soil microbiology and its effects on nutrient availability ... · soil soil life soil ph dec. 14,...

Kate Scow [email protected] Dept. of Land, Air & Water Resources Agricultural Sustainability Institute

Soil Microbiology and Its Effects on Nutrient Availability and Uptake in

Plants (and other things)

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

Most ecoecosystems concentrate biodiversity belowground

Above ground diversity is often intentionally low in managed systems

Soil is one of most diverse microbial habitats: Thousands of “species” can be detected in gram of soil. Most not yet iden>fied nor their func>on(s) known. Microbes include: Bacteria, Archaea, and Fungi. Of bacteria and archaea, ~1500 different taxa detected in CA cropping systems.

archaea

3

Types of soil organisms

diagram berdasarkan konsep Dr. Daniel Dindal, 1978

centipede

rove beetle

ant

millipede

mite

earthworm

organic debris

fungi

rove beetle

ground beetle

pseudo scorpion

mite

bacteria

roundworms

snail

mite

fly larvae

adult fly

flatworm

beetle

archaea

And archaea and fungi

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Contribute to biodiversity

Fight/suppress pests (IPM)

Build soil structure

Remove pesticides and nutrients in buffer strips

Support plant and animals via mutualism

Control and cycle plant nutrients

How microorganisms contribute to farms and gardens (the good, the bad and the ugly)

Source/sink of GHG

Biodegrade pesticides in field

Breakdown wastes, make compost

Develop antibiotic resistence (or not)

Fix nitrogen

Build soil organic matter

Contaminate food (or not)

Sequester carbon

Support farmer’s digestion and immunity

Synchrony

Drivers

Factors

Processes

Services

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Wat

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Crop rotation Organic Resource Quality Tillage

Climate Management

Plant and Soil

Biodiversity Soil Properties and processes

Carbon and

Nutrient Cycles

Nutrient Use Efficiency

Carbon Sequestration

Water Use Efficiency

Sustainable Agroecosystems Adapted from

Brussaard et al. 2007

e.g., Organic matter, texture Maintaining

soil structure

Microbes tightly coupled with plants and soil: can’t decouple biodiversity from soil


Climate Management

Plant and Soil Biodiversity

Soil Properties and processes

Carbon and

Nutrient Cycles





soil structure

BUILDING ORGANIC MATTER

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

Persistence of soil organic matter as an ecosystem property (2011) Schmidt et al. Nature 478, 49–56

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Plants & AnimalsSoil TypesOrganicFungus

Earth & ClimateLandslidesGeochemistryAcid Rain

ReferenceHumusSoilSoil lifeSoil pH

Dec. 14, 2012 — Remains of dead bacteria havefar greater meaning for soils than previouslyassumed. Around 40 per cent of the microbialbiomass is converted to organic soil components,write researchers from the Helmholtz Centre forEnvironmental Research (UFZ), the TechnischeUniversität Dresden (Technical University ofDresden) , the University of Stockholm, the Max-Planck-Institut für Entwicklungsbiologie (MaxPlanck Institute for Developmental Biology) and theLeibniz-Universität Hannover (Leibniz UniversityHannover) in the journal Biogeochemistry.

Until now, it was assumed that theorganic components of the soil werecomposed mostly of decomposedplant material which is directlyconverted to humic substances. In alaboratory experiment and in fieldtesting the researchers have nowrefuted this thesis. Evidently theeasily biologically degradable plantmaterial is initially converted tomicrobial biomass which thenprovides the source material to soilorganic matter.

Soil organic matter represent thelargest fraction of terrestrially boundcarbon in the biosphere. Thecompounds therefore play animportant role not only for soil fertilityand agricultural yields. They are alsoone of the key factors controlling theconcentration of carbon dioxide inthe atmosphere. Climatic changecan therefore be slowed down oraccelerated, according to themanagement of the soil resource.

In laboratory incubation experiment,the researchers initially labelledmodel bacteria with the stableisotope 13C and introduced the

bacteria to soil deriving from the long-term cultivationexperiment "Ewiger Roggenbau" in Halle/Saale. Following theincubation time of 224 days the fate of the carbon of bacterialorigin was determined. "As a result we found fragments ofbacterial cell walls in sizes of up to 500 x 500 nanometresthroughout our soil samples. Such fragments have also beenobserved in other studies, but have never been identified orquantified," declares Professor Matthias Kästner of the UFZ.The accumulation of the bacterial cell wall fragments appearsto be supported by peptides and proteins from the liquid interiorof the cells, which remain to a greater extent in the soil thanother cell components. These materials enable the formationof a film of organic molecules on the mineral components ofthe soil, on which the carbon from the dead bacteria isaccumulated and stabilised.

When the fragments of the bacterial cell walls dry out, theymay lose their rubber-like properties and can harden like glass.If the soil subsequently becomes moist again, however, undercertain circumstances they cannot be re-wetted -- an importantprerequisite for their degradation by other bacteria. This wouldprovide the simplest explanation for the stabilisation oftheoretically easily degradable carbon compounds in soil. "Thisnew approach explains many properties of organic soilcomponents which were previously viewed as contradictory,"says Matthias Kästner. In the late 1990s, Kästner and histeam arrived at this idea on the basis of earlier investigationson the degradation of environmental contaminants likeanthracene in polluted soils of former gas work sites. In these

The electron micrograph shows bacteria(Hyphomicrobium sp;;. Yellow) growing up partly onsolid surfaces, floors and sediment grains. Duringgrowth whatsoever cells die and deformed orfragmenting cell envelopes remain. Small-scalefragments of these shells (red) then set themicroparticulate matrix in soils and sediments.(Credit: Burkhard Schmidt-Brücken, Institute ofMaterial science/TU Dresden;; Colored by ChristianSchurig/ UFZ)

Related Stories

Findings On Biochar, Greenhouse GasEmissions and Ethylene (Dec. 13, 2011)— Adding a charred biomass materialcalled biochar to glacial soils can helpreduce emissions of the greenhouse

gases carbon dioxide and nitrous oxide, accordingto ... > read more

Rethinking Connection Between Soil as aCarbon Reservoir and Global Warming (Oct. 5,2011) — The soil plays a key role in theecosystem, economy and global carbon cycle.After the oceans, the humus is the largest carbonreservoir. If humus decreases, additional CO2 getsinto the ... > read more

Organic and Conventional Farming MethodsCompete to Eliminate Weed Seeds in Soil (Apr.21, 2011) — Weeds are hard to kill;; they seem tocome back no matter what steps people take toeradicate them. One reason is because of thepersistence of weed seeds in the soil. Organicfarming and conventional ... > read more

Can One-Time Tillage Improve No-Till? (June 28,2010) — Researchers test whether a one-timetillage of no-till could help manage certain perennialweeds, and reduce phosphorus stratification andrunoff. They also wanted to determine if a one-timetillage, ... > read more

Global Warming Is Changing OrganicMatter In Soil: Atmosphere CouldChange As A Result (Nov. 28, 2008) —New research shows that we should be

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Crop Residue May Be Too Valuable To HarvestFor Biofuels (July 19, 2008) — In the rush todevelop renewable fuels from plants, convertingcrop residues into cellulosic ethanol would seem tobe a slam dunk. However, that might not be such agood idea for farmers growing ... > read more

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See Also:

Plants & AnimalsSoil TypesOrganicFungus

Earth & ClimateLandslidesGeochemistryAcid Rain

ReferenceHumusSoilSoil lifeSoil pH

Dec. 14, 2012 — Remains of dead bacteria havefar greater meaning for soils than previouslyassumed. Around 40 per cent of the microbialbiomass is converted to organic soil components,write researchers from the Helmholtz Centre forEnvironmental Research (UFZ), the TechnischeUniversität Dresden (Technical University ofDresden) , the University of Stockholm, the Max-Planck-Institut für Entwicklungsbiologie (MaxPlanck Institute for Developmental Biology) and theLeibniz-Universität Hannover (Leibniz UniversityHannover) in the journal Biogeochemistry.

Until now, it was assumed that theorganic components of the soil werecomposed mostly of decomposedplant material which is directlyconverted to humic substances. In alaboratory experiment and in fieldtesting the researchers have nowrefuted this thesis. Evidently theeasily biologically degradable plantmaterial is initially converted tomicrobial biomass which thenprovides the source material to soilorganic matter.

Soil organic matter represent thelargest fraction of terrestrially boundcarbon in the biosphere. Thecompounds therefore play animportant role not only for soil fertilityand agricultural yields. They are alsoone of the key factors controlling theconcentration of carbon dioxide inthe atmosphere. Climatic changecan therefore be slowed down oraccelerated, according to themanagement of the soil resource.

In laboratory incubation experiment,the researchers initially labelledmodel bacteria with the stableisotope 13C and introduced the

bacteria to soil deriving from the long-term cultivationexperiment "Ewiger Roggenbau" in Halle/Saale. Following theincubation time of 224 days the fate of the carbon of bacterialorigin was determined. "As a result we found fragments ofbacterial cell walls in sizes of up to 500 x 500 nanometresthroughout our soil samples. Such fragments have also beenobserved in other studies, but have never been identified orquantified," declares Professor Matthias Kästner of the UFZ.The accumulation of the bacterial cell wall fragments appearsto be supported by peptides and proteins from the liquid interiorof the cells, which remain to a greater extent in the soil thanother cell components. These materials enable the formationof a film of organic molecules on the mineral components ofthe soil, on which the carbon from the dead bacteria isaccumulated and stabilised.

When the fragments of the bacterial cell walls dry out, theymay lose their rubber-like properties and can harden like glass.If the soil subsequently becomes moist again, however, undercertain circumstances they cannot be re-wetted -- an importantprerequisite for their degradation by other bacteria. This wouldprovide the simplest explanation for the stabilisation oftheoretically easily degradable carbon compounds in soil. "Thisnew approach explains many properties of organic soilcomponents which were previously viewed as contradictory,"says Matthias Kästner. In the late 1990s, Kästner and histeam arrived at this idea on the basis of earlier investigationson the degradation of environmental contaminants likeanthracene in polluted soils of former gas work sites. In these

The electron micrograph shows bacteria(Hyphomicrobium sp;;. Yellow) growing up partly onsolid surfaces, floors and sediment grains. Duringgrowth whatsoever cells die and deformed orfragmenting cell envelopes remain. Small-scalefragments of these shells (red) then set themicroparticulate matrix in soils and sediments.(Credit: Burkhard Schmidt-Brücken, Institute ofMaterial science/TU Dresden;; Colored by ChristianSchurig/ UFZ)

Related Stories

Findings On Biochar, Greenhouse GasEmissions and Ethylene (Dec. 13, 2011)— Adding a charred biomass materialcalled biochar to glacial soils can helpreduce emissions of the greenhouse

gases carbon dioxide and nitrous oxide, accordingto ... > read more

Rethinking Connection Between Soil as aCarbon Reservoir and Global Warming (Oct. 5,2011) — The soil plays a key role in theecosystem, economy and global carbon cycle.After the oceans, the humus is the largest carbonreservoir. If humus decreases, additional CO2 getsinto the ... > read more

Organic and Conventional Farming MethodsCompete to Eliminate Weed Seeds in Soil (Apr.21, 2011) — Weeds are hard to kill;; they seem tocome back no matter what steps people take toeradicate them. One reason is because of thepersistence of weed seeds in the soil. Organicfarming and conventional ... > read more

Can One-Time Tillage Improve No-Till? (June 28,2010) — Researchers test whether a one-timetillage of no-till could help manage certain perennialweeds, and reduce phosphorus stratification andrunoff. They also wanted to determine if a one-timetillage, ... > read more

Global Warming Is Changing OrganicMatter In Soil: Atmosphere CouldChange As A Result (Nov. 28, 2008) —New research shows that we should be

looking to the ground, not the sky, to see whereclimate change could have its most perilous impacton life on Earth. Scientists have shown that globalwarming ... > read more

Crop Residue May Be Too Valuable To HarvestFor Biofuels (July 19, 2008) — In the rush todevelop renewable fuels from plants, convertingcrop residues into cellulosic ethanol would seem tobe a slam dunk. However, that might not be such agood idea for farmers growing ... > read more

Fertile Soil Doesn't Fall from the Sky: Contribution of BacterialRemnants to Soil Fertility Has Been Underestimated Until Now

| 68.9K

Breaking News

Free Subscriptions

Feedback

Just In:Older Adults Made Less Forgetful

more breaking science news

Social Networks

Recommend ScienceDaily on Facebook, Twitter,and Google +1:

TweetTweet 23.5K FollowFollow 53.7K followers

+5708 Recommend this on Google

Other bookmarking and sharing tools:

... from NewsDaily.com

India to launchmission to Mars thisyear, says president"Vulcan" has biglead in bid to namePluto's newly discovered moonsNASA Mars rover ready to eat, analyze rockpowderMini planet found far beyond Earth's solar systemSubatomic calculations indicate finite lifespan foruniverseRussia asks: How do you stop space objectshitting Earth?Raytheon says aces missile-detection tests inU.S"Meteorite rush" begins as Russian scientistsfind fragmentsmore science news

In Other News ...Obama called top Republicans to discusslooming cuts: White HouseIn Federal Reserve bond-buying debate, officialsair opposing viewsFrench, Malian forces fight Islamist rebels in GaoIran installs advanced centrifuges to speed upnuclear workBerlusconi's last throw of the dice in Italy electionFrench hostages probably separated, HollandesaysJobs, factory, inflation data favor easy Fed policyWal-Mart eases investors fears, U.S. shoppersfeel painmore top news

Copyright Reuters 2008. See Restrictions.

... from ScienceDaily

Get the latest science news with our free emailnewsletters, updated daily and weekly. Or viewhourly updated newsfeeds in your RSS reader:Email NewslettersRSS Newsfeeds

... we want to hear from you!

Tell us what you think of ScienceDaily -- wewelcome both positive and negative comments.

Science News ... from universities, journals, and other research organizations Save Email Print Share

Like 218

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Like Send 47,738 people like this. Be the firstof your friends.

ShareShareShareShareShareShareShareShareShare

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Miltner et al.. SOM genesis: microbial biomass as a significant source. Biogeochemistry, 2011

tomato

Microbial Biomass

tomato wheat

If soil organic ma.er contains higher propor3on of microbial biomass carbon, is it be.er nutrient source?

Soil organic carbon 1.4% 1.0% 0.78%

Carbon/nitrogen ratio 9.4 10.2 11.5

Soil organic matter link to microbial biomass

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

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.

Soil Quality Website—West Australia http://soilquality.org.au/factsheets/making-sense-of-biological-indicators


Climate Management



Carbon and

Nutrient Cycles





soil structure

NUTRIENT CYCLING: N and P

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

Shaded circles show microbial processes or influences (diagram from Jackson et al., 2008 (Ann Rev Plant Biol 59))

and PHOSPHORUS??? Mineral P taken up in soil solution; general microbial activity increase P availability. Mycorrhizae help find and take up.

Organic P relies on decomposition of organic material to be released


Climate Management



Carbon and

Nutrient Cycles





soil structure

CREATING/MAINTAINING SOIL STRUCTURE

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 communities? How diverse are they?

Sequencing of 16/18S rRNA: probing or PCR, including clone libraries, pyrosequencing, DNA fingerprinting, metagenomics

Determines WHO is there based on universal phylogenetic standard, helps understand evolutionary relationships, gives idea of “potential”

How many/much are they? • Numbers • Biomass

Fumigation-extraction, PLFA, DNA, microscopic counts, quantitative PCR

Estimates amount of nutrients in microbial biomass. Gives an idea of how fast they carry out functions.

What functions do they perform? Degrades chemicals, produces chemicals • Associates with a symbiont • Kills someone • Competes with someone • Functions within some “niche” • Helps build soil structure

Substrate utilization, product formation (respirometry, GC, GC-MS, measure stable isotopes--natural abundance, labeled compounds). Presence/quantity of functional genes (Geochip, PCR or probing); RNA expression of functional genes

Measures the actual impacts of microorganisms on environment through what they remove, release, etc. Measures the potential and or activity of genes responsible for specific microbial processes

How are they doing? • Viability • Stress markers

ATP charge, PLFA stress markers, vital stains, RNA expression

Are organisms metabolically active? At full capacity? Are they stressed??

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 Areashttp://www.soilandhealth.org/01aglibrary/010117attrasoilmanual/010117attra.html

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

soil microbiology and its effects on nutrient availability ... · soil soil life soil ph dec. 14,...

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