The Effects Of Anthropogenic Stress On Nitrogen Cycling Microbial Communities In Temperate And Tropical Soils

In this dissertation several research studies are discussed that characterize the effects of anthropogenic, or human-induced, stress on both ammonia-oxidizing and total bacterial soil microbial communities. The disturbances of land-use change in tropical, South American rainforests and artificial warming and nitrogen (N) fertilization in temperate, North American forests were investigated as these disturbances represent past and current disturbances caused by human landscape alteration and climate change. Initially, the response of soil ammonia-oxidizing microbial communities to land-use change from primary rainforest to pasture and, finally, back to secondary forest was determined. Next, these analyses of land-use change effects were expanded to the total bacterial community in these rainforest soils sampled annually for three years. Lastly, the effects of increasing soil temperature and N-deposition on ammonia-oxidizing microbial communities in temperate forests were characterized. Land-use change affected ammonia-oxidizing communities in tropical soils. Both the abundance of ammonia-oxidizer marker genes and their community structure shifted due to land-use changes. Interestingly, phylogenetic analyses showed that community structural changes in ammonia-oxidizing thaumarchaea are driven by a shift away from primary rainforest, old pasture, and secondary forest clusters to separate clusters for young pasture. Additionally, there was a nearly complete disappearance in young pasture, old pasture, and secondary forest sites of a thaumarchaeal ammonia-oxidizing genus, the Nitrosotalea. We found that many of the bacterial community responses to land-use change stayed consistent between land-use types across all three years, especially in regards to OTU richness and Faith's phylogenetic diversity. Bacterial community turnover, or distance-decay, was significantly greater (P 0.05) in forests compared to pastures for two out of three years sampled. Lastly, two bacterial species, Rhodomicrobium udaipurense and Anaeromyxobacter dehalogens, were found to be exclusive indicator species for the pasture land-use type across all sampling time points. Finally, when investigating the effects of increasing soil temperatures and N-deposition rates on temperate forest soil N-cycling, potential N-mineralization and nitrification rates and chitinase enzyme activity showed no difference between treatments (P 0.05). Bacterial, fungal, and archaeal rRNA genes and thaumarchaeal amoA genes showed no significant difference between treatments. There were significant differences in ammonia-oxidizer community structure between control and heated plus nitrogen treatments. The majority of archaeal ammonia-oxidizer species were most closely related to Nitrosotalea and Nitrososphaera spp. However, the organic horizon in the heated plus nitrogen treatment was dominated by sequences most closely related to Nitrosopumilus maritimus. Taken together, these results can provide a conceptual foundation as to how anthropogenic stressors can alter microbial communities in tropical and temperate forests soils. These communities are critical to global biogeochemical cycling and climate regulation. By charactering how these communities respond to various anthropogenic stressors, the scientific community can begin to use this information to develop more holistic biogeochemical models to predict shifts in nutrient flow and greenhouse gas production.

Several textbooks and edited volumes are currently available on general soil fertility but‚ to date‚ none have been dedicated to the study of “Sustainable Carbon and Nitrogen Cycling in Soil.” Yet this aspect is extremely important, considering the fact that the soil, as the ‘epidermis of the Earth’ (geodermis)‚ is a major component of the terrestrial biosphere. This book addresses virtually every aspect of C and N cycling, including: general concepts on the diversity of microorganisms and management practices for soil, the function of soil’s structure-function-ecosystem, the evolving role of C and N, cutting-edge methods used in soil microbial ecological studies, rhizosphere microflora, the role of organic matter (OM) in agricultural productivity, C and N transformation in soil, biological nitrogen fixation (BNF) and its genetics, plant-growth-promoting rhizobacteria (PGPRs), PGPRs and their role in sustainable agriculture, organic agriculture, etc. The book’s main objectives are: (1) to explain in detail the role of C and N cycling in sustaining agricultural productivity and its importance to sustainable soil management; (2) to show readers how to restore soil health with C and N; and (3) to help them understand the matching of C and N cycling rules from a climatic perspective. Given its scope, the book offers a valuable resource for educators, researchers, and policymakers, as well as undergraduate and graduate students of soil science, soil microbiology, agronomy, ecology, and the environmental sciences. Gathering cutting-edge contributions from internationally respected researchers, it offers authoritative content on a broad range of topics, which is supplemented by a wealth of data, tables, figures, and photographs. Moreover, it provides a roadmap for sustainable approaches to food and nutritional security, and to soil sustainability in agricultural systems, based on C and N cycling in soil systems.

Advances in our understanding of the nitrogen cycle and the impact of anthropogenic activities on regional to global scales depend on the expansion of scientific studies to these fast-developing regions. This book presents a series of studies from across the Americas whose aim is to highlight key natural processes that control nitrogen cycling as well as discuss the main anthropogenic influences on the nitrogen cycle in both the tropical and temperate regions of the Americas.

Anthropogenic activity has clearly altered the N cycle contributing (among other factors) to climate change. This book aims to provide new biotechnological approach representing innovative strategies to solve specific problems related to the imbalance originating in the N cycle. Aspects such as new conceptions in agriculture, wastewater treatment, and greenhouse gas emissions are discussed in this book with a multidisciplinary vision. A team of international authors with wide experience have contributed up-to-date reviews, highlighting scientific principles and their environmental importance and integrating different biotechnological processes in environmental technology.

The cycling of nutrients, such as nitrogen (N), is arguably one of the most critical ecosystem services provided by soil. Nitrogen is the limiting nutrient for plant growth in many terrestrial ecosystems and can consequently regulate net primary production, plant diversity, and community composition. Transformations of available N, which are catalyzed by soil microorganisms, can also affect air and water quality, with possible implications for climate change and human health. In an era of global environmental change, it is paramount to gain a mechanistic understanding of how soil N is affected by anthropogenically derived perturbations such as exotic plant invasion and elevated nutrient deposition. Using a multifactor global change experiment, I assessed how three principal global change factors - exotic plant invasion, N deposition (simulated by N fertilization), and aboveground vegetation removal (to simulate cattle grazing or mowing) - affected soil N cycling, namely NH4 and NO3− availability and potential rates of nitrification and denitrification, in a California grassland. In order to increase understanding of how soil microbial communities regulate changes in N cycling, I concurrently measured broad-scale community structure of bacteria and archaea and the abundances of ammonia-oxidizing bacteria and archaea. I found that two invasive plants, Aegilops triuncialis and Elymus caput-medusae reduced soil N availability and nitrification and denitrification potentials compared to perennial-dominated native communities but not naturalized exotic communities. Aboveground vegetation removal, which is often used as a tool to manage invasive plant populations (through cattle grazing or mowing), tended to exacerbate the effects of invasion by further reducing nitrification potential and soil NO3− availability. Fertilization with NH4 NO3 consistently increased nitrification potential and soil NO3− availability, yet NH4 remained unaffected and denitrification potential was reduced. When combined, defoliation and N fertilization always produced additive effects. Finally, despite the sometimes dramatic shifts in N availability and potential rates that were observed, microbial community composition remained unaffected by changes in plant composition, N fertilization and defoliation. Overall, these findings provide evidence that N cycling is uniquely affected by each individual global change factor, and that the interactive effects of N fertilization and defoliation can be predicted based on combining single factor studies. These results also suggest that microbial communities composition is insensitive to global change in this system, and that microbial activity - as measured by rates of N cycling - is decoupled from community composition.

Nitrogen constitutes 78% of the Earth’s atmosphere and inevitably occupies a predominant role in marine and terrestrial nutrient biogeochemistry and the global climate. Callous human activities, like the excessive industrial nitrogen fixation and the incessant burning of fossil fuels, have caused a massive acceleration of the nitrogen cycle, which has, in turn, led to an increasing trend in eutrophication, smog formation, acid rain, and emission of nitrous oxide, which is a potent greenhouse gas, 300 times more powerful in warming the Earth’s atmosphere than carbon dioxide. This book comprehensively reviews the biotransformation of nitrogen, its ecological significance and the consequences of human interference. It will appeal to environmentalists, ecologists, marine biologists, and microbiologists worldwide, and will serve as a valuable guide to graduates, post-graduates, research scholars, scientists, and professors.

Human influence on the global nitrogen cycle (e.g., through fertilizer and wastewater runoff) has caused a suite of environmental problems including acidification, loss of biodiversity, increased concentrations of greenhouse gases, and eutrophication. These environmental risks can be lessened by microbial transformations of nitrogen; nitrification converts ammonia to nitrite and nitrate, which can then be lost to the atmosphere as N2 gas via denitrification or anammox. Microbial processes thus determine the fate of excess nitrogen and yet recent discoveries suggest that our understanding of these organisms is deficient. This dissertation focuses on microbial transformations of nitrogen in marine and estuarine systems through laboratory and field studies, using techniques from genomics, microbial ecology, and microbiology. Recent studies revealed that many archaea can oxidize ammonia (AOA; ammonia-oxidizing archaea), in addition to the well-described ammonia-oxidizing bacteria (AOB). Considering that these archaea are among the most abundant organisms on Earth, these findings have necessitated a reevaluation of nitrification to determine the relative contribution of AOA and AOB to overall rates and to determine if previous models of global nitrogen cycling require adjustment to include the AOA. I examined the distribution, diversity, and abundance of AOA and AOB in the San Francisco Bay estuary and found that the region of the estuary with low-salinity and high C:N ratios contained a group of AOA that were both abundant and phylogenetically distinct. In most of the estuary where salinity was high and C:N ratios were low, AOB were more abundant than AOA—despite the fact that AOA outnumber AOB in soils and the ocean, the two end members of an estuary. This study suggested that a combination of environmental factors including carbon, nitrogen, and salinity determine the niche distribution of the two groups of ammonia-oxidizers. In order to gain insight into the genetic basis for ammonia oxidation by estuarine AOA, we sequenced the genome of a new genus of AOA from San Francisco Bay using single cell genomics. The genome data revealed that the AOA have genes for both autotrophic and heterotrophic carbon metabolism, unlike the autotrophic AOB. These AOA may be chemotactic and motile based on numerous chemotaxis and motility-associated genes in the genome and electron microscopy evidence of flagella. Physiological studies showed that the AOA grow aerobically but they also oxidize ammonia at low oxygen concentrations and may produce the potent greenhouse gas N2O. Continued cultivation and genomic sequencing of AOA will allow for in-depth studies on the physiological and metabolic potential of this novel group of organisms that will ultimately advance our understanding of the global carbon and nitrogen cycles. Denitrifying bacteria are widespread in coastal and estuarine environments and account for a significant reduction of external nitrogen inputs, thereby diminishing the amount of bioavailable nitrogen and curtailing the harmful effects of nitrogen pollution. I determined the abundance, community structure, biogeochemical activity, and ecology of denitrifiers over space and time in the San Francisco Bay estuary. Salinity, carbon, nitrogen and some metals were important factors for denitrification rates, abundance, and community structure. Overall, this study provided valuable new insights into the microbial ecology of estuarine denitrifying communities and suggested that denitrifiers likely play an important role in nitrogen removal in San Francisco Bay, particularly at high salinity sites.

I studied the potential effects of a change in the amount, frequency and timing of precipitation on soil microbes and nitrogen cycling in the New Jersey Pinelands. I performed a two year field manipulation of precipitation amount and measured the response of the microbial community, potential net nitrogen mineralization and amino acid production. I found that soil microbes were not affected by rain exclusion or a doubling of rainfall. Nematode densities, but not community composition, were sensitive to precipitation amount. A large accumulation of ammonium in drought plots suggested sustained microbial activity under extreme drought conditions. I observed small changes in potential net nitrogen mineralization due to the effects of soil moisture on diffusion and immobilization. I measured the short-term response of the microbial community to a rewetting of dry soil and found a very rapid (three hour) change in the microbial community. The accumulation of ammonium within drought plots appears to have suppressed fungal biomass following the rewetting event. In a two year winter study, I found no long-term effect of supplemental winter rainfall on the soil microbial community. Elevated winter precipitation prevented ammonium accumulation, presumably by protecting plant roots from freeze damage. I found that supplemental watering insulates soil microbes from cold stress over the short-term (days), but that mid-winter declines in biomass due to cold soil. These experiments demonstrate that soil microbial communities in Pinelands soils are highly tolerant of abiotic stressors such as drought, upshock stress and soil freezing. Recovery from these disturbances is extremely rapid, occurring on the scale of hours to days. I conclude that changing precipitation patterns will not have a direct, long-term effect on soil microbial communities. Changes in precipitation patterns are more likely to alter nitrogen cycling rates via the influence on nitrogen diffusion and plant and microbial uptake. Furthermore, precipitation-induced changes in nematode densities may have important implications for nitrogen cycling in the New Jersey Pinelands.

The large and rapidly expanding body ofliterature related to nitrogen cycling in both managed and native terrestrial ecosystems reflects the importance accorded to the behaviour of this vital and often limiting nutrient. Research at the organism, ecosystem and landscape levels commonly addresses questions concerning nitrogen acquisition, internal cycling and retention. Goals for this research include increased agricultural productivity and a better understanding of human impact on local, regional and global nitrogen cycles. Nitrogen cycle research in tropical regions has a long and distinguished history. Research on different aspects of nitrogen cycling in ecosystems of the tropics has been carried out in many regions. In relatively few instances has there, however, been a focus on the biogeochemical cycles at the ecosystem level. The meeting resulting in this volume was an attempt to bring together existing information on nitrogen cycling in ecosystems of Latin America and the Caribbean and discuss this in an ecosystem context.