Response of fungal and actinobacterial communities to water-level drawdown in boreal peatland sites

"We used PCR-DGGE fingerprinting and direct sequencing to analyse the response of fungal and actinobacterial communities to changing hydrological conditions at 3 different sites in a boreal peatland complex in Finland. The experimental design involved a short-term (3 years; STD) and a long-term (43 years; LTD) water-level drawdown. Correspondence analyses of DGGE bands revealed differences in the communities between natural sites representing the nutrient-rich mesotrophic fen, the nutrient-poorer oligotrophic fen, and the nutrient-poor ombrotrophic bog. Still, most fungi and actinobacteria found in the pristine peatland seemed robust to the environmental variables. Both fungal and actinobacterial diversity was higher in the fens than in the bog. Fungal diversity increased significantly after STD whereas actinobacterial diversity did not respond to hydrology. Both fungal and actinobacterial communities became more similar between peatland types after LTD, which was not apparent after STD. Most sequences clustered equally between the two main fungal phyla Ascomycota and Basidiomycota. Sequencing revealed that basidiomycetes may respond more (either positively or negatively) to hydrological changes than ascomycetes. Overall, our results suggest that fungal responses to water-level drawdown depend on peatland type. Actinobacteria seem to be less sensitive to hydrological changes, although the response of some may similarly depend on peatland type. (C) 2009 Elsevier Ltd. All rights reserved.""We used PCR-DGGE fingerprinting and direct sequencing to analyse the response of fungal and actinobacterial communities to changing hydrological conditions at 3 different sites in a boreal peatland complex in Finland. The experimental design involved a short-term (3 years; STD) and a long-term (43 years; LTD) water-level drawdown. Correspondence analyses of DGGE bands revealed differences in the communities between natural sites representing the nutrient-rich mesotrophic fen, the nutrient-poorer oligotrophic fen, and the nutrient-poor ombrotrophic bog. Still, most fungi and actinobacteria found in the pristine peatland seemed robust to the environmental variables. Both fungal and actinobacterial diversity was higher in the fens than in the bog. Fungal diversity increased significantly after STD whereas actinobacterial diversity did not respond to hydrology. Both fungal and actinobacterial communities became more similar between peatland types after LTD, which was not apparent after STD. Most sequences clustered equally between the two main fungal phyla Ascomycota and Basidiomycota. Sequencing revealed that basidiomycetes may respond more (either positively or negatively) to hydrological changes than ascomycetes. Overall, our results suggest that fungal responses to water-level drawdown depend on peatland type. Actinobacteria seem to be less sensitive to hydrological changes, although the response of some may similarly depend on peatland type. (C) 2009 Elsevier Ltd. All rights reserved.""We used PCR-DGGE fingerprinting and direct sequencing to analyse the response of fungal and actinobacterial communities to changing hydrological conditions at 3 different sites in a boreal peatland complex in Finland. The experimental design involved a short-term (3 years; STD) and a long-term (43 years; LTD) water-level drawdown. Correspondence analyses of DGGE bands revealed differences in the communities between natural sites representing the nutrient-rich mesotrophic fen, the nutrient-poorer oligotrophic fen, and the nutrient-poor ombrotrophic bog. Still, most fungi and actinobacteria found in the pristine peatland seemed robust to the environmental variables. Both fungal and actinobacterial diversity was higher in the fens than in the bog. Fungal diversity increased significantly after STD whereas actinobacterial diversity did not respond to hydrology. Both fungal and actinobacterial communities became more similar between peatland types after LTD, which was not apparent after STD. Most sequences clustered equally between the two main fungal phyla Ascomycota and Basidiomycota. Sequencing revealed that basidiomycetes may respond more (either positively or negatively) to hydrological changes than ascomycetes. Overall, our results suggest that fungal responses to water-level drawdown depend on peatland type. Actinobacteria seem to be less sensitive to hydrological changes, although the response of some may similarly depend on peatland type. (C) 2009 Elsevier Ltd. All rights reserved."Peer reviewe

Excess soil moisture and fresh carbon input are prerequisites for methane production in podzolic soil

Boreal upland forests are generally considered methane (CH4) sinks due to the predominance of CH4 oxidizing bacteria over the methanogenic archaea. However, boreal upland forests can temporarily act as CH4 sources during wet seasons or years. From a landscape perspective and in annual terms, this source can be significant as weather conditions may cause flooding, which can last a considerable proportion of the active season and because often, the forest coverage within a typical boreal catchment is much higher than that of wetlands. Processes and conditions which change mineral soils from acting as a weak sink to a strong source are not well understood. We measured soil CH4 fluxes from 20 different points from regularly irrigated and control plots during two growing seasons. We also estimated potential CH4 production and oxidation rates in different soil layers and performed a laboratory experiment, where soil microcosms were subjected to different moisture levels and glucose addition simulating the fresh labile carbon (C) source from root exudates. The aim was to find the key controlling factors and conditions for boreal upland soil CH4 production. Probably due to long dry periods in both summers, we did not find occasions of CH4 production following the excess irrigation, with one exception in July 2019 with emission of 18 200 µg CH4 m−2 h−1. Otherwise, the soil was always a CH4 sink (median CH4 uptake rate of 260–290 and 150–170 µg CH4 m−2 h−1, in control and irrigated plots, respectively). The median soil CH4 uptake rates at the irrigated plot were 88 % and 50 % lower than at the control plot in 2018 and 2019, respectively. Potential CH4 production rates were highest in the organic layer (0.2–0.6 nmol CH4 g−1 d−1), but some production was also observed in the leaching layer, whereas in other soil layers, the rates were negligible. Potential CH4 oxidation rates varied mainly within 10–40 nmol CH4 g−1 d−1, except in deep soil and the organic layer in 2019, where potential oxidation rates were almost zero. The laboratory experiment revealed that high soil moisture alone does not turn upland forest soil into a CH4 source. However, a simple C source, e.g., substrates coming from root exudates with high moisture, switched the soil into a CH4 source. Our unique study provides new insights into the processes and controlling factors on CH4 production and oxidation, and the resulting net efflux that should be incorporated in process models describing global CH4 cycling

Are there environmental or agricultural benefits in using forest residue biochar in boreal agricultural clay soil?

Short-term agronomic and environmental benefits are fundamental factors in encouraging farmers to use biochar on a broad scale. The short-term impacts of forest residue biochar (BC) on the productivity and carbon (C) storage of arable boreal clay soil were studied in a field experiment. In addition, rain simulations and aggregate stability tests were carried out to investigate the potential of BC to reduce nutrient export to surface waters. A BC addition of 30 t ha−1 increased soil test phosphorus and decreased bulk density in the surface soil but did not significantly change pH or water retention properties, and most importantly, did not increase the yield. There were no changes in the bacterial or fungal communities, or biomasses. Soil basal respiration was higher in BC-amended plots in the spring, but no differences in respiration rates were detected in the fall two years after the application. Rain simulation experiments did not support the use of BC in reducing erosion or the export of nutrients from the field. Of the C added, on average 80% was discovered in the 0–45 cm soil layer one year after the application. Amendment of boreal clay soil with a high rate of BC characterized by a moderately alkaline pH, low surface functionalities, and a recalcitrant nature, did not induce such positive impacts that would unambiguously motivate farmers to invest in BC. BC use seems unviable from the farmer's perspective but could play a role in climate change mitigation, as it will likely serve as long-term C storage.202

Site fertility and soil water-table level affect fungal biomass production and community composition in boreal peatland forests

A substantial amount of below-ground carbon (C) is suggested to be associated with fungi, which may significantly affect the soil C balance in forested ecosystems. Ergosterol from in-growth mesh bags and litterbags was used to estimate fungal biomass production and community composition in drained peatland forests with differing fertility. Extramatrical mycelia (EMM) biomass production was generally higher in the nutrient-poor site, increased with deeper water table level and decreased along the length of the recovery time. EMM biomass production was of the same magnitude as in mineral-soil forests. Saprotrophic fungal biomass production was higher in the nutrient-rich site. Both ectomycorrhizal (ECM) and saprotrophic fungal community composition changed according to site fertility and water table level. ECM fungal community composition with different exploration types may explain the differences in fungal biomass production between peatland forests. Melanin-rich Hyaloscypha may indicate decreased turnover of biomass in nutrient-rich young peatland forest. Genera Lactarius and Laccaria may be important in nutrient rich and Piloderma in the nutrient-poor conditions, respectively. Furthermore, Paxillus involutus and Cortinarius sp. may be important generalists in all sites and responsible for EMM biomass production during the first summer months. Saprotrophs showed a functionally more diverse fungal community in the nutrient-rich site.Peer reviewe

Storm and Ips typographus disturbance effects on carbon stocks, humus layer carbon fractions and microbial community composition in boreal Picea abies stands

Tree-killing forest disturbances such as storms and bark beetle outbreaks can lead to notable changes in the carbon (C) balance and functioning of forest ecosystems. In this study, the effects of a storm in 2010 followed by an outbreak of European spruce bark beetle (Ips typographus L.) on tree, litter and soil C stocks as well as humus layer C fractions and microbial community composition were examined in boreal Norway spruce (Picea abies L.) stands. Tree (aboveground), litter detritus (distinguishable twig, bark and cones) and soil (humus layer and 0-6 cm mineral soil) C stocks were quantified for undisturbed (living trees), storm disturbed (in 2010) and I. typographus disturbed (tree mortality in circa 2013-2014) plots in 2015-2016. Additional humus layer samples were collected in 2017 for determination of total microbial biomass C, ergosterol (fungal biomass indicator) and K2SO4 extractable (labile) C concentrations, as well as fungal and bacterial community composition (DNA sequencing). Ectomycorrhizal (ECM) fungal mycelial growth in topsoil was also quantified. In spite of the differing initial development and intensity of the two disturbance types, there was little difference in humus layer C and microbiology between the storm and bark beetle disturbed plot types at the time of the study. This may be due to the longer time since the disturbance at the storm disturbed plots. The shift from tree biomass to necromass C stocks was not reflected in differences in SOC stocks or humus layer extractable C concentrations between undisturbed and disturbed plot types, but the amount of litter detritus on forest floor was similar (storm) or higher (beetle) in disturbed plots in comparison to undisturbed ones. Humus layer microbial biomass C and ergosterol concentrations and ECM fungal abundance were lower on disturbed plots in comparison to undisturbed plots. The disturbed plots were also indicated to have a slightly higher abundance of some saprotrophic fungi. Differences in the effects of the two disturbance types may occur when studied at differing spatial scales and at different times after disturbance. To understand the full impact of such disturbances on forest functioning and C balance, long-term monitoring studies will be required.Peer reviewe

Long-term impacts of organic and conventional farming on the soil microbiome in boreal arable soil

Long-term effects of organic and conventional farming systems in parallel on the microbiota of boreal arable soil from forage and cereal crop fields were investigated. Microbial activity was measured as basal respiration and microbial biomass C and N were determined by fumigation extraction. Microbial abundance was determined by gene copy numbers from bacterial and archaeal specific 16S rRNA genes and the fungal ITS2 region with quantitative PCR. Microbial community composition for soil bacteria and fungi, including arbuscular mycorrhiza, were conducted by amplicon sequencing with richness assessed from OTU reads. We detected changes in both bacterial and fungal community composition between the farming systems. Microbial activity and biomass C and N were higher in the organic system for cereal crop rotation compared to the respective conventional system. In the autumn, organic systems had higher microbial richness. As fungi were more abundant in the autumn, they may be responsible for both higher microbial activity and C sequestration in their biomass after harvesting, especially in the organic system for cereal crop rotation. Also, crop type and cow manure explained changes in fungal community composition. The typical bacterial community of the organic system for cereal crop rotation included many soil and plant health promoting bacterial groups. Fungi benefiting from organic farming practices, other than manure, may include endophytic taxa with a variety of functions as well as pathogenic and mycotoxin producing species. Overall, the results suggest that farming practices typical of organic farming, such as use of green manure and continuous plant cover have induced changes in the soil microbiome

Impacts of coniferous bark-derived organic soil amendments on microbial communities in arable soil – a microcosm study

A decline in the carbon content of agricultural soils has been reported globally. Amendments of forest industry side-streams might counteract this. We tested the effects of industrial conifer bark and its cascade process materials on the soil microbiome under barley (Hordeum vulgare L.) in clay and silt soil microcosms for 10 months, simulating the seasonal temperature changes of the boreal region. Microbial gene copy numbers were higher in clay soils than in silt. All amendments except unextracted bark increased bacterial gene copies in both soils. In turn, all other amendments, but not unextracted bark from an anaerobic digestion process, increased fungal gene copy numbers in silt soil. In clay soil, fungal increase occurred only with unextracted bark and hot water extracted bark. Soil, amendment type and simulated season affected both the bacterial and fungal community composition. Amendments increased bacteria originating from the anaerobic digestion process, as well as dinitrogen fixers and decomposers of plant cells. In turn, unextracted and hot water extracted bark determined the fungal community composition in silt. As fungal abundance increase and community diversification are related to soil carbon acquisition, bark-based amendments to soils can thus contribute to sustainable agriculture

Integrating Decomposers, Methane-Cycling Microbes and Ecosystem Carbon Fluxes Along a Peatland Successional Gradient in a Land Uplift Region

Peatlands are carbon dioxide (CO2) sinks that, in parallel, release methane (CH4). The peatland carbon (C) balance depends on the interplay of decomposer and CH4-cycling microbes, vegetation, and environmental conditions. These interactions are susceptible to the changes that occur along a successional gradient from vascular plant-dominated systems to Sphagnum moss-dominated systems. Changes similar to this succession are predicted to occur from climate change. Here, we investigated how microbial and plant communities are interlinked with each other and with ecosystem C cycling along a successional gradient on a boreal land uplift coast. The gradient ranged from shoreline to meadows and fens, and further to bogs. Potential microbial activity (aerobic CO2 production; CH4 production and oxidation) and biomass were greatest in the early successional meadows, although their communities of aerobic decomposers (fungi, actinobacteria), methanogens, and methanotrophs did not differ from the older fens. Instead, the functional microbial communities shifted at the fen-bog transition concurrent with a sudden decrease in C fluxes. The successional patterns of decomposer versus CH4-cycling communities diverged at the bog stage, indicating strong but distinct microbial responses to Sphagnum dominance and acidity. We highlight young meadows as dynamic sites with the greatest microbial potential for C release. These hot spots of C turnover with dense sedge cover may represent a sensitive bottleneck in succession, which is necessary for eventual long-term peat accumulation. The distinctive microbes in bogs could serve as indicators of the C sink function in restoration measures that aim to stabilize the C in the peat.Peer reviewe

Litter type affects the activity of aerobic decomposers in a boreal peatland more than site nutrient and water level regimes

The discussion paper published in Biogeosciences Discuss.: Straková, P., Niemi, R. M., Freeman, C., Peltoniemi, K., Toberman, H., Heiskanen, I., Fritze, H., and Laiho, R. 2011. Litter type affects the activity of aerobic decomposers in a boreal peatland more than site nutrient and water level regimes, Biogeosciences Discuss., 8, 1879-1916. doi:10.5194/bgd-8-1879-2011Peatlands are carbon (C) storage ecosystems sustained by a high water level (WL). High WL creates anoxic conditions that suppress the activity of aerobic decomposers and provide conditions for peat accumulation. Peatland function can be dramatically affected by WL drawdown caused by land-use and/or climate change. Aerobic decomposers are directly affected by WL drawdown through environmental factors such as increased oxygenation and nutrient availability. Additionally, they are indirectly affected via changes in plant community composition and litter quality. We studied the relative importance of direct and indirect effects of WL drawdown on aerobic decomposer activity in plant litter. We did this by profiling 11 extracellular enzymes involved in the mineralization of organic C, nitrogen, phosphorus and sulphur. Our study sites represented a three-stage chronosequence from pristine (undrained) to short-term (years) and long-term (decades) WL drawdown conditions under two nutrient regimes. The litter types included reflected the prevalent vegetation, i.e., Sphagnum mosses, graminoids, shrubs and trees. WL drawdown had a direct and positive effect on microbial activity. Enzyme allocation shifted towards C acquisition, which caused an increase in the rate of decomposition. However, litter type overruled the direct effects of WL drawdown and was the main factor shaping microbial activity patterns. Our results imply that changes in plant community composition in response to persistent WL drawdown will strongly affect the C dynamics of peatlands.Peer reviewe

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