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The handle http://hdl.handle.net/1887/37037 holds various files of this Leiden University
dissertation
Author: Lupatini, Manoeli
Title: Microbial communities in Pampa soils : impact of land-use changes, soil type
and climatic conditions
Issue Date: 2015-12-15
Acknowledgments
My PhD was an unforgettable time in my life. Many people have contributed to
make this journey wonderful and pleasant.
First of all, I would like to thank all people in the group “Environmental
biology and microbiology Prof. Marcos R. Fries” at Federal University of Santa
Maria. All bachelor, graduate students and professors contributed in some way
to the research described in this thesis. In particular, the field work was only
possible by the support provided by this group. Also, I would like to thank the
“Center for Interdisciplinary Research in Biotechnology ­ CIP­Biotec” at
Federal University of Pampa (UNIPAMPA), where I conducted the molecular
analyses of the soil microbiome and where I developed the skills to work with
bioinformatic tools. As important as the first groups, I would like to thank the
Microbial Ecology department and in particular the Kuramae research group
at Netherlands Institute of Ecology, NIOO­KNAW, in which I could improve
my knowledge of bioinformatics and statistical analysis. Being part of this
group was an immense pleasure!
Not only as colleagues, but also for their great friendship, I would like to thank
Afnan Suleiman and Alessandro Rosa. In different periods of my PhD, you
were very important to help me keep moving. Thank you, Afnan, since the
beginning of my PhD we have worked together in a fantastic way. Thank you,
Alessandro, by destiny or a strange coincidence, after completing the bachelor
and the master together in Brazil, we ended up sharing the same house in The
Netherlands during the PhD period there. So, we continued our philosophical
chats about all aspects of science which started years earlier. It was a pleasure
sharing the last year with such promising scientist!
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I am thankful to receive so much input in my studies from Luiz FW Roesch and
Rodrigo JS Jacques, especially for the great support, understanding and
patience in teaching me and discussing topics related with the studies
presented here. Also, immense thanks to LFW Roesch for the valuables
discussions on how to turn a pile of data into something scientifically relevant
and useful for the well­being of society.
With great pleasure I would like to express my sincere gratitude to all people
at NIOO during the the last year of my PhD. Mainly, I would like to thank to
Viviane, Ruth, Juan, Matheus, Julia, Paolo, Johnny, Olaf and Yin Yin, for the
work discussion, nice chats and a lot of coffee. Special thanks go to Victor
Carrion who supported me during all of my time at NIOO, with valuable
discussions about science, patience during the laboratory work and for a great
time outside of work. Thank you, Mattias and Norico, for being nice and patient
colleagues, and for your help and valuable discussions about bioinformatic and
statistical analysis. I specially acknowledge my family, my parents and sister for all the support.
Sometimes it was not easy to bridge the distance, but all your unconditional
love and encouragement made me a stronger person to overcome the hard
times.
If I did not mention someone here, it does not mean that I do not acknowledge
the help. This journey is almost finished. Good, bad or whatever, now, it is time
to look ahead and move forward.
Manoeli Lupatini
2015.12
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Curriculum vitae
Manoeli Lupatini was born on 30th of June1985 in Espumoso, Rio Grande do
Sul, Brazil. In 2002, she finished her secondary education at “Instituto
Estadual de Educação Dr. Ruy Piégas Silveira”, in Espumoso. In 2004, she
started the Bachelor in Agronomy at Federal University of Santa Maria, Santa
Maria, Brazil. On the first year of bachelor, after showing interest in two main
research topics, Soil Science and Microbial Ecology, she started an
undergraduate project studying the mycorrhizal fungi and the association with
plant community under the supervision of Dr. Z. I. Antoniolli. In her secondary
project, in the same laboratory, she performed research studying the potential
of microorganisms isolated from soil and rhizosphere to promote the plant
growth. In 2012, she continued with her MSc study in Soil Science at Federal
University of Santa Maria. For her masters thesis, she did research on soil
microbial ecology based on advanced molecular techniques using bioinformatic
tools and statistical approaches under the supervision of Dr. R.J.S. Jacques
and Dr. L.F.W. Roesch. For this work, she received a grant from "Coordenação
de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)". In 2012, she
started her PhD project "Microbiome dynamics in Pampa soils" described in
this thesis in collaboration with Federal University of Santa Maria, Federal
University of Pampa and Netherlands Institute of Ecology (NIOO/KNAW)
under the supervision of J.A. van Veen and Dr. E. Kuramae.
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Publications
Lupatini, M.; Suleiman, A. K. A.; Jacques, R. J. S.; Antoniolli, Z. I.; de
Siqueira Ferreira, A.; Kuramae, E. E. and Roesch, L. F. W. (2014). Network
topology reveals high connectance levels and few key microbial genera within
soils, Frontiers in Environmental Science 2:1­10.
Lupatini, M.; Suleiman, A. K. A.; Jacques, R. J. S.; Antoniolli, Z. I.; Kuramae,
E. E.; de Oliveira Camargo, F. A. and Roesch, L. F. W. (2013). Soil­borne
bacterial structure and diversity does not reflect community activity in Pampa
biome, PLoS ONE 8:e76465.
Suleiman, A. K. A.; Manoeli, L.; Boldo, J. T.; Pereira, M. G. and Roesch, L. F.
W. (2013). Shifts in soil bacterial community after eight years of land­use
change, Systematic and Applied Microbiology 36:137­144.
Lupatini, M.; Jacques, R. J. S.; Antoniolli, Z. I.; Suleiman, A. K. A.; Fulthorpe,
R. R. and Roesch, L. F. W. (2013). Land­use change and soil type are drivers of
fungal and archaeal communities in the Pampa biome, World Journal of
Microbiology and Biotechnology 29:223­233.
Silva, R.; Lupatini, M.; Trindade, L.; Antoniolli, Z.; Steffen, R. and Andreazza,
R. (2013). Copper resistance of different ectomycorrhizal fungi such as
Pisolithus microcarpus, Pisolithus sp., Scleroderma sp. and Suillus sp.,
Brazilian Journal of Microbiology 44:619­627.
Milanesi, P. M.; Blume, E.; Muniz, M. Fá. B.; Reiniger, L. R. S.; Antoniolli, Z. I.;
Junges, E. and Lupatini, M. (2013). Detecção de Fusarium spp. e Trichoderma
spp. e antagonismo de Trichoderma sp. em soja sob plantio direto, Semina:
Ciências Agrárias 34:3219­3234.
Poletto, I.; Lupatini, M.; Muniz, M. Fá. B. and Antoniolli, Z. I. (2012).
Caracterização e patogenicidade de isolados de Fusarium spp. causadores de
podridão­de­raízes da erva­mate, Floresta 42:95­104.
Redin, M.; dos Santos, G. d. F.; Miguel, P.; Denega, G. L.; Lupatini, M.;
Doneda, A. and de Souza, E. L. (2011). Impactos da queima sobre atributos
quimicos, fisicos e biológicos do solo, Ciência Florestal 21:381­392.
Stroschein, M. R. D.; Eltz, F. L. F.; Antoniolli, Z. I.; Lupatini, M.; Vargas, L.
K.; Giongo, A. and Pontelli, M. P. (2010). Symbiotic efficiency and genetic
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characteristics of Bradyrhizobium sp. strain UFSM LA 1.3 isolated from
Lupinus albescens (H. et Arn), Scientia Agricola 67:702­706.
Silva, R. F. d.; Lupatini, M.; Antoniolli, Z. I.; Leal, L. T. and Moro Junior, C.
A. (2011). Comportamento de Peltophorum dubium (Spreng.) Taub.,
Parapiptadenia rigida (Benth.) Brenan e Enterolobium contortisiliquum (Vell.)
Morong cultivadas em solo contaminado com cobre, Ciência Florestal 21:103­
110.
da Silva, R. F.; Antoniolli, Z. I.; Lupatini, M. and Trindade, L. L. (2011).
Ectomicorrização em quatro espécies florestais nativas do Rio Grande do Sul e
sua eficiência em solo contaminado por cobre, Ciência e Natura 33:95­109.
Antoniolli, Z. I.; Santos, Li. C. d.; Lupatini, M.; Leal, L. T.; Schirmer, G. K.
and Redin, M. (2010). Efeito do cobre na população de bactérias e fungos do
solo, na associação micorrizica e no cultivo de mudas de Eucalyptus grandis W.
Hill ex Maiden, Pinus elliottii Engelm e Peltophorum dubium (Sprengel)
Taubert, Ciência Florestal 20:419­428.
Menezes, J. P.; Lupatini, M.; Antoniolli, Z. I.; Blume, E.; Junges, E. and
Manzoni, C. G. (2010). Variabilidade genética na região its do rDNA de
isolados de Trichoderma spp.(biocontrolador) e Fusarium oxysporum f. sp.
Chrysanthemi, Ciência agrotécnica, Lavras 34:132­139.
Silva, R. F. d.; Antoniolli, Z. I.; Lupatini, M.; Trindade, L. L. and Silva, A. S. d.
(2010). Tolerância de mudas de Canafístula (Peltophorum dubium (SPRENG)
TAUB.) inoculadas com Pisolithus microcarpus a solo com excesso de cobre,
Ciência Florestal 20:147­156.
Mello, A. H. d.; Antoniolli, Z. I.; Kaminski, J.; Souza, E. L. d.; Schirmer, G. K.;
Machado, R. G.; Lupatini, M. and Moro Júnior, C. (2009). Estabelecimento a
campo de mudas de Eucalyptus grandis micorrizadas com Pisolithus
microcarpus (UFSC Pt 116) em solo arenoso, Ciência Florestal 19:149­155.
Antoniolli, Z. I.; Casali, C. A.; Denega, G. L.; Lupatini, M.; Steffen, R. B.;
Pujol, S. B. and de Quadros, V. J. (2009). Fauna edáfica em sistemas de cultivo
de batata, soja, feijão e milho, Ciência e Natura 31:115­130.
Lupatini, M.; de Mello, A. H. and Antoniolli, Z. I. (2008). Caracterização do
DNA ribossômico do isolado de Scleroderma UFSMSc1 de Eucalyptus grandis
W. Hill ex­maiden, Revista Brasileira de Ciência do Solo 32:2677­2682.
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Lupatini, M.; Bonnassis, P.; Steffen, R.; Oliveira, V. and Antoniolli, Z. (2008).
Mycorrhizal morphotyping and molecular characterization of Chondrogaster
angustisporus Giachini, Castellano, Trappe & Oliveira, an ectomycorrhizal
fungus from Eucalyptus, Mycorrhiza 18:437­442.
Steffen, R. B.; Antoniolli, Z. I.; Bosenbecker, V. K.; Steffen, G. P.; Lupatini,
M.; Campos, A. and Gomes, Cé. B. (2008). Avaliação de óleos essenciais de
plantas medicinais no controle de Meloidogyne graminicola em arroz irrigado,
Nematologia Brasileira 32:126­134.
Steffen, R. B.; Antoniolli, Z. I.; Kist, G. P.; Lupatini, M. and Gomes, Cé. B.
(2007). Caracterização bioquimica do nematóide das galhas (Meloidogyne spp.)
em lavouras de arroz irrigado na região central do Rio Grande do Sul, Ciência e
Natura 29:37­46.
dos Santos, Li. C.; Antoniolli, Z. I.; Leal, L. T. and Lupatini, M. (2007).
População de bactérias e fungos no solo contaminado com cobre nas minas de
camaquã, Ciência e Natura 29:105­114.
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