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Jenkins, Anthony Blaine. "Organic carbon and fertility of forest soils on the Allegheny Plateau of West Virginia." Morgantown, W. Va. : [West Virginia University Libraries], 2002. http://etd.wvu.edu/templates/showETD.cfm?recnum=2486.
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Thesis (M.S.)--West Virginia University, 2002.Title from document title page. Document formatted into pages; contains x, 282 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references.
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Hoyle, Frances Carmen. "The effect of soluble organic carbon substrates, and environmental modulators on soil microbial function and diversity /." Connect to this title, 2006. http://theses.library.uwa.edu.au/adt-WU2007.0050.
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Coyle, Kieran. "An investigation of the role of soil micro-organisms in phosphorus mobilisation : a report submitted to fulfil the requrements of the degree of Doctor of Philosophy." Title page, table of contents and abstract only, 2001. http://web4.library.adelaide.edu.au/theses/09PH/09phc8814.pdf.
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Wagai, Rota. "Climatic and Lithogenic Controls on Soil Organic Matter-Mineral Associations." Fogler Library, University of Maine, 2005. http://www.library.umaine.edu/theses/pdf/WagaiR2005.pdf.
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Watts, Dexter Brown. "Mineralization in soils amended with manure as affected by environmental conditions." Auburn, Ala. :, 2007. http://repo.lib.auburn.edu/2007%20Spring%20Dissertations/WATTS_DEXTER_20.pdf.
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Menefee, Dorothy. "Anthropogenic influences on soil microbial properties." Thesis, Kansas State University, 2016. http://hdl.handle.net/2097/32657.
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Master of ScienceDepartment of Agronomy
Ganga M. Hettiarachchi
Human activities have the potential to alter soil biochemical properties in a number of different ways. This thesis will focus on how agricultural practices (tillage and cropping system), climate change, and urban soil pollution (primarily lead and arsenic) affect soil biochemical properties. Two incubation studies were conducted to determine how human activities influence soil biochemical properties. The first study focused on how altered temperature and moisture regimes affected soil properties from four different agroecosystems. Four different soils were incubated under two different soil preparation methods (sieved <4mm and <0.25 mm), three different temperature treatments (12, 24, and 36°C), and two different moisture treatments (field capacity and 80% of field capacity) for 180 days. Destructive samples were taken at 7, 30, 60, 120, and 180 days and the soil microbial community was analyzed using phospholipid fatty acid analysis (PLFA). The second study investigated how soil amendment treatments (Mushroom Compost and Composted Biosolids) of an industrially contaminated site affected the biochemical properties of that soil. Surface soil samples collected 435 days after compost addition from urban garden test plots located adjacent to a former rail yard in Monon, Indiana. Soils were incubated for 30 days to stimulate microbial activity. Following incubation, the soil was analyzed for PLFA, soil enzymes, and available metal fractions. In the first study the greatest differences were found between the <4mm and the <0.25 mm size fractions – which highlights the effect of soil aggregation and structure on microbial populations. After aggregation effects, temperature treatment had the next largest effect on microbial populations, with the greatest biomass in the middle (24°C) treatment. The second study assessed different soil amendments on soil microbial properties and metal availability. Composted biosolids reduced metal availability and increased microbial enzyme activity and biomass.
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Sutanto, Yovita. "Manure from grazing cattle effects on soil microbial communities and soil quality in northern West Virginia pastures /." Morgantown, W. Va. : [West Virginia University Libraries], 2005. https://etd.wvu.edu/etd/controller.jsp?moduleName=documentdata&jsp%5FetdId=3933.
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Thesis (M.S.)--West Virginia University, 2005.Title from document title page. Document formatted into pages; contains vii, 72 p. : ill. (some col.), map. Includes abstract. Includes bibliographical references.
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Lanza, G. R., and Phillip R. Scheuerman. "Effect of Soil Amendments on In Situ Biodegradation in Creosote Contaminated Soils." Digital Commons @ East Tennessee State University, 1996. https://dc.etsu.edu/etsu-works/2910.
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Padua, Roberto R. "Purification and characterization of an antimicrobial compound secreted by a soil bacterium /." Abstract Full Text (HTML) Full Text (PDF), 2008. http://eprints.ccsu.edu/archive/00000530/02/1979FT.htm.
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Thesis (M.A.) -- Central Connecticut State University, 2008.Thesis advisor: Michael A. Davis. "... in partial fulfillment of the requirements for the degree of Master of Arts in Biomolecular Sciences." Includes bibliographical references (leaves 36-39). Also available via the World Wide Web.
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Au, William R. "Relationships between microbial physiological status and nitrogen availability in forest soils." Thesis, McGill University, 1998. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=21506.
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Although the physiological nitrogen demand of the soil microbial biomass is a major determinant of N mineralization in forest soils, the exact nature of the relationship is unclear. This study investigated the relationships between a respiration-based indicator of microbial physiological N demand (NIR) and N availability in forest soils. NIR was found to correlate significantly with net mineralized N in the field and annual foliar litterfall N fluxes. In a laboratory incubation, NIR was shown to be sensitive to changes in soil available C and N pools. These results demonstrated that microbial physiological N demand is determined by relative availabilities of labile C and N, and that it is significantly related to N cycling in forest soils. Results from a seasonal study of a forested watershed suggest that nutrient availability determined tree production and soil C availability, which in turn determined microbial physiological N demand and nitrogen dynamics in the forest.
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Edvantoro, Bagus Bina. "Bioavailability, toxicity and microbial volatilisation of arsenic in soils from cattle dip sites." Title page, Contents and Abstract only, 2000. http://web4.library.adelaide.edu.au/theses/09A/09ae24.pdf.
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Kinneer, Krista L. "Size fractionation of bacterial functional diversity within soils." Morgantown, W. Va. : [West Virginia University Libraries], 1999. http://etd.wvu.edu/templates/showETD.cfm?recnum=1095.
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Thesis (M.S.)--West Virginia University, 1999.Title from document title page. Document formatted into pages; contains x, 68 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 47-48).
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Bellinger, Christina G. "Commercial Soils as a Potential Vehicle for Antibiotic Resistance Transmission." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1503298572132004.
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Shillam, Laura-Lee. "Structural diversity and decomposition functions of volcanic soils at different stages of development." Thesis, University of Stirling, 2008. http://hdl.handle.net/1893/444.
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During a volcanic eruption, the extrusion of lava onto surfaces destroys biological activity creating virgin land surfaces. Through time this new land will be subject to soil formation and colonisation under relatively similar climatic conditions and parent materials. Soils formed from volcanic deposits present a unique opportunity to study microbial community development. Soils at different developmental stages and differing in vegetation cover were selected from four locations on the slopes of Mount Etna, Sicily. Three main research objectives were determined in order to test the hypothesis that the microbial communities from soils at later stages of development would have a greater biomass, be more diverse, be more efficient at utilising carbon sources and recover from an environmental disturbance at a greater rate. A field experiment was conducted to ascertain the long term in situ catabolic abilities of the microbial communities in each soil and to establish the effects of litter mixing on decomposition rate. Litter bags containing either Genista aetnensis (Etnean Broom), Pinus nigra (Corsican Pine) or a mixture of the two were buried at each of the sites and their decomposition monitored over a 2.5 year period. PLFA diversity, community composition and function was assessed for each of the soils. The soils were also subject to a disturbance and the recovery of key community parameters was monitored over a six month period in order to establish each soil community’s resistance and resilience to disturbance. A laboratory experiment was conducted in order to investigate functional diversity and decomposition functions of each soil community using a range of simple and complex substrates. The relationship between PLFA diversity and functional diversity was also investigated. No correlation was found between soil C and N contents, microbial biomass or soil respiration and soil developmental stage and there was no detectable difference in litter bag mass loss between the soil types. No non- additive effects were noted in mixed litters. The more developed soil had a greater PLFA diversity and PLFA biomass however the more developed soil was not more resistant or resilient to disturbance. Developed soils showed greater catabolic diversity compared with less developed soils broadly correlating with PLFA diversity. Despite increased PLFA diversity and functional diversity in the more developed soils, residue decomposition in situ was unaffected. Reduced PLFA diversity and community complexity did not result in reduced function. Soils at different developmental stages had similar catabolic responses and were able to degrade simple and complex substrates to a similar degree. Microbial diversity in soil has the potential to be very high thus resulting in a high rate of functional redundancy i.e. many species within the same community which have the same functional role. It is possible that only a few key functional groups present within the soil community contribute to the main decomposition function within the soil and were able to maintain function during perturbation. Both Etna soils had similar PLFA’s present in similar concentrations and these groups in general were maintained during disturbance. This suggests that total microbial community diversity may not be as important to community function as the presence of key functional groups.
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STETZENBACH, LINDA DALE ALLEN. "THE DEGRADATION AND UTILIZATION OF POLYCYCLIC AROMATIC HYDROCARBONS BY INDIGENOUS SOIL BACTERIA (NAPHTHALENE, FLUORENE, ANTHRACENE, PYRENE)." Diss., The University of Arizona, 1986. http://hdl.handle.net/10150/183810.
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The persistance of industrially derived polycyclic aromatic hydrocarbons in the subsurface may be significantly affected by the metabolism of soil bacteria. This study was conducted to determine the ability of indigenous soil bacteria to decrease the concentration of four polycyclic aromatic hydrocarbons (naphthalene, fluorene, anthracene, and pyrene) and to utilize the compounds as a substrate for growth. Soil cores from petroleum contaminated and non-contaminated sites contained 10⁵ - 10⁷ viable microorganisms per gram dry weight of soil. Gram negative rod-shaped bacteria predominated. Decreases in the concentration of the four polycyclic aromatic hydrocarbons were observed during incubation with bacterial isolates in aqueous suspension by the use of high performance liquid chromatography. Corresponding increases in bacterial numbers indicated utilization of the compounds as a carbon source. Soil samples from the contaminated sites contained greater numbers of bacteria utilizing anthracene and pyrene than soil samples from non-contaminated sites. Degradation rates of the four polycyclic aromatic hydrocarbons were related to the compound, its concentration, and the bacterium. Biodegradation of pyrene was positively correlated with the presence of oxygen. Pyrene was biodegraded by an Acinetobacter sp. under aerobic conditions but not under anaerobic or microaerophilic conditions. Studies with radiolabeled ¹⁴C-anthracene demonstrated utilization of the labeled carbon as a source of carbon by viable bacterial cells in aqueous suspension. Incorporation of ¹⁴C into cellular biomass however was not observed during incubation of ¹⁴C-anthracene in soil.
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Juck, David F. "Polyphasic examination of microbial communities in soils contaminated with organic pollutants." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=38209.
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A polyphasic approach was used to examine the impact of contamination on soil microbial community structure. Two systems were examined using a combined biochemical and molecular biological approach. Petroleum hydrocarbon contaminated soils from two Northern Canadian sites, representing long-term contamination, were examined using Biolog GN plates and PCR-denaturing gradient gel electrophoresis (DGGE) analysis of total community 16S rDNA. Results obtained using both methods demonstrated a positive correlation between samples that was based on the geographical origin of the samples, not on contamination level. In the second system, non-contaminated soil was contaminated with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) to monitor the effect of short- to medium-term contamination. Changes in the soil microbial community were examined using PCR-DGGE of total community 16S rDNA combined with RDX mineralization and chemical analysis of intermediates. The non-contaminated loam soil had an inherent RDX degradative capability and contamination of soil columns with 1000 mg RDX/kg soil did not significantly change the 16S rDNA bacterial community profile. The bacterial diversity remained high as estimated by the number of bands present in the DGGE and by NQ-78704 statistical rarefaction analysis of 16S rDNA clone RFLPs. The same soil, used in 10% soil slurries (w/v), demonstrated two apparently different RDX degradation mechanisms based on mineralization and chemical analysis. The differences were based on aerobic versus anaerobic conditions and the presence/absence of Na3 citrate. PCR-DGGE performed on 16S rDNA from aerobic slurries amended with Na3-citrate detected the stimulation of 3 operational taxonomic units, identified as Stenotrophomonas sp., Sphingomonas sp. and a member of the Alcaligenaceae. The results from the two systems examined (short- to medium-term and long-term contamination) demonstrated the utility of a polyphasic approach in the examina
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Owojori, Olugbenga J. (Olugbenga John). "Influence of clay content and salinity on the bioavailability and toxicity of metals (copper and zinc) to soil organisms." Thesis, Stellenbosch : University of Stellenbosch, 2009. http://hdl.handle.net/10019.1/1484.
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Thesis (PhD (Botany and Zoology))—University of Stellenbosch, 2009.ENGLISH ABSTRACT: Metal pollution is a problem of increasing global concern. It could arise from industrial activities, as well as pesticide use in agriculture, among other sources. For adequate protection of the soil ecosystem from metal toxicity, the bioavailability of metals must be properly evaluated. A plethora of soil factors affect the bioavailability of metals to soil organisms. These include pH, clay and organic matter contents, salinity among others. While much is known about the influence of some of these parameters, little is known on how clay content and salinity modify the bioavailability of metals to soil organisms. This study investigated the influence of clay content and salinity on partitioning, uptake and toxicity of two essential metals (Cu and Zn) to the earthworm Eisenia fetida in separate laboratory trials. Partitioning of the metals was evaluated with 0.01 M CaCl2, DTPA (di-ethylene-triamine-penta acetic acid), and nitric acid extractions. The metal content of worms was determined by acid digestion, while growth, cocoon production, and mortality were used as endpoints showing toxicity to metals and/or salinity. To test the validity of some of the laboratory results, a field study was undertaken, using the earthworm Aporrectodea caliginosa. Further, the study assessed the effect of salinity, using a battery of laboratory tests (acute, chronic and avoidance tests) with natural and/or artificial soils on four species of organisms (a collembolan Folsomia candida, a potworm Enchytraeus doerjesi and two earthworm species E. fetida and A. caliginosa), representing different feeding patterns and ecological roles in soil. Results showed that with increased clay content, there was increased availability of Cu in the substrate, and increased toxicity to E. fetida as shown by data for mortality and growth. The situation with Zn was less significant at sub-lethal concentrations but much so at lethal concentrations. DTPA and CaCl2 extracted metals revealed changes in partitioning of Cu and Zn with changes in clay content, but this trend was not always consistent. Both DTPA and CaCl2 revealed increased availability of Zn in substrates with increased salinity. Salinity had an additive to synergistic effect with Zn in toxicity to E. fetida. When combined with Cu, salinity also increased the availability of Cu as shown by CaCl2 extracted fraction, and had additive effect on toxicity of Cu to the earthworm. The field study did not succeed in in iv confirming the results of the laboratory study due to confounding role of flooding after heavy rainfall and subsequent leaching of salts and Cu. The results of the experiment on acute and chronic toxicity tests for NaCl on E. fetida showed LC50 of 5436 mg/kg NaCl and EC50 for growth and cocoon production of 4985 and 2020 mg/kg NaCl. These values showed that earthworms might be negatively affected in many soils containing fairly moderate concentrations of salts. Similarly, A. caliginosa could not survive in natural soil containing relatively low salt concentrations (EC = 1.62 dS/m) while reproduction was severely affected at lower EC value of 0.52 dS/m. F. candida and E. doerjesi could survive in the highest salinity soil (EC = 1.62 dS/m) used in this study but their reproduction was severely affected from 1.03 dS/m. Overall, it appears that of all the taxa used, earthworm species were the most sensitive to saline stress and could proof useful in determining ‘safe levels’ of salt in contaminated soils. The results of the avoidance test showed that A. caliginosa avoided both natural and artificial saline soil containing concentrations lower than those avoided by E. fetida. The conclusion is that the influence of clay content and salinity on the bioavailability of Cu and Zn depends largely on the metal in question, but generally speaking, bioavailability and toxicity of the metals were reduced with increased clay content while the opposite was true for salinity. If the species used in this study can be seen as fairly representative of a wide range of soil organisms, the conclusion is that salinisation of soil will be detrimental to most soil organisms at relatively low saline concentrations. Given the role of beneficial soil organisms in several soil processes which in turn contribute to soil fertility and sustainable use of land, it is recommended that any farming practices that may lead to an increase in salt content of agricultural soils should be discouraged.
AFRIKAANSE OPSOMMING: Metaalbesoedeling is ‘n probleem wat toenemende globale kommer veroorsaak. Dit kan ontstaan as gevolg van industriële aktiwiteite sowel as van plaagmiddelgebruik in die landbou en ander bronne.Ten einde die grondekostelsel genoegsaam te beskerm, moet die biobeskikbaarheid van metale ge-evalueer word. ‘n Verskeidenheid van grondfaktore be-invloed die biobeskikbaarheid van metale vir grondorganismes Hulle sluit onder andere in pH, klei, organiese inhoud en soutgehalte. Hoewel heelwat bekend is oor die rol van sommige van hierdie parameters, is min bekend oor hoe klei en soutgehalte die biobeskikbaarheid van metale vir grondorganismes kan modifieer. Hierdie studie het die invloed van kleiinhoud and soutgehalte op die verdeling/partisie, opname en toksisiteit van twee essensiële metale (Cu en Zn) vir die erdwurm Eisenia fetida in afsonderlike laboratoriumproewe ondersoek. Kompartementele verdeling van die metale is geevalueer deur middel van ekstraksie-metodes met 0.01 M CaCl2, DTPA (di-etileentriamien- penta asysnsuur), en salpertersuur ekstraksies. Die metaalinhoud van wurms is bepaal deur suurverterings en spektrofotometriese analises te doen terwyl groei, kokonproduksie en mortaliteit van organismes gebruik is as gevoeligheidseindpunte om toksisiteit van metale en soutgehalte aan te toon. Om die geldigheid van somige van die laboratoriumresultate te toets, is ‘n veldstudie ook onderneem met die erdwurm Aporrectodea caliginosa. Die effek van soutgehalte is verder ondersoek deur ‘n battery van laboratoriumtoetse met vier spesies (‘n kollembool Folsomia candida,’n potwurm Enchytraeus doerjesi en twee erdwurmspesies E. fetida en A. caliginosa), wat verskillende voedingspatrone verteenwoordig. Die resultate het getoon dat met toenmende klei-inhoud was daar ‘n toename in die beskikbaarheid van Cu vir opname vanuit die substraat, asook ‘n toename in toksisiteit vir E. fetida soos deur die gegewens vir mortaliteit en groei uitgewys. Die situasie met Zn was minder betekenisvol by subletale konsentrasies en selfs baie minder so by letale konsentrasies. DTPA en CaCl2 ge-ekstraheerde metale het veranderinge in die partisie/verdeling van Cu en Zn uitgewys met verandering in klei-inhoud, maar die tendens was nie altyd konstant nie. Beide DTPA en CaCl2 ekstraksie het toenemende beskikbaarheid van Zn in substrate uitgewys met toenemende soutinhoud. Soutinhoud het ‘n additiewe/toegevoegde tot sinergistiese vi toksisiteitseffek saam met Zn vir E. fetida. In kombinasie met Cu het soutgehalte ook die geskatte biobeskikbaarheid van Cu verhoog soos uitgewys deur die CaCl2, geekstraheerde fraksie, en het ‘n additiewe effek gehad op die toksisitiet van Cu vir die erdwurm. Die veldstudie kon nie die resultate van die laboratoriumstudie bevestig nie weens die belemmerende rol van vloede na swaar reënneerslae en daaropvolgende uitloging van soute en Cu. Die resultate van die eksperimentele ondersoek na die akute en chroniese effekte van NaCl op E. fetida het ‘n LC50 van 5436 mg/kg NaCl en EC50 vir groei en kokonproduksie van 4985 en 2020 mg/kg NaCl opgelewer. Hierdie waardes het aangetoon dat erdwurms moontlik negatief beinvloed kan word in baie gronde wat ‘n redelike gemiddelde konsentrasie van soute bevat. Soortgelyk kon A. caliginosa nie oorleef in natuurllike grond wat relatief lae soutkonsentrasies bevat het (EC=1.62 dS/m) nie terwyl voortplanting sterk ge-affekteer is by ‘n lae EC waarde van 0.52 dS/m. F. candida en E. doerjesi kon oorleef in die grond met die hoogste soutgehalte (EC= 1.62 dS/m) maar hulle voortplanting is ernstig geknou vanaf 1.03 dS/m. In geheel blyk dit dat van allle taksa wat gebruik is, erdwurms die sensitiefste was vir die stres wat deur soutgehalte veroorsaak is. Die kennis kan nuttig wees in die bepaling van “veilige vlakke” van sout in gekontamineerde gronde. Die resultate van die vermydingstoetse het getoon dat A. caliginosa beide natuurlike en kunsmatig versoute gronde vermy het by konsentrasies wat heelwat laer was as dié wat deur E. fetida vermy is Die gevolgtrekking is dat die invloed van klei en soutgehalte op die biobeskikbaarheid van Cu en Zn grootliks afhanklik is van die metale wat betrokke is en dat biobeskikbaarheid en toksisiteit normaalweg verminder het met verhoogde klei-inhoud, met die teenoorgestelde wat waar was in die geval van soutgehalte. Indien die spesies wat in die studie gebruik is beskou kan word as redelik verteenwoordigend van ‘n wye reeks van grondorganismes, is die gevolgtrekking dat versouting van gronde nadelig sal wees vir meeste grondorganismes, selfs by relatief lae soutkonsentrasies. In die lig van die rol wat nuttige grondorganismes speel in verskeie grondprosesse wat bydraend is tot grondvrugbaarheid en volhoubare gebruik van gronde, word dit aanbeveel dat enige boerderypraktyk wat mag lei tot verhoging van die soutinhoud van landbougronde ontmoedig moet word.
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Wang, Jing, and 王静. "Culture-independent analysis of anammox, AOA and AOB in paddy soil of Sanjiang Plain in Northeast China." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B4622158X.
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Slabbert, Etienne. "Microbial diversity of soils of the Sand fynbos." Thesis, Stellenbosch : Stellenbosch University, 2008. http://hdl.handle.net/10019.1/4082.
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Thesis (MSc (Microbiology))--Stellenbosch University, 2008.The soil environment is thought to contain a lot of the earth’s undiscovered biodiversity. The aim of this study was to understand the extent of microbial diversity in the unique ecosystem of the Western Cape’s fynbos biome. It is known that many processes give rise to this immense microbial diversity in soil. In addition the aim was to link microbial diversity with the soils physio-chemical properties as well as the plant community’s structure. Molecular methods especially automated ribosomal intergenic spacer analysis (ARISA) was used in the study. The most important property of environmental DNA intended for molecular ecology studies and other downstream applications is purity from humic acids and phenolic compounds. These compounds act as PCR inhibitors and need to be removed during the DNA extraction protocol. The fist goal in the study was to develop an effective DNA extraction protocol by using cationic locculation of humic acids. The combination of cationic flocculation with CuCl2 and the addition of PVPP and KCl resulted in a high yield of DNA, suitable for PCR amplification with bacterial and fungal specific primers. Determining the reproducibility and accuracy of ARISA and ARISA-PCR was important because these factors have an important influence on the results and effectiveness of these techniques. Primer sets for automated ribosomal intergenic spacer analysis, ITS4/ITS5, were assessed for the characterization of the fungal communities in the fynbos soil. The primer set delivered reproducible ARISA profiles for the fungal community composition with little variation observed between ARISAPCR’s. ARISA proved useful for the assessment and comparison of fungal diversity in ecological samples. The soil community composition of both fungal and bacterial groups in the Sand fynbos was characterized. Soil from 4 different Sand fynbos sites was compared to investigate diversity of eubacterial and fungal groups at the local as well as a the landscape scale. A molecular approach was used for the isolation of total soil genetic DNA. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified when performing bacterial ARISA from total soil community DNA (BARISA). Correspondingly, the internal transcribed spacers, ITS1, ITS2 and the 5.8S rRNA gene from the fungal rRNA operon were amplified when undertaking fungal ARISA (F-ARISA). The community structure from different samples and sites were statistically analysed. ARISA data was used to evaluate different species accumulation and estimation models for fungal and bacterial communities and to predict the total community richness. Diversity, evenness and dominance were the microbial communities were used to describe the extent of microbial iversity of the fynbos soils. The spatial ordination of the bacterial and fungal species richness and diversity was considered by determining the species area relationship and beta diversity of both communities. The correlation between the soil physio-chemical properties was determined. The plant community structure data was correlated with the fungal and the bacterial community structure. The results indicated that bacterial species numbers and diversity were continually higher at the local scale. Fungi however showed higher species turnover at the landscape scale. Bacterial community structure showed stronger links to the plant community structure whereas the fungi community structure conformed to spatial separation patterns. To further investigate the diversity of soil microbes the potential of genus specific primes was investigated. The genus Penicillium is widespread in the soil environment and the extent of its diversity and distribution is however not. For this reason Penicillium was chosen as a model organism. To expand the insight into the diversity of Penicillium species in the fynbos soil ecosystem, a rapid group specific molecular approach would be useful. Penicillium specific primers targeting the 18S rRNA ITS gene region were evaluated. Fungal specific primers ITS4 and ITS5, targeting the internal transcribed region (ITS) were used to target Penicillium specific in the soil sample. Nested PCR, using primer Pen-10 and ITS5, was then utilized to target Penicillium species specifically. The discrimination of Penicillium species was possible due to length heterogeneity of this gene region. Eight different peaks was detected in the soil sample with ARISA and eight different species could be isolated on growth media. The technique proved useful for the detection and quantification of Penicillium species in the soil.
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Du, Plessis Keith R. (Keith Roland). "Biological indicators of copper-induced stress in soil." Thesis, Stellenbosch : Stellenbosch University, 2002. http://hdl.handle.net/10019.1/52719.
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Thesis (MSc)--University of Stellenbosch, 2002.ENGLISH ABSTRACT: The concentrations of copper (Cu) in vineyard soils of the Western Cape range from 0.1 to 20 ppm. However, more than 160 tons of the fungicide copper oxychloride are annually being sprayed on these vineyards. This has raised concerns that Cu may accumulate in these soils, resulting in a negative impact on the soil biological processes, especially since the soils in the Western Cape are slightly acidic, making Cu more mobile and available for soil organisms than would have been the case in alkaline soils. The goal of the initial part of this study was therefore to identify those soil microbial communities indigenous to the Western Cape, which are most susceptible to Cu-induced stress as a result of the addition of copper oxychloride. These potential bioindicators of Cu-induced stress were first searched for in uncultivated agricultural soil from Nietvoorbij experimental farm. Consequently, a series of soil microcosms was prepared by adding various concentrations of Cu as a component of copper oxychloride, to each of eight aliquots of soil: 0 (control), 10, 20, 30, 40, 50, 100, 500 and 1000 ppm. The resulting concentrations of exchangeable Cu in these microcosms were found to be 2 (control), 12,23,34,42,59, 126,516 and 1112 ppm. Selected microbial communities in each microcosm were subsequently monitored over a period of 245 days. It was found that the culturable microbial numbers did not provide a reliable indication of the effect of Cu on community integrity. However, analyses of terminal-restriction fragment length polymorphism (T-RFLP) community fingerprints and especially analyses of the whole community metabolic profiles, revealed that shifts in the soil microbial communities took place as the Cu concentration increased. Direct counts of soil protozoa also revealed that the addition of Cu to the soil impacted negatively on the numbers of these eukaryotes. To confirm these findings in other soil ecosystems, the impact of copper oxychloride on whole community metabolic profiles and protozoan numbers were investigated in soils from Koopmanskloof commercial farm and Nietvoorbij experimental farm. These potential bioindicators were subsequently monitored in a series of soil microcosms prepared for each soil type by adding the estimated amounts of 0 (control), 30, 100 and 1000 ppm Cu as a component of copper oxychloride to the soil. The results confirmed the fmdings that elevated levels of copper impact negatively on the metabolic potential and protozoan numbers of soil. Consequently, it was decided to investigate a combination of protozoan counts and metabolic profiling as a potential bioindicator for Cu-induced stress in soil. Data collected from all the microcosms containing exchangeable Cu concentrations ranging from 1 ppm to 1112 ppm was used to construct a dendrogram using carbon source utilization profiles in combination with protozoan counts. It was found that the microcosms grouped into clusters, which correlated with the concentration of exchangeable Cu in the soil. Under the experimental conditions used in this study, the combination of protozoan counts and metabolic profiling seemed to be a reliable indicator of Cu-induced stress. However, this bioindicator must be further investigated in other soil types using other types of stress inducing pollutants. In addition to the above fmdings it was also found that the numbers of soil protozoa was particularly susceptible to Cu-induced stress in soils with a low soil pH. This is in agreement with the fmdings of others on the bio-availability of heavy metals in low pH soils. In these soils, nutrient cycling as a result of protozoan activity, may therefore be particularly susceptible to the negative impact of copper to the soil.
AFRIKAANSE OPSOMMING: Die konsentrasies van koper (Cu) in wingerdgronde van die Wes-Kaap wissel tussen 0.1 en 20 dpm. Meer as 160 ton van die fungisied koper-oksichloried word egter jaarliks op dié wingerde gespuit, wat kommer laat ontstaan het oor die moontlike akkumulasie van Cu in dié grond en die gevaar van 'n negatiewe impak op die biologiese prosesse in die grond. Die gevaar word vererger deur die feit dat die Wes-Kaapse grond effens suur is, wat Cu meer mobiel en beskikbaar maak vir grondorganismes as wat die geval sou wees in alkaliese grond. Die eerste doelstelling van hierdie studie was dus om die mikrobiese gemeenskappe in die grond, wat inheems is aan die Wes-Kaap, te identifiseer wat die meeste vatbaar is vir Cu-geïnduseerde stres as gevolg van die toevoeging van koper-oksichloried. Hierdie potensiële bioindikatore van Cu-geïnduseerde stres is eerstens gesoek in onbewerkte landbougrond van die Nietvoorbij-proefplaas. 'n Reeks grondmikrokosmosse is gevolglik berei deur verskillende konsentrasies Cu, as 'n komponent van koperoksichloried, by elk van agt hoeveelhede grond te voeg naamlik 0 (kontrole), 10,20, 30, 40, 50, 100, 500 en 1000 dpm. Die gevolglike konsentrasies van uitruilbare Cu in hierdie mikrokosmosse was 2 (kontrole), 12, 23, 34, 42, 59, 126, 516 en 1112 dpm. Geselekteerde mikrobiese gemeenskappe in elke mikrokosmos is vervolgens oor 'n tydperk van 245 dae bestudeer. Daar is gevind dat die kweekbare mikrobiese tellings nie 'n betroubare aanduiding kon gee van die uitwerking van Cu op gemeenskapsintegriteit nie. Die ontledings van terminale-restriksie fragment lengte polymorfisme (T-RFLP) gemeenskapsvingerafdrukke en veral van die metaboliese profiele van die totale gemeenskap, het getoon dat verskuiwings in die grondmikrobiese gemeenskappe plaasgevind het met 'n toename in Cu-konsentrasies. Direkte tellings van grondprotosoë het ook aangedui dat die toevoeging van Cu tot die grond 'n negatiewe uitwerking op die getalle van hierdie eukariote gehad het. Om dié resultate te bevestig, is die impak van koper-oksichloried op die metaboliese profiele van totale gemeenskappe en protosoë-getalle in ander grond-ekosisteme vervolgens bestudeer deur grond van die kommersiële plaas Koopmanskloof en die Nietvoorbij-proefplaas te gebruik. Dié potensiële bioindikatore is vervolgens bestudeer in 'n reeks grondmikrokosmosse, wat vir elke grondtipe voorberei is deur die toevoeging van beraamde hoeveelhede van 0 (kontrole), 30, 100 en 1000 dpm Cu as 'n komponent van koper-oksichloried. Die resultate het die bevindings bevestig dat verhoogde vlakke van Cu 'n negatiewe uitwerking het op die metaboliese potensiaal en op die protosoëgetalle in die grond. Daar is gevolglik besluit om 'n kombinasie van protosoë-tellings en metaboliese profiele te ondersoek as 'n potensiële bioindikator van Cu-geïnduseerde stres in grond. Data van al die mikrokosmosse wat uitruilbare Cu bevat, wisselend van 1 dpm tot 1112 dpm, is gebruik om 'n dendrogram te konstrueer wat koolstofbronbenuttingsprofiele in kombinasie met protosoë tellings gebruik. Daar is gevind dat die mikrokosmosse groepe vorm wat korrelleer met die konsentrasie uitruilbare Cu in die grond. Onder die eksperimentele kondisies wat in dié studie gebruik is, wil dit voorkom of die kombinasie van protosoë-tellings en metaboliese profiele 'n betroubare indikator van Cugeïnduseerde stres is. Hierdie bioindikator moet egter verder in ander grondtipes en met ander tipes stres-induserende besoedeling ondersoek word. By bogenoemde bevindings is daar ook gevind dat die getalle grondprotosoë besonder gevoelig is vir Cu-geïnduseerde stres in grond met In lae pH. Dit is in ooreenstemming met die bevindings van andere met betrekking tot die bio-beskikbaarheid van swaar metale in grond met 'n lae pH. In dié tipe grond mag nutriëntsiklering as gevolg van protosoë aktiwiteit besonder gevoelig wees vir die negatiewe uitwerking van koper in die grond.
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Caleb, Oluwafemi James. "Microbial community structure as an indicator of soil health in apple orchards." Thesis, Stellenbosch : University of Stellenbosch, 2010. http://hdl.handle.net/10019.1/4133.
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Thesis (MSc (Microbiology))--University of Stellenbosch, 2010.ENGLISH ABSTRACT: The relationship between various land management practices, soil properties and the soil microbial communities are complex and little is known about the effect of these interactions on plant productivity in agricultural systems. Although it would be advantageous to have a single organism or property that can be used as a measure of soil health, it may not be possible. Soil organisms which include both the microorganisms as well as soil fauna are subjected to the effect of their immediate environment. This microenvironment in turn is determined by the soil properties as well as above ground flora and their interactions. Most soil indicators interact with each other, and these interactions can modify or influence the soil properties. The complexities of the interactions between critical soil indicator values often preclude its practical use by land managers and policy makers. However, soil microbial communities (e.g. diversity and structural stability) may serve as a relative indicator of soil quality. These communities are sensitive to land management practices and changes in the microenvironment. The objective of this study was to gain an understanding of the complex relationships by investigating the effect of conventional, integrated and organic apple production systems on the physical, chemical and biological (particularly soil microbial diversity) properties of the soil. Automated Ribosomal Intergenic spacer analysis (ARISA) was used to characterise fungal (F-ARISA) and bacterial (B-ARISA) communities from soil samples obtained from an experimental apple orchard in Elgin, Grabouw. The intergenic spacer (ITS) region from the fungal rRNA operon was amplified using ITS4 and fluorescently FAM (6- carboxylfluorescein) labelled ITS5 primers. Similarly, the 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified using ITSR and FAM-labelled ITSF primers. The sensitivity of the technique allowed us to discriminate between the soil microbial communities of the different treatments. From our results we observed significant increase (p < 0.05) in the fungal community diversity between the February and April samples, while the bacterial community diversity was consistent (p > 0.05). Also, treatments with mulch showed a significantly higher microbial diversity than the other treatments at a 5 % significance level. Fungal communities showed significant correlation with the potassium concentration in the soil, while bacterial communities depicted a significant correlation with the soil phosphorous concentration. Based on the results we concluded that different management practices have a significant effect on the soil microbial communities and that these communities are particularly sensitive to small changes in the environment. However, there is still a need to determine what the composition of the soil microbial communities are to be able to correlate our observations with soil health.
AFRIKAANSE OPSOMMING: Die verhouding tussen verskillende landboubestuurspraktyke, grondeienskappe en die mikrobiese gemeenskappe in grond is kompleks en weinig is bekend oor die uitwerking van hierdie interaksies op die produktiwiteit van landboustelsels. Alhoewel dit voordelig sou wees om ‘n enkele organisme of eienskap te kan hê wat die gesondheid van grond kan meet, sal dit dalk nie moontlik wees nie. Grondorganismes wat die mikroörganismes sowel as die grondfauna insluit, is onderworpe aan die invloed van hulle onmiddelike omgewings. Hierdie mikro-omgewings op hulle beurt word weer beïnvloed deur die grondeienskappe sowel as die die oppervlak flora en hulle wisselwerkinge. Meeste van die grondaanwysers toon ook wisselwerkinge met mekaar, en hierdie wisselwerkinge kan die grondeienskappe beïnvloed or selfs verander. Die kompleksiteit van die wisselwerkinge tussen kritiese grond aanwysers is meestal die rede waarom dit nie deur grondbestuurders en beleidsmakers gebruik word nie. Dit is ongeag die feit dat grond mikrobiese gemeenskappe (bv. diversiteit en stukturele stabiliteit) mag dien as ‘n relatiewe aanwyser van grondkwaliteit. Hierdie gemeenskappe is sensitief vir bestuurspraktyke en veranderinge in die mikro-omgewing. Die doel van die studie was om die ingewikkelde verhoudings in die grondgemeenskappe te bestudeer en die uitwerking van konventionele, geïntegreerde en organiese appel produksie sisteme op die fisiese, chemiese en biologiese eienskappe (veral die grond mikrobiologiese diversiteit) te bepaal. Geoutomatiseerde Ribosomale Intergeniese Spasie Analise (ARISA) is gebruik om die fungus (F-ARISA) en bakteriese (B-ARISA) gemeenskappe van grondmonsters wat vanaf ‘n proef appelboord in Elgin (Grabouw) verkry is, te bepaal. Die intergeenspasie (ITS) area van die fungus rDNA operon is vermeerder deur die ITS4 en fluoresserende FAM (6-karboxylfluorescein) gemerkte ITS5 inleiers te gebruik. Soortgelyk is die 16S-23S intergeenspasie area van die bakteriese rDNA operon vermeerder deur ITSR en FAM-gemerkte ITSF inleiers te gebruik. Die sensitiwiteit van die tegniek laat ons toe om te onderskei tussen die grond mikrobiese gemeenskappe vanaf verskillende grondbehandelings. Vanuit die resultate kon ons aflei dat daar ‘n toename (p < 0.05) in die fungus gemeenskap diversiteit vanaf Februarie to April was terwyl die bakteriese gemeenskap ‘n konstante diversteit getoon het (p > 0.05). Behandelings met grondbedekking het ook ‘n beduidend hoër mikrobiese diversiteit getoon as ander behandelings. Fungus gemeenskappe het beduidende korrelasies getoon met kalium konsentrasies in die grond, terwyl bakteriese gemeenskappe ‘n beduidende korrelasie getoon het met grond fosfor konsentrasies. Gebaseer op die resultate kon ons aflei dat verskillende bestuurspraktyke ‘n uitwerking kan hê op die grond mikrobiese gemeenskappe en dat hierdie gemeenskappe sensitief is vir klein veranderinge in die omgewing. Dit sal egter nog nodig wees om die spesifieke samestelling van die grond mikrobiese gemeenskappe te bepaal voor ons hierdie waarnemings kan korreleer met grondgesondheid.
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Bushula, Vuyiswa Sylvia. "Native Fusarium species from indigenous fynbos soils of the Western Cape." Thesis, Link to the online version, 2008. http://hdl.handle.net/10019/1878.
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Millar, Neville. "The effect of improved fallow residue quality on nitrous oxide emissions from tropical soils." Thesis, Imperial College London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.268667.
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Marí, Marí Teresa. "Changes in soil biodiversity and activity along management and climatic gradients." Doctoral thesis, Universitat de Lleida, 2017. http://hdl.handle.net/10803/457976.
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Els anomenats “rangelands” són àrees sense cultivar, àmpliament pasturades per animals domèstics i salvatges, actualment amenaçats pels canvis climàtic i en l’ús del sòl. Els microorganismes del sòl tenen un paper clau tant en la descomposició com en diversos processos de l’ecosistema, fet pel qual composició i funció de la comunitat microbiana han estat utilitzats durant molt temps com a índexs de fertilitat del sòl.
Els rangelands europeus i africans comparteixen un origen antropogènic comú, però el clima i la gestió del sòl els afecten d’una manera diferent. És per això que aquesta tesi pretén analitzar la comunitat microbiana d’ambdós tipus d’ecosistemes, per tal d’observar els efectes d’algunes de les amenaces comunes des d’una perspectiva més global.
Mentre que la sobrepastura va demostrar tenir l’efecte més perjudicial sobre la funció microbiana en sòls kenyans, es va trobar un efecte més fort del clima sobre els prats europeus. Els fongs i els bacteris van covariar al llarg de gradients altitudinals i climàtics, però la comunitat bacteriana va mostrar una recuperació més ràpida després de les pertorbacions biològiques i físico-químiques del sòl.
Aquest conjunt d’estudis afegeix nous coneixements sobre l’estructura i funció dels rangelands africans i europeus, i convida a explorar noves línies de recerca que incloguin tant bacteris com fongs alhora d’estudiar la comunitat microbiana del sòl.Los llamados "rangelands" son áreas sin cultivar, ampliamente pastoreadas por animales domésticos y salvajes, actualmente amenazados por los cambios climático y de uso del suelo. Los microorganismos del suelo tienen un papel clave tanto en la descomposición como en diversos procesos del ecosistema, por lo que composición y función de la comunidad microbiana han sido utilizados durante mucho tiempo como índices de fertilidad del suelo. Los rangelands europeos y africanos comparten un origen antropogénico común, pero el clima y la gestión del suelo les afectan de una manera diferente. Es por ello que esta tesis pretende analizar la comunidad microbiana de ambos tipos de ecosistemas, a fin de observar los efectos de algunas de las amenazas comunes desde una perspectiva más global. Mientras que el sobrepastoreo demostró tener el efecto más perjudicial sobre la función microbiana en suelos kenianos, se encontró un efecto más fuerte del clima sobre los prados europeos. Los hongos y las bacterias covariaron a lo largo de gradientes altitudinales y climáticos, pero la comunidad bacteriana mostró una recuperación más rápida después de las perturbaciones biológicas y físico-químicas del suelo. Este conjunto de estudios añade nuevos conocimientos sobre la estructura y función de los rangelands africanos y europeos, e invita a explorar nuevas líneas de investigación que incluyan tanto bacterias como hongos en el estudio de la comunidad microbiana del suelo.
Rangelands are uncultivated areas extensively grazed by wild and domestic animals, currently threatened by land use and climatic changes. Soil microorganisms play a key role in decomposition and several ecosystem processes and the composition and function of the microbial community have been long used as indices of soil fertility. African and European rangelands share a common anthropogenic origin, but climate and management affect them in a different way. That is why this thesis aimed to analyze the microbial community of both in order to observe the effects of some common threats from a more global perspective. While overgrazing proved to have the most detrimental effect on the soil microbial function in Kenyan soils, a stronger effect of climate was found to affect European grasslands. Fungi and bacteria co-varied along altitudinal and climatic gradients, but the bacterial community showed a fast recovery after biological and soil physico-chemical disturbances. This group of studies adds new knowledge on the structure and function of the African and European rangelands, and invite to explore new lines of research including both fungal and bacterial consortia when studying the soil microbial community.
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Smith, Jacques J. "Microbial diversity and gene mining in Antarctic Dry Valley mineral soils." Thesis, University of the Western Cape, 2006. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_5762_1183463992.
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Soil communities are regarded as among the most complex and diverse assemblages of microorganisms with estimated bacterial numbers in the order of 10â?¹ cells.gâ?»¹
. Studies on extreme soils however, have reported lower cell densities, supporting the perception that the so-called extreme environments exhibit low species diversity. To assess the extent of microbial diversity within an extreme environment, the mineral soils of the Dry Valleys, Ross Dependency, Eastern Antarctica were investigated using 16S rDNA analysis.
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Roth, McKenzie L. "Analysis of Bacterial Abundance and Species Diversity in Various Soils." Ashland University Honors Theses / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=auhonors1355166102.
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Amasah, Reda. "Studies on the environmental microbiology and biogeochemistry of desert surface soils." Thesis, University of Sheffield, 2012. http://etheses.whiterose.ac.uk/2769/.
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Microorganisms play a key role in the functioning of the environment, particularly in relation to the biogeochemical cycles. Here, a study was made of the microbial activity of primitive desert surface soils in comparison with that exhibited by a fertile agricultural loam soil. The microbial transformations studied included nitrification, the hydrolysis of urea, the oxidation of elemental sulphur to sulphate and phosphate solubilisation; these processes were collectively used to study the biogeochemical activity of desert surface soils. Bacterial population densities in the desert surface soils, fertile loam soils and volcanic, cave rock samples were also determined. A variety of bacterial isolates from desert surface soils and cave rock samples have been identified using molecular identification techniques like DNA extraction, PCR amplification, determinations of 16S and 18S rRNA gene sequences. The isolation and characterization of extremophilic bacterial strains from a dormant volcano on the island of Reunion is reported, using molecular identification, morphological and physiological studies. As the area of the volcano, from which these bacteria were isolated, has not been recently active, it was considered of interest to determine if these bacteria grow, or merely survive, in a mesophilic environment. Nuclear magnetic resonance spectroscopy (NMR) was used to study the compatible solutes in these isolates when growing under high temperatures, low and high pH stresses and at various concentrations of NaCl. Finally, various environmental samples were tested in order to detect the presence of Mycoplasma using an EZ-PCR Mycoplasma Test Kit.
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Hoyle, Frances Carmen. "The effect of soluble organic carbon substrates, and environmental modulators on soil microbial function and diversity." University of Western Australia. School of Earth and Geographical Sciences, 2007. http://theses.library.uwa.edu.au/adt-WU2007.0050.
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[Truncated abstract] The principal aim of this thesis was to examine the response of the microbial community to the addition of small amounts (<50 μg C g-1 soil) of organic C substrates (‘trigger molecules’) to soil. This addition is comparative to indigenous soluble C concentrations for a range of soil types in Western Australia (typically measured between 20 and 55 μg C g-1 soil). Previously it has been reported that the application of trigger molecules to European soils has caused more CO2-C to be evolved (up to six fold) than was applied . . . Findings from this study indicated that there was an additional CO2 release (i.e. greater than the C added) on application of organic C substrates to some soil treatments. However, findings from this study indicate that the response of the microbial community to small additions of soluble C substrate is not consistent for all soil types and may vary due to greater availability of C, and supports the premise that microbial responses vary in a yet to be predicted manner between soil type and ecosystems. Differences in microbial response to the addition of soluble organic C are likely attributable to differences in soil attributes and environmental factors influencing both the diversity of microbes present and the frequency of food events. Theoretically, trigger molecules could also provide a possible control mechanism for microorganisms in arable farming systems. These mechanisms include stimulating either targeted pathogenic microorganisms that starve after depletion of a suitable substrate; or stimulating beneficial microorganisms to manipulate nutrient cycling, by targeting specific functional groups and altering mineralisation and immobilisation turnover rates.
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Khan, Nuraan. "Characterisation of microbial communities associated with hypolithic environments in Antarctic Dry Valley soils." Thesis, University of the Western Cape, 2008. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_7054_1269981243.
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The Eastern Antarctic Dry Valley region is a polar desert, where conditions of extreme aridity, high temperature fluctuations and high irradiation levels make it one of the most extreme environments on earth. Despite the harsh environment, the soils in this region yield a wide range of bacterial and eukaryotic phylotypes in greater abundance than previously believed. In the Dry Valleys, highly localized niche communities colonise the underside of translucent quartz rocks and present macroscopic growth.
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Van, Schoor Louise. "Effect of biological amendments on soil microbial properties and performance of pome fruit trees." Thesis, Stellenbosch : Stellenbosch University, 2009. http://hdl.handle.net/10019.1/4602.
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Thesis (PhD(Agric))--Stellenbosch University, 2009.ENGLISH ABSTRACT: The global movement in agriculture is towards more environmentally friendly, sustainable production practices, since the role of soil microbial functions in ensuring crop production and soil fertility has become more evident in agricultural systems. Furthermore, with the impeding phase-out of methyl bromide, apple replant disease (ARD) is becoming an increasingly important problem and biological management practises are needed. Since microbial activity is generally carbon-limited in agricultural soil, it is widely accepted that management practices providing a range of organic compounds on a regular basis will tend to maintain an active and diverse microbial population. It was hypothesised that the application of various biological amendments can affect soil microbial numbers and function, thereby having a positive effect on fruit tree growth and yield. The effect of continued applications of organic material, various microbial inoculants and biostimulants on tree performance were evaluated in conventional management systems. Field trials were established in a conventional pear orchard, potential apple replant disease sites, as well as an optimally managed, high density apple orchard under controlled fertigation. The use of compost, compost extracts, a Bacillus inoculant and humates were investigated intensively. Furthermore, to improve our understanding of soil biological systems a combination of simple, practical methods were used to evaluate the effect of biological amendments on soil microbial properties and effects were related to tree performance. Regular application of compost extract in combination with compost showed the most significant effect in improving tree performance in commercial pome fruit orchards under various conditions. In the pear orchard, cumulative yield over the first two seasons was improved by more than 50% compared to controls, while in the fertigated orchard yield was improved by 22%. Biological amendments also showed improved growth in orchards suffering from stunted growth symptoms typical of ARD. However, in severe ARD cases methyl bromide fumigation showed the most consistent effects. Other biological amendments which showed positive effects on yield were application of Bacillus inoculants (Biostart®) in combination with a labile C source and a low dosage humate product, as well as a combination of compost and humates. It was clear that a combination of labile organic matter and a diverse group of microorganisms showed most promise. Although for some specific treatments increased microbial numbers and activity may have resulted in improved tree performance, in general, changes in culture-based plate counts, soil enzyme activity and carbon utilisation profiles could not be used as an indicator of yield. It was suggested that improved synchronisation of nutrient release and plant uptake, as well as microbial phytohormone production, may play an important role in improving tree performance with application of biological amendments. More research is needed on the exact mechanisms through which compost extracts improve yield and studies on root growth proliferation, as well as effects in the rhizosphere are recommended.
AFRIKAANSE OPSOMMING: Binne lanbouverband is daar tans wêreldwyd die neiging om die uitwerking van produksie-praktykte op die omgewing in ag te neem en sodoende meer verantwoordelik op te tree. Omdat die belangrike rol wat grondmikro-organisme funksionering in volhoubare verbouingspraktyke speel nou deeglik besef word, word meer volhoubare bestuurspraktyke bepleit. Hiermee saam, noodsaak aspekte soos die uitfasering van metielbromied vir die beheer van appelhervestigingsiekte, dat biologiese bestuurspraktyke meer aandag geniet. Daar word geredelik aanvaar dat gereelde toediening en aanvulling van organiese materiaal ‘n aktiewe, diverse mikrobe populasie in die grond tot gevolg sal hê. Die hipotese is gestel dat die toediening van ‘n verskeidenheid biologiese produkte grondmikrobe getalle en werking gunstig kan beïnvloed. Dit kan moontlik weer aanleiding gee tot positiewe reaskies wat die groei en drag van vrugtebome betref. In hierdie studie is die uitwerking van voortgesette toedienings van organiese materiaal, mikrobiese inokulante, asook biostimulante, op die prestasievermoë van vrugtebome ondersoek. Veldproewe is uitgelê in ‘n konvensionele peerboord, verskeie boorde met moontlike appelhervestigingsiekte probleme, asook ‘n hoëdigtheidsaanplanting appelboord onder optimale bestuur. ‘n Deeglike ondersoek is gedoen met betrekking tot die gebruik van kompos, komposekstrak, Bacillus-inokulante en humate. Eenvoudige, praktiese metodes is aangewend om vas te stel hoe biologiese toevoegings grondmikrobe eienskappe beïnvloed en of dit verband hou met veranderinge in boomprestasie. Die studie het aangetoon dat die gereelde toediening van komposekstrak saammet kompos, betekenisvolle verbetering in boomprestasie van kernvrugboorde teweeg bring onder verskeie omstandighede. Die kumulatiewe opbrengs van ‘n peerboord is oor twee seisoene met meer as 50% verhoog teenoor die kontrole. In ‘n optimaal bestuurde appelboord onder sproeibemesting, is opbrengs met 22% verhoog in vergelyking met die kontrole. Biologiese toevoegings het ook groei verbeter in boorde waar appelhervestigingsiekte bome se groei vertraag het. In die geval van ernstige appelhervestigingsimptome het metielbromied egter steeds die mees konstante positiewe uitwerking gehad. Ander biologiese toevoegings wat ‘n gunstige uitwerking op opbrengs getoon het, was ‘n kombinasie van Bacillus inokulante, ‘n lae dosis humaat en ‘n aktiewe koolstofbron, asook kompos in kombinasie met humate. Dit is duidelik dat ‘n kombinasie van ‘n maklik afbreekbare koolstofbron (soos kompos) tesame met ‘n diverse groep mikroorganismes mees belowend is vir gebruik in biologiese verbouingssisteme. Resultate toon dat veranderings in aantal organismes gemeet deur plaattellings, die aktiwiteit van grondensieme, en verbruikspotensiaal van verskillende koolstofbronne, nie as ‘n aanduiding van boomprestasie gebruik kan word nie. Daar is voorgestel dat verbeterde sinkronisasie van voedingselementvrystelling en plantopname, sowel as produksie van plantgroeihormone deur mikrobe, moontlik ‘n rol speel by boomreaksies op biologiese toevoegings. Meer navorsing wat verband hou met die meganisme waardeur komposekstrak opbrengs verbeter, is nodig. Verder word studies op fynwortelontwikkeling sowel as aspekte van die wortelrisosfeer aanbeveel.
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Munier-Lamy, Colette. "Mobilisation et préconcentration de l'uranium dans les sols : Rôle des substances hymiques." Nancy 1, 1987. http://www.theses.fr/1987NAN10220.
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Arthur, Mickey Francis. "Soils containing 2,3,7,8-tetrachlorodibenzo-p-dioxin : aspects of their microbial activity and the potential for their microbially-mediated decontamination /." The Ohio State University, 1987. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487330761218489.
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Cutler, Anya. "Ecological Dynamics in Compost-Amended Soils and the Resulting Effects on Escherichia coli Survival." ScholarWorks @ UVM, 2016. http://scholarworks.uvm.edu/graddis/603.
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Escherichia coli (E. coli) are common and typically innocuous copiotrophic bacteria found in the mammalian gut microbiome. However, over the past 30 years, pathogenic E. coli have been responsible for several outbreaks of foodborne illness linked to contaminated produce. The introduction of Escherichia coli to an agricultural soil, via contaminated water, compost, or raw manure, exposes the bacterium to a medley of ecological forces not found in a mammalian gut environment. This study assesses a variety of abiotic and biotic soil factors that influence the ability of an "invasive" copiotrophic coliform bacterium to survive in compost-amended agricultural soil. The study included both field and laboratory components. In the lab experiment, a cocktail of rifampicin-resistant generic E.coli strains was added to sterile and non-sterile extracts of eight different composts and one soil sample from the field sites. E. coli abundance was monitored over a one-week period and composts were analyzed for their nutrient profile. In the field experiment, the same E. coli cocktail was sprayed on plots with the following treatments: 1) dairy windrow compost, 2) dairy vermicompost, 3) poultry windrow compost, or 4) no compost. E. coli abundance, soil water potential, soil temperature, extracellular enzyme activity, microbial respiration, phospholipid fatty acid biomarker abundance, and genetic sequencing of the microbial community were measured over a six-month field season.
The lab experiment showed that E. coli were able to grow well in sterile compost extracts, without microbial competition for nutrients. Conversely, E. coli populations were only able to survive in non-sterile soil extracts. These results suggest that copiotrophic organisms adapted for high-nutrient environments may depend on the extracellular enzyme activity of native oligotrophic organisms to acquire sufficient nutrients to survive in soils. Results of the field experiment showed clear and interdependent effects of soil moisture and nutrient availability on microbial community dynamics and E. coli survival. Data suggest that saturated soils cause a decrease in microbial extracellular enzyme activity, and drying-rewetting cycles can cause respiration bursts, nutrient mineralization, and shifts in community composition. The saturation of soils, which mobilizes nutrients and may result in a decrease in competition from aerobic organisms, correlated directly with increased survival of E. coli. Additionally, amendment with ammonium-rich poultry compost resulted in the maintenance of high levels of E. coli throughout the field season. Despite an increase in microbial biomass from dairy vermicompost amendment, poultry compost was the only compost that had a significant effect on E. coli survival. The results suggest that nitrogen availability and water potential are strong drivers of E. coli's survival in soils. Correlations among abiotic factors, community composition, and E. coli survival reveal insights into the complex relationships that occur in disturbed agricultural soil environments. Further research on E. coli's response to targeted organisms, abiotic soil properties, and nutrient inputs could have implications for agricultural considerations in food safety and microbial ecology.
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Lako, Joseph. "Analysis of ammonia-oxidizing bacteria associated with the roots of Proteaceae plant species in soils of Fynbos ecosystem." Thesis, University of the Western Cape, 2005. http://etd.uwc.ac.za/index.php?module=etd&.
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The major objective of this study was to investigate soil ammonia-oxidizing bacterial diversity and composition associated with plant roots of Proteaceae plants and to compare it with non-plant associated soil.
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Elliott, Geoffrey Nigel. "Diversity of Bacillus merA genes directly amplified from mercury polluted soils." Thesis, University of Liverpool, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366733.
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Ouimet, Nicole. "Laboratory measurements of soil microbial biomass and nitrogen mineralization from two Chinese soils as influenced by long-term applications of manure and inorganic fertilizers." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=68236.
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The purpose of this study was to investigate the results of two long-term fertilization experiments on soil organic C, total N, and mineralizable N in the Jiangsu Province of People's Republic of China. The soil samples that received manure over the years contained more soil organic C, and total N than the inorganic fertilized samples. Soil organic C was closely correlated with total N and there were correlations between crop yields and soil organic C contents and between crop yields and soil total N contents. Plant-available N was estimated using biological and chemical tests. Mineralized N formed under anaerobic incubation was low except for those soil samples that received manure. Microbial biomass C and N were estimated using the chloroform fumigation-incubation method (CFIM) and fumigation-extraction procedures. Biomass measurements by CFIM were more precise and reliable than values obtained by fumigation-extraction. Treatment differences in biomass were not significant. Estimates of biomass C and N were influenced by the choice of the control soil and the period of incubation used by the CFIM. Unfumigated (10-20 d) control soils were found to be the best control for samples. Extraction of mineralized N using O.5M NaHCO$ sb3$ after incubation overestimated biomass N since this extraction was found to extract non-biomass N.
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Summerville, Kevin M. "Effectiveness of Amendments and Microbial Treatments on Plant Growth in Urban Garden Soils." Youngstown State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1495712379969062.
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Casarez, Elizabeth Anne Joseph. "Microbial regulation of arsenic bioavailability and toxicity in soils." Diss., The University of Arizona, 2004. http://hdl.handle.net/10150/280678.
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The biogeochemical cycle of arsenic (As) is very complex. The current practice of measuring total arsenic concentrations, especially in soil environments, ignores any differences in arsenic form or bioavailability, and therefore misrepresents the risk of arsenic to human health. Biotic and abiotic transformations of arsenic change its mobility, availability, and toxicity. A key reaction is arsenite (As(III)) oxidation to arsenate (As(V)), a form that is less bioavailable and fifty times less toxic. The role of microorganisms may be key to understanding As(III) oxidation rates in soils. This research studies how As(III) oxidation rates may be altered when soil microorganisms have had previous arsenic exposure. My primary hypothesis is: Previous exposure to arsenic affects the soil microbial population, allowing it to more quickly oxidize, and therefore detoxify, additional arsenite challenges. Microcosms of soils with different histories of arsenic contamination were amended with As(III). As(III) oxidation rates were compared by monitoring the bioavailable (water-extractable) arsenic concentrations using high performance liquid chromatography--hydride generation--atomic fluorescence spectrometry. Although As(III) oxidation occurred in all biologically active soils, reaction rates were positively correlated with previous As exposure, even with fewer and less diverse microorganisms in the chronically contaminated soils. 16SrDNA denaturing gradient gel electrophoresis analysis detected an emerging band with sequence homology to Thiomonas sp. NO115 after the highest contaminated soil was given the highest amendments. Bacterial isolates from that soil also showed different As transformation abilities, even when under the same selection pressures. To determine if faster As(III) oxidation rates could be induced in an arsenic-naive soil, control soils were given multiple doses of As(III). Changes in As(III) oxidation rate were dependent on both the number of previous doses and the challenge dose. When a soil inoculated with microorganisms extracted from a pre-exposed soil was challenged with 500ppm As(III), As(III) disappearance was more similar to an adapted soil, showing that it was the change in the microbial population that was responsible for the change in the As(III) oxidation rate. By studying how microbial populations adapt to environmental stressors like As(III), we may better understand not only the microorganisms, but also the biogeochemistry of arsenic.
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Nye, Mark Edward. "Microbial Community Structure in Soils Amended With Glyphosate Tolerant Soybean Residue." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1396272020.
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Navarrete, Acacio Aparecido. "Bacterial ecology in Amazonian soils under deforestation and agricultural management." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-22042013-163134/.
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This thesis assessed effects of Amazonian deforestation on artificial association networks of bacteria to bacteria and to abiotic soil factors and networks based on categories of bacterial functions and abiotic soil factors, and sought a better insight into community of Acidobacteria in Amazon soils under agricultural management of soybean based on culture-dependent and molecular approaches. Bacterial community was studied based on next-generation sequencing technologies (Roche GS FLX Titanium and Illumina HiSeq 2000 platforms), quantitative real-time PCR, fingerprinting technique and basic procedures for bacteria culture. The general objective of this thesis was achieved by development of three different studies. The Study 1 analyzed the total bacterial community based on 16S ribosomal DNA pyrotag (425 thousand sequences), shotgun metagenomics (266 million sequences) and environmental parameters from soil samples collected in three real replicate of intact Amazon rainforest and adjacent deforested site after 2-4 months of forest clearing and burning in the Brazilian Amazon. This study showed that deforestation of Amazon forest soils led to a consistent decline in the abundance of Verrucomicrobia and alterations in verrucomicrobial community structure, and simplified association networks among different bacterial taxonomic groups and abiotic soil factors. In order to adapt to this condition function-based associations network were enhanced, indicating a higher degree of risk spreading for the maintenance of soil functioning. The Study 2, in turn, correlated relative abundance of Acidobacteria subgroups - based on approximately 33 thousand sequences of acidobacterial 16S rRNA genes - and abiotic soil factors, and showed differential response of Acidobacteria subgroups to abiotic soil factors in Amazon forest soils into soybean croplands. This study opened the possibilites to explore acidobacterial subgroups as early-warning bio-indicators of agricultural soil management effects in the Amazon area. Lastly, the Study 3 reported the culturability and molecular detection of Acidobacteria subgroups 1 and 3 concomitantly to other bacterial groups from Amazon soils on enriched culture medium with carbon source and incubated for relatively long period in hypoxic atmosphere (2% O2 [vol/vol], 2% CO2 [vol/vol] and 96% N2 [vol/vol]), and validated the combination of traditional procedures for bacteria culture and molecular techniques for recover and detection of Acidobacteria from Amazon soilsEste trabalho de tese avaliou o efeito do desmatamento sobre redes artificiais de associação entre grupos taxonômicos de Bacteria e fatores abióticos do solo e redes baseadas em funções bacterianas e fatores abióticos do solo, e utilizou técnicas moleculares e abordagem dependente de cultivo para compreender a dinâmica da comunidade de Acidobacteria em solos da floresta Amazônica convertidos em áreas agrícolas para produção de soja. Para estudo das comunidades bacterianas foram utilizadas tecnologias de sequenciamento de nova geração (plataformas 454 GS FLX Titanium da Roche e Illumina HiSeq 2000), PCR quantitativo em tempo-real, método de fingerprinting e procedimentos tradicionais para cultivo de bactérias. O objetivo geral desta tese foi alcançado com o desenvolvimento de três diferentes estudos. O Estudo 1 considerou aproximadamente 425 mil sequências do gene 16S rRNA de Bacteria e 266 milhões de sequências de DNA bacteriano obtidas por análise metagenômica a partir de solos coletados em três réplicas verdadeiras de floresta intacta na Amazônia e área desmatada adjacente após corte e queima da cobertura vegetal. Com isso, este estudo mostrou que o desmatamento declina a abundância e altera a estrutura de comunidade de Verrucomicrobia no solo e simplifica as redes artificiais de associação entre diferentes grupos bacterianos. A rede artificial de associação entre categorias funcionais e fatores de solo revelou-se mais complexa em solos desmatados, indicando um alto grau de dispersão de risco para a manutenção do funcionamento do solo. Por sua vez, o Estudo 2 correlacionou a abundância de subgrupos de Acidobacteria - com base em aproximadamente 33 mil sequências do gene 16S rRNA de Acidobacteria - com fatores abióticos do solo, e mostrou que subgrupos de Acidobacteria respondem diferentemente aos efeitos do manejo agrícola de solos da floresta Amazônica dentro de áreas de produção de soja. Este estudo abriu possibilidades de explorar subgrupos de Acidobacteria como bio-indicadores dos efeitos do manejo agrícola do solo na região da Amazônia. Por fim, o Estudo 3 reportou a culturabilidade e detecção molecular de Acidobacteria subgrupos 1 e 3 e outros grupos bacterianos presentes em solos Amazônicos em meio de cultura enriquecido com carbono e incubado sob atmosfera hipóxica (2% O2 [vol/vol], 2% CO2 [vol/vol] e 96% N2 [vol/vol]), atestando, assim, a combinação de procedimentos tradicionais de cultivo e técnicas moleculares para a recuperação e detecção de Acidobacteria de solos da Amazônia
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Perez-Guzman, Lumarie. "Microbial Activity, Abundance and Diversity in Organic and Conventional Agricultural Soils Amended with Biochars." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1503083433558626.
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Abdulaziz, Sami. "The microbiology and biogeochemistry of desert soils notably in relation to microbial phosphate solubulization." Thesis, University of Sheffield, 2013. http://etheses.whiterose.ac.uk/5086/.
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The aim of the work reported in this Thesis was to investigate the role of a range of microorganisms in the functioning of the desert environment, particularly in relation to the biogeochemical cycles. A study was made of the microbial activity of phosphate soils in comparison with that found in a fertile, temperate grassland soil. The microbial transformations studied included phosphate solubilization, the oxidation of elemental sulphur to sulphate, nitrification and the hydrolysis of urea by microbes and were collectively used to study the biogeochemical activity of soils. Bacterial and fungal population densities in the soils, temperate grassland, and phosphate mine spoil desert-vegetated soil samples were investigated. In all cases the highest activity of the individual components of the mineral cycles was not surprisingly, found in the temperate grassland (control soil). The highest activities in the desert soils were associated with vegetation cover, i.e. the establishment of a rhizosphere. A variety of bacteria and fungi were isolated from phosphate mine spoil desert-vegetated soil and desert non-vegetated soil samples were identified using molecular identification techniques based on DNA extraction, PCR amplification and determination of the sequences 16SrRNA and 18SrRNA genes. The isolates were: bacteria- Paracoccus sp., Rhizobium sp, Bacillus megaterium, Cupriavidus necator, Bacillus simplex and Bacillus foraminis and fungi Cochliobolus lunatus, Penicillium daleae, Mucor sp. and Aspergilus oryzae. The following desert soil fungi, solubilized insoluble phosphate: Cochliobolus lumans, Penicillium daleae and Mucor Sp. Using NMR it was shown that soluble phosphate was released into the medium and also taken up by the fungi and fixed as metal phosphates.
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Ferrera, Rodriguez Ofelia. "Rhizosphere microbial communities of Puccinella angustata thriving in pristine diesel-contaminated Arctic soils." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=104604.
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Petroleum hydrocarbon contamination has reached Arctic soils, Puccinellia angustata thrives in such habitats. Hydrocarbon removal during phytoremediation treatments strongly depends on the catabolic activities of root associated microorganisms. This research compared the rhizospheric microorganisms from P. angustata established at Arctic soils under different degrees of contamination with petroleum hydrocarbons to determine if this plant species has phytoremediation potential. The abundance, diversity, and activity of soil bacterial communities were investigated by means of plate and microscopic counts, strains isolation, 16S rRNA gene DGGE fingerprinting, functional gene PCR detection, microcosm hydrocarbon mineralization assays, and TPH quantification. This study was divided in three experimental stages. In the first stage a comparison of samples vegetated by five different plant species as well as four bulk samples, showed that P. angustata had greater enrichment of hydrocarbon-degrading bacteria than samples vegetated by other plant species. In the second stage, a comparison between the rhizosphere of P. angustata and bulk samples collected at pristine (Pr), hydrocarbon-contaminated but non-bioremediated (NBr) and hydrocarbon-contaminated and bioremediated (Br) Arctic soils, revealed that the presence of P. angustata enhanced the abundance and the activity of hydrocarbon-degrading microorganisms in two soils (Pr and NBr) but not at Br since this soil was subjected to fertilizations as bioremediation process. In the third stage, via growth chamber experiments, in which high Arctic summer conditions were simulated, P. angustata (with and without nitrogen fertilization) was assessed for phytoremediation of a soil artificially contaminated with diesel (10,000 mg Kg-1). Puccinellia showed tolerance to fresh diesel contamination and enhanced hydrocarbon-degrading bacteria that significantly increased the TPH removal. Also, the rhizosphere of P. angusatata had high bacterial diversity, encompassing members from Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes and Proteobacteria phyla. These findings indicate that P. angustata stimulates soil microflora responsible for biodegradation of hydrocarbons therefore it has potential for phytoremediating contaminated Arctic soils.Abbreviation: PCR (polymerase chain reaction), DGGE (Denaturing Gradient Gel Electrophoresis), TPH (Total Petroleum Hydrocarbons).La contamination par hydrocarbures pétroliers a touché les sols arctiques ; Puccinellia angustata se développe dans ces habitats. L'élimination de l'hydrocarbure pendant les traitements de phytoremédiation dépend fortement des activités cataboliques des microorganismes associés à la racine. Cette recherche a comparé les microorganismes rhizosphériques de P. angustata établis dans les sols arctiques à différents niveaux de contamination par hydrocarbures pétroliers pour déterminer si cette espèce de plante a du potentiel pour la phytoremédiation. L'abondance, la diversité, et l'activité des communautés bactériennes du sol ont été examinées au moyen de comptages sur plaque et microscopiques, isolement de souches, empreinte digitale par DGGE du gène 16S rRNA, détection fonctionnelle du gène par PCR, essais de minéralisation des hydrocarbures en microcosme et quantification de TPH. Cette étude a été divisée en trois étapes expérimentales. Dans la première étape, une comparaison d'échantillons globales et d'échantillons plantés de cinq espèces végétales différentes a montré que P. angustata avait une plus grande accumulation de bactéries de dégradation de l'hydrocarbure que les échantillons plantés avec d'autres espèces végétales. Dans la deuxième étape, une comparaison entre la rhizosphère de P. angustata et des échantillons globales pris des sols arctiques pures (Pr), des sols arctiques contaminés par hydrocarbures et non-bio-réhabilités (NBr) et des sols arctiques contaminés par hydrocarbures et bio-réhabilités (Br), a révélé que la présence de P. angustata a augmenté l'abondance et l'activité des microorganismes de dégradation d'hydrocarbures dans deux sols (Pr et NBr), mais pas dans le Br, parce que ce sol avait reçu des fertilisations comme processus de bioremédiation. Dans la troisième étape, au moyen d‘essais en chambres de croissance où les conditions d'été du Haut-Arctique étaient simulées, P. angustata (avec et sans fertilisation par hydrogène) a été évaluée pour la phytoremédiation d'un sol contaminé artificiellement avec du diesel (10,000 mg Kg-1). Puccinellia a montré tolérance à la contamination par diesel et a augmenté les bactéries de dégradation d'hydrocarbures, en améliorant ainsi beaucoup l'élimination des TPH. Aussi, la rhizosphère de P. angustata avait une haute diversité bactérienne, contenant des membres de phylums Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes et Proteobacteria. Ces conclusions indiquent que P. angustata stimule la microflore du sol qui est responsable de la biodégradation des hydrocarbures et, pourtant, pourrait aider la phytoremédiation des sols arctiques contaminés.Abréviations : PCR (Réactions en chaîne par polymérase), DGGE (Électrophorèse sur gel à gradient dénaturant),TPH (hydrocarbures pétroliers totaux)
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Bell, Terrence. "Identification of taxa-specific responses to bioremediation treatments in hydrocarbon-contaminated Arctic soils." Thesis, McGill University, 2013. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=114487.
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A warming climate and improved technology have allowed northern countries to more thoroughly explore and exploit Arctic resources. This increased activity has led to an elevated risk of petroleum contamination, and consequently, there is a need to develop strategies to effectively and efficiently degrade these contaminants on site. While many Arctic soil microorganisms are known to naturally metabolize petroleum hydrocarbons in contaminated sites, a process known as bioremediation, treatments directed at stimulating the hydrocarbon-degrading activity of these microbes (e.g. nutrient amendments) have varied in effectiveness.The objective of this study was to determine whether microbial taxa respond equally to disturbances of the soil environment by hydrocarbon contaminants and nutrient amendments, and whether the most efficient hydrocarbon degraders are naturally stimulated. To determine whether the bacteria inhabiting contaminated Arctic soils assimilate added nitrogen equally, a novel 15N-stable isotope probing approach was developed. After a month of in situ incubation, it was determined that many hydrocarbon-degrading bacteria had incorporated the added nitrogen, but to varying extents. The Alphaproteobacteria most effectively used the added nitrogen, as determined by both 16S rRNA and alkB gene enrichment, and this was noteworthy given that they were not expected to be the most effective hydrocarbon-degrading group.To assess whether the relative abundance of bacterial taxa in hydrocarbon-contaminated soils was determined by soil characteristics as opposed to hydrocarbon-degrading ability, 18 soils from across the Arctic were collected and treated with diesel and monoammonium phosphate. Bacterial diversity and community composition were determined through 16S rRNA gene sequencing on the Ion Torrent platform, while hydrocarbon degradation was measured using gas chromatography. It was found that Actinobacteria dominated soils with low organic matter, while Proteobacteria dominated those with high organic matter. In addition, the extent of bacterial diversity and the relative abundance of specific assemblages of Betaproteobacteria in uncontaminated soils were predictive of hydrocarbon degradation with and without nutrient amendments, respectively. Relative abundance of Betaproteobacteria was associated with efficient hydrocarbon degradation in the presence of added nutrients, suggesting that this may be an important group to target.Finally, to determine whether modifying the microbial community within a given soil would impact rates of hydrocarbon degradation, gentamicin and vancomycin were used to inhibit specific portions of the bacterial community. Bacterial 16S rRNA gene diversity and community composition were again determined using the Ion Torrent platform, qPCR was used to quantify bacterial and fungal populations within each treatment, and GC analysis was used to determine hydrocarbon degradation. Bacterial 16S rRNA gene abundance declined in soils treated with gentamicin, but diesel degradation was highest in the presence of both gentamicin and vancomycin. Bacterial community composition shifted under all treatments, and Xanthomonadaceae (Gammaproteobacteria) and Micrococcaceae (Actinobacteria) dominated soils treated with both antibiotics. Diesel degradation was much less effective when nutrients were also added to soils treated with gentamicin and vancomycin, possibly due to competition from a larger fungal population.Overall, these results suggest that more effective in situ treatments of hydrocarbon-contaminated Arctic soils are possible through selective targeting of efficient hydrocarbon-degrading consortia. Future research should aim to understand which soil microorganisms most quickly degrade various contaminants in situ, as well as the main biotic and abiotic factors that limit their activity.Le réchauffement climatique et l'amélioration de la technologie ont permis aux pays situés au nord du globe d'exploiter les ressources de l'Arctique comme jamais auparavant. L'accroissement de l'activité humaine augmente le risque de contamination par des produits pétroliers, d'où la nécessité de développer des stratégies afin d'être en mesure de dégrader ces contaminants de façon rapide et efficace. Bien que plusieurs des microorganismes qui peuplent le sol de l'Arctique possèdent la capacité de métaboliser des hydrocarbures, les traitements utilisés afin de stimuler l'activité de ces bactéries (ex. ajouts de nutriments) n'ont pas tous été aussi efficaces que souhaité.L'objectif de cette étude était de déterminer si les microorganismes réagissent de la même façon aux perturbations causées par les hydrocarbures et les ajouts de nutriments, et si les espèces efficaces dans la dégradation des hydrocarbures sont naturellement stimulées. Afin de déterminer si le taux d'assimilation de l'azote est le même pour toutes les bactéries qui vivent dans les sols contaminés de l'Arctique, une nouvelle technique de sondage à l'aide de l'isotope stable 15N a été développée. Après un mois d'incubation, nous avons déterminé que plusieurs groupes de bactéries ont incorporé l'azote, mais à des degrés divers. Les Alphaproteobacteria ont été les plus efficaces dans l'utilisation de l'azote, tel que démontré par l'enrichissement des gènes de l'ARNr 16S et alkB, ce qui constitue un fait intéressant étant donné qu'elles n'étaient pas considérées comme le groupe de bactéries le plus efficace dans la dégradation des hydrocarbures.Afin d'évaluer si l'abondance des espèces bactériennes est influencée plutôt par les caractéristiques du sol que par leurs capacités de dégradation, 18 sols prélevés dans différentes régions de l'Arctique ont été traités avec du diésel et des nutriments. La diversité et la composition des communautés microbiennes ont été déterminées par séquençage sur la plateforme Ion Torrent, alors que la chromatographie en phase gazeuse a permis de mesurer la dégradation des hydrocarbures. Le groupe des Actinobacteria prédominait dans les sols à faible teneur en substances organiques (<10%), tandis que le groupe des Proteobacteria prédominait dans les sols à haute teneur en substances organiques. De plus, la diversité bactérienne et l'abondance relative de certains groupes de Betaproteobacteria constituent un facteur prédictif de la dégradation efficace des hydrocarbures. L'abondance relative de Betaproteobacteria est associée à une dégradation efficace d'hydrocarbures en présence de nutriments, ce qui suggère qu'il s'agirait d'un bon groupe à cibler durant la biorémédiation.Enfin, dans le but de déterminer si une modification de la communauté microbienne influence la dégradation, des fractions de la communauté microbienne ont été inhibées à l'aide de la gentamicine et de la vancomycine. La dégradation du diesel donnait les meilleurs résultats en présence à la fois de la gentamicine et de la vancomycine. Tous les traitements utilisés ont provoqué des changements dans la composition de la communauté microbienne des sols et les groupes des Xanthomonadaceae (Gammaproteobacteria) et des Micrococcaceae (Actinobacteria) prédominaient dans les sols traités avec les deux antibiotiques. La dégradation du diesel était moins efficace lorsque des nutriments étaient également ajoutés en même temps que la gentamicine et la vancomycine, possiblement à cause de la compétition d'une population fongique plus importante.Ces résultats suggèrent qu'il est possible d'améliorer l'efficacité des traitements pour les sols arctiques contaminés par des hydrocarbures. Dans le futur, les recherches devraient se concentrer sur l'identification des microorganismes du sol qui dégradent le plus rapidement les divers contaminants associés à l'exploitation des hydrocarbures, ainsi que sur la compréhension des facteurs qui peuvent limiter leur activité.
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Samson, Heidi E. (Heidi Estrelita). "Psychrotolerant mucoralean fungi present in pristine mountain fynbos soil and vineyard soil from the Stellenbosch region." Thesis, Stellenbosch : Stellenbosch University, 2001. http://hdl.handle.net/10019.1/52423.
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Thesis (MSc)--University of Stellenbosch, 2001.ENGLISH ABSTRACT: Mucoralean fungi are mostly saprotrophs that are frequently encountered in soil habitats. Using an isolation temperature of circa 25°C, other workers obtained these fungi from a wide diversity of geographical areas in southern Africa. However, it is known that psychrotolerant mucoralean fungi, able to grow at 25°C as well as at 5°C, occur in pristine Alti Mountain Grassland. Nothing is known about the diversity of these psychrotolerant soil fungi in other vegetation types of South Africa. Consequently, in this study, the psychrotolerant fungal taxa and numbers in soil from a vineyard and from pristine Mountain Fynbos were determined using an incubation temperature of 4°C and a complex isolation medium. The latter contained agar, malt extract, peptone, yeast extract, penicillin and streptomycin sulphate. Soil samples were analysed in late summer, autumn and mid-winter. It was found that, for the samples taken in late summer and autumn, the diversity of mucoralean species in the soil differed between fynbos and vineyard. In winter however, no significant difference was detected between the Shannon's diversity indices of mucoralean species in the soil samples taken from the two habitats. It was found that in both soil types, the percentage mucoralean fungi on the plates increased from summer to winter. In addition, the numbers of detectable Morlierella subgenus Morlierella on the plates were higher in winter than in late summer. The diversity of mucoralean species obtained during winter in fynbos and vineyard soil was significantly less than the diversity of these species in Alti Mountain Grassland soil. To determine if the Morlierella subgenus Morlierella isolates from the fynbos and vineyard soil, and those obtained from Alti Mountain Grassland, differ in the ability to grow at low temperatures, the radial growth rate on malt extract agar at 4°C and BOC was determined for each isolate. The results indicate that not only did seasonal changes occur in the taxa within Morlierella subgenus Morlierella, but that the isolates dominating the soil in different seasons also differed in the ability to grow at low temperatures. The percentage of isolates that had reached greater colony diameters after B days of incubation at 4°C, was higher for the isolates obtained in the cold wet month of July than for those obtained in the warmer dryer month of February. Similar results were obtained with the radial growth experiments conducted at BOC. The Morlierella subgenus Morlierella isolates obtained in winter from fynbos and vineyard soil showed less variation in low temperature growth rate than the isolates of this taxon obtained in winter from Alti Mountain Grassland soil during a previous study. This variation corresponds to the greater number (20) of Morlierella subgenus Morlierella species found in the grassland soil. Altogether only seven species of this subgenus was detected during the present study in the fynbos and vineyard soil samples. It was speculated that this difference in diversity between the fynbos and vineyard isolates, and the grassland isolates obtained in a previous study, might have been as a result of differences in the habitat or the enumeration methods used. The phylogenetic relationship between different psychrotolerant isolates of Morlierella subgenus Morlierella originating from the soil of the fynbos, vineyard and Alti Mountain Grassland, was subsequently determine through comparison of ITS regions, within ribosomal RNA repeats. Consequently, 45 psychrotolerant Morlierella subgenus Morlierella isolates originating from the three soil habitats was compared on the basis ITS 1 nucleotide sequence composition and radial growth rate at 4°C. Phylogenetic analyses showed that the isolates could be grouped into two clusters correlating with the ability to grow at low temperatures. Each cluster was further subdivided into two subgroups. It was found that except for one subgroup and the reference strain occurring in another subgroup, all the subgroups contain isolates originating from a single soil habitat. Therefore, the ITS 1 sequence of these fungi seems to indicate the original habitat and ability to grow at low temperatures. This correlation of the ITS sequence with the ecological habitat of a fungus has also been observed by other workers for other fungal groups.
AFRIKAANSE OPSOMMING: Mucoraliese fungi is meestal saprotrofe wat dikwels in grondhabitatte aangetref word. Deur gebruik te maak van 'n isolasietemperatuur van circa 25°C, het ander werkers dié fungi van 'n wye verskeidenheid geografiese gebiede in suidelike Afrika verkry. Dit is egter bekend dat die psigrotolerante mucoraliese fungi, wat in staat is om by 2SoC en ook by SaC te groei, in ongeskonde Alti Berg-Grasland voorkom. Niks is egter bekend oor die diversiteit van dié psigrotolerante grondfungi in ander veldtipes van suidelike Afrika nie. Die psigrotolerante fungustaksa en -getalle in grond van 'n wingerd en van ongeskonde Berg Fynbos is gevolglik in dié studie bepaal deur gebruik te maak van 'n inkubasietemperatuur van 4"C en 'n komplekse isolasiemedium. Laasgenoemde het agar, moutekstrak, peptoon, gisekstrak, penisillien en streptomisiensulfaat bevat. Grondmonsters is in die laatsomer, herfs en midwinter geanaliseer. Daar is 'n verskil gevind tussen die diversiteit van die mucoraliese spesies in die grond van fynbos en dié van wingerd in die monsters wat in die laatsomer en midwinter geneem is. In die winter is daar egter geen beduidende verskil gevind tussen die Shannon diversiteitsindekse van mucoraliese spesies in die grondmonsters wat uit die twee habitatte getrek is nie. In albei grondtipes is daar gevind dat die persentasie mucoraliese fungi op die plate toegeneem het van somer tot winter. Daarby was die aantal waarneembare Morlierella subgenus Morlierella op die plate meer in die winter as in die laatsomer. Die diversiteit van mucoraliese spesies wat in die winter uit fynbos- en wingerdgrond verkry is, was beduidend minder as die diversiteit van dié spesies in Alti Berg-Grasland grond. Om te bepaal of die Morlierella subgenus Morlierella isolate van die fynbos- en wingerdgrond en dié van Alti Berg-Grasland van mekaar verskil ten opsigte van hul vermoë om by lae temperature te groei, is die radiale groeitempo op moutekstrak by 4"C en aoc vir elke isolaat bepaal. Die resultate dui aan dat daar nie alleen seisoenale veranderinge in die taksa binne Morlierella subgenus Morlierella voorkom nie, maar dat die isolate wat tydens verskillende seisoene uit die grond verkry is, ook ten opsigte van hul groeivermoë by lae temperature van mekaar verskil. Die persentasie isolate wat groter kolonie diameters bereik het ná B dae inkubasie by 4°C, was hoër vir die isolate van die koue, nat Juliemaand as vir dié wat in die warmer en droër Februariemaand verkry is. Soortgelyke resultate is verkry met radiale groei-eksperimente wat by BOC gedoen is. Die MortierelIa subgenus MortierelIa isolate wat in die winter uit fynbos- en wingerdgrond verkry is, het In kleiner variasie in hul groeitempo by lae temperature getoon as die isolate in dié takson wat tydens 'n vorige studie in die winter uit Alti Berg-Grasland grond verkry is. Dié variasie stem ooreen met die groter aantal (20) MortierelIa subgenus MortierelIa spesies wat in die graslandgrond gevind is. Slegs sewe spesies van dié subgenus is gedurende die huidige studie in die fynbos- en wingerdgrondmonsters waargeneem. Daar is gespekuleer dat dié verskil in diversiteit tussen die fynbos- en wingerdisolate en die graslandisolate van die vorige studie die gevolg mag wees van verskille tussen die habitat of die enumerasiemetodes wat gebruik is. Die filogenetiese verwantskap tussen verskillende psigrotolerante isolate van MortierelIa subgenus MortierelIa uit die grond van die fynbos, wingerd en Alti Berg-Grasland, is vervolgens bepaal deur 'n vergelyking van interne getranskribeerde spasieerder (ITS) areas, binne ribosomale RNS herhalings. Daar is gevolglik 45 psigrotolerante MortierelIa subgenus MortierelIa isolate uit die drie grondhabitatte met mekaar vergelyk op grond van die basis ITS 1 nukleotied opeenvolgingsamestelling en radiale groeitempo by 4°C. Filogenetiese analises het die isolate in twee groepe verdeel op grond van hul vermoë om by lae temperature te groei. Elke groep is verder in twee subgroepe verdeel. Daar is gevind dat behalwe vir een subgroep en die verwysingstam wat in 'n ander subgroep voorgekom het, elkeen van die subgroepe bestaan het uit isolate wat van 'n enkele grond habitat verkry is. Dit wil dus voorkom of die ITS 1 opeenvolging van dié fungi 'n aanduiding gee van die oorspronklike habitat en die vermoë om by lae temperature te groei. Dié korrelasie tussen die ITS opeenvolging en die ekologiese habitat van 'n fungus is ook deur ander werkers vir ander fungusgroepe waargeneem.
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Pillai, Suresh Divakaran. "Ecology and genetic stability of Tn5 mutants of bean rhizobia in Sonoran desert soils." Diss., The University of Arizona, 1989. http://hdl.handle.net/10150/184823.
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Five transposon Tn5 mutants of bean rhizobia (Rhizobium leguminosarum b.v. phaseoli) and the wild type strain were used in ecological studies to evaluate the efficacy of transposon Tn5 as a phenotypic marker in rhizobia for ecological studies in two Sonoran desert soils. All mutants possessed chromosomal insertions of the transposable element. Survival of each mutant strain was compared to that of the wild type strain under non stress, moisture stress and temperature stress conditions in Pima silty clay loam and Brazil to sandy loam. The genetic stability of Tn5 in terms of transposition of the element within the chromosome and the Tn5 coded antibiotic resistant phenotype was determined in cells recovered throughout the survival period. Under non stress conditions, the viable Tn5 mutant population decreased in size. Two mutants showed significantly (p < 0.01) lower populations than the wild type at the end of 30 days in the silty clay loam. In the sandy loam, four of the five mutant populations were significantly lower than the wild type. Tn5 was genetically stable in both soils. Under moisture stress conditions, the decline of the Tn5 mutant and wild type populations corresponded to a decline in soil moisture content. The finer textured soil afforded more protection to the cells than the coarse textured soil. There were no indications of Tn5 instability under moisture stress. In both soils under temperature stress, sizes of all populations declined rapidly and after 12 days, the mutant cells when screened using the Tn5 coded markers were significantly less in numbers than the wild type indicating a loss of Tn5 coded antibiotic resistance phenotype. There were no significant differences in numbers between wild type and mutant cells when screened using only the intrinsic markers. DNA:DNA hybridizations confirmed that the lack of Tn5 coded antibiotic resistance phenotype was probably not due to a deletion or transposition of the element. Under non stress conditions Tn5 is a useful ecological marker, but each Tn5 mutant has to be evaluated independently under specific environmental conditions to determine the efficacy of Tn5 as an ecological marker.
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Sengupta, Adti. "Studying Methanotrophic Bacterial Diversity in Ohio Soils Using High-Throughput Sequence Analysis." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1436956336.
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Vickers, J. C. "A taxonomic approach to the selective isolation, identification and screening of streptomycetes from soils." Thesis, University of Liverpool, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.356286.
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Spedding, Timothy Andrew. "Soil microbial dynamics in response to tillage and residue management in a maize cropping system." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=79133.
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The impact of tillage and residue management on soil microorganisms was studied over the maize (Zea mays L.) growing season in southwestern Quebec. Tillage and residue treatments were imposed on a sandy loam to loamy sand soil in fall 1991. Treatments consisted of no till, reduced tillage, and conventional tillage with crop residues either removed from (-R) or retained on (+R) experimental plots, laid out in a randomized complete block design. Soil microbial biomass carbon (SMB-C), soil microbial nitrogen (SMB-N) and phospholipid fatty acid (PLFA) concentrations were measured four times, at two depths (0--10 cm, 10--20 cm), over the 2001 growing season. Sample periods were: May 7th (pre planting), June 25 th, July 16th, and September 29th (prior to corn harvest). The effect of time was of a greater magnitude than those attributed to tillage or residue treatments. While SMB-C showed no seasonal change (160 mug C g-1 soil); SMB-N was responsive to mineral nitrogen fertilizer; and PLFA data showed an increase in fungi and total PLFA throughout the season. PLFA profiles showed better distinction between sampling period, and depth, than treatments. Of the two treatments, the effect of residue was more pronounced than that of tillage, with increased SMB-C and SMB-N (6.1% and 96%) in +R plots compared to -R plots. This study illustrated that measuring soil quality based on soil microbial components must take into account seasonal changes in soil physical, chemical conditions, and nutrient supply.
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Pfoller, Stacy Lynn. "DIVERSITY AND ACTIVITY OF SPHINGOMONAS IN PAH-IMPACTED SOILS AND SEDIMENTS." University of Cincinnati / OhioLINK, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=ucin984589035.
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