jurnal mikroba tanah

8/16/2019 Jurnal Mikroba Tanah

1/26

Kate [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)


2/26

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


3/26

Film


4/26

!"#$ &'"&'"#(#$&)# '"*'&*$+,$&

-."/.0&+#.$( -&1"23+"4*/

Above ground diversity is often intentionally low in managed systems


5/26

5".1 .# "*& "6 )"#$ /.0&+#& ).'+"-.,1 7,-.$,$#8 97"4#,*/# "6 :#;&'.<',* -& /&$&'$&/ .* 3+,) "6 #".1= !"#$ *"$ (&$ ./&*>?&/ *"+ $7&.+64*'>"*@#A B*"2*=

!.'+"- .*'14/&8 !"#$%&'"( *+"%"( ",- ./,0'= C6 -,'$&+., ,*/,+'7,&,D EFGHH /.I&+&*$ $,J, /&$&'$&/ .* KL '+";;.*3 #(#$&)#=

,+'7,&,

diagram berdasarkan konsep Dr. Daniel Dindal, 1

centipede

rovebeetle

ant

millipede

mite

earthworm

organic debris

fungi

rovebeetle

groundbeetle

pseudo scorpion

mite

bacteria

roundworms

snail

mite

flylarvae

adult fly

flatworm

beetle

,+'7,&,

And archaea and fungi


6/26

h t t p : / / i m a g e s . g o o g l e . c o m / i m g r e s ? i m g u r l = h t t p : / / w w

w . s a r e . o r g /

p u b l i c a t i o n s / e x p l o r e / i m a g e s / s c e n e w i d e 2 . j p g

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 badand the ugly)

Source/sinkof GHG

Biodegrade

pesticides in

field

Breakdown

wastes, make

compost

Develop antibioticresistence (or not)

Fix nitrogen

Build soil

organic matter

Contaminate

food (or not)

Sequester

carbon

Support farmer’s

digestion and immunity


7/26

Synchrony

Drivers

Factors

Processes

Services

W

a t e r /

N u t r i e n t

S u p p l y

W a t e r / N

u t r i e n t U s e

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 fromBrussaard et al. 2007

e.g., Organic

matter, texture

Maintaining

soilstructure

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


8/26

Crop rotation


Tillage

Climate Management

Plant and Soil

BiodiversitySoil Properties

and processes

Carbonand

Nutrient

Cycles




e.g., Organicmatter, texture

Maintaining

soil

structure

BUILDING

ORGANIC MATTER


9/26

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


10/26

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

TweetTweet 42

6

72

Share This:

See Also:

Dec. 14, 2012 — Remains of dead bacteria have

far greater meaning for soils than previously

assumed. Around 40 per cent of the microbial

biomass is converted to organic soil components,

write researchers from the Helmholtz Centre for

Environmental Research (UFZ), the Technische

Universität Dresden (Technical University of

Dresden) , the University of Stockholm, the Max-Planck-Institut für Entwicklungsbiologie (Max

Planck Institute for Developmental Biology) and the

Leibniz-Universität Hannover (Leibniz University

Hannover) in the journal Biogeochemistry .

Until now, it was assumed that theorganic components of the soil werecomposed mostly of decomposed

plant 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 soil

organic matter.

The electron micrograph shows bacteria(Hyphomicrobium sp;. Yellow) growing up partly on

solid surfaces, floors and sediment grains. During growth whatsoever cells die and deformed or fragmenting cell envelopes remain. Small-scalefragments of these shells (red) then set themicroparticulate matrix in soils and sediments.(Credit: Burkhard Schmidt-Brücken, Institute of Material science/TU Dresden; Colored by ChristianSchurig/ UFZ)

Fertile Soil Doesn't Fall from the Sky: Contribution of Bacterial

Remnants to Soil Fertility Has Been Underestimated Until Now

Science News ... from universities, journals, and other research organizations

Like 218

enlarge

Until now, it was assumed that the

organic 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 soil

organic matter.

Miltner et al.. SOM genesis: microbial biomass as a

significant source. Biogeochemistry, 2011


11/26

$"),$"

! . ' + " - . , 1 M . " ) , # #

$"),$" 27&,$

!" $%&' %()*+&, -*./( ,%+0*&+$ 1&)1/( 2(%2%(3%+ %" -&,(%4&*'

4&%-*$$ ,*(4%+5 &$ &0 4/./( +60(&/+0 $%6(,/7

Soil organic carbon1.4% 1.0% 0.78%

Carbon/nitrogen ratio

9.4 10.2 11.5

Soil organic matter link to microbial biomass


12/26

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 plantover season from organic matter in soil.

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


13/26

Crop rotation


Tillage

Climate Management

Plant and Soil


and processes

Carbonand

Nutrient

Cycles




e.g., Organic

matter, texture

Maintaining

soil

structure

NUTRIENT

CYCLING: N and P


14/26

NUTRIENT CYCLINGManaging the N cycle means managing

microbes

•

Plant N use efficiency often low,


15/26

Managing the N cycle means managing microbes

57,/&/ '.+'1 #7"2 ).'+"-.,1 ;+"'# "+ .*N4&*'(diagram from Jackson et al., 2008 (Ann Rev Plant Biol 59))


16/26

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 bereleased


17/26

Crop rotation


Tillage

Climate Management

Plant and Soil


and processes

Carbonand

Nutrient

Cycles




e.g., Organic

matter, texture

Maintaining

soil

structure

CREATING/MAINTAINING

SOIL

STRUCTURE


18/26

SOIL STRUCTURE

Role of organic matter and microbes in creating

structure: fueled by carbon inputs


19/26

Implications of structure for water movement and gas exchange


20/26

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.


21/26

Indicators: what do we measure to show how we are doing?


22/26

O*/.',$"+#D )&$+.'# 6"+ #".1 -."/.0&+#.$(

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 oractivity 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??


23/26

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


24/26

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 growingseason) 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 intosystem—our expanding knowledge of microbial communities

well help


25/26

Helpful tools and resources

•

Oregon State University Organic Fertilizer and Cover Crop

Calculator http://smallfarms.oregonstate.edu/calculator

•

NRCS Soil Health Initiativehttp://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/


26/26

jurnal mikroba tanah

Documents