In oligotrophic systems, where primary production is low and nitrogen is in short supply, nitrogen fixation process is intense. Although a few diazotrophs (eg. Trichodesmium) have been widely-studied, the rest of the diazotrophic community is still poorly understood. Furthermore, the global distribution of diazotrophs are yet to be clearly resolved. This dissertation assessed the distribution of diazotrophs in oligotrophic systems, particularly in the tropical and subtropical oceans, using genomics tools including next-generation sequencing. We first tested out a pair of nifH-specific primer that previously performed well in silico, but found that its application on seawater samples was biased towards paralogous, non-functional nitrogenase nifH genes. Instead, we found that the use of a nested PCR method using different primers sets to be more effective in amplifying functional nifH genes. Trichodesmium sp., UCYN-A and Pseudomonas sp. forms the core of the diazotrophic communities in oligotrophic oceans. Temperature is the primary driver of the abundances and distributions of these organisms in the Pacific, Atlantic and Indian Oceans, as well as in the oligotrophic Red Sea. Trichodesmium tends to dominate warm, surface waters, while UCYN-A prefers cooler environments and dwell in sub-surface waters in the Red Sea. Due to the dominance of Pseudomonas in the large-sized fraction samples, they are believed to be part of the Trichodesmium-associated consortia, although this requires further investigations. We also found non-cyanobacterial species of diazotrophs to be dominant previously-described hotspots of nitrogen fixation, and found evidence for the widespread of alternative nitrogenases (Cluster II). Using the Red Sea as an exemplar for future warming ocean, we found patterns of niche partitioning in the Red Sea diazotrophs, based on their distribution along seasons, latitude and depth. Our one-year observation of Red Sea Trichodesmium population witnessed the collapse of the population at temperatures above 32°C. This dissertation not only improve our understanding of the effects of future rising temperature on the natural populations of diazotrophs, but it also helps to establish a baseline understanding of the structure, spatial and temporal dynamics of Red Sea diazotrophs, which has not been discussed elsewhere.

Seagrasses are key coastal ecosystems, providing many ecosystem services. Seagrasses increase biodiversity as they provide habitat for a large set of organisms. In addition, their structure provides hiding places to avoid predation. Seagrasses can grow in shallow marine coastal areas, but several factors regulate their growth and distribution. Seagrasses can uptake different kinds of organic and inorganic nutrients through their leaves and roots. Nitrogen and phosphorous are the most important nutrients for seagrass growth. Biological nitrogen fixation is the conversion of atmospheric nitrogen into ammonia by diazotrophic bacteria. This process provides a significant source of nitrogen for seagrass growth. The nitrogen fixation is controlled by the nif genes which are found in diazotrophs. The main goal of the project is to measure nitrogen fixation rates on seagrass sediments, in order to compare among various seagrass species from the Red Sea. Moreover, we will compare the fixing rates of the Vegetated areas with the bare sediments. This project will help to ascertain the role of nitrogen fixing bacteria in the development of seagrass meadows.

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A native desert Rhizobium, AZ-M1, was isolated from a nodulated mesquite tree (Prosopis juliflora var. velutina) following inoculation of mesquite seed with a desert soil. This strain and a selected commercial strain (31A5) were used in a greenhouse study to determine their N fixation efficiency against applied N fertilizer. Strain AZ-M1 was a more efficient N fixer than 31A5. The survival rate of the two strains was tested in three different desert soils in a controlled laboratory study. The native strain AZ-M1 grew and survived in the soils over a period of one month. The commercial strain did not grow and the population decreased from 10⁸ cells gm⁻¹ of dry soil to below 10⁴ cells after 14 days. Soil factors affected survival of both strains. The competitiveness of the two strains was compared in a greenhouse experiment. The native isolate out competed strain 31A5 in nodule occupancy regardless of cell number when applied as a mixed inoculant. A high incidence of double occupancy was found in the root nodules when double strain inoculants were applied. The two rhizobia were fast growing rhizobia, lowering the pH of a defined medium. Strain AZ-M1 showed a high intrinsic resistance to 3 antibiotics among 12 tested. Strain AZ-M1 has been shown to be highly effective, fairly competitive and survive better in desert soils than strain 31A5.

One low salt tolerant alfalfa (Medicago sativa L.) cultivar and two germination salt tolerant alfalfa selections were compared for growth and N fixation at four salinity levels (0, -0.3, -0.6 and -1.2 Mpa). In the first experiment a Hoagland's solution at 5 ppm-N was used; in the second experiment the solution had a 1 ppm-N concentration and supplemental light was used. No significant differences were found among the cultivars. This provides additional support that germination salt tolerance is not necessarily related to salt tolerance for growth. Nitrogen fixed to the first harvest was 61, 48, 49, and 27% of the total shoot N for plants in the control, -0.3, -0.6, and -1.2 Mpa solutions, respectively. At the second harvest, N fixation percentages were 94, 89, 80, and 57% for the corresponding salinity levels which showed significant reduction in N fixation at -0.3 Mpa. The evaluation of N fixation was by 15N techniques.

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