Academic literature on the topic 'Soil microbiology – Research'
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Journal articles on the topic "Soil microbiology – Research"
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Mocali, Stefano, and Anna Benedetti. "Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology." Research in Microbiology 161, no. 6 (July 2010): 497–505. http://dx.doi.org/10.1016/j.resmic.2010.04.010.
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Al-Hashmi, Zeyana, and Said S. Al-Ismaily. "Environmental Soil Microbiology: A Novel Research-Oriented Laboratory Course for Undergraduate Students." Atlas Journal of Science Education 2, no. 2 (June 12, 2017): 77–83. http://dx.doi.org/10.5147/ajse.v2i2.79.
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Laboratory courses have a central and distinctive role in sci- ence education. The need of improving laboratory curricular materials in environmental soil microbiology education is a must more than ever as due to the followings: (i) emerg- ing of new types of soil biological problems associated with new manipulated environments, (ii) the intimacy of human, plants, and animals to soil microbial activities, and (iii) en- vironmental soil-connected issues is the area of current re- search interests. We present a novel research-oriented labo- ratory course for undergraduates in soil science, according to the need of reforming the laboratory curriculum as called by the National Science Education Standards to advocate in- quiry and cognitivity in teaching and learning. Our inquiry- based environmental soil microbiology laboratory course provides a good pedagogical opportunity in promoting criti- cal thinking, making predictions, proposing causative factors, and presenting consistent arguments to support a position through effective scientific writing. The novelty of our labora- tory curriculum relies on the integration of three main com- ponents namely the “skill learning”, “research experience”, and “effective writing skills” which ultimately may help in optimizing students thinking performance towards research oriented mindset. The course is divided into two modules (I
& II), where in module I students are introduced to the basic principles and techniques in soil microbiology. As for module II, students are assigned a research project to enhance their critical thinking and develop their conceptual skills in design- ing an experiment, problem solving, gathering and analy- sis of data, and scientific writing. The unit content can be modified to suit other specific laboratory curriculums in other branches of natural science without loss of students learning efficiency or impact.
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Al-Hashmi, Zeyana, and Said S. Al-Ismaily. "Environmental Soil Microbiology: A Novel Research-Oriented Laboratory Course for Undergraduate Students." Atlas Journal of Science Education 2, no. 2 (August 1, 2013): 77–83. http://dx.doi.org/10.5147/ajse.2013.0101.
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Kulmatiski, Andrew, and Karen H. Beard. "Reducing sampler error in soil research." Soil Biology and Biochemistry 36, no. 2 (February 2004): 383–85. http://dx.doi.org/10.1016/j.soilbio.2003.10.004.
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Alexander, Martin. "Highlights of Research in Division S-3-Soil Microbiology and Biochemistry Since 196." Soil Science Society of America Journal 50, no. 4 (July 1986): 839–40. http://dx.doi.org/10.2136/sssaj1986.03615995005000040001x.
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Geisen, Stefan, Martin Hartmann, and Christoph C. Tebbe. "The European Journal of Soil Biology: A catalyst for soil biodiversity research." European Journal of Soil Biology 102 (January 2021): 103262. http://dx.doi.org/10.1016/j.ejsobi.2020.103262.
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Meunier, Robert, and Saliha Bayır. "Metagenomics approaches in microbial ecology and research for sustainable agriculture." TATuP - Zeitschrift für Technikfolgenabschätzung in Theorie und Praxis 30, no. 2 (July 26, 2021): 24–29. http://dx.doi.org/10.14512/tatup.30.2.24.
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Technologies such as next generation sequencing (NGS) are transforming research fields at the methodological, conceptual, and organizational level. They open up new possibilities and bring with them new commitments and inherent limitations. We show from a philosophy of science perspective how NGS-based metagenomics has transformed microbial ecology and, with it, parts of agricultural soil science, which integrate ecological approaches with the aim to inform agricultural practices. We reconstruct agricultural science as design science (sensu Niiniluoto) and describe how the possibilities, commitments, and limitations of metagenomics approaches in microbial ecology shape values, situation assessments, and recommendations for interventions of soil microbiology in the context of sustainable agriculture.
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Dashko, Regina, and Anna Shidlovskaya. "Impact of microbial activity on soil properties." Canadian Geotechnical Journal 53, no. 9 (September 2016): 1386–97. http://dx.doi.org/10.1139/cgj-2015-0649.
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There are microorganisms in soils and their activity can have a positive or negative impact on soil properties and groundwater. The positive effect of microorganisms includes the self-purification and self-regulation of contaminated groundwater and soil. The negative effect on soil is the change in grain-size composition; the weakening of engineering properties of soils; and the development processes, such as biogas generation, microbial quick-sand formation, and soil liquefaction. This paper addresses the negative effects of microbial activity on soil. Research on the impact of microbial activity in an underground space has been motivated by observations associated with underground infrastructure, such as subway tunnels, utilities tunnels, deep mines including those with tailings, and infrastructure with shallow and deep foundations. An overview of microorganisms in soil and an analysis of microbial activity in soils under the influence of natural and human-made factors are presented. Field and laboratory experiments show the significant impact of microbial activity on the engineering properties and consistency of the soil. Due to the complexity of the process, a study of microbial activity in the soil profile requires an integration of microbiology, biochemistry, engineering geology, and geotechnical engineering knowledge and experience.
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Petersen, Joan, and Patrick Chan. "A College–High School Collaboration to Support Authentic Microbiology Research." American Biology Teacher 82, no. 4 (April 1, 2020): 201–8. http://dx.doi.org/10.1525/abt.2020.82.4.201.
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A partnership between a community college biology professor and a local high school teacher was established to engage high school students in authentic microbiology research. High school students isolated actinomycetes from soil samples and tested them for their ability to produce antimicrobial chemicals. They also designed and carried out their own experiments with these isolates. Laboratory reports, written assignments, and quizzes were used to assess the scientific learning of the subject covered by the research project. The students' attitudes about science and scientific research were assessed using a standardized survey and written reflection questions. In completing this project, the students applied their knowledge of the scientific method and experimental design to address authentic research questions. They also learned several hands-on laboratory skills, including serial dilution, aseptic technique, isolation of pure cultures, Gram staining, microscopy, and antimicrobial testing. Student feedback was overwhelmingly positive – many expressed an increased interest in pursuing a career in science, and most felt that the project helped them gain confidence in their ability to do science. This project illustrates the importance of establishing partnerships between secondary schools and academic institutions to successfully introduce research to younger students.
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Lestari, Widya, and Kamsia Dorliana Sitanggang. "KARAKTERISASI BAKTERI TANAH PERTANIAN ORGANIK DAN TANAH PERTANIAN ANORGANIK DAN UJI ANTAGONIS TERHADAP JAMUR AKAR PUTIH (Rigidoporus microporus)." JURNAL AGROPLASMA 7, no. 1 (May 20, 2020): 1–11. http://dx.doi.org/10.36987/agroplasma.v7i1.1684.
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Research on the Characterization and Antagonist Test of Organic Soil Bacteria and Inorganic Farm Soils Against White Root Fungi (Rigidoporus microporus), was studied at the USU FMIPA Microbiology Laboratory, Medan, in May 2018. The method used was the characterization of agricultural soil bacteria with scatter plates and Yeast media. Extract 1%, obtained 3 soil bacterial isolates namely Sp01, Sp02 and Sp03 and 3 isolates from the inorganic agricultural soils Spa1, Spa2, and Spa3 which were characterized by shape, color, elevation edge and edge of the colony. Sp02 and Sp03 bacteria have greater ability to inhibit the growth of Rigidoporus microporus than Sp01 with inhibition zones of 2.5 and 3.5 mm. Sp a1 bacterium has the highest inhibitory ability of 30 mm against Rigidoporus microporus compared to Spa2 and Spa3. Keywords: Bacteria, Rigidoporus microporus, Faarm soils
Dissertations / Theses on the topic "Soil microbiology – Research"
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Gullic, David Bryan. "Variations in the biodegradation potential of toluene with increasing depth in an unsaturated subsurface environment." Thesis, This resource online, 1990. http://scholar.lib.vt.edu/theses/available/etd-03042009-040343/.
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Liu, Yunhao. "Structural and biochemical analysis of HutD from Pseudomonas fluorescens SBW25 : a thesis submitted in fulfilment of the requirements for the degree of Master of Science in Molecular Biosciences at Massey University, Auckland, New Zealand." Massey University, 2009. http://hdl.handle.net/10179/1074.
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Pseudomonas fluorescens SBW25 is a gram-negative soil bacterium capable of growing on histidine as the sole source of carbon and nitrogen. Expression of histidine utilization (hut) genes is controlled by the HutC repressor with urocanate, the first intermediate of the histidine degradation pathway, as the direct inducer. Recent genome sequencing of P. fluorescens SBW25 revealed the presence of hutD in the hut locus, which encodes a highly conserved hypothetical protein. Previous genetic analysis showed that hutD is involved in hut regulation, in such a way that it prevents overproduction of the hut enzymes. Deletion of hutD resulted in a slow growth phenotype in minimal medium with histidine as the sole carbon and nitrogen source. While the genetic evidence supporting a role of hutD in hut regulation is strong, nothing is known of the mechanism of HutD action. Here I have cloned and expressed the P. fluorescens SBW25 hutD in E. coli. Purified HutD was subjected to chemical and structural analysis. Analytic size-exclusion chromatography indicated that HutD forms a dimer in the elution buffer. The crystal structure of HutD was solved at 1.80 Å (R = 19.3% and Rfree = 22.3%) by using molecular replacement based on HutD from P. aeruginosa PAO1. P. fluorescens SBW25 HutD has two molecules in an asymmetric unit and each monomer consists of one subdomain and two ß-barrel domains. Comparative structural analysis revealed a conserved binding pocket. The interaction of formate with a highly conserved residue Arg61 via salt-bridges in the pocket suggests HutD binds to small molecules with carboxylic group(s) such as histidine, urocanate or formyl-glutamate. The hypothesis that HutD functions via binding to urocanate, the hut inducer, was tested. Experiments using a thermal shift assay and isothermal titration calorimetry (ITC) analysis suggested that HutD binds to urocanate but not to histidine. However, the signal of HutD-urocanate binding was very weak and detected only at high urocanate concentration (53.23 mM), which is not physiologically relevant. The current data thus does not support the hypothesis of HutD-urocanate binding in vivo. Although the HutD-urocanate binding was not confirmed, this work has laid a solid foundation for further testing of the many alternative hypotheses regarding HutD function.
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Shi, Shengjing. "Influence of root exudates on soil microbial diversity and activity." Lincoln University, 2009. http://hdl.handle.net/10182/1549.
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Interactions between plant roots and soil microorganisms in the rhizosphere are critical for plant growth. However, understanding of precisely how root exudates influence the diversity and activity of rhizosphere microorganisms is limited. The main objective of this study was to investigate the effect of radiata pine (Pinus radiata) root exudates on rhizosphere soil microbial communities, with an emphasis on the role of low molecular weight organic anions. The study involved the development and validation of new methods for investigating rhizosphere processes in a purpose-built facility. This included development of an in situ sampling technique using an anion exchange membrane strip to collect a range of organic anions exuded from radiata pine roots grown in large-scale rhizotrons. These included tartarate, quinate, formate, malate, malonate, shikimate, lactate, acetate, maleate, citrate, succinate and fumarate. Soil microbial activity and diversity were determined using dehydrogenase activity and denaturing gradient gel electrophoresis. Links between organic anions in root exudates and rhizosphere soil microbial community structures were investigated by comparing wild type and genetically modified radiata pine trees which were grown in rhizotrons for 10 months. As expected, there was considerable temporal and spatial variability in the amounts and composition of organic anions collected, and there were no consistent or significant differences determined between the two tree lines. Significant differences in rhizosphere microbial communities were detected between wild type and genetically modified pine trees; however, they were inconsistent throughout the experiment. The shifts in microbial communities could have been related to changes in exudate production and composition. Based on results from the main rhizotron experiment, a microcosm study was carried out to investigate the influence of selected pine root exudate sugars (glucose, sucrose and fructose) and organic anions (quinate, lactate and maleate) on soil microbial activity and diversity. Soil microbial activity increased up to 3-fold in all of the sugar and organic anion treatments compared to the control, except for a mixture of sugars and maleate where it decreased. The corresponding impacts on soil microbial diversity were assessed using denaturing gradient gel electrophoresis and 16S rRNA phylochips. Addition of the exudate compounds had a dramatic impact on the composition and diversity of the soil microbial community. A large number of bacterial taxa (88 to 1043) responded positively to the presence of exudate compounds, although some taxa (12 to 24) responded negatively. Organic anions had a greater impact on microbial communities than sugars, which indicated that they may have important roles in rhizosphere ecology of radiata pine. In addition, a diverse range of potentially beneficial bacterial taxa were detected in soil amended with organic anions, indicating specific regulation of rhizosphere microbial communities by root exudates. This project highlighted the considerable challenges and difficulties involved in detailed investigation of in situ rhizosphere processes. Nonetheless, the findings of this study represent a significant contribution to advancing understanding of relationships between root exudates and soil microbial diversity, which will be further enhanced by refinement and application of the specific methodologies and techniques developed.
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Bertram, Janet. "Effects of cow urine and its constituents on soil microbial populations and nitrous oxide emissions." Diss., Lincoln University, 2009. http://hdl.handle.net/10182/1334.
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New Zealand’s 5.3 million strong dairy herd returns approximately 106 million litres of urine to pasture soils daily. The urea in that urine is rapidly hydrolysed to ammonium (NH₄⁺), which is then nitrified, with denitrification of nitrate (NO₃⁻) ensuing. Nitrous oxide (N₂O), a potent greenhouse gas (GHG), is produced via nitrification and denitrification, which are enzyme-catalysed processes mediated by soil microbes. Thus microbes are linked intrinsically to urine patch chemistry. However, few previous studies have investigated microbial dynamics in urine patches. Therefore the objective of these four experiments was to investigate the effects on soil microbial communities of cow urine deposition. Methods used included phospholipid fatty acid (PLFA) analyses of microbial community structure and microbial stress, dehydrogenase activity (DHA) assays measuring microbial activity, and headspace gas sampling of N₂O, ammonia (NH₃) and carbon dioxide (CO₂) fluxes. Experiment 1, a laboratory study, examined the influence of soil moisture and urinary salt content on the microbial community. Both urine application and high soil moisture increased microbial stress, as evidenced by significant changes in PLFA trans/cis and iso/anteiso ratios. Total PLFAs and DHA showed a short-term (< 1 week) stimulatory effect on microbes after urine application. Mean cumulative N₂O-N fluxes were 2.75% and 0.05% of the nitrogen (N) applied, from the wet (70% WFPS) and dry (35% WFPS) soils, respectively. Experiment 2, a field trial, investigated nutrient dynamics and microbial stress with plants present. Concentrations of the micronutrients, copper, iron and molybdenum, increased up to 20-fold after urine application, while soil phosphorus (P) concentrations decreased from 0.87 mg kg ⁻¹ to 0.48 mg kg⁻¹. Plant P was also lower in urine patches, but total PLFAs were higher, suggesting that microbes had utilised the available nutrients. Microbial stress again resulted from urine application but, in contrast to experiment 1, the fungal biomass recovered after its initial inhibition. Studies published during the course of this thesis reported that hippuric acid (HA) and its hydrolysis product benzoic acid (BA) significantly reduced N₂O-N emissions from synthetic cow urine, thus experiment 3 investigated this effect using real cow urine. Cumulative N₂O-N fluxes were 16.8, 5.9 and 4.7% of N applied for urine (U) alone, U+HA and U+BA, respectively. Since NH₃-N volatilisation remained unchanged, net gaseous N emissions were reduced. Trends in total PLFAs and microbial stress were comparable to experiment 1 results. Experiment 4 studied HA effects at different temperatures and found no inhibition of N₂O-N fluxes from HA-amended urine. However, mean cumulative N₂O-N fluxes were reduced from 7.6% of N applied at 15–20°C to 0.2% at 5–10°C. Total cumulative N emissions (N₂O-N + NH₃-N) were highest at 20°C (17.5% of N applied) and lowest at 10°C (9.8% of N applied). Microbial activity, measured as potential DHA, increased with increasing temperature. This work has clearly shown that the stimulation and inhibition of the soil microbial community by urine application are closely linked to soil chemistry and have significant impacts not only on soil nutrient dynamics but also on N₂O-N emissions and their possible mitigation.
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Bourguignon, Emmanuel. "Ecology and diversity of indigenous Trichoderma species in vegetable cropping systems." Lincoln University, 2008. http://hdl.handle.net/10182/641.
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The overall aim of this research was to improve the understanding of the ecology and diversity of Trichoderma species within the soil and rhizosphere of onion (Allium cepa L.) and potato (Solanum tuberosum L.) under intensive management in New Zealand. The indigenous Trichoderma population was measured in a field trial at Pukekohe over a three year period under six different crop rotation treatments. The treatments included two continuous onion and potato rotations (intensive), two onion/potato mixed rotation (conventional), and two green manure rotations (sustainable). Results showed that Trichoderma populations were stable in both the rhizosphere and bulk soil (1.5 x 10² to 8.5 x 10³ CFU g⁻¹ ODS). The planting and incorporation of an oat (Avena sativa L.) green manure in the sustainable rotations positively increased Trichoderma colony forming unit (CFU) numbers in the rhizosphere soil from 3.4 x 10² to 2.5 x 10³ g⁻¹ ODS. A Trichoderma species identification method was developed based on colony morphology. Representative isolates were verified using restriction fragment length polymorphism (RFLP) and DNA sequencing. The method allowed for rapid and reliable identification of isolated Trichoderma species. Five species were identified in the Pukekohe soil: T. asperellum, T. atroviride, T. hamatum, T. harzianum and T. koningii. Results showed identical species diversity between the rhizosphere, rhizoplane and bulk soil. The species did not strongly compete between each other for the rhizosphere ecological niche and differences in species proportions seemed to be caused by environmental factors rather than the rotation treatments. The incorporation of oat green manure in pots did not significantly promote the indigenous Trichoderma population size and diversity in the rhizosphere of onion plants up to 4 months old. The identified species were the same as in the field trial. The incorporation of onion scale residues was shown to result in low Trichoderma and high Penicillium CFU numbers and a reduction in plant size. Additionally, the presence of high levels (6.0 x 10⁵ CFU g⁻¹ ODS) of Penicillium CFU was negatively correlated with the presence of Trichoderma CFU. The effect of oat incorporation on Trichoderma saprophytic growth was also investigated in a soil sandwich assay and revealed no significant differences. A series of experiments indicated that onion extract obtained from dry onion scale residues had no antifungal activity against either Trichoderma or Penicillium and instead tended to promote their hyphal growth and sporulation. It also showed that competition between Penicillium and Trichoderma isolates was limited despite the ability of Penicillium to produce a wide range of inhibitory substances. Four indigenous Trichoderma species (T. atroviride, T. hamatum, T. harzianum and T. koningii) were shown to be rhizosphere competent in a split tube experiment over a 6 week period. The results of this experiment revealed that, the Trichoderma species clearly displayed differences in their ability to colonise the rhizosphere of young onion seedlings. Species such as T. koningii had the greatest rhizosphere colonising ability regardless of soil depth while T. harzianum displayed the weakest ability. Results also indicated that when inoculated as a mixture the four species competed with one another to colonise the rhizosphere. Overall, this research indicated that the studied crop rotation treatments and the use of oat as a green manure did not strongly promote indigenous Trichoderma populations. Species diversity was constant throughout the research with T. hamatum and T. koningii being the most frequently isolated species.
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Dore, Dalin Shelley. "Grapevine rhizosphere bacteria : influence of diversity and function on two root diseases : a thesis submitted in fulfilment of the requirements for the degree of Master of Science at Lincoln University /." Diss., Lincoln University, 2009. http://hdl.handle.net/10182/1305.
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The overall goal of this research was to determine what, if any, role grapevine rhizosphere bacteria play in the differing susceptibilities of New Zealand grown rootstocks to Cylindrocarpon black foot disease. The size and diversity of bacterial populations associated with the rhizospheres of grapevine rootstocks: 101-14, 5C, Schwarzmann and Riparia Gloire were evaluated. Dilution plating showed that total bacterial (P=0.012, P=0.005 for NA and KB, respectively) and fluorescent Pseudomonad (P=0.035) rhizosphere counts differed between rhizosphere and bulk soils but did not correlate with the differing susceptibilities of the rootstock varieties to black foot. No varietal differences were found for spore forming bacteria (P=0.201). SSCP banding patterns showed that species diversity was similar for most rootstocks, but that there were some differences in the composition of bacterial populations, probably attributable to vigour. Some functional characteristics of the bacteria isolated from the rhizospheres of the most and least susceptible rootstock varieties were assessed to investigate their potential to suppress the pathogen. In dual culture, bacteria from Riparia Gloire, 101-14 and the control soil all had little ability to antagonise Cylindrocarpon destructans. However, they differed in their degrees of activity for glucanase (P=0.000), protease (P=0.001) and siderophores (P=0.000). In all tests, bacterial isolates from the rhizosphere of 101-14 had the largest number of active isolates (P≤0.002); however, those from Riparia Gloire had the greatest degree of positive responses for the glucanase and siderophore assays. Bacterial isolates from the control soil produced few glucanases and no siderophores, but had the highest degree of protease activity. Bands excised and sequenced from SSCP gels frequently matched to other ‘uncultured bacteria’ in GenBank, as well as to other bacterial phyla, classes and genera commonly isolated from soil and sediment samples. These included members of the Firmicutes, Proteobacteria (α, δ, γ), Verrucomicrobia, Acidobacteria and Chromatiales. The pathogenicity of C. destructans and Fusarium oxysporum was investigated by inoculating soil containing wounded ungrafted rootstocks of 101-14, 5C, Schwarzmann and Riparia Gloire. Results indicated that F. oxysporum might be a more aggressive pathogen than C. destructans. Inoculation with F. oxysporum or C. destructans increased disease severity, P=0.018 and P=0.056, respectively at 0 cm. Rootstock variety influenced disease severity caused by C. destructans (P<0.001) and F. oxysporum (P=0.090), with rootstocks 101-14 and 5C being most susceptible to C. destructans, and Riparia Gloire and Schwarzmann most susceptible to F. oxysporum. There was also an indication that inoculation with one pathogen increased plant susceptibility to the other, with increased F. oxysporum infection in the C. destructans inoculated treatments of Riparia Gloire and Schwarzmann (P<0.05). The effect of carbohydrate stress (leaf trimming) and inoculation on C. destructans disease severity, incidence, and rootstock rhizosphere bacterial populations was evaluated by inoculating the soil containing one year old plants of Sauvignon Blanc scion wood grafted to rootstocks 101-14 and Schwarzmann. Disease severity and incidence was similar for both Schwarzmann (8.4% and 29.3%, respectively) and 101-14 (14.9% and 31.0%, respectively). When data for the moderate and no stress treatments were combined, because their effects were similar, the disease severity was significantly higher for the highly stressed plants(P=0.043). Stress did not influence disease incidence (P=0.551). Infection occurred in the non-inoculated plants, but disease severity was higher in the plants inoculated with C. destructans than those that were not. Root dry weight of highly stressed plants was lower than in both the moderately stressed (P=0.000) and unstressed plants (P=0.003). An interaction between inoculation and stress (P=0.031) showed that inoculated and highly stressed plants had the lowest root dry weight but there was no effect of rootstocks (P=0.062). There was no significant effect of carbohydrate stress (P=0.259) or inoculation (P=0.885) on shoot dry weight. SSCP banding patterns showed that bacterial diversity was generally similar between rootstocks, but stress and inoculation altered rhizosphere bacterial communities. This study has demonstrated that functionality of grapevine rhizosphere bacteria do differ between grapevine rootstock varieties that have different susceptibilities to black foot disease, but that this role needs to be further investigated if more accurate and practically relevant conclusions are to be drawn.
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Chng, Soon Fang. "Microbial factors associated with the natural suppression of take-all in wheat in New Zealand : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Lincoln University, Canterbury, New Zealand /." Diss., Lincoln University, 2009. http://hdl.handle.net/10182/863.
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Take-all, caused by the soilborne fungus, Gaeumannomyces graminis var. tritici (Ggt), is an important root disease of wheat that can be reduced by take-all decline (TAD) in successive wheat crops, due to general and/or specific suppression. A study of 112 New Zealand wheat soils in 2003 had shown that Ggt DNA concentrations (analysed using real-time PCR) increased with successive years of wheat crops (1-3 y) and generally reflected take-all severity in subsequent crops. However, some wheat soils with high Ggt DNA concentrations had low take-all, suggesting presence of TAD. This study investigated 26 such soils for presence of TAD and possible suppressive mechanisms, and characterised the microorganisms from wheat roots and rhizosphere using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). A preliminary pot trial of 29 soils (including three from ryegrass fields) amended with 12.5% w/w Ggt inoculum, screened their suppressiveness against take-all in a growth chamber. Results indicated that the inoculum level was too high to detect the differences between soils and that the environmental conditions used were unsuitable. Comparison between the Ggt DNA concentrations of the same soils collected in 2003 and in 2004 (collected for the pot trial), showed that most soils cropped with 2, 3 and 4 y of successive wheat had reduced Ggt DNA concentrations (by 195-2911 pg g-1 soil), and their disease incidences revealed 11 of the 29 test soils with potential take-all suppressiveness. Further pot trials improved the protocols, such that they were able to differentiate the magnitudes of suppressiveness among the soils. The first of the subsequent trials, using 4% w/w Ggt inoculum level, controlled conditions at 16°C, 80% RH with alternate 12 h light/dark conditions, and watering the plants twice weekly to field capacity (FC), screened 13 soils for their suppressiveness against take-all. The 13 soils consisted of 11 from the preliminary trial, one wheat soil that had been cropped with 9 y of wheat (considered likely to be suppressive), and a conducive ryegrass soil. The results revealed that 10 of these soils were suppressive to take-all. However, in only four of them were the effects related to high levels of microbial/biological involvement in the suppression, which were assessed in an experiment that first sterilised the soils. In a repeat trial using five of the soils H1, H3, M2, P7 (previously cropped with 3, 3, 4 and 9 y successive wheat, respectively) and H15 (previously cropped with 5 y of ryegrass), three of them (H1, H3 and M2) had reduced Ggt DNA concentrations (>1000 pg g-1 soil reductions), and were confirmed to be suppressive to take-all. A pot trial, in which 1% of each soil was transferred into a γ-irradiated base soil amended with 0.1% Ggt inoculum, indicated that soils H1 and H3 (3 y wheat) were specific in their suppressiveness, and M2 (4 y wheat) was general in its suppressiveness. The microbial communities within the rhizosphere and roots of plants grown in the soils, which demonstrated conduciveness, specific or general suppressiveness to take-all, were characterised using PCR-DGGE, and identities of the distinguishing microorganisms (which differentiated the soils) identified by sequence analysis. Results showed similar clusters of microorganisms associated with conducive and suppressive soils, both for specific and general suppression. Further excision, re-amplification, cloning and sequencing of the distinguishing bands showed that some actinomycetes (Streptomyces bingchengensis, Terrabacter sp. and Nocardioides sp.), ascomycetes (Fusarium lateritium and Microdochium bolleyi) and an unidentified fungus, were associated with the suppressive soils (specific and general). Others, such as the proteobacteria (Pseudomonas putida and P. fluorescens), an actinomycete (Nocardioides oleivorans), ascomycete (Gibberella zeae), and basidiomycete (Penicillium allii), were unique in the specific suppressiveness. This indicated commonality of some microorganisms in the take-all suppressive soils, with a selected distinguishing group responsible for specific suppressiveness. General suppressiveness was considered to be due to no specific microorganisms, as seen in soil M2. An attempt to induce TAD by growing successive wheat crops in pots of Ggt-infested soils was unsuccessful with no TAD effects shown, possibly due to variable Ggt DNA concentrations in the soils and addition of nutrients during the experiment. Increasing numbers of Pseudomonas fluorescens CFU in the rhizosphere of plants, during successive wheat crops was independent of the Ggt DNA concentrations and disease incidence, suggesting that increases in P. fluorescens numbers were associated with wheat monoculture. This study has demonstrated that TAD in New Zealand was due to both specific and general suppressiveness, and has identified the distinguishing microorganisms associated with the suppression. Since most of these distinguishing microorganisms are known to show antagonistic activities against Ggt or other soilborne pathogens, they are likely to act as antagonists of Ggt in the field. Future work should focus on validating their effects either individually, or interactively, on Ggt in plate and pot assays and under field conditions.
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Aiken, Jane Tracy, University of Western Sydney, College of Health and Science, and School of Natural Sciences. "A soil microbial response to urban wastewater application : bacterial communities and soil salinity." 2006. http://handle.uws.edu.au:8081/1959.7/29055.
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Soils research at the University of Western Sydney, Hawkesbury Campus, was undertaken to investigate bacterial communities and soil salinity in an applied study. Microbial ecology was used to inform an understanding of conditions in soil irrigated with treated effluent. Several hypotheses were investigated examining changes in ecological organization conducted under laboratory and field conditions. Results indicated that relative abundance distributions for candidate forms of the bacteria community associated with higher and lower salinity, as defined using canonical correlation analysis, were reproducible between laboratory incubation experiments and field samples. The investigation is the first to apply the ecological parameter of richness and abundance to a study of microbial communities and their environment in order to determine soil conditions for sites irrigated with treated effluent. The thesis tests the theory and application of applying quantitative ecology to microbial community analysis.Doctor of Philosophy (PhD)
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"Using an Ecohydrology Model to Explore the Role of Biological Soil Crusts on Soil Hydrologic Conditions at the Canyonlands Research Station, Utah." Master's thesis, 2015. http://hdl.handle.net/2286/R.I.34907.
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abstract: Biological soil crusts (BSCs) dominate the soil surface of drylands in the western United States and possess properties thought to influence local hydrology. Little agreement exists, however, on the effects of BSCs on runoff, infiltration, and evaporative rates. This study aims to improve the predictive capability of an ecohydrology model in order to understand how BSCs affect the storage, retention, and infiltration of water into soils characteristic of the Colorado Plateau. A set of soil moisture measurements obtained at a climate manipulation experiment near Moab, Utah, are used for model development and testing. Over five years, different rainfall treatments over experimental plots resulted in the development of BSC cover with different properties that influence soil moisture differently. This study used numerical simulations to isolate the relative roles of different BSC properties on the hydrologic response at the plot-scale. On-site meteorological, soil texture and vegetation property datasets are utilized as inputs into a ecohydrology model, modified to include local processes: (1) temperature-dependent precipitation partitioning, snow accumulation and melt, (2) seasonally-variable potential evapotranspiration, (3) plant species-specific transpiration factors, and (4) a new module to account for the water balance of the BSC. Soil, BSC and vegetation parameters were determined from field measurements or through model calibration to the soil moisture observations using the Shuffled Complex Evolution algorithm. Model performance is assessed against five years of soil moisture measurements at each experimental site, representing a wide range of crust cover properties. Simulation experiments were then carried out using the calibrated ecohydrology model in which BSC parameters were varied according to the level of development of the BSC, as represented by the BSC roughness. These results indicate that BSCs act to both buffer against evaporative soil moisture losses by enhancing BSC moisture evaporation and significantly alter the rates of soil water infiltration by reducing moisture storage and increasing conductivity in the BSC. The simulation results for soil water infiltration, storage and retention across a wide range of meteorological events help explain the conflicting hydrologic outcomes present in the literature on BSCs. In addition, identifying how BSCs mediate infiltration and evaporation processes has implications for dryland ecosystem function in the western United States.Dissertation/Thesis
Masters Thesis Geological Sciences 2015
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Turner, Dee Ann. "Monitoring, characterizing, and preventing microbial degradation of ignitable liquids on soil." Thesis, 2013. http://hdl.handle.net/1805/5046.
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Indiana University-Purdue University Indianapolis (IUPUI)Organic-rich substrates such as soil provide an excellent carbon source for bacteria. However, hydrocarbons such as those found in various ignitable liquids can also serve as a source of carbon to support bacterial growth. This is problematic for fire debris analysis as samples may be stored at room temperature for extended periods before they are analyzed due to case backlog. As a result, selective loss of key components due to bacterial metabolism can make identifying and classifying ignitable liquid residues by their chemical composition and boiling point range very difficult. The ultimate goal of this project is to preserve ignitable liquid residues against microbial degradation as efficiently and quickly as possible. Field and laboratory studies were conducted to monitor microbial degradation of gasoline and other ignitable liquids in soil samples. In addition to monitoring degradation in potting soil, as a worst case scenario, the effect of soil type and season were also studied. The effect of microbial action was also compared to the effect of weathering by evaporation (under nitrogen in the laboratory and by the passive headspace analysis of the glass fragments from the incendiary devices in the field studies). All studies showed that microbial degradation resulted in the significant loss of n-alkanes and lesser substituted alkylbenzenes predominantly and quickly, while more highly substituted alkanes and aromatics were not significantly affected. Additionally, the residential soil during the fall season showed the most significant loss of these compounds over the course of 30 days. To combat this problem, a chemical solution is to be immediately applied to the samples as they are collected. Various household and commercial products were tested for their efficacy at low concentrations to eliminate all living bacteria in the soil. Triclosan (2% (w/v) in NaOH) proved to be the most effective at preserving ignitable liquid residues for at least 30 days.
Books on the topic "Soil microbiology – Research"
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Microbial bioremediation of non-metals: Current research. Norfolk: Caister Academic Press, 2011.
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Soil Microbial Systems Laboratory (U.S.). In-depth laboratory review October 19-21, 1994: Soil Microbial Systems Laboratory : soil quality, sustainable agriculture, composted waste, arbuscular mycorrhizae, pesticide metabolism, bioremediation, biocontrol management system. Beltsville, Md.]: The Laboratory, 1994.
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1953-, Dion Patrice, and Nautiyal Chandra Shekhar, eds. Microbiology of extreme soils. Berlin: Springer, 2008.
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Podila, Gopi K., and Ajit Varma. Basic Research & Applications of Mycorrhizae (Microbiology Series) (Microbiology Series). Anshan Ltd, 2006.
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(Editor), Gudni G. Hardarson, and William J. Broughton (Editor), eds. Molecular Microbial Ecology of the Soil: Results from an FAO/IAEA Co-ordinated Research Programme, 1992-1996 (Developments in Plant and Soil Sciences). Springer, 1999.
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G, Hardarson, Broughton William, FAO/IAEA Co-ordinated Research Programme, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture. Soil and Water Management & Crop Nutrition Section., and FAO/IAEA Agriculture and Biotechnology Laboratory. Soil Science Unit., eds. Molecular microbial ecology of the soil: Results from an FAO/IAEA Co-ordinated Research Programme, 1992-1996. Dordrecht: Kluwer Academic Publishers, 1998.
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(Editor), Kan Wang, Alfredo Herrera-Estrella (Editor), and Marc van Montagu (Editor), eds. Transformation of Plants and Soil Microorganisms (Biotechnology Research). Cambridge University Press, 2004.
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Begon, M., ed. Advances In Ecological Research (Advances in Ecological Research). Academic Press, 1997.
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K, Podila Gopi, and Varma A. 1939-, eds. Basic research and applications of Mycorrhizae. Kent, U.K: Anshan, 2006.
Find full textBook chapters on the topic "Soil microbiology – Research"
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St. Martin, Chaney C. G., Judy Rouse-Miller, Piterson Vilpigue, and Richard Rampersaud. "Application of Nanotechnology to Research on the Microbiology of Composting." In Soil Biology, 203–14. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-39173-7_10.
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Schmidt, E. L. "Soil Microbiology: The Prologue and the Promise." In Future Developments in Soil Science Research, 127–32. Madison, WI, USA: Soil Science Society of America, 2015. http://dx.doi.org/10.2136/1987.futuredevelopmentssoil.c14.
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Adhya, Tapan Kumar, and K. Annapurna. "Soil Microbiology Research in the Coming Decades: Translational Research Opportunities." In Advances in Soil Microbiology: Recent Trends and Future Prospects, 1–8. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-6178-3_1.
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Cheng, H. H. "Future Developments in Soil Microbiology and Biochemistry - An Introduction." In Future Developments in Soil Science Research, 125–26. Madison, WI, USA: Soil Science Society of America, 2015. http://dx.doi.org/10.2136/1987.futuredevelopmentssoil.c13.
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Sexstone, A. J., V. G. M. Calabrese, and R. C. Derk. "The Role of Soil Microbiology Research in the Northeastern United States." In Agricultural Research in the Northeastern United States: Critical Review and Future Perspectives, 27–35. Madison, WI, USA: American Society of Agronomy, 2015. http://dx.doi.org/10.2134/1993.agriculturalresearchinnortheastern.c4.
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Groffman, Peter M. "Soil Microbiology: Contributions from the Gene to the Global Scale." In Agricultural Research in the Northeastern United States: Critical Review and Future Perspectives, 19–26. Madison, WI, USA: American Society of Agronomy, 2015. http://dx.doi.org/10.2134/1993.agriculturalresearchinnortheastern.c3.
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Yu, T. R. "Introduction." In Chemistry of Variable Charge Soils. Oxford University Press, 1997. http://dx.doi.org/10.1093/oso/9780195097450.003.0004.
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The constitution and properties of soils have their macroscopic and microscopic aspects. Macroscopically, the profile of a soil consists of several horizons, each containing numerous aggregates and blocks of soil particles of different sizes. These structures are visible to the naked eye. Microscopically, a soil is composed of many kinds of minerals and organic matter interlinked in a complex manner. In addition, a soil is always inhabited by numerous microorganisms which can be observed by modern scientific instruments. To study these various aspects, several branches of soil science, such as soil geography, soil mineralogy, and soil microbiology, have been developed. If examined on a more minute scale, it can be found that most of the chemical reactions in a soil occur at the interface between soil colloidal surface and solution or in the solution adjacent to this interface. This is because these colloidal surfaces carry negative as well as positive charges, thus reacting with ions, protons, and electrons of the solution. The presence of surface charge is the basic cause of the fertility of a soil and is also the principal criterion that distinguishes soil from pure sand. The chief objective of soil chemical research is to deal with the interactions among charged particles (colloids, ions, protons, electrons) and their chemical consequences in soils. As depicted in Fig. 1.1, these charged particles are closely interrelated. The surface charge of soil colloids is the basic reason that a soil possesses a series of chemical properties. At present, considerable knowledge has been accumulated about the permanent charge of soils. On the other hand, our understanding is still at an early stage about the mechanisms and the affecting factors of variable charge. The quantity of surface charge determines the amount of ions that a soil can adsorb, whereas the surface charge density is the determining factor of adsorbing strength for these ions. Because of the complexities in the composition of soils, the distribution of positive and negative charges is uneven on the surface of soil colloidal particles. Insight into the origin and the distribution of these charges should contribute to a sound foundation of the surface chemistry of soils.
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Li, Jie Jack. "Reflections." In Laughing Gas, Viagra, and Lipitor. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780195300994.003.0014.
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In this book, I have chronicled eight categories of medicines. As a testament to the changing times, the old European master-apprentice relationship between drug discoverers is a thing of the past. This truth is exemplified by the feud between Selman Waksman and Albert Schatz (see chapter 2). I have no doubt that Waksman sincerely believed that he was the one responsible for the discovery of streptomycin. After all, streptomycin was the fruit of decades of his endeavor with soil microbiology in general and actinomycetes in particular. Schatz happened to be at the right place at the right time. Waksman’s conviction would have been completely acceptable if it had taken place just a century ago. Since the new millennium, vilifying the pharmaceutical industry has become fashionable. One of the crimes that the pharmaceutical industry is accused of committing involves the so-called me-too drugs. Even Merck’s former head of research Ed Scolnick once declared: “We at Merck do not do me-toos, if it is not innovative, we are not interested.” But history is replete with examples in which incremental improvements of a prototype yielded much better drugs. The first ACE inhibitor was teprotide, a peptide with nine amino acids, inspired by a Brazilian snake venom extract. Peptides did not survive in the stomach juice, which broke them down into amino acids. Therefore, the prototype teprotide could be used only by IV injection. With brilliant insight, David Cushman and Miguel Ondetti at Squibb Pharmaceuticals designed and synthesized captopril. Captopril was the first oral ACE inhibitor, which contributed tremendously to the management of hypertension. In theory, captopril is indeed a “me-too” drug to teprotide, but most patients would certainly prefer to take an oral drug than to have injections for the same purpose. Because captopril has a short duration of action, it has to be taken more than once a day. It possessed a trio of shortcomings: bone marrow suppression (due to a decrease in circulating white blood cells), skin rash, and a loss of taste.