Project description:Increasing levels of atmospheric carbon dioxide (CO2) and rates of nitrogen (N)-deposition to forest ecosystems are predicted to alter the structure and function of soil fungal communities, but the spatially heterogeneous distribution of soil fungi has hampered investigations aimed at understanding such impacts. We hypothesized that soil physical and chemical properties and fungal community composition would be differentially impacted by elevated atmospheric CO2 (eCO2) and N-fertilization in spatially separated field samples, in the forest floor, 0-2, 2-5, and 5-10?cm depth intervals in a loblolly pine Free-Air Carbon Dioxide Enrichment (FACE) experiment. In all soils, quantitative PCR-based estimates of fungal biomass were highest in the forest floor. Fungal richness, based on pyrosequencing of the fungal ribosomal large subunit gene, increased in response to N-fertilization in 0-2?cm and forest floor intervals. Composition shifted in forest floor, 0-2 and 2-5?cm intervals in response to N-fertilization, but the shift was most distinct in the 0-2?cm interval, in which the largest number of statistically significant changes in soil chemical parameters (i.e., phosphorus, organic matter, calcium, pH) was also observed. In the 0-2?cm interval, increased recovery of sequences from the Thelephoraceae, Tricholomataceae, Hypocreaceae, Clavicipitaceae, and Herpotrichiellaceae families and decreased recovery of sequences from the Amanitaceae correlated with N-fertilization. In this same depth interval, Amanitaceae, Tricholomataceae, and Herpotriciellaceae sequences were recovered less frequently from soils exposed to eCO2 relative to ambient conditions. These results demonstrated that vertical stratification should be taken into consideration in future efforts to elucidate environmental impacts on fungal communities and their feedbacks on ecosystem processes.
Project description:Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil.
Project description:Fungi underpin almost all terrestrial ecosystem functions, yet our understanding of their community ecology lags far behind that of other organisms. Here, red paddy soils in subtropical China were collected across a soil depth profile, comprising 0-to-10-cm- (0-10cm-), 10-20cm-, and 20-40cm-deep layers. Using Illumina MiSeq amplicon sequencing of the internal transcribed spacer (ITS) region, distance-decay relationships (DDRs), and ecological models, fungal assemblages and their spatial patterns were investigated from each soil depth. We observed significant spatial variation in fungal communities and found that environmental heterogeneity decreased with soil depth, while spatial variation in fungal communities showed the opposite trend. DDRs occurred only in 0-10cm- and 10-20cm-deep soil layers, not in the 20-40cm layer. Our analyses revealed that the fungal community assembly in the 0-10cm layer was primarily governed by environmental filtering and a high dispersal rate, while in the deeper layer (20-40cm), it was primarily governed by dispersal limitation with minimal environmental filtering. Both environmental filtering and dispersal limitation controlled fungal community assembly in the 10-20cm layer, with dispersal limitation playing the major role. Results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Effectively, "everything is everywhere, but the environment selects," although only in shallower soils that are easily accessible to dispersive fungal propagules. This work highlights that perceived drivers of fungal community assembly are dependent on sampling depth, suggesting that caution is required when interpreting diversity patterns from samples that integrate across depths.IMPORTANCE In this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Therefore, the results of this study highlight that perceived drivers of fungal community assembly are dependent on sampling depth and suggest that caution is required when interpreting diversity patterns from samples that integrate across depths. This is the first study focusing on assemblages of fungal communities in different soil layers on a relatively large scale, and we thus believe that this study is of great importance to researchers and readers in microbial ecology, especially in microbial biogeography, because the results can provide sampling guidance in future studies of microbial biogeography.
Project description:Soil organic carbon (SOC) and soil total nitrogen (STN) are major soil indicators for soil quality and fertility. Accurate mapping SOC and STN in soils would help both managed and natural soils and ecosystem management. This study developed an improved similarity-based approach (ISA) to predicting and mapping topsoil (0-20 cm soil depth) SOC and STN in a coastal region of northeastern China. Six environmental variables including elevation, slope gradient, topographic wetness index, the mean annual temperature, the mean annual temperature, and normalized difference vegetation index were used as predictors. Soil survey data in 2012 was designed based on the clustering of the study area into six climatic vegetation landscape units. In each landscape unit, 20-25 sampling points were determined at different landform positions considering local climate, soil type, elevation and other environmental factors, and finally 126 sampling points were obtained. Soil sampling from the depth of 0-20 cm were used for model prediction and validation. The ISA model performance was compared with the geographically weighted regression (GWR), regression kriging (RK), boosted regression trees (BRT) considering mean absolute prediction error (MAE), root mean square error (RMSE), coefficient of determination (R 2), and maximum relative difference (RD) indices. We found that the ISA method performed best with the highest R2 and lowest MAE, RMSE compared to GWR, RK, and BRT methods. The ISA method could explain 76% and 83% of the total SOC and STN variability, respectively, 12-40% higher than other models in the study area. Elevation had the largest influence on SOC and STN distribution. We conclude that the developed ISA model is robust and effective in mapping SOC and STN, particularly in the areas with complex vegetation-landscape when limited samples are available. The method needs to be tested for other regions in our future research.
Project description:Vineyard soil microbial communities potentially mediate grapevine growth, grape production as well as wine <i>terroir</i>. Simultaneously assessing shifts of microbial community composition at the intra-vineyard scale allows us to decouple correlations among environmental variables, thus providing insights into vineyard management. Here we investigated bacterial and fungal community compositions and their relationships with edaphic properties in soils collected from a commercial vineyard at four different soil depths (0-5, 5-10, 10-20, and 20-40 cm). Soil organic carbon (SOC) content, invertase activity and phosphatase activity decreased along depth gradient in the 0-20 cm soil fraction (<i>P</i> < 0.001). The soil bacterial biomass and ?-diversity were significantly higher than those of fungi (<i>P</i> ? 0.001). Statistical analyses revealed that SOC content, pH, C/N ratio and total phosphorus (TP) were significant determinants of soil bacterial (<i>R</i> = 0.494, <i>P</i> = 0.001) and fungal (<i>R</i> = 0.443, <i>P</i> = 0.001) community structure. The abundance of dominated bacterial phyla (<i>Proteobacteria</i>, <i>Acidobacteria</i> and <i>Actinobacteria</i>) and fungal phyla (<i>Ascomycota</i>, <i>Zygomycota</i> and <i>Basidiomycota</i>) slightly varied among all soil samples. Genus <i>Lactococcus</i>, which comprised 2.72% of the soil bacterial community, showed increasing pattern with depth. Importantly, <i>Candidatus Nitrososphaera</i>, <i>Monographella</i> and <i>Fusarium</i> were also detected with high abundances in soil samples, indicating their ecological function in soil nitrogen cycle and the potential risk in grapevine disease. Overall, this work detected the intra-vineyard variation of bacterial and fungal communities and their relationships with soil characteristics, which was beneficial to vineyard soil management and grapevine disease prevention.
Project description:Soil acidification instead of alkalization has become a new environmental issue caused by urbanization. However, it remains unclear the characters and main contributors of this acidification. We investigated the effects of an urbanization gradient on soil acidity of Pinus massoniana forests in Pearl River Delta, South China. The soil pH of pine forests at 20-cm depth had significantly positive linear correlations with the distance from the urban core of Guangzhou. Soil pH reduced by 0.44 unit at the 0-10 cm layer in urbanized areas compared to that in non-urbanized areas. Nitrogen deposition, mean annual temperature and mean annual precipitation were key factors influencing soil acidification based on a principal component analysis. Nitrogen deposition showed significant linear relationships with soil pH at the 0-10 cm (for ammonium N(NH4+(-N)), P < 0.05; for nitrate N(NO3-(-N)), P < 0.01) and 10-20 cm (for NO3-(-N), P < 0.05) layers. However, there was no significant loss of exchangeable non-acidic cations along the urbanization gradient, instead their levels were higher in urban than in urban/suburban area at the 0-10 cm layer. Our results suggested N deposition particularly under the climate of high temperature and rainfall, greatly contributed to a significant soil acidification occurred in the urbanized environment.