Markéta Marečková

e-mail: sagova@vurv.cz

Microorganisms in soil

• Soil structure and its • Soil ecosystem • Trophic relationships • Key processes• Estimation, models and evaluation

Soil is the most complex environment

Ecosystem

BioticAbiotic

Structure Function

Soil ecosystem

dominated by

heterotropic organisms

•bedrock•darkness

porous mixtureof solids, liquids and gases

•plant nutrition•decomposition of

OM

quantity & quality of C

predation

Methods of study

Solids

Porous material of solids, liquids and gasesBedrock : e.g. limestone,dolomite (neutral to alkaline), silicate (acidic)

Determines the basic soil pH.Humus: Humic acids are aromatic and aliphatic remains of lignin, aminoacids

and sugars. Humus is a product of decomposition, microbial or chemical. Humus is usually acid and is negatively charged.

Clay particles: large surface, together with humus influence ion exchange. Negatively charged.

\ Adsorbtion afinity: Al 3+ > Ca 2+ = Mg 2+ > K+ = NH3+ >Na+

Abiotic factors

Maier et al., 2000

Abiotic soil components

mineral particles

mineralparticles

mineralparticles pores pores pores

organic matter organic matter

sand silt gravel

Velikost porů, odpovídající procesy a organismy.

Na velikostní úrovni jílových částic (μm) se vyskytují pouze bakterie a houbová vlákna. Na úrovni prachu (0.063 mm) a písku (2 mm) se vyskytují kořenové vlášení, kořeny, prvoci, hlístice.

Struktura půdy

oživení porů

Meier et al., 2002

Water, liquids

Water is the main limiting factor in soilwater content is correlated to organic matter content

Pore size:

macropores > 0.08 mm, gravitation water, plants mesopores 0.08 -0.03 mm,capillary water micropores 0.03-0.005 mm,inside agregates, bacteriaultramicropores 0.005-0.0001mm,inside clay particles cryptopores < 0.0001mm, too small even for macromolecules

Abiotic factors

Maier et al., 2000

Water potential: force necessary for movement of a certain amount of water under a given pressure and material

Adhesion (binding force to solid surfaces – matrix potential, Ψm)Binding to ions (osmotic potencial, ΨS)Gravitation force (gravitation potencial, Ψg)

Reaches negative values because it is compared to free water. Given in pressure units.

Free and bound waterAbiotic soil components

surface forces, Ψm, - 31 až – 10000 atm

capillary forces, ΨS -0.1 až -30 atm

gravitation forces, Ψg 0 až -0.5 atm

Maier et al., 2000

Soil structure

examples of characteristics

pH vodivost Ca Mg Al Fe humus % organic

μS mg/kg mg/kg mg/kg mg/kg % %

Alpilles 7.54 256 5900 184 3.0 1.0 2.3 16.1

Bozi Dar 3.27 47 1290 106 5.3 1.4 40.6 95.7

Devin 7.87 200 6210 163 3.0 1.0 1.4 12.0

Kotyz 7.52 310 7600 191 3.0 1.2 3.7 26.6

Meluzina 5.03 86 2700 137 10.4 2.5 18.5 7.6

Nechranice 6.08 64 3470 618 3.0 1.0 7.2 11.6

Oblik 7.9 200 6090 307 3.0 1.0 0.5 21.5

Podyji 5.55 75 2010 404 4.1 2.9 3.2 10.2

Rynholec 6.31 53 2840 83 6.5 1.0 0.1 7.2

Saline Giraud 8.12 21350 3150 67 3.0 1.0 0.0 3.3

slanisko Nesyt 7.97 537 3390 1250 3.0 1.0 0.5 6.6

Srbsko 7.65 141 4740 141 3.0 1.0 0.5 8.2

Slepici vrch 4.57 24 100 29 3.0 1.0 0.7 1.5

Trebon 4.01 80 1160 289 3.4 4.4 3.8 9.1

Habitat of microorganisms: variable in space and time

stratified by physical and chemical forces and important

nutrients– C, organické látky, 02, N, P, S microhabitat

• soil particles• rhizosphere• air bubbles • sufaces of

organisms

Soil structure and life niches

life formactive cells, spores, fillaments, collonies, biofilms

(obydlí)

Viruses,phages

Living forms

Diversity of viruses in various soilsLiving forms

•Comparison of agricultural, forest and alpine soils.

•Highest diversity (Simpson index) was found in forest soils

•The highest percentage of viruses were bacteriophages

Proteobacteria: pseudomonads, myxobacteria, rhizobia AcidobacteriaActinobacteria: streptomycets, corynebacteriaVerrucomicrobiaFirmicutes: bacilli, clostridia, laktobacilliPlanctomycetes

Streptomyces

Chondromyces

Myxococcus Bacillus

Living forms

Bacteria

109 cells and thousands of species per gram soil. Culivativable part is only from tenths to tens of percent Aerobic dominate the anaerobic in regular soil several times. Spatial variability is enourmous.

Living forms

Molds

Aspergillus

Algae

Cryptomonas

Blue greens

Nostoc

Blue green algae and algae live only in top several cm of soil. They often make a crust or a biofilm and they are adapted to very dry environment even deserts.

Algae and Fungi

Living forms

AmoebasAcanthamoeba

Paranema

Heterotrophic flagellates

Protozoa

Living forms

Euplotes, Stylonychia

Cilliates

Nemathods

Springtails

Orchesella

Mites

Living forms

Mammals

Microtus arvalis

Oligochaetes

Lumbricullus variegatus

Živé složky půdy

Soil horizonsstructure

In soil, organic and anorganic material is layered to soil horizons. They are created byplant litter and water from rain and groundwater.

Abundance and biomass of soil populations

Scale analysis (A) Distribution of soil patches colonized by bacteria in a two-dimensional grid with an indication of the four sizes of microsamplesused. (B) Same distribution after the test for the presence of bacteria. The black and white elementary units represent positive and negative results, respectively. (C) Corresponding curves obtained after sampling, showing the percentages of positive microsamples as a function of the four microsample sizes. Different types of distribution of bacteria are shown in rows a, b, and c.

Grundmann et al.2004

Distribution by source

Resources occur in soil mostly at aggregates of different sizes. E.g. in upper soil there are larger pieces of OM than in the lower soil. Bacteria aggregate as site of sources.

structure

Example: The highest number of bacteria phylotypes occurred in the clay fraction. Protection from predation. Fertilization does not change this relationship. Also highest diversity in the smaller pores – association with particles is stronger than the nutrient exchange

Sessitch et al.2001

T-RFLP profiles in three fractions of differently treated soils

Inhabiting pore according to its size structurete

rmin

al f

rag

men

t le

ng

ht

Organic matter main factor influencing productivity of soil environment. ovlivňuje:•plant nutrition •community composition•water content•agregate stability•erosion control

The main source of OM is the higher plants. One part of plants is quickly mineralized to CO2, phosphates, sulfates, nitrates etc. and used by other organisms. the other part is decomposed only partly and makes up humus. The ration of both components differes between sites, the most important factors being pH and moisture. Clay component and humus are the source of soil fertility. Both processes mineralization and humification are driven by bacteria and fungi. Bacteria and fungi add to humus also by their bodies which make a biomass of 40-200 g m-2.

„Hot spots“ sites of highest mircorbial activity. 90% of activity goes on in 10% of soil volume. E.g. rhizosphere and burries of animals

structure Organic matter sources

Relationships between contents of C, N, bacteria and fungi in soil at 5 diffrent sites (beech, pine, meadow, organic field, convention field at 5 and 25 oC.

Sites differ by:fungi abundance but not that of bacteriaFungi quantity correlated with C and negatively with N. Bacteria correlate with temperature.

DOC dissolved organic carbon,DON dissolved organic nitrogen

Example

bacteria fungi

NH4+ NO3

-

DOC DON

Nutritionstructure

All processes are faster at higher temperature. Respiration is similar at all sites. Mineralization N, imobilization C and nitrification are the highest in a meadow and smalest in a forest

Example

Rate of soil processes function

mineralization

imobilization N nitrification

Soil bacteria according to the K-r selection

K organisms: slow metabolism, consumption of nutrients from small amoutns of poorly available sources, large genomes, filamentous forms, adaptation to harsh conditions (cold, deserts), stay at sites

r organisms: fast growing, fast reactions to a new source, consumption of available sources at good living conditions, coccal forms, fast growth, tolerate stress

Streptomyces, Micromonospora, Streptosporangium (podřády), myxobakterie

Burkholderia, Xanthomonas, Agrobacterium, entherobakterie

Nutrient consumptionstructure

C content in soil by source

microbial C total Cug/g %

arable land 70 - 720 1.0 - 3.8250 - 1080 3.0 - 6.0420 - 980 2.5 - 5.5

meadow 2670 2.9470 21120 1.9

forest 420 - 1770 0.9 - 2.6800 - 1670 1.2 - 6.0

1670 2.1subtropical forest 330 - 1090 0.9 - 1.8

200 - 790 0.7 - 1.3alpine meadow 1000 - 2750 1.7 - 2.8

structure

Examples of organic C content and microbial C content. In meadow ecosystems microbial content is higher.

•Soil trophic pyramid is not well known•Dominating process is decompostion Predation influences dynamics of the energy exchange processes •The best methods to describe are isotope probing •Limitation by C except in the rhizosphere (and by water as at all terrestrial ecosystems)

Trophic pyramidprocesses

secundary decomposers

PP

primary decomposers

predators I

predators II

nutrition

litter

shredded litter,microorganisms

decomposers, PP

predators I

chemolithotrophie

Trophic relationships in soil environment

natural meadow ecosystem

wheat monoculture

Agroecosystem is simplified,no mycorhiza, N2 fixation, limited nematods and increasing effect of cilliates

Trophic processesprocesses

Plant community

exudates litter

bacteria

protists

Carbon and other nutrients

ener

get

ic c

anal

bac

teri

al

fun

gal

Basic flows of energy and nutrients in soil ecosystems

Two basic types of food webs:

• based on exudates• based on litter

Food web in rhizosphere is fast. Production and biomass are several times higher than in the litter web. Interactions between plants, bacteria and protozoa are called a microbial loop. In this community, predators effectively control bacterial growth but the effect of secondary predators is low. Nutrients cycle locally and are not spread around. Plants give up to 40 % of assimilated carbon to rhizosphere microorganisms.

Bacterial food web is more typical for high pH , higher N, and lower soil moisture. Typical of fast overturn. Predators are protozoa and nematods. It is controlled by nutrients (bottom up).Fungal – oposite, controlled by predation(top down)

procesess Trophic relationships

Example:

A field with convention farming (full) and a field with organic farming (dashed) were followedduring a year.Biomass of bacteria and fungi correlated with temperature.Maximum of bacterial biomasswas reached in relationship to soil moisture. This demonstrates limitation with water in a soil community. Bacterivorous nematods were highest in winter, which shows high tolerance to T and avoiding of predators.

Trophic relationships

Bloem et al., 1994

predation predationpredation

grazingsubstrate processing

pore formationlitter fragmentation

bioturbation

Energy flow

Habitat formation

Function of organisms by body size organismů

Trophic interactions are fast while habitat formation is a long term process

Primary production

ChemolithotrophyFixace CO2

Energie: oxidace železa, amonných solí, sirníků, síry, kovů, dusitanů

Bernhart et al., 2007Jourdan et al., 2005

function

Zastoupení autotrophů podle qPCR Zastoupení autotrofů v průběhu tří let

Predation

soil predators: bakterivorous: protozoa, nematods, and bacterial predators phtophagous: mites, springtails

the main cause of bacterial mortality in soil

•no cyclic relationships•high redundancy causes high stability,•many prey species•fast nutrient cycle, mineralization

Predation in soil: consumption of heterotrophic organisms with detritus

Maier et al., 2000

Escape from predation:attachement to soil, small pores, pathogenicity, antibiosis, filaments, biofilm.

Protection from digestion: release of toxines, intracellular parazitism

Function

predation

Salinas et al., 2007

Movement of protozoa in soil: flagellates 2-4 cm, amoebas 3-6 cm, cilliates 1-2 cm

Consumption rate of bactria by prozoa. 5000 bacterial cells per min 800 kg of bacteria per ha per year

Predation

Ekelund et al., 2001

funkce

Correlation between the number of protozoaand bacteria at different sites in Danmark.The regular relationship on the figure demonstrates the possibility of bacteria control by protozoa at those sites.

Example:

Pisum sativum - Streptomyces lydicus – Rhizobium sp.

Streptomyces lydicus collonizes rhizosphere:

increases the number of nodules i.e. supports infections by nitrogen fixing Rhizobium sp.,increases the nodule surface, supports growth of rhizobia mostly by supplying Fe and other nutrients

Fe, other nutrients? Pisum sativum

S. lydicus Rhizobium sp.

nutrientsexudates, O2?

N source

Fe, other nutrients

N source ?

Tokala et al., Appl. Environ. Microbiol. 68, 2161-2171, 2002.

Mutualisms of three species

Tokala et al., Appl. Environ. Microbiol. 68, 2161-2171, 2002.

Nodes with a streptomycetes Nodes without streptomycetes

Nodes with streptomycetes have a large surface, which enables better nutrient utilization

Microorgansims are limited by specific requirements to moisture and temperature.They have limited or no capability to move. Microorganisms are dependent on dispersion by other organisms.

Everything is everywhere but the environment selects.

Limitation

Adaptation

Microorganisms are adapted to utilization of any organic substrate. Dispose of often large genomes, which contains pathways expresed under different conditions.Microorganisms grow quickly in the lab but very slowly in nature, one generationbetween 6 and 18 months, they are waiting for the ideal conditions to come. V laboratoři rostou velmi rychle, ale v přírodě je obrat mezi 6 a 18 měsíci.

Limitations of microbial processes function

Limitations of microbial processesfunction

Horizontal relationships – competition, comensalism, antibiosisNot well studies. Comensalisms occurs in C utilization. Cooperation in utilization of recalcitrant forms or in anaerobic conditions.

Example: „Disease supressive soils“

Use of antibiosis in agriculture. Disease suppressive soils are known for suppression of a specific pathogen, fungi, bacteria or nemathods. The most well known is disease suppression of take all wheat disease cause by mold Gauemanomyces graminis by antibiotics produced by pseudomonads.

• 11%

• 20%

• Inoculated• Not inoculated

• Inoculated• Not inoculated

• Suppressive• Conducive

Disease suppressive soilsexample Tievaliopsis basicola

microarray for identification of 1500 bacterial genera

differences in composition of communities in disease suppressive and conducive soils

conducive suppressive

Kyselkova et al., ISME 2009

Biodegradation

Microorganisms oxidating carbohydrates:bacteria, molds, yeasts, bluegreen algae, algae

Only aerobic processdependence on temperature, pH and sources of anorganic nutrients

Xenobiotics: (pesticids, polychlorinated bifenyls, explosives, tints, chlorinated solvents etc.)some are structurally related to natural compounds – slow degradation by existing enzymes

degradation of completely foreign compounds takes much longer, degradation pathways must be developed

Genomes of microorganisms – what is necessary

Glass et al.: Essential genes of a minimal bacterium

PNAS 2006;103;425-430

„minimal bacteria“ - Mycoplasma genitalium482 protein coding genes, since 2002 Nanoarchaeum equitans, 491 kb)

→ 382 from the total of 482 genes of M.genitalium are essential

Genomes of microorganisms – what is necessary

Haggblom et al.

Degradation of MTBE, methyl tert-butyl ether

One bacteria in 109 which can degrade it. Took 5 years to find it using enrichment cultivation.

Biodegradation of oil

Bacteria aggregate in high numbers at the edge between water and organic phase, or are present directly inside the organic phase

Biodegradation of oil

Functional metagenomic profiling of nine biomes

Nature 452, April 200815 milion od sequences were evaluateddivided by metabolisms and functions

9 bioms: underground, saline, sea, coral, freshwater, fish, terrestrial animals, microbial, and moskyto

Sekvence divided also by the originto viral and microbial

Separation of sequences by canonic ordination analysis

Microbial and viral set differes significantly

Processes dominating for microorganisms:cell wall building, sulfur, signalization, movement, respiration, building of proteins

Viral processes:membrane transport, potassium, phosphorus, cell division, DNA, virulence, sekundary metabolites, fatty acids

mikrobiální

virový

Climatic changes in relationship to soil microorganisms