UNIVERSIDADE ESTADUAL PAULISTA – UNESP  

JABOTICABAL CAMPUS 

 

 

 

 

 

 

 

 

 

 

CO2 EMISSION AND O2 UPTAKE OF SOIL UNDER DIFFERENT SYSTEMS 

 

 

 

 

Risely Ferraz de Almeida 

Agronomic Engineer 

 

 

 

 

 

 

 

 

 

 

 

 

2017 



UNIVERSIDADE ESTADUAL DE SÃO PAULO – UNESP  

JABOTICABAL CAMPUS 

 

 

 

 

 

 

 

 

 

CO2 EMISSION AND O2 UPTAKE OF SOIL UNDER DIFFERENT SYSTEMS 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  

 

 

 

2017 

Risely Ferraz de Almeida 

Advisor: Prof. Dr. Newton La Scala Júnior  

Thesis presented to the College of 

Agricultural and Veterinarian Sciences 

– UNESP, Jaboticabal Campus, as 

partial fulfillment of the requirements 

for the degree of Doctor in Soil 

Science 



 

 

 

 

 

 

 

 

  

Almeida, Risely Ferraz 

A447c CO2 Emission and O2 uptake of soil under different systems. – – 

Jaboticabal, 2017 

 ix, 56 p. : il. ; 29 cm 

  

 Tese (doutorado) - Universidade Estadual Paulista, Faculdade de 

Ciências Agrárias e Veterinárias, 2017 

 Orientador: Newton La Scala Júnior 

Banca examinadora: Liziane de Figueiredo Brito, Alan Rodrigo 

Panosso, Zigomar Menezes de Souza, Zigomar Menezes de Souza 

 Bibliography 

  

 1. Soil respiration. 2. O2 uptake. 3. Biochar. I. Título. II. 

Jaboticabal-Faculdade de Ciências Agrárias e Veterinárias. 

  

CDU 631.433.3 

  

Ficha catalográfica elaborada pela Seção Técnica de Aquisição e Tratamento da 
Informação – Serviço Técnico de Biblioteca e Documentação - UNESP, Câmpus de 
Jaboticabal. 

 

 

 

 

 

 

 

 



 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 



AUTHOR’S CURRICULUM DATA 

 

RISELY FERRAZ DE ALMEIDA – Daughter of Rhonda Graça Ferraz and 

Valternor Ferreira de Almeida, was born on September 29, 1986, in Vitória da 

Conquista, Bahia state, Brazil. She earned her Bachelor of Science Degree in 

Agronomy in February, 2012 at Universidade Estadual do Sudoeste da Bahia 

(UESB), Vitória da Conquista campus. At that same time, she attended the Instituto 

Federal de Tecnologia da Bahia (IFBA) where she got her technical degree in 

Environment Science. On March 2012, she entered the M.Sc. Program at the 

Universidade Federal de Uberlândia (UFU), Uberlândia campus, and received her 

M.Sc. Degree in Agronomy (Soil Science) in 2014. In March, 2014, she joined to the 

Graduate Program in Agronomy (Soil Science) at the São Paulo State University 

(UNESP/FCAV), Jaboticabal campus to get her doctorate degree. For that, she 

developed two soil projects at: the São Paulo State University (UNESP), Ilha Solteira 

campus; and University of Minnesota, St Paul campus - USA. These projects have 

been part of her doctoral thesis. Then she submitted the doctoral thesis to an 

examination panel, and received her Ph.D. Degree in Agronomy (Soil Science) from 

UNESP/FCAV on February 2017. As results of her background and expertise is 

associated with environmental and agricultural sciences, especially on the following 

research topics: sugarcane management, climate change, soil CO2 emission, soil 

carbon, biochar, soil use and management. 

 

 

 

 

 

 

 

 

 

 

 

 

 



 

I DEDICATE  

 

To God for blessing me all the time. 

 

 

 

 

To my beloved mother, Rhonda Graça Ferraz,                                                                                                                     

my greatest example of being a better person. This is for you! 

 

 

 

 

I OFFER  

 

To my family for being the base of my life 

To my friends for being the family that I chose 

 

 

 

 

 

 

 

 

 

 



ACKNOWLEDGEMENTS 

 

First and foremost, to God for helping and taking care of me wherever I am 

and for being her loved daughter. 

I am grateful to my advisors Newton La Scala Júnior, Kurt A. Spokas and Alan 

Rodrigo Panosso, who helped me a lot with the processes of learning and writing this 

doctoral dissertation. 

I am grateful to Maria José Servidone Trizólio, Norival Inácio, Shirley 

Aparecida Martineli de Sousa, Mara Regina Moitinho, Daniel De Bortoli Teixeira, 

Eduardo Barreto de Figueiredo, Ricardo de Oliveira Bordonal, Bruna Oliveira, 

Gustavo Andre and Clariana Valadares Xavier from the Department of Exact 

Sciences of the Faculty of Agrarian and Veterinary Sciences, Jaboticabal campus of 

the São Paulo State University (FCAV–UNESP), for being available for any help.  

My sincere gratitude to all members of the Department of Soil, Water, and 

Climate of the University of Minnesota, especially Prof. Kurt Spokas and Martin 

DuSaire who kindly received me and from whom I learned a lot. They gave me 

support and facilities for conducting all the laboratory experiments, to the United 

States Department of Agriculture, Agricultural Research Service (USDA-ARS). It was 

an incredible honor and opportunity to work with them. 

I am grateful to the Coordination for the Improvement of Higher Education 

Personnel (CAPES) for funding and supporting this research. I would like to say 

thank you to the Graduate Program in Agronomy (Soil Science) of the Faculty of 

Agrarian and Veterinary Sciences, Jaboticabal campus of the São Paulo State 

University (FCAV–UNESP). 

I am a blessed person because I have a wonderful family. I am very grateful 

for having my beloved mother (Rhonda Graça Ferraz), my brothers (Randler Ferraz 

Almeida and Victor Ferraz de Almeida), grandmother and grandfather (Maria Emilia 

Rodrigues de Souza and Eliziário Graça Ferraz), uncles (Roberto Graça Ferraz, 

Andreia Martins Ferraz, Roger Graça Ferraz, Alessandra Almeida Ferraz e Marcelo 

Martins Menecurse) and cousins (Caio Ferraz Menecurse, Robert Gustavo Almeida 

Ferraz and Joao Pedro Alves Ferraz) in my life. They have given me their friendship, 

support and love. They are the base of my life. 

I also would like to thank my American family. How they are special for me and 

were very important when I was living in the USA. Therefore, I want to say thank you 

to my American mothers (Beth Obern and Cristine Hart) who gave love and showed 



me that no matter where I am I can have a beloved family. My American friends, 

Laíse Sousa, Juliano Sousa, Christopher J. James, Marcos Santos, David E Eby, Jeff 

Stwart, Corey Ross, Jordyn P. Anklam and Iracema Wood. I say thank you for their 

friendship, support and experiencing unforgettable moments together.  

To my Brazilian friends I want to thank them for being with me all the time. Part 

of my success I offer to them. I do not have words to say how special Bruna Cristina 

Sanches and Scheyla Esteves are in my life. They are the sisters who I do not have 

in this life. I also say thank you to Roberta Carmargo de Oliveira, Camila Silveira 

Haddad, Raquel Pinheiro, Elienay Ferreira da Silva, Luma Castro, Fernanda Martins, 

Thaisa Moreti, Nilvan Melo and Juciléia Irian do Santos for sharing great and bad 

moment at UNESP. The academic life was better because I had them in my life   

Finally, to all that have contributed somehow, please feel represented here, 

you know who you are! 

I am very thankful for everything I have! 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 



vii 
 

 SUMMARY 

 

 Page 
ABSTRACT viii 
RESUMO ix 
1.0 CHAPTER 1 - General considerations 1 
1.1 Introduction and Justification 1 
1.2 Sugarcane production in Brazil 1 
1.3 Soil Attributes related to CO2 emission 2 
1.4 Soil Attributes related to O2 uptake 4 
1.5 Relationship between O2 uptake and CO2 emission 6 
1.6 Use of Biochar in soil 6 
References 7 
2.0 CHAPTER 2 - Use of O2 uptake as an index of CO2 respiration in 
sugarcane areas under different managements 

16 

Abstract 16 
2.1 Introduction 17 
2.2 Material and Methods 18 
2.3 Results 23 
2.4 Discussion 27 
2.5 Conclusion 33 
References 33 
3.0 CHAPTER 3 - How O2 uptake can help us understand the CO2 sorption 
processes by biochar? 

38 

Abstract 38 
3.1 Introduction 39 
3.2 Material and Methods 40 
3.3 Results 43 
3.4 Discussion 49 
3.5 Conclusion 52 
References 52 
4.0 CHAPTER 4 – General conclusions 58 
  
  
 

 

 

 

 

 

 

 

 



viii 
 

CO2 EMISSION AND O2 UPTAKE OF SOIL UNDER DIFFERENT SYSTEMS 

 

ABSTRACT - The soil O2 and CO2 concentration are the two most important gases 

related to soil microorganisms. Thus, this thesis was developed to observe the 

concentration and relationship between carbon dioxide (CO2) and oxygen (O2) under 

different residue systems. For that, we run two soil experiments in Brazil and the 

USA, respectively. The first experiment was developed to examine the relationship 

between CO2 and O2 using soil moisture and O2 as a soil respiration predictor in a 

sugarcane area under different managements of residues (mechanical harvesting - 

GH versus straw burning - BH). Therefore, the first experimental results are 

described in the Chapter 2 and entitled “Use of O2 uptake as an index of CO2 

respiration in sugarcane areas under different managements”. We run the second soil 

experiment measuring biochar’s impact on CO2 production or sorption and O2 uptake 

in amended soils. Thus, we studied three soil types (Rosemount - RM; Potting soil 

Sunshine - PS; and UM) and five different biochars (Pine chip biochar - ICM; Royal 

Oak hardwood lump charcoal - RO; Accurel activated charcoal - AAC; Bamboo - B; 

and Macadamia nut - MC) and control treatment (Soil without biochar). Consequently, 

the results are described in the Chapter 3 and entitled “How O2 uptake can help us 

understand the CO2 sorption processes by biochar?”. Thus, we can conclude with our 

results that the concentration and relationship between FCO2 and FO2 depend on 

different systems and soil conditions, for example: soil crop residue managements, 

soil moisture and use of biochar. The FO2 is positively correlated with FCO2 at 

biological condition with respiratory quotient (RQ) values close to 1.0. Moreover, we 

can observe that RQ values higher than 1 are results of soil–gas exchange fluxes 

after precipitation or higher available on O2. Thus, the FO2 can be used as an index 

for categorizing the source of FCO2 respiration. To finish, we can observe that the 

biochar can be used to sequester CO2 from the atmosphere by the absence of 

biological activities in a short period of time. However, we believe that more study 

should be developed to elucidate the CO2 and O2 sorption by biochars and their 

reactions (biological and/or chemical) when added biochar in soil. 

Keywords: Biochar, Soil crop residue, Biological respiration, Respiratory quotient  

 

 

 

 



ix 
 

EMISSÃO DE CO2 E CAPTURA DE O2 DO SOLO EM DIFERENTES SISTEMAS 

 

RESUMO - O oxigênio (O2) e o dióxido de carbono (CO2) no solo são os dois 

principais gases relacionados com a atividade dos microorganismos no solo. Assim, 

esta tese foi desenvolvida para observar a concentração e a relação entre a 

concentração do  CO2 e O2 sob diferentes sistemas de resíduos. Para isso, 

realizamos dois experimentos de solo no Brasil e nos EUA, respectivamente. O 

primeiro experimento foi desenvolvido para examinar a relação entre fluxo de CO2 

(FCO2) e o fluxo de O2 (FO2) usando a umidade do solo e o O2 como um predictor 

da respiração do solo em uma área de cana-de-açúcar sob diferentes manejos de 

resíduos (colheita mecânica - GH versus colheita queimada – BH). Portanto, os 

resultados do primeiro experimento estão descritos no Capítulo 2 e sendo intitulado 

de "Uso da captura de O2 como índice de respiração de CO2 em áreas de cana-de-

açúcar sob diferentes manejos". O segundo experimento do solo observou o impacto 

do biochar na emissão ou sorção de CO2 e O2 nos solos. Assim, foram estudados 

três tipos de solos (Rosemount - RM, Potting Sol Sunshine - PS e UM), cinco 

biochars diferentes (biochar de chip de pinho - ICM, biochar de Carvalho Oak Royal - 

RO, biochar Acurel ativado - AAC, biochar de Bambu - B; biochar de Macadâmia - 

MC) e o tratamento controle (solo sem biochar). Consequentemente, os resultados 

foram descritos no Capítulo 3 e intitulado "Como a captura de O2 pode nos ajudar a 

entender os processos de sorção de CO2 via biochar?". Assim, nós podemos 

concluir com os nossos resultados que a concentração e relação entre FCO2 e FO2 

dependem dos diferentes sistemas e condições dos solos estudados, tais como: 

manejo de resíduos de culturas do solo, umidade do solo e uso de biochar. O FO2 

está positivamente correlacionado com o FCO2 via atividade biológica e com valores 

de coeficientes respiratório (RQ) próximos de 1,0. Além disso, podemos observar 

que valores de RQ maiores que 1 são resultados dos fluxos de troca solo-gás após 

precipitação ou maior disponibilidade de O2 no meio. Assim, o FO2 pode ser 

utilizado como um índice para categorizar uma fonte de respiração de CO2. Para 

concluir, o biochar pode ser utilizado para sequestrar CO2 da atmosfera em curto 

período de tempo. No entanto, acreditamos que mais estudos devem ser 

desenvolvidos para elucidar a sorção de CO2 e O2 pelo biochar e suas reações 

(biológicas e/ou químicas) quando adicionado biochar no solo. 

Palavras-chave: Biochar, Resíduo da cultura no solo, Respiração biológica, 

Quoeficiente respiratório 



1 
 

 

1. CHAPTER 1 – General considerations 

1.1 Introduction and Justification 

 The soil air constituents as well as soil water content are important aspects 

controlling biological activities (plant and microorganism respiration) (MOREIRA; 

SIQUEIRA, 2006; LEPSCH, 2011; BRADY; WEIL, 2013). The soil air contains mainly 

nitrogen (N2), oxygen (O2), carbon dioxide (CO2) and water vapor, and they are the 

most important gases in soil (GLINSKI; STEPNIEWSKI, 1985). Normally, the CO2 

concentration in soil is higher than in the atmosphere, while O2 concentration is lower 

(LEPSCH, 2011; MARSCHNER, 2012).    

 The soil O2 and CO2 concentration are the two most important gases related to 

soil microorganisms, capture, and soils and root respiration, respectively, (GLINSKI; 

STEPNIEWSKI, 1985). Stepniewski et al. (2005) have mentioned the importance of a 

better understanding of the oxygen cycle, and they have called this cycle, that 

describes the stock, absorption, movement, functions and determination of O2 

concentration in the environment. 

The CO2 cycle also has been mentioned by other researchers, such as: La 

Scala Júnior et al. (2000), Xu and Qi (2001), Epron et al. (2006), Panosso et al 

(2009), Corrade et al. (2013), Almeida et al. (2014), Moitinho et al. (2014) and 

Almeida et al. (2015), who have explained the relationships among the CO2 and soil 

attributes and characteristic under different systems, uses and managements. 

 Therefore, this thesis was developed with the hypotheses that the CO2 

emission has a close relationship with O2 under residues systems. Moreover, to 

understand and clarify the concentration and relationship of O2 and O2 with RQ.  

Thus, this thesis has the objectives of: (i) examine the relationship between 

FCO2 and FO2 using soil moisture, RQ and O2 as a soil respiration predictor in a 

sugarcane area under different managements (mechanical harvesting versus straw 

burning) (Chapter 2); and (ii) measuring biochar’s impact on CO2 production or 

sorption and O2 uptake in amended soils (Chapter 3). 

 

1.2 Sugarcane production in Brazil 

Brazil is currently the largest sugarcane producer and has an average stalks 

yield at 684.7 millions of tons in 2016/17 (CONAB, 2016) and an estimated 20 Mg ha-

1 of residues on the soil surface after harvest (URQUIAGA et al., 1991; OLIVEIRA et 

al., 1999).  



2 
 

The management of sugarcane with mechanized harvesting without burning or 

straw removal from the soil contributes to a more sustainable management option for 

sugarcane production (FIGUEIREDO; LA SCALA, 2011). However, sugarcane 

harvesting continues to be undertaken using two distinct practices in Brazil: 

mechanical harvesting with straw burning (BH) and without burning (GH) (PANOSSO 

et al., 2011).  

 Some researchers, such as Panosso et al. (2011), Bicalho et al. (2014) and 

Moitinho et al. (2015) have been studying sugarcane area and looking at the 

relationship of soil attributes to CO2 emission. They have found a higher relation of 

soil CO2 emission with temperature and precipitation (PANOSSO et al., 2011), and 

soil physical attributes, such as: soil porosity (PANOSSO et al., 2011; PANOSSO et 

al., 2012; BICALHO et al., 2014; MOITINHO et al., 2015), texture (SIGNOR et al., 

2014) soil bulk density (CHAVES; FARIAS, 2008; SIGNOR et al., 2014), soil moisture 

(SILVA et al., 2014; IAMAGUTI et al., 2015), and others, like soil mineralogy (LA 

SCALA et al., 2000).  

Moreover, some soil chemical attributes under sugarcane also have been 

cited, such as: pH value (SIGNOR et al., 2014), cation exchange capacity (LA 

SCALA JÚNIOR et al., 2000), and available nutrients (SIGNOR et al., 2014). The 

organic components, the soil carbon stock (MENDONZA et al., 2000; CHAVES; 

FARIAS, 2008), and ratio of carbon and nitrogen (SIGNOR et al., 2014) and microbial 

activity (MENDONZA et al., 2000), also are important.  

 

1.3 Soil Attributes related to CO2 emission  

The CO2 is included in the global carbon cycle, and that cycle occurs in soil, 

plant and atmosphere where the CO2 emission is an important component (RAICH; 

SCHLESINGER, 1992). The soil CO2 emission is a result of root respiration and 

microorganism respiration via a biological process (MELILLO et al., 2002; LAL, 

2009).  

On the other hand, the soil CO2 emission also is a result of soil chemical 

process (MARQUES et al., 2000; DELBEM, 2011 and ANGERT et al., 2015). 

According to ANGERT et al. (2015) the use of calcareous materials in the soil is an 

example of a chemical process that improves CO2 emission. Furthermore, the use of 

nitrogenous fertilizer through the urea reaction another example (MARQUES et al., 

2000; DELBEM, 2011). Therefore, the CO2 emission is a result of biological and 

chemical reactions in soils. In addition, the climate and the physical, chemical and 



3 
 

biological soil attributes, as well as soil organic matter, are responsible for increasing 

or decreasing the CO2 emissions (LAL, 2009).  

The main climatic variables that directly influence the CO2 emission from the 

soil into the atmosphere are temperature (soil and atmosphere) and precipitation 

(humidity) (Duiker; Lal, 2000; ALMEIDA et al., 2009). In fact, this occurs because 

these variables can help improve the soil microbiology, providing adequate conditions 

for soil organic matter degradation (DUIKER; LAL, 2000; SILVA-OLAYA et al., 2013)  

The temperature is considered the most important factor for microbial activity 

(BENJAMIN et al., 2003; KYAW THA PAW et al., 2006; and LAL, 2009; CHEN et al., 

2011). According to Fang and Moncrieff (2001) and Stanford et al. (1973) the 

temperature can improve the microbial activity with the exponential increase of soil 

respiration and consequently the CO2 emission occurring at temperature between 5 

and 35°C.  

Among the soil physical attributes we can describe some soil properties and 

characteristic, such as soil texture (CAMPOS et al., 1999; DILUSTRO et al., 2005), 

soil porosity (CHEN et al., 2010; PANOSSO et al., 2011), bulk density (XU; QI, 2001), 

moisture (GARDINI et al, 1991; HOWARD; HOWARD, 1993; CHEN et al. 2011) and 

the soil mineralogy (LA SCALA et al., 2000; XU; QI, 2001; EPRON et al., 2006), that 

have the same ability to control the CO2 emission from soils. 

The soil porosity has been cited as the most significant soil physical attribute 

that influences the CO2 diffusion into soil (EHLERS et al., 1969), and its relationships 

have been observed by Xu and Qi, (2001), Ranjard and Richaume (2001) Epron et 

al. (2006), Panosso et al. (2012), Bicalho et al. (2014) and Moitinho et al (2015). 

According to Ehlers et al. (1969) and Fang et al. (1998) the relationship is stronger 

because the CO2 diffusion (movement) is lower in soils with a low amount of pores, 

mainly in micropores. Moreover, the soil pores are a natural habitat for microbial 

communities (RANJARD; RICHAUME, 2001).  

The soil moisture is another important physical attribute related to CO2 

emission. Some researchers such as Gardini et al. (1991) and Howard and Howard 

(1993) consider the soil moisture the key abiotic factor that affects the CO2 emission 

process. According to Chen et al. (2011) soils with higher soil moisture and air 

availability can promote up to an 80% increase in CO2 emission. This occurs because 

the soil moisture can improve microorganism and root activity (LAL; KIMBLE, 1995; 

SMITH et al., 2003), and gas diffusion through the soil pores (HILLEL, 1998; 

IGNATIUS, 1999; SMITH et al., 2003; COSTA et al., 2008). However, conditions of 



4 
 

higher soil moisture values (>50%) happens increase of denitrification by anaerobic 

microorganisms and production of N2O (nitrous oxide) (DALAL et al., 2003). 

The more significant soil chemical attributes we can describe are the pH value 

(RETH et al., 2005; FUENTES et al., 2006), cation exchange capacity (LA SCALA 

JÚNIOR et al., 2000), and the nutrients available, such as phosphorus (DUAH-

YENTUMI et al., 1998), magnesium (XU; QI, 2001), nitrogen (ALMEIDA, 2014). The 

organic components are also important, such as the carbon stock (LONGDOZ et al., 

2000; AMADO et al., 2001; SÁ et al., 2001; ALMEIDA et al., 2015) and carbon and 

nitrogen ratio (TIAN et al, 1997; COSTA et al., 2008). 

We can consider the soil organic matter, microorganism activity and root 

distribution and density as biological soil attributes. According to Longdoz et al. 

(2000) and Panosso et al. (2011) the biological soil attributes have short and high 

relationship with the CO2 produced from the soil. Almeida et al (2015) have been 

observing that soil label carbon has the highest correlation with CO2 because it is 

easily decomposed by soil microorganisms. 

 

1.4 Soil Attributes related to O2 uptake 

 The air in the soil has a function of suppling O2 for a soil organism (micro 

fauna and aerobic microorganisms), and plant respiration (photosynthesis and 

chemosynthesis) (MALAVOLTA, 2006; CHEN et al., 2011). During plant respiration, 

the O2 is used for chemosynthesis (VAN DOVER, 2000; SMITH, 2002) as the primary 

electron acceptor in aerobic conditions, whereas under anaerobic conditions the 

nitrate, carbon dioxide, sulphur and sulphate can be the primary electron acceptor 

(SMITH, 2002). In photorespiration process the O2 is used as a substrate by rubisco 

activity (carboxylation enzyme) in C3 plants in oxygenase (O2 absorption to CO2 

production in photorespiration) and carboxylase (CO2 absorption at photosynthesis) 

(NAGANUMA, 1998; MARENCO et al., 2014).  

The O2 available in the soil depends on its fast and continuous exchange 

between the soil and the atmosphere (CHEN et al., 2011). According to soil available 

O2 we can classify the soil as normoxic, hypoxia and anoxia (DREW, 1997; CHEN et 

al., 2011). The normoxic is when the soil has sufficient O2 availability for root and 

microorganism activity. Hypoxia is considered the point between normoxic and 

anoxia, and anoxia is the total absence of soil O2 (DREW, 1997). According to Chen 

et al.  (2011) in hypoxia it is possible to observe the low exchange of gases between 



5 
 

the soil and the atmosphere, and it occurs with a decrease of root growth and 

microorganism activity.  

There are some soil chemical, physical and biological attributes that can be 

used as available O2 diagnostics in soil. For instance, soil color, water-filled pore 

space, air permeability, redox potential, available iron and enzymatic activities 

(GLINSKI; STEPNIEWSKI, 1985). Therefore, the soil conditions can be an indicator 

of O2 availability, and it has become very important to understand the available soil 

O2 conditions (BRADY; WEIL, 2013). Some researchers have been working to better 

understand the O2 flux behavior and the relationship between the O2 and soil 

attributes, researchers such as: Berry and Norris (1949), Currie (1965), Cary and 

Holder (1982), Cook (1995), Armstrong and Drew (2002), Cook and Knight (2003) 

Cook et al. (2007) and Cheng et al. (2012).  

Some physical soil attributes have been described as having a close 

relationship with available O2, such as: soil porosity (QUASTEL, 1965; HILLEL, 1998; 

BRADY; WEIL, 2013), macroporosity and microporosity (SIERRA et al., 1995, 

SCANLON et. al., 2002; BRADY; WEIL, 2013), bulk density (KYAW THA PAW et al., 

2006) and soil aggregation (OUYANG; BOERSMA, 1992; SIERRA et al., 1995; 

KYAW THA PAW et al., 2006). According to Glinski and Stepniewski (1985) the soil 

porosity is the simplest and probably the oldest soil attribute that can be used as an 

available O2 indicator.   

The water filled pores have been cited as an important attribute to understand 

the soil O2 available (DILLY 2001; COOK et al. 2007; ELBERLING et al., 2011; 

BRADY; WEIL, 2013) because both O2 and water occupy soil pores (QUASTEL, 

1965). In addition, O2 has a low solubility in water (HILLEL, 1998), and the O2 

diffusion coefficient decreases when the soils become saturated with water 

(SCANLON et al., 2002). The soil microbiological activity is also other important soil 

attribute to help understand the available soil O2 (BERRY; NORRIS, 1949; GLINSKI; 

STEPNIEWSKI, 1985; BRADY; WEIL, 2013). The activity takes place because the O2 

is consumed by soil organism and plant root respiration (BRADY; WEIL, 2013). 

Consequently, higher plant root concentrations and biological activity trigger higher 

O2 consumption. This has been observed in soil layers close to soil surfaces (KYAW 

THA PAW et al., 2006).  

   

 

 



6 
 

1.5 Relationship between O2 uptake and CO2 emission 

The relationship between O2 and CO2 concentration by respiration is 

described as inversely proportional and normally the CO2 presents a higher 

concentration than O2 (LESPCH, 2011). This occurs because of the respiration, 

where 1 mol of O2 is consumed per 1 mol of CO2 produced. That relation is called soil 

respiratory activity and can be determined by calculating the RQ (microbial 

respiratory quotient) according to Dilly (2001).  

The balance and concentration of CO2 and O2 in soil depend on some factors, 

such as (1) The gas exchange facility between soil and atmosphere; (2) Biological 

process (STOBOVOI, 2001; LEPSCH, 2011), and (3) Chemical reactions (COOK et 

al. 2004). 

In soil higher biological activity takes place with lower available O2 and higher 

CO2 produced by plant root respiration (GLINSKI; STEPNIEWSKI, 1985; COOK et al. 

1998; COOK et al., 2007; LESPCH, 2011) and microorganism respiration 

(ORCHARD; COOK, 1983; STOBOVOI, 2001; DILLY, 2001). Some chemical 

reactions can consume O2 (COOK et al. 2004) or produce CO2 in soil (MARQUES et 

al., 2000; DELBEM, 2011). 

Some soil CO2 experiments have been developed with CO2 results in different 

systems, managements and soil uses without inclusion of available O2 or correlation 

between CO2 and O2 results, such as:  Xu and Qi (2001), Epron et al. (2006), 

Panosso et al. (2009), Panosso et al. (2012), Bicalho et al. (2014), Almeida et al. 

(2015) and Moitinho et al. (2015). Indeed, the relationship between O2 and CO2 

becomes very important when seeking to understand the biological or chemical soil 

system.  

 

1.6 Use of Biochar in soil 

Biochar is classified as a fine-grained and porous substance, similar in 

appearance to charcoal, that is produced by pyrolysis of biomass under oxygen-

limited conditions (CHEN, 2011). The Biochar has a relatively structured carbon 

matrix with an extensive surface area and high degree of porosity (SOHI et al., 2009). 

There are different kinds of biochars (SPOKAS; REICOSKY, 2009; SPOKAS et 

al., 2013), and they have been produced from different materials (animal manures 

and lignocellulosic feedstocks) (NOVAK et al., 2013), production processes (heating 

biomass and oxygen environment) (LAIRD et al., 2009) and aging (surface, oxidation 

and alteration) (SPOKAS; REICOSKY, 2009; SPOKAS, 2013). These processes and 



7 
 

process parameters, are particularly important to biochar quality, such as: 

temperature, and the nature of the feedstock (SOHI et al., 2009). 

The use of biochar in soil has been cited as a technique to sequester carbon 

(GOLDBERG, 1985; LEHMANN, 2007; AMELOOT et al., 2013; THOMAZINI et al., 

2015) and has received considerable interest as a material to improve crop 

production (LEHMANN et al., 2006; LEHMANN, 2007; LAIRD, 2008) and soil nutrient 

availability (soil fertility), such as nitrogen (PARK et al., 2011; LENTZ et al., 2014; 

AGEGNEHU et al., 2015) and other soil nutrients, such as phosphorus (LAIRD et al., 

2010; AGEGNEHU et al., 2015), potassium, magnesium and calcium (LAIRD et al., 

2010).  

Moreover, the biochar in soil has been correlated with an increase in soil 

microbiological and enzymatic activity (LEHMANN et al., 2011), carbon degradation 

by microorganisms (HARRIS et al., 2003; BRUNN et al., 2008; LEHMANN et al., 

2011; AGEGNEHU et al., 2015), and providing habitat for soil microbes 

(PIETIKAINEN et al., 2000), and increased organic carbon content (PENDERGAST-

MILLER et al., 2011; LENTZ et al., 2014).  

The relationship between the uses of biochar with CO2 emission has also been 

observed by some researchers, such as Major et al. (2009), Zimmerman et al. 

(2011), Lehmann et al. (2011), Lentz et al. (2014) and Lin et al. (2014). However, 

their results depend on kinds of soil and biochar observed (NOVAK; BUSSCHER, 

2009) and there is limited information regarding the associated underlying 

mechanisms (CHEN et al., 2011). 

 

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16 
 

2. CHAPTER 2: Use of O2 uptake as an index of CO2 respiration in sugarcane                 

                       areas under different managements 

 

ABSTRACT – The oxygen uptake (FO2) and carbon dioxide emissions (FCO2) in 

soils are important gases, and their concentrations can help understanding the 

relation of soil especially in environments where this is driven by aerobic microbial 

activity. This study was developed to examine the relationship and profile of flux of 

carbon dioxide (FCO2) using the soil moisture and the flux of oxygen (O2) as a soil 

respiration predictor in a sugarcane area under different residues managements 

(mechanical harvesting - GH versus straw burning - BH). We noticed that there was a 

lower and relatively constant FCO2 and FO2 when the soil moisture has a variation of 

6.0 to 8.6% to both managements. However, the BH (87.07 ±19.45 g CO2 m-2) 

presented the higher cumulative CO2 emission, which is 53.68% higher than GH 

(52.31 ± 15.41 g CO2 m-2). The relationship between FCO2 and soil moisture was 

positive in both treatments, BH (r= 0.74) and GH (r= 0.69), whereas the soil moisture 

showed a negative correlation with O2 uptake under GH (r=-0.46; P<0.00). 

Furthermore, there was a positive correlation between FCO2 and FO2 under BH (r = 

0.74; P<0.00), and the respiration quotient (RQ) was constant and lower than 1 

before the precipitation. So, the FCO2 and FO2 profiles and correlation depended on 

soil, crop residue managements and the FO2 can be used as an index for 

categorizing the source of CO2 respiration. The RQ values higher than 1 were results 

of soil–gas exchange fluxes after precipitation. 

Keywords: Soil biological activity, Soil crop residue, Respiratory quotient, 

Mechanized planting-harvesting 

 

 

 

 

 

 

 

 

 

 



17 
 

2.1 Introduction 

Measurement of oxygen uptake (FO2) in soils is important, as it could help in 

understanding the relation to soil carbon dioxide emissions (FCO2), especially in 

environments where this is driven by aerobic microbial activity (STERN et al. 1999). 

Therefore, this characterization can be useful in determining the impact of soil carbon 

losses under different agricultural managements. These gaseous exchange rates 

(FO2 and FCO2) are intimately related to the global carbon cycle, considering the FO2 

as a reflection of the carbon cycle (KEELING; SHERTZ 1992) and the relation 

between them can be a process key to the global carbon cycle (DILLY, 2003) 

The soil respiration (CO2 emission) occurs in soils driven by biochemical 

processes directly related to the respiration of roots and organic matter 

decomposition by microbial activity (LAL, 2009; MELILLO et al., 2002). These 

microbes are mainly aerobic, whose activity increases soil CO2 gas concentrations to 

2.0-3.0% (STERN et al., 1999).  

In the soil atmosphere after CO2 production and accumulation, pressure driven 

mass flow and diffusion are the main mechanisms responsible for FO2 and FCO2 

transport in the soil (HILLEL, 1998), and resulting exchange of gases between the 

soil and the atmosphere (COOK et al., 2008). It must be remembered that the soil 

atmosphere composition is a balance between the metabolism and growth conditions 

of anaerobic and aerobic microorganisms (GARDINI et al., 1991). 

The gaseous diffusion is primarily responsible for driving FO2 and FCO2 into the 

soil (BENJAMIN et al., 2003) and their transport is due to the concentration gradient 

between the atmosphere and soil gas phase (BALL; SMITH, 1991; PEREIRA; 

CRUCIANI, 2009). Since, these concentration gradients are in opposite directions for 

these two gases, their fluxes will be in opposite directions (CO2 outwards; and O2 

inwards towards the soil).  

The soil physical attributes directly influence the gaseous exchange with the 

atmosphere, among them are: the water filled pores - WFP (COOK et al., 2008), soil 

moisture (PANOSSO et al., 2011), soil depth (CAMPBELL, 1985; COOK, 1995), soil 

texture, soil water availability (CHEN et al., 2011) and the tillage management 

(BICALHO et al., 2014). Furthermore, available soil oxygen (CHEN et al., 2011), soil 

nitrogen and carbon and organic matter (ALMEIDA et al., 2015) also control microbial 

rates. Therefore, soil nutrients, such as: phosphor, magnesium and calcium, also 

have an influence on the gaseous exchange with the atmosphere (DUAH-YENTUMI 



18 
 

et al., 1998; XU; QI, 2001), by influencing the production or consumption rates of soil 

gases. 

Soil management and use also are other factors that can influence the FCO2 

and FO2. Brazil is currently the largest sugarcane producer and has an average an 

average stalks yield at 684.7 millions of tons in 2016/17  (CONAB, 2016) with an 

estimated 20 Mg ha-1 of residues on the soil surface after harvest (URQUIAGA et al., 

1991; OLIVEIRA et al. 1999).  

The management with mechanized harvesting of sugarcane without burning or 

removal of the straw on the soil contributes to a more sustainable management 

option for sugarcane production (FIGUEIREDO; LA SCALA, 2011). However, sugar 

cane harvesting continues to be undertaken using two distinct practices in some 

Brazilian states: mechanical harvesting with straw burning (BH) and without burning 

(GH) (PANOSSO et al., 2011). 

To hypothesis that different residues managements can change the O2, CO2 

concentrations and relationship with them in sugarcane area this study was run to 

examine the relationship between FCO2 and FO2 using soil moisture, RQ and O2 as a 

soil respiration predictor in a sugarcane area under different managements 

(mechanical harvesting versus straw burning). 

 

2.2 Material and methods 

2.2.1 Characterization of the study area 

The study was conducted in an area under sugarcane cultivation (Saccharum 

spp.) during July, 2014 (July 4-14th) in Mato Grosso do Sul state, near the 

municipality of Aparecida do Taboado (20º19'S and 51º13'W). The soil was classified 

as an oxisol according of Soil Survey Staff (2014), with sandy clay loam texture in the 

0-0.2 m layer (Table 1 and Figure 2.1). 

The region has a tropical humid climate classified as Aw (PEEL et al., 2007) 

which has a rainy summer season (Sept–Jun) and a dry winter (Jun-Aug), with an 

average annual rainfall of 1595 mm in 2014. During the field measurement in July, 

2014, there was precipitation in the 13 th and the 14th day with a daily rainfall of 6.1 

and 1.5 mm, respectively (Climate Channel at UNESP Ilha Solteira, 

http://clima.feis.unesp.br).  

The effect of residue management was evaluated in two sections of the 

production field that were under different straw managements (Sections). Section 1: 

with mechanical harvesting and straw burning (BH); and Section 2: with mechanical 



19 
 

harvesting (GH) and maintenance of the straw. Normally the mechanical harvesting 

can add the average of 20 Mg of crop residue ha-1. However, this quantity will depend 

on the variety used and harvest stage (CORREIA; DURIGAN, 2004; TOFOLI et al., 

2009; ALMEIDA et al., 2014). Both sections were the same cultivation and harvest 

management with the sugarcane productivity of 63 and 46 Mg ha-1 in 2013 and 2014, 

respectively. 

 

 
Figure 2.1. Areas under sugarcane cultivation (Saccharum spp.) with different straw 
managements: mechanical harvesting (GH) and straw burning (BH).   

 

The study area was 21.77 ha cultivated with sugarcane, CTC variety, and a 

population of 60,000 plants per hectare. Historically, the study area has been used 

for sugarcane production (for 20+ years). The soil was prepared and sugarcane was 

planted using the conventional system (soil disturbance), application of dolomitic 

limestone (Dose of 1.5 t ha-1), gypsum (Dose of 1.0 t ha-1) and gypsum. The 

mechanized planting was performed with furrowing (average depth of 0.35 to 0.4 m), 

placing 18 buds per m-2. 

The fertilization was performed in the furrow with the distribution of 250 kg ha-1 

of mono-ammonium phosphate (MAP), equivalent to 120 kg ha-1 of P2O5 and 27 kg 

ha-1 of N-NH4+. Subsequently, topdressing was done with the liquid formula 05-00-13 

+ 0.3% Zn + 0.3% B, in the amount of 1,000 L ha-1, equivalent to 50 kg ha-1 N, 130 kg 

ha-1 of K2O, 3 kg ha-1 of Zn and B. After the first cutting, ratoon fertilization was 



20 
 

performed based on the best management practices applying 90 kg ha-1 N, 30 kg ha-

1 of P2O5 and 110 kg ha-1 of K2O.  

The sugarcane harvest was done mechanically and with burning for BH in 2014. 

However, for GH the sugarcane harvest was done mechanically and without burning. 

In sampling time, the sugarcane plants were 20 cm high and it was approximately 2 

weeks after their 2rd cutting (harvest) in 2014. Thus, the area did not have plants in 

higher growth stages. 

Field sampling was conducted by selecting 10 points with at least 5 m spacing 

from each management sector. We used 10 points because the oxygen sensor takes 

about 15 minutes to analyze one simple. The results of the analyses of the soils from 

the two sections (0-0.2 m layer) are shown in Table 1. Physical and chemical 

attributes did not show differences between the systems observed.  

This table presents the soil physical (Sand, Silt and Clay) and chemical 

properties (hydrogen ionic potential-pH; soil organic matter-SOM; phosphorus-P; 

sulfur-S; calcium-Ca+2; potassium-K+; magnesium-Mg+2 and aluminum-Al+3) beside 

the soil porosity (Macro, micro porosity and Total porosity) and water full pores 

(WFP). These analytical results were analyzed through Embrapa methodology 

(1997). 

 

Table.  1. Physical and chemical attributes of a Red-Yellow Latosol in use with 
sugarcane with mechanized harvesting with the presence of straw (GH) and straw 
burning (BH). 

  Soil chemical attributes 
  pH SOM P S Ca+2 K+ Mg+2 Al+3 

 
- g dm-3 -------- mg dm-3 -------- 

------------------------mmolc dm-3 -------------------
- 

BH 5.11±0.0 16.30±0.5 8.0±0.2 5.5±0.2 19.7±1.1 1.36±0.0 9.1±0.8 0.8±0.2 
GH 5.18±0.0 15.90±0.2 8.2±0.2 5.3±0.2 22.0±0.8 1.26±0.1 8.7±0.5 0.9±0.31 

 
Soil chemical attributes Soil physical attributes 

 
Sand Silt Clay Macro Micro TP WFP 

 
-------------- g Kg-1-------------- --------------%-------------- 

 
BH 613±1.0 101.0±1.0 286.0±0.0 14.6±2.0 29.0±0.6 43.69±1.6 18.73±5.6 
GH 602±0.3 111.5±0.3 286.0±0.0 11.1±1.3 31.58±1.0 42.75±1.0 18.49± 6.4 

In the table: the hydrogen ionic potential is represented by pH; soil organic matter-SOM; 
phosphorus-P; sulfur-S; calcium-Ca+2; potassium-K+; magnesium-Mg+2; aluminum-Al+3; cation 
exchange capacity-CTC; Microporosity (Macro); Microporosity (Micro); Total pore (TP); water 
full pores (WFP). The physical and chemical attributes were compared using the Student’s t 

test (P≤0. 05) 

 

The water-filled pores (WFP) was calculated using Equation 1 by Linn and 

Doran (1984). Where the soil moisture was the volumetric water content percent (%) 

and the total soil porosity percent (TP). To calculate the TP (TP= (1 - PB/PP)*100) we 



21 
 

used the soil particle density (PP) was assumed to be 2.65 Mg m-3 and soil bulk 

density (PB) in Mg m-3. 

 

                                                                                                                                                                                             Eq. (1) 

 

2.2.2 Soil sample and CO2, O2 soil moisture analyzed 

          PVC rings (polyvinyl chloride), 10 cm in diameter and 8.5 cm in height were 

previously installed and fixed at the sample points. After 24 hours, the CO2 emissions 

(FCO2), O2 uptake (FO2) and temperature in 6 separate measurement days (July 4th, 

6th, 8th, 10th, 12th and 14th) totaling 10 observation days. We used this period of 

time because we wanted to observe the relationship of these variables to the soil 

without the confounding contribution from crop growth at higher stages. The soil 

measurements were collected in the morning between 7 and 8 am. 

To collect FCO2 we used an IRGA (LI-COR 8100A) which has a closed 

circulation system with an internal volume of 854 mL and a soil contact area of 84 

cm² (LI-COR Inc. Linclon, NE, USA). The IRGA has an infrared (IR) system that 

measures the CO2 concentration by optical infrared absorption spectroscopy (Figure 

2.2a). 

Figure 2.2 The IRGA system (a) and O2 sensor used in this experiment. 

 

The soil moisture was measured using a portable TDR system (Time Domain 

Reflectometry; HydrosenseTM; Campbell Scientific, Australia) that determined the soil 

moisture according to the dielectric constant of the travel time of an electromagnetic 

pulse in the space between the two end points (2 rods, 12 cm high) inserted into the 

soil adjacent to the PVC collars (0-10 cm).  

 100  
TP

moisture soil  = %WFP

a b 



22 
 

The soil FO2 was monitored by an O2 sensor (CM-021; CO2 Meter, Inc., 

Ormond Beach, FL, USA) with a full scale span of 0–25% (v/v). This sensor is 

portable and utilizes ultraviolet light (UV) fluorescence to assess the oxygen 

concentration (Figure 2.2b). The sensor result was read using the software (Gaslab) 

to calculate the soil O2 uptake rate.  

With the CO2 and O2 results we calculated the respiratory quotient - RQ (mol 

mol-1) according to Dilly (2001), Dilly (2003) and Wolinska (2011), where the RQ is a 

ratio of the CO2 emission and O2 uptake. 

 

2.2.3 Calculus of soil FO2  

 The soil O2 uptake rate (dO2/dt) was calculated by a linear interpolation of the 

concentration values as a function of time, during the first 300 seconds of sampling.  

Specifically, the soil FO2 was calculated by Eq. (2) taking into account the pressure, 

temperature and volume of the gas trapped in the chamber. In Equation (1), FO2(t) is 

the amount of O2 measured at time t, the dO2 is the concentration change in relation 

to the unit of time (dt) in the area of the collar surface (A) (JASSAL et al., 2012; 

GIACOMO et al., 2014).  

                                                                 

                                                                                                                       Eq. (2) 

The initial O2 readings are in concentration units of parts per million (ppm). The 

PVC had a volume of 0.00066 m3 and area 0.008 m2. The volume measured by the 

sensor (ppm) was converted to moles of O2 using the ideal gas law, Equation (3). 

            Eq. (3) 

 

 

After Equation 2, we calculated the O2 uptake by time (dO2/dt). In Equation (4), 

the ΔV is the O2 uptake (dO2/dt), P is the pressure (Pa), T is the atmospheric 

temperature (K) and R  is the universal constant of perfect gases (J mol−1 K−1).  

 

                                                                                                          Eq. (4) 

 

 

 

 

2.2.4 Data processing and statistical analysis   

Adt
dO

tFO


 2
2 )(

nRT
FO


  V P 

2

P(V) = (n)RT                                         



23 
 

The soil moisture, O2 uptake, CO2 emission and RQ daily mean were calculated 

using N (number) of 10 per day and compared by Student’s t-test (P≤0.05) per each 

management sector. Consequently, the FCO2, FO2 and total RQ were calculated 

using all days observed with an N of 60 per treatment. Thus, an integration of the 

area under the FCO2 and FO2 curves were calculated using the Origin 7 program 

(Origin Lab Corporation 2002). Thereafter, the treatment results were compared by 

Student’s t-test (P≤0.05). 

The relationship between soil CO2 emission and O2 uptake with soil moisture 

was calculated using regression analysis and the Pearson correlation for both 

managements. The analysis of presuppositions was conducted using residuals 

analysis and identifying the outliers and influent values by Leverage statistics. The 

normality of residuals was verified by test Cramer-von-misses at 5% probability.  

 

2.3 Results  

2.3.1 Daily behavior of soil variables 

The soil CO2 emission on the 4th, 6th, 8th and 10th day were similar, especially 

in GH, with means  of 0.95; 1.32; 0.76 and 0.83 µmol m-2 s-1 and 1.65; 1.54; 1.41 and 

1.52 µmol m-2 s-1 for GH and BH, respectively (Figure 2.3d).  

We can see that both treatments showed lower and relatively constant CO2 

emission when the soil moisture had 6.44 to 8.6% and 6.0 to 7.4% for BH and GH, 

respectively (Figure 2.3b). However, after the 10th day the CO2 emission and soil 

moisture increased with means of 4.87 and 2.26 µmol m-2 s-1 and 14.33 and 14.11% 

for BH and GH (Figure 2.3d, b). This maximum observed soil moisture value followed 

a precipitation event of 6.1 mm (Figure 2.3a). 

The BH had higher CO2 emission in all days observed with a statistical 

difference in GH according to student test (p≤0.05) on the 4th, 8th, 10th, 12th and 14th 

day. The highest BH difference occurred on the 12th day of study, with a CO2 

emission increase of 54.0% compared to the GH treatment (Figure 2.3d). 

The temporal variability of soil O2 uptake was inverse compared to the CO2 

emission in this study. The O2 uptake was lower with variation of 0.22 to 0.46 and 

0.20 to 0.40 mg m-2 s-1 on the first days (4th and 10th). 1110 However, after the 

precipitation event the O2 uptake had a decrease of 73.0% for BH and GH 

treatments, respectively (Figure 2.3c). 



24 
 

When comparing the treatments we can also notice that the soil O2 uptake did 

not present a difference between the treatments for all days observed according to 

the student t-test (p≤0.05). The BH and GH mean for all days observed were 0.24 

and 0.25 mg m-2 s-1, respectively (Figure 2.3c). 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 2.3. Precipitation (mm) (a), soil moisture (%) (b), O2 uptake (mg O2 m-2 s-1) 
(c), CO2 emission (µmol m-2 s-1) (d) and respiratory quotient - RQ (mol mol-1) (e) in 
soil with sugarcane managements with mechanized harvesting GH) and burned straw 
(BH). In the Figure 3b and d: days identified with lower-case when distinct, differ by 
the Student’s t-test (P≤0.05).  

(a) 

(b) 

(c) 

(d) 

(e) 



25 
 

  The RQ behavior was very similar to the CO2 emission, soil moisture and 

precipitation behaviors (Figure 2.3). In other words, the RQ was constant, lower than 

1, and had a mean variation from 0.9 to 0.27 and 0.17 to 0.31 for GH and BH 

treatment from the 4th to 10th days, respectively. However, after precipitation (12th 

day) the RQ was higher than 1 and obtained the highest RQ mean in BH (1.38 ± 0.46 

mol mol-1), while in GH the mean was lower than 1 (0.77 ± 0.46 mol mol-1).  

 

2.3.2 Accumulated FCO2, FO2 and RQ  

The cumulative FO2 had means of 202.52 (±49.62) and 267.41 (±73.6) g O2 m-

2, respectively, for the GH and BH managements (Figure 2.4a). When compared by 

student t-test (P≤0.05) we did not find a significant statistical difference between 

harvesting techniques on the FO2 uptake.  

The BH also had higher CO2 emission cumulative (87.07 ±19.45 g CO2 m-2), 

when compared with GH (52.31 ± 15.41 g CO2 m-2). However, for CO2 emission, the 

BH is significantly different (P≤0.05) with a 50.0% increase compared to the GH 

treatment (Figure 2.4a).  

The cumulative ratio between CO2 and O2, represented by RQ total, was lower 

than 1 in both treatments with means of 0.59 (±0.18) and 0.43 (±0.13), respectively 

for BH and GH (Figure 2.4b). When comparing the RQ for both treatment we did not 

see a significant statistical difference between them by the Students t test.  

 

Figure. 2.4. Soil CO2 emission cumulative (g CO2 m-2), soil O2 uptake cumulative (g 
O2 m-2) (a) and RQ total (mol mol-1) (b) in the ground with sugarcane managements 
with mechanized harvesting (GH) and burned harvesting (BH). In the figure: bars 
identified with upper-case letters when distinct, differ by the Student’s t-test (P≤0.05). 

 



26 
 

2.3.3 Relationships between soil CO2 emission and O2 uptake with soil moisture 

Soil  

The relationship between CO2 emission and soil moisture was positive and 

significant in both treatments (Figure 2.5a, c). However, the BH had the higher 

correlation (r= 0.74) than GH (r= 0.69).  

Despite the fact that the high correlation of soil moisture with CO2, when we 

compared the soil moisture with O2 uptake, was not significant for the BH treatment. 

However, the soil moisture for GH showed the negative correlation with O2 uptake 

(r=-0.46), Figure 2.5b and d.  

 

 

Figure. 2.5. Relationship between soil CO2 emission (µmol m² s-1) and O2 uptake 
(mg of O2 m-2 s-1) (a and c), and CO2 emission (µmol m² s-1) and soil moisture (%) (b 
and d), in sugarcane soil with mechanized harvesting (GH) and burned harvesting 
(BH). 

The relationship between CO2 emission and O2 uptake had opposite results for 

the BH and GH treatments. In BH, the correlation was negative and significant, but in 

GH there was no correlation between them (Figure 2.6). We also noticed that the GH 

(31.6%1.05) had a higher microporosity distribution compared with BH 

(29.0%0.60). However, GH had a lower macroporosity distribution with a decrease 



27 
 

of 23.9% (Table 1). Furthermore, the WFP was higher in BH (18.73%5.6) compared 

to GH (18.496.4) 

Figure. 2.6 Relationship between soil CO2 emission (µmol m-2 s-1) (a) and soil O2 
uptake (mg of O2 m-2 s-1) (b) in sugarcane soil with mechanized harvesting (GH) and 
burned harvesting (BH).  

 

2.4 Discussion 

2.4.1 CO2 and O2 results (Daily and accumulated) 

We noticed a relative consistent magnitude of the FCO2 on the 4th, 6th, 8th and 

10th day for GH and BH which suggests a corresponding stability in soil microbial 

activity (Figure 2.3). The microbial stability occurs after the soil carbon mineralization 

of soil organic matter (CUNHA et al., 2011; BADÍA et al., 2013; KNICKER et al., 

2013) and leads to higher emissions with higher microbial activity (LUO et al., 2006).  

However, we are not able to separate it into the components since the net emission 

comes from the biological activity of soil microbial respiration and root respiration as 

noticed by Stern et al. (1999), Lal (2009) and Melillo et al. (2002).  

The higher CO2 emission (Daily and Accumulated) in BH, compared to GH 

(Figure 2.3 and 2.4), has been observed in other studies, such as Panosso et al. 

(2009), Panosso et al. (2011) and Corradi et al. (2013) working with a similar Oxisol 

soil and BH and GH managements in the São Paulo state region. This difference 

could be explained by the higher nutrient availability in the BH treatment, due to 

burning, which has been mentioned by Marques et al. (2009) and Panosso et al. 

(2011). However, in our experiment we did not observe a significant difference in soil 

nutrients available in BH and GH. On the other hand, we noticed that the BH 

treatment presented higher macroporosity and PT, and lower microporosity 



28 
 

compared with GH (Table 1). The high porosity in BH could have been the result of 

burned sugarcane residue. Therefore, after the burned the porosity could have 

increased due to the opening of potentially charred root channels. Remembering that 

both the BH and GH had the same mechanical harvesting traffic and soil preparation.  

The relationship between soil porosity and CO2 emission has been reported by 

Xu and Qi (2001), Epron et al. (2006), Panosso et al. (2012) and Bicalho et al. 

(2014). It is so important that, according to Moitinho et al. (2015), when studying the 

FCO2 variability (spatial and temporal) it is necessary to include soil porosity 

variability. Wick et al. (2012) also mentioned that the soil porosity can help to explain 

the soil CO2 emission results.  

The soil porosity is responsible for soil gaseous transport (XU; QI 2001; 

EPRON et al., 2006) and movement of organic and inorganic solutions throughout 

the soil (RANJARD; RICHAUME, 2001). Consequentially, a porosity with a higher 

macroporosity proportion facilitates soil oxygenation, microbiological activity and 

increases FCO2 (FANG et al., 1998).  

Additionally, a larger portion of macropores would result in potentially faster 

infiltration rates, since the water would preferentially fill larger pores first (HILLEL, 

1980).  Moreover, soil porosity represents the natural habitat for microbial 

communities (RANJARD; RICHAUME, 2001).  

The lower FCO2 in GH to be a result of the sugarcane residues on the soil 

surface. In addition, these residues have a high C/N ratio (83.63) (ALMEIDA et al., 

2015), lignin (25.80%) (COSTA et al., 2013), cellulose (72.90%) (ALMEIDA et al., 

2009), and lower crude protein concentration (2.50%) (PEREIRA et al., 2000). These 

characteristic are important parameters in nutrient dynamics (LAL, 2004) and 

consequently, there is reduced accumulated CO2 due to slow residue decomposition 

(ALMEIDA et al., 2014).  

Some researchers have been noticed that the surface residue is an additional 

barrier for diffusive transport. It also certainly contributes to increased water retention 

(OHASHI; GYOKUSEN, 2007; CONCILIO et al., 2009) and decreased evaporation, 

thus providing a buffer for abrupt temperature fluctuations (MARQUES et al., 2009). It 

has happened because of the mechanical sugarcane harvest added an average 

thickness between 10 and 12 cm of accumulated residues on the soil surface 

(OLIVEIRA et al., 1999; ALMEIDA et al., 2015). However, we did not notice the 

increased water retention (soil moisture) at GH in our experiment (Figure 2.3b). 



29 
 

Differently from CO2, the O2 uptake did not present a significant difference in 

the BH and GH treatments (for all days observed and O2 accumulated), Figure 1 and 

2. Concentration profiles of O2 have a correlation with soil porosity (HILLEL, 1998; 

BRADY; WEIL, 2013), and the results, because the soil porosity is where the O2 can 

be found (GLINSKI; STEPNIEWSKI, 1985; HILLEL, 1998). This relationship is so 

important to soil microbial activity that Glinski and Stepniewski (1985) mentioned that 

the soil porosity is the oldest and simplest soil attribute that can be used as soil O2 

indicator.  

 

2.4.2 Relationships between soil CO2 emission and O2 uptake with soil moisture   

The temporal variability of soil O2 uptake was inverse when compared to CO2 

emission after precipitation, in our study (Figure 2.3). In the other words, after the 

precipitation, the O2 uptake decreased and CO2 increased in both treatments (Figure 

2.3c). Thus, the soil moisture can be considered as the key abiotic factor that affects 

the CO2 emission (GARDINI et al., 1991; HOWARD; HOWARD, 1993) and O2 uptake 

processes (GARDINI et al., 1991).  

Some researchers believe that soil moisture and soil aeration are the main 

factors that influence the CO2 emission into the atmosphere (FANG; MONCRIEFF, 

2001; COOK; ORCHARD, 2007; WEI et al., 2014). In fact, the soil temperature is 

another attribute that can also have an important influence (BENJAMIN et al., 2003; 

KYAW THA PAW et al., 2006; LAL, 2009; CHEN et al., 2011). Higher soil moisture 

has been observed to promote up to an 80% increase in FCO2 (CHEN et al., 2011) as 

a result of higher microorganism and root activity (LAL; KIMBLE, 1995; SMITH et al., 

2003) and lower diffusion of gases through the soil pores (HILLEL, 1998; IGNATIUS, 

1999; SMITH et al., 2003).  

That positive correlation between CO2 and soil moisture is reported for BH and 

GH treatments (Figure 3). It has also been observed by Ignatius (1999), Epron et al. 

(2006), Lal (2009), Moitinho et al. (2014) and Wei et al. (2014). Furthermore, Corradi 

et al. (2013) hypothesized that this correlation was positive and linear in soil moisture 

variations of 38-47% for an Oxisol with high clay content (636 g kg-1). According to 

Doran et al. (1990) and Chen et al. (2011) the highest soil respiration rates occur 

having between 40 and 70% water-filled pore (WFP) space in a majority of soils. In 

our experiment, the WFP was less than 70% of all treatments and days observed 

(Table 1).   



30 
 

The high correlation between FCO2 and soil moisture in BH was correlated to 

higher macroporosity and lower microporosity, as we saw in our results (Figure 2.5 

and Table 1). Moreover, the higher correlation coefficient in the BH, compared to GH, 

suggests that there is a high sensitivity of burned residue management to soil 

moisture variations. This results because of the connection between soil 

macroporosity and transport rates (SILVA et al., 2005). This concept is supported by 

the results of Ruser et al. (2006), in which they explained that the soil moisture did 

not influence the CO2 emissions as much as the differences in porosity between 

compacted inter-row soils and the un-compacted inter-row, where compacted soil has 

fewer macrospores and more microspores at bulk densities of 1.24 and 1.65 g cm-3, 

respectfully. Ceddia et al. (1999) noticed the water infiltration in sugarcane areas has 

a variation according to soil aggregations and porosity and normally the infiltration is 

faster in soil with higher macroporosity than microporosity.   

 Decreased O2 uptake after precipitation events was also observed by Linn 

and Doran (1984) and Gardini et al. (1991). Water infiltration reduces the amount of 

O2 in soil pores (COOK et al., 2007), and the water is a very effective at limiting the 

gas exchange (O2) between the soil atmosphere and air atmosphere (ARMSTRONG; 

DREW, 2002; ELBERLING et al., 2011). Moreover, in that condition, there is a strong 

correlation between O2 uptake and water filled pores (QUASTEL, 1965; COOK et al., 

1998).  

 

2.4.3 Relationships between soil CO2 emission and O2 uptake  

The FCO2 and FO2 were inversely correlated in the BH treatment. However, 

we did not notice a relationship between them in the GH treatment. We also observed 

that the FO2 was higher than FCO2 in both treatments. The higher O2 was also 

noticed by Angert et al. (2015) studying temperate and alpine forest ecosystems, and 

the relationship between FCO2 and FO2 in soil has also been noticed by Kyaw Tha 

Paw et al. (2006). With this result we can notice that there is a CO2 increase as result 

of O2 uptake in soil with a soil moisture variation of 6.44 to 14.5%.  This relationship 

is more expressive in management without surface residue.   

To understand and explain the FO2 as a respiration predictor we used the 

calculated respiration coefficient (RQ), where RQ values close to 1, is a result of 

aerobic respiration in soil with WFP lower than 70% and, this aerobic reaction has a 

higher metabolic efficiency. It should be remembered that RQ is determined on the 

basis of the CO2 emission and O2 uptake rate (DILLY, 2001). Some researchers, 



31 
 

such as Stotzky (1960), Alef (1995) and Dilly (2003), utilize RQ to elucidate the 

relation between the FCO2 and FO2. The RQ index has also been used as a criteria 

of the soil microbial activity across different WFP conditions (STOTZKY, 1960). 

We observed that the RQ was lower than 1 for BH and GH treatment before 

the precipitation on the days observed. Therefore, the RQ was higher than 1 after 

precipitation (12th day), with soil moisture variations from 6.4 to 14.5% and WFP 

values lower than 32.0% for BH and GH, respectively.  In other words, the RQ was 

higher than 1 under soil aerobic conditions.  

According to Linn and Doran (1984) the increase of RQ values of 1.3 to 1.7 

occurs with an increase of soil water and WFP value higher than 70%.  Nevertheless, 

in our experiment on the 12th day presented precipitation and the WFP value was not 

>70%, and the treatments had WFP values of 30.7% and 31.7% for BH and GH, 

respectively. Therefore, under this WFP condition, there was an aerobic respiratory 

predominance, as described by Franzluebbers et al. (1999), who noticed the 

maximum respiratory activity of soil microbial biomass at WFP levels ranging 

between 27% and 68%. 

Values of RQ >1 are suggestive of chemical and physical soil processes (e.g., 

Soil–gas exchange fluxes).  According to Angert et al. (2015), the variations in the 

RQ ratios in soil profiles can be a result of soil–gas exchange fluxes associated with 

biological respiration. Linn and Doran (1984) and Lal (2009) state that the physical 

process (soil–gas exchange fluxes) of water infiltration (percolation) triggers the 

expulsion of significant amounts of soil gases (e.g. CO2). Chemical additions can also 

trigger CO2 fluxes, such as liming (SILVA et al., 2015; ANGERT et al., 2015) and 

urea additions (MARQUES et al., 2000; DELBEM, 2011). However, the CO2 emission 

in the Mediterranean climate calcareous soils can be described by a diffusion process 

alone (ANGERT et al., 2015).   

High RQ values (> 1) can also occur with certain environmental conditions 

(ALEF, 1995), such as available soil or substrate compositions, the soil microbial 

community current nutritional conditions (DILLY, 2001; KUTZNER, 2013), carbon 

source (KUTZNER, 2013) or higher water contents (LINN; DORAN, 1984; GARDINI 

et al., 1991; IKEDA; NAKAMURA, 1996). Therefore, some environmental conditions 

may control the RQ ratio (DILLY, 2001). 

We believe that our results support the use of RQ as a respiration predictor 

with RQ values lower than 1; a situation that helps to explain the alterations in soil O2 

and CO2 fluxes. We also believe that our results can assist in the formulations of 



32 
 

mechanistic models for soil gas emissions (e.g. COOK, 1995; COOK et al., 2007; 

COOK; KNIGHT, 2003).  

 

2.5 Conclusion 

The FO2 is inversely correlated with soil moisture in the GH treatment. There is a 

positive correlation between soil moisture and FCO2. 

The FCO2 and FO2 profiles and correlation depend on soil  and crop residue 

managements. 

The FO2 can be used as an index for categorizing the source of CO2 respiration. The 

RQ values higher than 1 are results of soil–gas exchange fluxes after precipitation. 

 

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