.12.2020): 937–47. http://dx.doi.org/10.3329/bjb.v49i4.52501.
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Composition and concentration of the bacterial communities in air of using a culture-dependent plate exposure technique and air sampling with filter were analysed. An average value of 2.8 x 103 bacterial CFU/m3 was found in different seasons. A total of 8 bacterial genera were identified among 58 species. The most predominant bacteria were Bacillus (73%), Planococcus (9%), Staphylococcus (6%), Micrococcus (4%), Deinococcus (2%), Arthrobacter (2%), Microbacterium (2%), and Exiguobacterium (2%). The distribution of predominant airborne bacteria varied greatly between different sampling sites and seasons and was limited by environmental parameters, as well as human activities.
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He, Ping-An, i Li Xia. "Oligonucleotide Profiling for Discriminating Bacteria in Bacterial Communities". Combinatorial Chemistry & High Throughput Screening 10, nr 4 (1.05.2007): 247–55. http://dx.doi.org/10.2174/138620707780636646.
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Harcombe, W. R., i J. J. Bull. "Impact of Phages on Two-Species Bacterial Communities". Applied and Environmental Microbiology 71, nr 9 (wrzesień 2005): 5254–59. http://dx.doi.org/10.1128/aem.71.9.5254-5259.2005.
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ABSTRACT A long history of experimental work has shown that addition of bacteriophages to a monoculture of bacteria leads to only a temporary depression of bacterial levels. Resistant bacteria usually become abundant, despite reduced growth rates relative to those of phage-sensitive bacteria. This restoration of high bacterial density occurs even if the phages evolve to overcome bacterial resistance. We believe that the generality of this result may be limited to monocultures, in which the resistant bacteria do not face competition from bacterial species unaffected by the phage. As a simple case, we investigated the impact of phages attacking one species in a two-species culture of bacteria. In the absence of phages, Escherichia coli B and Salmonella enterica serovar Typhimurium were stably maintained during daily serial passage in glucose minimal medium (M9). When either of two E. coli-specific phages (T7 or T5) was added to the mixed culture, E. coli became extinct or was maintained at densities that were orders of magnitude lower than those before phage introduction, even though the E. coli densities with phage reached high levels when Salmonella was absent. In contrast, the addition of a phage that attacked only Salmonella (SP6) led to transient decreases in the bacterial number whether E. coli was absent or present. These results suggest that phages can sometimes, although not always, provide long-term suppression of target bacteria.
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Stephens, Colton R. A., Breanne M. McAmmond, Jonathan D. Van Hamme, Ken A. Otter, Matthew W. Reudink i Eric M. Bottos. "Analysis of bacterial communities associated with Mountain Chickadees (Poecile gambeli) across urban and rural habitats". Canadian Journal of Microbiology 67, nr 8 (sierpień 2021): 572–83. http://dx.doi.org/10.1139/cjm-2020-0320.
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Host-associated microbial communities play important roles in wildlife health, but these dynamics can be influenced by environmental factors. Urbanization has numerous effects on wildlife; however, the degree to which wildlife-associated bacterial communities and potential bacterial pathogens vary across urban–rural/native habitat gradients remains largely unknown. We used 16S rRNA gene amplicon sequencing to examine bacterial communities found on Mountain Chickadee (Poecile gambeli) feathers and nests in urban and rural habitats. The feathers and nests in urban and rural sites had similar abundances of major bacterial phyla and dominant genera with pathogenic members. However, richness of bacterial communities and potential pathogens on birds were higher in urban habitats, and potential pathogens accounted for some of the differences in bacterial occurrence between urban and rural environments. We predicted habitat using potential pathogen occurrence with a 90% success rate for feather bacteria, and a 72.2% success rate for nest bacteria, suggesting an influence of urban environments on the presence of potential pathogens. We additionally observed similarities in bacterial communities between nests and their occupants, suggesting bacterial transmission between them. These findings improve our understanding of the bacterial communities associated with urban wildlife and suggest that urbanization impacts the composition of wildlife-associated bacterial communities.
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Dionisio, Francisco, Ivan Matic, Miroslav Radman, Olivia R. Rodrigues i François Taddei. "Plasmids Spread Very Fast in Heterogeneous Bacterial Communities". Genetics 162, nr 4 (1.12.2002): 1525–32. http://dx.doi.org/10.1093/genetics/162.4.1525.
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Abstract Conjugative plasmids can mediate gene transfer between bacterial taxa in diverse environments. The ability to donate the F-type conjugative plasmid R1 greatly varies among enteric bacteria due to the interaction of the system that represses sex-pili formations (products of finOP) of plasmids already harbored by a bacterial strain with those of the R1 plasmid. The presence of efficient donors in heterogeneous bacterial populations can accelerate plasmid transfer and can spread by several orders of magnitude. Such donors allow millions of other bacteria to acquire the plasmid in a matter of days whereas, in the absence of such strains, plasmid dissemination would take years. This “amplification effect” could have an impact on the evolution of bacterial pathogens that exist in heterogeneous bacterial communities because conjugative plasmids can carry virulence or antibiotic-resistance genes.
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Montalvo, Naomi F., i Russell T. Hill. "Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts". Applied and Environmental Microbiology 77, nr 20 (19.08.2011): 7207–16. http://dx.doi.org/10.1128/aem.05285-11.
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ABSTRACTThe giant barrel spongesXestospongiamutaandXestospongiatestudinariaare ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences fromX.mutaandX.testudinariashowed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the twoXestospongiaspecies, as well as sequences found also in other sponge species and are dominated by three bacterial groups,Chloroflexi,Acidobacteria, andActinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the twoXestospongiaspecies, and also with the genusXestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.
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Wade, W. G., i E. M. Prosdocimi. "Profiling of Oral Bacterial Communities". Journal of Dental Research 99, nr 6 (14.04.2020): 621–29. http://dx.doi.org/10.1177/0022034520914594.
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The profiling of bacterial communities by the sequencing of housekeeping genes such as that encoding the small subunit ribosomal RNA has revealed the extensive diversity of bacterial life on earth. Standard protocols have been developed and are widely used for this application, but individual habitats may require modification of methods. This review discusses the sequencing and analysis methods most appropriate for the study of the bacterial component of the human oral microbiota. If possible, DNA should be extracted from samples soon after collection. If samples have to be stored for practical reasons, precautions to avoid DNA degradation on freezing should be taken. A critical aspect of profiling oral bacterial communities is the choice of region of the 16S rRNA gene for sequencing. The V1-V2 region provides the best discrimination between species of the genus Streptococcus, the most common genus in the mouth and important in health and disease. The MiSeq platform is most commonly used for sequencing, but long-read technologies are now becoming available that should improve the resolution of analyses. There are a variety of well-established data analysis pipelines available, including mothur and QIIME, which identify sequence reads as phylotypes by comparing them to reference data sets or grouping them into operational taxonomic units. DADA2 has improved sequence error correction capabilities and resolves reads to unique variants. Two curated oral 16S rRNA databases are available: HOMD and CORE. Expert interpretation of community profiles is required, both to detect the presence of contaminating DNA, which is commonly present in the reagents used in analysis, and to differentiate oral and nonoral bacteria and determine the significance of findings. Despite advances in shotgun whole-genome metagenomic methods, oral bacterial community profiling via 16S rRNA sequence analysis remains a valuable technique for the characterization of oral bacterial populations.
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Bates, Scott T., Garrett W. G. Cropsey, J. Gregory Caporaso, Rob Knight i Noah Fierer. "Bacterial Communities Associated with the Lichen Symbiosis". Applied and Environmental Microbiology 77, nr 4 (17.12.2010): 1309–14. http://dx.doi.org/10.1128/aem.02257-10.
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ABSTRACTLichens are commonly described as a mutualistic symbiosis between fungi and “algae” (ChlorophytaorCyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated byAlphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associatedRhizobialeslineage (LAR1; putative N2fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N2fixers (e.g.,Azospirillum,Bradyrhizobium, andFrankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses.
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Guo, Yufang. "Bacterial communities by design". Nature Food 3, nr 5 (maj 2022): 303. http://dx.doi.org/10.1038/s43016-022-00527-6.
Pełny tekst źródłaRozprawy doktorskie na temat "Bacterial communities"
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Jayaswal, Gaurav. "Spatial confinement of bacterial communities". Doctoral thesis, Università degli studi di Padova, 2015. http://hdl.handle.net/11577/3423866.
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The subject of bacterial swimming has intrigued scientists for decades and recently there has been a growing interest in the study of collective swimming behavior of bacteria in a confined geometry. This thesis deals with a systematic experimental investigation of the density distribution of bacterial solutions of different concentration.
Two different types of bacteria, Pseudomonas and E. coli, have been used owing to their diverse propelling mechanism. E. coli behavior has been studied in detail, instead there are no reports in the literature regarding Pseudomonas, to the best of our knowledge.
The experimental set up consisted of two glass plates separated by spacers which define the confinement region. The separation distance ranged from 100 to 250 microns. The two plates were functionalized with bovine serum albumin (BSA) to avoid bacterial adhesion to the glass. The bacterial suspension was subjected to adjustment of buoyancy by addition of a density matching fluid like Percoll.
In agreement with previous studies, we found a significant enhancement of density close to the walls for both bacteria. This effect does not seem to be affected by either the separation distance or the solution concentration. These results were compared with those obtained by numerical simulations of self-propelled rod like particles which do not interact with each other apart from steric interactions. The preliminary data support the experimental outcome suggesting that steric interactions alone are sufficient to produce the observed enhancement effect.Il moto di batteri ha attratto gli scienziati da decenni e, ultimamente, c’è stato un crescente interesse nello studio del moto collettivo di batteri in geometrie confinate. Questa tesi descrive uno studio sperimentale della distribuzione di densità di soluzioni di batteri di concentrazione diversa confinate tra due pareti parallele. Si sono usati due tipi di batteri, Pseudomonas ed E. coli, che presentano diversi meccanismi di propulsione. Il comportamento di E. coli è stato studiato in dettaglio, invece non ci sono lavori in letteratura riguardanti Pseudomonas, per quello che sappiamo. L’apparato sperimentale consisteva di due vetrini separati da spaziatori che definivano la regione confinante. La distanza di separazione variava da 100 a 250 micron. I due vetrini erano funzionalizzati con albumina di serio bovino per evitare l’adesione dei batteri al vetro. Alla sospensione era stato aggiunto del percoll per aggiustare la spinta idrostatica agente sui batteri. In accordo con precedenti studi, abbiamo trovato un significativo aumento di densità in prossimità delle pareti per entrambi i tipi di batteri. Questo effetto non sembra essere influenzato né dalla distanza di separazione, né dalla concentrazione della soluzione. Questi risultati sono stati confrontati con quelli ottenuti da simulazioni numeriche di particelle auto-propellenti c he interagiscono solo mediante interazioni steriche. I dati preliminari supportano l’osservazione sperimentale suggerendo che le sole interazioni steriche sono sufficienti a produrre addensamento dei batteri alle pareti.
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Benskin, Clare McWilliam Haldane. "Bacterial communities in the avian gut". Thesis, Lancaster University, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.539637.
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Fidalgo, Cátia Isabel Assis. "Endophytic bacterial communities of Halimione portulacoides". Doctoral thesis, Universidade de Aveiro, 2017. http://hdl.handle.net/10773/22661.
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Doutoramento BiologiaOs sapais são ecossistemas marinhos altamente produtivos que frequentemente recebem contaminantes de natureza antropogénica. A Ria de Aveiro encontra-se no noroeste de Portugal e contém numerosos sapais. Halimione portulacoides é um dos halófitos mais importantes em sapais Europeus e tem sido amplamente estudada devido ao seu potencial para ser usada em fins de fitorremediação, e como bioindicador de contaminação de sedimentos. Bactérias endofíticas podem apresentar capacidade promotora do crescimento de plantas (PCP), quer diretamente por produção de fito-hormonas e aquisição de nutrientes, quer indiretamente via competição com fitopatogenos. No presente trabalho, a diversidade de bactérias endofíticas da planta de sapal H. portulacoides da Ria de Aveiro é explorada extensivamente. Isolados de bactérias endofíticas foram obtidos e caracterizados quanto à sua taxonomia, capacidade de produzir enzimas e características PCP. As características mais observadas foram atividade celulolítica, xilanolítica e desaminase de 1-aminociclopropano-1-carboxilato, e a produção da auxina ácido indol-3-acético. Os resultados revelaram um enorme potencial da coleção para PCP in vitro e in vivo. A coleção de isolados foi também explorada para procurar diversidade não descrita. Como resultado, dez novas espécies de bactérias foram amplamente caracterizadas e descritas: Microbacterium diaminobutyricum, Saccharospirillum correiae, Altererythrobacter halimionae, Altererythrobacter endophyticus, Zunongwangia endophytica, Salinicola halimionae, Salinicola aestuarina, Salinicola endophytica, Salinicola halophytica e Salinicola lusitana. Consequentemente, o presente trabalho expôs a endosfera de H. portulacoides como um foco de diversidade bacteriana desconhecida. A composição taxonómica da comunidade endofítica foi averiguada via sequenciação do gene 16S rRNA da coleção de isolados, e mais profundamente com a utilização de sequenciação de alto rendimento independente do cultivo. A última abordagem revelou cinco filos principais: Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes e Firmicutes. Destes, apenas Planctomycetes não foi obtido na coleção de isolados. As comunidades diferiram de acordo com o local (no ensaio dependente do cultivo, para locais contaminados e não-contaminado) e tecido (em ambos os ensaios) de amostragem. As principais famílias obtidas no endofitoma nuclear foram Oceanospirillaceae em tecidos de parte aérea, e Enterobacteriaceae e Kiloniellaceae em tecidos de raiz. O trabalho apresentado providenciou uma compreensão profunda das bactérias endofíticas presentes no halófito H. portulacoides, e expôs o seu potencial como foco de bactérias não descritas e bactérias promotoras do crescimento de plantas.
Salt marshes are highly productive marine ecosystems that often act as a sink for contaminants of anthropogenic nature. The Ria de Aveiro lagoon is located in the north-west of Portugal and comprises numerous salt marshes. Halimione portulacoides is one of the most important halophytes in European salt marshes and has been widely researched for its potential for phytoremediation, and as a bioindicator of sediment contamination. Endophytic bacteria can present plant growth promotion (PGP) abilities, either directly by production of phytohormones and nutrient uptake, or indirectly via competition with phytopathogens. In the present work, the diversity of endophytic bacteria from the salt marsh plant H. portulacoides from Ria de Aveiro is extensively explored. Endophytic bacterial isolates were obtained and characterized for their taxonomy, ability to produce specific enzymes and PGP traits. The most observed traits were cellulolytic, xylanolytic and 1-aminocyclopropane-1-carboxylate deaminase activities, and the production of the auxin indol-3-acetic acid. The results revealed an enormous potential of the collection for in vitro and in vivo PGP. The collection of isolates was also explored for undescribed diversity. As a result, ten novel bacterial species were thoroughly characterized and described: Microbacterium diaminobutyricum, Saccharospirillum correiae, Altererythrobacter halimionae, Altererythrobacter endophyticus, Zunongwangia endophytica, Salinicola halimionae, Salinicola aestuarina, Salinicola endophytica, Salinicola halophytica and Salinicola lusitana. Consequently, the present work exposes the endosphere of H. portulacoides as a hotspot of unknown bacterial diversity. The taxonomic composition of the endophytic community was assessed via 16S rRNA gene sequencing of the isolate collection, and with more depth using culture-independent high-throughput sequencing. The latter approach revealed five main phyla: Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes and Firmicutes. From these, only Planctomycetes was not obtained in the isolate collection. The communities differed according to sampling site (for the culture-dependent assay, for contaminated and non-contaminated sites) and tissue (in both assays). The main families found in the core endophytome were Oceanospirillaceae for aboveground tissues, and Enterobacteriaceae and Kiloniellaceae for belowground tissues. The present work provided a deep understanding of the endophytic bacteria present in the halophyte H. portulacoides, and exposed its potential as a hotspot of undescribed bacteria and plant growth promoting bacteria.
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Riddell, Andrew. "Characterisation of bacterial communities within chronic wounds". Thesis, Cardiff University, 2012. http://orca.cf.ac.uk/41930/.
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Chronic wounds are a rapidly growing clinical problem across the world, expensive to healthcare systems and severely injurious to the quality of life of those affected. Such wounds have been shown to contain bacteria within biofilms which can be difficult to identify and treat, and are implicated in the lack of healing. The aim of this study was to improve our understanding of the characterisation of these bacterial communities within chronic wounds. This was achieved through the collection of 18 unique chronic wound samples of various phenotypes and 9 acute wound samples. The two bacterial species, Staphylococcus .aureus and Pseudomonas. aeruginosa, most commonly isolated from chronic wounds and known to be prolific biofilm formers and formidable human pathogens were the focus of this study. Both PCR and culture demonstrated the presence of one or both species in all chronic wound samples and the presence of S. aureus in some acute samples. Novel monoclonal antibodies were developed to TNase (of S.aureus) and LPS (of P. aeruginosa) and their ability to detect the bacteria in vitro in a simulated chronic wound environment was evaluated. The action of these monoclonal antibodies were calibrated and evaluated through the use of fluorescent microscopy, and direct and competition ELISA. Following this biofilms of S.aureus and P. aeruginosa both single species and mixed were evaluated utilising Peptide Nucleic Acid Flourescent In Situ Hybridisation, and the Confocal Laser Scanning Microscope to demonstrate the architecture of the biofilms produced and the locations of the bacteria within the biofilm. Microbiologically using both culture and PCR, the widespread presence of S. aureus and P. aeruginosa throughout human chronic wound samples was demonstrated. The ELISA and fluorescent microscopy illustrated the feasibility of MABs as a rapid and accurate detection system for identifying bacteria within chronic wounds. The PNA FISH accurately identified individual species in mixed biofilms through multiplex staining. It also visually demonstrated the tissue invasion of S. aureus, adhesive properties of P. aeruginosa and the synergy of these virulence factors in mixed biofilms. This study has met its aims in that it has provided further evidence of techniques which could be successfully applied to rapidly identify bacteria within a chronic wound environment, and to characterise the structure and composition of bacterial biofilms formed within these wounds. It provides a basis for the development of future clinically relevant rapid bacterial detection systems, and for the academic study of bacteria within the biofilm phenotype.
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Co, Julia Yin-Ting. "The influence of mucins on bacterial communities". Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/99569.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2015.Cataloged from PDF version of thesis.
Includes bibliographical references.
Mucus is the hydrogel layer that coats all wet epithelia in the body. By supporting commensal microbes and preventing pathogenic invasion, mucus maintains host-microbe homeostasis. Mucin polymers, the primary gel-forming component of mucus, are an important mediator of mucus-microbe interactions. In this thesis, I demonstrate that mucins impact bacterial communities in their physical structure as well as microbe-microbe and microbe-host dynamics. In Chapter 2, 1 study the ability of mucin surface coatings to suppress bacterial surface attachment, the first step in biofilm formation, for Streptococcus pneumoniae and Staphylococcus aureus. Mucin-bound glycans were identified as a critical structural component of mucin coatings that are necessary for bacterial repulsion. In Chapter 3, 1 investigate how mucins impact established Pseudomonas aeruginosa biofilms. The data reveal that mucins cause disassembly and structural rearrangement in P. aeruginosa biofilms in a mucin concentration and flow rate dependent manner. In Appendix A, I show evidence for the involvement of the bacterial flagella in mucinmediated biofilm disruption. Deletion of flagellar capfliD or flagellar stators motABCD results in biofilms that are resistant to mucin-mediated dissociation. In Appendix B, I examine how mucins affect dual-species bacterial communities. I show that mucins promote S. aureus survival during co-culture with P. aeruginosa and also suppress the anti-staphylococcal effects of P. aeruginosa pyocyanin. In Appendix C, I explore the impacts of mucins on P. aeruginosa quorum sensing, an important pathogenic determinant in P. aeruginosa infections. I found that mucins suppress the expression of P. aeruginosa Las and Rhl quorum sensing genes as well as downstream virulence factors. In Appendix D, I assess how mucins modulate P. aeruginosa-epithelium interactions. The data show that mucins hinder the ability of P. aeruginosa to attach to epithelial cells in vitro. Additionally, mucins suppressed P. aeruginosa-associatede pithelial cytotoxicity in a mucin concentration dependent manner. Together, this thesis demonstrates that mucins modulate microbial communities in their behavior and interactions. Understanding how mucus and mucins impact microbes provides insight to host-microbe relationships, as well as for the development of novel bacteria-regulating strategies.
by Julia Yin-Ting Co.
Ph. D.
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Kanso, Sungwan, i n/a. "Molecular Studies of Bacterial Communities in the Great Artesian Basin Aquifers". Griffith University. School of Biomolecular and Biomedical Science, 2004. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20040219.140509.
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16S rRNA gene analysis has shown that bacterial diversity in the GAB bores studied was limited to the genera Hydrogenobacter in the phylum Aquificae, Thermus in the phylum Deinococcus-Thermus, Desulfotomaculum in the phylum Firmicutes, the alpha-, beta- and gamma-classes of the phylum Proteobacteria and the phylum Nitrospirae. There was no clone closely related to members of the delta-proteobacteria and epsilon-proteobacteria classes detected. The number of bacterial strains directly isolated from the Fairlea and the Cooinda bores were far less than the numbers of distinctive phylotypes detected by the 16S rRNA gene characterisation. In addition none of the bacterial strains directly isolated from the water samples were represented in the 16S rRNA gene clone libraries. Similar discrepancies between the bacterial populations obtained from the 16S rRNA gene analysis and those obtained from direct isolation have been reported in the literature (Dunbar et al., 1999; Kampfer et al., 1996; Suzuki et al., 1997; Ward et al., 1998; Ward et al., 1997). However, in general, the phyla with which the isolates were affiliated were the same as those phyla to which the clones belonged. The environmental changes introduced (by bringing the artesian water up to the surface and exposing it to four types of metal coupons made of carbon steels identified by codes ASTM-A53B, ASTM-A53, AS-1074 and AS-1396 and commonly used in bore casings) led to changes in the bacterial community structures. In general, the species which proliferated in the communities before and after the changes were different. The diversity of the bacterial species in the community decreased following the environmental changes. Clones dominating the clone libraries constructed from newly established bacterial communities also differed from the clones dominating the libraries constructed from the bacterial communities which had existed naturally in the bores. These trends toward change in the bacterial communities were observed at both the Fairlea and the Cooinda bore sites. All four metal types incubated in the Fairlea bore water lost between 3.4 and 4.7% of their original weight. In contrast none of the metals incubated in Cooinda bore water lost weight. Clone library A1 showed that the natural population of the Fairlea bore was dominated by clone A1-3, which represented a novel species related to the isolate boom-7m-04. But after metal incubation (and recording of the metal weight loss), the bacterial community was dominated by clone PKA34B, which has a 95% similarity in its 16S rRNA gene sequence with Desulfotomaculum putei. Desulfotomaculum species are known to cause metal corrosion due to their byproduct H2S. But the low level of phylogenetic relatedness found does not provide enough information to speculate on whether the species represented by clone PKA34B is a member of the genus Desulfotomaculum or not. However, the fact that clone PKA34B dominated the PKA clone library by 50% makes the species it represents a suspected candidate likely to be involved with the metal weight loss at the Fairlea bore. In contrast, clone library 4381 showed that the natural population of the Cooinda bore was dominated by clone 4381-15 representing a species distantly related to a hydrogen oxidiser Hydrogenophaga flava (95% similarity). The dominating clone of the new community formed after metal incubation was clone COO25, which has 99% similarity with Thermus species that have not been reported to be involved with metal corrosion to my knowledge. In this project detection, identification and comparative quantification by 16S rRNA gene-targeted PCR probing with probes 23B and 34B were successfully developed for a Leptothrix-like species and for a Desulfotomaculum-like species represented by clones PKA23B and PKA34B respectively. This method of probing permits a fast, sensitive and reproducible detection, identification and at least a comparative quantification of the bacteria in the environment without the need for culturing. Therefore it is extremely suitable for use in bacterial population monitoring. PCR probing with the 34B probe has a potential commercial use as a means of screening for bores with a potential high risk of corrosion due to this Desulfotomaculum-like species. Direct isolation of bacteria from the GAB water has resulted in the isolation of seven strains from the Fairlea bore and eight from the Cooinda bore. Among these isolates, three novel strains were studied in detail. Reports on the characterisation of strain FaiI4T (T=Type strain) from the Fairlea bore (Kanso & Patel, 2003) and strain CooI3BT from the Cooinda bore have been published (Kanso et al., 2002). The data generated during this project add to our current information and extend our knowledge about the bacterial communities of the GAB's sub-surface environment. This information will provide a basis for further ecological studies of the GAB. Studies on involvement of certain groups of bacteria with the corrosion of metals used in bore casings could provide a foundation for further studies to develop maintenance and managing strategies for the GAB bores.
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Kanso, Sungwan. "Molecular Studies of Bacterial Communities in the Great Artesian Basin Aquifers". Thesis, Griffith University, 2004. http://hdl.handle.net/10072/366613.
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16S rRNA gene analysis has shown that bacterial diversity in the GAB bores studied was limited to the genera Hydrogenobacter in the phylum Aquificae, Thermus in the phylum Deinococcus-Thermus, Desulfotomaculum in the phylum Firmicutes, the alpha-, beta- and gamma-classes of the phylum Proteobacteria and the phylum Nitrospirae. There was no clone closely related to members of the delta-proteobacteria and epsilon-proteobacteria classes detected. The number of bacterial strains directly isolated from the Fairlea and the Cooinda bores were far less than the numbers of distinctive phylotypes detected by the 16S rRNA gene characterisation. In addition none of the bacterial strains directly isolated from the water samples were represented in the 16S rRNA gene clone libraries. Similar discrepancies between the bacterial populations obtained from the 16S rRNA gene analysis and those obtained from direct isolation have been reported in the literature (Dunbar et al., 1999; Kampfer et al., 1996; Suzuki et al., 1997; Ward et al., 1998; Ward et al., 1997). However, in general, the phyla with which the isolates were affiliated were the same as those phyla to which the clones belonged. The environmental changes introduced (by bringing the artesian water up to the surface and exposing it to four types of metal coupons made of carbon steels identified by codes ASTM-A53B, ASTM-A53, AS-1074 and AS-1396 and commonly used in bore casings) led to changes in the bacterial community structures. In general, the species which proliferated in the communities before and after the changes were different. The diversity of the bacterial species in the community decreased following the environmental changes. Clones dominating the clone libraries constructed from newly established bacterial communities also differed from the clones dominating the libraries constructed from the bacterial communities which had existed naturally in the bores. These trends toward change in the bacterial communities were observed at both the Fairlea and the Cooinda bore sites. All four metal types incubated in the Fairlea bore water lost between 3.4 and 4.7% of their original weight. In contrast none of the metals incubated in Cooinda bore water lost weight. Clone library A1 showed that the natural population of the Fairlea bore was dominated by clone A1-3, which represented a novel species related to the isolate boom-7m-04. But after metal incubation (and recording of the metal weight loss), the bacterial community was dominated by clone PKA34B, which has a 95% similarity in its 16S rRNA gene sequence with Desulfotomaculum putei. Desulfotomaculum species are known to cause metal corrosion due to their byproduct H2S. But the low level of phylogenetic relatedness found does not provide enough information to speculate on whether the species represented by clone PKA34B is a member of the genus Desulfotomaculum or not. However, the fact that clone PKA34B dominated the PKA clone library by 50% makes the species it represents a suspected candidate likely to be involved with the metal weight loss at the Fairlea bore. In contrast, clone library 4381 showed that the natural population of the Cooinda bore was dominated by clone 4381-15 representing a species distantly related to a hydrogen oxidiser Hydrogenophaga flava (95% similarity). The dominating clone of the new community formed after metal incubation was clone COO25, which has 99% similarity with Thermus species that have not been reported to be involved with metal corrosion to my knowledge. In this project detection, identification and comparative quantification by 16S rRNA gene-targeted PCR probing with probes 23B and 34B were successfully developed for a Leptothrix-like species and for a Desulfotomaculum-like species represented by clones PKA23B and PKA34B respectively. This method of probing permits a fast, sensitive and reproducible detection, identification and at least a comparative quantification of the bacteria in the environment without the need for culturing. Therefore it is extremely suitable for use in bacterial population monitoring. PCR probing with the 34B probe has a potential commercial use as a means of screening for bores with a potential high risk of corrosion due to this Desulfotomaculum-like species. Direct isolation of bacteria from the GAB water has resulted in the isolation of seven strains from the Fairlea bore and eight from the Cooinda bore. Among these isolates, three novel strains were studied in detail. Reports on the characterisation of strain FaiI4T (T=Type strain) from the Fairlea bore (Kanso & Patel, 2003) and strain CooI3BT from the Cooinda bore have been published (Kanso et al., 2002). The data generated during this project add to our current information and extend our knowledge about the bacterial communities of the GAB's sub-surface environment. This information will provide a basis for further ecological studies of the GAB. Studies on involvement of certain groups of bacteria with the corrosion of metals used in bore casings could provide a foundation for further studies to develop maintenance and managing strategies for the GAB bores.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Biomedical Sciences
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Rodriguez, Caballero Adrian. "STUDY OF BACTERIAL COMMUNITIES : – A WASTEWATER TREATMENT PERSPECTIVE". Licentiate thesis, Mälardalens högskola, Akademin för hållbar samhälls- och teknikutveckling, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:mdh:diva-11884.
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In this thesis, the application of molecular microbiology methods to understand wastewater treatment bio-reactions is described. Two different wastewater treatment systems were chosen for the experimental work. Firstly; the activated sludge processes at two different facilities in Sweden (Västerås and Eskilstuna) were investigated and compared in a context where low temperatures can affect the efficiency of the nitrogen removal performance in terms of nitrification. Initially, fluorescence in situ hybridization (FISH) was utilised in order to quantify some of the species involved in ammonia and nitrite oxidation at Västerås, providing information on how the different communities react to decreasing temperatures. Then, the polymerase chain reaction (PCR), cloning-sequencing method was employed in order to study the composition of the ammonia oxidizing bacteria (AOB) community at the same two wastewater treatment plants (WWTPs). Secondly; the potential use of constructed wetlands for the treatment of winery wastewater was studied. High ethanol concentration artificial wastewater with and without inorganic nutrients (nitrates and phosphates) was fed in a set of pilot-scale constructed wetlands. Pollutant removal performance and enzyme activity tests were carried out. Additionally, the bacterial community structure was investigated by means of denaturing gradient gel electrophoresis (DGGE). In the first set of studies it was shown that the AOB population which plays a major role in nitrifying reactors presented a seasonal shift and a higher diversity at Västerås during winter time, while the nitrification performance maintained stable levels and the ammonia removal efficiency increased. Thus, the higher ammonia removal efficiency at Västerås could be related to the diversity of the AOB population composition. Lastly, when constructed wetlands were in focus, the differential effects of ethanol and nutrients over the chemical oxygen demand (COD) removal performance were proven. In fact, the addition of nutrients on one of the experimental wetlands increased the COD (ethanol) removal and supported the maintenance of a bacterial population similar to the control wetland (no ethanol added). In conclusion, both studies proved a strong relationship between process performance (pollution removal) and the dynamics of the bacterial communities involved.
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Haglund, Ann-Louise. "Attached Bacterial Communities in Lakes – Habitat-Specific Differences". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4627.
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Beeton, S. "Biotransformation of T-2 toxin by bacterial communities". Thesis, University of Kent, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234437.
Pełny tekst źródłaKsiążki na temat "Bacterial communities"
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Klepac-Ceraj, Vanja. Diversity and phylogenetic structure of two complex marine microbial communities. Ft. Belvoir: Defense Technical Information Center, 2004.
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Microbiology, American Society for, red. Oral microbial communities: Genomic inquiry and interspecies communication. Washington, DC: ASM Press, 2011.
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Nyberg, Karin. Impact of organic waste residues on structure and function of soil bacterial communities with emphasis on ammonia oxidizing bacteria. Uppsala: Swedish University of Agricultural Sciences, 2006.
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D, Allsopp, Colwell Rita R. 1934- i Hawksworth D. L, red. Microbial diversity and ecosystem function: Proceedings of the IUBS/IUMS workshop held at Egham, UK, 10-13 August 1993 in support of the IUBS/UNESCO/SCOPE "DIVERSITAS" programme. Wallingford, Oxon, UK: CAB International, in association with United Nations Environment Programme, 1995.
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Santelli, Cara M. Promotion of Mn(II) oxidation and remediation of coal mine drainage in passive treatment systems by diverse fungal and bacterial communities. [Washington]: American Society for Microbiology, 2010.
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Exploring denitrifying communities in the environment. Uppsala: Swedish University of Agricultural Sciences, 2006.
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Rosenberg, Eugene. The Prokaryotes: Prokaryotic Communities and Ecophysiology. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013.
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Braddock, Joan F. Petroleum hydrocarbon-degrading microbial communities in Beaufort-Chukchi Sea sediments. Fairbanks, AK: Coastal Marine Institute, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2004.
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Braddock, Joan F. Petroleum hydrocarbon-degrading microbial communities in Beaufort-Chukchi Sea sediments. Fairbanks, AK: Coastal Marine Institute, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2004.
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Polar microbiology: The ecology, biodiversity, and bioremediation potential of microorganisms in extremely cold environments. Boca Raton: Taylor & Francis, 2010.
Znajdź pełny tekst źródłaCzęści książek na temat "Bacterial communities"
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Friedrich, Michael W. "Bacterial Communities on Macroalgae". W Ecological Studies, 189–201. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-28451-9_10.
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Bourne, David G., i Nicole S. Webster. "Coral Reef Bacterial Communities". W The Prokaryotes, 163–87. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-30123-0_48.
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Caldwell, Douglas E., Gideon M. Wolfaardt, Darren R. Korber i John R. Lawrence. "Do Bacterial Communities Transcend Darwinism?" W Advances in Microbial Ecology, 105–91. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4757-9074-0_4.
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Hattori, Tsutomu, Hisayuki Mitsui, Reiko Hattori, Shuichi Shikano, Krystyna Gorlach, Yasuhiro Kasahara i Adel El-Beltagy. "Analysis of the Bacterial Community according to Colony Development on Solid Medium". W Microbial Communities, 229–35. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60694-6_21.
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van Verseveld, Henk W., Wilfred F. M. Röling, Diman van Rossum, Anniet M. Laverman, Stef van Dijck, Martin Braster i Fred C. Boogerd. "Phenetic and Genetic Analyses of Bacterial Populations in Fermented Food and Environmental Samples". W Microbial Communities, 19–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60694-6_3.
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Cerone, Antonio, i Enrico Marsili. "A Formal Model for the Simulation and Analysis of Early Biofilm Formation". W From Data to Models and Back, 134–51. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-70650-0_9.
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AbstractBiofilms are structured communities of bacterial cells adherent to a surface. This bacterial state is called sessile.This paper focuses on the modelling of the transition between planktonic and sessile state using Real-time Maude as the modelling language. With more and more bacteria joining the sessile community, the likelihood of producing a biofilm increases. Once the percentage of bacterial cells that adheres to the surface reaches a threshold, which is specific for the considered bacterium species, a permanent biofilm is formed. An important challenge is to predict the time needed for the formation of a biofilm on a specific surface, in order to plan when the material infrastructure that comprises such a surface needs to be cleaned or replaced. We exploit the model-checking features of Real-time Maude to formally prove that a regular cleaning or replacement of the infrastructure prevents the biofilm formation.
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Wünsche, Lothar, C. Härtig, H. O. Pucci i W. Babel. "Combined Application of Biolog and MIS/SHERLOCK for Identifying Bacterial Isolates from Hydrocarbon-polluted Argentinian Soils". W Microbial Communities, 49–56. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60694-6_5.
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Manapure, Abha, Raghvendra Pratap Singh i Alok R. Rai. "Bacterial Community Composition Dynamics in Rice Rhizosphere: A Metagenomic Approaches". W Microbes in Microbial Communities, 133–52. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-5617-0_6.
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Xie, Hua, i Richard J. Lamont. "Bacterial Peptides Targeting Periodontal Pathogens in Communities". W Emerging Therapies in Periodontics, 175–86. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-42990-4_11.
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Freilich, Shiri, i Eytan Ruppin. "Toward the Educated Design of Bacterial Communities". W Beneficial Microorganisms in Multicellular Life Forms, 177–88. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21680-0_12.
Pełny tekst źródłaStreszczenia konferencji na temat "Bacterial communities"
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Ashlock, Daniel, i Andrew McEachern. "A simulation of bacterial communities". W 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology - Part of 17273 - 2011 Ssci. IEEE, 2011. http://dx.doi.org/10.1109/cibcb.2011.5948465.
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Radojević, Ivana, Aleksandar Ostojić i Nenad Stefanović. "APPLICATION OF DATA MINING IN THE ECOLOGICAL ANALYSIS OF THE IMPACT OF BACTERIAL COMMUNITIES IN DIFFERENT RESERVOIRS". W 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.186r.
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Using data mining techniques, this study analyzes the influence and dependance of bacterial communities that are determined in routine monitoring of open water quality status, such as heterotrophic bacteria (psychrophiles and mesophiles). The SeLaR database was used, which, in addition to various studies of integrated data related to the reservoirs of Serbia, is the basis for advanced data analysis – utilizing statistical methods and data mining. Data for reservoirs with different morphometric qualities, different positions, trophic status, and dominant bacterial community were analyzed. In this research, classification, and analysis of influential parameters, as well as scenario analysis was applied. The results indicate that a designed data mining system can analyze the state and influence of bacterial communities with different parameters that are determined both in standard routine analysis, and in some more specialized studies. This study showed that designed data mining system can serve as flexible, effective, and practical tool for monitoring water quality using bacterial communities in reservoirs.
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Radojević, Ivana, Aleksandar Ostojić i Vesna Ranković. "Ecological applications based on bacterial community abundance in reservoirs using an artificial neural network approach". W 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.317r.
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The objective of this study is to analyze the influence and predict abundance the heterotrophic bacteria (psychrophile; mesophile) and facultative oligotrophic bacteria as a reflection of ecological relationships in reservoirs and water quality. We used artificial neural networks (ANNs) to develop models based on input variables derived from two different reservoirs. The neural network models were developed using experimental data which is collected for ten years. Although reservoirs have a different position, different morphometric qualities, trophic state and dominant bacterial community there is a possibility of predicting these bacterial communities with the same input parameters. Comparing the modeled values by ANN with the experimental data indicates that neural network models provide accurate results. The important conclusion of this work is that ANNs can provide a flexible and applicable tool in monitoring water quality across bacterial communities in reservoirs.
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Yin, Chuntao. "Disease-induced changes in the rhizosphere microbiome reduced root disease". W IS-MPMI Congress. IS-MPMI, 2023. http://dx.doi.org/10.1094/ismpmi-2023-5r.
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Rhizosphere microbiota, referred to as the second genome of plants, are crucial to plant health. Increasing evidence reveals that plants can change their rhizosphere microbiome and promote microbial activity to reduce plant disease. However, how plant and phytopathogens factor in combination to structure the rhizosphere microbiome and govern microbial selection for adaptation to disease stress remains incompletely understood. In this study, rhizosphere microbiota from successive wheat plantings under the pressure of the soilborne pathogen Rhizoctonia solani AG8 were characterized. Amplicon sequence analyses revealed that bacterial and fungal communities clustered by planting cycles. The addition of AG8 enhanced the separation of the rhizosphere microbiota. The alpha diversity of bacteria and fungi significantly decreased over planting cycles. Compared with rhizosphere bacterial communities, AG8 was a major driver structuring fungal communities. Pathogen-infected monocultures enriched a group of bacterial genera with potential antagonistic activities or abilities for plant growth promotion or nitrogen fixation. Further, eleven bacterial species exhibited antagonistic activities toward Rhizoctonia spp., and four of them displayed broad antagonism against multiple soilborne fungal pathogens. These findings support the potential to improve plant health through manipulating rhizosphere microbiota.
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Bray, J., J. C. Joaquin, G. Brelles-Marino i N. Abramzon. "Destruction of Bacterial Communities using Gas Discharge Plasma." W IEEE Conference Record - Abstracts. 2005 IEEE International Conference on Plasma Science. IEEE, 2005. http://dx.doi.org/10.1109/plasma.2005.359149.
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Nadeau, Jay, Randall Mielke i Samuel Clarke. "Quantum dot conjugates for SEM of bacterial communities". W SPIE Scanning Microscopy, redaktorzy Michael T. Postek, Dale E. Newbury, S. Frank Platek i David C. Joy. SPIE, 2009. http://dx.doi.org/10.1117/12.824201.
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Barani, Navid, i Kamal Sarabandi. "Theory of Electromagnetic-Based Communication within Bacterial Communities". W 2019 IEEE International Symposium on Antennas and Propagation and USNC-URSI Radio Science Meeting. IEEE, 2019. http://dx.doi.org/10.1109/apusncursinrsm.2019.8889323.
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Ragan, Regina, William J. Thrift, Antony S. Cabuslay i Allon I. Hochbaum. "Illuminating bacterial communities with plasmonic nanoantennas (Conference Presentation)". W Plasmonics: Design, Materials, Fabrication, Characterization, and Applications XVII, redaktorzy Takuo Tanaka i Din Ping Tsai. SPIE, 2019. http://dx.doi.org/10.1117/12.2535513.
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Ziganshina, E. E., i A. M. Ziganshin. "BACTERIAL DIVERSITY OF OILFIELD WATERS OF THE REPUBLIC OF TATARSTAN". W X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-79.
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Oilfield waters are characterized by distinct microbial communities due to several environmental factors. In this work, the bacterial diversity of oilfield water samples of the Republic of Tatarstan (Russia) was analyzed. The objects of research were bacterial cultures from formation and injection waters. The bacterial communities in oilfield waters were represented by members of the phyla Firmicutes, Proteobacteria and Actinobacteria.
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Lalinska-Volekova, Bronislava, Hana Majerova, Ivona Kautmanova, Tomas Farago, Dana Szaboova i Jana Brcekova. "MICROBIAL COMPOSITION OF NATURAL Fe OXYHYDROXIDES AND ITS INFLUENCE ON ARSENIC AND ANTIMONY SORPTION". W 22nd SGEM International Multidisciplinary Scientific GeoConference 2022. STEF92 Technology, 2022. http://dx.doi.org/10.5593/sgem2022/5.1/s20.037.
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The presented paper represents a comprehensive analysis of hydrous ferric oxides (HFOs) precipitated from Fe rich drainage waters contaminated by arsenic and antimony. Ochre samples from three abandoned Sb deposits were collected in three different seasons and were characterized from the mineralogical, geochemical, and microbiological point of view. They were formed mainly by poorly crystallized 2-line ferrihydrite, with the content of arsenic in samples ranging from 0.7 wt.% to 13 wt.% and content of antimony ranging from 0.025 wt.% up to 1.2 wt.%. Next-generation sequencing approach with 16S RNA, 18S RNA and ITS markers was used to characterize bacterial, fungal, algal, metazoal and protozoal communities occurring in the HFOs. In the 16S RNA, the analysis dominated bacteria (96.2 %) were mainly Proteobacteria (68.8 %) and Bacteroidetes (10.2 %) and to less extent also Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Nitrosprae and Chloroflexi. Alpha and beta diversity analysis revealed that the bacterial communities of individual sites do not differ significantly, and only subtle seasonal changes were observed. This study provides evidence of diverse microbial communities that exist in drainage waters and are highly important in the process of mobilization or immobilization of the potentially toxic elements.
Raporty organizacyjne na temat "Bacterial communities"
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DeLong, Edward F., i Alice L. Alldredge. Influence of Bacterial Communities on Particle Aggregation. Fort Belvoir, VA: Defense Technical Information Center, wrzesień 1997. http://dx.doi.org/10.21236/ada635364.
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Crowley, David E., Dror Minz i Yitzhak Hadar. Shaping Plant Beneficial Rhizosphere Communities. United States Department of Agriculture, lipiec 2013. http://dx.doi.org/10.32747/2013.7594387.bard.
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PGPR bacteria include taxonomically diverse bacterial species that function for improving plant mineral nutrition, stress tolerance, and disease suppression. A number of PGPR are being developed and commercialized as soil and seed inoculants, but to date, their interactions with resident bacterial populations are still poorly understood, and-almost nothing is known about the effects of soil management practices on their population size and activities. To this end, the original objectives of this research project were: 1) To examine microbial community interactions with plant-growth-promoting rhizobacteria (PGPR) and their plant hosts. 2) To explore the factors that affect PGPR population size and activity on plant root surfaces. In our original proposal, we initially prqposed the use oflow-resolution methods mainly involving the use of PCR-DGGE and PLFA profiles of community structure. However, early in the project we recognized that the methods for studying soil microbial communities were undergoing an exponential leap forward to much more high resolution methods using high-throughput sequencing. The application of these methods for studies on rhizosphere ecology thus became a central theme in these research project. Other related research by the US team focused on identifying PGPR bacterial strains and examining their effective population si~es that are required to enhance plant growth and on developing a simulation model that examines the process of root colonization. As summarized in the following report, we characterized the rhizosphere microbiome of four host plant species to determine the impact of the host (host signature effect) on resident versus active communities. Results of our studies showed a distinct plant host specific signature among wheat, maize, tomato and cucumber, based on the following three parameters: (I) each plant promoted the activity of a unique suite of soil bacterial populations; (2) significant variations were observed in the number and the degree of dominance of active populations; and (3)the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This research demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations. Based on the studies from the US team, we suggest that the effective population size PGPR should be maintained at approximately 105 cells per gram of rhizosphere soil in the zone of elongation to obtain plant growth promotion effects, but emphasize that it is critical to also consider differences in the activity based on DNA-RNA correspondence. The results ofthis research provide fundamental new insight into the composition ofthe bacterial communities associated with plant roots, and the factors that affect their abundance and activity on root surfaces. Virtually all PGPR are multifunctional and may be expected to have diverse levels of activity with respect to production of plant growth hormones (regulation of root growth and architecture), suppression of stress ethylene (increased tolerance to drought and salinity), production of siderophores and antibiotics (disease suppression), and solubilization of phosphorus. The application of transcriptome methods pioneered in our research will ultimately lead to better understanding of how management practices such as use of compost and soil inoculants can be used to improve plant yields, stress tolerance, and disease resistance. As we look to the future, the use of metagenomic techniques combined with quantitative methods including microarrays, and quantitative peR methods that target specific genes should allow us to better classify, monitor, and manage the plant rhizosphere to improve crop yields in agricultural ecosystems. In addition, expression of several genes in rhizospheres of both cucumber and whet roots were identified, including mostly housekeeping genes. Denitrification, chemotaxis and motility genes were preferentially expressed in wheat while in cucumber roots bacterial genes involved in catalase, a large set of polysaccharide degradation and assimilatory sulfate reduction genes were preferentially expressed.
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Weiss, Shimon. Inorganic voltage nanosensors for bioelectricity studies in bacterial communities. Office of Scientific and Technical Information (OSTI), wrzesień 2019. http://dx.doi.org/10.2172/2229451.
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Michel Jr., Frederick C., Harry A. J. Hoitink, Yitzhak Hadar i Dror Minz. Microbial Communities Active in Soil-Induced Systemic Plant Disease Resistance. United States Department of Agriculture, styczeń 2005. http://dx.doi.org/10.32747/2005.7586476.bard.
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Induced Systemic Resistance (ISR) is a highly variable property that can be induced by compost amendment of potting media and soils. For example, previous studies showed that only 1 of 79 potting mixes prepared with different batches of mature composts produced from several different types of solid wastes were able to suppress the severity of bacterial leaf spot of radish caused by Xanthomonas campestris pv. armoraciae compared with disease on plants produced in a nonamended sphagnum peat mix. In this project, microbial consortia in the rhizosphere of plants grown in ISR-active compost-amended substrates were characterized. The plants used included primarily cucumber but also tomato and radish. Rhizosphere microbial consortia were characterized using multiple molecular tools including DGGE (Israel) and T -RFLP (Ohio) in both ISR-active field plots and potting media. Universal as well as population-specific bacterial and fungal PCR primers were utilized. T -RFLP analyses using universal bacterial primers showed few significant differences in overall bacterial community composition in ISR-active and inactive substrates (Ohio). In addition, the community members which were significantly different varied when different ISR-activecomposts were used (Ohio). To better characterize the shifts in microbial community structure during the development of ISR, population specific molecular tools were developed (Israel, Ohio).-PCR primers were designed to detect and quantify bacterial groups including Pyrenomycetes, Bacillus, Pan toea, Pseudomonas, Xanthomonas and Streptomyces as well as Trichoderma and Fusarium; two groups of fungi that harbor isolates which are ISR active (Isreal and Ohio). Bacterial consortia associated with cucumber plants grown in compost-amended potting mixtures were shown to be dominated by the phylogenetic taxon Bacteroidetes, including members of the genus Chryseobacterium, which in some cases have been shown to be involved in biocontrol (Israel). Nested-PCR-DGGE analyses coupled with long l6S rDNA sequencing, demonstrated that the Chryseobacteriumspp. detected on seed and the root in compost-amended treatments were derived from the compost itself. The most effective ISR inducing rhizobacterial strains were identified as Bacillus sp. based on partial sequencing of l6S rDNA. However, these strains were significantly less effective in reducing the severity of disease than Trichoderma hamatum382 (T382). A procedure was developed for inoculation of a compost-amended substrate with T -382 which consistently induced ISR in cucumber against Phytophthora blight caused by Phytophthora capsiciand in radish against bacterial spot (Ohio). Inoculation of compost-amended potting mixes with biocontrol agents such as T -382 and other microbes that induce systemic resistance in plants significantly increased the frequency of systemic disease control obtained with natural compost amendments.
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Busby, Ryan, David Ringelberg i Carina Jung. Flavonoids Differentially Influence Rhizosphere Bacterial Communities from Native and Introduced Lespedeza Roots. Engineer Research and Development Center (U.S.), sierpień 2018. http://dx.doi.org/10.21079/11681/28063.
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Matin, A., T. Schmidt i D. Caldwell. Role of starvation genes in the survival of deep subsurface bacterial communities. Final report. Office of Scientific and Technical Information (OSTI), listopad 1998. http://dx.doi.org/10.2172/674896.
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Gottlieb, Yuval, i Bradley A. Mullens. Might Bacterial Symbionts Influence Vectorial Capacity of Biting Midges for Ruminant Viruses? United States Department of Agriculture, wrzesień 2010. http://dx.doi.org/10.32747/2010.7699837.bard.
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- Original objectives and revision: The feasibility study performed in the last year was aimed at determining the symbiotic profiles of eight selected Culicoidesspecies in Israel and the USA by: Comparing bacterial communities among geographic populations of primary bluetongue virus (BTV) vectors. Comparing bacterial communities between adults of field-collected, mammal-feeding BTV vectors and non-vectors. Comparing bacterial communities within and between mammal feeders and bird feeders, with special attention to species with unique immature habitats. We made an effort to collect the eight species during the beginning of the project, however, due to the short available collection season, and the significant changes in habitats available for Israeli Culicoides, we initially determined the symbiotic profile of five species: two BTV vectors (C. sonorensis, C. imicola), one mammal feeders with unknown vectoring ability (C. schultzei), one bird feeder (C. crepuscularis), and one unique habitat species (C. cacticola). In addition, upon preliminary symbiont identification we focused our effort on relevant specific symbionts. Background: Biting midges (Culicoides, Diptera: Ceratopogonidae) are vectors of many major viral diseases affecting farm animals, including BT, which is listed among the most damaging by the World Organization for Animal Health (OIE) and has recently emerged in completely unexpected areas (Northern Europe). One of the strategies to reduce the vectorial capacity of insect vectors is by manipulating their specific symbionts either to affect the vector species or to influence performance of the disease agent within it. Despite significant efforts to elucidate the vectorial capacity of certain Culicoidesspecies, and the critical basis of variability in infection, almost no attention has been given to symbiotic interactions between the vector and its bacterial tenants. It is now established that bacterial symbionts have major influences on their host biology, and may interact with disease agents vectored by their hosts. - Major conclusions, solutions, achievements: During the feasibility project we have found two major bacterial symbionts in Israeli and American Culicoides. In Israel we discovered that C. imicola, a known vector of BT, and C. schultzeigp. a suspected vector of BT, carry the symbiotic bacterium Cardinium, a reproductive manipulator symbiont. In C. imicolathe infection rate was close to 50%, and in C. schultzeiit was lower, and restricted to one of two species within Schultzeigroup. In 3 American species (C. sonorensis, C. crepuscularis, C. cacticola) we found the bacterium Burkholderiasp. In all species tested we have also found other bacterial species in diverse quantities and frequencies. - Implications, both scientific and agricultural: Finding specific symbionts in Culicoidesvector species is the first step in developing symbiont based control (SBC) strategies. Both identified symbionts are known from other insects, and Cardiniumis also known as a reproductive manipulator that can cause cytoplasmic incompatibility, an important phenomenon that can be used for spreading desired traits in infected populations. The role of the symbionts in Culicoideshost can be target for manipulation to reduce the vectorial capacity of the host by either changing its fitness so that it is unable to serve as a vector, or by directly changing the symbiont in a way that will affect the performance of the disease agent in its vector. Since Burkholderiaperhaps can be cultured independently of the host, it is a promising candidate for the later option. Thus, we have now opened the door for studying the specific interactions between symbionts and vector species.
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Gottlieb, Yuval, Bradley Mullens i Richard Stouthamer. investigation of the role of bacterial symbionts in regulating the biology and vector competence of Culicoides vectors of animal viruses. United States Department of Agriculture, czerwiec 2015. http://dx.doi.org/10.32747/2015.7699865.bard.
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Symbiotic bacteria have been shown to influence host reproduction and defense against biotic and abiotic stressors, and this relates to possible development of a symbiont-based control strategy. This project was based on the hypothesis that symbionts have a significant impact on Culicoides fitness and vector competence for animal viruses. The original objectives in our proposal were: 1. Molecular identification and localization of the newly-discovered symbiotic bacteria within C. imicola and C. schultzei in Israel and C. sonorensis in California. 2. Determination of the prevalence of symbiotic bacteria within different vector Culicoides populations. 3. Documentation of specific symbiont effects on vector reproduction and defense: 3a) test for cytoplasmic incompatibility in Cardinium-infected species; 3b) experimentally evaluate the role of the symbiont on infection or parasitism by key Culicoides natural enemies (iridescent virus and mermithid nematode). 4. Testing the role(s) of the symbionts in possible protection against infection of vector Culicoides by BTV. According to preliminary findings and difficulties in performing experimental procedures performed in other insect symbiosis systems where insect host cultures are easily maintained, we modified the last two objectives as follows: Obj. 3, we tested how symbionts affected general fitness of Israeli Culicoides species, and thoroughly described and evaluated the correlation between American Culicoides and their bacterial communities in the field. We also tried alternative methods to test symbiont-Culicoides interactions and launched studies to characterize low-temperature stress tolerances of the main US vector, which may be related to symbionts. Obj. 4, we tested the correlation between EHDV (instead of BTV) aquisition and Cardinium infection. Culicoides-bornearboviral diseases are emerging or re-emerging worldwide, causing direct and indirect economic losses as well as reduction in animal welfare. One novel strategy to reduce insects’ vectorial capacity is by manipulating specific symbionts to affect vector fitness or performance of the disease agent within. Little was known on the bacterial tenants occupying various Culicoides species, and thus, this project was initiated with the above aims. During this project, we were able to describe the symbiont Cardinium and whole bacterial communities in Israeli and American Culicoides species respectively. We showed that Cardinium infection prevalence is determined by land surface temperature, and this may be important to the larval stage. We also showed no patent significant effect of Cardinium on adult fitness parameters. We showed that the bacterial community in C. sonorensis varies significantly with the host’s developmental stage, but it varies little across multiple wastewater pond environments. This may indicate some specific biological interactions and allowed us to describe a “core microbiome” for C. sonorensis. The final set of analyses that include habitat sample is currently done, in order to separate the more intimately-associated bacteria from those inhabiting the gut contents or cuticle surface (which also could be important). We were also able to carefully study other biological aspects of Culicoides and were able to discriminate two species in C. schultzei group in Israel, and to investigate low temperature tolerances of C. sonorensis that may be related to symbionts. Scientific implications include the establishment of bacterial identification and interactions in Culicoides (our work is cited in other bacteria-Culicoides studies), the development molecular identification of C. schultzei group, and the detailed description of the microbiome of the immature and matched adult stages of C. sonorensis. Agricultural implications include understanding of intrinsic factors that govern Culicoides biology and population regulation, which may be relevant for vector control or reduction in pathogen transmission. Being able to precisely identify Culicoides species is central to understanding Culicoides borne disease epidemiology.
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Minz, Dror, Eric Nelson i Yitzhak Hadar. Ecology of seed-colonizing microbial communities: influence of soil and plant factors and implications for rhizosphere microbiology. United States Department of Agriculture, lipiec 2008. http://dx.doi.org/10.32747/2008.7587728.bard.
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Original objectives: Our initial project objectives were to 1) Determine and compare the composition of seed-colonizing microbial communities on seeds, 2) Determine the dynamics of development of microbial communities on seeds, and 3) Determine and compare the composition of seed-colonizing microbial communities with the composition of those in the soil and rhizosphere of the plants. Revisions to objectives: Our initial work on this project was hampered by the presence of native Pythium species in the soils we were using (in the US), preventing us from getting accurate assessments of spermosphere microbial communities. In our initial work, we tried to get around this problem by focusing on water potentials that might reduce damage from native Pythium species. This also prompted some initial investigation of the oomycete communities associated seedlings in this soil. However, for this work to proceed in a way that would allow us to examine seed-colonizing communities on healthy plants, we needed to either physically treat soils or amend soils with composts to suppress damage from Pythium. In the end, we followed the compost amendment line of investigation, which took us away from our initial objectives, but led to interesting work focusing on seed-associated microbial communities and their functional significance to seed-infecting pathogens. Work done in Israel was using suppressive compost amended potting mix throughout the study and did not have such problems. Our work focused on the following objectives: 1) to determine whether different plant species support a microbial induced suppression of Pythium damping-off, 2) to determine whether compost microbes that colonize seeds during early stages of seed germination can adequately explain levels of damping-off suppression observed, 3) to characterize cucumber seed-colonizing microbial communities that give rise to the disease suppressive properties, 4) assess carbon competition between seed-colonizing microbes and Pythium sporangia as a means of explaining Pythium damping-off suppression. Background: Earlier work demonstrated that seed-colonizing microbes might explain Pythium suppression. Yet these seed-colonizing microbial communities have never been characterized and their functional significance to Pythium damping-off suppression is not known. Our work set out to confirm the disease suppressive properties of seed-colonizing microbes, to characterize communities, and begin to determine the mechanisms by which Pythium suppression occurs. Major Conclusions: Compost-induced suppression of Pythium damping-off of cucumber and wheat can be explained by the bacterial consortia colonizing seeds within 8 h of sowing. Suppression on pea was highly variable. Fungi and archaea play no role in disease suppression. Potentially significant bacterial taxa are those with affinities to Firmicutes, Actinobacteria, and Bacteroidetes. Current sequencing efforts are trying to resolve these taxa. Seed colonizing bacteria suppress Pythium by carbon competition, allowing sporangium germination by preventing the development of germ tubes. Presence of Pythium had a strong effect on microbial community on the seed.
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Arias-Thode, Y. M., Ken Richter, Adriane Wotawa-Bergen, D. B. Chadwick, Jinjun Kan i Kenneth Nealson. Development of Microbial Fuel Cell Prototypes for Examination of the Temporal and Spatial Response of Anodic Bacterial Communities in Marine Sediments. Fort Belvoir, VA: Defense Technical Information Center, styczeń 2014. http://dx.doi.org/10.21236/ada610308.
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