The Response Of Soil Microbial Communities To Vegetable Cropping Systems Analyzed For Rna And Dna Based Sampling

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The Response of Soil Microbial Communities to Vegetable Cropping Systems Analyzed for RNA- and DNA-based Sampling

Author : Lorena Gomez-Montano
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (18 download)

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Book Synopsis The Response of Soil Microbial Communities to Vegetable Cropping Systems Analyzed for RNA- and DNA-based Sampling by : Lorena Gomez-Montano

Download or read book The Response of Soil Microbial Communities to Vegetable Cropping Systems Analyzed for RNA- and DNA-based Sampling written by Lorena Gomez-Montano and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Soil microbial communities play fundamental and complex roles in the productivity of agriculture. However, we still have a limited understanding of the response of microbial communities to different farming systems, such as organic and conventional fertility management regimens. We applied high-throughput sequencing to develop a better understanding of how soil microbial communities (bacteria and fungi) in vegetable production respond to organic or conventional soil fertility management. Specifically, my three studies examined the following questions: 1. How do soil microbial communities from cDNA and DNA samples compare in organic and conventional fertility treatments? 2. How do soil microbial communities in a tomato cropping season respond to long-term organic vs. conventional soil fertility treatments? 3. How do soil bacterial and fungal communities respond to high tunnels, plastic mulch and organic amendments across a tomato cropping season? The first two questions were addressed at the Kansas State University Horticulture and Extension Center in Olathe, KS, using organic and conventional field plots with three levels of fertilizer. We sampled the plots during the development of a tomato crop. The third question was addressed at a commercial farm in Lawrence, KS, during its transition to organic vegetable production, during a tomato crop. The Lawrence experiment included as treatments field plots versus high tunnels, and three organic nutrient amendments. We used 454-pyrosequencing of bacterial and fungal ribosomal markers to compare total resident (DNA) and active microbial communities (cDNA, which is DNA synthesized from a single stranded RNA template) for our first question. We used Illumina MiSeq metabarcoding of bacterial and fungal ribosomal markers for our second and third questions. In all three studies we evaluated bacterial and fungal community responses using Simpson ́s diversity index, Simpson ́s evenness and richness for each experiment. For the first question, when we compared DNA and cDNA, bacterial diversity was higher in cDNA samples from organic compared to conventional management. In addition, fungal diversity from cDNA samples was higher than from DNA samples. In contrast, in the second question, bacterial and fungal diversity indices did not differ in the tomato crop under organic and conventional management systems. For our third question, high tunnels did not affect bacterial or fungal diversity. Use of plastic mulch for a tomato crop in open field plots did not affect bacterial richness, but decreased fungal richness compared to open field plots without plastic mulch. High-throughput sequencing provides a new perspective on the structure and dynamics of these communities. Information from this approach will ultimately improve our ability to manage soil for sustainable productivity by promoting beneficial microorganisms and suppressing pathogenic ones.

Determinants of Microbial Community Structure and Substrate Utilization Potential in Soils of Vegetable Cropping Systems

Author : Mary Edith Schutter
Publisher :
ISBN 13 :
Total Pages : 386 pages
Book Rating : 4.:/5 (45 download)

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Book Synopsis Determinants of Microbial Community Structure and Substrate Utilization Potential in Soils of Vegetable Cropping Systems by : Mary Edith Schutter

Download or read book Determinants of Microbial Community Structure and Substrate Utilization Potential in Soils of Vegetable Cropping Systems written by Mary Edith Schutter and published by . This book was released on 2000 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Oregon Long-Term Soil Quality Project was initiated to identify soil properties that respond rapidly to alternative management practices. Such practices included winter cover cropping, which was implemented at two experimental research stations and several grower fields throughout the Willamette Valley. The goal of this thesis was to identify the major impacts of cover cropping on soil microbial community structure, diversity, and substrate utilization potential. Microbial community structure was assessed by extracting fatty acids from soil and analyzing community fatty acid methyl ester (FAME) profiles. Two different methods for extracting fatty acids were tested; these were the ester linked method and the MIDI method developed by Microbial ID, Inc. (Newark, DE). Both methods discriminated among communities from different soils, but the types and relative amounts of fatty acids extracted differed by method. Microbial communities also were characterized by their potential to utilize a diverse range of carbon substrates using the Biolog assay. In a laboratory incubation study, the Biolog assay demonstrated that the types and overall diversity of substrates utilized were affected by the complexity of carbon substrate added to soil. In addition, Biolog diversity was significantly correlated with community FAME richness (r = 0.59). FAME and Biolog assays were applied to field soils of the Soil Quality Project. Changes occurred in microbial FAME structure and Biolog potential in response to winter cover cropping, but effects often were not observed until incorporation of cover crops to soil. In some soils containing cover crop residues, there were greater amounts of eukaryotic FAME markers compared to winter-fallow soils, suggesting greater fungal and protozoan populations in cover-cropped soil. Biolog diversity also was greater in cover-cropped soil compared to fallow soil, which may reflect the utilization of cover crop residues by soil microorganisms during the summer months. Community patterns across different sizes of soil aggregates also were assessed. Biolog diversity was heterogeneously distributed among aggregates, and winter cover cropping elevated FAME diversity across all but the largest (2.0-5.0 mm) aggregate size class. This thesis also identified season and soil type as strong determinants of microbial community structure.

Soil Microbial Communities in Agroecosystems

Author : Deborah Ann Bossio
Publisher :
ISBN 13 :
Total Pages : 234 pages
Book Rating : 4.:/5 (56 download)

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Book Synopsis Soil Microbial Communities in Agroecosystems by : Deborah Ann Bossio

Download or read book Soil Microbial Communities in Agroecosystems written by Deborah Ann Bossio and published by . This book was released on 1996 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt:

16s Ribosomal RNA Analysis to Detect Soil Microbial Community Shifts in Response to Changing Agricultural Practices from Row Crops to Short Rotation Woody Crops

Download 16s Ribosomal RNA Analysis to Detect Soil Microbial Community Shifts in Response to Changing Agricultural Practices from Row Crops to Short Rotation Woody Crops PDF Online Free

Author : Julia O'Neal Stair
Publisher :
ISBN 13 :
Total Pages : 392 pages
Book Rating : 4.:/5 (431 download)

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Book Synopsis 16s Ribosomal RNA Analysis to Detect Soil Microbial Community Shifts in Response to Changing Agricultural Practices from Row Crops to Short Rotation Woody Crops by : Julia O'Neal Stair

Download or read book 16s Ribosomal RNA Analysis to Detect Soil Microbial Community Shifts in Response to Changing Agricultural Practices from Row Crops to Short Rotation Woody Crops written by Julia O'Neal Stair and published by . This book was released on 1998 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Effects of Organic and Conventional Agricultural Practices on Soil Microbial Communities and Molecular Detection of Soil Borne Disease

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Author : Holli K. Milner
Publisher :
ISBN 13 :
Total Pages : 83 pages
Book Rating : 4.:/5 (94 download)

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Book Synopsis Effects of Organic and Conventional Agricultural Practices on Soil Microbial Communities and Molecular Detection of Soil Borne Disease by : Holli K. Milner

Download or read book Effects of Organic and Conventional Agricultural Practices on Soil Microbial Communities and Molecular Detection of Soil Borne Disease written by Holli K. Milner and published by . This book was released on 2014 with total page 83 pages. Available in PDF, EPUB and Kindle. Book excerpt: Author's abstract: Agricultural practices affect soil microbial communities and health through the input of pesticides, herbicides, fertilizers, and cycling of crop rotation. By examining the microbial community structure, we analyzed how microbial species respond to the environment that individual farms create. Early detection of soil borne disease is essential for agricultural success. However, monitoring incidence of disease based on plant growth response to pathogenic inoculation may not reveal the amount of pathogenic DNA in soil. A comparative study of tomato production systems was conducted by analysis of soil microbial community structure from four farms in Southeast Georgia for the years 2012 and 2013, and incidence level of disease and plant growth of tomato plants grown in greenhouse soil were measured. The results indicated that the soil fungal, bacterial, and animal communities were unique to each farm (ANOSIM P

Plant Root Interaction With Associated Microbiomes to Improve Plant Resiliency and Crop Biodiversity

Author : Nikolay Vassilev
Publisher : Frontiers Media SA
ISBN 13 : 2889712788
Total Pages : 442 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Plant Root Interaction With Associated Microbiomes to Improve Plant Resiliency and Crop Biodiversity by : Nikolay Vassilev

Download or read book Plant Root Interaction With Associated Microbiomes to Improve Plant Resiliency and Crop Biodiversity written by Nikolay Vassilev and published by Frontiers Media SA. This book was released on 2021-09-10 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Nucleic Acids and Proteins in Soil

Author : Paolo Nannipieri
Publisher : Springer Science & Business Media
ISBN 13 : 354029449X
Total Pages : 468 pages
Book Rating : 4.5/5 (42 download)

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Book Synopsis Nucleic Acids and Proteins in Soil by : Paolo Nannipieri

Download or read book Nucleic Acids and Proteins in Soil written by Paolo Nannipieri and published by Springer Science & Business Media. This book was released on 2006-09-22 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: With millions of different bacterial species living in soil, the microbial community is extremely complex, varying at very small scales. Microbe-driven functions are essential for most processes in soil. Thus, a better understanding of this microbial diversity will be invaluable for the management of the various soil functions. Nucleic Acids and Proteins in Soil combines traditional approaches in soil microbiology and biochemistry with the latest techniques in molecular microbial ecology. Included are methods to analyse the presence and importance of nucleic acids and proteins both inside and outside microbial cells, the horizontal gene transfer which drives bacterial diversity, as well as soil proteomes. Further chapters describe techniques such as PCR, fingerprinting, the challenging use of gene arrays for structural and functional analysis, stable isotope probing to identify in situ metabolic functions, and the use of marker and reporter genes in soil microbial ecology.

Standard Soil Methods for Long-Term Ecological Research

Author : G. Philip Robertson
Publisher : Oxford University Press
ISBN 13 : 0198028261
Total Pages : 481 pages
Book Rating : 4.1/5 (98 download)

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Book Synopsis Standard Soil Methods for Long-Term Ecological Research by : G. Philip Robertson

Download or read book Standard Soil Methods for Long-Term Ecological Research written by G. Philip Robertson and published by Oxford University Press. This book was released on 1999-10-28 with total page 481 pages. Available in PDF, EPUB and Kindle. Book excerpt: Standardized methods and measurements are crucial for ecological research, particularly in long-term ecological studies where the projects are by nature collaborative and where it can be difficult to distinguish signs of environmental change from the effects of differing methodologies. This second volume in the Long-Term Ecological Research (LTER) Network Series addresses these issues directly by providing a comprehensive standardized set of protocols for measuring soil properties. The goal of the volume is to facilitate cross-site synthesis and evaluation of ecosystem processes. Chapters cover methods for studying physical and chemical properties of soils, soil biological properties, and soil organisms, and they include work from many leaders in the field. The book is the first broadly based compendium of standardized soil measurement methods and will be an invaluable resource for ecologists, agronomists, and soil scientists.

Molecular Approaches to Soil, Rhizosphere and Plant Microorganism Analysis

Author : John Eric Cooper
Publisher : CABI
ISBN 13 : 1845931831
Total Pages : 309 pages
Book Rating : 4.8/5 (459 download)

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Book Synopsis Molecular Approaches to Soil, Rhizosphere and Plant Microorganism Analysis by : John Eric Cooper

Download or read book Molecular Approaches to Soil, Rhizosphere and Plant Microorganism Analysis written by John Eric Cooper and published by CABI. This book was released on 2006 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants have evolved both general and highly specialized defence mechanisms that function to prevent diseases caused by the majority of microbial pathogens they encounter. Highly specialized defence is governed by specific interactions between pathogen avr (avirulence) genes' loci and alleles of the corresponding plant disease resistance (R) loci. These defences can be very dynamic as microbes from the same species can act differently in their co-evolution with the specific host plant, which in turn has similarly evolved its response to external threats. There have been major developments in the field of plant-microbe interactions in recent years, due to newly developed techniques and the availability of genomic information. Molecular Plant-Microbe Interactions explores these new discoveries, focusing primarily on the mechanisms controlling plant disease resistance, the cross-talk among the pathways involved and the strategies used by the pathogens to suppress these defences. By exploring developments in plant defences, pathogen's counter-defences and mutually beneficial plant-microbe interactions, this book will be useful for researchers and students in plant pathology and plant biology-related areas.

Microorganisms as Indicators of Soil Health

Author : Mette Neiendam Nielsen
Publisher :
ISBN 13 : 9788777726583
Total Pages : 82 pages
Book Rating : 4.7/5 (265 download)

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Book Synopsis Microorganisms as Indicators of Soil Health by : Mette Neiendam Nielsen

Download or read book Microorganisms as Indicators of Soil Health written by Mette Neiendam Nielsen and published by . This book was released on 2002 with total page 82 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Bacterial Community Structure in Soils of the Oldest Agronomic Experiment Fields in the United States, the Morrow Plots, and of the Original Tallgrass Prairie

Download Bacterial Community Structure in Soils of the Oldest Agronomic Experiment Fields in the United States, the Morrow Plots, and of the Original Tallgrass Prairie PDF Online Free

Author : Abiramasundari Ganesan
Publisher :
ISBN 13 :
Total Pages : 94 pages
Book Rating : 4.:/5 (112 download)

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Book Synopsis Bacterial Community Structure in Soils of the Oldest Agronomic Experiment Fields in the United States, the Morrow Plots, and of the Original Tallgrass Prairie by : Abiramasundari Ganesan

Download or read book Bacterial Community Structure in Soils of the Oldest Agronomic Experiment Fields in the United States, the Morrow Plots, and of the Original Tallgrass Prairie written by Abiramasundari Ganesan and published by . This book was released on 2019 with total page 94 pages. Available in PDF, EPUB and Kindle. Book excerpt: Diversity of soil microbial communities and their influence on plants growth are widely studied to develop and improve sustainable agricultural practices. Soil-microbe interactions are very complex to interpret given that it involves other biotic and abiotic environmental factors, and the traditional culture-based methods followed by physicochemical analysis are either extremely laborious or not robust enough to investigate the broad picture and intricate details of these complex interactions. The use of molecular technologies like qPCR has resolved some of the shortcomings of culture-based methods, but still exhibited biases in both qualitative and quantitative analyses of microbial communities. New molecular techniques that focus on high throughput DNA sequencing techniques such as 454 pyrosequencing and the MiSeq sequencing platforms revolutionized the field of microbial diversity studies. These techniques are widely used in projects such as the Earth Microbiome Project (EMP), a collective attempt to establish microbial fingerprints in different environments of the planet. Additional applications include studies on long-term effects of crop rotation and different fertilization regimen on bacterial community structure. We tried to build on these studies and assess microbial community structure in the Morrow Plots, the oldest agronomic experimental fields in the United States, and adjacent tallgrass prairie with emphasis on members of the genus Frankia. The Morrow Plots were established in 1876 on tallgrass prairie soils to evaluate the effects of different cropping systems and soil treatments on crop yields, and include the oldest continuous corn plots in the world. Illumina-based l 6S rRNA V3 gene amplicon sequencing retrieved a total of 26.4 7 M effective sequences obtained from 44 samples, i.e. 12 soils with different vegetation and fertilization regimen, and 3 to 6 replicates per soil, with 313,695 to 906,328 reads per sample. At a sequencing depth of 300,000 sequences for each sample, Acidobacteria, Actinobacteria, Proteobacteria and Verrumicrobia were the most abundant bacterial phyla present across all soil samples accounting for 74±4% of the reads. Crop rotation increased diversity of the bacterial community, which was also affected by the fertilization regimen. Reads representing frankiae accounted for 0.1 to 1.0% of all reads, with generally higher percentages in fertilized soils. Reads represented frankiae of clusters la, 2, 3, and 4, but also a group of frankiae that could not reliably be assigned to a cultured relative. The results provide evidence of long-term establishment of Frankia populations in agricultural soils under different management conditions.

Evaluation of Corn-based and Perennial Bioenergy Cropping Systems

Author : Laura A. Lipps
Publisher :
ISBN 13 :
Total Pages : 132 pages
Book Rating : 4.:/5 (688 download)

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Book Synopsis Evaluation of Corn-based and Perennial Bioenergy Cropping Systems by : Laura A. Lipps

Download or read book Evaluation of Corn-based and Perennial Bioenergy Cropping Systems written by Laura A. Lipps and published by . This book was released on 2010 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Soil Microbial Community, Soil Aggregation and Cropping System

Author : Sabine Caniquitte
Publisher :
ISBN 13 :
Total Pages : 124 pages
Book Rating : 4.:/5 (316 download)

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Book Synopsis Soil Microbial Community, Soil Aggregation and Cropping System by : Sabine Caniquitte

Download or read book Soil Microbial Community, Soil Aggregation and Cropping System written by Sabine Caniquitte and published by . This book was released on 2008 with total page 124 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Impacts of Cropping Systems on Soil Health and Microbial Ecology

Author : Korbla Edwin Akley
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (919 download)

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Book Synopsis Impacts of Cropping Systems on Soil Health and Microbial Ecology by : Korbla Edwin Akley

Download or read book Impacts of Cropping Systems on Soil Health and Microbial Ecology written by Korbla Edwin Akley and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Declining soil health is the underlying cause of decreasing agricultural productivity and environmental degradation. To address this challenge, research was conducted to determine how: (1) cover crops affect soil health in Kansas, USA and (2) direct seeding mulch-based cropping (DMC) systems affect soil health in Nyankpala, Ghana. Soil health indicators assessed include: biomass yield (kg ha−1), soil microbial respiration (SMR), soil microbial C and N (MBC & MBN), potentially mineralizable N (PMN), dissolved organic carbon (DOC), soil organic C (SOC), soil total nitrogen (TN), phospholipid fatty acid analysis (PLFA), water stable aggregate (WSA), bulk density, pH, N, P, K, Ca and Mg. DMC systems from Ghana yielded significantly greater biomass compared to the control. High biomass produced by DMC systems did not increase SOC and PMN relative to the control. Fertilizer application had a significant impact on biomass production, which resulted in a significant increase in SOC and PMN in the 0-5 cm soil layer. Soil pH was significantly reduced by cropping systems and fertilizer in the 0-5 cm soil layer. Microbial biomass N, TN, SMR, N, P, Ca and Mg were not affected by the DMC cropping systems. Application of mineral fertilizer increased SMR, MBN, TN, N, and P. Soil K was also significantly affected by cropping systems and mineral fertilizer. The combination of mineral fertilizer and plant residues would be needed to improve soil health and increase crop productivity in the Guinea Savanna Zone of Ghana. Liming would be required to address low soil pH. In the USA, of all the soil health indicators examined, actinomycetes, gram-positive bacteria, fungi-bacteria ratio (F:B), SMR, MBN and WSA, were those significantly influenced by cover crops. The interactive effect of cover cops and N fertilizer also affected gram-positive bacteria, total PLFA, MBN, F:B ratio and WSA. Cover crop residues contributed to the observed differences in these indicators. The low response of soil health indicators suggest further evaluations are needed to determine the effectiveness of the indicators.

Soil Microbial Dynamics and Nitrogen Availability in Organic, Low Input and Conventional Cropping Systems

Author : Nirmala Gunapala
Publisher :
ISBN 13 :
Total Pages : 422 pages
Book Rating : 4.:/5 (54 download)

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Book Synopsis Soil Microbial Dynamics and Nitrogen Availability in Organic, Low Input and Conventional Cropping Systems by : Nirmala Gunapala

Download or read book Soil Microbial Dynamics and Nitrogen Availability in Organic, Low Input and Conventional Cropping Systems written by Nirmala Gunapala and published by . This book was released on 1994 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt:

The Importance of Soil Organic Matter

Author : Alexandra Bot
Publisher : Food & Agriculture Org.
ISBN 13 : 9789251053669
Total Pages : 96 pages
Book Rating : 4.0/5 (536 download)

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Book Synopsis The Importance of Soil Organic Matter by : Alexandra Bot

Download or read book The Importance of Soil Organic Matter written by Alexandra Bot and published by Food & Agriculture Org.. This book was released on 2005 with total page 96 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soil organic matter - the product of on-site biological decomposition - affects the chemical and physical properties of the soil and its overall health. Its composition and breakdown rate affect: the soil structure and porosity; the water infiltration rate and moisture holding capacity of soils; the diversity and biological activity of soil organisms; and plant nutrient availability. This document concentrates on the organic matter dynamics of cropping soils and discusses the circumstances that deplete organic matter and their negative outcomes. It then moves on to more proactive solutions. It reviews a "basket" of practices in order to show how they can increase organic matter content and discusses the land and cropping benefits that then accrue.--Publisher's description.

Linking Soil Microbiology and Environmental Conditions to Variability in Nitrous Oxide Production in Bioenergy Cropping Systems

Author : David Sean Duncan
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (969 download)

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Book Synopsis Linking Soil Microbiology and Environmental Conditions to Variability in Nitrous Oxide Production in Bioenergy Cropping Systems by : David Sean Duncan

Download or read book Linking Soil Microbiology and Environmental Conditions to Variability in Nitrous Oxide Production in Bioenergy Cropping Systems written by David Sean Duncan and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Agroecosystems may differ in multiple ecosystem properties, among them nitrous oxide (N2O) production and soil microbial community composition. We hypothesized that perenniality, plant species richness, and exogenous nitrogen inputs all influence N2O production directly through regulation of substrate concentrations and other environmental conditions and indirectly through changes to soil microbial functional characteristics. We studied the interplay among cropping systems, microbial communities, and N2O production in the context of an agronomic trial of potential bioenergy feedstock cropping systems. We measured N2O production from 2009-2014 and collected accompanying data on soil temperature, water-filled pore space, and inorganic nitrogen concentrations. Individual N2O fluxes and aggregate annual N2O emissions were lower in perennial systems relative to annual ones, but were not consistently influenced by plant species richness in perennial systems. Environmental variables defined upper limits for N2O fluxes, but did little to explain cropping system effects or their lack. We explored microbial community differences between continuous corn and prairie systems using membrane lipid profiling, amplicon sequencing, and functional gene annotations from shotgun metagenomic sequencing. The strength of cropping system effects differed among methods, with the strongest effects observed in lipid profiles. We used elastic net modeling to correlate community profiles to aggregate N2O emissions. Only the corn system could be effectively modeled, with the best models created from 16S rRNA amplicons and functional gene abundances. We used bacterial functional gene abundance profiles to characterize microbial communities across a broader range of cropping systems. The strength of cropping system effects varied among site years. Ecological factors such as perenniality and species diversity did not determine abundance patterns for either the full set of genes explored or for groups of genes with similar functions. Similarly, individual denitrification pathway genes did not systematically differ among cropping systems. Cropping system effects on N2O production and functional gene abundances were weaker than anticipated. Despite this, elastic net modeling linked gene abundance patterns to variation in N2O emissions with considerable accuracy. This indicates that within-cropping system variability in N2O production and functional genes are in some way connected.