A critical review of some of the more important aspects of the neo-realistic philosophy, as expounded in Professor Holt's book "The concept of consciousness.".

Thesis (Ph.D.)--Boston University N.B.: Page 12 is missing from original thesis

Community ecology of denitrifying bacteria in arable land

Denitrifying bacteria comprise a functional guild that under anaerobic conditions is able to use nitrogenous compound for respiration. Agricultural soils are often fertilized with nitrogen, and the reduction of nitrate and nitrite to nitric oxide, nitrous oxide and dinitrogen via the denitrification pathway, leads to gaseous emissions from the nitrogenous compounds, a subject of great environmental and economic concern. This thesis examined denitrifiers, nitrate reducers, ammonia oxidizers and total bacteria, in terms of community structure, abundance and function in different arable soils. Denitrifying bacteria were described using the signature genes that encode the analytic subunits of denitrification enzymes. Appropriate targets and methods for this were evaluated. An assessment was carried out of how these biological factors are affected by different fertilizer and management practices. The spatial distribution of the denitrifying bacteria, and how this was correlated to soil properties, was also explored. Long-term application of different organic and mineral fertilizers altered both the community structure and function of the different bacterial groups. However, fertilization practices producing the most different community structure were not correlated to the treatments with the most different activities. Thus activities were not coupled to community composition. However, a study with different carbon additions, with and without nitrogen additions, showed that nitrogen addition increased the microbial activity and biomass, and in this case community composition was correlated with potential activity. In long-term fertilization, pH, C:N ratio and organic carbon content were important drivers shaping the community composition of the denitrifiers and total bacteria. Determination of the structure and size of denitrifying bacteria at field scale revealed significant relationships between denitrifying community composition, size and activity, and soil factors. These results are important in identifying the resource-based niches for denitrifiers at scales relevant for developing sustainable land management and agricultural practices

Antiviral Activities and Putative Identification of Compounds in Microbial Extracts from the Hawaiian Coastal Waters

Marine environments are a rich source of significant bioactive compounds. The Hawaiian archipelago, located in the middle of the Pacific Ocean, hosts diverse microorganisms, including many endemic species. Thirty-eight microbial extracts from Hawaiian coastal waters were evaluated for their antiviral activity against four mammalian viruses including herpes simplex virus type one (HSV-1), vesicular stomatitis virus (VSV), vaccinia virus and poliovirus type one (poliovirus-1) using in vitro cell culture assay. Nine of the 38 microbial crude extracts showed antiviral potencies and three of these nine microbial extracts exhibited significant activity against the enveloped viruses. A secosteroid, 5α(H),17α(H),(20R)-beta-acetoxyergost-8(14)-ene was putatively identified and confirmed to be the active compound in these marine microbial extracts. These results warrant future in-depth tests on the isolation of these active elements in order to explore and validate their antiviral potential as important therapeutic remedies

Effect of Biocontrol Agent Pseudomonas fluorescens 2P24 on Soil Fungal Community in Cucumber Rhizosphere Using T-RFLP and DGGE

Fungi and fungal community play important roles in the soil ecosystem, and the diversity of fungal community could act as natural antagonists of various plant pathogens. Biological control is a promising method to protect plants as chemical pesticides may cause environment pollution. Pseudomonas fluorescens 2P24 had strong inhibitory on Rastonia solanacearum, Fusarium oxysporum and Rhizoctonia solani, etc., and was isolated from the wheat rhizosphere take-all decline soils in Shandong province, China. However, its potential effect on soil fungal community was still unknown. In this study, the gfp-labeled P. fluorescens 2P24 was inoculated into cucumber rhizosphere, and the survival of 2P24 was monitored weekly. The amount decreased from 108 to 105 CFU/g dry soils. The effect of 2P24 on soil fungal community in cucumber rhizosphere was investigated using T-RFLP and DGGE. In T-RFLP analysis, principle component analysis showed that the soil fungal community was greatly influenced at first, digested with restriction enzyme Hinf I and Taq I. However, there was little difference as digested by different enzymes. DGGE results demonstrated that the soil fungal community was greatly shocked at the beginning, but it recovered slowly with the decline of P. fluorescens 2P24. Four weeks later, there was little difference between the treatment and control. Generally speaking, the effect of P. fluorescens 2P24 on soil fungal community in cucumber rhizosphere was just transient

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites