Markéta Marečková e-mail: sagova @vurv.cz

1. Markéta Marečková e-mail: sagova@vurv.cz

2. Microorganisms in soil • Soil structure and its • Soil ecosystem • Trophic relationships • Key processes • Estimation, models and evaluation Soil is the most complex environment

3. Ecosystem Abiotic Biotic Function Structure

4. Soil ecosystem dominated by heterotropic organisms • bedrock • darkness predation quantity & quality of C • plant nutrition • decomposition of OM porous mixture of solids, liquids and gases

5. Methods of study

6. Solids Abiotic factors Porous material of solids, liquids and gases Bedrock : 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+ Maier et al., 2000

7. Abiotic soil components sand silt gravel mineral particles mineral particles mineral particles pores pores pores organic matter organic matter

8. Struktura půdy oživení porů 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. Meier et al., 2002

9. Water, liquids Abiotic factors Water is the main limiting factor in soil water content is correlated to organic matter content Pore size: macropores>0.08mm, gravitation water, plants mesopores0.08 -0.03mm,capillary water micropores0.03-0.005mm,inside agregates, bacteria ultramicropores0.005-0.0001mm,inside clay particles cryptopores<0.0001mm, too small even for macromolecules Maier et al., 2000

10. Free and bound water Abiotic soil components 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. surface forces,Ψm, - 31 až – 10000 atm capillary forces, ΨS-0.1 až -30 atm gravitation forces, Ψg0 až -0.5 atm Maier et al., 2000

11. Soil structure examples of characteristics

12. Soil structure and life niches Habitat of microorganisms: variable in space and time stratified by physical and chemical forces and important nutrients– C, organické látky, 02, N, P, S (obydlí) microhabitat life form • soil particles • rhizosphere • air bubbles • sufaces of organisms active cells, spores, fillaments, collonies, biofilms

13. Living forms Viruses, phages

14. Diversity of viruses in various soils Living forms • Comparison of agricultural, forest and • alpine soils. • Highest diversity (Simpson index) was • found in forest soils • The highest percentage of viruses were • bacteriophages

15. Living forms Bacteria Proteobacteria: pseudomonads, myxobacteria, rhizobia Acidobacteria Actinobacteria: streptomycets, corynebacteria Verrucomicrobia Firmicutes: bacilli, clostridia, laktobacilli Planctomycetes Chondromyces 109cells 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. Myxococcus Streptomyces Bacillus

16. Algae and Fungi Living forms Molds Blue greens Nostoc Algae Aspergillus Cryptomonas 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.

17. Protozoa Living forms Amoebas Acanthamoeba Heterotrophic flagellates Paranema

18. Living forms Cilliates Euplotes, Stylonychia Nemathods

19. Living forms Mites Springtails Orchesella

20. Živé složky půdy Oligochaetes Lumbricullus variegatus Mammals Microtus arvalis

21. Soil horizons structure In soil, organic and anorganic material is layered to soil horizons. They are created by plant litter and water from rain and groundwater.

22. Abundance and biomass of soil populations

23. Distribution by source structure 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. Scale analysis (A) Distribution of soil patches colonized by bacteria in a two-dimensional grid with an indication of the four sizes of microsamples used. (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

24. structure Inhabiting pore according to its size terminal fragment lenght T-RFLP profiles in three fractions of differently treated soils Sessitch et al.2001 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

25. Organic matter sources structure • Organic matter • main factor influencing productivity of soil environment. ovlivňuje: • plant nutrition • community composition • water content • agregate stability • erosion control „Hot spots“ sites of highest mircorbial activity. 90% of activity goes on in 10% of soil volume. E.g. rhizosphere and burries of animals 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.

26. DOC DON NH4+ NO3- fungi bacteria Nutrition structure Example 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 bacteria Fungi quantity correlated with C and negatively with N. Bacteria correlate with temperature. DOC dissolved organic carbon, DON dissolved organic nitrogen

27. Rate of soil processes function Example mineralization 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 nitrification imobilization N

28. structure Nutrient consumption 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 Streptomyces, Micromonospora, Streptosporangium (podřády), myxobakterie r organisms: fast growing, fast reactions to a new source, consumption of available sources at good living conditions, coccal forms, fast growth, tolerate stress Burkholderia, Xanthomonas, Agrobacterium, entherobakterie

29. structure C content in soil by source Examples of organic C content and microbial C content. In meadow ecosystems microbial content is higher.

30. processes Trophic pyramid • 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) nutrition predators II predators I predators I decomposers, PP PP chemolithotrophie shredded litter, microorganisms secundary decomposers primary decomposers litter

31. Trophic relationships in soil environment natural meadow ecosystem wheat monoculture Agroecosystem is simplified, no mycorhiza, N2 fixation, limited nematods and increasing effect of cilliates

32. Plant community exudates litter bacteria energetic canal fungal bacterial protists Carbon and other nutrients Trophic processes processes • 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) Basic flows of energy and nutrients in soil ecosystems

33. Trophic relationships procesess

34. Trophic relationships Example: A field with convention farming (full) and a field with organic farming (dashed) were followed during a year. Biomass of bacteria and fungi correlatedwith temperature. Maximum of bacterial biomass was 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. Bloem et al., 1994

35. predation predation predation grazing substrate processing Energy flow pore formation litter fragmentation bioturbation Habitat formation Function of organisms by body size organismů Trophic interactions are fast while habitat formation is a long term process

36. Primary production function Chemolithotrophy Fixace CO2 Energie: oxidace železa, amonných solí, sirníků, síry, kovů, dusitanů Zastoupení autotrophů podle qPCR Zastoupení autotrofů v průběhu tří let Jourdan et al., 2005 Bernhart et al., 2007

37. Predation Predation in soil:consumption of heterotrophic organisms with detritus the main cause of bacterial mortality in soil soil predators: bakterivorous: protozoa, nematods, and bacterial predators phtophagous: mites, springtails • no cyclic relationships • high redundancy causes high stability, • many prey species • fast nutrient cycle, mineralization Maier et al., 2000

38. Function predation Escape from predation: attachement to soil, small pores, pathogenicity, antibiosis, filaments, biofilm. Protection from digestion: release of toxines, intracellular parazitism Salinas et al., 2007

39. Predation funkce Consumption rate of bactria by prozoa. 5000 bacterial cells per min 800 kg of bacteria per ha per year Movement of protozoa in soil: flagellates 2-4 cm, amoebas 3-6 cm, cilliates 1-2 cm Example: Correlation between the number of protozoa and bacteria at different sites in Danmark. The regular relationship on the figure demonstrates the possibility of bacteria control by protozoa at those sites. Ekelund et al., 2001

40. Mutualisms of three species Pisum sativum - Streptomyces lydicus – Rhizobium sp. Streptomyces lydicuscollonizes 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 N source nutrients exudates, O2? N source ? Rhizobium sp. S. lydicus Fe, other nutrients Tokala et al., Appl. Environ. Microbiol. 68, 2161-2171, 2002.

41. Nodes with a streptomycetes Nodes without streptomycetes Nodes with streptomycetes have a large surface, which enables better nutrient utilization Tokala et al., Appl. Environ. Microbiol. 68, 2161-2171, 2002.

42. Limitations of microbial processes function Limitation 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. 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 generation between 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.

43. Limitations of microbial processes function Horizontal relationships – competition, comensalism, antibiosis Not 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 graminisby antibiotics produced by pseudomonads.

44. Conducive • Suppressive • 20% • Inoculated • Not inoculated • Inoculated • Not inoculated • 11% Disease suppressive soils exampleTievaliopsis basicola microarray for identification of 1500 bacterial genera suppressive conducive differences in composition of communities in disease suppressive and conducive soils Kyselkova et al., ISME 2009

45. Microorganisms oxidating carbohydrates: bacteria, molds, yeasts, bluegreen algae, algae Only aerobic process dependence 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 Biodegradation

46. Genomes of microorganisms – what is necessary Glass et al.: Essential genes of a minimal bacterium PNAS 2006;103;425-430 „minimal bacteria“ - Mycoplasma genitalium 482 protein coding genes, since 2002 Nanoarchaeum equitans, 491 kb) → 382 from the total of 482 genes of M.genitalium are essential

47. 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.

48. Biodegradation of oil Bacteria aggregate in high numbers at the edge between water and organic phase, or are present directly inside the organic phase

49. Biodegradation of oil