Response of the soil fungal community to multi-factor environmental changes in a temperate forest

Both environmental and climatic changes are known to influence soil microbial biomes in terrestrial ecosystems. However, there are limited data defining the interactive effects of multi-factor environmental disturbances, including N-deposition, precipitation, and air temperature, on soil fungal communities in temperate forests. A 3-year outdoor pot experiment was conducted to examine the temporal shifts of soil fungal communities in a temperate forest following N-addition, precipitation and air temperature changes. The shifts in the structure and composition of soil fungal communities were characterized by denaturing gradient gel electrophoresis and DNA sequencing. N-addition regimen induced significant alterations in the composition of soil fungal communities, and this effect was different at both higher and lower altitudes. The response of the soil fungal community to N-addition was much stronger in precipitation-reduced soils compared to soils experiencing enhanced precipitation. The combined treatment of N-addition and reduced precipitation caused more pronounced changes in the lower altitude versus those in the higher one. Certain fungal species in the subphylum Pezizomycotina and Saccharomycotina distinctively responded to N fertilization and soil water control at both altitudes. Redundancy discrimination analysis showed that changes in environmental factors and soil physicochemical properties explained 43.7% of the total variability in the soil fungal community at this forest ecosystem. Variations in the soil fungal community were significantly related to the altitude, soil temperature, total soil N content (TN) and pH value (P < 0.05). We present evidence for the interactive effects of N-addition, water manipulation and air temperature to reshape soil fungal communities in the temperate forest. Our data could provide new insights into predicting the response of soil micro-ecosystem to climatic changes.     

Diversity of laccase genes from basidiomycetes in a forest soil

Fungal oxidative exo-enzymes lacking substrate specificity play a central role in the cycling of soil organic matter. Due to their broad ecological impact and available knowledge of their gene structure, laccases appeared to be appropriate markers to monitor fungi with this kind of oxidative potential in soils. A degenerate PCR-primer pair Cu1F/Cu2R, specific for basidiomycetes, was designed to assess directly the diversity of laccase genes in soils. PCR amplification of mycelial cultures and fruit-bodies of a wide spectrum of basidiomycetes, covering all functional groups (saprophytes, symbionts, and pathogens), produced multiple DNA fragments around 200 bp. A neighbor-joining tree analysis of the PCR-amplified laccase sequences showed a clear species-specificity, but also revealed that most fungal taxa possess several laccase genes showing a large sequence divergence. This sequence diversity precluded the systematic attribution of amplified laccase of unknown origin to specific taxa. Amplification of laccase sequences from DNA, extracted from a brown (moder) forest soil, showed a specific distribution of laccase genes and of the corresponding fungal species in the various soil horizons (O_h, A_h, B_v). The most organic O_h-horizon displayed the highest gene diversity. Saprophytic fungi appeared to be less widespread through the soil horizons and displayed a higher diversity of laccase genes than the mycorrhizal ones.     

Effects of long-term CO2 fumigation on fungal communities in a temperate forest soil

This study aimed at determining the impact of long-time elevated CO₂ fumigation on fungal communities in a temperate forest soil. In addition to the CO₂ concentration, both time and its interaction with the CO₂ affected the activity of 1,4-β-N-acetylglucosaminidase that is mainly of the fungal origin in the soil. No significant change in Shannon's indexes (from 18S rDNA-PCR-DGGE) was observed between the ambient and elevated CO₂ treatments. Analysis of time-course indicated that the succession of soil fungal community was altered by the elevated CO₂ fumigation, and the variations in the soil samples under Pinus koraiensis Sieb. et Zucc were larger than those under the Pinus sylvestriformis (Takenouchi) T. Wang ex Cheng samples. The results suggest that the increase in atmospheric CO₂ concentrations could alter the temporal patterning of soil fungal communities.     

Experimental warming effects on the microbial community of a temperate mountain forest soil

Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO₂ (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.     

Microbial community structure and activity in a Colorado Rocky Mountain forest soil scarred by slash pile burning

Tree thinning and harvesting produces large amounts of slash material which are typically disposed of by burning, often resulting in severe soil heating. We measured soil chemical properties and microbial community structure and function over time to determine effects of slash pile burning in a ponderosa pine forest soil. Real time data were collected for soil temperature, heat flux, and soil moisture contents in one of two slash piles burned in April 2004. During the burn, soil temperatures reached 300 °C beneath the pile center and 175 °C beneath the pile edge. Slash pile burning increased soil pH, extractable N and P, and decreased total C levels within the first 15 cm of soil. Burning reduced soil bacterial biovolumes within the first 15 cm of soil and fungal biovolumes within the first 5 cm of soil. One month after the burn, soil microbial communities under the pile center were enriched in Gram-positive bacterial fatty acid markers compared to communities from under the pile edge and control (nonburned) soil. Fifteen months later, soil chemical properties had not returned to background levels, and microbial community structure in fire-affected soil, regardless of pile location, was distinct from communities of control soil. In fire-affected soil, concentrations of fungal fatty acid biomarkers were low and arbuscular mycorrhizal fungal biomarkers were absent, regardless of pile location. Slash pile burning also reduced fungal and bacterial respiration and resulted in large fluctuations in microbial potential N mineralization and immobilization activities. By altering soil properties important to soil conservation and plant reestablishment, slash pile burning negatively impacts forest ecosystems at localized scales.     

Influence of repeated prescribed burning on the soil fungal community in an eastern Australian wet sclerophyll forest

A long-term prescribed burning experiment, incorporating replicated plots that receive burning biennially (2 yr burn) or quadrennially (4 yr burn) and unburned controls, has been maintained in a wet sclerophyll forest at Peachester, Queensland, Australia since 1972. In 2003 we extracted DNA from soil collected from the experimental plots and investigated the influence of the burning on the soil fungal community by comparing denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified partial rDNA internal transcribed spacer regions (ITS1). Canonical analysis of principal coordinates (CAP) of the DGGE profiles of the upper 10 cm of the soil profile grouped the data strongly according to treatment, indicating that both burning regimes significantly altered fungal community structure compared to the unburned controls. In contrast, no obvious trend was observed for soil from a depth of 10-20 cm of the profile. Sequencing of selected DGGE bands found no obvious patterns of presence/absence of taxonomic groups between the treatments. Analysis of soil nitrogen and carbon by mass spectrometry indicated that total soil C and N, along with both gross and net N mineralisation, were significantly lower in 2 yr plots compared to control and 4 yr plots.     

Comparison of the functions of the barley nicotianamine synthase gene HvNAS1 and rice nicotianamine synthase gene OsNAS1 promoters in response to iron deficiency in transgenic tobacco

Barley ( Hordeum vulgare L.) nicotianamine synthase gene ( HvNAS1 ) expression in barley is strongly induced by Fe deficiency in the roots and rice ( Oryza sativa L.) nicotianamine synthase gene ( OsNAS1 ) expression in rice is induced by Fe deficiency both in the roots and in the shoots. In dicots, NAS genes are not strongly induced by Fe deficiency, and they function to maintain Fe homeostasis. Rice OsNAS1promoter::GUS or barley HvNAS1promoter::GUS was introduced into tobacco ( Nicotiana tabacum L.) and tissue specificities and systemic regulation of their expression were compared. A split-root experiment revealed that the HvNAS1 promoter exhibited functions similar to those of Fe-acquisition-related genes in tobacco roots, suggesting that this promoter responded to certain Fe-deficiency systemic signals and to the Fe concentration in the rhizosphere. The HvNAS1 promoter might harbor a type of universal system of gene expression for Fe acquisition. However, the OsNAS1 promoter did not respond to local application of Fe to the roots and induced GUS activities in mature leaves in response to Fe deficiency. This promoter might possess numerous types of cis -acting sequences that are involved in Fe metabolism.     

Bioactivity in limed soil of a spruce forest

Summary The stimulative effect of lime on the bioactivity of various soil horizons was demonstrated by the ATP test, and respiration and microcalorimetric measurements, but not by FDA hydrolysis or the iron reduction test. The latter showed clear inhibition. When the natural structure of layers was saved while sampling, a smaller stimulation of bioactivity was observed than in the case of mixing natural layers. No stimulation was recorded when the lime layer was removed.     

Relationships among fine roots, fungal hyphae and soil microarthropods among different soil microhabitats in a temperate coniferous forest of Chamaecyparis obtusa

The relationships between roots and soil communities are not well understood. We used the ingrowth-core method with L-, FH-, and M-layer substrates to investigate the relationships among soil organic carbon, fine root biomass, hyphal length and the numbers of soil microarthropods. The study was carried out in a temperate forest of the arbuscular mycorrhizal conifer, Chamaecyparis obtusa. The relationships among fine roots, fungi and soil microarthropods were different among soil substrates and faunal taxa. Soil carbon contents, fine root biomass, hyphal length and soil-microarthropod numbers were the highest in the FH-substrate, and the lowest in the M-substrate. For each substrate, the total numbers of soil microarthropods did not positively correlated with soil organic carbon. A positive correlation between fine root biomass and the soil microarthropod numbers was significant only in the M-substrate, but not in the L- and FH-substrates. In M-substrates, strong positive correlations were found between fine root biomass or hyphal length and Mesostigmata or Oribatida numbers, but Collembola numbers were not corelated. Further studies of the regulation mechanism of soil food web structures should note that the soil microarthropods have different responses to C sources according to soil conditions and trophic interactions.     

Organic matter dynamics in a temperate forest soil following enhanced drying

Climate models predict an increase in global surface temperature and a change in precipitation intensity during this century. For Europe, extended drought periods followed by heavy rainfall are expected. The consequences for soil organic matter (SOM) dynamics are poorly understood. In this study, we investigated the effect of changing soil moisture regime on SOM quality under field conditions. For this purpose, a throughfall exclusion (TE) experiment was conducted in the summers 2006 and 2007 on a Haplic Podzol under a 140 years old Norway spruce stand using a roof installation followed by re-wetting compared to non-manipulated control plots. Total organic carbon, lignin (stable carbon pool), plant and microbial sugars (labile carbon pool) and microbial biomass (phospholipid fatty acids) were determined before, during and after the experiment in the L, O, A and B horizons. No significant treatment effects could be observed for SOM quantity. Amounts of lignin and soil microbial biomass were also not affected by the moisture regime but structure of soil microbial community. In the L and organic layers, gram + bacteria and actinomycetes were reduced during water stress, while gram- bacteria, fungi and protozoa increased during drought. Warmer and drier weather led to a dominance of fungi while a cooler and moister regime favoured bacteria, at least in the L horizon. An increasing PLFA (cy17:0 + cy19:0)/(16:1ω7c + 18:1ω7c) ratio in the O layer and A horizon suggests that the microbes suffered from water stress in these horizons. This agrees with a decreasing contribution of microbial sugars to SOM with decreasing water content in the O and A horizons. Although the original plant material exhibited increasing plant sugar content with increasing dryness, the contribution of the plant sugars to total soil organic carbon (SOC) generally decreased with decreasing water content. Physical-chemical changes of soil structure can theoretically change the sugar extractability from soils and/or chemical changes of sugars structure can probably affect the analysis. Therefore, chemical alteration and stabilization could be responsible for sugar decrease in soil with increasing dryness explaining the contrast compared to the original plant material.     

Fire severity shapes plant colonization effects on bacterial community structure,microbial biomass,and soil enzyme activity in secondary succession of a burned forest

The increasing frequency and severity of wildfires has led to growing attention to the effects of fire disturbance on soil microbial communities and biogeochemical cycling. While many studies have examined fire impacts on plant communities, and a growing body of research is detailing the effects of fire on soil microbial communities, little attention has been paid to the interaction between plant recolonization and shifts in soil properties and microbial community structure and function. In this study, we examined the effect of a common post-fire colonizer plant species, Corydalis aurea, on soil chemistry, microbial biomass, soil enzyme activity and bacterial community structure one year after a major forest wildfire in Colorado, USA, in severely burned and lightly burned soils. Consistent with past research, we find significant differences in soil edaphic and biotic properties between severe and light burn soils. Further, our work suggests an important interaction between fire severity and plant effects by demonstrating that the recolonization of soils by C. aurea plants only has a significant effect on soil bacterial communities and biogeochemistry in severely burned soils, resulting in increases in percent nitrogen, extractable organic carbon, microbial biomass, β-glucosidase enzyme activity and shifts in bacterial community diversity. This work propounds the important role of plant colonization in succession by demonstrating a clear connection between plant colonization and bacterial community structure as well as the cycling of carbon in a post-fire landscape. This study conveys how the strength of plant–microbe interactions in secondary succession may shift based on an abiotic context, where plant effects are accentuated in harsher abiotic conditions of severe burn soils, with implications for bacterial community structure and enzyme activity.     

Decreases in soil moisture and organic matter quality suppress microbial decomposition following a boreal forest fire

Climate warming is projected to increase the frequency and severity of wildfires in boreal forests, and increased wildfire activity may alter the large soil carbon (C) stocks in boreal forests. Changes in boreal soil C stocks that result from increased wildfire activity will be regulated in part by the response of microbial decomposition to fire, but post-fire changes in microbial decomposition are poorly understood. Here, we investigate the response of microbial decomposition to a boreal forest fire in interior Alaska and test the mechanisms that control post-fire changes in microbial decomposition. We used a reciprocal transplant between a recently burned boreal forest stand and a late successional boreal forest stand to test how post-fire changes in abiotic conditions, soil organic matter (SOM) composition, and soil microbial communities influence microbial decomposition. We found that SOM decomposing at the burned site lost 30.9% less mass over two years than SOM decomposing at the unburned site, indicating that post-fire changes in abiotic conditions suppress microbial decomposition. Our results suggest that moisture availability is one abiotic factor that constrains microbial decomposition in recently burned forests. In addition, we observed that burned SOM decomposed more slowly than unburned SOM, but the exact nature of SOM changes in the recently burned stand are unclear. Finally, we found no evidence that post-fire changes in soil microbial community composition significantly affect decomposition. Taken together, our study has demonstrated that boreal forest fires can suppress microbial decomposition due to post-fire changes in abiotic factors and the composition of SOM. Models that predict the consequences of increased wildfires for C storage in boreal forests may increase their predictive power by incorporating the observed negative response of microbial decomposition to boreal wildfires.     

Pollution-induced tolerance of soil bacterial communities in meadow and forest ecosystems polluted with heavy metals

Pollution-induced community tolerance (PICT) allows finding a cause–effect relationship between pollution and adverse changes in a community. In our previous study we found that functional diversity of bacterial communities decreased significantly with increasing metal concentration, in both forest humus and meadow topsoil. Thus, the aim of the present study was to test whether tolerance of soil bacterial communities had increased as an effect of long-term metal pollution. Bacterial tolerance was tested with the use of the Biolog^® ECO plates in soils originating from the most polluted and the least polluted sites from three forest and five meadow transects located near smelters in Avonmouth (England), Clydach (Wales), and Głogów and Olkusz (Poland). We found that tolerance of bacterial communities was significantly increased in polluted meadow soils when compared to control meadow soils. On the contrary, no increase in tolerance was detected in polluted forest humus.     

Biochar soil amendment increased bacterial but decreased fungal gene abundance with shifts in community structure in a slightly acid rice paddy from Southwest China

Biochar’s role on greenhouse gas emission and plant growth has been well addressed. However, there have been few studies on changes in soil microbial community and activities with biochar soil amendment (BSA) in croplands. In a field experiment, biochar was amended at rates of 0, 20 and 40 t ha⁻¹ (C0, C1 and C2, respectively) in May 2010 before rice transplantation in a rice paddy from Sichuan, China. Topsoil (0–15 cm) was collected from the rice paddy while rice harvest in late October 2011. Soil physico-chemical properties and microbial biomass carbon (MBC) and nitrogen (MBN) as well as selected soil enzyme activities were determined. Based on 16S rRNA and 18S rRNA gene, bacterial and fungal community structure and abundance were characterized using terminal-restriction fragment length polymorphism (T-RFLP) combined with clone library analysis, denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR assay (qPCR). Contents of SOC and total N and soil pH were increased but bulk density decreased significantly. While no changes in MBC and MBN, gene copy numbers of bacterial 16S rRNA was shown significantly increased by 28% and 64% and that of fungal 18S rRNA significantly decreased by 35% and 46% under BSA at 20 and 40 t ha⁻¹ respectively over control. Moreover, there was a significant decrease by 70% in abundance of Methylophilaceae and of Hydrogenophilaceae with an increase by 45% in Anaerolineae abundance under BSA at 40 t ha⁻¹ over control. Whereas, using sequencing DGGE bands of fungal 18S rRNA gene, some bands affiliated with Ascomycota and Glomeromycota were shown inhibited by BSA at rate of 40 t ha⁻¹. Significant increases in activities of dehydrogenase, alkaline phosphatases while decreased β-glucosidase were also observed under BSA. The results here indicated a shift toward a bacterial dominated microbial community in the rice paddy with BSA.     

Inputs of nitrogen and organic matter govern the composition of fungal communities in soil disturbed by overwintering cattle

Overwintering cattle outdoors causes soil surface disturbance, substantial increases of soil N_tot, C_org, and P and a shift in pH to alkaline levels. Since fungi predominate in unfertilized soils with acidic pH and have filamentous hyphae, we hypothesized that changes caused by overwintering cattle outdoors (trampling, excreta returns, and changes in soil chemistry) will lead to suppressed species richness, lower biomass, and alter the structure of fungal communities. The research was conducted on an upland pasture used more than 10 years for cattle overwintering. Both culture-dependent and -independent methods were used for the determination of either fungal species composition (cultivation; DGGE) or biomass (numbers of CFU; concentration of fungal PLFA marker 18:2ω6,9). Soils under three different levels of cattle disturbance (S - severe, M - moderate, C - no disturbance/control) were investigated during three subsequent years. In addition, the DGGE analysis of soils was completed by comparison with analysis of fresh cattle excrements (Ex). The composition of fungal communities showed significantly higher richness and a substantial shift in species composition in cattle-disturbed soils (S, M) in comparison to the non-disturbed soil (C). The number of separated DGGE bands was significantly higher in S (30.67 ± 1.63; mean ± SD) and M (25.50 ± 1.64) soils than in the C soil (19.33 ± 1.75). Sequencing of typical bands revealed common fungal genera - Alternaria, Penicillium, Fusarium, Rhizopus, Isaria, and Metarhizium. Profiles of the S soil were enriched by bands of rumen-born anaerobic fungi (Neocallimastix, Cyllamyces) occurring mainly in profiles of excrements, where relatively low band richness (14.33 ± 1.15) was observed. The increasing level of cattle disturbance induced an increase in the biomass of complex fungal community over the three-year experimental period from 3.39 ± 2.11 (mean ± SD) nmol of fungal PLFA per gram of the C soil to 5.87 ± 3.16 in the M soil and 9.21 ± 4.69 in the S soil. Concentrations of soil N_tot and C_org were evaluated as the parameters significantly correlating with biomass as well as composition of the fungal community.     

Long term repeated burning in a wet sclerophyll forest reduces fungal and bacterial biomass and responses to carbon substrates

Soils from a long term experiment, established in 1972, incorporating replicated treatments of burning every 2 and 4 years with control plots were sampled in 2005 to determine the changes in microbial community structure, measured using phospholipid fatty acids (PLFAs) and functional diversity measured using multiple substrate induced respiration (SIR) tests (MicroResp™). Microbial biomass (total PLFA) in the 2 year burn treatments was 50% less than both the control and 4-year burn treatments. There was also concomitantly less respiratory activity which mirrored the known changes in soil C and substrate quality. Contrary to other studies soil bacterial PLFAs were reduced as much as fungal PLFAs in the 2-year burn and the short term (6 h) SIR of arginine, lysine, galactose and trehalose were significantly inhibited in the 2-year burn soils. The data suggest that a 4-year burn is a more sustainable practice for maintaining the original structure and function of the forest belowground ecosystem.     

Spatial distribution of fungal communities in a coastal grassland soil

In grasslands, saprotrophic fungi, including basidiomycetes, are major decomposers of dead organic matter, although spatial distributions of their mycelial assemblages are little described. The aim of this study was to characterise the scale and distribution of saprotrophic fungal communities in a coastal grassland soil using terminal restriction fragment length polymorphism (T-RFLP).Soil fungi were sampled at Point Reyes, California, USA, by taking forty-five 26 mm diam. cores in a spatially defined manner. Within each sampled core, complete core sections at 1-2 cm and 14-15 cm depths were removed and sub-sampled for DNA extraction and amplification using the primer pairs ITS1F-FAM/ITS4 (general fungi) or ITS1F-FAM/ITS4B (basidiomycete-specific).Nonmetric Multidimensional Scaling showed that general fungal communities could be clearly separated by depth, although basidiomycete communities could not. There were no strong patterns of community similarity or dissimilarity for general or basidiomycete fungal communities at horizontal geographical distances from 25 cm to 96 m in the upper horizon. These results show considerable vertical, but little horizontal, variability in fungal community structure in a semi-natural grassland at the spatial scales measured here.     

Tree species effects on soil enzyme activities through effects on soil physicochemical and microbial properties in a tropical montane forest on Mt. Kinabalu, Borneo

Tree species influence on the soil mineralization process can regulate overall nutrient cycling in a forest ecosystem, which may occur through their effects on substrate quality, soil physicochemical properties and soil microbial community. We investigated tree species effects on soil enzyme activities in a tropical montane forest on Mt. Kinabalu, Borneo. Specifically, we analyzed C- and P-degrading enzyme activities, as well as the relationships among the enzyme activities, soil physicochemical properties, substrate quality (C, N, and P concentrations), and microbial composition in the top 5 cm soils beneath conifers (Dacrycarpus imbricatus and Dacrydium gracilis) and broadleaves (Lithocarpus clementianus, Palaquium rioence, and Tristaniopsis clementis). Activities of acid phosphatase and β-d-glucosidase were significantly different among the tree species. Soil moisture, total C and N content and microbial lipid abundance (a proxy for microbial composition) could influence the enzyme activities although the relative contributions of microbial composition to the enzyme activities might be smaller. A higher acid phosphatase activity beneath Dacrydium than those beneath the other tree species can compensate for a lower concentration of P in available fractions beneath Dacrydium. This localized mineralization activity could subsequently influence soil nutrient availability in this forest.