Soil resources and soil microbial processes in agro-environments Aiming at improved agricultural. practices

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1 Sustainable cultivation methods for agriculture increasing soil crop cover and optimizing ecosystem services of soil microorganisms (SUCCESS) Soil resources and soil microbial processes in agro-environments Aiming at improved agricultural practices Timo Sipilä Henvi, Global Environmental Change Programme MTT, Changing Climate and Agriculture

2 Content 1. Introduction 2. SUCCESS-project 3. Subproject 3 - Microbial deliverables for sustainable agricultural practices -Methodological outline 4. Expected research results

3 Agricultural adaptation to climate change is needed Predicted impacts of the climate change in Finland - Elevated winter temperatures and precipitation, and shortened snow cover period - Main part of annual agricultural erosion and nutrient loading is generated outside the growing season Erosion and nutrient leaching to the freshwaters and to the Baltic sea is accelerating in course of climate change Adaptation requires - Prevention of winter time erosion - Methods to suppress plant pathogens and pests emerging in course of climate change - Winter time crop cover reduces the erosion and land degradation out side the growing season

4 Crop cover intensity has a effect on soil erosion Winter crop cover: can be achieved using reduced autumn ploughing or with perennial crops Zero tillage Reduced tillage Crop cover Tillage intensity Autumn ploughing

5 Crop residues in conservation tillage may hamper in spring Slower drying and warming of soil Risk of yield losses Increased risk of soil and crop residue born plant diseases New sustainable agricultural practices have to be developed

6 Mind map of potential effects conservation tillage vs. ploughing Expenses Crop yield Ploughing Biodiversity Erosion, land degradation and nutrient leaching Eutrophication of waterways Biological Control Conservation tillage Amount of fungal patogens Use of chemical pesticides

7 Agricultural field sites Several long and short-term field experiments located on clayey soils in Jokioinen, in southwestern part of Finland. Tillage intensity: Mono cultured fields with different tillage intensities Crop rotations in different tillage intensities Crop rotations fields: 1) Spring wheat (Triticum aestivum) monoculture. 2) Crop rotations Spring wheat, spring barley, turnip rape, and pea.

8 Monocultured plots at KaSu-experimental field (Ojainen, Jokionen, 2008 autumn)

9 SUCCESS-project Aim is to develop innovative and feasible agro-environmental technology for improvement of environmental sustainability of cultivation methods Subproject 1 Agrotechnological maintenance of crop cover Subproject 2 Fungi to accelerate decomposition of crop residues Subproject 3 Soil suppressiveness against plant diseases Social impact

Subproject 1: Agrotechnological maintenance of crop cover Amount, handling and location of crop residues Automatic continuous monitoring of soil physical properties and weather, soil structure

10 Subproject 1: Agrotechnological maintenance of crop cover Amount, handling and location of crop residues Automatic continuous monitoring of soil physical properties and weather, soil structure around the year Modeling of soil air interface with different crop covers (evaporation, soil warming/drying) Nutrient balance and crop development Wireless automatic weather stations at the field site

11 Automatic continuous monitoring of soil physical/chemical properties, weather and soil structure

Producer of novel cellulytic and hemicellulytic enzymes Fungi are isolated from straw

12 Subproject 2 Fungi to accelerate decomposition of crop residues Isolation saprotrophic fungi Testing the decomposer efficiency Identification of antagonistic signal compounds Producer of novel cellulytic and hemicellulytic enzymes Fungi are isolated from straw bags that are overwintered in different soil depth of field experiments (Surface, -10 and -20 cm)

13 Subproject 3: Soil suppressiveness against plant diseases Biotests for estimation of agricultural soil suppression capacity to soil and crop residue born cereal pathogens Identification of potentially suppressive microbes Bacterial and fungal pure cultures: laboratory studies on suppression mechanisms

14 Soil fungistasis Fungistasis = Restriction of germination and growth of fungi induced by (in)direct contact with soil Fungistasis affects both plant-pathogenic and saprophytic fungi Pathogens are more sensitive to fungistasis than saprotrophs Positive and negative consequences for plant disease development In general fungistasis for a pathogenic fungal species is found to be positively correlated disease suppressiveness of soils

Soil pathogen suppression capacity Soils have different capacity to suppress plant pathogens Suppression is dependent on: suppression - Physical and chemical soil properties - Fungal life-history -

15 Soil pathogen suppression capacity Soils have different capacity to suppress plant pathogens Suppression is dependent on: suppression - Physical and chemical soil properties - Fungal life-history - Soil microbial activity/community composition Biological factors seems to be important in soil pathogen suppression soils General suppression 4 Soil suppression is possible to divide in to pathogen specific and general suppression Specific suppression to certain pathogen De Boer 2008 Berner et al 2003

Microbial antagonism of plant pathogens Several

pathogens The bacterial populations from soils with

be characterised Population markers correlating

isolation of biocontrol strains Antagonism: the

16 Microbial antagonism of plant pathogens Several micro-organism have capacity to suppress plant pathogens The bacterial populations from soils with different plant pathogen suppression capacity can be characterised Population markers correlating with soil suppression capacity can be used to guide isolation of biocontrol strains Antagonism: the action of any microbes that suppress the activity of a plant pathogen

1,40E+09 340 Modern soil microbiology, Van Elsas et al 2006 Great plate count anomaly = cultivation micro-organism leads to

17 Soil microbial communities have huge uncharted potential Metagenome size (Bp) DNA source E. coli genome equivalents E. coli 4,10E+06 1 Pasture soil 3,40E Forest soil 2,50E Forest soil, cultivated prokaryotes 1,40E Arable soil 1,40E Modern soil microbiology, Van Elsas et al 2006 Great plate count anomaly = cultivation micro-organism leads to substantially lower amount and diversity of micro-organism than cultivation independent methods Soil microbial community stained with DAPI Plating of bacteria

18 Microbial community analysis Most efficient way to study diverse microbial communities is sequence analysis of amplified marker genes from environmental DNA/RNA extracts 16S rrna gene is most frequently used marker gene due to its universal nature and phylogenetic robustness Recent development of massive parallel sequencing technology has opened a new window to microbial communities

19 Molecular analysis of microbial communities DNA/RNA extraction PCR = polymerase chain reaction community fingerprinting T-RFLP cloning + RFLP microbial community in agricultural soil DGGE DNA sequencing + phylogenetic analysis ATGCCTAGCCTAGC... ATGGCTTGCGTTGC... ATCGCAAGCCTTGG...

20 Methodological outline (Subproject 3) Field soils with different agricultural practises Characterization of soil fungistasis Soil plant pathogen supression capacity Microbial markers specific to soil suppression Characterization of microbial populations Method to assess biocontrol potential of soils Evaluation of general disease suppression Management of agricultural microbial Universitycommunities of Helsinki to improve general disease suppression Soil plant pathogen supression bioassay

21 Expected research results Subproject 1 Physical model of soil and air interface around the year with different crop cover Subproject 2 Agricultural saprophytic fungi important in straw residue biodegradation and their enzymes in cellulose biodegradation Producer of novel cellulytic and hemicellulytic enzymes Subproject 3 Management of the resident soil microbial community to increase general disease suppression of soil microbes, diminish the activity of soil born plant pathogens and to improve plant health."

22 SUCCESS-project partners Agrotechnological maintenance of crop cover Dept. of Agrotechnology, Laura Alakukku (Coordinator) (Soil and environmental technology) Dept of biological and environmental sciences, (Environmental sciences) Fungi to accelerate decomposition of crop residues Dept of Applied Chemistry and Microbiology, Annele Hatakka (Environmental biotechnology ) MTT Agrifood Research Finland Soil suppressiveness against plant diseases Dept of biological and environmental sciences, (Kim Yrjälä) (General microbiology) MTT Agrifood Research Finland MTT Agrifood Research Finland, Ansa Palojärvi (Coordinator at MTT) International cooperation: Wietse de Boer, Centre for Terrestrial Ecology, Netherlands. Göran Bergkvist, SLU, Department of Crop Production Ecology, Sweden.

23 Thank you for your attention!!!

Insight into microbial world molecular biology research in environmental microbiology

Insight into microbial world molecular biology research in environmental microbiology Aleksandra Ziembi ska The Silesian University of Technology, Environmental Biotechnology Department aleksandra.ziembinska@polsl.pl