Louise Jackson Dept. of Land, Air and Water Resources University of California at Davis

Transcription

1 Louise Jackson Dept. of Land, Air and Water Resources University of California at Davis

2 How much biodiversity should we try to conserve and why? Increased population and food demand Globalization of agriculture Human-induced rapid environmental change CBD commitment to sustain and protect biodiversity

3 Hypothesis: Biodiversity-based agriculture supports food security, helps to conserve wild biodiversity, and increases ecosystem services across the landscape Use of unique varieties, crop rotations, cover crops, insectary plantings, soil food webs, IPM, hedgerows, farmscape complexity, riparian corridors, habitat preservation, etc. How to test and implement: Integrated landscape approach Innovation + partnerships within local communities Investment: R&D, governance, and institutional support Global awareness and connectivity DIVERSITAS agrobiodiversity Network 2005; Jackson et al. COSUST 2010; Brussaard et al. COSUST 2010

4 Land sharing integrating biodiversity conservation and food production on the same land, using wildlife-friendly farming methods Land sparing separating land for conservation from land for crops, with high-yield farming facilitating the protection of remaining natural habitats from agricultural expansion Phalan et al. Science 2011 Sumatra Agroforest (c: M. van Noordwijk) Ghana Forest (c: B. Phalan)

5 Process by which farming systems increasingly: increase productivity and income substitute human labor with mechanization and fossil fuels use nonrenewable, purchased inputs, e.g., inorganic fertilizers and agrochemicals for pest suppression rely on more frequent cropping, less fallow/set aside, less cover crops and less organic matter amendments enlarge the sizes of fields and/or farms occupy most of the landscape lose biodiversity Matson et al. Science 1997 California conventional farmland

6 Biodiversity and agricultural intensification Plant-soil nitrogen cycling and agricultural intensification Biodiversity and ecosystem function approach in California s Central Valley Excess N + loss of soil biodiversity with high-input, highly productive agriculture Organic farm: re-establishment of plant/soil biodiversity and nutrient retention? AM fungi: function and diagnostic tools Linking multiple scales and functions: (gene landscape farmers)

7 What indicators and diagnostics of N cycling and retention? Jackson et al. Ann Rev Plant Biol 2008

8 Meta-analysis of 206 N addition expts Increase in: Plant and litter N (50%) Total soil N (6%) Nitrate (430%) N 2 O (135%) Leaching (460%) Decrease in: Microbial N (-6%) Lu et al. New Phytol 2011 Agricultural ecosystems (open bars) Non-agricultural ecosystems (closed bars)

9 Van Groenigen et al. Nature 2011 Meta-analysis of CO 2 enrichment expts eco 2 stimulated N 2 O emissions Less transpiration Higher soil moisture More roots and labile C

10 Biodiversity and agricultural intensification Plant-soil nitrogen cycling and agricultural intensification Biodiversity and ecosystem function approach in California s Central Valley Excess N + loss of soil biodiversity with high-input, highly productive agriculture Organic farm: re-establishment of plant/soil biodiversity and nutrient retention? AM fungi: function and diagnostic tools Linking multiple scales and functions: (gene landscape farmers)

11 Waterways in a I50 km 2 landscape in California s Central Valley Irrigated row crops to grazed dryland savanna GIS analysis to obtain representative data across the landscape Ecological assessments & farmer interviews (sites shown) Agricultural intensification index: non-renewable inputs + landscape complexity at each site Culman et al. Landscape Ecol 2010 Young-Mathews et al. Agroforestry Systems 2010 Sánchez-Moreno et al. Soil Biol Biogeochem 2011

12 Residuals of abundance vs. richness of soil biota and plants NO 3 - : strongest effect of all soil variables Low slopes Slight decrease with NO 3 - except microbial feeding nematodes Sánchez-Moreno et al. Soil Biol Biogeochem 2011 Log soil nitrate at 0-15 cm depth (μg NO 3- -N g -1 soil) Dry grazed grassland & savanna (open circles) Irrigated row crops & orchards (closed circles)

13 Organic > Conventional Renewable inputs Biodiversity Soil C and N Arbuscular mycorrhizae Soil microbial biomass Ecology-based management strategies USDA Organic Foods Act IFOAM Innovation Markets increasing Tanimura & Antle Monterey Co. California Fetzer Vineyards Mendocino Co. California Rominger Farms Yolo Co. California

14 How does organic management affect nutrients and soil biota in wooded and cultivated farm habitats? Selecting a farmscape Similar soil in all habitats Participatory research Monitoring for 2 years Associations between biodiversity and ecosystem function Smukler et al. Ag Ecosyst Env 2010 fields riparian ditch Tomato and grain fields, riparian, hedgerow, drainage ditch and pond habitats at Rominger organic farm in Yolo County, CA

15 16 Anion Exchange Resin Bags x Nitrate-N (0-30 cm depth) 40 kg N ha -1 in crop season 10 kg N ha -1 in winter Nitrate leaching (60 cm depth) in anion resin bags 10 to 80 kg N ha -1 yr -1 Slightly higher in ditches Infiltration lowest in tailwater ponds and ditches N 2 O emissions (mean) 5 to 7 μg N m -2 hr -1 (fields) 15 μg N m -2 hr -1 (ditches) NO3 - -N (g m -2 ) Infiltration rate (cm minute -1 ) DOC (mg L -1 ) a abc a z Year 1 Year 2 a z a yz Infiltration ab b Lysimeter Dissolved Organic Carbon a x x ab ab Riparian Corridor Hedgerow South Field North Field Tailwater Pond Ditches x c b ab z b b y a b 30 cm Years 1&2 60 cm Year 1 60 cm Year 2 z b y b x

16 No differences between wooded and cultivated habitats in: Amount of fungal PLFA Number of fungal feeding nematodes Higher soil OM in wooded than cultivated habitats 15% higher total soil C 150% higher soil mic. biomass Why lack of increase in soil biota with higher soil OM? Field management? Few reservoirs of biodiversity in the landscape? Fungal markers: 16:1w5c, 18:1w9c, 18:3 006c (6,9,12) Earthworm Nematode (number 100 g -1 soil) PLFA (nmol g dry soil -1 ) 100 AB Nematodes PLFA x- A a- a- A xy- xya- a- A AB a- ab- Gram+ Gram- Fungi Actinomycetes Unclassified Riparian Corridor Hedgerows South Field North Field Tailwater Pond Ditches A AB a- A AB b- y- Bacterial-Feeders Fungal-Feeders Predators Omnivores Plant Parasites and Herbivores C B a- a- abc- abbc- c- a- xy- xy- ab- b- b- B BC AB 0-15 cm depth

17 Biodiversity and agricultural intensification Plant-soil nitrogen cycling and agricultural intensification Biodiversity and ecosystem function approach in California s Central Valley Excess N + loss of soil biodiversity with high-input, highly productive agriculture Organic farm: re-establishment of plant/soil biodiversity and nutrient retention? AM fungi: function and diagnostic tools Linking multiple scales and functions: (gene landscape farmers)

18 Field studies of two tomato genotypes rmc = Mycorrhiza defective mutagenized mutant 76R MYC+ = Mycorrhizal wild-type progenitor Organic vegetable-alfalfa farm 15 years of organic farming Mycorrhizal colonization 30% Similar PLFA and nematode communities with both genotypes 3 treatments in root in-growth rings 0, 6.5 & 65.0 g NH 4+ -N g -1 soil Indicators of ecological functions of AM (?) 76R MYC+ rmc Microarray Expression of specific gene(s) Diagnostic tool OR Open profiling platform Profile of gene sequences Diagnostic tool Ruzicka et al. Pl Soil 2011; BMP Pl Biol 2010; Cavagnaro et al. Pl Soil 2005

19 Microarray: MYC+ genotype changed expression of 174 genes on chip qpcr: LeAMT4 and LeAMT5 are AMspecific similar to L. japonicus LjAMT2.2 and M. truncatula MtAMT

20 Affymetrix tomato microarray is limited to known tomato genes Fungal genes are expressed in arbuscule Mycorrhizal-regulated tomato genes not on microarray Use next generation sequencing for de novo transcriptome analysis Tomato has a reference genome sequence, AMF does not Use 454 sequencing to capture long reads and create better contiguous assemblies Myc+ genotype s specific transcripts (Plant and Fungal) = (Water injected WT - Water injected rmc)

21 Contigs (joined reads) blasted against NCBI nr database (all organisms) and against tomato genome 27,870 annotated as plant/tomato 765 annotated as fungal 1354 did not match any known gene sequences 17 annotated as virus 57 annotated as nonplant and non-fungal 2210 mycorrhizal specific contigs identified >40% not previously recognized (959/2210) Could be used for ecological interpretation without IDs contigs unique to the MYC+ genotype tomato fungi other no hit

22 Biodiversity and agricultural intensification Plant-soil nitrogen cycling and agricultural intensification Biodiversity and ecosystem function approach in California s Central Valley Excess N + loss of soil biodiversity with high-input, highly productive agriculture Organic farm: re-establishment of plant/soil biodiversity and nutrient retention? AM fungi: function and diagnostic tools Linking multiple scales and functions: (gene landscape farmers)

23 What are informative indicators of N availability in organically-managed systems? What are the trade-offs for multiple ecosystem functions (soil quality, C stocks, production) in response to management? Bowles, in progress 13 sites representing the range of environmental and management conditions for organic vegetable production for Yolo Co., CA

24 root gene expression soil biogeochemistry linking farmer attitudes and markets management interventions soil biota productivity

25 Jackson et al. Ann Rev Plant Biol 2008

26 Biodiversity-based agriculture and land-sharing support multiple ecosystem services, requiring a multi-scale approach. High-input agriculture reduces diversity of plant and soil communities and reactive N, even in non-agricultural habitats. Mechanisms and diagnostics for biodiversity-mediated N processes in agriculture could better combine soil biogeochemistry, plant physiology, and genetics. Biodiversity-based N management needs contextual integration of soil ecology, location, markets, and farmer attitudes. Thank you for listening, and to many collaborators especially Howard Ferris, Allan Hollander, Sara Sánchez- Moreno, and Daniel Schachtman, as well as

27 Sean Smukler Felipe Barrios- Masias Steve Culman Annie Young-Mathews Tim Cavagnaro Dan Ruzicka Amanda Hodson Tim Bowles Philipp Raab

28 Our 454 data = 1.2 million sequence reads (average length 300 nt) WT MYC+ rmc myc- 1.2 million reads assembled into 30,063 contig sequences Relative expression determined by # of reads from each sample type in a given contig assembly. WT MYC+ rmc myc- 6 1

29 UNDER LOW NITROGEN TREATMENT Key tomato genes involved in N uptake and assimilation were differentially regulated in mycorrhizal and nonmycorrhizal roots Higher in rmc Higher in wt 29

30 Relative Signal Intensity Microarray Relative Expression qrt-pcr Relative Expression (n=5) Relative Expression n=6 AM fungi supplies roots with additional N high N assimilation Asparagine Synthetase P interaction < WT rmc P < P = control low N high N Glutamine synthetase P interaction = P < control low N high N AS and GS more highly expressed at high nitrogen conditions More highly expressed in WT roots compared to rmc under limiting nitrogen conditions 30

31 Microarray Relative LN(Signal Expression Relative Intensity) Expression (n=5) Microarray Relative Expression LN(Signal Intensity) Nitrate uptake pathway in nonmycorrhizal roots LN(Signal Intensity) Microarray Relative Expression Copper Nitrate Transporter transporter 1.1-like genes P genotype = WT rmc Copper transporter genes Nitrate Reductase NR 4 P interaction = WT P = rmc Copper transporter genes Nitrite Reductase Nii P interaction WT = rmc P = control low N high N COPT2 Cu chaperone control low N high N COPT2 Cu chaperone Transcriptome data suggests direct root uptake of nitrate is reduced in mycorrhizal roots under limiting N conditions control low N high N COPT2 Cu chaperone 31

32 Functional categorization of mycorrhizal-specific fungal contigs Category # contig sequences % of MYC+ specific contigs Selected gene functions of interest cell growth and division % cell division cycle family member, cell polarity protein cell structure % cyctoskeleton proteins, histone family members disease defense % ferrooxidoreductase, cu-zn superoxide dismutase energy % malate dehydrogenase, nadp-dependent mailc enzyme, isocitrate dehydrogenase intracellular trafficking % synaptobrevin vesicle-associated membrane protein, rab gdpdissociation inhibitor metabolism % inorganic pyrophosphatase, chitin synthase export chaperone, ornithine aminotransferase, hexokinase, chitin synthase, glycerol dehydrogenase protein storage and destination % secondary metabolism % cytochrome p450 signal transduction % gtp-binding protein, rho gtpase, g-protein complex alpha subunit transcription % RNA polymerase, RNA binding, no dna-binding transcription factors found translation % ribosomal proteins, initiation and elongation factors transporter % see next slide unknown %

33 mid-1990s NO N y 2 6 NHx Galloway et al., 2003b 5 NO N y 2 NHx N 2 + 3H NH 3