No description available.

No description available.

Soil microorganisms are critical to many processes in the environment such as decomposition and nutrient cycling; yet little is known about how functional processes performed by soil microbial communities respond to and recover from perturbation. The influences of microbial community structure, rhizosphere interactions and environmental factors on soil microbial community function were examined in a temperate upland grassland soil. Two contrasting methods were used to manipulate microbial community structure in soil microcosms. In a constructive approach, soil was g-irradiated and reinoculated with a progressively diluted soil suspension, producing 4 levels of microbial inoculum. In a deconstructive approach, soil was chloroform-fumigated for 0, 1/2, 2 or 24 h. Both sets of soils were then incubated for 8 months until a similar microbial biomass size was attained. Samples of each soil were either heat-stressed (40°C for 24h) or amended with Cu (1000 mg kg -1). Functional capability was assessed over 28 days following stress by monitoring the short-term decomposition of native plant residues. The progressively fumigated and g-irradiated and reinoculated soils were either amended to 200 mg kg-1 N or unfertilized, and planted with an indigenous grass, Agrostis capillaris L. cv. Highland for eight months. Temporal and rhizosphere effects were shown to influence the resilience of soil microbial function to perturbation. A field study of the grassland site and microbial toxicity assessment of soil pore water extracts using a lux-marked biosensor, E. coli HB101 (pUCD607), demonstrated that land management practices influenced functional resilience to Cu perturbation through changes in Cu bioavailability. Resilience of the decomposition process in the upland grassland soil was shown to be significantly affected by the type of perturbation applied, prevailing structure of the soil microbial community, temporal variation and land management practices.

Little is known of the ecological structure of macro-invertebrate assemblages that live in the soil and leaf litter of British woodlands. This is the first study to investigate these assemblages at the whole community level, examining them at a range of resolutions from higher taxonomic unit (HTU) to species-level diversity and abundance across seven major groups including beetles, spiders and earthworms. Using the National Vegetation Classification (NVC) as a framework, 17 different wet and dry woodland types were sampled across England to examine the macro-invertebrate soil and litter communities, to compare and contrast the range of functional roles in each case, and to uncover the complex vegetational and environmental factors that influence invertebrate assemblage composition and structure. As the most widespread and invertebrate diverse woodland in the UK, an additional ten oak woodlands were sampled to explore the influence of geographic and climatic variables upon the patterns of soil/litter macro-invertebrates. The key findings suggest that soil moisture is most influential in determining the invertebrate species composition in all woodland types, indicating the wet woodlands are not only different to each other but to all other woodlands, and that the dry woodlands are more similar. Geographic location and soil type were found to have most influence on the diversity and abundance of both plant and invertebrate species in the dry woodlands. Air temperature is a key environmental influence on the oak woodlands as they can be grouped by geographic area, namely northern, western and central England localities. An oak woodland was further investigated for temporal patterns of soil invertebrates over a 12-month period. Findings indicate that most invertebrate species and functional groups peak in abundance at two key periods during the year: spring/early summer and later summer/autumn, this coincides with food availability for these groups at these times.

No description available.

No description available.

The rock-soil interface (critical zone) is where a variety of important earth system processes occur, such as the sequestration of CO2 and pedogenesis from rock weathering. This zone is an important sub-surface region of microbial activity in extreme environments because bedrock hydrolyses providing nutrients and cations (Le. Ca2 Mg2., Na) otherwise unavailable to flora and fauna. Yet, the diversity and role of microorganisms in weathering at the critical zone is not well understood. This thesis examines microbial communities in vegetated and unvegetated critical zones near Skorradalur Lake, Iceland. A suite of analyses were carried out to determine the environmental conditions, diversity, function and trophic survival strategy employed by bacteria at the sub-surface critical zone. Molecular analysis of the bacterial 16S rRNA gene indicates that the presence of plants at the soil surface influences the bacterial diversity and composition. Cultivation of microorganisms produced several bacterial isolates; most of which were capable of mineral phosphate solubilisation. However, isolate growth rates and copper tolerance show most isolates inhabit areas of sub-optimal growth potential. Environmental factors such as temperature and pH may influence bacterial divers ity, although the presence of organics may override these other influences. The trophic conditions at sites without higher plants may have a role in bacterial weathering as the availability of organics has resulted in a diverse heterotrophic community capable of utilizing bacterial necromass as a carbon source rather than plant derived carbon. This work has shown for the first time the bacterial diversity of the sub-surface critical zone in this region. Moreover, this bacterial diversity is influenced by plants and the potentially associated organics. Areas devoid of plants harboured a diverse heterotrophic bacterial community that employ weathering as a genera list function. Experiments show that bacteria increase the rate of phosphate weathering, although it may be a generalist function rather than specific to any individual taxon.

Whilst much is known about the physics and erosion of soil surfaces on a millimetre scale, little is known about the associated microbiology, particularly in temperate arable systems. The vast majority of research regarding microbial interactions at soil surfaces has concerned microbiotic crusts. However, such surface crusts take many years to form and then only in relatively undisturbed soil systems. Arable soil surfaces are subject to relatively extreme environmental conditions, potentially undergoing rapid changes in relation to temperature, water status and solar radiation compared to deeper soil zones. These extreme environmental parameters are likely to have a large impact on the biota found at the arable soil surface when compared to that which occurs in deeper soil zones. Phenotypic profiling using phospholipid fatty acid (PLFA) analysis, microbial biomass, and chlorophyll concentration were used to characterise soil microbial communities with the aim of quantifying differences within the surface layers of arable systems on a millimetre scale. This field work was supported with a series of microcosm-scale studies in which parameters such as length of time between disturbance events and the quality of light reaching the soil surface were controlled. Using microcosms subjected to simulated rainfall and imaged using X-ray computed tomography scanning, the effects of the soil surface microbiota on associated physical properties including structural integrity, porosity, erodibility and hydrological properties were investigated. This research showed that given sufficient time between disturbance events, environmental parameters such as temperature and wet:dry cycling were sufficient to drive the formation of a distinct soil surface phenotype, which appeared to be consistently confined to an order of depth of circa 1 mm. It was notable that the PLFA 16:0 was consistently associated with discrimination between phenotypes between soil surface layers. Calculation of the ratio of fungal to bacterial PLFA biomarkers showed a consistently higher ratio of fungi to bacteria present in the soil surface layer to a depth of circa 1 mm, providing evidence that fungi grow preferentially over the soil surface compared to through the soil matrix. Further investigation demonstrated that light, particularly at photosynthetically active wavelengths, was the main driving factor in the establishment of the distinct soil surface phenotypes. The inocula which drove the formation of such soil-surface community phenotypes, especially the photoautotrophic components, was demonstrated to derive predominantly from aerial sources. Functionally the nature of the soil surface community was found to affect run-off generation and shear strength at the surface. There was no significant impact of the soil surface microbiota on erodibility or water infiltration rates, although whilst distinct surface phenotypes had developed in this experimental circumstance, these were relatively deficient in photoautotrophs compared to other microcosm experiments and field circumstances, and hence extrapolation of this conclusion is not sound. This project has demonstrated that a soil surface ecological niche may exist in other unexplored soil surfaces and highlights the needs to explore this possibility and to examine any associated functional consequence should such niches be found to exist.

No description available.

Viruses have been shown to be responsible for considerable bacterial mortality and nutrient cycling in aquatic systems. As yet no detailed studies have been published on the role of viruses in natural soil bacterial communities despite common knowledge that viruses exist in the soil. This thesis sought to address some key questions on the ecology of soil bacterial viruses and their hosts. Disturbance through soil desiccation, nutrient inputs, rhizosphere effects and protozoan predation pressure were investigated. The first study of lysogeny in natural soil systems was also undertaken. The work presented here utilised tools and techniques commonplace in aquatic systems research and applied them to soil. A novel protocol was developed based on physical extraction of bacteria and viruses from soil and direct counting with epifluorescence microscopy. Physical extraction was achieved using shaking, ultrasound sonication and low speed centrifugation. The fluorochrome SYBR Gold was used to stain nucleic acid of extracted bacteria and viruses, and image analysis software used to determine bacterial cell volumes. Bacterial and viral abundances were in the region of 107-109 per gram of soil over a range of soil types. Significant fluctuations in viral and bacterial abundances were recorded at timescales of less than 24 h. Glucose and nitrogen addition led to substantial increases in bacterial and viral abundance. Loss of soil moisture resulted in peaks of viral abundance in sandy soils but not in a clay soil. A six-week microcosm study demonstrated that phage were not a significant regulator of bacterial abundance. Low levels of lysogeny were recorded over a range of soils when measured explicitly with Mitomycin C. The implication from that study was that viruses in soil behave differently to those in aquatic systems. Bacterial and viral abundances were highly coupled in most instances, irrespective of the potential activity of bacteria. Further fundamental studies are recommended.