Metagenomics of the Microbial Nitrogen Cycle

Theory, Methods and Applications

Author: Diana Marco



Category: Nature

Page: 288

View: 495

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


Publisher: Stanford University




View: 219

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.

Rhizosphere Microbes

Soil and Plant Functions

Author: Sushil Kumar Sharma

Publisher: Springer Nature


Category: Technology & Engineering

Page: 682

View: 536

Plants create a dynamic micro-biosphere in the soil, around the roots, called as ‘rhizosphere’, which harbors diverse number of microorganisms for sustaining their growth and development. A soil with diverse and multi-traits microbial communities is considered healthy to enhance crop productivity. In the last decades, rhizosphere biology has gained attention due to unraveling of new mechanisms, processes and molecules in the rhizosphere that contributes towards the promotion of plant productivity. The rhizospheric microbes and associated processes are being utilized for harnessing potential of soils in effective and sustainable functioning in the agro-ecosystems. Broadly, the book discusses rhizospheric microbes and their role in modulating functions of soil and crop plant. Specifically, it highlights conventional and modern aspects of rhizosphere microbes such as – microbiome in the rhizosphere, microbes as an indicator and promoter of soil health, rhizosphere microbes as biofertilizer, biostimulator and biofortifyer, microbial signaling in the rhizosphere, recent tools in deciphering rhizobiome, and regulatory mechanisms for commercialization of biofertilizer, biopesticide and biostimulator. The book is useful for agriculture scientist, biotechnologist, plant pathologist, mycologist, and microbiologist, farming community, scientist of R&D organization, as well as teaching community, researcher and student and policy maker.

Nitrogen Cycle

Ecology, Biotechnological Applications and Environmental Impacts

Author: Jesus Gonzalez-Lopez

Publisher: CRC Press


Category: Technology & Engineering

Page: 292

View: 703

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.

Microbial Biomass: A Paradigm Shift In Terrestrial Biogeochemistry

Author: Tate Kevin Russel

Publisher: World Scientific


Category: Technology & Engineering

Page: 348

View: 738

Microbial Biomass informs readers of the ongoing global revolution in understanding soil and ecosystem microbial processes. The first paper on the subject was written by David Jenkinson in 1966, and here new insights and expansions are given on the fascinating world of soil microbial processes. In terms of contemporary issues, it also serves to support urgent efforts to sustainably manage land to feed a growing world population without compromising the environment. It presents new methods of investigation which are leading to more sustainable management of ecosystems, and improved understanding of ecosystem changes in an increasingly warmer world. The book approaches the topic by looking at the emergence of our understanding of soil biological processes, and begins by tracing the conception and first measurement of soil microbial biomass. Following this, changes in ecosystems, and in natural ecosystem processes are discussed in relation to land management issues and global change. Microbial biomass and its diversity are recognized as key factors in finding solutions for more sustainable land and ecosystem management, aided by new molecular and other tools. Information from the use of these tools is now being incorporated into emerging microbial-explicit predictive models, to help us study changes in earth system processes. Perfect for use in research and practice, this book is written for undergraduate and graduate students, researchers and professionals of agronomy, chemistry, geology, physical geography, ecology, biology, microbiology, silviculture and soil science.

Microbial Probiotics for Agricultural Systems

Advances in Agronomic Use

Author: Doris Zúñiga-Dávila

Publisher: Springer


Category: Science

Page: 256

View: 145

The book is a comprehensive compilation of the most recent advances in the practical approach of the use of microbial probiotics for agriculture. Unlike the rest of the publications about biofertilizers, this book bridges the gap between the lab studies (molecular, physiological, omics, etc.) and the agronomic application.

Mining of Microbial Wealth and MetaGenomics

Author: Vipin Chandra Kalia

Publisher: Springer


Category: Medical

Page: 461

View: 672

The existence of living organisms in diverse ecosystems has been the focus of interest to human beings, primarily to obtain insights into the diversity and dynamics of the communities. This book discusses how the advent of novel molecular biology techniques, the latest being the next-generation sequencing technologies, helps to elucidate the identity of novel organisms, including those that are rare. The book highlights the fact that oceans, marine environments, rivers, mountains and the gut are ecosystems with great potential for obtaining bioactive molecules, which can be used in areas such as agriculture, food, medicine, water supplies and bioremediation. It then describes the latest research in metagenomics, a field that allows elucidation of the maximum biodiversity within an ecosystem, without the need to actually grow and culture the organisms. Further, it describes how human-associated microbes are directly responsible for our health and overall wellbeing.“/p>

Metagenomics and Microbial Ecology

Techniques and Applications

Author: Surajit De Mandal

Publisher: CRC Press


Category: Nature

Page: 214

View: 978

Microorganisms comprise the greatest genetic diversity in the natural ecosystem, and characterization of these microbes is an essential step towards discovering novel products or understanding complex biological mechanisms. The advancement of metagenomics coupled with the introduction of high-throughput, cost-effective NGS technology has expanded the possibilities of microbial research in various biological systems. In addition to traditional culture and biochemical characteristics, omics approaches (metagenomics, metaproteomics, and metatranscriptomics) are useful for analyzing complete microbial communities and their functional attributes in various environments. Metagenomics and Microbial Ecology: Techniques and Applications explores the most recent advances in metagenomics research in the landscape of next-generation sequencing technologies. This book also describes how advances in sequencing technologies are used to study invisible microbes as well as the relationships between microorganisms in their respective environments. Features: Covers a wide range of concepts, investigations, and technological advancement in metagenomics at the global level. Highlights the novel and recent approaches to analyze microbial diversity and its functional attributes. Features a range of chapters that present an introduction to the field and functional insight into various ecosystems.


Microbiology Fundamentals and Biotechnological Applications

Author: Eun Yeol Lee

Publisher: Springer Nature


Category: Science

Page: 278

View: 225

This book offers a comprehensive overview of the microbiological fundamentals and biotechnological applications of methanotrophs: aerobic proteobacteria that can utilize methane as their sole carbon and energy source. It highlights methanotrophs’ pivotal role in the global carbon cycle, in which they remove methane generated geothermally and by methanogens. Readers will learn how methanotrophs have been employed as biocatalysts for mitigating methane gas and remediating halogenated hydrocarbons in soil and underground water. Recently, methane has also attracted considerable attention as a potential next-generation carbon feedstock for industrial biotechnology, because of its abundance and low price. Methanotrophs can be used as biocatalysts for the production of fuels, chemicals and biomaterials including methanobactin from methane under environmentally benign production conditions. Sharing these and other cutting-edge insights, the book offers a fascinating read for all scientists and students of microbiology and biotechnology.