Dissertations / Theses on the topic 'Microbial amendments'

Low microbial activity and associated nutrient cycling are concerns in agricultural problem soils. The objectives of this study were to investigate microbial response on problem soils to amendments, drying-wetting cycles, and the interaction of amendments and drying-wetting cycles. In this laboratory study, soil carbon dioxide (CO2) flux was measured from thermal desorption treated soils and saline soils in response to Proganics, spent lime, and composted beef manure applications. Microbial activity was measured through CO2 flux and its rate of change, permanganate oxidizable C, and residual inorganic nitrogen. Proganics had the greatest ability to elevate and sustain microbial activity on problem soils, but spent lime and compost had the greatest potential to improve microbial mediated nitrogen mineralization. In conclusion, spent lime and compost can be effective amendments for improving soil quality of saline and thermal desorption treated problem soils to increase microbial activity and associated nitrogen cycling.

This dissertation examined the microbial ecology of Listeria monocytogenes in three distinctly different environments: a cheese microbial community; a farm environment; and a soil microbial community. The aim of the first study was to investigate the effects of L. monocytogenes on the composition of the surface microflora on washed rind soft cheese. Two trials with washed rind cheeses that were inoculated with 100cfu cm⁻² of a L. monocytogenes six strain cocktail were conducted. The first trial had to be terminated early (day 28) as contamination of Pseudomonas spp. from the initial brine did not produce the expected characteristics of the cheese during the aging period. For the second trial, cheese samples were aged in the lab for 60 days according to the cheesemakers specifications. Surface cheese rind samples were collected from both control and inoculated cheeses every 7 days. Cheese rind samples were analyzed through the standard BAM method for enumeration of L. monocytogenes and through amplification of the V4 region of 16S rRNA and ITS regions for identification of the surface rind bacterial and fungal communities, respectively. Our data showed that Pseudomonas spp. significantly changed the composition of the microorganisms found on the surface of the rind while L. monocytogenes had little effect. In addition, although the concentration of L. monocytogenes increased to levels of 10⁶ cfu cm⁻² based on the enumeration data, the genetic data was not able to identify it in the flora due to the fact that other genera were found at much higher concentrations, which is a limitation of molecular methods used for identification of pathogens in foods. For the second study the presence and incidence of L. monocytogenes on farms that either produce raw milk cheese or supply the milk for raw milk cheese production was investigated. Five farms were visited and in total 266 samples were collected from barn, environmental, and milk sites. L. monocytogenes prevalence was found to be at 6% from all the farms tested with 10 isolates found in the barn samples, 5 from environmental sites and 1 from milking equipment. Samples were identified to the genus level through a modified BAM method and speciated though multiplex PCR. Included in the pathogenic isolates was a DUP-1042B L. monocytogenes strain that has been implicated in major outbreaks, which emphasizes the adaptability and persistence of highly pathogenic stains in food manufacturing environments. Results from this study continue to support the fact that contaminated silage can be an important reservoir of the pathogen in a dairy farm setting. From our data and field observations we identified that drinking water sources for the animals is also an important reservoir of L. monocytogenes in farm environments. More importantly this study has shown the importance of continuous monitoring of environmental sites for the presence of the pathogen, particularly in silage. Lastly manure amended soils in the northeastern U.S. were tested for the presence and survival of rifampicin resistant Escherichia coli (rE. coli), generic E. coli (gE. coli) and Listeria spp.. Both gE.coli and rE.coli samples were processed using either direct enumeration, MPN or bag enrichment methods. Samples were taken from both tilled and surface dairy solid manure-amended plots. Listeria samples were processed using a modified BAM method. Listeria presence was constant throughout the study. In contrast, rE. coli and gE. coli levels declined with time. The main conclusions of this study were that soil type, location and physical characteristics have a significant role in the survival of bacterial populations of rE. coli, gE. coli and Listeria spp. in soil. Dairy solids application does not seem to have a long term effect on the natural microbial population of soils. Tilling of soils results in increased survival of the bacterial population due to the fact that it increases soil pore size and facilitates moisture entry, which in turn has been shown to increase bacterial survival rates. Data from this research will assist in the creation of preventative measures that lead to the elimination of pathogen reservoirs. It will be further used to verify that a 120 day interval following manure application should be sufficient to ensure food safety of edible crops subsequently planted on these soils.

Soil microbial communities are affected extensively by addition of amendments to their environment. Of particular concern is the addition of poultry litter, which contains a substantial C, energy, and nutrient supply, but also antibiotic resistance genes (ARG), antimicrobials, and a multitude of microbial species. This project seeks to primarily assess if there is a change in bacterial community structure in response to poultry litter amendments to pasture land across geographically independent land across northern Georgia. It may be that changes in the relative abundance of bacterial communities also result in alteration in ARGs, and the community resistance to antibiotics (“resistome”) which in turn increases the potential threat of antibiotic resistance genes. While another part of this study will determine changes in integrons and specific ARGs, this project will focus on changes in bacterial communities and the potential functional changes in the community, which in turn have consequences for ARG levels and its horizontal transfer to various members of the soil community. Addition of waste from livestock is a historical method for increasing nutrients needed in the soil for the cultivation of crops, and in turn causes pronounced shifts in soil microbial communities due to the addition of large amounts of carbon, nutrients, foreign microbes, and other material. This study is unique because it utilizes a novel and relatively large landscape-scale to determine if there are discernable and repeatable patterns of bacterial community structure change in response to amendment regardless of exact soil type or source of chicken litter amendment. In the future, these data can also provide insight into the changes in the relative abundance antibiotic related genes associated with community change.
M.S.
Soil is complicated, both in terms of its physical makeup and the organisms that live inside of it. Predicting changes in soil based on the addition of foreign material such as chemicals or biological waste is not an easy process, and whether or not it is even possible to reliably predict those changes is a matter of some dispute. This study is designed to illustrate that such changes can in fact be reliably and consistently predicted even with regard to the addition of complicated materials to the soil. In this study, specifically, the material in question is chicken litter. A mix of the bedding and waste produced by chickens, litter is commonly handled by composting and is added to soil in farms as a fertilizer rich in organic matter. It is possible to point at specific elements of the soil such as the chemistry and bacteria and see how it is changed with the addition of chicken litter, which allows us to determine the nature and extent of the change that chicken litter has on soil. This study is conducted on a larger scale than similar experiments conducted in the past, making it apparent that these relationships exist on a repeated basis. It is the object of this study to pave the way and make it easier for scientists in the future to determine these relationships in other unique contexts.

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.

The effects of managing soil with organic amendments were examined with respect to soil microbial community dynamics, macroaggregate formation, and plant physio-genetic responses. The objective was to examine the possibility of managing soil microbial communities via soil management, such that the microbial community would provide agronomic benefits. In part one of this research, effects of three amendments (hairy vetch residue, manure, compost) on soil chemical and microbial properties were examined relative to formation of large macroaggregates in three different soils. Vetch and manure promoted fungal proliferation (measured via two biomarkers: fatty acid methyl ester 18:2ω6c and ergosterol) and also stimulated the greatest macroaggregate formation. In part two of this research, effects of soil management (same amendments as above, inorganic N fertilization, organic production) on soil chemical and microbial properties were examined relative to the expression of nitrogen assimilation and defense response genes in tomato (Solanum lycopersicum L.). Soil management affected expression of a nitrogen assimilation gene (GS1, glutamine synthetase) and several defense-related genes. The GS1 gene was downregulated with inorganic N fertilization, expression of the pathogenesis-related PR1b gene (which codes for the pathogenesis-related PR1b protein) was increased in plants grown in soil amended with compost, vetch, and N fertilizer, and expression of three other defense-related genes coding for chitinase (ChiB), osmotin (Osm), and β-1,3-glucanase (GluA) were decreased in plants from soil amended with manure and in plants from the organically managed soil. Differential expression of defense-related genes was inversely related to the relative abundance of Gram-negative bacteria. The relative abundance of the 18:1ω7c Gram‑negative bacterial biomarker was greatest in manure treated soil and in organically managed soil (which recieves seasonal manure applications). These treatments also had the lowest expression of ChiB, Osm, and GluA, leading to speculation that manure, through increases in Gram-negative bacteria, may have suppressed populations of soil organisms that induce a defense response in plants, possibly allowing for less-stressed plants. Outcomes of this research may be useful for those interested in developing management strategies for maintaining or improving soil structure as well as those interested in understanding management effects plant physio-genetic responses.

Human activities that disrupt soil properties are fundamentally changing ecosystems. Soil degradation decreases microbial abundance and activity, leading to changes in nutrient availability, soil organic matter, and plant growth and establishment. Land use and land cover change are widespread and increasing in semiarid regions of the southwestern US, which results in reductions of native plant and microbial abundance and community diversity. Here we studied the effects of soil degradation and amendments (biochar and woodchips) on microbial activity, soil carbon and nitrogen availability, and plant growth of ten semi-arid plants species native to the southwestern US. Results show that woodchip amendments result in poor overall plant growth, while biochar amended soils promoted plant growth when soil quality was reduced. Additionally, amendments had a strong influence on microbial activity, while the presence and species identity of plants did not. Biochar amended soils led to increases in the potential activities of enzymes involved in the degradation of carbon, nitrogen, and phosphorus rich substrates. Woodchips, caused an increase of potential activity in enzymes involved in the degradation of sugar and proteins. These results show that microbes and plants respond differently to soil treatments and suggest that microbial responses may function as earlier indicators of the success of re-vegetation attempts.

Thesis (Ph.D.)--University of Missouri-Columbia, 2004.
(tm) after EM in title is for Trademark symbol. Typescript. Vita. Includes bibliographical references (leaves 120-142). Also available on the Internet.

Les émissions de COVs jouent un rôle central sur la pollution atmosphérique. Les sources biogéniques des COVs sont entre 10 et 11 fois plus élevées que les émissions des COVs provenant par des sources anthropiques. Récemment, l'importance de la caractérisation des flux de COVs par les sols et les microorganismes a été soulignée. En effet, les émissions des COVs provenant du sol et des microorganismes sont des possibles précurseurs des particules atmosphériques et de la formation d'O3. En particulier, ce travail est centré sur la caractérisation des émissions de COVs par des sols amendés avec des PROs en détectant les émissions toute de suite après l’apport, 1 an et 2 ans après l’apport des PROs. De plus, l'influence de la diversité microbienne du sol sur les émissions de COV a également été analysée. Les émissions de COVs ont été détectées à l'aide de la technique PTR-QiTOF-MS et la totalité des expériences a été réalisées dans des conditions de laboratoire contrôlées en utilisant des chambres dynamiques pour la détection des COVs émis par les échantillons. Les résultats ont montré que les différentes PROs émettent des quantités COVs variables et que les propriétés chimiques et physiques du sol influençaient également les émissions. L’analyse de l'influence de la biodiversité microbienne sur les émissions de COVs a montré que si la diversité microbienne est plus élevée, les émissions de COVs par les sols sont plus faibles. En outre, la diversité des COVs diminue lorsque les émissions de COVs par le sol sont plus élevées. Enfin, l'étude de la dynamique des émissions de COVs par de microcosmes récemment amendés avec du PRO, a montré que le flux des émissions de COV augmentait dans les premières 49 heures après l'apport des PRO en raison d'une perturbation de la communauté microbienne dans le sol
VOCs emissions play a pivotal role on the atmospheric pollution. Biogenic sources of VOCs are between 10 and 11 times higher than VOC emissions from anthropogenic sources. Recently, the importance of the characterization of the VOC fluxes by soils and microorganisms has been highlighted. Instead, VOCs emissions from soil and microorganisms are possible precursors of the particulate matter and the O3 formation. This work is focused on the characterization of the VOCs emissions by soils amended with OWPs over the long and short terms application. The influence of the microbial diversity in soil on VOCs emissions was also analysed. VOC emissions were detected using the PTR-QiTOF-MS technique and all the experiments were performed under controlled laboratory condition using dynamic chambers for the detection of the VOCs emissions from samples. The results showed that different OWPs released different quantity of VOCs emissions and also the chemical and physical properties of the soil were linked to the emissions. Analyses on the influence of microbial biodiversity on VOCs emissions have shown that while the microbial diversity was higher VOC emissions by soils were lower. Furthermore, the diversity of the VOCs decreases when the VOCs emissions by soil are higher. Finally, the study of the dynamics of VOC emissions from microcosms amended with fresh OWPs, showed that the VOC emission flux increased in the first 49 hours after the OWP amendment, due to a disturbance of the microbial community in the soil

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2002.
Abstract inserted. Appendix reprints four papers and manuscripts co-authored with others. Includes bibliographical references. Also partially issued electronically via World Wide Web in PDF format; online version lacks appendix.

El suelo desempeña funciones de gran importancia para el sustento de la vida en este planeta pero la desertificación producida en el mismo, en las zonas áridas o semiáridas, repercute notoriamente en una abundante pérdida de materia orgánica, y por tanto de carbono orgánico, la cual afecta negativamente a la calidad y la sostenibilidad del suelo. La recuperación del carbono orgánico del suelo hacia unos valores umbrales suficientes para poder gestionar sus funciones básicas es de vital importancia. Por este motivo, la presente Tesis Doctoral tiene como Objetivo entender el ciclo del carbono en suelos semiáridos y el desarrollo de estrategias para la restauración de estos suelos. Para ello nos hemos centrado particularmente en la capacidad que presenta este tipo de suelo para responder a fuentes de carbono exógenas derivadas de residuos vegetales, el papel que desempeña la comunidad microbiana en la degradación de estas fuentes de carbono, y su relación con los ciclos biogeoquímicos de los elementos importantes (C, N y P), con particular incidencia en el del carbono. Se maneja como Hipótesis general de trabajo de esta Tesis Doctoral el hecho de que las comunidades microbianas de suelos áridos y semiáridos tienen una limitada capacidad para el procesamiento de sustratos carbonados, a consecuencia del escaso contenido en materia orgánica que presentan habitualmente estos suelos. Con el objetivo de obtener una información completa sobre la dinámica del carbono orgánico y las enmiendas orgánicas de origen vegetal en relación con las poblaciones microbianas asociadas a su procesamiento, se abordan experimentos en condiciones controladas de laboratorio y campo. La primera parte de la Tesis (Capítulos 1, 2 y 3) se realizó en condiciones controladas de laboratorio, mediante la utilización de tres moléculas de origen vegetal de distinta complejidad: glucosa, celulosa y lignina; dichas moléculas son parte fundamental de los propios restos vegetales que entran al suelo de forma natural. Estas moléculas se utilizaron en su forma enriquecida en 13C (isótopo estable del carbono) con el objetivo de trazar a alta resolución la dinámica de estas materias orgánicas y las poblaciones microbianas implicadas en su procesamiento. En estos experimentos se aplicaron, entre otras, técnicas basadas en el análisis de la composición isotópica del CO2, fracciones hidrosolubles de C, y de sustancias húmicas, así como la composición isotópica de ácidos grasos (PLFA-SIP). Mediante este conjunto de técnicas se pudo trazar exhaustivamente el ciclo del C, evaluando su persistencia, mineralización y las poblaciones microbianas asociadas con la dinámica de estas moléculas. La segunda parte de la Tesis (Capítulos 4 y 5) se realizó a nivel de campo, lo cual representa un escenario real para el estudio de la restauración de suelos. En el Capítulo 4, se evaluó el efecto a largo plazo de enmiendas orgánicas de origen vegetal (residuos de poda fresco y compostado) y de su dosis (150 y 300 t ha-1) en las propiedades químicas, bioquímicas y microbiológicas de un suelo semiárido. Para ello se emplearon diferentes técnicas para medir los cambios en la actividad microbiana después de la adición de la materia orgánica, así como el análisis de ácidos grasos fosfolípidos y el perfil fisiológico de las comunidades microbianas para estudiar los cambios en la biomasa y estructura de la comunidad. En el Capítulo 5, se estudió el efecto que ejerce la adición enmiendas orgánicas a largo plazo en las enzimas involucradas en el ciclo del carbono bajo condiciones semiáridas, además de su influencia en la biomasa y la estructura de la comunidad microbiana. Además, se pretendió completar el conocimiento del ciclo del carbono en este tipo de suelos mediante el estudio de la diversidad de isoenzimas que presentan la celulasa y β-glucosidasa empleando la zimografía. Los cambios provocados en el tamaño de la biomasa microbiana y la estructura de la comunidad microbiana por la adición de las enmiendas fueron estudiados mediante el análisis de los ácidos grasos fosfolípidos. Haciendo una visión global de esta Tesis Doctoral, podemos concluir que los suelos semiáridos, a pesar de su avanzado estado de degradación y no recibir abundantes entradas de C orgánico, presentan una alta disponibilidad biótica para gestionar materia orgánica de origen vegetal de distinto nivel de complejidad y estabilidad. Se ha observado que sólo una pequeña fracción de la comunidad microbiana es capaz de degradar las formas más complejas de carbono, pero esta fracción microbiana es fundamental para el inicio del ciclo del carbono en suelos semiáridos y, por tanto, para la sostenibilidad de estas áreas. Además, las entradas de materia orgánica al suelo mejoran la calidad de los suelos semiáridos a largo plazo, aumentando el contenido en carbono orgánico en los mismos, favoreciendo el crecimiento de la biomasa microbiana y variando la estructura funcional de la comunidad microbiana, como una adaptación ecológica a la presencia de nuevos metabolitos en el suelo derivados de dichas materias orgánicas. Por otro lado, la adición de moléculas compuestas únicamente por carbono, no sólo ejerce un efecto sobre el ciclo del carbono si no que también influye sobre otros ciclos biogeoquímicos como el del nitrógeno o el fósforo como hemos podido ver por los cambios producidos en la actividad enzimática relacionada con estos elementos. Este hecho implica que estos ciclos no pueden considerarse independientes si no que actúan de forma conjunta para condicionar la calidad y sostenibilidad de un suelo.
Soil plays a highly important role in sustaining life on earth but soil desertification, in arid and semiarid areas, negatively impacts on a significant loss of organic matter, and therefore of organic carbon, which negatively affects the quality and sustainability of the soil. In such degraded soils, it is of vital importance to restore levels of soil organic carbon to sufficient thresholds to maintain its basic functions. For this reason, the aim of this Doctoral Dissertation is to understand the carbon cycling of semiarid soils and the development of strategies for soil restoration. To reach this goal we have focused on the following topics in particular: the ability of this type of soil to respond to exogenous sources of carbon derived from plants; the role of the microbial community in the degradation of these carbon sources; and the link between these carbon sources and the biogeochemical cycling of the important elements (C, N and P), with a particular focus on carbon. The general working Hypothesis of this Doctoral Thesis is that the microbial communities in arid and semiarid soils have a limited capacity for processing carbonaceous substrates as a result of the low content of organic matter usually found in these soils. In order to obtain complete information concerning the dynamics of organic carbon and plant-derived organic amendments with respect to the microbial populations associated with processing of this organic matter, we conducted experiments in both controlled laboratory and field conditions. The first part of the thesis (Chapters 1, 2 and 3) was carried out in controlled laboratory conditions using three molecules of varying complexity: glucose, cellulose and lignin. These molecules are an essential part of the natural plant inputs to soil. We used glucose, cellulose and lignin molecules enriched with 13C (a stable isotope of carbon) in order to track the dynamics of these organic materials and the microbial populations involved in their processing in high resolution. In these experiments we applied, among other techniques, those based on the analysis of the isotopic composition of CO2, water-soluble fractions of C and of humic substances and the isotopic composition of fatty acids (PLFA-SIP). These techniques made it possible to thoroughly track the C cycle, evaluating the persistence and mineralisation of C in addition to the microbial populations associated with the dynamics of the added molecules. The second part of the thesis (Chapters 4 and 5) was carried out in the field, which represents a real setting for the study of soil restoration. In Chapter 4, we evaluated the long-term effects of plant-derived organic amendments (fresh and composted pruning waste) and of the applied dose (150 and 300 t ha-1) on the chemical, biochemical and microbiological properties of a semiarid soil. Different techniques were used to measure the changes in microbial activity after the addition of organic matter. Furthermore, phospholipid fatty acid analysis and the microbial community-level physiological profile were used to study changes in the biomass and the structure of the microbial community Finally, in the Chapter 5, we studied the long-term effect of organic amendments on the enzymes involved in the carbon cycle in semiarid conditions. In this chapter, we also evaluated the influence of organic amendments on microbial biomass and community structure. Furthermore, we aimed to complete our knowledge of the carbon cycle in semiarid soils by studying the diversity of isoenzymes exhibiting cellulase and β-glucosidase activity by zymography. Changes caused by the amendments in the biomass and the structure of the microbial community were studied by phospholipid fatty acid analysis . Taking a global picture of this Doctoral Thesis, we have reached the conclusion that semiarid soils, despite their advanced state of degradation and the fact they have not received much organic C input, nevertheless have a high level of biotic availability for handling plant-derived organic matter of different levels of complexity and stability. We observed that only a small fraction of the microbial community is able to degrade the more complex forms of carbon, but this microbial fraction is crucial for starting the carbon cycle in semiarid soils and therefore for the sustainability of semiarid areas. Moreover, adding organic matter to the soil improves the quality of semiarid soils in the long term. Indeed, organic amendments increase the content of organic carbon in such soils at long-term, favour the growth of the microbial biomass and change the functional structure of the microbial community as an ecological adaptation to the presence of new soil metabolites derived from the organic matter added. Furthermore, the addition of molecules composed solely of carbon not only has an effect on the carbon cycle but also influences other biogeochemical cycles such as the nitrogen and phosphorus cycles, which we were able to observe through changes in the enzyme activity related to these elements. This implies that these cycles cannot be considered as independent from one another but that they in fact act together to determine the quality and sustainability of a soil.

The chemical and physical processes controlling contaminant fate and transport in the vadose zone limit the options for application of many remedial technologies. Foam delivery technology (FDT) has been developed as a potential solution to overcome these limitations for remediating subsurface and deep vadose zone environments using reactive amendments. Although there are many advantages to utilizing FDT for treatment in the deep vadose zone, little information is available on how the addition of these surfactants and remedial amendments affect the indigenous microbial communities in the deep vadose zone as well as the impact of biological transformations of surfactant-based foams on remediation efforts. The purpose of this study was to develop a rapid method for assessment of microbial communities in contaminated subsurface environments. This research was divided into two phases: (1) assess the toxicity of proposed FDT components on a single bacterial species, Shewanella oneidensis MR-1; and (2) determine the effects of these components on a microbial community from the vadose zone. In Phase I, S. oneidensis MR-1 was exposed to proposed FDT components to assess potential growth inhibition or stimulation caused by these chemicals. S. oneidensis MR-1 cultures were exposed to the surfactants sodium laureth sulfate (SLES), sodium dodecyl sulfate (SDS), cocamidopropyl betaine (CAPB), and NINOL 40-CO, and the remedial amendment, calcium polysulfide (CPS). Results from this phase revealed that the relative acute toxicity order for these compounds was SDS>>CPS>>NINOL40-CO>SLES≥CAPB. High concentrations of SDS were toxic to the growth of S. oneidensis MR-1 but low concentrations were stimulatory. This benchtop system provided a capability to assess adverse microbial-remediation responses and contributed to the development of in situ remedial chemistries before they are deployed in the field. For Phase II, sediments from the BC Cribs and Trenches (BCCT) area of the Hanford Site, WA, were characterized before and after exposure to potential FDT components. First, the phylogenetic and metabolic diversity of sediment from the BCCT was assessed by sequencing the microbial community and measuring the metabolic activity. The sediment was also incubated with various concentrations of SDS, CAPB, and CPS. Phylogenetic analysis detected phylotypes from the Alpha-, Beta-, Delta-, and Gammaproteobacteria, and Actinobacteria. Unlike the S. oneidensis MR-1 studies conducted in Phase I, the surfactants and CPS stimulated the metabolic activity of the native microbial communities. The observed stimulation could be caused by sorption of the chemicals to the sediment particles, or utilization of the surfactants by the microbial communities. These findings emphasize the importance of monitoring microbial activity at remediation sites in order to determine short and long term efficacy of the treatment, compliance with regulatory mandates, and act as an early warning indicator of unintended changes to the subsurface.

Coastal sediments are major sites for microbially-mediated nitrate reduction, In particular denitrification. Estuarine sediments are prime locations for this process due to anthropogenic ally generated nitrate pollution from agricultural sources and wastewater treatment plants. The Colne estuary (UK) is one such hypernutrified estuary, receiving significant inputs of nitrate and ammonium. Rates of denitrification have been previously characterised along the estuary and found to be highest at the estuary head and lowest at the mouth. The aim of this current study was to investigate spatial and temporal variation in microbial community structure along nutrient and salinity gradients of the estuary, as well as assess the bacterial and archaeal community composition and denitrification potential of the sediments located at the mouth of the estuary and via the use of slurry microcosm experiments to examine the responses of bacterial communities to changes in levels of nitrate and organic carbon. Molecular techniques based on both the microbial taxonomic marker gene (16S rRNA) and denitrification (nirS, nirK) genes were employed to investigate these changes in community structure and composition. Distinct sediment bacterial communities were present at the low salinity and marine sites of the estuary with seasonal variability observed at the lowest salinity site (Hythe) and monthto- month variation at the brackish and marine sites (Alresford and Brightlingsea). The marine bacterial community was dominated by proteobacteria, with Crenarchaeota the dominant archaeal phylum. The potential for denitrification was investigated in the marine sediments, with denitrifying populations distinct from those previously described in low salinity sediments of the Colne. In microcosm experiments, bacterial communities in sediments amended with only nitrate, or nitrate and acetate showed major shifts in community composition relative to those in unamended sediments. This research has revealed a diverse microbial community structure exists along the Colne estuary and demonstrates considerable capacity for nitrate removal at the mouth of the estuary and that changes in nitrate and organic carbon can result in major changes in sediment microbial community composition.

[Truncated abstract] Weeds are a major limitation to agricultural and horticultural production and the main method of control is the use of herbicides. In addition to the resulting chemical pollution of the environment, the wide spread and continues use of herbicides have resulted in many weeds developing resistance to commonly used herbicides. This study investigated the potential of using green manures as a cultural method of control of weed invasion in agricultural fields. To understand the general mechanisms involved in the suppression of seed germination in green manure amended soils, seeds of crop species with little or no dormancy requirements were used in certain studies. Lettuce (Lactuca sativa) and cress (Lepidium sativum) seeds were sown to a sandy soil amended with green manures of lupin (Lupinus angustifolius), Brassica juncea, or oats (Avena sativa) to determine if the amendments affected seed germination and/or decay. It was hypothesised that the addition of plant material would increase the microbial activity of the soil thereby increasing seed decay, under laboratory and greenhouse conditions. Initial experiments used lettuce, cress and lupin seeds. Lettuce and cress are commonly used as standard test species for seed viability studies. Subsequent experiments used seeds of annual ryegrass (Lolium rigidum), silver grass (Vulpia bromoides), wild radish (Raphanus raphanistrum) and wild oat (Avena fatua) as these weed species are commonly found throughout agricultural regions in Western Australia. Amending the soil with lupin or Brassica green manure was established as treatments capable of developing environments suppressive to seed germination. Lupin residues as green manure showed the strongest inhibition of seed germination and seed decay. The decay of certain seeds was enhanced with changes to soil microbial activity, dissolved organic carbon and carbon and nitrogen amounts in lupin amended soil. Seeds of weed species were decayed in lupin amended soil, but showed varied degree of decay. Annual ryegrass and silver grass were severely decayed and wild oat and wild radish were less decayed, in lupin amended soil.

Manure is a commonly used soil fertilizer, but there are concerns that this practice could affect the spread of antibiotic resistance genes (ARGs) from farm to fork. A microcosm-scale study evaluated the effect of prior antibiotic use (manure-based soil amendments generated from dairy and beef cattle with or without antibiotic administration), composting, and soil type on the quantity of ARGs and the microbial community composition of dairy and beef manure applied soil. ARGs were analyzed through novel metagenomic techniques and quantitative polymerase chain reaction of sul1, tet(W), and 16S rRNA gene, while the microbial community composition was determined via 16S rRNA amplicon sequencing. The results indicated that while prior antibiotic administration elevated the relative abundance of ARGs and changed the microbial community of raw manure applied soils, composting reduced this effect. However, compost applied soils still had a higher relative abundance of ARGs than the unamended soils and occasionally soil applied with raw manure of untreated cattle. Soil type may be a mediating factor as there were differences observed between the three soil types (sandy loam, silty clay loam, and silty loam) with sandy loam amended soils often having the least attenuation of ARGs. As the relative abundance of ARGs was still elevated and the microbial community composition still significantly different from the unamended soils after 120 days, these results suggest that 120 days is not a long enough waiting period between biological soil amendments and crop harvest for ARG dissipation.
Master of Science

Laboratory batch and long-term column experiments were conducted to investigate the effects of wood-chip biochar and coal-derived activated carbon amendment on the microbiology of a volatile petroleum hydrocarbon (VPH) - contaminated gravelly sand. First, a stable isotope-labelled mono aromatic compound – toluene was used as a model VPH to gain insights into the mineralization of VPHs by soil microorganisms in the presence and absence of biochar or activated carbon. The biodegradation of a mixture of 12 VPHs was subsequently monitored in batch microcosms over a duration of 6-19 days by measuring headspace CO2 concentration. Further analysis was carried out by characterizing changes in the soil microbial community composition using next generation sequencing techniques – 454 pyrosequencing and Ion torrent sequencing. Increases in the levels of headspace CO2 in contaminated soil batches as compared to live and abiotic controls to which no VPHs were added indicated a stimulation of microbial activity in the batches through VPH addition. By fitting a maximum specific growth rate of 0.6 h-1 (in line with published rates), it was possible to match model predictions of 45CO2 and 44CO2 concentrations with the experimentally determined data. Half-saturation constants of 4.06 x 103 mgL-1, 7.76 x 102 mgL-1 and 1.83 x 102 mgL-1 were predicted for soil, soil & BC and soil & AC respectively, much higher than values reported in the literature. Differences in the half-saturation constant suggests that sorbent amendment affects the microbial ecology, by making microorganisms which can utilize substrates at lower concentrations more competitive. Yield coefficients (g biomass-C relative to g (biomass-C + CO2-C)) compared more closely in the nutrient (N & P) amended soils ranging from 4.83±0.46 in soil and biochar to 7.86±0.72 in unamended soil, than in the batches without nutrients, 4.1±3.1 in soil & BC, 17.7±5.2 in soil and 13.7±4.6 in soil & AC. Sorbent amendment thus reduced yield coefficients, thereby slowing the growth of VPH degrading biomass. Microbial community structure analysis revealed an increase in the relative abundance ranking of members of the genera Pseudomonas, Pseudoxanthomonas, and Arenimonas by up to 32 folds and in the families Nocardioidaceae and Pseudomonadaceae by at least 32 folds in sorbent amended and unamended soil batches and columns compared to their initial soil conditions. Consequently, amending soils with 2% BC or AC changed the biokinetics of VPH degradation by rendering VPHs less bioavailable, but did not appear to have any detrimental effects on the VPH degrading bacteria both in the short- and long-term, and may serve as a sustainable, cost-effective approach for enhancing the natural attenuation of VPHs in soil, thus addressing the challenge of petroleum hydrocarbon contamination.

As agrarian society developed, the most fertile soils able to sustain the nutritional requirements needed for high crop yield were assigned to farming, while the more penurious soils were left to uphold the forest ecosystems. Some temperate forests are developed on acidic soils considered to be nutrient poor, as much of the inorganic nutrients are entrapped in poorly weatherable soil minerals and not easily accessed by plant roots. In an undisturbed ecosystem, the largest contribution of available nutrients comes from the recycling of organically bound nutrients via the decomposition of dead plant material. If biomass is removed, for instance with a more intensified exploitation of the forest ecosystems including whole tree harvesting, this source of nutrients is consequently decreased. The importance of soil mineral weathering as a source of nutrients, and especially that promoted by soil biota, is thereby emphasized. This thesis addresses biotic parameters associated with mineral weathering. Different aspects of soil solution sampling strategies and analysis of different organic ligands as well as biomarkers for the estimation of fungal biomass were investigated. These chemical parameters were also evaluated as indicators of microbial activity in relation to mineral nutrient availability in soil. With the assumption that the current nutrient status of a soil will affect the microbial interest of certain minerals as sources of inorganic nutrients, a mineral amendment trial was performed in a Swedish boreal forest soil. Overall, the amended soil presented good nutrient status, but with a possible shortage of iron. Due to this, it was hypothesized that the amended mineral with the highest iron content i.e. biotite would cause an elevation of microbial activity in its vicinity when compared to the bulk soil. The level of microbial activity in the vicinity of the amended minerals was evaluated via quantification of organic acids and siderophores, as well as estimation of fungal biomass and enzymatic activity. The highest microbial activity was measured for the O horizon of the investigated podzol, although nothing indicated an elevated association with the amended minerals. In the E horizon, however, elevation in microbial activity was observed in the vicinity of the biotite mineral when compared with bulk soil, although only a few of the investigated parameters differed significantly when evaluated separately.   To enable this study, a highly sensitive analytical method employing liquid chromatography and mass spectrometry was developed to quantify a number of hydroxamate siderophores. On-line pre-concentration enabled detection of these organic ligands in the pico-molar range – a necessity when analyzing natural samples. Furthermore, an analytical method was developed for the estimation of fungal biomass via quantification of chitin-derived glucosamine, which also employed liquid chromatography and tandem mass spectrometry. Unlike currently available methods, the one presented in this thesis did not involve analyte derivatization, which resulted in high sample throughput while simultaneously avoiding complications involved with the additional derivatization procedure. The distribution of a group of organic ligands known as aromatic low molecular mass organic acids was also studied in a boreal forest podzol soil. Different sampling and samples preparation techniques, namely tension-lysimeters, soil centrifugation and liquid-soil extraction, were compared when analyzing soil solution components. Significant differences in analyte amount and species type were found between these sampling techniques. Some of the differences could be accounted for by variation in soil composition at different depths of the investigated podzol, but others could be attributed to structural differences within the studied analyte group. This clearly illustrated the intricacy of sampling and analysis when working with a sample matrix as complex and diverse as soil. As previously, liquid chromatography and mass spectrometry was used to quantify the analytes of interest. A highly sensitive analytical method was developed that was able to detect eleven aromatic low molecular mass organic acids in the nano-molar range. High selectivity was ensured by applying multiple reaction monitoring enabled by collision induced fragmentation of the analytes.
FORE

Alors que l'épandage de déchets huileux à forte dose sur des sols non cultivés est utilisé pour éliminer les hydrocarbures, les épandages à faible dose sur les terres cultivées ont été peu envisagés. Aussi, des essais ont été conduits au laboratoire et au champ afin de suivre le devenir et les effets, dans le système sol-plante-microorganismes, d'hydrocarbures appliqués à faible dose sous la forme de déblais de forage. Ont été pris en compte la phytotoxicité, le transfert sol-plante, la biodégradation en absence et en présence de plante et l'infiltration des hydrocarbures. Les résultats des études en laboratoire montrent que les hydrocarbures perturbent la germination et la croissance des végétaux. La phytotoxicité dépend de la dose, du type de molécule et varie en fonction des espèces végétales. Aucun transfert d'hydrocarbures dans les parties aériennes du maïs n'est observé. Dans le sol, la majorité des hydrocarbures est dégradée et le résidu final de la biodégradation est constitué de molécules cycliques. En présence de plante, la dégradation est plus rapide et l'exsudation racinaire est un facteur important de stimulation de la dégradation des hydrocarbures dans la rhizosphère. Au champ, l'infiltration sélective des hydrocarbures légers et de certains métabolites dans le profil de sol et dans les eaux de drainage est observée. L’importance du phénomène dépend de la quantité et du type d'hydrocarbures et des conditions pédoclimatiques. L’épandage de déblais de forage en plein champ entraine une légère diminution du rendement des deux premières cultures. Aucun hydrocarbure pétrogénique n'est retrouvé dans les plantes. Dans ces conditions, la vitesse de disparition des hydrocarbures est proportionnelle à la dose d'épandage. Les alcanes linéaires, ramifiés et certains aromatiques sont dégradés alors que les composés cycliques persistent. L’apport de petites quantités de déblais de forage pourrait constituer une alternative au landfarming intensif des déchets huileux. Cependant, la présence de molécules mobiles et toxiques peut avoir des conséquences négatives sur l'agrosystème

The reuse of litter in broiler production can lead to litter pathogen buildup and high levels of ammonia in broiler housing, thus resulting in poor broiler performance. This study evaluated the effects of two microbial litter amendments on litter characteristics, ammonia production and broiler performance. Experiment one, consisting of three trials, utilized eight pens approximately 3 x 3.2 m (10 x 10.5 ft) to rear broilers to 49 d of age. Experiment two, consisting of one trial, utilized twelve 1.8 x 3.7 m (6 x 12 ft) pens to rear broilers to 42 d of age. Used litter was obtained from separate commercial broiler farms for each experiment and placed into the pens at an average depth of 11 cm (4.3 in). Feed consumption and mortality were recorded for each pen for each trial. Ammonia production was measured by placing an enclosed chamber over the litter and measuring the headspace ammonia concentration after 20 minutes for both experiments. Experiment one also utilized a two minute ammonia flux technique. Ammonia measurements were taken at the time of litter treatment, at chick placement, and once per week for the remainder of the grow-out. Litter samples were collected at the same time and location as ammonia measurements. At the end of all trials, caked litter was removed from each pen, weighed and sampled. Litter and cake samples were analyzed for total aerobic and anaerobic microbial counts in experiment 1. Experiment 2 analyzed aerobic litter samples only. Paw scores were also recorded at the end of each trial for all birds using a 3-point scale. Data was subjected to ANOVA using the GLM procedure with means deemed significantly different at P < 0.05. Statistical differences were seen sparingly in different parameters in both experiments; however these differences were random in their distribution and showed no trend. Final results indicated that the microbial litter amendments had no effect on broiler performance, litter characteristics or ammonia production.

A three year field study was conducted on two different tailings, Bethlehem (silt loam) and Trojan (sand), to determine the effects of fertilizer and biosolids amendments on selected soil physical, chemical and microbial parameters. Following addition of biosolids at rates of 50, 100, 150, 200 and 250 Mg ha⁻¹ soil bulk density decreased linearly. Biosolids addition resulted in an increase in water retention (gravimetric) at field capacity and wilting point but no significant change in water holding capacity were noted. On a volumetric basis water holding capacity decreased with increasing biosolids addition for the silt loam site, but showed no change for the sandy site. Soil pH was generally not impacted by treatment while electrical conductivity, soil organic matter, total carbon and cation exchange capacity all increased with increasing levels of biosolids. Addition of biosolids resulted in an increase in total heterotrophic aerobes, total anaerobes, sulfate reducers, iron reducers and denitrifiers. The chemical fertilizer amendment did not alter soil physical or chemical parameters from that of the control.

The boreal forest area around Flin Flon, MB, and Creighton, SK, has been the site of a metal mining and smelting complex since the 1930s. Smelter emissions, coupled with forest logging, forest fires, and subsequent soil erosion, have led to severe vegetation dieback and the development of soils containing a mixture of metals in varying concentrations. In affected areas, existing vegetation typically is stunted. Limestone applications to affected soils have served to increase pH and, in some instances, the vegetation has responded positively; however, in some areas limestone application has failed to restore vegetation, leading to an interest in examining the suitability of other soil amendments to affect revegetation in these areas. Typically revegetation programs focus on aboveground vegetation responses; however, healthy plant growth often is dependent on the presence of an equally healthy soil microbial community. Thus, this study attempted to link revegetation success with responses of the soil microbial community structure to various soil amendments. Two studies were conducted to determine the influence of soil amendments (biochar, municipal and manure compost, glauconite, and an arbuscular mycorrhizal/ectomycorrhizal inoculant) on plant growth and microbial community structure in two soils from the Flin Flon area, classified as containing high and low metal concentrations. The two studies evaluated the growth of boreal forest understory species American vetch (Vicia americana) and tufted hairgrass (Deschampsia caespitosa) and overstory species jack pine (Pinus banksiana) and trembling aspen (Populus tremuloides) after addition of soil amendments, and the subsequent effects on microbial community structure. Greenhouse experiments evaluated plant growth for a period of 8 weeks (understory species) or 19 weeks (overstory species), after which plants were analyzed for changes in biomass and metal accumulation in plant tissue. Soils were analyzed for available metal concentrations, as well as microbial biomass carbon and nitrogen, and phospholipid fatty acid concentration, which is a measure of microbial community structure. Significant effects were seen on plant growth and microbial community structure due to the metal concentrations in the soil, but no one amendment consistently impacted plant growth or metal uptake, or any measured microbial parameter. The results of this study indicate the variability of plant growth and microbial functioning in soils from the study site, as well as the inherent challenges associated with revegetating heavy metal affected soils, and underline the need for further research on plant growth and microbial community structure at this site.

Mestrado em Engenharia do Ambiente - Especialização em Tecnologias Ambientais - Instituto Superior de Agronomia
Organic amendments were made to a naturally burned soil (BS), unburned soil (fresh soil) and soils treated at 65, 105 and 250 oC simulating fire effects. Digested pig slurry (PS), composted municipal solid waste (MSW) and a mixture of both residues were applied to soil samples and incubated for 2 months. To determine the effects of fire and organic amendments on soil microorganisms and if changes occurred in their functional diversity, microbial community level physiological profiles were assessed using different carbon substrates. Substrate induced respiration and basal respiration were determined by the MicroRespTM method. BS showed greater respiration values than other treatments, suggesting that the ability of soil microorganisms to use carbon substrates was not reduced in BS, probably due to low fire intensity. PS seemed to be more effective improving microbial activity in BS, while in 65 and 105 oC soils MSW was more successful. Fresh soil often showed lower respiration than 65 and 105 oC soils suggesting a change in microbial communities after treatment, eventually with destruction of less tolerant microorganisms and consequent increase of available organic matter. Microorganisms introduced by organic residues seemed to play an important role in microbial respiration recovery.---------------------------------Foram aplicados resíduos orgânicos a um solo queimado (SQ) em fogo florestal, solo não queimado (solo fresco) e solos tratados a 65, 105 e 250 oC em estufa. Chorume de porco digerido (CP), resíduo solo urbano compostado (RSU) e uma mistura destes dois resíduos foram adicionados aos solos e incubados durante dois meses. Para avaliar os efeitos do fogo e da aplicação de resíduos aplicados nos microrganismos do solo e se as mudanças ocorreram ao nível da sua diversidade funcional, determinaram-se os perfis fisiológicos da comunidade microbiana através da utilização de diferentes substratos carbonados, pelo método MicroRespTM. O SQ apresentou maior respiração, sugerindo que a capacidade dos microrganismos utilizarem os substratos não ficou reduzida pelo fogo, que provavelmente foi de baixa intensidade. O CP terá sido mais eficiente a melhorar a actividade microbiana no SQ, e nos solos a 65 e 105 oC o RSU. O solo fresco obteve frequentemente menores valores de respiração que os solos tratados a 65 e 105 oC, sugerindo uma mudança nas comunidades microbianas após tratamento, com eventual destruição de microrganismos menos tolerantes e aumento de matéria orgânica disponível. Os microrganismos introduzidos pelos resíduos parecem desempenhar um papel importante na recuperação da respiração microbiana.

Research Doctorate - Doctor of Philosophy (PhD)
Soil organic carbon (SOC) plays a critical role in soil health and also in maintaining its ecological service. The stabilization of SOC involves physical, chemical, and biological processes in soil. Soil microorganisms serve as a carbon (C) biological sink as well as biochemical agents in C transformation in soil. The plant litter inputs and root exudates provide microorganisms with both labile and recalcitrant C sources. The C availability and soil habitat environment alter microbiota, consequently impacting the organic C decomposition processes in soil. Anthropogenic disturbances such as organic amendments, contaminants, tillage and grazing practices impact soil ‘biophysicochemical’ properties. The addition of organic C sources such as manure composts and biochar can lead to processes such as priming effect and microbial population shifts. In metal contaminated soils, organic-metal bonding can be beneficial to the immobilization of heavy metals, thereby reducing their bioavailability and biotoxicity. Microorganisms also develop strategies for the purpose to adapt to soil environment stress conditions. These stress tolerance processes include alteration of microbial community composition, and the redistribution of energy between catabolism (respired CO₂) and anabolism (biomass C). Although a number of studies have examined soil C biogeochemical dynamics, very few comprehensive studies have been reported on the role of soil microorganisms in relation to the mobilization and immobilization ((im)mobilization) processes of organic C dynamics. In this research, soil microbial function and community composition in relation to C dynamics as affected by environmental factors were investigated. The definition of ‘microbial carbon use efficiency’ (CUE) was introduced for the purpose of assessing the fraction of microbially decomposed organic C that is subsequently assimilated into microbial biomass. The specific objectives of this research include: (i) to determine microbial CUE involving different approaches in relation with various sources of C and nitrogen (N) inputs; (ii) to investigate the influence of land use practices on soil microbial functions in relation to CUE; (iii) to evaluate metal stress on microbial function in relation to CUE; and (iv) to examine the influence of biochar on metal toxicity in relation to microbial CUE. The first experiment was aimed to compare four approaches to measure microbial CUE using isotopic labelled glucose as an organic C source. The first approach (C_s) for microbial CUE measurement was based on monitoring C depletion, while the second (C_m) and third (C_p) approaches were based on detecting of microbial biomass accumulation, the forth approach (C_r) was aimed at calculating the ratio of the increased microbial biomass to the decreased C content. The microbial CUE values varied amongst the four approaches, and the C_m values were generally higher than other measurements. Because the main aims of the subsequent experiments were to understand the microbial mediation of soil C and the accumulation of C in microbial community, the microbial CUE measurement based on the accumulation of microbial biomass C (C_m) was used in the remaining chapters. In the first experiment, the ¹³C labelled glucose was evenly applied to soils to trace the C flow as measured by the release of CO₂, C incorporation into microbial biomass, and C remaining as undecomposed C input. Microbial phospholipid fatty acids (PLFAs) were extracted and analysed as biomarkers in order to identify the microbial community composition. Results revealed that organic amendment coupled with mineral N [(NH₄)₂SO₄] stimulated both microbial activity and biomass, leading to a positive priming effect (PE). However, as different C:N ratios were introduced in this experiment, the PE intensity stimulated by different exogenous C and mineral N sources showed variation amongst C sources, similar to microbial CUE values as determined by above approaches. The labile C source (glucose) with low N contributed to relatively higher microbial PE. Microbial community varied with C input sources, the readily available C source (glucose) favoured bacteria community growth over fungi, while fungi population increased with mineral N application. In conclusion, microbial CUE measurements are related to the methods and parameters used, and the C use preference and community composition are highly dependent on the exogenous C and mineral sources. Based on the microbial CUE measurement results of the first experiment, the second experiment used soils from three land use systems: cropping, pasture and natural forest soil. Three types of organic amendments were introduced: glucose as a labile C source, and wheat straw and macadamia nutshell biochar as a relatively recalcitrant C material. Microbial biomass C, and basal and substrate-induced respiration were measured to determine microbial CUE. Microbial community composition was determined based on the measurement of PLFAs. Land use history generally affects soil physiochemical and microbial properties. The natural forest soil had the highest organic C content while having relatively low soil nutrient contents. Because of constant disturbance and management, cropping soil had relatively lower values in microbial activity and biomass. Although there were no significant differences of microbial CUE values in soils from different land systems, the organic amendments lead to distinct microbial CUE values. Therefore, the exogenous C source applied to cropping land during cultivation played a more important role in terms of microbial C use preference. Glucose input significantly (p > 0.05) increased microbial respiration with less biomass formation, thereby resulting in a decrease in microbial CUE, while wheat straw and biochar inputs increased microbial CUE compared to glucose. However, microbial community composition differed among land use systems. Fungi was dominant in natural forest soil while bacteria population was larger in cropping and pasture soils. The type of organic amendment inputs also altered microbial community composition. The addition of an easily degradable C source such as glucose stimulated a growth in Gram-positive bacteria, while biochar input favoured fungi population growth. The biotoxicity of heavy metal(loid)s was evaluated by monitoring microbial CUE and community composition in soil samples spiked with Cd(II) and Pb(II), both individually and in combination. The bioavailable metal concentrations, soil properties, and microbial parameters including microbial respiration, biomass and microbial PLFAs were determined at two sampling periods during the 49 days incubation experiments. Microbial CUE was determined as the ratio of accumulated biomass to decomposed C amount. Metal contamination had no significant effect on (p > 0.05) on soil properties such as pH and EC, while significantly (p < 0.05) inhibiting microbial activity and biomass formation. Notably, the microbial CUE decreased due to metal contamination, and the higher heavy metal concentration lead to lower microbial CUE values. Both total PLFAs and PLFA diversity decreased under metal stress. The microbial community composition and PLFA patterns also differed among treatments. Heavy metal pollution had greater negative influences on fungi population compared to bacteria. This might result in a vulnerable soil ecosystem with less resilience ability. Based on the third experiment, biochar was introduced as an effective method for the remediation of metal contaminated soils. In this fourth experiment, Cd and Pb spiked soils treated with macadamia nutshell biochar (5% w/w) were monitored during a 49 days incubation period. Soil properties, metal bioavailability, microbial respiration, and microbial biomass C were measured after the incubation period. Microbial CUE was calculated from the ratio of C incorporated into microbial biomass to the C mineralised. Microbial community composition was determined by measuring microbial PLFAs. Results showed that total PLFA concentration decreased to a greater extent in metal contaminated soils than uncontaminated soils. Microbial CUE also decreased due to metal toxicity. However, biochar addition alleviated the metal toxicity, and increased total PLFA concentration. Both microbial respiration and biomass C increased due to biochar application, and CUE was significantly (p < 0.01) higher in biochar treated soils than untreated soils. Heavy metals reduced the microbial C sequestration in contaminated soils by negatively influencing the CUE. The improvement of CUE through biochar addition in the contaminated soils could be attributed to the decrease in metal bioavailability, thereby mitigating the biotoxicity to soil microorganisms. In conclusion, microbial properties are essential indicators in the determination of soil health. The microbial CUE values vary depending on the measurement adopted. As such, there is a need for a comprehensive conceptual understanding and unified method of determination of microbial CUE. For the purpose of this research, the microbial CUE measured based on the accumulation of microbial biomass was more appropriate to examine microbial function in terms of microbial C utilization. Land use histories, organic amendments and environmental factor all alter the direction and dimension of microbial CUE, as well altering the microbial community composition. Especially certain microbial species such as bacteria and fungi could reveal soil functional status because of the difference in C use and allocation preference among these communities. Biochar could be beneficial to microbiota under metal stress, not only because of its high C content, but also because of its remediation ability as metal sorbents.