Academic literature on the topic 'Microbes found'
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Journal articles on the topic "Microbes found"
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Barras, Colin. "Deepest land microbes ever found." New Scientist 249, no. 3323 (2021): 14. http://dx.doi.org/10.1016/s0262-4079(21)00308-0.
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Gewin, Virginia. "Live Microbes Found in Ancient Ice." Frontiers in Ecology and the Environment 3, no. 3 (2005): 128. http://dx.doi.org/10.2307/3868533.
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Marshall, Michael. "Earth's earliest microbes found in rocks." New Scientist 243, no. 3250 (2019): 14. http://dx.doi.org/10.1016/s0262-4079(19)31850-0.
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Wang, Qianhong, Zheng Hao, Ruirui Ding, Huabing Li, Xiangming Tang, and Feizhou Chen. "Host Dependence of Zooplankton-Associated Microbes and Their Ecological Implications in Freshwater Lakes." Water 13, no. 21 (2021): 2949. http://dx.doi.org/10.3390/w13212949.
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Zooplankton is colonized by quite different microbes compared with free-living and particle-associated bacteria, serving as a non-negligible niche of bacteria in aquatic ecosystems. Yet detailed analysis of these bacterial groups is still less known, especially in freshwater lakes. To widen our knowledge of host-microbe interaction and bacterial ecosystem functions, we chose two specific populations of zooplankton, i.e., cladoceran Moina and copepod Calanoids, as hosts from five natural lakes, and illustrated detailed features of their associated bacteria. Through 16S rRNA gene sequencing, we found microbes colonized on Calanoids presented significantly higher α-diversity, stronger bacterial interaction and metabolic function potentials than for Moina. It was also notable that zooplankton-associated bacteria showed a high potential of fatty acid metabolism, which is beneficial for host’s development. Moreover, we found that zooplankton-associated microbes may exert profound effects on biogeochemical cycles in freshwater lakes, since several bacterial members able to participate in carbon and nitrogen cycles were found abundant. Overall, our study expands current understanding of the host-microbe interaction and underlying ecological dynamics in freshwater ecosystem.
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Li, Wei Tse, Anjali S. Iyangar, Rohan Reddy, et al. "The Bladder Microbiome Is Associated with Epithelial–Mesenchymal Transition in Muscle Invasive Urothelial Bladder Carcinoma." Cancers 13, no. 15 (2021): 3649. http://dx.doi.org/10.3390/cancers13153649.
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The intra-tumor microbiome has recently been linked to epithelial–mesenchymal transition (EMT) in a number of cancers. However, the relationship between EMT and microbes in bladder cancer has not been explored. In this study, we profiled the abundance of individual microbe species in the tumor samples of over 400 muscle invasive bladder carcinoma (MIBC) patients. We then correlated microbe abundance to the expression of EMT-associated genes and genes in the extracellular matrix (ECM), which are key players in EMT. We discovered that a variety of microbes, including E. coli, butyrate-producing bacterium SM4/1, and a species of Oscillatoria, were associated with expression of classical EMT-associated genes, including E-cadherin, vimentin, SNAI2, SNAI3, and TWIST1. We also found significant correlations between microbial abundance and the expression of genes in the ECM, specifically collagens and elastin. Lastly, we found that a large number of microbes exhibiting significant correlations to EMT are also associated with clinical prognosis and outcomes. We further determined that the microbes we profiled were likely not environmental contaminants. In conclusion, we discovered that the intra-tumoral microbiome could potentially play a significant role in the regulation of EMT in MIBC.
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Rediske, Andrea M. "Beautiful Images and Practical Examples Found in Idaho Microbes." Journal of Microbiology & Biology Education 17, no. 2 (2016): 308. http://dx.doi.org/10.1128/jmbe.v17i2.1113.
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Kaur, Amandeep, and Sangeeta Sharma. "Biogenic Synthesis of Gold Nanoparticles and their Applications: A Review." Asian Journal of Chemistry 31, no. 12 (2019): 2679–97. http://dx.doi.org/10.14233/ajchem.2019.22105.
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The purpose of the present study is to explore the merits and demerits of various biogenic synthesis route of gold nanoparticles using plant materials and microbes. Literature survey indicated that microbe mediated synthesis route is found to be quite effective buttheavailability and feasibility of microbes, enzyme control conditions is of great challenge for the researchers. Among all the available bio-reductants for the synthesis of gold nanoparticles rhizome of Zinger officinale (ginger) has been found more advantageous in accordance with availability, stability, applicability, reaction time, etc. for the fabrication of gold nanoparticles.
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Deng, Lei, Yibiao Huang, Xuejun Liu, and Hui Liu. "Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations." Bioinformatics 38, no. 4 (2021): 1118–25. http://dx.doi.org/10.1093/bioinformatics/btab792.
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Abstract Motivation Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial agents. Therefore, screening of microbe–drug associations can benefit greatly drug research and development. With the increase of microbial genomic and pharmacological datasets, we are greatly motivated to develop an effective computational method to identify new microbe–drug associations. Results In this article, we proposed a novel method, Graph2MDA, to predict microbe–drug associations by using variational graph autoencoder (VGAE). We constructed multi-modal attributed graphs based on multiple features of microbes and drugs, such as molecular structures, microbe genetic sequences and function annotations. Taking as input the multi-modal attribute graphs, VGAE was trained to learn the informative and interpretable latent representations of each node and the whole graph, and then a deep neural network classifier was used to predict microbe–drug associations. The hyperparameter analysis and model ablation studies showed the sensitivity and robustness of our model. We evaluated our method on three independent datasets and the experimental results showed that our proposed method outperformed six existing state-of-the-art methods. We also explored the meaning of the learned latent representations of drugs and found that the drugs show obvious clustering patterns that are significantly consistent with drug ATC classification. Moreover, we conducted case studies on two microbes and two drugs and found 75–95% predicted associations have been reported in PubMed literature. Our extensive performance evaluations validated the effectiveness of our proposed method. Availability and implementation Source codes and preprocessed data are available at https://github.com/moen-hyb/Graph2MDA. Supplementary information Supplementary data are available at Bioinformatics online.
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Замшин, А. И. "Correspondence About the article of the Privat-docent V. F. Maslovkago: "To the doctrine of self-infection of maternity hospitals"." Journal of obstetrics and women's diseases 6, no. 5 (2020): 530–31. http://dx.doi.org/10.17816/jowd65530-531.
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Privat-docent V. F. Maslovsky in his work "On the doctrine of self-infection of maternity hospitals", which appeared in the April book "Journal of obstetrics and women's diseases" for the current year, reproaches me for limiting myself to studying only the biological properties of microbes found, and says (p.332): "it is currently impossible to determine the property of microbes according to the state of culture, due to insufficient information about their biological properties."In this regard, I should note that it is the biological properties of known microbes that are currently being studied; in particular, this can be said about the desired microbe in my workstaph. R. aureus.
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Mwafulirwa, Samuel. "Isolation Characterization and Diversity of Indigenous Pesticide Degrading Microbes from Selected Agro Ecological Zones of Malawi." Asian Plant Research Journal 11, no. 3 (2023): 29–40. http://dx.doi.org/10.9734/aprj/2023/v11i3213.
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Pesticide xenobiotics have a great impact on bio argumentation, bio-magnification, and environment degradation regardless of being adopted by green revolution technologies. Bioremediation is widely accepted because it’s cheap, practical at the same time environmentally friendly. Bioremediation advocates indigenous microbes use to degrade pesticides, therefore a study has been performed to show prospects of degrading microorganisms. The study isolated microbes from different agro ecological zones to assess their capacity to utilize some pesticide as sole carbon source complimented by the presence of laccase gene. Biochemical test and genetic characterization using 16S rDNA genes were used in identification. Diversified species and strains of genus Enterobacter, Klebsiella, Pseudomonas, Pantoea and Leclercia, were found to degrade cypermethrin and acetochlor but no microbe was found to degrade dimethoate. The study adds new strain of microbes involved in degradation of cypermethrin and acetochlor and also strains that that can degrade both. The study puts proposition that pest infestation in fields is a result of abundance of xenobiotic degrading microbes due to natural selection pressure not pesticide resistance of the pest.
Dissertations / Theses on the topic "Microbes found"
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Halder, Aparna. "Identification and studies on microbes found in tannery effluents." Thesis, University of North Bengal, 2006. http://ir.nbu.ac.in/handle/123456789/1396.
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Blank, Carrine E., Hong Cui, Lisa R. Moore, and Ramona L. Walls. "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions." BIOMED CENTRAL LTD, 2016. http://hdl.handle.net/10150/614758.
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Background: MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. Results: MicrO currently has similar to 14550 classes (similar to 2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by similar to 24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. Conclusions: By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we intend MicrO to be a powerful new tool to increase the computing power of bioinformatics tools such as the automated text mining of prokaryotic taxonomic descriptions using natural language processing. We also intend MicrO to support the development of new bioinformatics tools that aim to develop new connections between microbial phenotypes and genotypes (i.e., the gene content in genomes). Future ontology development will include incorporation of pathogenic phenotypes and prokaryotic habitats.
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Phuti, Moukangoe Getrude. "Synthesis, characterization and antimicrobial activity of cobalt and cobalt sulphide nanoparticles against selected microbes that are found in wastewater." Thesis, 2018. http://hdl.handle.net/10352/447.
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M. Tech (Department of Biotechnology, Faculty of Applied and Computer Sciences) Vaal University of Technology.<br>Water shortages, water pollution and climate changes are highly interrelated global issues. These have raised immense concerns about serious adverse effects on the quality, treatment and re-use of wastewater. A major role of water is for vitality of life on earth. Water is recognized as source of evolution from origin to degree of civilization, since it is an essential resource its treatment becomes a necessity for day to day for life.
Nanoparticles and their application in treatment of wastewater is becoming a major area of research. It is mainly applicable to the removal of major contaminants like microorganisms. This study was carried out with an objective to investigate the antibacterial and antifungal potentials of nanoparticles. Cobalt and cobalt complexes of urea and thiourea were synthesized and characterized using UV-Vs, PL, FTIR, TEM, SEM, XRD and TGA techniques. The Co particles are in a mixture of rod, agglomerates with irregular shape around 50 – 100 nm in diameter. The Co/Thiourea particles appear to be around 10 – 30nm in size. The Co complexed with urea images showed spherical to hexagonal shape with 50 nm size in diameter.
The antimicrobial activity was determined using Minimum Inhibitory and bactericidal concentration and the well diffusion method. The antibacterial and antifungal activities of ratios (1:1, 1:2, 1:3, 2:1 μg/mL) of doped cobalt nanoparticles were tested against a panel of five Gramnegative bacteria - (Escherichia coli, Pseudomonas aeruginosa, Shigella enterica, Salmonella typhi and Salmonella sonnei) human pathogenic bacteria; and two fungal strains - Aspergillus niger and Candida albicans. Zones of inhibition as a consequence of nanoparticles were compared with that of different standards like Neomycin for antibacterial activity and Amphotericin B for antifungal activity. The results showed a remarkable inhibition of the bacterial growth against the tested organisms. The most striking feature of this study is that Cobalt, Urea and Thiourea nanoparticles have antifungal activity comparable or more effective (as in case of Thiourea on A. niger) than Amphotericin B and nearly promising antibacterial activity although not comparable to Neomycin.
Books on the topic "Microbes found"
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Kirchman, David L. Genomes and meta-omics for microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0005.
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The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far. Genomic studies have also highlighted the importance of genes exchanged (“horizontal gene transfer”) between organisms, seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use metagenomics to sequence all microbes in a community. This approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Genomes from single cells isolated by flow cytometry have also provided insights about the ecophysiology of both bacteria and protists. Oligotrophic bacteria have streamlined genomes, which are usually small but with a high fraction of genomic material devoted to protein-encoding genes, and few transcriptional control mechanisms. The study of all transcripts from a natural community, metatranscriptomics, has been informative about the response of eukaryotes as well as bacteria to changing environmental conditions.
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Kirchman, David L. Community structure of microbes in natural environments. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0004.
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Community structure refers to the taxonomic types of microbes and their relative abundance in an environment. This chapter focuses on bacteria with a few words about fungi; protists and viruses are discussed in Chapters 9 and 10. Traditional methods for identifying microbes rely on biochemical testing of phenotype observable in the laboratory. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the laboratory using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50% of the total microbial abundance. Dispersal of bacteria and other small microbes is thought to be easy, leading to the Bass Becking hypothesis that “everything is everywhere, but the environment selects.” Among several factors known to affect community structure, salinity and temperature are very important, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower growing defensive specialists to survive. Cultivation-independent approaches indicate that fungi are more diverse than previously appreciated, but they are less diverse than bacteria, especially in aquatic habitats. The community structure of fungi is affected by many of the same factors shaping bacterial community structure, but the dispersal of fungi is more limited than that of bacteria. The chapter ends with a discussion about the relationship between community structure and biogeochemical processes. The value of community structure information varies with the process and the degree of metabolic redundancy among the community members for the process.
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Birch, Jonathan. The Philosophy of Social Evolution. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198733058.001.0001.
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From microbes to humans, the natural world is full of spectacular examples of social behaviour. In the 1960s, W. D. Hamilton introduced three key innovations—now known as Hamilton’s rule, kin selection, and inclusive fitness—that changed the way we think about how social behaviour evolves, beginning a research program now known as social evolution theory. This is a book about the philosophical foundations and future prospects of that program. Part I, ‘Foundations’, provides a philosophical analysis of Hamilton’s core ideas, with some modifications along the way. We will see that Hamilton’s rule provides a compelling way of organizing our thinking about the ultimate causes of social behaviour; and we will see how, in inclusive fitness, Hamilton found a fitness concept with a special role to play in explaining cumulative adaptation. Part II, ‘Extensions’, shows how these ideas, when extended in certain ways, can help us understand cooperation in micro-organisms, cooperation among the cells of a multicellular organism, and culturally evolved cooperation in the earliest human societies. In all these cases and more, living things cooperate because they are related, where the concept of relatedness picks out relevant statistical patterns of similarity in the transmissible basis (genetic or otherwise) of social traits.
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Kirchman, David L. The ecology of viruses. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0010.
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In addition to grazing, another form of top-down control of microbes is lysis by viruses. Every organism in the biosphere is probably infected by at least one virus, but the most common viruses are thought to be those that infect bacteria. Viruses come in many varieties, but the simplest is a form of nucleic acid wrapped in a protein coat. The form of nucleic acid can be virtually any type of RNA or DNA, single or double stranded. Few viruses in nature can be identified by traditional methods because their hosts cannot be grown in the laboratory. Direct count methods have found that viruses are very abundant, being about ten-fold more abundant than bacteria, but the ratio of viruses to bacteria varies greatly. Viruses are thought to account for about 50% of bacterial mortality but the percentage varies from zero to 100%, depending on the environment and time. In addition to viruses of bacteria and cyanobacteria, microbial ecologists have examined viruses of algae and the possibility that viral lysis ends phytoplankton blooms. Viruses infecting fungi do not appear to lyse their host and are transmitted from one fungus to another without being released into the external environment. While viral lysis and grazing are both top-down controls on microbial growth, they differ in several crucial respects. Unlike grazers, which often completely oxidize prey organic material to carbon dioxide and inorganic nutrients, viral lysis releases the organic material from hosts more or less without modification. Perhaps even more important, viruses may facilitate the exchange of genetic material from one host to another. Metagenomic approaches have been used to explore viral diversity and the dynamics of virus communities in natural environments.
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Vaughan, David. 5. Minerals and the living world. Oxford University Press, 2014. http://dx.doi.org/10.1093/actrade/9780199682843.003.0005.
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‘Minerals and the living world’ considers various mineral–microbe interactions, biomineralization, and how minerals interact with the human body and human health. Biomineralization is the process where living organisms produce minerals such as calcite, apatite, and silica. An example is the unicellular, ocean-living radiolaria that have complex silica skeletons. After death their skeletal remains sink to the ocean floor and can be seen preserved in cherts and flints. Human biominerals can be divided into those which are an essential part of the bodies’ systems, such as hydroxylapatite found in bones and teeth, and those which are unexpected and pathological mineral deposits, such as calcium oxalate and asbestiform minerals.
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Ruxton, Graeme D., William L. Allen, Thomas N. Sherratt, and Michael P. Speed. Secondary defences. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780199688678.003.0006.
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In this chapter we consider defences that are usually deployed during, or just before, contact between a prey and its predator: so-called ‘secondary’ defences. Secondary defences are found right across the tree of life and therefore come in very many forms, including: 1.) chemical defences; 2.) mechanical defences; and 3.) behavioural defences. Here we review selected examples that provide useful illustrations of the ecological and evolutionary characteristics associated with secondary defences. We discuss costs of secondary defences, placing emphasis on the consequences of such costs, especially as they relate to forms of social interaction. We show also that the acquisition of secondary defences may modify niche, life history, and habitat range of prey animals and review a well-known and significant study of predator–prey co-evolution of defensive toxins of prey and resistance to those toxins in predators. We include a small selection of examples and ideas from the plant and microbe defence literature where we think a broader perspective is helpful. We begin the chapter by considering the evolutionary mechanisms that favour secondary defence evolution.
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Rickard, David. Framboids. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780190080112.001.0001.
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Framboids may be the most astonishing and abundant natural features you have never heard of. These microscopic spherules of golden pyrite consist of thousands of even smaller microcrystals, often arranged in stunning geometric arrays. There are probably 10<sup>30</sup> on Earth, and they are forming at a rate of 10<sup>20</sup> every second. This means that there are a billion times more framboids than sand grains on Earth, and a million times more framboids than stars in the observable universe. They are all around us: they can be found in rocks of all ages and in present-day sediments, soils, and natural waters. The sulfur in the pyrite is mainly produced by bacteria, and many framboids contain organic matter. They are formed through burst nucleation of supersaturated solutions of iron and sulfide, followed by limited crystal growth in diffusion-dominated stagnant sediments. The framboids self-assemble as surface free energy is minimized and the microcrystals are attracted to each other by surface forces. Self-organization occurs through entropy maximization, and the microcrystals rotate into their final positions through Brownian motion. The final shape of the framboids is often actually polygonal or partially facetted rather than spherical, as icosahedral microcrystal packing develops. Their average diameter is around 6 microns and the average microcrystal size is about 0.1 microns. There is no significant change in these dimensions with time: the framboid is an exceptionally stable structure, and the oldest may be 2.9 billion years old. This means that they provide samples of the chemistry of ancient environments.
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Richards, Greg, Les Hall, and Steve Parish. Natural History of Australian Bats. CSIRO Publishing, 2012. http://dx.doi.org/10.1071/9780643103757.
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To hold a little microbat in your hand, its body the size of the end of your thumb, is nothing but astounding. Its head is nearly the size of a man’s fingernail, its tiny ears are twitching as it struggles to get free, and then it bares its teeth to try and scare you into letting it go. Inside that tiny head is a powerhouse of information. Some of our little bats know the entire landscape of our east coast, and can pinpoint a cave entrance in dense forest 500 km from its last home. When they get there they know what to do – where to forage, which bat to mate with and how to avoid local predators. 
 A Natural History of Australian Bats uncovers the unique biology and ecology of these wonderful creatures. It features a description of each bat species found in Australia, as well as a section on bat myths. The book is enhanced by stunning colour photographs from Steve Parish, most of which have never been seen before.
Book chapters on the topic "Microbes found"
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Štrbáňová, Soňa. "Fruitful Years. What Alice Found in the Microbes." In SpringerBriefs in Molecular Science. Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-49736-4_3.
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Pinzari, Flavia, and Beata Gutarowska. "Extreme Colonizers and Rapid Profiteers: The Challenging World of Microorganisms That Attack Paper and Parchment." In Microorganisms in the Deterioration and Preservation of Cultural Heritage. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-69411-1_4.
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AbstractMicroorganisms form the backbone of life on Earth. Over billions of years, they have colonized and shaped every possible niche on the planet. Microbes have modelled both the land and the sea, and have created favourable conditions for multicellular organisms to thrive in. Our understanding of how microbial diversity is distributed across natural environments and how microbes affect ecosystems is constantly evolving as public databases are set up and new techniques based on massive sequencing are developed. The microbiome found in a particular anthropogenic environment is generally much less complex than those found in natural ones: there is less competition and the main actors are often linked to survival mechanisms regulated by a few limiting factors. Despite this simplicity, it is very difficult to link cause and effect when seeking to identify the role of individual organisms. In the case of biodeterioration of paper and parchment, even when analysing the individual components of a simple phenomenon, it is not always easy to understand the mechanisms at play. Works of art are unique objects and the elements that determine the arrival and establishment of one or more microorganisms and the direction that the biodeterioration process takes are always different. In some cases, however, there are common denominators and predictable mechanisms. The variables that come into play are examined below.
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Pinhey, Sally, and Margaret Tebbs. "The role of fungi." In Plants for soil regeneration: an illustrated guide. CABI, 2022. http://dx.doi.org/10.1079/9781789243604.0005.
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Abstract This chapter focuses on the role of fungi. Fungi are a vital part of the mixture of microorganisms found in healthy soil. Fungal associations between plant roots and beneficial fungi are known as mycorrhizae (meaning 'fungus' and 'root'), and form a beneficial or symbiotic relationship with plants growing in the soil. Mycorrhizal fungi also facilitate plant interactions with other soil microbes. These include pathogens, and bacteria that produce vitamins and protect against attack. The most common of the mycorrhizae are divided into the following: (1) ectomycorrhizae; (2) endomycorrhizae; (3) arbuscular mycorrhizae; (4) ericoid mycorrhizae; and (5) orchid mycorrhiza. The role of saprophytes, pathogens and actinomycetes are also discussed.
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Miles, Sarah M., Ron Gestler, and Sandra M. Dworatzek. "Bioremediation of Petroleum Hydrocarbons in the Subsurface." In Advances in the Characterisation and Remediation of Sites Contaminated with Petroleum Hydrocarbons. Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-34447-3_14.
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AbstractDue to human activity and, to a lesser extent, natural processes, petroleum hydrocarbons continue to pollute the environment. These contaminants of concern can be found globally and their remediation is key to restoring affected sites to safe and functional status. Conventional treatment of sites contaminated with petroleum hydrocarbons relies heavily on remediation approaches that are often financially prohibitive or may be technically impractical and that sometimes produce undesirable by-products. Using microbes that occur in nature (if not always at the site), can be a viable treatment with distinct advantages. Understanding the environment, contaminants, and natural biological processes occurring are key aspects for effective application of remediation techniques that rely on biological processes. Whether by stimulating the native microbial community, or, secondarily, by augmenting the native community with known degrader populations to degrade the target compounds, bioremediation is a practical, effective, and sustainable natural solution to a wide array of contamination around the globe. This chapter explores approaches to bioremediation of both soil and groundwater contaminated by petroleum hydrocarbons, describing how the approaches work and the benefits and challenges associated with them. It focuses on the use of aerobic and anaerobic microbial bioremediation, phytoremediation, and mycoremediation to address petroleum hydrocarbons.
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Kelly, Alan. "From Sweetness to Structure." In Molecules, Microbes, and Meals. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780190687694.003.0008.
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When we refer to food as containing “sugar,” we tend to picture white crystals we buy in bags or pour from sachets into our coffee, but to a food scientist sugar is not a single thing, but a type of thing. While, most commonly, when we say sugar we refer to sucrose, in reality there are many sugars that can be found in (or added to) food. They all have in common the chemical characteristic that they are carbohydrates, which means, as the name suggests, that they are based on carbon and water (giving hydrated carbon), and indeed the three core elements found in all sugars are carbon, hydrogen, and oxygen. One of the simplest sugars, molecularly speaking, is glucose, in which there are 6 carbon atoms, 6 oxygen atoms and 12 hydrogen atoms (so it is like 6 carbons plus 6 water molecules, as each water molecule has two hydrogens to one oxygen). These are arranged, not in a long chain, as in the proteins we discussed in the previous chapter, but rather in a ring structure (not technically round, but more like a hexagon might appear if you gave it a good twist). Glucose is the main sugar found in biology, being found in our bodies and also produced by plants by photosynthesis. Another simple sugar is fructose, found widely in fruit and honey, which has an even simpler structure, a pentagon structure, but again has 6 carbon atoms bound together with 6 oxygens and 12 hydrogens, while a rarer one (at least in its unbound state) is galactose, again with the same number of the core atoms but arranged in yet another slightly different state. Here is a wonderful example of the significance of chemistry for food, where the exact same number of atoms of the same three elements can naturally be found in (at least) three different arrangements, which reflect subtly different molecular shapes but yet give compounds that differ greatly in their sweetness, solubility, reaction with other components in food, and many other properties.
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Muthukrishnan, Lakshmipathy. "Encountering the Survival Strategies Using Various Nano Assemblages." In Handbook of Research on Nano-Strategies for Combatting Antimicrobial Resistance and Cancer. IGI Global, 2021. http://dx.doi.org/10.4018/978-1-7998-5049-6.ch007.
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The technological advancements have not only made humans more civilized but have also caused the micro-organisms to develop several survival strategies via antimicrobial resistance to keep pace. Such highly developed microbial systems have been classified as superbugs, exhibiting Trojan-horse mechanism. This uncertain behaviour in microbes has challenged humans to scour around novel moiety to shield themselves from the detrimental effects. One such natural phenomenon that has drawn the attention of researchers is the metal-microbe interaction where microbes were found to be controlled during their interaction with metals. Fine tuning could bestow them with enhanced physico-chemical properties capable of controlling life-threatening micro-organisms. Nano forms of metals (nanoparticles, quantum dots, polymeric nanostructures) exhibiting medicinal properties have been implied toward biomedical theranostics. This chapter highlights the mechanistic antimicrobial resistance and the containment strategy using various nano assemblage highlighting its fabrication and bio-molecular interaction.
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Ali, Arslan, Maimona Sadia, Muhammad Zeeshan Ahmad, et al. "UNLOCKING THE SECRETS OF PLANT-MICROBE INTERACTIONS: HARNESSING BIOTECHNOLOGY FOR CROP IMPROVEMENT." In Futuristic Trends in Biotechnology Volume 3 Book 1. Iterative International Publisher, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/v3bfbt1p1ch2.
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Plants and microbes have many different associations, from advantageous symbiotic relationships to harmful pathogenic interactions. Understanding these interactions at the molecular level has important ramifications for agriculture since it presents novel ways to increase crop output, cut back on chemical inputs, and encourage sustainable farming methods. The complex connections between plants and microbes are discussed in this chapter, particularly emphasizing those interactions and the possibilities for employing biotechnology to raise agricultural yield. It begins by underlining the significance of plant-microbe interactions in agriculture. These interactions have an impact on the cycling of nutrients, soil fertility, and plant defense systems. For instance, helpful microbes can increase plant nutrient absorption efficiency, increase plant disease resistance, and help plants adapt to abiotic conditions like salt and drought. Biotechnology can unlock the potential for crop improvement by understanding the molecular processes behind these interactions. The potential of biotechnology to study and influence the interactions between plants and microbes is then highlighted. Researchers can now identify specific microbial taxa and genes involved in beneficial interactions using high-throughput sequencing techniques like metagenomics and transcriptomics, which help them to unravel the intricate networks of plant-microbe associations. Omics technologies shed light on the genetic and biochemical changes that occur in plants as a result of these interactions, elucidating mechanisms for nutrient uptake, stress tolerance, and defense responses. The chapter goes into further detail about the use of genetic engineering and synthetic biology to alter plant-microbe interactions. Researchers can insert genes or regulatory elements involved in these interactions to enhance favorable relationships and provide plants with desirable features. Crop improvement can also be achieved using biocontrol agents and microorganisms promoting plant development. Advanced imaging techniques, such as confocal microscopy and fluorescence in situ hybridization, enable the detection and identification of microbial dispersion inside plant tissues, providing greater knowledge of symbiotic interactions. Moreover, cutting-edge techniques like CRISPR-Cas9-based genome editing show promise for precise modification of genes in plants and microorganisms, opening new avenues for studying functional genomics in plant-microbe interactions. Field research and on-farm trials complement molecular technologies, providing insights into the effectiveness of biotechnological treatments in real-world agricultural contexts. Concerning previous case studies, it was found that microbes play a vital role in plant growth promotion by different processes. It was concluded that unraveling the secrets of plant-microbe interactions through biotechnology offers exciting prospects for crop improvement and sustainable agriculture. By understanding and manipulating these interactions at the molecular level, researchers can enhance nutrient cycling, disease control, stress tolerance, and overall plant health, ultimately revolutionizing modern agriculture and promoting environmental sustainability.
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Džunková, Mária. "Single-cell Genomics for Uncovering Relationships between Bacteriophages and their Hosts." In Genetic Diversity - Recent Advances and Applications [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.108118.
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Microbial single-cell genomics represents an innovative approach to study microbial diversity and symbiosis. It allows us to recover genomes of microbes possessing specific features of our interest, or detect relationships between microbes found in close proximity to each other (one microbe inside of the other or microbes attached to each other). It can be used for linking phages with their bacterial hosts in different kinds of environmental samples, which often contain an enormous diversity of yet uncultured bacterial species and novel bacteriophages. In the typical microbial single-cell genomics workflow, fluorescence-activated cell sorting (FACS) is used to collect bacterial cells of interest, based on their cell size, internal granularity, or fluorescence. Femtograms of DNA from each sorted particle are then amplified up to the quantities required by the standard sequencing library preparation kits. Single-cell assemblies then reveal presence of phages in sorted bacterial cells. In case of highly abundant viral species, single-cell genomics can be coupled with metagenomics (shotgun sequencing of the total microbial community), which can provide insights into the bacteria-bacteriophage population fluctuations in time or space. In this chapter, we explain the details of uncovering relationships between bacteriophages and their hosts coming from so-called viral or bacterial dark matter.
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Sharma, Gayatri. "Microbes as Artists of Life." In Symbiosis in Nature [Working Title]. IntechOpen, 2023. http://dx.doi.org/10.5772/intechopen.109532.
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Scientists have been knocking the wood to ascertain the symbiotic relationships of tiny living creatures, that is, microorganisms with other beings such as plants, animals, insects, and humans. The concept of “symbiosis” got its existence in 1879, which means “living together.” Microorganisms show a great deal of diverse interactions such as commensalism (moochers), mutualism (both benefitted), and parasitism (one benefitted and other unharmed) with other living beings and mutualism being the most common of all, thus forming a range of antagonistic to cooperative symbiotic relationships. These tiny creatures interact with plants by forming lichens (fungi and algae), mycorrhizae (plants and roots of higher plants), root noodles (Rhizobium) and acting as keyworkers in plant’s rhizosphere promoting growth and development. Microbial community also extends itself to kingdom Animalia establishing relationships with phylum Mammalia including humans, animals, and the most abundant species of phylum Arthropoda, that is, insects such as termites, which have colonization of bacteria in gut to digest wood cellulose. Scientists have discovered that most studied organisms—mussels found in deep-sea hydrothermal vents too live in a mutualistic association whereby bacteria get protection and mussels get nutrition as bacteria use chemicals from hydrothermal fluid producing organic compounds.
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A. Waoo, Ashwini, and Shivangi Agnihotri. "Dynamic Interplay of Soil and Microbes for Sustainable Ecological Balance." In Industrial Applications of Soil Microbes. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/9789815039955122010011.
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A microorganism is a term given to small living beings whose size is measured in microns. Bacteria, fungi, algae, and protozoans are a few of them that reside in the air, water, and soil. This review is about the microorganisms found in soil. These microorganisms have different functions in soil decomposition of dead organic matter, such as ecological food web balance, and making nutrients available to plants. Recently, their role in alleviating different abiotic stresses like salinity and drought has been marvelous. These microbes are also being used in biopesticide form, which is environmentally friendly and safe for other living organisms. Bacteria convert the inaccessible nutrients from dead matter into usable forms. Actinomycetes give off the typical smell of soil, and these microorganisms are also being used as a source of therapeutic medicines. Fungi are helpful in the way that they break down impossible nutrients, which are then available to other microbes. They also colonize plant roots and thus aid in plant growth. Algae promote submerged aeration as their photosynthesis is faster and adds more oxygen. Algae also help prevent the loss of nitrates that help in building soil structures by promoting the weathering of rocks. Nematodes help maintain the ecological equilibrium of their habitat. Viruses are the mode of gene transfer between organisms in the soil. Thus, these microorganisms have different functions in the soil to maintain the soil's structure and the balance between the environment and its living beings.
Conference papers on the topic "Microbes found"
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Sharma, Mohita, Dongshan An, Kristen Baxter, Matthew Henderson, Lem Edillon, and Gerrit Voordouw. "Understanding the Role of Microbes in Frequent Coiled Tubing Failures." In CORROSION 2016. NACE International, 2016. https://doi.org/10.5006/c2016-07815.
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Abstract The use of coiled tubing (CT) has strongly increased in the oil and gas industry in recent years. Potential corrosion problems arise from re-use of low quality water in closed loop coiled tubing operations. Water chemistry, corrosion rates, microbial counts and microbial community compositions were monitored for 5 samples from Field 1 and for 15 samples from Field 2 (Canada). The samples from Field 1 represented a failure with general corrosion rates of 0.1 mm/yr. The general corrosion rates of Field 2 samples for incubations initiated in the lab ranged from 0.09 to 1.31 mm/yr (average 0.25 mm/yr). The high rate of 1.31 mm/yr was for a recycled injection water (S19) taken from a tank prior to re-injection. Interestingly, general corrosion rates for this recycled injection water (S19) for incubations initiated onsite were also very high (0.89, 0.84 and 0.99 mm/yr). Acid Producing Bacteria (APB) like Pseudomonas and Iron Reducing Bacteria (IRB) like Shewanella were found in all samples. These may have created acidic environments accelerating the corrosion. Sand (7-8 g/L) and other components found in Field 2 samples may have contributed to sand erosion-corrosion. In summary, it appeared that low pH, sand and microbes can significantly increase CT corrosion.
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Jia, Ru, Hasrizal Bin Abd Rahman, Dongqing Yang, and Tingyue Gu. "Investigation of the Impact of an Enhanced Oil Recovery Polymer on Microbial Growth and MIC." In CORROSION 2018. NACE International, 2018. https://doi.org/10.5006/c2018-10567.
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Abstract In the oil and gas industry, water flooding, often with a polymer additive, is used in enhanced oil recovery (EOR) to increase reservoir pressure because reservoirs are aging. This practice causes operational concerns because water flooding brings nutrients and microbes downhole, which may allow microbes to flourish. Polymers such as carboxymethyl cellulose sodium are used in EOR to increase the viscosity of the injection water. However, there is a possibility that EOR polymers may be utilized as a carbon source by microbes downhole causing reservoir souring and microbiologically influenced corrosion (MIC). In this work, carboxymethyl cellulose sodium (3,000 ppm by mass) was found to be utilized by an oilfield biofilm consortium containing various microbes including sulfate reducing bacteria (SRB) and biodegradation microbes during a 30-day anaerobic incubation test at 37°C. The polymer utilization increased the planktonic cell count and SRB sessile cell count in anaerobic vials with 100 ml artificial seawater. After the 30-day incubation, the polymer utilization led to 16% viscosity loss. The utilization also slightly increased weight loss and pitting corrosion on C1018 carbon steel.
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Geissler, Brett. "Identification of Compounds That Effectively Block Microbial H2S Production." In CORROSION 2017. NACE International, 2017. https://doi.org/10.5006/c2017-09551.
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Abstract Microbial reduction of sulfur compounds is a concern in many industries due to the toxicity and corrosivity of the chief metabolic waste product, hydrogen sulfide (H2S). In the oil and gas industry, production of H2S by microbes within the petroleum reservoir is extremely detrimental to production and often leads to complete shut-in of wells and entire assets due to these concerns. Hundreds of different genera of bacteria and archaea are capable of generating H2S from an array of sulfur-containing compounds, although the key enzymes involved are relatively well conserved. We have identified a class of inhibitory molecules that abrogate sulfidogenesis by numerous diverse microbial populations found within oilfield produced fluids. Using bottle tests and laboratory-scale bioreactors designed to more closely mimic field conditions, very low doses of two different versions of this class of compounds were found to effectively prevent H2S generation and decrease the number of sulfide-producing microbes from the population. Although not proven experimentally, by decreasing the amount of H2S generated, these compounds will likely be able to decrease the levels of microbiologically influenced corrosion normally associated with sulfidogenic populations of microbes.
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Yin, Bei, and Kenneth Wunch. "Combined Effects of Microbes and Nitrate on SRB Growth, Souring and Corrosion." In CORROSION 2017. NACE International, 2017. https://doi.org/10.5006/c2017-09425.
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Abstract Controlling reservoir souring is critical to successful production and asset protection in hydrocarbon recovery. Nitrate injection has been used in water flooding for controlling biogenic sulfide in oil reservoirs. Souring control via nitrate implementation is based on the interactions between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB). As a result, it is important to understand how the NRB and SRB population profile controls the effectiveness of nitrate on SRB growth, sulfide levels, and corrosion. In laboratory studies, the impact of NRB (including denitrifiers (N2NRB) and nitrite-producing NRB (NO2NRB)) and SRB (including SRB with and without nitrate-reducing ability) composition on nitrate effectiveness was evaluated. A stationary testing method and a porous media flow reactor method were used for these studies. The effect of different NRB, including NO2NRB and sulfide-oxidizing NRB (SONRB) on corrosion of carbon steel beads in the presence and absence of nitrate was also investigated using porous media flow reactors. It was found that the effectiveness of nitrate on sulfide level, SRB growth, and metal corrosion can be dynamically affected by the composition of SRB and NRB present in the testing systems.
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Geissler, Brett, Alicia M. Jones, and Vic Keasler. "Prevalence and Distribution of Sulfide Generating Microbes in the Oil and Gas Industry." In CORROSION 2016. NACE International, 2016. https://doi.org/10.5006/c2016-07569.
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Abstract Hydrogen sulfide generation is one of the key detriments linked to microbial activity in the oil and gas industry and is the most likely cause of most microbiologically influenced corrosion. H2S is extremely corrosive to most metals and can significantly devalue produced fluids and gases as well as raise HS&E concerns for production facilities. Microbial sulfidogenesis has historically been linked to only a few types of sulfate reducing bacteria that are capable of growth in Modified Postgate’s B medium, but recent advances in microbial identification techniques have shown that the sulfide generating population in the industry is made up of over 190 different genera. Metabolic studies have shown that the vast majority of these microbes require thiosulfate, elemental sulfur, (bi) sulfite, and other sulfur compounds for energy production, and can therefore not be cultured using standard oilfield methods. This paper discusses the prevalence and distribution of the varied population of sulfide generating bacteria and archaea that have been identified by DNA sequencing from over 7000 samples obtained from numerous sites throughout hydrocarbon production facilities found all over the world.
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Dharani, R., R. Deepalakshmi, S. N. Padma Devi, S. Nithya Meenakshi, and D. Nalini. "Influence of Soil Fungi on Corrosion of Mild Steel Plates." In CORROSION 2018. NACE International, 2018. https://doi.org/10.5006/c2018-10839.
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Abstract Metal corrosion is an electrochemical reaction between the environment and a metal, in which microbes are thought to play a very important role. These microorganisms do not only cause corrosion, but they can also inhibit or protect against corrosion. Fungi are the most dessicant – resistant microorganisms and are ubiquitous in atmospheric environments. About five fungal organisms were isolated using Starkey media from the soil of corroded pipeline tank. The influence of these fungal isolates on both rusted and non – rusted mild steel plates were studied for a period of 25 days. Among the five fungal isolates, Non – rusted Isolate (NR) – 1 and Rusted Isolate (R) – 3 showed minimum corrosion reaction on mild steel plates, based on the results of weight loss and dissolved iron content. The results revealed that the two isolates showed minimum rate of corrosion on mild steel plates due to the passive mechanism of microbes upon the plates. Therefore the above isolates (NR -1 and R- 3) was identified using molecular markers and it was found to be Aspergillus flavus and Alternaria alternata respectively.
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Geissler, Brett, Alicia Jones, Marty Setinc, Alex Koerner, and Damon Binek. "Field Trial Findings of a Novel Sulfidogenesis Inhibitory Compound." In CORROSION 2019. NACE International, 2019. https://doi.org/10.5006/c2019-13168.
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Absrract Due to its contribution to microbiologically influenced corrosion and potential HS&E consequences, hydrogen sulfide (H2S) presents many challenges to oil and gas production operations. Microbiologically generated H2S is often more difficult to address, because it is not present at the onset of production, but becomes a problem over the course of the lifetime of a well/asset. Many different types of microbes are responsible for H2S production and reservoir souring. These microbes are capable of reducing, not only sulfate, but most available sulfur compounds that are present in the reservoir. A new class of compounds was recently identified and characterized in the lab as effective inhibitors or microbial sulfidogenesis. In this work, we present results from a field trial conducted using one of these chemistries. The trial showed that this novel inhibitor retained activity under downhole conditions and resulted in significant reductions in the H2S produced within the reservoir as well as the levels found at the central gathering facility. These findings further support the potential of these compounds as solutions to reservoir souring and highlight the need for additional field applications.
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Xu, Lingjun, Adnan Khan, Sarah A. Aqeel, and Tingyue Gu. "Monitoring Oil Pipeline MIC and Its Mitigation Offline Using a True Biofilm Test Kit and a Mechanistic MIC Model." In CONFERENCE 2025. AMPP, 2025. https://doi.org/10.5006/c2025-00286.
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Microbiologically influenced corrosion (MIC) is caused by microbial biofilms. In this work, the water phase of an oilfield oil-water sample was assessed using a new disposable electrochemical biofilm/MIC test kit consisting of two solid-state electrodes in a 10 mL serum vial for biofilm growth, biocorrosivity and biocide efficacy. The water sample was found to be low in microbes and nutrients. To simulate “worst-case scenario,” the water sample was subcultured at 37oC using enriched artificial seawater (EASW) for three rounds before being used as the seed culture for further MIC and biocide tests. Its main corrosive microbes were identified as sulfate reducers from a metagenomics analysis. The 7-d X60 carbon steel weight loss was 1.1 ± 0.2 mg/cm2 (2.9 mpy uniform corrosion rate). With 20 ppm tetrakis hydroxymethyl phosphonium sulfate (THPS) in EASW, it dropped to 0.5 ± 0.2 mg/cm2 (1.3 mpy), and with 50 ppm THPS, it became negligible (0.08 mpy). The corresponding MIC pit depths were 10.5 μm, 8.9 μm, and no well-defined pits, respectively. With the weight loss data, the corrosion resistance (Rp) from linear polarization resistance and corrosion current density (icorr) from Tafel scans were correlated with biofilm aggressiveness in our existing mechanistic model for MIC prediction with and without biocide treatment.
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Kleina, L. G., M. H. Czechowski, J. S. Clavin, W. K. Whitekettle, and C. R. Ascolese. "Performance and Monitoring of a New Nonoxidizing Biocide: the Study of BNPD/ISO and ATP." In CORROSION 1997. NACE International, 1997. https://doi.org/10.5006/c1997-97403.
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Abstract A bromo, nitropropanediol/isothiazolone blend (BNPD/ISO) was evaluated in an industrial cooling system to assess its performance and potential as an alternative to the oxidizing biocide program (gaseous chlorine) currently in use. Finding effective alternatives to gaseous chlorine is important because of safety and handling issues. Furthermore, chlorine has the associated problems of increasing cooling water corrosion rates, degradation of wood cooling structures, impaired efficacy at high pH, and sensitivity to organics and reducing agents in the water. The goals of this study were two-fold: First, to determine whether BNPD/ISO could be used as a chlorine alternative in an industrial system with equal or better performance at economically viable use levels; Second, to develop rapid, effective monitoring for nonoxidizing biocides in this system that would maximize useful application information without consuming large quantities of time and effort. The BNPD/ISO blend controlled the planktonic and sessile microbes in the cooling system. The solution to monitoring nonoxidizing biocides was determined to be ATP technology. ATP monitoring methodology was compared to standard microbiological field monitoring methods. ATP monitoring provided real-time data and was found to be an excellent monitor of nonoxidizing biocide efficacy. ATP methodology performed equally well in the presence of chlorine. Results of the effects of biocide on microbes were obtained within one hour after feeding the biocide. The total time needed to process the samples and obtain results was less than ten minutes. Field application data and results are discussed.
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Tidwell, Timothy J., Renato De Paula, Zach Broussard, and Victor Keasler. "A Comprehensive Approach to Diagnosing a Solution for a South Texas Production System with Severe MIC." In CORROSION 2016. NACE International, 2016. https://doi.org/10.5006/c2016-07770.
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Abstract Microbially Influenced Corrosion is primarily caused by sessile microbes found within a biofilm. The ultimate goal of many biocide treatments is the removal of any biofilm within that system. These cells may be killed but remain in place, be removed but not killed, or may be both killed and removed. Many of the factors that determine the fate of sessile cells are poorly understood. For example, deciding to treat a system with a low dose of biocide for a long period of time or to treat with a high dose of biocide for a short period of time may yield drastically different results in terms of reducing the risk of microbially influenced corrosion. In this study, we show a comprehensive approach to growing in vitro biofilms to conduct sessile kill studies for product qualification.
Reports on the topic "Microbes found"
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Boulin, Tiphaine, and Hannah Moody. The microbiome and breast cancer. Breast Cancer UK, 2024. https://doi.org/10.71450/56839173.
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The human microbiome, all the microbes and their genes found in the human body, plays a key role in influencing health and the development of diseases. The role of the gut microbiome has been extensively studied in relation to breast cancer risk, showing that dysbiosis, an imbalance in bacterial composition or distribution, of the gut microbiota is linked to a higher risk of breast cancer through different mechanisms. Other microbiomes and breast cancer risk are being studied, such as the breast, breast skin and oral microbiomes; however, to date, the strongest links identified are with the gut microbiome.
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Baldwin, Richard. PR-015-084508-R01 Contaminants in Sales Gas Pipelines Sources Removal and Treatment. Pipeline Research Council International, Inc. (PRCI), 2010. http://dx.doi.org/10.55274/r0010029.
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The objective of this project is to provide information about a problem material found in gas pipelines called "black powder". It is a mixture or a chemical compound of iron sulfides, iron oxides, dirt, sand, salts, chlorides, water, glycols, hydrocarbons and compressor oils, mill scale, or other materials. The most common constituents, iron compounds of sulfur or oxygen, are corrosion products. In addition to chemical formation, black powder can be formed by microbes normally found in gas pipelines. This material causes machinery, measurement, and pipeline maintenance problems. This research investigates the forms of iron sulfides, their characteristics, and methods of formation and whether the molecular form can be an indicator of the source of the material. A sampling protocol was developed for proper collection of materials for analysis. Seventeen corrosion samples were collected and analyzed for material constituents and microbial content. The results of this testing were anonymously tabulated in a database. Other tasks in this project include guidelines for removal, handling, and disposal of the material. It discusses symptomatic versus root cause treatments for the prevention and control of black powder, and the corporate culture necessary to manage the problem. It presents recently developed technologies for cleaning or treating a pipeline containing black powder, such as cleaning and anti-microbial agents containing THPS which dissolve iron sulfides, and the use of magnetic filtration. The final task describes concepts for identifying the location of black powder in an operating pipeline and places to look and methods to use to best determine the distribution of the material.
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Lindow, Steven, Yedidya Gafni, Shulamit Manulis, and Isaac Barash. Role and In situ Regulation of Growth Regulators Produced in Plant-Microbe Interactions by Erwinia herbicola. United States Department of Agriculture, 1992. http://dx.doi.org/10.32747/1992.7561059.bard.
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The main objective of this work was to gain a better understanding of how some strains of Erwinia herbicola have evolved into serious plant pathogens while also commonly existing as epiphytes on the surface of healthy plants. The focus of our studies was to determine the nature of, and regulation, of virulence factors, including the phytohormones IAA and cytokinins, which are encoded on a large plasmid (pPATH) found in gall-forming strains of this species. In addition, the in situ regulation and contribution to epiphytic fitness of a second, chromosomal, IAA biosynthetic locus (ipdC) was determined to ascertain the relative contribution of the two redundant IAA-biosynthetic pathways to the biology of E. herbicola. Genes (pre-etz and etz) conferring production of cytokinins were clustered immediately 3' of the iaaM and iaaH genes conferring IAA boisynthesis on pPATH. A new insertion-like element, IS1327, was also found immediately 3' of etz on pPATH, suggesting that these virulence factors were all introduced onto pPATH from another pathogenic bacterium. Mutants of E. herbicola in which etz, iaaH, and iaaM, but not ipdC, were disrupted caused smaller galls to form on gypsophila plants. In contrast, ipdC but not iaaH or iaaM mutants of E. herbicola exhibited reduced ability to grow and survive on plant surfaces. Transcription of ipdC was induced when cells were on plants compared to in culture, suggesting that idpC may play a selective role in fitness on leaves.
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Chen, Yona, Jeffrey Buyer, and Yitzhak Hadar. Microbial Activity in the Rhizosphere in Relation to the Iron Nutrition of Plants. United States Department of Agriculture, 1993. http://dx.doi.org/10.32747/1993.7613020.bard.
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Iron is the fourth most abundant element in the soil, but since it forms insoluble hydroxides at neutral and basic pH, it often falls short of meeting the basic requirements of plants and microorganisms. Most aerobic and facultative aerobic microorganisms possess a high-affinity Fe transport system in which siderophores are excreted and the consequent Fe complex is taken up via a cognate specific receptor and a transport pathway. The role of the siderophore in Fe uptake by plants and microorganisms was the focus of this study. In this research Rhizopus arrhizus was found to produce a novel siderophore named Rhizoferrin when grown under Fe deficiency. This compound was purified and its chemical structure was elucidated. Fe-Rhizoferrin was found to alleviate Fe deficiency when applied to several plants grown in nutrient solutions. It was concluded that Fe-Rhizoferrin is the most efficient Fe source for plants when compared with other among microbial siderophores known to date and its activity equals that of the most efficient synthetic commercial iron fertilizer-Fe EDDHA. Siderophores produced by several rhizosphere organisms including Rhizopus Pseudomonas were purified. Monoclonal antibodies were produced and used to develop a method for detection of the siderophores produced by plant-growth-promoting microorganisms in barley rhizosphere. The presence of an Fe-ferrichrome uptake in fluorescent Pseudomonas spp. was demonstrated, and its structural requirements were mapped in P. putida with the help of biomimetic ferrichrome analogs. Using competition experiments, it was shown that FOB, Cop B and FC share at least one common determinant in their uptake pathway. Since FC analogs did not affect FOB or Cop-mediated 55Fe uptake, it could be concluded that these siderophores make use of a different receptor(s) than FC. Therefore, recognition of Cop, FOB and FC proceeds through different receptors having different structural requirements. On the other hand, the phytosiderophores mugineic acid (MA and DMA), were utilized indirectly via ligand exchange by P. putida. Receptors from different biological systems seem to differ in their structural requirements for siderophore recognition and uptake. The design of genus- or species-specific drugs, probes or chemicals, along with an understanding of plant-microbe and microbe-microbe relationships as well as developing methods to detect siderophores using monoclonal antibodies are useful for manipulating the composition of the rhizosphere microbial population for better plant growth, Fe-nutrition and protection from diseases.
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Shpigel, Nahum Y., Ynte Schukken, and Ilan Rosenshine. Identification of genes involved in virulence of Escherichia coli mastitis by signature tagged mutagenesis. United States Department of Agriculture, 2014. http://dx.doi.org/10.32747/2014.7699853.bard.
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Mastitis, an inflammatory response of the mammary tissue to invading pathogenic bacteria, is the largest health problem in the dairy industry and is responsible for multibillion dollar economic losses. E. coli are a leading cause of acute mastitis in dairy animals worldwide and certainly in Israel and North America. The species E. coli comprises a highly heterogeneous group of pathogens, some of which are commensal residents of the gut, infecting the mammary gland after contamination of the teat skin from the environment. As compared to other gut microflora, mammary pathogenic E. coli (MPEC) may have undergone evolutionary adaptations that improve their fitness for colonization of the unique and varied environmental niches found within the mammary gland. These niches include competing microbes already present or accompanying the new colonizer, soluble and cellular antimicrobials in milk, and the innate immune response elicited by mammary cells and recruited immune cells. However, to date, no specific virulence factors have been identified in E. coli isolates associated with mastitis. The original overall research objective of this application was to develop a genome-wide, transposon-tagged mutant collection of MPEC strain P4 and to use this technology to identify E. coli genes that are specifically involved in mammary virulence and pathogenicity. In the course of the project we decided to take an alternative genome-wide approach and to use whole genomes bioinformatics analysis. Using genome sequencing and analysis of six MPEC strains, our studies have shown that type VI secretion system (T6SS) gene clusters were present in all these strains. Furthermore, using unbiased screening of MPEC strains for reduced colonization, fitness and virulence in the murine mastitis model, we have identified in MPEC P4-NR a new pathogenicity island (PAI-1) encoding the core components of T6SS and its hallmark effectors Hcp, VgrG and Rhs. Next, we have shown that specific deletions of T6SS genes reduced colonization, fitness and virulence in lactating mouse mammary glands. Our long-term goal is to understand the molecular mechanisms of host-pathogen interactions in the mammary gland and to relate these mechanisms to disease processes and pathogenesis. We have been able to achieve our research objectives to identify E. coli genes that are specifically involved in mammary virulence and pathogenicity. The project elucidated a new basic concept in host pathogen interaction of MPEC, which for the best of our knowledge was never described or investigated before. This research will help us to shed new light on principles behind the infection strategy of MPEC. The new targets now enable prevalence and epidemiology studies of T6SS in field strains of MPEC which might unveil new geographic, management and ecological risk factors. These will contribute to development of new approaches to treat and prevent mastitis by MPEC and perhaps other mammary pathogens. The use of antibiotics in farm animals and specifically to treat mastitis is gradually precluded and thus new treatment and prevention strategies are needed. Effective mastitis vaccines are currently not available, structural components and effectors of T6SS might be new targets for the development of novel vaccines and therapeutics.
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Yedidia, I., H. Senderowitz, and A. O. Charkowski. Small molecule cocktails designed to impair virulence targets in soft rot Erwinias. United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134165.bard.
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Chemical signaling between beneficial or pathogenic bacteria and plants is a central factor in determining the outcome of plant-microbe interactions. Pectobacterium and Dickeya (soft rot Erwinias) are the major cause of soft rot, stem rot, and blackleg formed on potato and ornamentals, currently with no effective control. Our major aim was to establish and study specific bacterial genes/proteins as targets for anti-virulence compounds, by combining drug design tools and bioinformatics with experimental work. The approach allowed us to identify and test compounds (small molecules) that specifically interfere with the activities of these targets, by this impairing bacterial virulence. Two main targets were selected within the frame of the BARD project. The first is the ATP-binding cassette (ABC) transporters and methyl-accepting chemotaxis proteins (MCP) that have been characterized here for the first time in Pectobacteriaceae, and the second is the quorum sensing (QS) machinery of Pectobacterium with its major proteins and in particular, the AHL synthase ExpI that was identified as the preferred target for inhibition. Both systems are strongly associated with bacterial virulence and survival in planta. We found that Pectobacteriaceae, namely Dickeya and Pectobacterium, encode more ABC transporters and MCP in their genomes, compared to other bacteria in the order. For MCP, soft rot Pectobacteriaceae not only contain more than 30 MCP genes per strain, but also have more diverse ligand binding domains than other species in the Enterobacteriales. These findings suggest that both ABC transporters and MCP are important for soft rot Pectobacteriaceae pathogenicity. We now have a selection of mutants in these proteins that may be further explored to understand their direct involvement in virulence. In parallel, we studied the QS central proteins in pectobacteria, the signaling molecule N-acyl-homoserine lactone synthase, ExpI, and the response regulator ExpR, and established their phylogenetic relations within plant pathogenic Gram negative bacteria. Next, these proteins were used for virtual screening of millions of compounds in order to discover new compounds with potential to interfere with the QS machinery. Several natural compounds were tested for their interference with virulence related traits in Pectobacterium and their capability to minimize soft rot infections. Our findings using microcalorimetric binding studies have established for the first time direct interaction between the protein ExpI and two natural ligands, the plant hormone salicylic acid and the volatile compound carvacrol. These results supported a model by which plants interfere with bacterial communication through interkingdom signaling. The collaborative project yielded two research papers and a comprehensive review, which included new computational and bioinformatics data, in Annu. Rev. Phytopathol., the highest ranked journal in phytopathology. Additional two papers are in preparation. In order to transform the fundamental knowledge that have been gained during this collaborative BARD project into agricultural practice, to control soft rot bacteria, we have submitted a continual project.
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Fluhr, Robert, and Maor Bar-Peled. Novel Lectin Controls Wound-responses in Arabidopsis. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7697123.bard.
Full textAbstract:
Innate immune responses in animals and plants involve receptors that recognize microbe-associated molecules. In plants, one set of this defense system is characterized by large families of TIR–nucleotide binding site–leucine-rich repeat (TIR-NBS-LRR) resistance genes. The direct interaction between plant proteins harboring the TIR domain with proteins that transmit and facilitate a signaling pathway has yet to be shown. The Arabidopsis genome encodes TIR-domain containing genes that lack NBS and LRR whose functions are unknown. Here we investigated the functional role of such protein, TLW1 (TIR LECTIN WOUNDRESPONSIVE1). The TLW1 gene encodes a protein with two domains: a TIR domain linked to a lectin-containing domain. Our specific aim in this proposal was to examine the ramifications of the TL1-glycan interaction by; A) The functional characterization of TL1 activity in the context of plant wound response and B) Examine the hypothesis that wounding induced specific polysaccharides and examine them as candidates for TL-1 interactive glycan compounds. The Weizmann group showed TLW1 transcripts are rapidly induced by wounding in a JA-independent pathway and T-DNA-tagged tlw1 mutants that lack TLW1 transcripts, fail to initiate the full systemic wound response. Transcriptome methodology analysis was set up and transcriptome analyses indicates a two-fold reduced level of JA-responsive but not JA-independent transcripts. The TIR domain of TLW1 was found to interact directly with the KAT2/PED1 gene product responsible for the final b-oxidation steps in peroxisomal-basedJA biosynthesis. To identify potential binding target(s) of TL1 in plant wound response, the CCRC group first expressed recombinant TL1 in bacterial cells and optimized conditions for the protein expression. TL1 was most highly expressed in ArcticExpress cell line. Different types of extraction buffers and extraction methods were used to prepare plant extracts for TL1 binding assay. Optimized condition for glycan labeling was determined, and 2-aminobenzamide was used to label plant extracts. Sensitivity of MALDI and LC-MS using standard glycans. THAP (2,4,6- Trihydroxyacetophenone) showed minimal background peaks at positive mode of MALDI, however, it was insensitive with a minimum detection level of 100 ng. Using LC-MS, sensitivity was highly increased enough to detect 30 pmol concentration. However, patterns of total glycans displayed no significant difference between different extraction conditions when samples were separated with Dionex ICS-2000 ion chromatography system. Transgenic plants over-expressing lectin domains were generated to obtain active lectin domain in plant cells. Insertion of the overexpression construct into the plant genome was confirmed by antibiotic selection and genomic DNA PCR. However, RT-PCR analysis was not able to detect increased level of the transcripts. Binding ability of azelaic acid to recombinant TL1. Azelaic acid was detected in GST-TL1 elution fraction, however, DHB matrix has the same mass in background signals, which needs to be further tested on other matrices. The major findings showed the importance of TLW1 in regulating wound response. The findings demonstrate completely novel and unexpected TIR domain interactions and reveal a control nexus and mechanism that contributes to the propagation of wound responses in Arabidopsis. The implications are to our understanding of the function of TIR domains and to the notion that early molecular events occur systemically within minutes of a plant sustaining a wound. A WEB site (http://genome.weizmann.ac.il/hormonometer/) was set up that enables scientists to interact with a collated plant hormone database.