Yao Pan’s research while affiliated with Netherlands Institute of Ecology and other places

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Publications (5)


Supplementary Material
  • Data
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February 2017

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5 Reads

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Yao Pan

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Jaap Bloem

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Figure 1. Multiple factor analysis of the bacterial and fungal communities (Hellinger-transformed data) together with the microbial biomass and microbial activity, according to the (a) organic amendment (Control, Manure, Lucerne, Corn and Straw) and (b) time (32, 69 and 132 days) with (c) Hierarchy of Multiple Factor Analysis considering the clusters (C1, C2, C3, C4, C5, C6) of corresponding variables and the amount of inertia gained in the clustering cut-off.  
Figure 2. Percentage of inertia for each of the first 10 dimensions from the Multiple factor analysis of the bacterial and fungal communities (Hellinger-transformed data) together with microbial biomass and activity, according to the group of variables (a) (T: treatments – N source x Time; B: bacterial community; F: classified fungal community; unF: unclassified fungal community; Ac: variables of microbial biomass and active community) and (b) the percentage of total inertia related to each dimension.  
Figure 3. Multiple factor analysis of the bacterial and fungal community (Hellinger-transformed data) together with the microbial biomass and activity and C and N mineralization rate, according to the (a) organic amendment (Control, Manure, Lucerne, Corn and Straw) and (b) time (Nov and Jan) and (c) Hierarchy Clustering from the Multiple factor analysis of the bacterial and fungal community Hellinger-transformed data sets together with the microbial biomass and activity and C and N mineralization rate and the amount of inertia gained in the clustering cut-off. C1: cluster 1, C2: cluster 2, C3: cluster 3.  
Figure 4. Percentage of inertia for each of the first 10 dimensions from the Multiple factor analysis of the bacterial and fungal community (Hellinger-transformed data) together with the microbial biomass and activity and C and N mineralization rate, according to the group of variables (a) (T: treatments – N source x Time; B: bacteria community; F: classified fungal community; unF: unclassified fungi community; Ac: variables of active community and microbial biomass; Min: carbon and nitrogen mineralization rate) and (b) the percentage of total inertia related to each dimension.  
Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

February 2017

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257 Reads

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54 Citations

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.



Figure 1. Between-Class Analysis (BCA) of the (A) plant, (B) bacterial, (C) fungal community compositions and (D) soil factor factors based on correspondence analysis (A–C) or principal components analysis (D) over the long-term control (C), liming (L), nitrogen (N), nitrogen-potassium-phosphorus (NPK) and phosphorus (P) treatments of the Ossekampen experiment are presented. Group significances were assessed by Monte-Carlo tests.  
Figure 2. Co-inertia analysis (COIA) between correspondence analysis of plant and fungal community composition across the long-term control (C), liming (L), nitrogen (N), nitrogen-potassium-phosphorus (NPK) and phosphorus (P) treatments of the Ossekampen experiment (cumulative projected inertia = 86%). Significance of co-structure was assessed by a Monte-Carlo test. Circle = Plant; Square = Fungi.  
Figure 3. Co-inertia analysis (COIA) between correspondence analysis of plant and bacterial community composition across the long-term control (C), liming (L), nitrogen (N), nitrogen-potassium-phosphorus (NPK) and phosphorus (P) treatments of the Ossekampen experiment (cumulative projected inertia = 88%). Significance of the co-structure was assessed by a Monte-Carlo test. Circle = Plant; Square = Bacteria.  
Figure 4. Co-inertia analysis (COIA) between correspondence analysis of bacterial and fungal community composition across the long-term control (C), liming (L), nitrogen (N), nitrogen-potassium-phosphorus (NPK) and phosphorus (P) treatments of the Ossekampen experiment (cumulative projected inertia = 92%). Significance of the co-structure was assessed by a Monte-Carlo test. Circle = Bacteria; Squere = Fungi.  
Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

March 2016

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1,296 Reads

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134 Citations

Inorganic fertilization and mowing alter soil factors with subsequent effects–direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions.


Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil

July 2014

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369 Reads

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239 Citations

FEMS Microbiology Ecology

Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem. This study demonstrated that bacterial community composition but not functions shifted in long-term N-, P-, K- and NPK-fertilized grassland. This study demonstrated that bacterial community composition but not functions shifted in long-term N-, P-, K- and NPK-fertilized grassland.

Citations (3)


... The soil samples we reanalyzed for heavy metal content using inductively coupled plasma mass spectrometry (ICP-MS). This method is widely used in trace element analysis and allows for the determination of a wide range of elements in a single sample [65,66] procedure was used to prepare the samples for analysis. Briefly, the samples were dried at 60°C for 48 hours, ground to a fine powder using a mortar and pestle, and passed through a 2 mm sieve. ...

Reference:

Environmental and Health Consequences of Heavy Metals in Crude Oil-Polluted Soils in Ihwrekreka Community
Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

... Our results suggest that crop rotation had distinct impact on the soil microbiota and fungi was more sensitive to crop rotation (Figure 9). This result is consistent with the finding by Cassman et al. (2016), who reported that fungal community are closely associated with plant in long-term fertilized grassland. Overall, crop rotation was the main factor in shaping soil microbiota, while straw return with less impact. ...

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

... NPK 17-17-17 is among the products of highest commercialisation in the fertiliser markets of Uganda [53]. NPK 17:17:17 fertiliser typically contain nitrate nitrogen [54], which plays a vital role in providing essential nutrients to plant growth. Residents engaged in agricultural activities around MB and NG use NPK 17:17:17 fertiliser which are mainly trans-ported by the rain runoff to the MB and NG. ...

Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil
  • Citing Article
  • July 2014

FEMS Microbiology Ecology