Relevant bibliographies by topics / Native microbes

Academic literature on the topic 'Native microbes'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Native microbes"

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Koziol, Liz, Thomas P. McKenna, and James D. Bever. "Native Microbes Amplify Native Seedling Establishment and Diversity While Inhibiting a Non-Native Grass." Plants 12, no. 5 (March 6, 2023): 1184. http://dx.doi.org/10.3390/plants12051184.

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Although several studies have shown increased native plant establishment with native microbe soil amendments, few studies have investigated how microbes can alter seedling recruitment and establishment in the presence of a non-native competitor. In this study, the effect of microbial communities on seedling biomass and diversity was assessed by seeding pots with both native prairie seeds and a non-native grass that commonly invades US grassland restorations, Setaria faberi. Soil in the pots was inoculated with whole soil collections from ex-arable land, late successional arbuscular mycorrhizal (AM) fungi isolated from a nearby tallgrass prairie, with both prairie AM fungi and ex-arable whole soil, or with a sterile soil (control). We hypothesized (1) late successional plants would benefit from native AM fungi, (2) that non-native plants would outcompete native plants in ex-arable soils, and (3) early successional plants would be unresponsive to microbes. Overall, native plant abundance, late successional plant abundance, and total diversity were greatest in the native AM fungi+ ex-arable soil treatment. These increases led to decreased abundance of the non-native grass S. faberi. These results highlight the importance of late successional native microbes on native seed establishment and demonstrate that microbes can be harnessed to improve both plant community diversity and resistance to invasion during the nascent stages of restoration.
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Cai, Chaonan, Yingying Zhao, Yongge Yuan, and Junmin Li. "Parasitism Shifts the Effects of Native Soil Microbes on the Growth of the Invasive Plant Alternanthera philoxeroides." Life 13, no. 1 (January 4, 2023): 150. http://dx.doi.org/10.3390/life13010150.

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Soil microbes play an important role in plant invasion, and parasitic plants regulate the growth of invasive plants. However, the mechanisms by which parasitic plants regulate the effects of soil microbes on invasive plants have not been investigated. Here, we used the invasive plant Alternanthera philoxeroides and the holoparasitic plant Cuscuta grovonii to test whether and how C. grovonii parasitism shifts the effect of native soil microbes on the growth of A. philoxeroides. In a factorial setup, A. philoxeroides was grown in pots with the presence versus absence of parasitism and the presence versus absence of native soil microbes. The findings showed that native soil microbes increased the biomass and clonal growth of A. philoxeroides only in the absence of a parasite, whereas parasitism decreased the biomass and clonal growth of A. philoxeroides only in the presence of soil microbes. In addition, the presence of soil microbes increased the deleterious effects of the parasite on A. philoxeroides. These results indicate that parasitism can shift the effects of native soil microbes on the growth of the invasive plant A. philoxeroides. Our results enrich the understanding of the mechanisms underlying the success of plant invasion.
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Fox, Jeffrey L. "Native Microbes' Role in Alaskan Clean-Up." Nature Biotechnology 7, no. 9 (September 1989): 852. http://dx.doi.org/10.1038/nbt0989-852.

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Alfonzetti, Matthew, Sebastien Doleac, Charlotte H. Mills, Rachael V. Gallagher, and Sasha Tetu. "Characterizing Effects of Microbial Biostimulants and Whole-Soil Inoculums for Native Plant Revegetation." Microorganisms 11, no. 1 (December 24, 2022): 55. http://dx.doi.org/10.3390/microorganisms11010055.

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Soil microbes play important roles in plant health and ecosystem functioning, however, they can often be disturbed or depleted in degraded lands. During seed-based revegetation of such sites there is often very low germination and seedling establishment success, with recruitment of beneficial microbes to the rhizosphere one potential contributor to this problem. Here we investigated whether Australian native plant species may benefit from planting seed encapsulated within extruded seed pellets amended with one of two microbe-rich products: a commercial vermicast extract biostimulant or a whole-soil inoculum from a healthy reference site of native vegetation. Two manipulative glasshouse trials assessing the performance of two Australian native plant species (Acacia parramattensis and Indigofera australis) were carried out in both unmodified field-collected soil (trial 1) and in the same soil reduced in nutrients and microbes (trial 2). Seedling emergence and growth were compared between pelleted and bare-seeded controls and analyzed alongside soil nutrient concentrations and culturable microbial community assessments. The addition of microbial amendments maintained, but did not improve upon, high levels of emergence in both plant species relative to unamended pellets. In trial 1, mean time to emergence of Acacia parramattensis seedlings was slightly shorter in both amended pellet types relative to the standard pellets, and in trial 2, whole-soil inoculum pellets showed significantly improved growth metrics. This work shows that there is potential for microbial amendments to positively affect native plant emergence and growth, however exact effects are dependent on the type of amendment, the plant species, and the characteristics of the planting site soil.
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Lewin, Gina R., Apollo Stacy, Kelly L. Michie, Richard J. Lamont, and Marvin Whiteley. "Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes." Proceedings of the National Academy of Sciences 116, no. 39 (August 19, 2019): 19685–94. http://dx.doi.org/10.1073/pnas.1907619116.

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Recent evidence suggests that the genes an organism needs to survive in an environment drastically differ when alone or in a community. However, it is not known if there are universal functions that enable microbes to persist in a community and if there are functions specific to interactions between microbes native to the same (sympatric) or different (allopatric) environments. Here, we ask how the essential functions of the oral pathogen Aggregatibacter actinomycetemcomitans change during pairwise coinfection in a murine abscess with each of 15 microbes commonly found in the oral cavity and 10 microbes that are not. A. actinomycetemcomitans was more abundant when coinfected with allopatric than with sympatric microbes, and this increased fitness correlated with expanded metabolic capacity of the coinfecting microbes. Using transposon sequencing, we discovered that 33% of the A. actinomycetemcomitans genome is required for coinfection fitness. Fifty-nine “core” genes were required across all coinfections and included genes necessary for aerobic respiration. The core genes were also all required in monoinfection, indicating the essentiality of these genes cannot be alleviated by a coinfecting microbe. Furthermore, coinfection with some microbes, predominately sympatric species, induced the requirement for over 100 new community-dependent essential genes. In contrast, in other coinfections, predominately with nonoral species, A. actinomycetemcomitans required 50 fewer genes than in monoinfection, demonstrating that some allopatric microbes can drastically alleviate gene essentialities. These results expand our understanding of how diverse microbes alter growth and gene essentiality within polymicrobial infections.
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Zhang, Guangyi, Luji Yu, Panlong Liu, Zheng Fan, Tingmei Li, Tao Chen, and Xiaojing Zhang. "Ammonium removal by native microbes and activated sludge within the Jialu River basin and the associated microbial community structures." Water Science and Technology 76, no. 12 (September 20, 2017): 3358–67. http://dx.doi.org/10.2166/wst.2017.495.

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Abstract To explore the availability of native microbes and activated sludge for ammonium removal, the native microbes and activated sludge in Jialu River basin were investigated in terms of ammonium-removing activities and their microbial communities using spectrophotometry and high-throughput sequencing. NH4+-N and total nitrogen (TN) in the targeted river ranged from 2.45 ± 1.76 to 8.56 ± 2.54 mg/L and from 3.42 ± 2.79 to 13.49 ± 5.06 mg/L, respectively. Both the native microbes and activated sludge had strong ammonium-removing activities with the removal efficiencies of more than 94%. High-throughput sequencing results indicated that, after five batches of operation, the class Gammaproteobacteria (28.55%), Alphaproteobacteria (14.55%), Betaproteobacteria (13.89%), Acidobacteria (8.82%) and Bacilli (7.04%) were dominated in native community, and there was a predominance of Gammaproteobacteria (21.57%), Betaproteobacteria (16.33%), Acidobacteria (12.41%), Alphaproteobacteria (10.01%), Sphingobacteriia (6.92%) and Bacilli (6.66%) in activated sludge. These two microbial sources were able to remove ammonium, while activated sludge was more cost-effective.
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Nafady, Nivien Allam, Mohamed Bahy-El-Din Mazen, Mohamed Mahmoud Mohamed Ahmed, and Omaima Abdel Monsef. "Transfer of Nickel from Polluted Soil to Pisum sativum L. and Raphanus sativus L. under Composted Green Amendment and Native Soil Microbes." Agriculture (Pol'nohospodárstvo) 63, no. 2 (August 1, 2017): 52–66. http://dx.doi.org/10.1515/agri-2017-0005.

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Abstract The effect of compost, inoculation with native soil microbes and their residual effects on bioavailability of nickel by peas (Pisum sativum L.) and radish (Raphanus sativus L.) grown on polluted soil were investigated in pot experiments. Plants were amendment with different compost levels (0, 0.2, 0.4, 0.6% of soil dry weight) and inoculated with different native soil microbes (4 fungal species, one bacterial species, 4 species of arbuscular mycorrhizal fungi) isolated from the polluted soil under study. Significant increases in the biomass of pea and radish plants were observed as a result of amendment application and their residual effects. The mycorrhizal dependency (MD) of pea plants was lower than of radish plants. The highest reductions of Ni levels in both plants were observed by the simultaneous applications of compost with microbes or mycorrhizal fungi to polluted soils. Soil pH increased significantly (p < 0.05) as a result of applying native microbes especially with arbuscular mycorrhizal fungi (AMF) alone or combined with compost. The DTPA extractability of soil Ni was significantly decreased with increasing soil pH (p < 0.05). The minimum transfer factor of Ni from polluted soil were 0.067 and 0.089 for pea and radish plants, respectively which were attained as a result of applying compost (0.6% of soil weight) inoculated with mycorrhizal fungi. From the results, we can conclude that the use of compost and native soil microbes as a soil remediate could be an effective strategy for soil remediation.
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Fahey, Catherine, and Stephen Luke Flory. "Soil microbes alter competition between native and invasive plants." Journal of Ecology 110, no. 2 (November 8, 2021): 404–14. http://dx.doi.org/10.1111/1365-2745.13807.

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Liu, Manxi, Lu Xia, Ruinan Liu, Zongjun Gao, Cong Han, Jianguo Feng, Jing Wang, Wanlong Qu, and Tongju Xing. "Degradation of High-Concentration Nitrate Nitrogen in Groundwater: A Laboratory Study." Journal of Chemistry 2021 (May 28, 2021): 1–13. http://dx.doi.org/10.1155/2021/4797946.

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To investigate effective and reasonable methods for the remediation of nitrate nitrogen pollution in groundwater, two groups of laboratory denitrification experiments were conducted: one on the effect of native denitrifying microbes in groundwater and another on the effect of artificially added denitrifying microbes. The water used in the experiment was typical groundwater with a high concentration of nitrate nitrogen. The temperature was controlled at 15°C. Both groups of experiments established four types of culture environments: anaerobic, anaerobic with an added carbon source (glucose), aerobic, and aerobic with an added carbon source (glucose). The results indicated that native denitrifying microbes in the groundwater have almost no ability to remove high concentrations of nitrate nitrogen. However, artificially added denitrifying microbes can effectively promote denitrification. Artificially added denitrifying microbes had the highest activity in an anaerobic environment in which a carbon source had been added, and the rate removal of a high concentration of nitrate nitrogen in groundwater was the highest and reached as high as 89.52%.
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Rudgers, Jennifer A., and Samuel Orr. "Non-native grass alters growth of native tree species via leaf and soil microbes." Journal of Ecology 97, no. 2 (March 2009): 247–55. http://dx.doi.org/10.1111/j.1365-2745.2008.01478.x.

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Dissertations / Theses on the topic "Native microbes"

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Kiesel, Carola Angelika [Verfasser], Jean Charles [Akademischer Betreuer] Munch, and Jens [Akademischer Betreuer] Aamand. "Enhanced degradation of isoproturon in soils: sustainability of inoculated, microbial herbicide degraders, and adaptation of native microbes / Carola Angelika Kiesel. Gutachter: Jean Charles Munch ; Jens Aamand. Betreuer: Jean Charles Munch." München : Universitätsbibliothek der TU München, 2014. http://d-nb.info/1064523145/34.

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Fähndrich, Laura. "Tasting Bubbling Naturecultures and Touching M/other’s Hands : Aesthesias of Microbial Touch Points." Thesis, Linnéuniversitetet, Institutionen för design (DE), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-96876.

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This project explores co-being and interdependencies between human and more-than-human, the microbes, through the medium of fermentation and the (hidden) communities this practice embodies. Therewith not only resisting commodification and alienation from our food but facing our very own identity, and the human-made construct of human exceptionalism and detachment of nature and culture. The cells in ’our’ human body are outnumbered by the cells of other microorganisms. They even actively influence many of the bodily functions associated with the concept of ’self‘ (our brain, immune system and genome).1 Considering this, what does it even mean to be human? What does it mean to be me, If not cherishing and embracing the more-than-human, more-than-one-culture collective? The Korean word 손맛 ’son-mat’/ ’hand-taste’ refers to the inherited quality, love and care that went into preparing the (often associated with mother‘s) dish, something uniquely connected to the cook. While the microbes in sourdough can be linked to the baker‘s hand microbes, the baker‘s microbes have also shown to beaffected by the interaction with sourdough (Herman‘s (see picture to the right) microbial culture) with the scientific findings exposing our mutual interaction. This son-mat within fermentation I see as a symbolized touching point where our human realm and the microbial invisible microcosmos meet and become tangible. To emphasize this co-being, I work with our bodily senses, using design to bridge, making the insensible sensible, tangible, and audible. Staying curious and sprawling with my design approaches of creating narratives with the more-than-human, aimed to evoke questions and reflections of us and our culture. What happens when we share culture (human and microbial)? Through our hands, eating and digesting parts of others and becoming-with. To share culture means to see that humans and ’non-humans‘ are one. To taste that our culture is shared. And to feel that nature and culture are not two but one. Can you taste it?
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Laneuville, Ballester Sandra Isabel, and Ballester Sandra Isabel Laneuville. "Étude de l'interaction associative entre la β-lactoglobuline et le xanthane natif ou le xanthane traité aux hautes pressions hydrodynamiques." Doctoral thesis, Université Laval, 2004. http://hdl.handle.net/20.500.11794/18223.

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L’interaction associative entre la β-lactoglobuline et le xanthane (natif ou traité par hautes pressions hydrodynamiques) résultant en la formation de complexes électrostatiques a été étudiée par diverses techniques chimiques et physiques. L’objectif principal était d’approfondir les connaissances fondamentales au niveau moléculaire sur les interactions protéines – polysaccharides anioniques. Il a été trouvé que le mécanisme de séparation de phases associative suivi par ce système est une nucléation et croissance qui résultant en la formation de diverses structures fractales. Notamment, des différences de taille, de structure interne (compacité) et de solubilité ont été obtenues selon, entre autres, le pH et le ratio protéine – xanthane qui dirigent les processus de structuration dans le système en gouvernant, respectivement, la densité de charge des molécules et les effets d’équilibre de masse. L’importance et l’effet des forces de cisaillement appliquées (ou non) ainsi que la méthode d’acidification utilisée pendant la séparation de phases ont aussi été démontrés. Ainsi, lorsque la complexation a lieu sous cisaillement, la taille et la structure des complexes sont déterminées par un processus de restructuration induit par une compétition entre les forces électrostatiques attractives et les forces de rupture dues à l’écoulement. D’autre part, il a été démontré que le degré d’agrégation du xanthane est responsable des différentes structures formées puisque c’est le polysaccharide qui agit comme support lors de la complexation. Particulièrement, à des taux d’acidification lents, la taille des complexes peut être contrôlée en modifiant le poids moléculaire du xanthane. Les propriétés fonctionnelles des complexes obtenus peuvent ainsi être modifiées et façonnées en ajustant divers paramètres initiaux (ratio protéine – xanthane, poids moléculaire du xanthane) ainsi que les conditions présentes lors de leur fabrication (cisaillement, vitesse d’acidification). La fonctionnalité des complexes comme substituts de matière grasse a été évaluée dans des formulations modèles de garniture à biscuit ou glaçage à gâteaux. Les complexes ont conféré de bons attributs de viscosité et de texture aux échantillons faibles en gras.
L’interaction associative entre la β-lactoglobuline et le xanthane (natif ou traité par hautes pressions hydrodynamiques) résultant en la formation de complexes électrostatiques a été étudiée par diverses techniques chimiques et physiques. L’objectif principal était d’approfondir les connaissances fondamentales au niveau moléculaire sur les interactions protéines – polysaccharides anioniques. Il a été trouvé que le mécanisme de séparation de phases associative suivi par ce système est une nucléation et croissance qui résultant en la formation de diverses structures fractales. Notamment, des différences de taille, de structure interne (compacité) et de solubilité ont été obtenues selon, entre autres, le pH et le ratio protéine – xanthane qui dirigent les processus de structuration dans le système en gouvernant, respectivement, la densité de charge des molécules et les effets d’équilibre de masse. L’importance et l’effet des forces de cisaillement appliquées (ou non) ainsi que la méthode d’acidification utilisée pendant la séparation de phases ont aussi été démontrés. Ainsi, lorsque la complexation a lieu sous cisaillement, la taille et la structure des complexes sont déterminées par un processus de restructuration induit par une compétition entre les forces électrostatiques attractives et les forces de rupture dues à l’écoulement. D’autre part, il a été démontré que le degré d’agrégation du xanthane est responsable des différentes structures formées puisque c’est le polysaccharide qui agit comme support lors de la complexation. Particulièrement, à des taux d’acidification lents, la taille des complexes peut être contrôlée en modifiant le poids moléculaire du xanthane. Les propriétés fonctionnelles des complexes obtenus peuvent ainsi être modifiées et façonnées en ajustant divers paramètres initiaux (ratio protéine – xanthane, poids moléculaire du xanthane) ainsi que les conditions présentes lors de leur fabrication (cisaillement, vitesse d’acidification). La fonctionnalité des complexes comme substituts de matière grasse a été évaluée dans des formulations modèles de garniture à biscuit ou glaçage à gâteaux. Les complexes ont conféré de bons attributs de viscosité et de texture aux échantillons faibles en gras.
The associative interaction between β-lactoglobulin and xanthan gum (native or treated by high hydrodynamic pressures) resulting in the formation of electrostatic complexes was studied by several chemical and physical techniques. The main objective was to develop a fundamental knowledge of this system at a molecular level, to better understand the interactions between proteins and anionic polysaccharides. The associative phase separation in this system proceeded via a nucleation and growth mechanism that resulted in the formation of distinct fractal structures. Namely, differences in size, internal structure (compactness), and solubility were obtained depending principally on the pH and initial protein to polysaccharide ratio; which, in turn governed molecular charge density and mass action equilibrium effects determining the structuration processes. The important effects of the acidification method and the shearing forces applied during complexation were also identified. Particularly, it was revealed that when shear forces were applied during complexation the size and the structure of interpolymeric complexes were determined by restructuring processes set by a competition between attractive electrostatic forces and rupture forces caused by flow. Moreover, it was found that the aggregation pattern of xanthan gum was responsible for the formation of the different structures since it is the polysaccharide that acts as the support during complexation. Accordingly, at slow rates of acidification, a modification of the molecular weight of xanthan gum can control the size of the complexes. Therefore, the characteristics and functional properties of the complexes can be modified and tailored by adjusting the initial parameters and the conditions present during their manufacture.
The associative interaction between β-lactoglobulin and xanthan gum (native or treated by high hydrodynamic pressures) resulting in the formation of electrostatic complexes was studied by several chemical and physical techniques. The main objective was to develop a fundamental knowledge of this system at a molecular level, to better understand the interactions between proteins and anionic polysaccharides. The associative phase separation in this system proceeded via a nucleation and growth mechanism that resulted in the formation of distinct fractal structures. Namely, differences in size, internal structure (compactness), and solubility were obtained depending principally on the pH and initial protein to polysaccharide ratio; which, in turn governed molecular charge density and mass action equilibrium effects determining the structuration processes. The important effects of the acidification method and the shearing forces applied during complexation were also identified. Particularly, it was revealed that when shear forces were applied during complexation the size and the structure of interpolymeric complexes were determined by restructuring processes set by a competition between attractive electrostatic forces and rupture forces caused by flow. Moreover, it was found that the aggregation pattern of xanthan gum was responsible for the formation of the different structures since it is the polysaccharide that acts as the support during complexation. Accordingly, at slow rates of acidification, a modification of the molecular weight of xanthan gum can control the size of the complexes. Therefore, the characteristics and functional properties of the complexes can be modified and tailored by adjusting the initial parameters and the conditions present during their manufacture.
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Xiao, Xin-Yi, and 蕭歆怡. "Native microbes selection and inoculation for manufacturing ethanol and acetic acid." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/ypfeue.

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碩士
國立高雄第一科技大學
環境與安全衛生工程系碩士班
106
In Taiwan, microbrewery and ethanol-to-acid business commonly use forgein microbial species for fermentation. The climate effects result in the control of fermentation process using the forgein species rather strigent. Moreover, the limited use of the native species in fermentation constrains their potential uses in fermentation business. Thus, in this study native species for fermentation were to be inoculated and preserved, and there efficiency in fermentation checked. The objectives include: (1) to select the most highly efficient ethanol-producing and ethanol-oxidizing microbial species, (2) to study the important factors in fermenting sugar and ethanol, and (3) to test the feasible method in preserving the selected microbial species. During this study, grape liquor was used to produce ethanol and to inoculate the ethanol-producing species; and a commercial red wine and Taiwan beer was used for ethanol to acid conversion and to inoculate the ethanol-oxidizing microbial species. Gas chromatograph with a flame ionization detector (GC-FID) was used to monitor the ethanol and acid content, along with pH and microbial changes. The results demonstrated that at pH=6, Temperature= 25 oC, sugar of 20 grams, initial microbial counts at 8.5×104 CFU/mL, total volume of 300 mL and no mixing conditions, the most highest ethanol production concluded. Three fruits, pineapple, banana and grape, were fermented with the obtained microbial species, and the grape run had the highest ethanol production of 2.7% on day 12. The ethanol/sugar ratio was 0.45, which was lower than the literature value of 0.85-1.37. Also after 12 days the beer-incubated ethanol oxidizing microbes produced 2-3% acid at pH=6 and temperature= 25 oC. The acid/ethanol (beer) was 1.53, which was higher than literature value of 0.63-0.69. Finally, the results of using wet or dried flour for the preservation of the obtained microbial species revealed that the initial microbial counts of wet and dried flours were 5.17×106 and 5.95×105 CFU/g, respectively, which were dropped to 1.69×106 and 1.49×105 CFU/g after 14 days, respectively. About 40 and 10% ethanol production observed if the microbes restored from wet and dried flour, respectively. Similarly, the ethanol-oxidizing bugs in the wet and dried flour were 2.17×106及1.34×106 CFU/g, and were dropped to 3.67×105及9.06×104 CFU/g after 14 days. The lost of microbes in the preserving flour deserves more attention when performing the microbial preservative operation. Key words: ethanol-producing species, sugar to ethanol, ethanol-oxidizing species, ethanol to acid, preservation of microbial species
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Books on the topic "Native microbes"

1

B, Sheehan Kathy, ed. Seen and unseen: Discovering the microbes of Yellowstone. Guilford, Conn: Falcon, 2005.

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Schaible, Ulrich E., and Haas Albert. Intracellular niches of microbes: A pathogens guide through the host cell. Weinheim: Wiley-VCH, 2009.

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1925-, Pimentel David, ed. Biological invasions: Economic and environmental costs of alien plant, animal, and microbe species. Boca Raton: CRC Press, 2002.

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Biological invasions: Economic and environmental costs of alien plant, animal, and microbe species. 2nd ed. Boca Raton, FL: CRC Press, 2011.

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Alien Species and Evolution: The Evolutionary Ecology of Exotic Plants, Animals, Microbes, and Interacting Native Species. Island Press, 2004.

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Alien Species and Evolution: The Evolutionary Ecology of Exotic Plants, Animals, Microbes, and Interacting Native Species. Island Press, 2004.

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Haas, Albert, and Ulrich E. Schaible. Intracellular Niches of Microbes: A Microbes Guide Through the Host Cell. Wiley & Sons, Incorporated, John, 2009.

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Intracellular Niches of Microbes: A Microbes Guide Through the Host Cell. Wiley-Interscience, 2009.

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Sheehan, Kathy B., Brett Leigh Dicks, Joan M. Henson, and David J. Patterson. Seen and Unseen: Discovering the Microbes of Yellowstone. Falcon, 2005.

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Kirchman, David L. Elements, biochemicals, and structures of microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0002.

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Microbiologists focus on the basic biochemical make-up of microbes, such as relative amounts of protein, RNA, and DNA in cells, while ecologists and biogeochemists use elemental ratios, most notably, the ratio of carbon to nitrogen (C:N), to explore biogeochemical processes and to connect up the carbon cycle with the cycle of other elements. Microbial ecologists make use of both types of data and approaches. This chapter combines both and reviews all things, from elements to macromolecular structures, that make up bacteria and other microbes. The most commonly used elemental ratio was discovered by Alfred Redfield who concluded that microbes have a huge impact on the chemistry of the oceans because of the similarity in nitrogen-to-phosphorus ratios for organisms and nitrate-to-phosphate ratios in the deep oceans. Although statistically different, the C:N ratios in soil microbes are remarkably similar to the ratios of aquatic microbes. The chapter moves on to discussing the macromolecular composition of bacteria and other microbes. This composition gives insights into the growth state of microbes in nature. Geochemists use specific compounds, “biomarkers”, to trace sources of organic material in ecosystems. The last section of the chapter is a review of extracellular polymers, pili, and flagella, which serve a variety of functions, from propelling microbes around to keeping them stuck in one place.
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Book chapters on the topic "Native microbes"

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le Roux, Johannes J. "Molecular ecology of plant-microbial interactions during invasions: progress and challenges." In Plant invasions: the role of biotic interactions, 340–62. Wallingford: CABI, 2020. http://dx.doi.org/10.1079/9781789242171.0340.

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Abstract Microbes are omnipresent, yet their interactions with invasive plants remain understudied. This is surprising, given the importance of microbes in plant community ecology and their influence on plant performance in new environments. Recent advances in molecular genetic approaches have opened the door to studying this unseen majority in great detail and to understand how they fit into ecological interaction networks. Molecular approaches allow rapid assessments of microbial diversity at reasonable cost while providing both taxonomic and evolutionary information. Here I discuss how these approaches have contributed to a better understanding of plant-microbial interactions in the context of biological invasions. By drawing insights from various case studies, I illustrate how next-generation sequencing (DNA barcoding) has revolutionized the way we understand such interactions. Tight-knit and coevolved mutualist (e.g. mycorrhizal) and antagonist (e.g. pathogen) interactions appear particularly promising to understand the structure and function of invasive plant-microbial interaction networks, the impacts of invasive plants on native networks and the vulnerability of native networks to infiltration by non-native species. I also discuss novel ways in which molecular data can aid the study of invasive plant-microbial interactions, such as incorporating phylogenetic data into network analyses to better understand the role of evolutionary history in network dynamics and how such dynamics respond to plant invasions. DNA barcoding of microbes also presents unique challenges to the study of network ecology, such as uncertainty in the legitimacy and efficiency of interactions. Future research should incorporate overall plant-associated microbial communities (microbiomes) into interaction networks to better understand the role microbes play during plant invasions.
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Smith-Ramesh, Lauren M. "Allelopathic disruptions of biotic interactions due to non-native plants." In Plant invasions: the role of biotic interactions, 270–80. Wallingford: CABI, 2020. http://dx.doi.org/10.1079/9781789242171.0270.

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Abstract Allelopathy, or the process by which plants influence the growth and performance of their neighbours through the release of chemicals, may play a key role in mediating the impacts of non-native invasive species on their neighbours. The Novel Weapons Hypothesis purports that non-native invasive species are in part successful because they produce harmful allelochemicals to which resident species are particularly susceptible because residents lack a shared evolutionary history with the invader. While allelopathic non-native invaders may reduce the growth and performance of neighbours through direct phytotoxicity, they may more often exert negative impacts through disruption of biotic interactions among resident species. Allelopathy by non-native plants may disrupt mutualisms between resident plants and microbes, plant-herbivore interactions or existing competitive and facilitative interactions among resident plants. For example, several non-native plants are known to disrupt the mutualism between resident plants and mycorrhizal fungi, reducing resident plant fitness to the benefit of the invader. Allelopathic non-natives may also disrupt interactions among resident plants and their herbivores when allelochemicals also influence herbivore behaviour or fitness. Alternatively, biotic interactions can also be protective for resident species, which may be less susceptible to the impacts of non-native species when their mutualisms are intact. As we advance our understanding of allelopathy and its role in mediating the impacts of invasive plant species, we may gain new insights by viewing invasions within a network context rather than focusing on pairwise interactions.
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O'Malley, Maureen. "The Microbial Nature of Humans." In In the Company of Microbes, 42–46. Washington, DC, USA: ASM Press, 2016. http://dx.doi.org/10.1128/9781555819606.ch12.

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Elio. "The Fastest Flights in Nature." In In the Company of Microbes, 139–40. Washington, DC, USA: ASM Press, 2016. http://dx.doi.org/10.1128/9781555819606.ch34.

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Feng, Zengwei, Honghui Zhu, and Qing Yao. "Multi-Disciplinary Nature of Microbes in Agricultural Research." In Microbes in Agri-Forestry Biotechnology, 1–34. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003110477-1.

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Khan, Tabeer, Sidra Abbas, Anila Fariq, and Azra Yasmin. "Microbes: Nature’s Cell Factories of Nanoparticles Synthesis." In Exploring the Realms of Nature for Nanosynthesis, 25–50. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-99570-0_2.

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Oremland, Ronald S., and John Stolz. "Dissimilatory Reduction of Selenate and Arsenate in Nature." In Environmental Microbe-Metal Interactions, 199–224. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818098.ch9.

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Kanvinde, Lalita, M. H. Soliman, H. Wardhan, Lise Nowell, D. Fox, and G. R. K. Sastry. "Studies on the Diazotrophic Nature of Agrobacterium." In Molecular genetics of plant-microbe interactions, 309–12. Dordrecht: Springer Netherlands, 1987. http://dx.doi.org/10.1007/978-94-009-4482-4_79.

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Adebayo, E. A., I. C. Oladipo, J. A. Badmus, and A. Lateef. "Beneficial Microbes as Novel Microbial Cell Factories in Nanobiotechnology: Potentials in Nanomedicine." In Materials Horizons: From Nature to Nanomaterials, 315–42. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-33-4777-9_11.

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Yarzábal, Luis Andrés, and Eduardo J. Chica. "Potential for Developing Low-Input Sustainable Agriculture in the Tropical Andes by Making Use of Native Microbial Resources." In Plant-Microbe Interactions in Agro-Ecological Perspectives, 29–54. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-6593-4_2.

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Conference papers on the topic "Native microbes"

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Lyakhovchenko, N. S., V. Yu Senchenkov, D. A. Myagkov, D. A. Pribylov, A. A. Chepurina, I. A. Nikishin, A. A. Avakova, et al. "Determination of the taxonomic affiliation of the native isolate of the pigment-forming bacterium, separated from the Vezelka river of the city of Belgorod." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.157.

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The paper presents the results of a study of an aboriginal isolate of a pigment-forming bacterium isolated from the Vezelka River in the city of Belgorod, which makes it possible to determine its taxonomic affiliation.
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Ontivero, Roberto Emanuel, Lucía V. Risio, Hebe J. Iriarte, and Mónica A. Lugo. "Effect of Land-Use Change on Arbuscular Mycorrhizal Fungi Diversity in an Argentinean Endemic Native Forest." In The 2nd International Electronic Conference on Diversity (IECD 2022)—New Insights into the Biodiversity of Plants, Animals and Microbes. Basel Switzerland: MDPI, 2022. http://dx.doi.org/10.3390/iecd2022-12430.

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Chai Ching Hsia, Ivy, Mohd Firdaus Abdul Wahab, Nur Kamilah Abdul Jalil, Abigail Harriet Goodman, Hazratul Mumtaz Lahuri, and Sahriza Salwani Md Shah. "Accelerated Methanogenesis for the Conversion of Biomethane from Carbon Dioxide and Biohydrogen at Hyperthermophilic Condition." In International Petroleum Technology Conference. IPTC, 2023. http://dx.doi.org/10.2523/iptc-22744-ea.

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Abstract Methanogenesis is the conversion of carbon dioxide (CO2) to methane (CH4) using microbes. In the context CO2 utilization, methanogenesis process in the utilizing native microbes from a particular reservoir can be a very slow process without any external intervention. To accelerate the conversion rate and methane yield, this study investigates the use of agriculture by-product such as palm oil mill effluent (POME) as substrates as well as potential microbial isolates that can produce biohydrogen at high temperatures. This paper covers the three laboratory assessments of microbes from anaerobic sludge from a local palm oil mill, use of POME to augment the microbial growth, and physicochemical manipulation to identify key parameters that increases CH4 yield and rate: i) biohydrogen production ii) biomethane production, and iii) syntrophic reactions. All experiments are conducted at 70°C which is considered a hyperthermophilic condition for many microbes. Biohydrogen production achieved with highest H2 production of 66.00 (mL/Lmedium). For biomethane production, the highest production rate achieved was 0.0768 CH4 µmol/mL/day which 10,000X higher than 19.6 pmol/mL/day used as a benchmark. Syntrophic reaction with both types of hydrogen-producing and methanogen in the same reactor, and pure H2 and CO2 supplemented externally was able to achieve the highest methane production of 10.095 µmol/mL and 2.524 µmol/ml/day. Methane production rate is 2.5 times faster than without external gasses being introduced. Introduction of external CO2 to the syntrophic reaction is to mimic actual carbon injection and storage in the reservoir. Our paper shows that stimulation of microbes using POME as substrates and H2/CO2 supplementation are important in accelerating the rate of methane production and yield. Future work will focus on optimizing the gas ratio, pH of growth media, and performing syntrophic reaction in porous media to emulate conditions of a reservoir.
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Dias, Andrew D., David M. Kingsley, Douglas B. Chrisey, and David T. Corr. "Fabrication of Hybrid Cell-Microbead Constructs Using Laser Direct-Write of Alginate Microbeads and Adherent Breast Cancer Cells." In ASME 2013 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/sbc2013-14521.

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Microbeads are becoming popular tools in tissue engineering as 3D microstructure hydrogels. The gel nature of microbeads enables them to sequester soluble factors and mammalian cells, and their high surface area-to-volume ratio allows diffusion between the bead and the environment [1,2]. Microbeads are thus good systems for drug delivery and can serve as 3D microenvironments for cells. To fully maximize their potential as delivery systems and microenvironments, it is highly desirable to create spatially-precise hybrid cultures of microbeads and mammalian cells. Precise placement of microbeads in proximity to patterned cells will allow the study of spatial cellular interactions, paracrine signaling, and drug delivery.
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Markova, Yu A., L. A. Belovezhets, M. S. Tretyakova, A. M. Cheremnykh, and A. A. Levchuk. "The nature of the carbon source as a modulator of the response of bacteria to biologically active compounds (for example, colchicine and protatranes)." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.163.

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When assessing the impact of biological active compounds (colchicine and protatranes) on Rhodococcus erythropolis against the background of various carbon sources, an unusual effect of low concentrations of colchicine was revealed, that expressed in sharp stimulation of bacterial metabolism.
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Baranskaya, M. I., and L. A. Chaikovskaya. "Bacteria Lelliottia nimipressuralis CCM 32-3 - the producer of organic acids." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.034.

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Statsyuk, N. V., L. A. Shcherbakova, O. D. Mikityuk, T. A. Nazarova, and V. G. Dzhavakhiya. "Mycotoxin degradation by microbial metabolites." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.234.

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Extracellular metabolites of Gliocladium roseum GRZ7 are able to destroy aflatoxin B1 and zearalenone (by 61.9 and 68%, respectively). The determined optimum pH and temperature confirm the enzymatic nature of these metabolites.
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Vetchinkina, E. P., V. Yu Gorshkov, N. E. Gogoleva, Yu V. Gogolev, and V. E. Nikitina. "Comparative analysis of transcriptomes of different morphological structures of the basidiomycete Lentinus edodes." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.270.

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A comparative analysis of transcriptomes at the vegetative and generative stages of the development of Lentinus edodes basidiomycetes was carried out. The nature of differential gene expression was described, and the activated/repressed metabolic pathways were visualized.
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Yevstigneyeva, S. S., Yu P. Fedonenko, and A. V. Shelud’ko. "Biofilms of Azospirillum brasilense and Azospirillum lipoferum and their resistance to abiotic stresses." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.282.

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The biofilms of the bacteria A. brasilense and A. lipoferum are resistant to salt (over 400 mM NaCl in the medium) and temperature (up to 48° C) stresses. The nature of resistance to these stressors is determined by the type of biofilm.
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O’Connell, Grace D., Clare Gollnick, Gerard A. Ateshian, Ravi V. Bellamkonda, and Clark T. Hung. "Beneficial Effects of Chondroitinase ABC Release From Lipid Microtubes Encapsulated in Chondrocyte-Seeded Hydrogel Constructs." In ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53832.

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Tissue-engineered cartilage using a hydrogel scaffold is capable of achieving native compressive properties and glycosaminglycan (GAG) content [1]; however, promoting collagen growth towards native values has been challenging. As the cells in the cartilage constructs deposit matrix over time in culture, transport of nutrients to the construct center becomes increasingly hindered [2]. Digestion of mature tissue engineered constructs with chondroitinase (chABC) temporarily suppresses the GAG content, allowing an increase in the collagen content and eventually improving the mechanical properties after GAG content recovers [1]. However, adding chABC into the feeding media limits its effectiveness to the construct’s periphery, reflecting enzyme diffusion gradients. Additionally, long-term use of chABC, without re-application, is limited since its enzymatic activity degrades within 5 days at 37°C [3]. Lee and co-workers have developed a method for delivering thermostabilized chABC using sugar trehalose and hydrogel-microtubes for applications desiring extended enzyme release [4]. Lipid microtubes loaded with thermostabilized chABC may be incorporated into an agarose hydrogel scaffold to provide long-term release of the enzyme uniformly throughout the construct [3]. The objective of this study was to test the hypothesis that chABC-filled microtubes will enhance in vitro development of engineered cartilage.
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Reports on the topic "Native microbes"

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Minz, Dror, Eric Nelson, and Yitzhak Hadar. Ecology of seed-colonizing microbial communities: influence of soil and plant factors and implications for rhizosphere microbiology. United States Department of Agriculture, July 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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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, August 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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Dickman, Martin B., and Oded Yarden. Genetic and chemical intervention in ROS signaling pathways affecting development and pathogenicity of Sclerotinia sclerotiorum. United States Department of Agriculture, July 2015. http://dx.doi.org/10.32747/2015.7699866.bard.

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Abstract: The long-term goals of our research are to understand the regulation of sclerotial development and pathogenicity in S. sclerotior11111. The focus in this project was on the elucidation of the signaling events and environmental cues involved in the regulation of these processes, utilizing and continuously developing tools our research groups have established and/or adapted for analysis of S. sclerotiorum, Our stated objectives: To take advantage of the recent conceptual (ROS/PPs signaling) and technical (amenability of S. sclerotiorumto manipulations coupled with chemical genomics and next generation sequencing) developments to address and extend our fundamental and potentially applicable knowledge of the following questions concerning the involvement of REDOX signaling and protein dephosphorylation in the regulation of hyphal/sclerotial development and pathogenicity of S. sclerotiorum: (i) How do defects in genes involved in ROS signaling affect S. sclerotiorumdevelopment and pathogenicity? (ii) In what manner do phosphotyrosinephosphatases affect S. sclerotiorumdevelopment and pathogenicity and how are they linked with ROS and other signaling pathways? And (iii) What is the nature of activity of newly identified compounds that affect S. sclerotiori,111 growth? What are the fungal targets and do they interfere with ROS signaling? We have met a significant portion of the specific goals set in our research project. Much of our work has been published. Briefly. we can summarize that: (a) Silencing of SsNox1(NADPHoxidase) expression indicated a central role for this enzyme in both virulence and pathogenic development, while inactivation of the SsNox2 gene resulted in limited sclerotial development, but the organism remained fully pathogenic. (b) A catalase gene (Scatl), whose expression was highly induced during host infection is involved in hyphal growth, branching, sclerotia formation and infection. (c) Protein tyrosine phosphatase l (ptpl) is required for sclerotial development and is involved in fungal infection. (d) Deletion of a superoxidedismutase gene (Sssodl) significantly reduced in virulence on both tomato and tobacco plants yet pathogenicity was mostly restored following supplementation with oxalate. (e) We have participated in comparative genome sequence analysis of S. sclerotiorumand B. cinerea. (f) S. sclerotiorumexhibits a potential switch between biotrophic and necrotrophic lifestyles (g) During plant­ microbe interactions cell death can occur in both resistant and susceptible events. Non­ pathogenic fungal mutants S. sclerotior111n also cause a cell death but with opposing results. We investigated PCD in more detail and showed that, although PCD occurs in both circumstances they exhibit distinctly different features. The mutants trigger a restricted cell death phenotype in the host that unexpectedly exhibits markers associated with the plant hypersensitive (resistant) response. Using electron and fluorescence microscopy, chemical effectors and reverse genetics, we have established that this restricted cell death is autophagic. Inhibition of autophagy rescued the non-pathogenic mutant phenotype. These findings indicate that autophagy is a defense response in this interaction Thus the control of cell death, dictated by the plant (autophagy) סr the fungus (apoptosis), is decisive to the outcome of certain plant­ microbe interactions. In addition to the time and efforts invested towards reaching the specific goals mentioned, both Pls have initiated utilizing (as stated as an objective in our proposal) state of the art RNA-seq tools in order to harness this technology for the study of S. sclerotiorum. The Pls have met twice (in Israel and in the US), in order to discuss .נחd coordinate the research efforts. This included a working visit at the US Pls laboratory for performing RNA-seq experiments and data analysis as well as working on a joint publication (now published). The work we have performed expands our understanding of the fundamental biology (developmental and pathogenic) of S. sclerotioז111וז. Furthermore, based on our results we have now reached the conclusion that this fungus is not a bona fide necrotroph, but can also display a biotrophic lifestyle at the early phases of infection. The data obtained can eventually serve .נ basis of rational intervention with the disease cycle of this pathogen.
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