managing soil microbial communities with organic amendments to promote soil aggregate

181 Pages·2017·0.84 MB·English

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Theses and Dissertations--Plant and Soil
Plant and Soil Sciences
Sciences
2013
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Shawn T. Lucas
University of Kentucky, [email protected]
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Lucas, Shawn T., "MANAGING SOIL MICROBIAL COMMUNITIES WITH ORGANIC AMENDMENTS TO
PROMOTE SOIL AGGREGATE FORMATION AND PLANT HEALTH" (2013). Theses and Dissertations--Plant
and Soil Sciences. 24.
https://uknowledge.uky.edu/pss_etds/24
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The document mentioned above has been reviewed and accepted by the student’s advisor, on
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Shawn T. Lucas, Student
Dr. Elisa M. D'Angelo, Major Professor
Dr. Mark S. Coyne, Director of Graduate Studies
MANAGING SOIL MICROBIAL COMMUNITIES WITH ORGANIC
AMENDMENTS TO PROMOTE SOIL AGGREGATE FORMATION AND PLANT
HEALTH

_________________________________

DISSERTATION
_________________________________

A dissertation submitted in partial fulfillment of the
requirements for the degree of Doctor of Philosophy in the
College of Agriculture
at the University of Kentucky

By
Shawn T. H. Lucas

Lexington, KY

Co-Directors: Dr. Elisa M. D’Angelo, Professor of Soil Science
and Dr. Mark A. Williams, Professor of Horticulture

Lexington, Kentucky

Copyright © Shawn T.H. Lucas 2013
ABSTRACT OF DISSERTATION

MANAGING SOIL MICROBIAL COMMUNITIES WITH ORGANIC
AMENDMENTS TO PROMOTE SOIL AGGREGATE FORMATION AND PLANT
HEALTH

The effects of managing soil with organic amendments were examined with
respect to soil microbial community dynamics, macroaggregate formation, and plant
physio-genetic responses. The objective was to examine the possibility of managing soil
microbial communities via soil management, such that the microbial community would
provide agronomic benefits. In part one of this research, effects of three amendments
(hairy vetch residue, manure, compost) on soil chemical and microbial properties were
examined relative to formation of large macroaggregates in three different soils. Vetch
and manure promoted fungal proliferation (measured via two biomarkers: fatty acid
methyl ester 18:2ω6c and ergosterol) and also stimulated the greatest macroaggregate
formation. In part two of this research, effects of soil management (same amendments as
above, inorganic N fertilization, organic production) on soil chemical and microbial
properties were examined relative to the expression of nitrogen assimilation and defense
response genes in tomato (Solanum lycopersicum L.). Soil management affected
expression of a nitrogen assimilation gene (GS1, glutamine synthetase) and several
defense-related genes. The GS1 gene was downregulated with inorganic N fertilization,
expression of the pathogenesis-related PR1b gene (which codes for the pathogenesis-
related PR1b protein) was increased in plants grown in soil amended with compost,
vetch, and N fertilizer, and expression of three other defense-related genes coding for
chitinase (ChiB), osmotin (Osm), and β-1,3-glucanase (GluA) were decreased in plants
from soil amended with manure and in plants from the organically managed soil.
Differential expression of defense-related genes was inversely related to the relative
abundance of Gram-negative bacteria. The relative abundance of the 18:1ω7c
Gram-negative bacterial biomarker was greatest in manure treated soil and in organically
managed soil (which recieves seasonal manure applications). These treatments also had
the lowest expression of ChiB, Osm, and GluA, leading to speculation that manure,
through increases in Gram-negative bacteria, may have suppressed populations of soil
organisms that induce a defense response in plants, possibly allowing for less-stressed
plants. Outcomes of this research may be useful for those interested in developing
management strategies for maintaining or improving soil structure as well as those
interested in understanding management effects plant physio-genetic responses.

KEYWORDS: Soil management, Organic amendments, Soil microbial community, Soil
structure, Plant gene expression

Shawn T.H. Lucas
__________________________________________
Student’s Signature

May 30, 2013
__________________________________________
Date
MANAGING SOIL MICROBIAL COMMUNITIES WITH ORGANIC
AMENDMENTS TO PROMOTE SOIL AGGREGATE FORMATION AND PLANT
HEALTH

By

Shawn T. H. Lucas

Dr. Elisa M. D’Angelo
__________________________________________
Co-Director of Dissertation

Dr. Mark A. Williams
__________________________________________
Co-Director of Dissertation

Dr. Mark S. Coyne
__________________________________________
Director of Graduate Studies

May 30, 2013
__________________________________________
Date
Dedicated to my wonderful wife Jessica Breen Hays Lucas, and my sons Eli and Jonah,
for (sometimes begrudgingly, but always lovingly) supporting and sustaining me through
the course of this work.
ACKNOWLEDGEMENTS
Through my time at the University of Kentucky, the list of people who I need to thank
has continually grown. In particular I would like to thank the people acknowledged in
this section. Without their help this project would not have been successful. I would like
to give my utmost thanks my Co-Advisors: Dr. Elisa M. D’Angelo and Dr. Mark A.
Williams for their invaluable mentoring and support through the course of this research
and for the opportunity to work and learn with them. I would like to thank my committee
members: Dr. Mary Arthur, Dr. Seth DeBolt, and Dr. David McNear for their sharing
their advice, assistance, lab space, and time. I also appreciate the service of Dr. Larry
Grabau on an earlier iteration of my committee. Olga Tsyusko, Rick Lewis, and Dr.
Mohammad Babar Ali provided helpful advice in learning the intricacies of qPCR.
Georgia Zeigler and Joe Kupper provided technical assistance and moral support. Julie
Beale helped with microscopy of fungi. Dr. Mark Coyne and Dr. John Grove were
invaluable for sharing their expertise in navigating the rules and regulations of the
graduate program, as well as their advice as it pertained to this project. Dr. Richard Dick
and Nicola Lorenz of The Ohio State University provided initial training in the fatty acid
methyl ester method. Fred Brown of Irvine, KY provided the Yeager soil used in this
research. This research was partially supported by a grant (GS08-065) from the USDA
Sustainable Agriculture Research and Education program. Finally, I would like to thank
the Department of Horticulture and The Department of Plant and Soil Science for
support.

vi
TABLE OF CONTENTS

Acknowledgements ……………………………………………………………… vi
List of Tables ……………………………………………………………… x
List of Figures ……………………………………………………………… xi

Chapter 1: A Review of Literature on Soil Management, Soil Microbial
Communities, Soil Structure, and Plant Physio-Genetic
Responses………………………………………………….... 1
Introduction………………………………………….. 1
The Soil Microbial Community……………………... 2
Soil Aggregation: Interaction between Soil Organic
Matter and Soil Microoganisms……………………... 4
Soil Microbial-Plant Interactions to Promote Plant
Health………………………………………………... 8
Managing the Soil Microbial Community with
Organic Amendments……………………...……….... 11
Can the Microbial Community be managed to
Promote Beneficial Agronomic Outcomes?……....…. 13

Chapter 2: Improving Soil Structure by Promoting Fungal Abundance
with Organic Soil Amendments.............................................. 15
Introduction.................................................................. 15
Materials and Methods................................................. 19
Soil Collection and Processing............................ 19
Soil Incubation Experiment.................................. 20
Size Distribution of Water Stable Aggregates...... 22
Fatty Acid Methyl Ester Extraction and
Quantification...................................................... 22
Ergosterol Extraction and Quantification........... 25
Statistics............................................................... 26
Results.......................................................................... 27
Effects of Organic Amendments on Soil
Properties............................................................. 27
Effects of Organic Amendments on Formation of
Large Macroaggregates....................................... 27
Effects of Organic Amendments on Soil
Microbial Communities........................................ 28
Discussion.................................................................... 31
Effects of Organic Amendments on Soil
Chemical Properties............................................ 31
Effects of Organic Amendments on Soil
Microbial Communities........................................ 33
Effects of Organic Amendments on Formation of
Large Macroaggregates....................................... 35

vii
Relationships Between Macroaggregate
Formation and Microbial Community Structure. 38
Conclusions.................................................................. 40
Tables........................................................................... 42
Figures.......................................................................... 45

Chapter 3: Can Soil Management-induced Differential Gene
Expression in Tomato (Solanum lycopersicum L.) be Linked
to Management-driven Shifts in the Soil Microbial
Community?............................................................................ 49
Introduction.................................................................. 49
Materials and Methods................................................. 52
Soil Collection and Treatment Preparation......... 52
Collection and Processing of Experimental
Plant and Soil Samples........................................ 55
Chemical analysis of soils, amendments, and
plants.................................................................... 55
Fatty Acid Methyl Ester Extraction and
Quantification...................................................... 57
Ergosterol Extraction and Quantification........... 58
Gene Expression Analysis of Tomato Plants....... 59
Statistics............................................................... 62
Results.......................................................................... 63
Effects of Soil Management on Soil
Properties............ 63
Effects of Soil Management on Soil Microbial
Communities......................................................... 64
Effects of Soil Management on Tomato Plant
Characteristics..................................................... 66
Effects of Soil Management on Tomato Gene
Expression............................................................ 67
Discussion.................................................................... 68
Effects of Soil Management on Soil Properties
and Plant Characteristics.................................... 68
Effects of Soil Management on Soil Microbial
Communities......................................................... 72
Effects of Soil Management on Expression of
Selected Tomato Genes........................................ 80
Relationships Between Tomato Gene Expression
and Plant, Soil, and Microbial Characteristics... 88
Conclusions.................................................................. 93
Tables........................................................................... 95
Figures.......................................................................... 101

Chapter 4 Conclusions, Implications, and Future Directions.................. 105
Research Findings and Implications............................ 105
viii