Soil Microbiology and Its Effects on Nutrient Availability and Uptake in Plants (And Other Things)

Soil Microbiology and Its Effects on Nutrient Availability and Uptake in Plants (and other things)

Dept. of Land, Air & Water Resources Agricultural Sustainability Institute Outline • Soil biodiversity and farming (short film) • Role of soil microbes in growing things – Organic matter – Nitrogen cycling – Phosphorus cycling – Soil structure • Managing soil biology for plant growth and sustainability • Indicators—how do we measure how we are doing? • Discussion Film Above ground diversity is often intentionally low in managed systems

Most ecoecosystems concentrate biodiversity belowground Soil is one of most diverse microbial habitats: Thousands of “species” can be detected in gram of soil. Most not yet idenﬁed nor their funcon(s) known.

Microbes include: Bacteria, Archaea, and Fungi. Of bacteria and archaea, ~1500 diﬀerent taxa detected in CA cropping systems. Types of soil organisms

centipede rove pseudo scorpion beetle

ant

flatworm

mite ground beetle

adult fly fly roundworms larvae rove beetle mite beetle bacteria millipede

fungi archaea snail archaea

mite And archaea and fungi earthworm

organic debris diagram berdasarkan konsep Dr. Daniel Dindal, 1978

3 Breakdown wastes, make Remove pesticides and compost nutrients in buffer strips Build soil Contribute to structure biodiversity Develop antibiotic resistence (or not)

Contaminate food (or not) Support plant and animals via mutualism Sequester carbon Fix nitrogen Biodegrade pesticides in ﬁeld

Source/sink Build soil of GHG organic matter Control and cycle Support farmer’s Fight/suppress

pests (IPM) publications/explore/images/scenewide2.jpg publications/explore/images/scenewide2.jpg http://images.google.com/imgres?imgurl=http://www.sare.org/ plant nutrients digestion and immunity How microorganisms contribute to farms and gardens (the good, the bad and the ugly) Microbes tightly coupled with plants and soil: can’t decouple biodiversity from soil

Drivers Climate Management Crop rotation Organic Resource Quality Tillage Water/ Nutrient Supply Plant and Factors Soil Soil Properties

Biodiversity and processes Synchrony

Carbon e.g., Organic Processes Maintaining and matter, texture soil Nutrient structure Cycles

Nutrient Use Efﬁciency Water Use Efﬁciency Services Carbon Sequestration Water/Nutrient Use Water/Nutrient

Sustainable Agroecosystems Adapted from Brussaard et al. 2007 BUILDING Climate Management Crop rotation ORGANIC MATTER Organic Resource Quality Tillage

Plant and Soil Soil Properties Biodiversity and processes

Carbon e.g., Organic and Maintaining matter, texture soil Nutrient structure Cycles

Nutrient Use Efﬁciency Water Use Efﬁciency

Carbon Sequestration Soil organic matter (SOM) formation

Microbes are enzymatic drivers and also “feedstock” for SOM

Persistence of soil organic matter as an ecosystem property (2011) Schmidt et al. Nature 478, 49–56 News Articles Videos Images Books Reference Search ... Go

Health & Medicine Mind & Brain Plants & Animals Earth & Climate Space & Time Matter & Energy Computers & Math Fossils & Ruins

Science News ... from universities, journals, and other research organizations Save Email Print Share Fertile Soil Doesn't Fall from the Sky: Contribution of Bacterial Just In: Older Adults Made Less Forgetful Remnants to Soil Fertility Has Been Underestimated Until Now more breaking science news Dec. 14, 2012 — Remains of dead bacteria have Social Networks enlarge far greater meaning for soils than previously Recommend ScienceDaily on Facebook, Twitter, assumed. Around 40 per cent of the microbial and Google +1: biomass is converted to organic soil components, 47,738 people like this. Be the first News Articles Videos Images Books Reference Search ... L ikGeo Send write researchers from the Helmholtz Centre for of your friends. 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Arr o(uLned 4ib0 pneirz ce Unt onf ithvee mriscriotbyial and Google +1: ShaSrehaSrehaSrehaSrehaSrehaSrehaSrehaSreha|re 68.9K biomass is converted to organic soil components, Like Send 47,738 people like this. Be the first Hannover) in the journwarilte B reisoeagrceheorsc frhome mthei Hsetlrmyh.oltz Centre for of your friends. Environmental Research (UFZ), the Technische Tweet 23.5K Follow 53.7K followers UUnntiivle nrsoitäwt ,D riet swdeans ( Taeschsnuicmale Udn ivtherasitt yt hofe Breaking News ... from NewsDaily.com Share This: oDrgreasndeicn ) c, tohme Upnoivneersnittys o fo Sft otchkeho slmo, itlh ew Mearex- The electron micrograph shows bacteria+5708 Recommend this on Google Planck-Institut für Entwicklungsbiologie (Max Other bookmarking and sharing tools: cPolmanpcko Isnsetidtu tme fors Dtleyv eolofp dmeenctoalm Bipoolosgye)d and the (Hyphomicrobium sp;. 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SOM genesis: microbial biomass as a NASA Mars rover ready to eat, anaplyozew rodcker Persistencemicrobia ofl b soiliom organicass w matterhich t ashe ann ecosystem propertySchuri g(2011)/ UFZ Schmidt) et al. Nature 478, 49–56 provides the source material to soil signiﬁcant source. Biogeochemistry, 2011 powder provides the source material to soil Mini planet found far beyond Earth's solar system See Also: oSregea Anlsioc: matter. organic matter. Mini planet found far beyond Earth's solar system Related Stories Subatomic calculations indicate finite lifespan for Soil organic matter represent the Related Stories Plants & Animals universe Subatomic calculations indicate finite lifespan for largest fraction of terrestrially bound SoiSl ooil rTgypaesnic matter represent the Findings On Biochar, Greenhouse Gas Plants & Animals carbon in the biosphere. The Russia asks: How do you stop spaucen oibvjeectrsse Organic Emissions and Ethylene (Dec. 13, 2011) largest fraction ocfo mteporurnedss tthreiarelfolyre pblaoy uannd hitting Earth? Soil Types Fungus — Adding a charred biomass material important role not only for soil fertility Findings On Biochar, Greenhouse Gas carbon in the biosphere. The called biochar to glacial soils can help Raytheon says aces missile-detectRionu tsesstsi ain asks: How do you stop space objects Earth & Climate and agricultural yields. They are also Organic reducEe memisssisoniso onf tshe agrneednh oEustehyleneU. S(Dec. 13, 2011) Landslides one of the key factors controlling the hitting Earth? compounds therefore play an gases carbon dioxide and nitrous oxide, according "Meteorite rush" begins as Russian scientists Fungus Geochemistry concentration of carbon dioxide in — Adding a charred biomass material important role not only for soil fertility to ... > read more find fragments Acid Rain the atmosphere. 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Or view throughout our soil samplespr.o vSideu tcheh s ifmrpalegstm exeplnantastio hn faorv thee satalsbilois abtioen eofn poenr lsifei sont eEanrtch.e S coiefn twistse headve ssheowend thsa t ignlo btahl e hsouorliyl .u pOdartegda nnewiscfeeds in your RSFS rreandecr:h hostages probably separated, Hollande warming ... > read more observed in other studies, bthueotr ehticaalvlye e ansiley vdeegra dbabelee cnar biodne cnomtipfoiuends oin rsoil. "This Email Newsletters says new approach explains many properties of organic soil farming and conventional ... > read more Crop Residue May Be Too Valuable To Harvest components which were previously viewed as contradictory," RSS Newsfeeds quantified," declares Professor Matthias Kästner of the UFZ. For Biofuels (July 19, 2008) — In the rush to says Matthias Kästner. In the late 1990s, Kästner and his Jobs, factory, inflation data favor easy Fed policy Cdaevnel oOp rennew-aTbliem fueels Tfroiml lpalagntes, cIomnveprtrinog ve No-Till? (June 28, The accumulation of the batecatme arriraivle dc aet tlhli sw idaeal lo nf rtaheg bmasies noft esa rlaierp inpvesatigrastions Feedback ... we want to hear from you! crop residues into cellulosic ethanol would seem to on the degradation of environmental contaminants like Wal-Mart eases investors fears, U.S. shoppers to be supported by peptides and proteins from the liquid interior 2b0e1 a 0sl)a m— du nRk. eHsoweeaverrc, thhaet rmsig htte nsot tb ew shuceh taher a one-time anthracene in polluted soils of former gas work sites. In these Tell us what you think of ScienceDailfye --e wle pain of the cells, which remain to a greater extent in the soil than tiglloaodg idee ao fofr nfaorm-etrisl lg rcowoinugl .d.. h> erelapd mmoreanagew eclceomrtea bionth poesirtieven anndia nel gative comments. other cell components. These materials enable the formation weeds, and reduce phosphorus stratification and more top news of a film of organic molecules on the mineral components of runoff. They also wanted to determine if a one-time the soil, on which the carbon from the dead bacteria is tillage, ... > read more accumulated and stabilised. Copyright Reuters 2008. See Restrictions. Global Warming Is Changing Organic When the fragments of the bacterial cell walls dry out, they Matter In Soil: Atmosphere Could may lose their rubber-like properties and can harden like glass. Change As A Result (Nov. 28, 2008) — Free Subscriptions ... from ScienceDaily If the soil subsequently becomes moist again, however, under New research shows that we should be certain circumstances they cannot be re-wetted -- an important looking to the ground, not the sky, to see where Get the latest science news with our free email prerequisite for their degradation by other bacteria. This would climate change could have its most perilous impact newsletters, updated daily and weekly. Or view provide the simplest explanation for the stabilisation of on life on Earth. Scientists have shown that global hourly updated newsfeeds in your RSS reader: warming ... > read more theoretically easily degradable carbon compounds in soil. "This Email Newsletters new approach explains many properties of organic soil Crop Residue May Be Too Valuable To Harvest components which were previously viewed as contradictory," RSS Newsfeeds For Biofuels (July 19, 2008) — In the rush to says Matthias Kästner. In the late 1990s, Kästner and his develop renewable fuels from plants, converting team arrived at this idea on the basis of earlier investigations Feedback ... we want to hear from you! crop residues into cellulosic ethanol would seem to on the degradation of environmental contaminants like be a slam dunk. However, that might not be such a anthracene in polluted soils of former gas work sites. In these Tell us what you think of ScienceDaily -- we good idea for farmers growing ... > read more welcome both positive and negative comments. Soil organic matter link to microbial biomass

Soil organic carbon 1.4% 1.0% 0.78%

Carbon/nitrogen ratio 9.4 10.2 11.5 Microbial Biomass

tomato tomato wheat

If soil organic maer contains higher proporon of microbial biomass carbon, is it beer nutrient source? Microbial biomass is early indicator of changes in total soil organic carbon.

Microbial biomass is indicator of how much N available to plant over season from organic matter in soil.

Microbial biomass nitrogen and release of nitrogen decreasing with depth (Murphy et al., 1998).

Soil Quality Website—West Australia http://soilquality.org.au/factsheets/making-sense-of-biological-indicators NUTRIENT Climate Management Crop rotation CYCLING: N and P Organic Resource Quality Tillage

Plant and Soil Soil Properties Biodiversity and processes

Carbon e.g., Organic and Maintaining matter, texture soil Nutrient structure Cycles

Nutrient Use Efﬁciency Water Use Efﬁciency

Carbon Sequestration NUTRIENT CYCLING Managing the N cycle means managing microbes

• Plant N use efficiency often low, <50% of N added is taken up into plants immediately

• Uptake is regulated by relationships between soil microorganisms and plants. Large amount of fertilizer, NOT MATTER THE FORM, goes through microbes before plant gets it. Managing the N cycle means managing microbes

(diagram from Jackson et al., 2008 (Ann Rev Plant Biol 59)) Shaded circles show microbial processes or inﬂuences andMineral PHOSPHORUS??? P taken up Organic P relies on in soil solution; general decomposition of microbial activity organic material to be increase P availability. released Mycorrhizae help ﬁnd and take up. CREATING/MAINTAINING SOIL Climate Management Crop rotation STRUCTURE Organic Resource Quality Tillage

Plant and Soil Soil Properties Biodiversity and processes

Carbon e.g., Organic and Maintaining matter, texture soil Nutrient structure Cycles

Nutrient Use Efﬁciency Water Use Efﬁciency

Carbon Sequestration SOIL STRUCTURE Role of organic matter and microbes in creating structure: fueled by carbon inputs Implications of structure for water movement and gas exchange

Management practices for managing microbes in soil • Manipulate what they eat: C/N ratio of organics, degradability, physical availability, electron acceptors (e.g. oxygen), other nutrients, specific enzyme co-factors (?)

• Other soil amendments: biochar, calcium, signaling compounds?

• Manipulate their environment: water and oxygen content, pH, “architecture”. Less harsh chemicals. Less physical disturbance. Minimize periods of no cover.

• Inhibit/select for specific microbial groups? Nitrification inhibitors? Or through substrates?

• Promote symbiotic relationships with plants that short-circuit some of the soil processes providing N—less physical disturbance for mycorrhizal fungi?

• Inoculate with consortia, specific strains?….often equated with “soil biology” but evidence for efficacy is inconsistent. Lot to learn. Indicators: what do we measure to show how we are doing? Indicators, metrics for soil biodiversity Indicator How measure Why useful

Who are they and who is in their Sequencing of 16/18S rRNA: Determines WHO is there based on communities? How diverse are probing or PCR, including clone universal phylogenetic standard, they? libraries, pyrosequencing, DNA helps understand evolutionary fingerprinting, metagenomics relationships, gives idea of “potential”

How many/much are they? Fumigation-extraction, PLFA, DNA, Estimates amount of nutrients in • Numbers microscopic counts, quantitative microbial biomass. Gives an idea of • Biomass PCR how fast they carry out functions.

What functions do they perform? Substrate utilization, product Measures the actual impacts of Degrades chemicals, produces formation (respirometry, GC, GC- microorganisms on environment chemicals MS, measure stable isotopes--natural through what they remove, release, • Associates with a symbiont abundance, labeled compounds). etc. • Kills someone • Competes with someone Presence/quantity of functional • Functions within some “niche” genes (Geochip, PCR or probing); Measures the potential and or • Helps build soil structure RNA expression of functional genes activity of genes responsible for specific microbial processes How are they doing? ATP charge, PLFA stress markers, Are organisms metabolically active? • Viability vital stains, RNA expression At full capacity? Are they stressed?? • Stress markers Challenges and benefits in managing soil biology rather than relying only on chemically based systems

• Much of what we think of as “soil” processes is actually biological activity.

• “Indirect” management practices often more fruitful than direct manipulation of biology

• Everything is connected – Challenging because can’t isolate specific factors – Good in that can manage for multiple benefits – Important to evaluate trade-offs and identify indicators Challenges and benefits in managing soil biology rather than relying only on chemically based systems (2)

• Takes time to invest in system w/eye on future (not this growing season) to get it to where the positive benefits are substantial and consistent.

• Resistance/resilience of agroecosystems is largely due to biological systems

• May not have quick fixes to problems (e.g., chemicals in organic or more biological system)—so need to design resilience into system—our expanding knowledge of microbial communities well help

Helpful tools and resources • Oregon State University Organic Fertilizer and Cover Crop Calculator http://smallfarms.oregonstate.edu/calculator

• NRCS Soil Health Initiative http://www.nrcs.usda.gov/wps/portal/nrcs/main/soils/health/

• Cornell University Soil Health Initiative http://soilhealth.cals.cornell.edu/

• “Soils are Alive” online textbook (Australian Soil Club) http://www.soilhealth.com/soils-are-alive/

• Sustainable Soil Management (Appropriate Technology Transfer for Rural Areas http://www.soilandhealth.org/01aglibrary/010117attrasoilmanual/010117attra.html

• Film: Symphony of the Soil http://www.symphonyofthesoil.com/