Metla Project 3366

Coniferous forest soil microbial activity and community structure

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Duration: 2003-2010   Keywords: C-cycle, ash, carbon dioxide, fire, methane, mikrobial community , molecular biology
Research project group: Distinct projects 1 - Structure and function of forest ecosystems


About 1 % of the soil microorganisms can be cultivated for identification. New molecular based methods allow the identification of organisms from environmental samples without the need of cultivation. This project relates microbial communities to their performance in the global C-cycle (CO2, CH4). Field work will be performed in natural and cultivated forest as well as in ash fertilized, burned or trampled (weir) study sites.


Results CH4-cycle Wetlands, including peatlands, are the main source of natural emissions of the green house gas methane. Even though rate of CH4 release and production have been monitored in boreal peatlands, the communities of methanogenic Archaea, responsible for the CH4 formation, remain poorly described.

The diversity of methanogens was investigated, at different depths, in the most representative microsite (Eriophorum lawn) of the Salmisuo fen. Amplification of portions of the mcr gene revealed a change of populations with depth. Sequences from the upper layers of the fen grouped in a novel “Fen cluster”, related to Methanomicrobiales. Sequences retrieved from the deeper layers of the fen were related to hydrogenotrophs from the Rice Cluster-I.

Characterisation of methanogen communities from two well-defined fen microsites, Eriophorum lawn and hummock, indicated a population change in upper layers, and homogenous communities in deeper layers. 16SrRNA phylogenetic analyses revealed that upper layers of hummock were dominated by Methanomicrobiales related sequences, and that members of Methanosarcinales occupied upper parts of the Eriophorum lawn. Novel methanogenic sequences were found at both sites at both depths. Vegetation characterising the microsites probably influences methanogenic communities, and pathways in the anaerobic layers of the fen.

Samples from all depths of the drained Pelso-Resula bog contained a majority of mcr sequences related to the hydrogenotroph Rice cluster-I. An ash fertilisation trial demonstrated that ash treatment marginally increased peat pH without affecting the major methanogen groups. Nevertheless, some Fen cluster-related sequences were retrieved from fertilized plots only, suggesting a group specific response to environmental changes.

Galand P., Juottonen H., Fritze H. & Yrjälä K. 2004: Methanogen communities in a drained bog: effect of ash fertilization. Microbial Ecology (in press) Galand P., Fritze H. & Yrjälä K 2003: Microsite-dependent changes in Methanogenic Populations in a Boreal Oligotrophic Fen. Environmental Microbiology 5: 1133-1143. Galand P., Saarnio S., Fritze H. & Yrjälä K. 2002: Depth related diversity of methanogen Archaea in Finnish oligothrophic fen. FEMS Microbiology Ecology 42: 441-449. Jaatinen K., Knief K., Yrjälä K., Dunfield P. & Fritze H. 2004: Methanotrophic bacteria in boreal forest soil - effects of fire. FEMS Microbiology Ecology 50: 195-202 Galand P., Juottonen H., Fritze H. & Yrjälä K. 2005: Methanogen communities in a drained bog: effect of ash fertilization. Microbial Ecology 49: 209-217 Galand P, Fritze H, Conrad R & Yrjälä K. 2005: Pathways for methanogenesis and diversity of methanogenic Archaea in three boreal peatland ecosystems. Applied Environmental Microbiology 71: 2195-2198. Juottonen H, Galand P, Tuittila E-S, Laine J, Fritze H. & Yrjälä K. 2005: Methanogen communities and bacteria along an ecohydrological gradient in a northern raised bog complex. Environmental Microbiology 7: 1547-1557 Wood ash

The use of wood ash in forestry has been questioned because the potential risk associated with its cadmium (Cd) content (1-30 mg kg-1). In agriculture, wood ash is only allowed for use as fertilizer when its Cd content is below 3 mg kg-1. This restriction has not been applied to forest soils and there is a lack of knowledge about the potential harmful effects of the Cd in wood ash on forest ecosystems. This paper summarizes our recent studies on the microbial communities of boreal coniferous forest humus exposed to Cd-containing wood ash treatment. The main objectives of our studies were to test if the Cd in wood ash has the potential to affect the humus layer microflora of coniferous upland forests and if the Cd has the potential to enter the human food chain. These objectives were tested both in laboratory and field experiments with ash and ash spiked with Cd (in laboratory 400 or 1000 mg Cd kg-1 as CdO or CdCl2; in field 400 mg Cd kg-1 as CdO). In one study the dissolution of ash was accelerated by irrigating it with simulated acid rain (SAR).

Wood ash increased humus layer pH and microbial activities (respiration or thymidine incorporation rates) and changed its microfloral community structure (Biolog®, PLFA, 16S or 18S rDNA PCR-DGGE) in both laboratory and field and experiments. Spiking ash with Cd induced no further changes in the above-mentioned variables as ash alone. The Cd added with wood ash did not become bioavailable as detected with a bacterial biosensor Bacillus subtilis BR151(pTOO24). The form and level of Cd added in the ash had no further effect on the microbiological variables studied. Irrigation of ash with SAR did not increase the amount of bioavailable Cd, although the dissolution rate of the ash was increased. The concentration of Cd in soil water and in the berries of Vaccinium uliginosum and V. vitis-idaea, and the amount of humus bioavailable Cd did not increase with the ash or ash spiked with Cd although the ash spiked with Cd increased the amount of humus total and extractable Cd in the 4 year field study. Only the ash spiked with Cd and not the unspiked "normal" wood ash resulted in significantly higher Cd concentrations in the mushroom Lactarius rufus and a slight increase in the berries of Empetrum nigrum (first year only). Fritze H., Perkiömäki J., Saarela U., Katainen R., Tikka P., Yrjälä K., Karp M., Haimi J. & Romantschuk M. 2000: Effect of Cd-containing wood ash on the microflora of coniferous forest humus. FEMS Microbiology Ecology 32: 43-51. Fritze H., Perkiömäki J., Petänen T., Pennanen T., Romantschuk M., Karp M. & Yrjälä K. 2001: A microcosmos study on the effects of Cd-containing wood ash on the coniferous forest humus fungal community and Cd bioavailability. Journal of Soils and Sediments 1: 146-150. Perkiömäki J. & Fritze H. 2002: Short and long-termed effects of wood ash on the boreal forest microbial community. Soil Biology and Biochemistry 34: 1343-1353. Perkiömäki J. & Fritze H. 2003: Does simulated acid rain increase the leaching of cadmium from wood ash to toxic levels for coniferous forest humus microbes? FEMS Microbiology Ecology 44: 27-33. Perkiömäki J., Tom-Petersen A., Nybroe O. & Fritze H. 2003: Boreal forest microbial community after long-term field exposure to acid and metal pollution and its potential remediation by using wood ash. Soil Biology & Biochemistry 35: 1517-1526. Perkiömäki J., Kiikkilä O., Moilanen M., Issakainen J., Tervahauta A. & Fritze H. 2003: Cadmium-containing wood ash in a pine forest: effects on humus microflora and cadmium concentrations in mushrooms, berries and needles. Canadian Journal of Forest Research 33: 2443-2451. Perkiömäki, J., Levula, T. & Fritze, H 2004: A reciprocal decomposition experiment of Scots pine needles 19 yr after wood ash fertilization. Soil Biology & Biochemistry 36:731-734. Yrjälä, K, Katainen, R., Jurgens, G., Saarela, U., Saano, A., Romantschuk, M. & Fritze, H. 2004: Wood ash fertilization alters the forest humus Archaea community. Soil Biology & Biochemistry 36:199-201. Perkiömäki J & Fritze H 2005: Cadmium in upland forests after vitality fertilization with wood ash - a summary of soil microbiological studies into the potential risk of cadmium release. Biology and Fertility of Soils 41: 75-84. Forest weir Malmivaara-Lämsä, M. & Fritze H. 2003: Effect of wear and above ground forest site type characteristics on the soil microbial community structure in an urban setting. Plant and Soil 256: 187-203.

Forest habitat fragmentation

The objectives of this thesis were (i) to experimentally investigate the effects of habitat fragmentation on soil decomposers, and (ii) to examine whether such studies of soil decomposer communities can be used as a tool to provide generally applicable information on the consequences of habitat fragmentation. Special emphasis was put on testing the utility of habitat corridors in mitigating the expected negative effects of fragmentation. The experiments were conducted both in the laboratory and in the field. The results show that the soil decomposer organisms are, in general, relatively insensitive to habitat fragmentation. However, some predatory and rare, non predatory microarthropod species were an exception to this rule, being negatively affected by restricted habitat size. The functioning of corridors in alleviating fragmentation induced effects was practically undetected. Despite this, corridors were shown to facilitate the colonisation of new habitats by both soil fauna and microbes, suggesting that the corridors may benefit a whole community instead of only one or a few species. It was also shown that resource quality is a fundamental factor in determining .the abundance of soil decomposers in fragmented habitats. The present studies were novel in the sense that they investigated the responses of a wide variety of organisms, from basal resources to top predators. Although it is unlikely that the results can be straightforwardly extrapolated to larger scales, they nevertheless suggest that not all communities, and species therein, unanimously suffer from habitat fragmentation. On the other hand, the fragmentation responses of soil microarthropods may not differ that much from those of aboveground organisms operating at larger scales. The results of this thesis support the applicability of studying soil food webs as a tool for solving questions related to both applied and theoretical ecology.

Rantalainen, M-L., Fritze, H., Haimi, J., Kiikkilä, O., Pennanen, T. & Setälä, H 2004: Do enchytraeid worms and habitat corridors facilitate the colonisation of habitat patches by soil microbes? Biology and Fertility of Soils 39: 200-208. Rantalainen M-L, Kontiola L, Haimi J, Fritze H & Setälä H. 2004: Influence of resource quality on the composition of soil decomposer community in fragmented and continuous habitat. Soil Biology & Biochemistry 36:1983-1996 Rantalainen M-L, Fritze H, Haimi J, Pennanen T & Setälä H. 2005: Species richness and food web structure of soil decomposer community as affected by the scale of habitat fragmentation and habitat corridors. Global Change Biology 11: 1614-1627 Rantalainen M-L, Fritze H, Haimi J, Pennanen T & Setälä H. 2005: Colonisation of newly established habitats by soil decomposer organisms: the effect of habitat corridors in relation to colonisation distance and habitat size. Applied Soil Ecology 28:67-77

Project leader: Fritze, Hannu
The Finnish Forest Research Institute, Vantaa Unit, PO Box 18 (Jokiniemenkuja 1), FI-01301 VANTAA, FINLAND
Phone: +358 29 532 5416

Other researchers: Duran-Torres, Gilberto (2010), Peltoniemi, Krista (2006-09), Rajala, Tiina, VA (2007), Tuomivirta, Tero, VA (2006-10)

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Updated 31.12.2013