Cross-cutting activities: Soil quality (prepared by Peter Motavalli) Soil metagenomics

Peter Motavalli, Bunjirtluk Jintaridth, Johannes Lehmann, Keith Goyne, and Jere Gilles ASSESSING AND MANAGING SOIL QUALITY FOR SUSTAINABLE AGRICULTURAL SYSTEMS SANREM-CRSP CROSS-CUTTING INITIATIVE

Soil degradation is a major global environmental problem, resulting in increased poverty and severe environmental problems (e.g., decreased biodiversity and water quality) (Eswaran et al., 1997).Soil degradation is a major global environmental problem, resulting in increased poverty and severe environmental problems (e.g., decreased biodiversity and water quality) (Eswaran et al., 1997). For example, the loss of potential productivity due to soil erosion world wide is estimated to be equivalent to some 20 million tons of grain per year (UNEP, 1999).For example, the loss of potential productivity due to soil erosion world wide is estimated to be equivalent to some 20 million tons of grain per year (UNEP, 1999). INTRODUCTION

Almost 75% of Central America’s, 45% of South America’s, and 11% of Asia’s agricultural land have been seriously degraded. (Scherr, 1999; Heerink, 2001).Almost 75% of Central America’s, 45% of South America’s, and 11% of Asia’s agricultural land have been seriously degraded. (Scherr, 1999; Heerink, 2001). Three-quarters of Africa’s farmland has severe soil degradation caused by wind and soil erosion and loss of mineral nutrients (Heano and Baanante, 2006).Three-quarters of Africa’s farmland has severe soil degradation caused by wind and soil erosion and loss of mineral nutrients (Heano and Baanante, 2006). INTRODUCTION (CONT.)

Definition : “ the capacity of a soil …. to sustain biological productivity, maintain environmental quality, and promote plant and animal health” (Doran and Parkin,1994). SOIL QUALITY

Soil quality depends on the capacity of a soil to perform a desired ecosystem functionSoil quality depends on the capacity of a soil to perform a desired ecosystem function Soil functions –Soil functions –  sustaining biological activity, diversity, and productivity  regulating and partitioning water and solute flow  filtering, degrading, immobilizing and detoxifying organic and inorganic species  storing and cycling of nutrients  providing structural support SOIL QUALITY (CONT.)

Biological indicators – (e.g., microbial community structure and activity)Biological indicators – (e.g., microbial community structure and activity) Chemical indicators – (e.g., pH, CEC)Chemical indicators – (e.g., pH, CEC) Physical indicators – (e.g., infiltration, bulk density, water-holding capacity)Physical indicators – (e.g., infiltration, bulk density, water-holding capacity) Soil organic matter is an important soil quality index because of its integral role in soil biological, physical and chemical processes (Carter, 2002)Soil organic matter is an important soil quality index because of its integral role in soil biological, physical and chemical processes (Carter, 2002) SOIL QUALITY (CONT.) USDA Soil Quality Test Kit

Assess community perceptions and indicators of soil quality, including differences in perceptions of soil quality due to gender, environment and socio-economic factors.Assess community perceptions and indicators of soil quality, including differences in perceptions of soil quality due to gender, environment and socio-economic factors. Determine the effectiveness of spectroscopic- based (i.e., near-infrared, mid-infrared, and visible range) analytical methods to evaluate soil organic matter fractions and soil quality in degraded and non-degraded soils in a wide range of environments.Determine the effectiveness of spectroscopic- based (i.e., near-infrared, mid-infrared, and visible range) analytical methods to evaluate soil organic matter fractions and soil quality in degraded and non-degraded soils in a wide range of environments. To collaborate in the evaluation of soil metagenomic methods as an indicator of soil degradation.To collaborate in the evaluation of soil metagenomic methods as an indicator of soil degradation. OBJECTIVES

Will use participatory workshops of community members and professionalsWill use participatory workshops of community members and professionals What are the specific soil quality indicators that community members use to evaluate soil quality among the different soil types and crops?What are the specific soil quality indicators that community members use to evaluate soil quality among the different soil types and crops? How has soil quality changed over time and why?How has soil quality changed over time and why? The communities will be surveyed to determine the characteristics of a field soil quality testing procedure that would be appropriate for their conditions and for evaluating sustainable agricultural management practices.The communities will be surveyed to determine the characteristics of a field soil quality testing procedure that would be appropriate for their conditions and for evaluating sustainable agricultural management practices. METHODOLOGY

COMMUNITY PERCEPTIONS OF SOIL RESOURCES AND SOIL-RELATED PROBLEMS IN BOLIVIA Soil-related problems are only one of several factors limiting crop production.Soil-related problems are only one of several factors limiting crop production. Soil management problems identified were:Soil management problems identified were: Low soil quality and soil fertility (low soil nutrient content, high clay content and stoniness) Low soil quality and soil fertility (low soil nutrient content, high clay content and stoniness) Excessive water and wind-induced soil erosion Excessive water and wind-induced soil erosion Insufficient soil moisture due to lower rainfall Insufficient soil moisture due to lower rainfall Inadequate soil management practices (Inappropriate tractor tillage practices, lack of a suitable crop rotation strategy, insufficient soil fertility inputs, and overgrazing by sheep) Inadequate soil management practices (Inappropriate tractor tillage practices, lack of a suitable crop rotation strategy, insufficient soil fertility inputs, and overgrazing by sheep)

Soils will be collected from depths of 0-10 to cm from degraded and non-degraded agricultural fields (i.e., Sanborn Field, Bolivian, Ecuadorian, Zambian, and Asian studies)Soils will be collected from depths of 0-10 to cm from degraded and non-degraded agricultural fields (i.e., Sanborn Field, Bolivian, Ecuadorian, Zambian, and Asian studies) The soil will be freeze-dried, ground and sieved to a size fraction <2 mm diameter.The soil will be freeze-dried, ground and sieved to a size fraction <2 mm diameter. Climatic information will be obtained.Climatic information will be obtained. All samples will be analyzed by using spectroscopic methods.All samples will be analyzed by using spectroscopic methods. Soil texture, pH, CEC, total organic C, total N, water-soluble total organic C and total N, particulate organic matter C and N, soil test P (Bray 1 P), exch. K, Ca, and Mg will be determined.Soil texture, pH, CEC, total organic C, total N, water-soluble total organic C and total N, particulate organic matter C and N, soil test P (Bray 1 P), exch. K, Ca, and Mg will be determined. METHODOLOGY

Labile C Determination Using KMnO 4 (Weil, 2003) Evaluating two methods: FIELD METHODS Portable field spectrometer – 550 nmPortable field spectrometer – 550 nm Field chartField chart

Portable Field Near Infrared (NIR) Spectrometer Determination of soil organic C using a portable field NIR spectrometer, Fieldspec Pro FR (Stevens et al., 2006)Determination of soil organic C using a portable field NIR spectrometer, Fieldspec Pro FR (Stevens et al., 2006) It may relate to use of remotely sensed infrared imagery to improve diagnostic capabilities to assess plant and soil health.It may relate to use of remotely sensed infrared imagery to improve diagnostic capabilities to assess plant and soil health. For this study, we will do the NIR analysis of soil samples in the laboratory and not in the field.For this study, we will do the NIR analysis of soil samples in the laboratory and not in the field. FIELD METHODS

Coordinate soil quality survey with collaborators in the SANREM ProjectsCoordinate soil quality survey with collaborators in the SANREM Projects Distribute and organize field tests with soil quality kits with collaboratorsDistribute and organize field tests with soil quality kits with collaborators Obtain soil samples and site histories from degraded and non-degraded sites in coordination with SANREM and soil metagenomic projectsObtain soil samples and site histories from degraded and non-degraded sites in coordination with SANREM and soil metagenomic projects Develop laboratory methodologies and conduct analyses.Develop laboratory methodologies and conduct analyses. Two graduate students (one Thai and one Bolivian)are being trained.Two graduate students (one Thai and one Bolivian)are being trained. TASKS

Soil metagenomics

Metagenomics: The study of the genetic make-up of a whole community, such as the soil bacterial community We are sequencing ribosomal DNA to distinguish microbial taxa and characterize microbial communities (and exploring the use of microarrays for functional gene analysis) SOIL METAGENOMICS

Objectives Characterize soil microbial communities from soils representing a range of levels of degradation Identify microbial taxa that are indicators for levels of degradation, especially those that may indicate the process of degradation has begun but is still reversible Link soil community structure to both the general soil biophysical context and the social science context in order to understand human impacts and drivers of human decision-making for soil management SOIL METAGENOMICS

Research plan We are linking with SANREM studies of soil degradation in Bolivia, Zambia, and Ecuador Project began 2008 SOIL METAGENOMICS

Research steps Collaboratively determine the best sampling sites and sampling procedures to represent a range of soil degradation and quality Extract DNA from each soil sample Sequence DNA corresponding to each sample and evaluate the resulting lists of microbes Analyze microbial community composition and model relationship with soil degradation, other soil properties, and socioeconomic context Translate genomics results: Community outreach and recommendations for management and policy Performed in Bolivia and Ecuador, associated with a training workshop and implementation of a basic molecular lab

Current status Lorena Gomez is the MS student at KSU (US) and she has begun training for the project and preparation of the soil metagenomics workshop materials We will recruit MS students at UMSA (Bolivia) and in Ecuador We will analyze our first samples from Zambia in July We will present a workshop on soil metagenomics in La Paz and analyze Bolivian samples in August We will sample in Ecuador later in 2008 SOIL METAGENOMICS

QUESTIONS?COMMENTS?SUGGESTIONS?