Metagenomics Of Microbial Communities Involved In Nitrogen Cycling
DOWNLOAD
Download Metagenomics Of Microbial Communities Involved In Nitrogen Cycling PDF/ePub or read online books in Mobi eBooks. Click Download or Read Online button to get Metagenomics Of Microbial Communities Involved In Nitrogen Cycling book now. This website allows unlimited access to, at the time of writing, more than 1.5 million titles, including hundreds of thousands of titles in various foreign languages. If the content not found or just blank you must refresh this page
Metagenomics Of Microbial Communities Involved In Nitrogen Cycling
DOWNLOAD
Author :
language : en
Publisher:
Release Date : 2016
Metagenomics Of Microbial Communities Involved In Nitrogen Cycling written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Metagenomics Of The Microbial Nitrogen Cycle
DOWNLOAD
Author : Diana Marco
language : en
Publisher: Caister Academic Press Limited
Release Date : 2014
Metagenomics Of The Microbial Nitrogen Cycle written by Diana Marco and has been published by Caister Academic Press Limited this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with Science categories.
The nitrogen (N) cycle is one of the most important nutrient cycles on the planet, and many of its steps are performed by microbial organisms. During the cycling process, greenhouse gases are formed, including nitrous oxide and methane. In addition, the use of nitrogen fertilizers increases freshwater nitrate levels, causing pollution and human health problems. A greater knowledge of the microbial communities involved in nitrogen transformations is necessary to understand and counteract nitrogen pollution. This book - written by renowned researchers who are specialized in the most relevant and emerging topics in the field - provides comprehensive information on the new theoretical, methodological, and applied aspects of metagenomics and other 'omics' approaches used to study the microbial N cycle. The book provides a thorough account of the contributions of metagenomics to microbial N cycle background theory. It also reviews state-of-the-art investigative methods and explores new applications in water treatment, agricultural practices, climate change, among others. The book is recommended for microbiologists, environmental scientists, and anyone interested in microbial communities, metagenomics, metatranscriptomics, and metaproteomics of the microbial N cycle.
Microbial Nitrogen Cycling Dynamics In Coastal Systems
DOWNLOAD
Author : Annika Carlene Mosier
language : en
Publisher: Stanford University
Release Date : 2011
Microbial Nitrogen Cycling Dynamics In Coastal Systems written by Annika Carlene Mosier and has been published by Stanford University this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
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.
Soil Nitrogen Ecology
DOWNLOAD
Author : Cristina Cruz
language : en
Publisher: Springer Nature
Release Date : 2021-05-24
Soil Nitrogen Ecology written by Cristina Cruz and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-05-24 with Science categories.
This book highlights the latest discoveries about the nitrogen cycle in the soil. It introduces the concept of nitrogen fixation and covers important aspects of nitrogen in soil and ecology such as its distribution and occurrence, soil microflora and fauna and their role in N-fixation. The importance of plant growth-promoting microbes for a sustainable agriculture, e.g. arbuscular mycorrhizae in N-fixation, is discussed as well as perspectives of metagenomics, microbe-plant signal transduction in N-ecology and related aspects. This book enables the reader to bridge the main gaps in knowledge and carefully presents perspectives on the ecology of biotransformations of nitrogen in soil.
Research On Nitrification And Related Processes Part B
DOWNLOAD
Author :
language : en
Publisher: Academic Press
Release Date : 2011-06-15
Research On Nitrification And Related Processes Part B written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-06-15 with Science categories.
The global nitrogen cycle is the one most impacted by mankind. The past decade has changed our view on many aspects of the microbial biogeochemical cycles, including the global nitrogen cycle, which is mainly due to tremendous advances in methods, techniques and approaches. Many novel processes and the molecular inventory and organisms that facilitate them have been discovered only within the last 5 to 10 years, and the process is in progress. Research on Nitrification and Related Processes, Part B provides state-of-the-art updates on methods and protocols dealing with the detection, isolation and characterization of macromolecules and their hosting organisms that facilitate nitrification and related processes in the nitrogen cycle as well as the challenges of doing so in very diverse environments. Provides state-of-the-art update on methods and protocols Deals with the detection, isolation and characterization of macromolecules and their hosting organisms Deals with the challenges of very diverse environments
Omics Enabled Evaluation Of Microbial Communities In Acidic Environmental Systems
DOWNLOAD
Author : Diana Ayala
language : en
Publisher:
Release Date : 2021
Omics Enabled Evaluation Of Microbial Communities In Acidic Environmental Systems written by Diana Ayala and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.
Mining activity accelerates the generation of an extremely toxic fluid known as acid mine drainage (AMD). AMD has low pH and high sulfate, iron, and other metal(loid)s content. Environments impacted by AMD are uninhabitable for most biota. However, acid-tolerant and acidophilic microorganisms thrive under AMD harsh conditions relying on sulfur and iron compounds as main electron donors and acceptors. They are resistant to metal toxicity and can even promote metal precipitation. Many of these microorganisms are now applied in greener technologies for mining and AMD remediation purposes. In the first part of this dissertation, I studied microbial communities responsible for ferrous iron oxidation in lab-scale low-pH reactors. Such reactors constitute a cost-effective alternative for the removal of iron, Fe(II), from AMD. Like many microbial reactors, their overall function can be affected by environmental perturbations such as changes in pH. However, reactors, previously operated by Dr. William Burgos's group at different pH values and Fe(II) concentrations, were shown to be stable with respect to the general rate of microbial Fe(II) oxidation. In chapter 2, I focused on studying biofilms collected at three different times from the reactors when operated under the same chemical conditions (e.g., pH = 2.7 and influent [Fe(II)] = 300 mg.L-1). The microbial communities had differential growth of multiple autotrophic Fe(II) oxidizers affiliated with Acidithiobacillus, Ferrovum, and Leptospirillum genera. Metagenomic analyses of these communities revealed differences in the metabolic potential of the dominant taxa for key metabolic functions such as Fe(II) oxidation, carbon fixation, oxygen reduction, nitrogen acquisition, and biofilm formation. The distinct metabolic potential of the autotrophic Fe(II) oxidizers allowed their access to different resources over time and coexistence in the biofilm. The distribution of key metabolic functions across the multiple coexisting taxa supported functional redundancy and imparted stability to the reactors with respect to Fe(II) oxidation at low pH. In the second part of this dissertation, I focused on microbial communities living in the acidic pit lake Cueva de la Mora (CM) located in the Iberian Pyrite Belt in Spain. CM is a stratified lake with dramatic physico-chemical gradients and increasing metal concentrations with depth. It is one of the most extensively characterized acidic pit lakes in the world. However, knowledge gaps existed with respect to active microbial activity shaping the unique geochemistry of CM and potentially contributing to the lake's natural attenuation. By using a combination of metagenomics and metatranscriptomics, I studied the in situ microbiology of this acidic pit lake from three perspectives: metal resistance (Chapter 3), element cycling (Chapter 4), and contributions to biosulfidogenesis (Chapter 5). CM has three distinct microbial communities characterizing the upper layer, chemocline, and deep layer of the lake. Chapter 3 described the microbial composition of each layer by shotgun metagenomics only. Chapter 4 included results from amplicon sequencing. The upper layer was dominated by the green algae Coccomyxa onubensis from the phylum Chlorophyta. Surprisingly, despite having very limited available light, C. onubensis was also present in the chemocline along with bacteria mainly from the phylum Proteobacteria. Desulfomonile spp. were the most abundant bacteria in the chemocline followed by taxa affiliated with the order Ca. Acidulodesulfobacterales (non-described previously). Until now, the deep layer was largely uncharacterized. Currently, the metagenomic analysis revealed abundance of the archaea Euryarchaeota along with bacteria from the superphylum Patescibacteria. Other abundant bacteria were part of the phyla Actinobacteria, Chloroflexi, and Nitrospirae. Findings with respect to microbial metal resistance in CM were described in Chapter 3. A database of 222 metal resistant genes (MRGs) was constructed and used to compare MRGs across the three communities representing each layer of the lake. Genes (from metagenomes) and transcripts (from metatranscriptomes) annotated as MRGs were quantified per layer and classified by mechanisms of resistance and metal(loid). Eukaryotes, bacteria, and archaea expressed different metal resistance strategies. Expression of genes involved in resistance to the most toxic metals was not correlated to dissolved metal concentrations, especially for As and Cu. Finally, MRG expression patterns were studied among in silico populations (represented by metagenome assembled genomes - MAGs) from the same depth, and differences in metal resistance mechanisms among members of the same community were found. Chapter 4 focused on the active roles of predominant phyla in carbon, sulfur, iron, and nitrogen cycling in CM. The green algae Coccomyxa onubensis were active in the upper layer and chemocline and provided organic carbon to the less abundant heterotrophic bacteria in the upper layer and chemocline. Organic carbon associated with settling ferric iron minerals dissolved in the deep layer might fuel the heterotrophic activity of the most abundant taxa in the deep layer: Thermoplasmatales (Euryarchaeota). Autotrophic activity was observed in the chemocline and deep layer mainly associated with bacteria from the phylum Proteobacteria, Actinobacteria, Chloroflexi, and/or Nitrospirae. As expected, microbial sulfide/sulfur oxidation was active in the chemocline associated with Desulfomonile and Ca. Acidulodesulfobacterium populations which were also involved in sulfate reduction. Sulfide/sulfur oxidation was surprisingly active in the deep layer associated with the most abundant taxa (Euryarchaeota) and other less abundant bacteria such as Actinobacteria populations. The abundance of transcripts involved in oxygen respiration in the deep layer was also unexpected and related to potential sulfur-oxidizing populations. Activity for microbial sulfate reduction in the deep layer was associated with uncultured taxa from Actinobacteria, Chloroflexi, Nitrospirae, Firmicutes, and Proteobacteria. Fe(II) oxidation was mainly observed in the chemocline contributed by Ferrovum, Leptospirillum, and Ca. Acidulodesulfobacterium taxa. Although expected in the chemocline, no genomic information was gathered to support activity for Fe(III) reduction. The deep layer had Fe(III) reduction activity associated with low abundant Geobacter bacteria. Nitrogen fixation, nitrate reduction, and ammonia oxidation were active in the chemocline with Ca. Acidulodesulfobacterium populations as main contributors. In contrast the upper layer presented active assimilatory nitrogen metabolisms associated with Coccomyxa, and the deep layer presented dissimilatory nitrate reduction associated with uncultured Actinobacteria and Proteobacteria. Chapter 5 described novel acidophilic populations involved in active biosulfidogenesis in the deep layer of CM. Biosulfidogenesis is the generation of sulfide by microbial reduction of oxidized sulfur compounds. Sulfide precipitates dissolved metals as metal-sulfides that can be removed from the system. Despite the high sulfate and metal concentrations of the deep layer of CM, biosulfidogenic taxa had not been reported before. In Chapter 5, I reconstructed eighteen high quality MAGs from the deep layer that represented abundant phyla such as Euryarchaeota, Parcubacteria, Actinobacteria, Chloroflexi, and Nitrospirae. A phylogenetic analysis of the MAGs revealed their novelty as no similar culture or uncultured genomes to the MAGs were found. Thirteen of these MAGs had at least one gene, and three MAGs presented most genes and transcripts involved in sulfate reduction. The three MAGs belonged to the Actinobacteria, Chloroflexi, and Nitrospirae phyla, with no previous representatives of acidophilic and mesophilic sulfate reducers. These populations were predicted to be actively contributing to biosulfidogenesis in the deep layer. In accordance with Chapter 4 findings, MAGs representing some of the abundant populations in the deep layer had predicted activity for oxidation of sulfur compounds. These results suggest that CM has the potential of natural attenuation of metals by biosulfidogenesis, but such potential is diminished by cryptic sulfur cycling.
The New Science Of Metagenomics
DOWNLOAD
Author : National Research Council
language : en
Publisher: National Academies Press
Release Date : 2007-06-24
The New Science Of Metagenomics written by National Research Council and has been published by National Academies Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-06-24 with Science categories.
Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.
Microbial Control Of The Nitrogen Cycle
DOWNLOAD
Author : Lourdes Girard
language : en
Publisher: Frontiers Media SA
Release Date : 2020-07-02
Microbial Control Of The Nitrogen Cycle written by Lourdes Girard and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-07-02 with categories.
Linking Microbial Communities
DOWNLOAD
Author : Feng Ju
language : en
Publisher: Open Dissertation Press
Release Date : 2017-01-26
Linking Microbial Communities written by Feng Ju and has been published by Open Dissertation Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-01-26 with Technology & Engineering categories.
This dissertation, "Linking Microbial Communities, Environmental Factors and Performance of Biological Treatment Reactors Using Metagenomics" by Feng, Ju, 鞠峰, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: The thesis was conducted to reveal the associations among microbial communities, environmental factors (i.e., operational and physicochemical conditions) and performance of biological treatment reactors of activated sludge (AS) and anaerobic digestion (AD) using metagenomics. Moreover, environmental and biological factors that govern microbiome assembly and population dynamics were examined with emphasis on core, functional and uncultured microorganisms. Additionally, occurrence of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs) in digested sludge and their removal and dissemination during AD were evaluated. Full-scale AS reactors in wastewater treatment plants (WWTPs) were extensively investigated both spatially (50 grab samples, 27 reactors, 17 cities) and temporally (58 monthly samples, 1 reactor, Hong Kong). Metagenomics and network analysis of spatio-temporal data show that AS bacterial communities are nonrandomly assembled by taxonomic relatedness, which is induced by multiple deterministic processes, including habitat filtering and competition. Moreover, bacterial communities in full-scale municipal AS reactor follow no apparent seasonal succession over five years and biological interactions dominate over environmental conditions (mainly sludge retention time (SRT) and inorganic nitrogen) in determining bacterial assembly and population dynamics. Additionally, a core set of cosmopolitan functional microorganisms (e.g., nitrogen-cycling-related bacteria) widely occur in globally distributed AS reactors. Besides AS systems in WWTPs, performance of downstream AD reactors that receive primary and/or secondary sludge is also related with biological and environmental factors. First, multivariate, correlation and network analyses of three-year data of two full-scale municipal AD reactors show that methane production and percentage are significantly correlated (P-values Last, comparative genomics of 23 prokaryotic genomes reconstructed from phenol-degrading methanogenic reactors reveals that temperature difference induced colonization of sulfate/sulfite/sulfur (20oC) or nitrate/nitrite-respiring (37℃) sub-communities as competitors of methanogens, which differentiates methanogenesis from phenol. The discovery of interspecific competition justifies attempts towards biological manipulation for maximizing methanogenesis in anaerobic reactors. Combined, this thesis presents a large-scale meta
Research On Nitrification And Related Processes Part A
DOWNLOAD
Author : Martin G. Klotz
language : en
Publisher: Academic Press
Release Date : 2011-01-10
Research On Nitrification And Related Processes Part A written by Martin G. Klotz and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-01-10 with Reference categories.
State-of-the-art update on methods and protocols dealing with the detection, isolation and characterization of macromolecules and their hosting organisms that facilitate nitrification and related processes in the nitrogen cycle as well as the challenges of doing so in very diverse environments. Provides state-of-the-art update on methods and protocols Deals with the detection, isolation and characterization of macromolecules and their hosting organisms Deals with the challenges of very diverse environments