Structural and functional response of soil microbiota to addition of plant substrate are moderated by soil Cu levels

In soils, the microbially mediated decomposition of plant residue is a key process with wide ranging effects on ecosystem functioning and stability. Understanding the impact of contamination on this process is of high importance. We investigated the effects of long-term (6 years) copper exposure on the capacity of soil microbiota to decompose newly added resources; dried and ground Medicago truncatula stubble. In addition, the effects on the microbial community structure across the three domains were explored using polymerase chain reaction–denaturing gradient gel electrophoresis rRNA gene profiling. Ecological distances in community structure between treatments was calculated (Kulczynski) and effects tested using PERMANOVA. Clear dose–response relationships were present between microbial respiration (CO₂ evolution) and soil Cu level in soils receiving medic, but not under basal conditions (i.e., no medic added). These show that relatively labile forms of C are needed to drive microbial ecotoxicological responses and that microbial adaptation to the presence of Cu in the soils—after >6 years exposure—was functionally limited. Bacterial, archaeal and fungal communities showed significant (P < 0.05) levels of structural change in soils across the Cu gradient, demonstrating that species replacement had occurred following strong selective pressure. Addition of medic resources to the soils caused significant shifts in the bacterial and archaeal community structure (P < 0.001), which occurred across the entire range of soil Cu levels. For the fungal community, a significant interaction effect was present between Cu and medic addition (P = 0.002). At low Cu levels, medic addition caused large shifts in community structure, but this was negligible under high Cu levels. This was reflected in significant changes in the level of community structural dispersion at low compared with high Cu levels. As such, we show that Cu limits the capacity of soil fungal communities to rapidly respond to new resource capture. Given the primary role of soil fungi in plant material decomposition, this may have wide ranging impacts on wider ecosystem processes including nutrient cycling, trophic interactions, food web stability and energy transfer.     

A single application of Cu to field soil has long-term effects on bacterial community structure, diversity, and soil processes

Long-term diversity-disturbance responses of soil bacterial communities to copper were determined from field-soils (Spalding; South Australia) exposed to Cu in doses ranging from 0 through to 4012 mg Cu kg⁻¹ soil. Nearly 6 years after application of Cu, the structure of the total bacterial community showed change over the Cu gradient (PCR-DGGE profiling). 16S rRNA clone libraries, generated from unexposed and exposed (1003 mg Cu added kg⁻¹ soil) treatments, had significantly different taxa composition. In particular, Acidobacteria were abundant in unexposed soil but were nearly absent from the Cu-exposed sample (P<0.05), which was dominated by Firmicute bacteria (P<0.05). Analysis of community profiles of Acidobacteria, Bacillus, Pseudomonas and Sphingomonas showed significant changes in structural composition with increasing soil Cu. The diversity (Simpsons index) of the Acidobacteria community was more sensitive to increasing concentrations of CaCl-extractable soil Cu (Cu_Ext) than other groups, with decline in diversity occurring at 0.13 Cu_Ext mg kg⁻¹ soil. In contrast, diversity in the Bacillus community increased until 10.4 Cu_Ext mg kg⁻¹ soil, showing that this group was 2 orders of magnitude more resistant to Cu than Acidobacteria. Sphingomonas was the most resistant to Cu; however, this group along with Pseudomonas represented only a small percentage of total soil bacteria. Changes in bacterial community structure, but not diversity, were concomitant with a decrease in catabolic function (BioLog). Reduction in function followed a dose-response pattern with Cu_Ext levels (R²=0.86). The EC₅₀ for functional loss was 0.21 Cu_Ext mg kg⁻¹ soil, which coincided with loss of Acidobacteria diversity. The microbial responses were confirmed as being due to Cu and not shifts in soil pH (from use of CuSO₄) as parallel Zn-based field plots (ZnSO₄) were dissimilar. Changes in the diversity of most bacterial groups with soil Cu followed a unimodal response - i.e. diversity initially increased with Cu addition until a critical value was reached, whereupon it sharply decreased. These responses are indicative of the intermediate-disturbance-hypothesis, a macroecological theory that has not been widely tested in environmental microbial ecosystems.     

Impact of wheat straw decomposition on successional patterns of soil microbial community structure

The dynamics of indigenous bacterial and fungal soil communities were followed throughout the decomposition of wheat straw residue. More precisely, such dynamics were investigated in the different soil zones under the influence of decomposing wheat straw residue (i.e. residues, soil adjacent to residue = detritusphere, and bulk soil). The genetic structures of bacterial and fungal communities were compared throughout the decomposition process long by applying B- and F-ARISA (for bacterial and fungal-automated ribosomal intergenic spacer analysis) to DNA extracts from these different zones. Residue decomposition induced significant changes in bacterial and fungal community dynamics with a magnitude of changes between the different soil zones ordered as followed: residue > detritusphere > bulk soil, confirming the spatial structuration of the sphere of residue influence to the 4-6 mm soil zone in contact with residue. Furthermore, significant differences in the structure of bacterial and fungal communities were apparent between the early (14 and 28 days) and late (from 56 to 168 days) stages of decomposition. These could be related to ecological attributes such as the succession of r- (copiotrophs) and K- (oligotrophs) strategists. Microbial diversity at the early (28 days) and late (168 days) stages of degradation was further analysed by a molecular inventory of 16S and 18S rDNA in DNA extracts from the residue zone. This confirmed the succession of different populations during residue decomposition. Fluorescent Pseudomonas spp. and Neurospora sp. were dominant in the early stage with subsequent stimulation of Actinobacteria and Deltaproteobacteria taxa, as well as Basidiomycota fungal taxa and Madurella spp. According to the ecological attributes of these populations, microbial succession on fresh organic residue incorporated in soil would be dominated by copiotrophs and r-strategists in the early stages, with oligotrophs (K-strategists) increasing in relative abundance as substrate quantity and/or quality declines over time.     

The effect of electrokinetics on soil microbial communities

There is growing interest in the potential of applying an electric field to soil to move and stimulate the degradation of contaminants, but we know little of the impact of this approach on exposed microbial communities. The effect of electrokinetics (3.14 A m⁻²) on soil bacterial and fungal communities was studied using soil cartridge microcosms (13 cm×5.4 cm×5.9 cm). After 27 days of electrokinetics, a zone of low pH (<4) was detected close to the anode. Soil exposed to electrokinetics and immediately adjacent to the anode demonstrated an increase in carbon substrate utilisation potential (≤290%) and microbial respiration rates. The diversity and structure of the bacterial community showed little response to electrokinetics, with the exception of soil close to the anode. Here, an increase in the percentage of Gram-positive species isolated was identified, most notably of Bacillus megaterium. Overall, the only detectable response of the microbial community was observed in soil immediately adjacent to the anode. The results of this study provide evidence that the application of electrokinetics has no serious negative effect on ‘soil microbial health’, thus endorsing its validity as a viable soil remediation technology.     

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.     

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.     

Does soil ergosterol concentration provide a reliable estimate of soil fungal biomass?

Our aim was to determine if soil ergosterol concentration provides a quantitative estimate of the soil fungal biomass concentration, as is usually assumed. This was done by comparing soil ergosterol measurements with soil fungal biomass (fungal biomass C) concentrations estimated by microscopic measurements and by the selective inhibition technique linked to substrate-induced respiration (SIR). The measurements were compared in a silty-clay loam soil given a range of previous treatments designed to increase or decrease the soil fungal biomass and so also to change the soil ergosterol concentration. The treatments used were ryegrass amendment, to increase the total and fungal biomass, and CHCl₃-fumigation and the addition of the biocides, captan, bronopol and dinoseb, to decrease both ergosterol and fungal biomass C concentrations. The mineralization of ergosterol following addition to sand innoculated with soil extract, and to a sandy loam soil, was also determined. The added ergosterol was little, if at all, degraded following addition to either sand or the unfumigated or fumigated soil during a 10 d aerobic incubation. Similarly, pesticide addition did not significantly change soil ergosterol concentrations yet the soil fungal biomass C concentration decreased significantly. Thus, the ratio: (soil ergosterol concentration/soil fungal biomass C concentration) was much higher in the pesticide-treated soils than the control soil. Following ryegrass amendment, soil ergosterol concentration increased from about 6-12 μg⁻¹ soil within 5 d and then decreased gradually to about 7 μg g⁻¹ soil by 20 d incubation. Changes in fungal biomass C (measured by direct microscopy) closely mirrored changes in soil ergosterol over this period. However, when the amended soil was fumigated and then incubated for a further 5 d, the initial ergosterol concentration declined from 7 to 5 μg g⁻¹ soil by 20 d incubation (a decline of about 0.4). The comparable decline in fungal biomass C was about eight-fold. Thus the ratio of ergosterol to fungal biomass C increased from 0.005 to about 0.01. There was a significant correlation (r>0.84, P<0.001) between soil ergosterol concentration and fungal biomass measured by either SIR or microscopy. However, three data points played a vital role in the correlation. When these points were excluded the relationship was very poor (r<0.4). Our results therefore suggest that substantial amounts of ergosterol may exist, other than in living cells, for considerable periods, with little, if any mineralization. Thus, these results indicate that ergosterol and fungal biomass C concentrations are not always closely correlated, due to the slow metabolism of ergosterol in recently dead fugal biomass and/or the existence of exocellular ergosterol in soil.     

Microfungal communities in soil,litter and casts of Lumbricus terrestris L. (Lumbricidae): a laboratory experiment

The anecic earthworm Lumbricus terrestris L. was kept in laboratory microcosms containing beech forest soil without litter, with beech leaf litter or with lime leaf litter. The structure of microfungal communities in soil, litter and fresh and aged (100 days) earthworm faeces was analysed using the washing and plating technique. The passage of mineral soil through the gut of L. terrestris affected the structure of the fungal community only little. In contrast, in the litter treatments the structure of the fungal community in fresh earthworm casts significantly differed from that in soil and litter. The majority of soil and litter inhabiting fungi survived passage through the gut of L. terrestris and the fungal community in casts consisted of a mixture of soil and litter inhabiting fungi. However, the frequency of Cladosporium spp., Alternaria spp., Absidia spp., and other taxa was strongly reduced in fresh casts. The degree of colonization of litter particles (number of isolates per number of plated particles) also decreased, but some fungi (mainly Trichoderma spp.) benefited from gut passage and flourished in fresh casts. During ageing of cast material the dominance structure of the fungal community changed. Both the degree of colonization of organic particles and the species diversity increased and approached that in soil. However, the structure of the fungal community in casts remained cast specific even after 100 days of incubation. It is concluded that the feeding and burrowing activity of L. terrestris accelerates the colonization of litter by the edaphic mycoflora but also extends the range of occurrence of litter-associated fungi into mineral soil layers.     

Improving soil structure by promoting fungal abundance with organic soil amendments

Building soil structure in agroecosystems is important because it governs soil functions such as air and water movement, soil C stabilization, nutrient availability, and root system development. This study examined, under laboratory conditions, effects of organic amendments comprised of differing proportions of labile and semi-labile C on microbial community structure and macroaggregate formation in three variously textured soils where native structure was destroyed. Three amendment treatments were imposed (in order of increasing C lability): vegetable compost, dairy manure, hairy vetch (Vicia villosa Roth). Formation of water stable macroaggregates and changes in microbial community structure were evaluated over 82 days. Regardless of soil type, formation of large macroaggregates (LMA, >2000 μm diameter) was highest in soils amended with vetch, followed by manure, non-amended control, and compost. Vetch and manure had greater microbially available C and caused an increase in fungal biomarkers in all soils. Regression analysis indicated that LMA formation was most strongly related to the relative abundance of the fungal fatty acid methyl ester (FAME) 18:2ω6c (r = 0.55, p < 0.001), fungal ergosterol (r = 0.58, p < 0.001), and microbial biomass (r = 0.57, p < 0.001). Non-metric multidimensional scaling (NMS) ordination of FAME profiles revealed that vetch and manure drove shifts toward fungal-dominated soil microbial communities and greater LMA formation in these soils. This study demonstrated that, due to their greater amounts of microbially available C, vetch or manure inputs can be used to promote fungal proliferation in order to maintain or improve soil structure.     

Discriminating the effects of agricultural land management practices on soil fungal communities

The structure of fungal communities was examined in soil subjected to 5 years of different agricultural land management and tomato production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of fungal rDNA internal transcribed spacer-1 (ITS-1) regions was used to create genomic fingerprints of the soil fungal communities. Three years after initiation of land management practices, univariate analysis of genetic diversity failed to detect differences among soil fungal communities in plots managed organically, conventionally or maintained free of vegetation by continuous tillage (disk fallow). Genetic diversity was significantly higher in plots maintained as a perennial pasture grass (Paspalum notatum var Argentine bahiagrass) or as an undisturbed weed fallow. The composition of soil fungal communities within organic, pasture grass or disk fallow plots were separated into unique clusters by non-parametric multivariate analysis of their Bray-Curtis similarity matrices, computed from the relative abundance of ITS-1 amplicons, while the composition of communities within disk fallow and conventional plots could not be distinguished from each other. Diversity of soil fungal communities was significantly reduced following the cultivation of tomato in year four when compared to the diversity in plots where tomato was not cultivated. Divergence in the composition of soil fungal communities was observed following the cultivation of tomato under all land management regimes except organic, where communities continued to remained clustered based upon similarities among their ITS-1 amplicons. Divergence in the composition of fungal communities became more pronounced following two major hurricanes (Francis and Jeanne, September 2004) except for communities in the organic and pasture grass plots. Following the completion of a second tomato crop in year 5, genetic diversity and richness was similar under all land management regimes except the pasture grass, where it remained significantly higher. By contrast, following two consecutive years of tomato production, unique but mutually similar compositions of fungal communities were detected only in plots subjected to the organic land management regime. This was supported by observations that fungal communities were dominated by a 341 bp rDNA amplicon fragment in all land management regimes except the organic. Cloning and sequencing indicated that the 341 bp fragment generated by LH-PCR had a sequencing size of 343 bp, which was most closely related to Fusarium oxysporum. Thus, land management practices that disturb or disrupt soil fungal communities will significantly reduce their diversity. However, the composition of soil fungal communities is more strongly influenced by land management practices and communities within an organically management system were more resistant to anthropogenic and meteorological disturbances.     

Elevated enzyme activities in soils under the invasive nitrogen-fixing tree Falcataria moluccana

Like other N-fixing invasive species in Hawaii, Falcataria moluccana dramatically alters forest structure, litterfall quality and quantity, and nutrient dynamics. We hypothesized that these biogeochemical changes would also affect the soil microbial community and the extracellular enzymes responsible for carbon and nutrient mineralization. Across three sites differing in substrate texture and age (50-300 years old), we measured soil enzyme activities and microbial community parameters in native-dominated and Falcataria-invaded plots. Falcataria invasion increased acid phosphatase (AP) activities to >90 μmol g⁻¹ soil h⁻¹ compared to 30-60 μmol g⁻¹ soil h⁻¹ in native-dominated stands. Extracellular enzymes that mineralize carbon and nitrogen also increased significantly under Falcataria on the younger substrates. By contrast, total microbial biomass and mycorrhizal abundance changed little with invasion or substrate. However, fungal:bacterial ratios declined dramatically with invasion, from 2.69 and 1.35 to <0.89 on the 50- and 200-year-old substrates, respectively. These results suggest that Falcataria invasion alters the composition and function of belowground soil communities in addition to forest structure and biogeochemistry. The increased activities of AP and other enzymes that we observed are consistent with a shift toward phosphorus limitation and rapid microbial processing of litterfall C and N following Falcataria invasion.     

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.     

The effect of mixing ground leaf litters to soil on the development of pitch pine ectomycorrhizal and soil arthropod communities in natural soil microcosm systems

The addition of leaf litter to soil influences both the nutrients and polyphenols of soil. It is likely that contrasting nutrient and polyphenolic composition of different plant litters may affect plant growth, mycorrhizal and soil arthropod communities. We report results from a microcosm experiment of effects of incorporation of three single leaf litter species and a mixture of all three on pitch pine seedling growth, their ectomycorrhizal community and soil arthropod community. The three litter species (pine, oak and huckleberry) represent co-dominant species within the New Jersey pine barrens ecosystem. We show that the leaf litters have different composition of nutrients and polyphenols, with rooting matrix containing pine litter having lower inorganic nitrogen content (1.6 μg g⁻¹) than oak (19.9 μg g⁻¹) and huckleberry (4.4 μg g⁻¹), but oak litter having the highest extractable phosphorus (13.3 cf. 0-0.08 μg g⁻¹) and total phenol content and lowest condensed tannin content. These differences were imparted to rooting matrix of homogenized humic (Oa) layer of pine barrens soil to which milled leaf litter was added and used in the microcosms. Pitch pine seedlings grew significantly better in un-amended rooting matrix (0.33±0.02 g) than any of the litter treatments (0.15±0.02-0.17±0.01 g) and tissue P concentrations tracked phosphate concentrations in the rooting matrix. Total P accumulation into plant tissue was higher in oak than control, attributable to a significantly higher (P<0.05) accumulation in roots (3.3±0.19 mg g⁻¹) compared to other species (1.1±0.04-2.3±0.08 mg g⁻¹). No relationship was seen between tissue N concentration and soil N, but seedlings growing in huckleberry litter amended soil accumulated less N than control. The effect of leaf litters on the ectomycorrhizal community composition were determined by PCA (first two axes accounted for 81% of the variance) and stepwise multiple regression analysis. These analyses showed that huckleberry leaf litter had a significant impact on mycorrhizal community composition with morphotypes Cg and DB being more abundant in the presence of huckleberry litter (178±13 cf. 68±15-106±15 for Cg and 141±11 cf. 88±23-111±18 for DB) and its influence of elevating nitrate nitrogen, organic nitrogen, total phenols and protein precipitation content of the rooting matrix. Mycorrhizal morphotypes BS and SB were significantly more abundant in the community where these soil factors were low in the absence of leaf litter addition. Total ectomycorrhizal abundance was negatively related to hydrolysable tannin concentration in the rooting matrix (r²=0.132, P<0.05). There was no influence of leaf litter type on mite density (dominated by non-burrowing phthiracarids), but collembolan density (dominated by Folsomia spp) showed a greater than threefold reduction in population density in the presence of leaf litter (F=6.47, P<0.05). Collembolan density was positively correlated with mycorrhizal morphotypes GS and SB (P<0.05) and negatively related to morphotypes DB (P<0.05) and soil extractable NH₄-N (P<0.05), suggesting a possible selection of fungal species in their diet and a relationship between collembola and nitrification.     

Physiological, biochemical and molecular responses of the soil microbial community after afforestation of pastures with Pinus radiata

Afforestation and deforestation are key land-use changes across the world, and are considered to be dominant factors controlling ecosystem functioning and biodiversity. However, the responses of soil microbial communities to these land-use changes are not well understood. Because changes in soil microbial abundance and community structure have consequences for nutrient cycling, C-sequestration and long-term sustainability, we investigated impacts of land-use change, age of stand and soil physico-chemical properties on fungal and bacterial communities and their metabolic activities. This study was carried out at four sites in two geographical locations that were afforested on long-established pastures with Pinus radiata D. Don (pine). Two of the sites were on volcanic soils and two on non-volcanic soils and stand age ranged from 5 to 20 y. Microbial communities were analysed by biochemical (phospho-lipid fatty acids; PLFA) and molecular (multiplex-terminal restriction fragment length polymorphism; M-TRFLP) approaches. Both site and stand age influenced microbial properties, with changes being least detectable in the 5-y-old stand. Land use was a key factor influencing soil metabolic activities as measured by physiological profiling using MicroResp. Pasture soils had higher microbial biomass (P < 0.001), and metabolic activities (P < 0.001), and basal respiration rates were up to 2.8-times higher than in the pine soils. Microbial abundance analysis by PLFA showed that the fungal to bacterial ratio was higher in the pine soils (P < 0.01). Community analysis suggested that soil bacterial communities were more responsive to site (principal component 1; P < 0.001) than to land use (principal component 5; P < 0.001). In contrast, the fungal community was more affected by land-use change (principal component 1; P < 0.001) than by site, although site still had some influence on fungal community structure (principal component 2; P < 0.001). Redundancy analysis also suggested that bacterial and fungal communities responded differently to various soil abiotic properties, land-use change and location of sites. Overall, our results indicate that the change in land use from pasture to P. radiata stands had a direct impact on soil fungal communities but an indirect effect, through its effects on soil abiotic properties, on bacterial communities. Most of the changes in bacterial communities could be explained by altered soil physico-chemical properties associated with afforestation of pastures.     

Molecular characterization and glomalin production of arbuscular mycorrhizal fungi colonizing a heavy metal polluted ash disposal island, downtown Venice

In this work the arbuscular mycorrhizal (AM) fungal communities colonizing a polluted ash dump island, downtown Venice, were studied by using a multimodal approach. The island, Sacca San Biagio, was covered with a thick layer of municipal solid waste residues produced by an incinerator operating from 1973, to 1984. Such residues contained high levels of heavy metals (Cu, Pb and Zn). We characterized the AMF communities present in soils on Sacca San Biagio island by using molecular methods. Nine AM fungal sequence types were detected in the roots of three plant species, representative of the dominant flora, by using partial SSU ribosomal RNA genes. The most abundant sequence types corresponded to Glomus intraradices/Glomus fasciculatum, and to Glo18, a sequence detected so far only in planta. Two sequences were new to science. Glomalin-related soil protein (GRSP), extracted from rhizosphere soil of dominant plant species, ranged from 1.6 to 2.3 mg g⁻¹. The occurrence of an active AM fungal community able to live in such harsh environment was evinced by the correlation between mycorrhizal colonization and GRSP content.     

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.     

Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil

Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum J. H. Owen, results in considerable yield losses for cucumber plants. A bio-organic fertilizer (BIO), which was a combination of manure composts with antagonistic microorganisms, and an organic fertilizer (OF) were evaluated for their efficiencies in controlling Fusarium wilt. Application of the BIO suppressed the disease incidence by 83% and reduced yield losses threefold compared with the application of OF. Analysis of microbial communities in rhizosphere soils by high-throughput pyrosequencing showed that more complex community structures were present in BIO than in OF treated soils. The dominant taxonomic phyla found in both samples were Proteobacteria, Firmicutes, Actinobacteria and Acidobacteria among bacteria and Ascomycota among fungi. Abundance of beneficial bacteria or fungi, such as Trichoderma, Hypoxylon, Tritirachium, Paenibacillus, Bacillus, Haliangium and Streptomyces, increased compared to the OF treatment, whereas the soil-borne pathogen, Fusarium, was markedly decreased. Overall, the results of this study demonstrate that the application of the BIO was a useful and effective approach to suppress Fusarium wilt and that the high-throughput 454 pyrosequencing was a suitable method for the characterization of microbial communities of rhizosphere soil of cucumber.     

Is the soil microbial community related to the basal area of trees in a Scots pine stand?

The main energy sources of soil microorganisms are litter fall, root litter and exudation. The amount on these carbon inputs vary according to basal area of the forest stand. We hypothesized that soil microbes utilizing these soil carbon sources relate to the basal area of trees. We measured the amount of soil microbial biomass, soil respiration and microbial community structure as determined by phospholipid fatty acid (PLFA) profiles in the humus layer (FH) of an even-aged stand of Scots pine (Pinus sylvestris L.) with four different basal area levels ranging from 19.9 m² ha⁻¹ in the study plot Kasper 1 to 35.7 m² ha⁻¹ in Kasper 4. Increasing trend in basal respiration, total PLFAs and fungal-to-bacterial ratio was observed from Kasper 1 to Kasper 3 (basal area 29.2 m² ha⁻¹). The soil microbial community structure in Kasper 3 differed from that of the other study plots.     

Use of an artificial root to examine the influence of 8-hydroxyquinoline on soil microbial activity and bacterial community structure

Invasive plant species have been shown to alter the microbial community composition of the soils they invade and it is suggested that this below-ground perturbation of potential pathogens, decomposers or symbionts may feedback positively to allow invasive success. Whether these perturbations are mediated through specific components of root exudation are not understood. We focussed on 8-hydroxyquinoline, a putative allelochemical of Centaurea diffusa (diffuse knapweed) and used an artificial root system to differentiate the effects of 8-hydroxyquinoline against a background of total rhizodeposition as mimicked through supply of a synthetic exudate solution. In soil proximal (0-10 cm) to the artificial root, synthetic exudates had a highly significant (P < 0.001) influence on dehydrogenase, fluorescein diacetate hydrolysis and urease activity. In addition, 8-hydroxyquinoline was significant (p = 0.003) as a main effect on dehydrogenase activity and interacted with synthetic exudates to affect urease activity (p = 0.09). Hierarchical cluster analysis of 16S rDNA-based DGGE band patterns also identified a primary affect of synthetic exudates and a secondary affect of 8-hydroxyquinoline on bacterial community structure. Thus, we show that the artificial rhizosphere produced by the synthetic exudates was the predominant effect, but, that the influence of the 8-hydroxyquinoline signal on the activity and structure of soil microbial communities could also be detected.     

Short-term C4 plant Spartina alterniflora invasions change the soil carbon in C3 plant-dominated tidal wetlands on a growing estuarine Island

Spartina alterniflora is an invasive C₄ perennial grass, native to North America, and has spread rapidly along the east coast of China since its introduction in 1979. Since its intentional introduction to the Jiuduansha Island in the Yangtze River estuary, Spartina alterniflora community has become one of the dominant vegetation types. We investigated the soil carbon in the Spartina alterniflora community and compared it with that of the native C₃Scirpus mariqueter community by measuring total soil carbon (TC), soil organic carbon (SOC), total soil nitrogen (TN), and the stable carbon isotope composition (δ¹³C) of various fractions. TC and SOC were significantly higher in Spartina alterniflora in the top 60 cm of soil. However, there was no significant difference in soil inorganic carbon (IC) between the two communities. Stable carbon isotopic analysis suggests that the fraction of SOC pool contributed by Spartina alterniflora varied from 0.90% to 10.64% at a soil depth of 0-100 cm with a greater percentage between 20 and 40 cm deep soils. The δ¹³C decreased with increasing soil depth in both communities, but the difference in δ¹³C among layers of the top 60 cm soil was significant (p<0.05), while that for the deeper soil layers (>60 cm) was not detected statistically. The changes in δ¹³C with depth appeared to be associated with the small contribution of residues from Spartina alterniflora at greater soil depth that was directly related to the vertical root distribution of the species.