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Author: Sharon Faye Smith
Publisher:
ISBN:
Category :
Languages : en
Pages : 348
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Book Description
Soil microorganisms help maintain nutrient cycling, control carbon sequestration, impact plant productivity, and influence several soil chemical and physical properties; yet, the processes that control the microbial composition of soil and how environmental changes may affect the composition and activity of these organisms at different scales remains a difficult and intriguing puzzle for soil scientists, ecologists, and modelers. Wetlands are endangered and important ecosystems that provide several services, which are directly linked to soil function. However, few wetland assessments consider the soil environment and microbial ecology. Linking soil microbial community composition and distribution patterns to soil physio-chemical properties would provide fundamental information for the further exploration of how biogeochemical properties relate to ecosystem function, and pave the way towards developing new wetland success indicators. By using spatial ecology concepts along with soil metabarcoding, this research provides insight into the fungal and bacterial community composition and their relationship to the soil environment within a mounded wet prairie in southern United States. Generalized dissimilarity modeling (GDM), a form of nonlinear matrix regression, and amplicon metabarcoding was applied to simultaneously quantify the relative effects of geographic distance, elevation, and soil properties driving microbial community composition. The wet prairie surveyed in this research contained high spatial heterogeneity of soil chemical and physical properties, as well as distinct microtopography, which influenced the composition and diversity of soil microbial communities. The GDMs explained 28.3 and 41.5% of the total variation in bacterial and fungal beta diversity, respectively. Soil texture was an important and unexpected driver of both fungal and bacterial composition and diversity within the study site. Bacterial alpha diversity increased and fungal alpha diversity decreased with increasing sand content within the site. Sand content was also greatest on mounds in the site. Future wetland restoration studies should consider the influence of spatial heterogeneity of soil texture and micro-topography on microbial diversity, as it may affect the success of future restoration efforts. Understanding how soil microbial ecology connects to the soil environment at an ecosystem level can help inform future restoration practices, and can also be used to improve our predictive capabilities on a global scale for ecosystem services like carbon sequestration. The future applications of soil metagenomic data to infer ecosystem function and predict responses to a changing world are promising, but there are still many hurtles to overcome. While sequence databases are continuously growing, many metagenomic sequences still can't be aligned or assigned to a functional pathway. Thus, our ability to use metagenomic data for ecological models or to predict soil microbial response to climate change is dependent on continued efforts to characterize microbes and their associated environments.
Author: Sharon Faye Smith
Publisher:
ISBN:
Category :
Languages : en
Pages : 348
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Book Description
Soil microorganisms help maintain nutrient cycling, control carbon sequestration, impact plant productivity, and influence several soil chemical and physical properties; yet, the processes that control the microbial composition of soil and how environmental changes may affect the composition and activity of these organisms at different scales remains a difficult and intriguing puzzle for soil scientists, ecologists, and modelers. Wetlands are endangered and important ecosystems that provide several services, which are directly linked to soil function. However, few wetland assessments consider the soil environment and microbial ecology. Linking soil microbial community composition and distribution patterns to soil physio-chemical properties would provide fundamental information for the further exploration of how biogeochemical properties relate to ecosystem function, and pave the way towards developing new wetland success indicators. By using spatial ecology concepts along with soil metabarcoding, this research provides insight into the fungal and bacterial community composition and their relationship to the soil environment within a mounded wet prairie in southern United States. Generalized dissimilarity modeling (GDM), a form of nonlinear matrix regression, and amplicon metabarcoding was applied to simultaneously quantify the relative effects of geographic distance, elevation, and soil properties driving microbial community composition. The wet prairie surveyed in this research contained high spatial heterogeneity of soil chemical and physical properties, as well as distinct microtopography, which influenced the composition and diversity of soil microbial communities. The GDMs explained 28.3 and 41.5% of the total variation in bacterial and fungal beta diversity, respectively. Soil texture was an important and unexpected driver of both fungal and bacterial composition and diversity within the study site. Bacterial alpha diversity increased and fungal alpha diversity decreased with increasing sand content within the site. Sand content was also greatest on mounds in the site. Future wetland restoration studies should consider the influence of spatial heterogeneity of soil texture and micro-topography on microbial diversity, as it may affect the success of future restoration efforts. Understanding how soil microbial ecology connects to the soil environment at an ecosystem level can help inform future restoration practices, and can also be used to improve our predictive capabilities on a global scale for ecosystem services like carbon sequestration. The future applications of soil metagenomic data to infer ecosystem function and predict responses to a changing world are promising, but there are still many hurtles to overcome. While sequence databases are continuously growing, many metagenomic sequences still can't be aligned or assigned to a functional pathway. Thus, our ability to use metagenomic data for ecological models or to predict soil microbial response to climate change is dependent on continued efforts to characterize microbes and their associated environments.
Author: Rama Kant Dubey
Publisher: Springer
ISBN: 3030155161
Category : Nature
Languages : en
Pages : 118
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Book Description
This book explores the significance of soil microbial diversity to understand its utility in soil functions, ecosystem services, environmental sustainability, and achieving the sustainable development goals. With a focus on agriculture and environment, the book highlights the importance of the microbial world by providing state-of-the-art technologies for examining the structural and functional attributes of soil microbial diversity for applications in healthcare, industrial biotechnology, and bioremediation studies. In seven chapters, the book will act as a primer for students, environmental biotechnologists, microbial ecologists, plant scientists, and agricultural microbiologists. Chapter 1 introduces readers to the soil microbiome, and chapter 2 discusses the below ground microbial world. Chapter 3 addresses various methods for exploring microbial diversity, chapter 4 discusses the genomics methods, chapter 5 provides the metaproteomics and metatranscriptomics approaches and chapter 6 details the bioinformatics tools for soil microbial community analysis, and chapter 7 concludes the text with future perspectives on further soil microbial uses and applications.
Author: Jay Shankar Singh
Publisher: Elsevier
ISBN: 0323858945
Category : Science
Languages : en
Pages : 611
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Book Description
Microbes in Land Use Change Management details the various roles of microbial resources in management of land uses and how the microbes can be used for the source of income due to their cultivation for the purpose of biomass and bioenergy production. Using various techniques, the disturbed and marginal lands may also be restored eco-friendly in present era to fulfil the feeding needs of mankind around the globe. Microbes in Land Use Change Management provides standard and up to date information towards the land use change management using various microbial technologies to enhance the productivity of agriculture. Needless to say that Microbes in Land Use Change Management also considers the areas including generation of alternative energy sources, restoration of degraded and marginal lands, mitigation of global warming gases and next generation -omics technique etc. Land use change affects environment conditions and soil microbial community. Microbial population and its species diversity have influence in maintaining ecosystem balance. The study of changes of microbial population provides an idea about the variation occurring in a specific area and possibilities of restoration. Meant for a multidisciplinary audience Microbes in Land Use Change Management shows the need of next-generation omics technologies to explore microbial diversity. Describes the role of microbes in generation of alternative source of energy Gives recent information related to various microbial technology and their diversified applications Provides thorough insight in the problems related to landscape dynamics, restoration of soil, reclamation of lands mitigation of global warming gases etc. eco-friendly way using versatility of microbes Includes microbial tools and technology in reclamation of degraded, disturbed and marginal lands, mitigation of global warming gases
Author: Lauren Alteio
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Soil is considered one of the most diverse ecosystems on Earth, harboring diversity of organisms across the three domains of life. It is spatially and chemically heterogeneous: properties that intertwine in a complex matrix to support organismal diversity and function across different scales. Soil microorganisms both respond to and drive changes in ecosystems through metabolic activities. A single gram of soil is teeming with millions of cells comprised of thousands of species. Much of this diversity remains uncharacterized due to technical and methodological challenges faced by soil ecologists. Due to the complex physicochemical properties of soil and cross-feeding interactions between organisms, it is difficult to culture microorganisms in isolation. The immense biological diversity of soils also reduces bioinformatic genome assembly efficiency, therefore obscuring the scope of diversity. As one of Earth's main reserviors of stored carbon, containing roughly one-third of carbon globally, terrestrial ecosystems may serve as a carbon source under future climate scenarios and drive further climate change. Despite challenges associated with the study of soil microorganisms, it remains critical to discover and describe diversity of microbial communities in soils if we are to understand resilience of our ecosystems to climate change. Surveys of microbial diversity and function in soil have been conducted using amplicon sequencing, metagenomics, and metatranscriptomics, however a large knowledge gap persists in the characterization of diversity and ecological niches of elusive microorganisms. These are organisms that are typically recalcitrant to laboratory culture, and may appear in relatively low abundance in soil communities or exhibit a high degree of population microheterogeneity, thereby resulting in poor representation in genome assemblies. The focus of my dissertation research is the application of complementary genomic techniques in order to uncover more of the previously unknown microbial diversity contained in forest soils, and link this diversity to higher-level ecosystem function. Much of what is known about soil diversity has been contributed through cultivation-independent investigations, however diversity estimates indicate that we are only beginning to scratch the surface of bacterial, archaeal, and viral diversity in forest soils. We are therefore vastly underestimating the roles these organisms play in biogeochemical processes, such as the release of CO2 to the atmosphere through respiration. However, the scope of microbial diversity and their suite of metabolic functions remain challenging to link to ecosystem level processes due to methodological limitations. For chapter 1 of my dissertation, I worked in collaboration with researchers at the University of Vienna using extensive literature searches to explore the different spatial scales at which we study microbial diversity and function with the goal of linking microorganisms and their role as drivers of higher level processes. This work suggests that the level at which microorganisms interact, termed the 'microbial consortium', is a key scale which provides insights into microbial diversity, function, and enables scaling up from the single cell to the ecosystem. In chapter 2, I applied complementary metagenomic techniques to the discovery of soil biological diversity, including bulk metagenomics and a pooled, cell-sorting approach coupled to high-throughput sequencing, termed mini-metagenomics. In combination, these approaches uncover the genetic diversity of elusive microorganisms at the Harvard Forest Long-Term Ecological Research (LTER) site. Together, these approaches have generated some of the highest quality metagenome assembled genomes (MAGs) to date from this LTER experimental site, and have revealed a swath of diversity beyond the organisms typically found in high abundance in the soil. I demonstrate how complementary metagenomic techniques facilitate the discovery of biological diversity by highlighting the expanded knowledge of potential intracellular bacteria in the phylum Bacteroidetes. In chapter 3, I characterize the metabolism of representatives in the phylum Acidobacteria subdivision 2, which are abundant in forest soils but have yet to be described as there are no available genome sequences in this taxonomic group. Finally, chapter 4 describes sixteen novel giant viruses which have been discovered in Harvard Forest soil for the first time in collaboration with researchers at the Joint Genome Institute. These expand knowledge of phylogenetic diversity of the nucelocytoplasmic large DNA viruses (NCLDV) by 21%, and further demonstrate the utility of complementary metagenomic approaches in uncovering diversity of elusive viral entities in addition to microbial life. Observed changes at Prospect Hill, the longest-running soil warming experimental site at Harvard Forest, reveal increases in soil microbial respiration, increases in nitrogen mineralization, decreases in soil organic matter and decreases in the overall microbial biomass of these soils in response to warming. Based on these findings, we can expect similar changes to occur at the Barre Woods warming experiment, which was established at the Harvard Forest LTER site in 2002. Additionally, we may anticipate similar changes in temperate forest soils as the Earth's climate changes and surface temperatures continue to rise. With these changes, the microbial community must change and adapt to shifting nutrient and substrate availability, moisture conditions and changing soil structure. This dissertation work supports our understanding of the expansion of niches for soil microorganisms with oligotrophic growth strategies and flexible metabolism. These traits will enable soil organisms to cope with a nutrient-limited environment that is predicted to occur in response to long-term climate change.
Author: Tapan Kumar Adhya
Publisher: Springer
ISBN: 9811061785
Category : Science
Languages : en
Pages : 208
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Book Description
This book presents a comprehensive collection of articles illustrating the importance of microbial community structure and function for ecosystem sustainability and environmental reclamation. It addresses a diverse range of topics, including microbial diversity, physiology, genomics, ecosystem function, interaction, metabolism, and the fruitful use of microbial communities for crop productivity and environmental remediation. In addition, the book explores issues ranging from general concepts on the diversity of microorganisms in soil, and ecosystem function to the evolution and taxonomy of soil microbiota, with future prospects. It covers cutting-edge methods in soil microbial ecological studies, rhizosphere microflora, the role of organic matter in plant productivity, biological nitrogen fixation and its genetics, microbial transformation of plant nutrients in soil, plant-growth-promoting rhizobacteria, and organic matter transformation. The book also discusses the application of microbes in biodegradation of xenobiotic contaminants. It covers bio-fertilizers and their role in sustainable agriculture and soil health, biological control of insect pests and plant pathogens, and the latest tools of omics in soil microbiology, i.e. genomics, proteomics, transcriptomics and metabolomics, which offer pioneering approaches to the exploration of microbial structure and function.
Author: Laura Zucconi
Publisher: Frontiers Media SA
ISBN: 288971618X
Category : Science
Languages : en
Pages : 187
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Book Description
Author: Robert L. Tate, III
Publisher: John Wiley & Sons
ISBN: 1119114357
Category : Science
Languages : en
Pages : 592
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Book Description
An updated text exploring the properties of the soil microbial community Today, the environmentally oriented specialties of microbiology are shifting from considering a single or a few microbial species to focusing on the entire microbial community and its interactions. The third edition of Soil Microbiology has been fully revised and updated to reflect this change, with a new focus on microbial communities and how they impact global ecology. The third edition still provides thorough coverage of basic soil microbiology principles, yet the textbook also expands students’ understanding of the role the soil microbial community plays in global environmental health and human health. They can also learn more about the techniques used to conduct analysis at this level. Readers will benefit from the edition’s expanded use of figures and tables as well as the recommendations for further reading found within each chapter. Considers the impact of environmental perturbations on microbial community structure as well as the implications for soil system functions Discusses the impact of soil microbial communities on food and health related issues Emphasizes the importance of soil microbial communities on the sustainability of terrestrial ecosystems and solutions to global issues This third edition is a suitable text for those studying soil microbiology and soil ecology at the undergraduate or graduate level. It also serves as a valuable reference tool for professionals working in the fields of reclamation and soil management.
Author: Pravat Kumar Shit
Publisher: Springer Nature
ISBN: 3031092708
Category : Science
Languages : en
Pages : 732
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Book Description
This book demonstrates the measurement, monitoring, mapping and modelling of soil pollution and land resources. This book explores state-of-the-art techniques based on open sources software & R statistical programming and modelling in modern geo-computation techniques specifically focusing on the recent trends in data mining/machine learning techniques and robust modelling in soil resources. Soil and agricultural systems are an integral part of the global environment and human well‐being, providing multiple goods and services essential for people worldwide and crucial for sustainable development. Soil contamination is an environmental hazard and has become a big issue related to environmental health. The challenge of the twenty-first century is to reduce the contaminant load and bring it to below permissible level. The contamination is not only a problem affecting local environments at the place of occurrence but also spreading to other regions because of easy transportation of pollutants. This leads to direct and indirect contamination of land and aquatic systems, surface water and groundwater, inducing significant risks for natural ecosystems. In this context, the spatial modelling, prediction, efficient use, risk assessment, protection and management of soil resources in the agriculture system are the key to achieving sustainable development goals and ensuring the promotion of an economically, socially and environmental sustainability future. The aim of this book on soil contaminants and environmental health: application of geospatial technology is to identify the soil and sediment quality, sources of contaminants and risk assessment and focuses on the decision-making and planning point of view through GIS data management techniques. This book covers major topics such as spatial modelling in soil and sediments pollution and remediation; radioactive wastes, microbiology of soil and sediments, soil salinity and sodicity, pollution from landfill sites, soil erosion and contamination from agricultural activities, heavy metal pollution and health risk; environmental impact and risk assessment, sustainable land use, landscape management and governance, soil degradation and risk assessment, agricultural soil pollution, pollution due to urban activities, soil pollution by industrial effluents and solid wastes, pollution control and mitigation in extreme environments. The content of this book is of interest to researchers, professionals and policy-makers whose work is in soil science and agriculture practices. The book equips with the knowledge and skills to tackle a wide range of issues manifested in geographic data, including those with scientific, societal and environmental implications.
Author: Jieyun Wu
Publisher:
ISBN:
Category : Bacterial communities
Languages : en
Pages : 502
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Book Description
One of the central goals of the field of microbial biogeography is to better understand spatial patterns of microbial community diversity and how communities respond to gradients in environmental conditions, be they natural or anthropogenic in origin. The main aim of this thesis was to investigate how gradients in environmental conditions (i.e., across a mountain elevational gradient and across different land-use types) affect soil microbial community structure, diversity and functional traits, and to assess how these communities respond to differing environmental variables, using next-generation sequencing technologies. Elevation gradients are commonly used to explore impact climate impacts on biological communities since declines in temperature with increased elevation can generate substantial climate gradients over small spatial scales. However, inconsistent spatial patterns in soil bacterial community structure observed across elevation gradients imply that communities are affected by a variety of factors at different spatial scales. Here, I investigated the biogeography of soil bacteria across broad (i.e., a ~ 1500 m mountain elevation gradient) and fine sampling scales (i.e., both aspects of a mountain ridge) using 16S rRNA gene sequencing. Across equivalent distances, variation in bacterial community composition changed more with variation in site aspect than elevation. Bacterial community composition and richness were most strongly associated with soil pH, despite the large variability in multiple soil climate variables across the site. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. Similar to , inconsistent elevational patterns in soil fungal community diversity suggest that these communities are driven by a complex underlying mechanism. Thus, to enhance understanding of whether distinct biogeographic patterns can be distinguished between different microorganisms and how such gradients influence the potential interactions among individual taxa, I assessed variation in the co-occurrence of different fungal taxa at different elevations along the aforementioned mountain ridge, using fungal internal transcribed spacer (ITS1) DNA sequencing. Fungal community composition changed significantly along the gradient, and their co-occurrences were less frequent with increasing elevation. Such changes with elevation were associated with soil nutrient concentrations, likely driven by the relative ability of different taxa to compete for nutrients at different environmental concentrations. Evidence of nutrient-driven shifts in fungal community diversity and function in soil will enhance our understanding of underground nutrient cycling and the likely impacts of climate change and agricultural disturbance on soil microbial communities. To further explore gradients in the functional potential of soil bacterial communities along an elevation gradient, I devised a method to 'infer' metagenomics data from bacterial 16S rRNA gene sequences. I evaluated the applicability of my 'inferred metagenomics' approach, by comparing bacterial community composition derived from the original bacterial data to communities derived only from the 400 taxa for which genomic information is available. The results generated from these two datasets were highly similar, suggesting that the subset of 'inferred' community was largely reflective of that of the wider environmental community. Further analysis indicates that bacteria with larger genome size appear to prevail across the elevation gradient, suggesting that microorganisms might successfully cope with harsh or various environmental conditions by retaining a larger burden of potential genes and related functions. These findings highlight the potential for using inferred genomic information, based on bacterial 16S rRNA gene data, to generate a general functional trait-based picture of microbial biogeographical patterns. Apart from studies on elevational patterns of soil microbial communities, many other environmental gradients impact distributions of bacterial communities, including gradients of anthropogenic disturbance. Therefore, I studied how pastoral land management practices affect soil bacteria, both in agricultural soils and adjacent forest fragments along 21 transects bisecting pasture-forest boundaries. Decreased compositional dispersion of bacterial communities in the grazed pasture soils resulting in a net loss of diversity caused by community homogenisation after forest-to-pasture conversion. Additionally, a greater richness of pastureonly taxa for sites with a fence on the boundary between the two land uses revealed that boundary fences play an important role in protecting the integrity of soil bacterial communities in forests surrounded by agricultural land via restricting livestock invasion. The observed variation in bacterial community richness and composition was most related to changes in soil physicochemical variables commonly associated with agricultural fertilisation. Overall, my findings demonstrate clear, and potentially detrimental, effects of agricultural disturbance on bacterial communities in forest soils adjacent to pastoral land. This thesis reports the findings of a comprehensive evaluation of the impact of different environmental gradients on soil microbial community composition and functional potential, encompassing sample data collected across different spatial scales and land use types, as well as between different microbial phylogenetic groups. These results confirm that spatial patterns in both bacterial and fungal community structure are driven by various interacting environmental variables related with natural gradients or agricultural disturbances.
Author: Carmelo Dazzi
Publisher: Springer Nature
ISBN: 3031527445
Category :
Languages : en
Pages : 671
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Book Description
