Soil microbial diversity across different agroecological zones in New South Wales

332 Pages·2017·37.08 MB·English

Soil microbial diversity across
different agroecological zones in
New South Wales

Vanessa Pino V.

Faculty of Agriculture and Environment
The University of Sydney
New South Wales, Australia

A thesis submitted in partial fulfillment of the requirements for the degree of
Doctor of Philosophy

Pino, V. 2016. Soil Microbial Diversity Across Different Agroecological Zones in New South Wales.

A synergistic relationship between soil diversity (pedodiversity) and soil microbial diversity
(biodiversity) seems axiomatic. Soil microbial communities regulate the essentials
biogeochemical cycles (e.g. N and C cycles) on which rely the functioning and services of soil
ecosystems (e.g. food production, C storage). On its own, the soil matrix provides and regulates
living conditions by which these microbial communities are structured and functional.
Nonetheless, the multi-dimensionality of this pedodiversity-biodiversity relationship is still poorly
understood. A better insight into this synergy would enable us to quantify/qualify and so sustain,
protect, and hopefully improve, those processes underpinning soil functioning (e.g. promote N-
fixation and C sequestration). From a soil scientific perspective, we hypothesise that the
structural and functional extent of soil microbial communities relies on multivariate soil units
(e.g. soil horizons, profiles, classes) instead of any single discrete ‘environmental factor’ (e.g. soil
pH, precipitation) and; vice-versa, the structure of these communities can become a well-defined
biological property of these soil entities. We began exploring the multidimensional disposition
of this biotic-abiotic functioning by modeling the biogeographical patterns of soil microbial
communities - richness and diversity - using biomolecular sequencing, pedometrics, and digital
mapping approaches.

As a first exploratory analysis, this particular thesis evaluated local diversity (α-diversity) of
bacteria, archaea and fungi communities using a latitudinal (NS ) and a longitudinal (WE )
-transect -transect
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Pino, V. 2016. Soil Microbial Diversity Across Different Agroecological Zones in New South Wales.
transect of about 900 km each across New South Wales (NSW), Australia. Along these transects,
soil ecosystems were sampled at 48 different locations from paired conserved (e.g. woodlands)
and disturbed (e.g. cropping) ecosystems. Afterward, soil biophysicochemical attributes were
estimated using 16SrDNA and ITS metabarcoding (11,557,499 sequences; 423,740 OTUs) and
pedometric approaches (19 soil properties; 13 environmental covariates).

The microbial structural patterns, abundance and local diversity (α-diversity), were assessed in
relation to the soil physicochemical properties using both linear and quadratic associations and
other multivariate analysis (e.g. PCA, bootstrap regression modelling and, mapping). This
enabled the spatial prediction and mapping of the three microbial kingdoms at a resolution of
1#km across all of NSW. Our maps showed soil microbial diversity, richness, and abundance
following a combination of soil and environmental attributes in which western NSW has of
higher diversity compared with eastern NSW. Despite this gradient, fungi and archaea were
consistently lower and higher in Vertosols (Australian Soil Classification System), respectively,
whereas the distribution of bacteria is less clear. Our results suggest that the structure of
microbial communities is intimately related with most physicochemical soil attributes but this
association, whether linear or not, varies not only upon one single soil properties but a group of
them. At the same time, the extent and direction of these relations vary accordingly the different
microbial taxa (e.g. by phylum). Therefore, microbial diversities are more consistent with
grouped features defining soil entities (e.g. horizons and profiles classes) rather than on
individual soil attributes. Our further work will include more evidence for these conclusions by
analysing microbial and pedological dissimilarities (e.g. β-diversity) in a multiscale approach.
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Pino, V. 2016. Soil Microbial Diversity Across Different Agroecological Zones in New South Wales.

“Mapu mew iñchiñ ta ngen-ngenkülelaiñ,
iñchiñ may ta mapu ngeiñ” (mapundungun)

La tierra no es nuestra.
Nosotros somos de la tierra
(proverbio mapuche).

There are two immediate thoughts that come to mind after completing this Ph.D. dissertation.
First, that the magical world beneath our feet never ceases to impress me and it seems, after all
this hard work, I must sincerely be in love with. My second appreciation is that, more than ever
before, I know how much I do not know that still challenges my curiosity – which I think is a very
valuable motivation for a scientist.

At the end of this journey, I would like to express my sincere gratitude to my supervisor Alex
McBratney for his guidance but mostly for having given me, since the start, the freedom to decide
to work on soil biology and then the confidence for letting me be a part of such a beautiful project.
Many thanks to Neil Wilson and Rosalind Deaker for their co-supervision and initiation into soil
microbiology and molecular techniques. Thanks Neil for your confidence on my laboratory skills.
I also would like to thank all my friends, colleagues and technical stuff that gave a bit of their
time to help me when carrying out fieldtrips, laboratory work, data analysis or simply those fun
Fridays sharing some beers. Uta, Kanika, Yolima, Phil, Lori, Ivan, Stacey, Liana, Ed, Patito,
Claudia, Damien & Poppy, Budi, Jay, Olivier, Jessica, Mirja, Kasia, and many more.

Many thanks to my Australian family and loved ones that brought laughter, love and fun to my
days away from my Chile. Chalmers family (Flo, Paul, Sofi, Maryam, Jose, Clara), Sandrita & all
the CCFO dancers (I leap into heaven when dancing with you), Patito, Romi & The wonderland
home, and Claryto (que no alcanzaste a editar este pedacito de texto). A special thank you to
Mario Fajardo, we absolutely did this together, thanks for your unconditional friendship, love,
support and cafesongos every day.

Finally, I would like to dedicate this work to my family. To my dad, my mom and my Grandma,
Irene, Jose Luis and Normita, thanks for always encouraging me to be independent and strong;
to my siblings Muriel, Belen, Moises and Zaira, love you all. To my two big families; my many
uncles, aunties, cousins and nieces; and to my Chilean friends who are always looking after me;
childeltas, callejeras, las carmelas, georgies and others.

Muchas gracias a todos!
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Pino, V. 2016. Soil Microbial Diversity Across Different Agroecological Zones in New South Wales.
Summary  i 
Acknowledgements  iii 
Chapter 1  1 
Soil Biodiversity & Pedodiversity: Synergies and Parallels  1 
SYNERGIES AND PARALLELS OF SOIL BIODIVERSITY‐PEDODIVERSITY  3 
MODELLING MICROBIAL BIOGEOGRAPHICAL PATTERNS  16 
OVERVIEW OF BIOMOLECULAR SEQUENCING APPROACHES  20 
OVERVIEW OF SOIL MICROBIAL DIVERSITY METRICS  34 
Chapter 2  76 
Designing a Sampling Scheme for Microbial Diversity Analysis in New South Wales  76 
NEW SOUTH WALES IN THE CONTEXT OF THE AUSTRALIAN CONTINENT  79 
THE ENVIRONMENTS FACED BY SOIL MICROORGANISMS IN NSW  83 
DESIGNING THE TRANSECTS  121 
FIELDTRIPS AND SOIL SAMPLES COLLECTION  127 
ENVIRONMENTAL GRADIENT ALONG THE TRANSECTS  142 
Chapter 3  150 
Soil Microbial & Physicochemical Measurements  150 
INTRODUCING THE SOIL MICROBIAL AND PHYSICOCHEMICAL CHARACTERISATION  153 
SOIL MICROBIAL TAXONOMIC CHARACTERISATION  156 
SOIL PHYSICOCHEMICAL CHARACTERISATION  200 
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Pino, V. 2016. Soil Microbial Diversity Across Different Agroecological Zones in New South Wales.
Chapter 4  213 
Soil microbial α‐diversity across New South Wales  213 
MEASURING MICROBIAL DIVERSITY  216 
MODELLING AND MAPPING SOIL MICROBIAL DIVERSITY  276 
Chapter 5  303 
Conclusions & Future Work  303 
FINAL DISCUSSION  304 
FINAL CONCLUSIONS  315 
FUTURE WORK  316 
APPENDIX 1  317 
APPENDIX 2  318 
APPENDIX 3  322 
APPENDIX 4  324 

v

Soil Biodiversity &
Pedodiversity: Synergies and

Parallels
Outlines
Understanding the spatial soil biodiversity-pedodiversity relationship can provide useful information
when understanding soil microbial structural patterns in different environmental gradients. In this
research, this relation has been demonstrated by providing a robust and deep analysis of the soil
microbial structural diversity in relation to the soil physicochemical characteristics of a longitudinal and
latitudinal environmental gradient across NSW, Australia. This chapter provides the foundation for
this study, informing the relevance of soil microbial studies in the new era of modern microbiology and
pedometrics science.
Chapter1.Soil Biodiversity & Pedodiversity: Synergies and Parallels.
Summary
This chapter provides a general perspective on how this study contributes to characterizing soil
microbial communities (biodiversity) in the context of their soil environment (pedodiversity).
Apart from each other, soil microbial ecology and soil science have been recently realised
important advances in the study of soil biota and soil physicochemical properties but still these
disciplines did not converge their knowledge to a common and complete understanding.
Heretofore, soil scientists have developed modern approaches predicting the distribution of soils
around the globe as well as its physicochemical arrangements but barely taking into
consideration the soil biological components. On its own, ecologists have increased our concern
about soil microbiota putting a considerable effort these days on understanding their
structural/functional diversity and biogeographical patterns. We advise that soil heterogeneity
(pedodiversity) is already being predicted on a global scale on the basis of soil formation
factors/processes for which these pedological approaches might indeed define the spatial
patterns of soil microbial communities. This notion lies behind the framework for our aims and
the methodological advantages in this investigation.

In this chapter, we also examine the benefits of this new understanding. Indeed, the prediction
of soil microbial patterns in the entire context of their soil environment would able not only to
qualify but quantify their influence upon biogeochemical processes in the soil functioning (e.g.
for ensuring food production). Any advance towards the quantification of soil processes and
functioning enables its assessment for decision-making and regulatory policies for soil
protection (Soil Security).
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