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Supplementary Material and Methods on The ISME Journal website
Microbial succession in a chronosequence of chalk grasslands
Eiko E. Kuramae1, 2, Hannes A. Gamper1, Etienne Yergeau1, 3, Yvette M. Piceno4, Eoin L. Brodie4, Todd Z. DeSantis4, Gary L. Andersen4, JohannesA. van Veen1,5 and GeorgeA. Kowalchuk1,2
1Departmentof Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Heteren, The Netherlands; 2Institute of Ecological Science, Free University Amsterdam, Amsterdam, The Netherlands; 3Biotechnology Research Institute, National Research Council of Canada, Montréal, Canada; 4Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, USA; 5Institute of Biology, Leiden University, Leiden, The Netherlands
Site description and soil sampling and chemical analyses
Two secondary grassland succession series were defined in nature reserves in the province of Limburg, The Netherlands. The first series were selected at Wrakelberg (stages: W0-W4), on a slope (15-20º inclination) exposed to the SW, and the second series at Gerendal (stages: G0-G4) in fields with variable inclinations and exposures. Conventional arable fields with winter wheat (Triticum aestivum) represented the arable fields as reference of succession (W0/G0). Three grasslands, whose soils were last plowed about 17, 22, and 36 years ago, formed intermediate succession stages (W1/G1, W2/G2, W3/G3, respectively). The soils of the oldest succession stages were most probably never plowed and never fertilized, which is verified for at least the last 66 years.
Soil samples were taken at each of the 10 sites at the end of winter 2007 along linear transects of 20 m (Wrakelberg) or 10 m (Gerendal). At each site, five (A, B, C, D, E (Wrakelberg) or three A, C, E (Gerendal) within-field replicate composite soil samples were made by combining two cores (10-cm depth, 2cm diameter) taken less than 10 cm apart. This yielded a total of 40 composite soil samples (25 Wrakelberg and 15 Gerendal).The soils were sieved to < 3mm, thereby excluding larger root fragments and pieces of chalk.
Chemical soil analyses were performed according to Novozsamsky et al.(1984). Briefly, soil pH was determined in 1:2.5 (w/w) suspensions of lyophilized soil:H2O and 0.01M CaCl2. Available P was measured colorimetrically in 0.01M CaCl2 suspensions by the Molybdenum blue method and mineral N as the NH4+ and NO3- concentrations in KCl extracts, using a Traacs 800 autoanalyzer .
Plant species
A total of 52plant species were counted per 1m2 in five biological replicates per succession stage for plant species richness and diversity (Simpson index and Shanon Weaver index) at Wrakelberg site. The plant species were Arhenatherum elatius, Avenula sp., Avenula sp. (hard), Brachypodium pinatum, Briza media, Campanula sp., Carex flacca, Carex cariophyllaceae, Cirsium sp., Centaurea scabiosa, Convolvulus arvensis, Crataegus sp., Dactylis glomerata, Daucus carota, Euphrasia stricta, Festuca ovina, Galium mollugo, Genista tinctoria, Gymnadenia conopsea, Hieracium pilosella, Hypericum perforatum, Inula conyza, Knautia arvense, Leontodon hispidus, Leucanthemum vulgare, Linum catharticum, Lolium perenne, Lotus corniculatus, Medicago lupulina, Ononis repens, Oreganum vulgare, Pimpinella saxifraga, Plantago lanceolata, Poa sp., Poligola comosa, Potentilla sp., Prunella vulagris, Prunus avium, Ranunculus sp., Reseda lutea, Rhinanthus minor, Rosa sp., Rubus sp., Sanguisorba minor, Scabiosa columbaria, Senecio sp., Thymus pulegioides, Trifolium pratense, Trifolium sp.,Triticun aestivum, Vicia sp., Viola sp.
Nucleic acids extraction and 16S rRNA gene amplification
Five biological replicates per succession stage of Wrakelberg and three biological replicates per succession stages of Gerendal, totalling 40 samples were used for DNA isolation. Each sample was DNA extracted from 0.25g of soil, using the Power Soil kit (MoBio, Carlsbad, CA, USA) with bead-beating at 5.5 m s-1 for 10 min. Total DNA concentration was quantified on a ND-1000 spectrophotometer (Nanodrop Technology, Wilmington, DE, USA). 16S rRNA gene amplification was performed by using the bacterial-specific primers, 27F (5’-AGAGTTTGATCCTGGCTCAG-3’) and 1492R (5’-GGTTACCTTGTTACGACTT-3’) (Wilson et al., 1990), and the archaeal-specific primers, 4fa (5’- TCCGGTTGATCCTGCCRG-3’) and 1492R (5’-AGAGTTTGATCCTGGCTCAG-3’). PCR amplifications were carried out with 1× Ex Taq buffer (Takara Bio Inc, Japan), 0.8 mM dNTP, 0.02 units l-1Ex Taq polymerase, 0.4 mg ml-1 BSA, and 1.0 M of each primer. Three independently PCR amplifications were performed with the annealing temperatures 48C, 51.9C and 58C for both, bacteria and Archaea, with an initial denaturation 95C (3 min), 25 cycles amplification cycles with denaturation 95C (30 s), annealing (30 s), and extension 72C (60 s), followed by a final extension at 72C (7 min). PCR products of bacteria and PCR products of archaea were separately pooled, and a 2 l sub sample was quantified on 2% agarose by using E-gel Low Range Quantitative DNA ladder (Invitrogen, USA). The volume of pooled PCR reactions was reduced to less than 40 l with micrometer YM100 spin filters (Millipore, Billerica, MA). Regression analysis confirmed that quantity of PCR amplicon applied to the array was not correlated with any organism abundances as estimated by fluorescence intensity of hybridization (data not shown).
Phylochip processing, scanning, and normalization
The pooled PCR products described above were spiked with known concentrations of amplicons derived from yeast (YEL002C_WPB1, YEL024W_RIP1, YER022W_SRB4, YER148W_SPT15, YFL039C_ACT1) and prokaryotic metabolic genes (i.e. Bacillusthuringiensis,Mesorhizobiumloti, Pseudomonasaeruginosa, etc). This amplicon mix was fragmented to 50-200 bp using DNase I (0.02 U/ug DNA; Invitrogen) and One-Phor-All buffer following Affymetrix’s protocol. The mixture was then incubating at 25C for 20 min, 98C for 10 min. before labelling. Biotin labelling was carried out by using GeneChip DNA labelling reagent following manufacturer’s instructions (Affymetrix). Next the labelled DNA was denatured at 99C for 5 min and hybridized to custom-made Affymetrix GeneChips (16S PhyloChips) (DeSantis et al., 2007), at 48C and 60 rpm for 16 h in a hybridization chamber. PhyloChip washing and staining were performed according to standard Affymetrix protocols (Masuda and Church, 2002). Each PhyloChip was scanned and recorded as a pixel image, and initial data acquisition and intensity determination were performed using standard Affymetrix software (GeneChip microarray analysis suite, version 5.1). To account for scanning intensity variation from array to array, the intensities resulting from the internal standard probe sets were natural-log-transformed. Adjustment factors for each PhyloChip were calculated by fitting a linear model with the least-squares method. A PhyloChip's adjustment factor was subtracted from each probe set's natural log of intensity.
Background subtraction, noise calculation, and detection and quantification were essentially as previously reported (Brodie et al., 2006).The probe pair was considered positive when the difference in intensity between the perfect match and mismatch probes was at least 130 times the square noise value (N). A taxon was considered present in the sample when 90% or more of its assigned probe pairs for its corresponding probe set were positive (positive fraction (PosFrac) >=0.90). OTU richness of a sample was simply the number of OTU considered positive for a given sample. Relative OTU intensities were calculated by dividing the average signal of the probes aiming at a given OTU by the total average signal for all the OTUs that were identified as present. OTUs which PosFrac did not exceed 0.90 were set to zero scored as not detected. The relative abundance values were used directly for most analyses, and were also summed up to the Phylum level for other analyses.
Real-time PCR
Real-time PCR quantifications for Acidobacteria, Actinobacteria, Alphaproteobacteria, Bacteroidetes, Betaproteobacteria, Firmicutes and bacteria were performed using primers and cycling conditions previous described (Fierer et al., 2005), and fungi were quantified according to Lueders et al. (Lueders et al., 2004). Real-time PCR quantifications were carried out on soil DNA as previously described (Yergeau et al., 2007). Known template standards were made from PCR-amplified full-length 16S or 18S genes recovered from previously characterized clones.Most samples, and all standards, were assessed in at least two different runs to confirm the reproducibility of the quantification. Results of real-time PCR quantifications for the different phyla/classes were calculated as a percentage of total bacteria, by dividing the phyla/class 16S rRNA gene abundance by total bacterial 16S rRNA gene abundance.
Statistical Analyses
In order to evaluate if similarities between samples based on OTU composition, soil factors and plant community were significantly related, Mantel test on similarity/distance matrices was carried out, based on Mantel’s r (rm) with 999 permutations using P. Legendre’s statistical package Casgrain and Legendre (2001). The choice of similarity/distance indices for the different datasets followed the rationale detailed in Legendre and Legendre (1998): Bray-Curtis distance for OTU relative intensity and plant biomass, Jaccard similarity for OTU presence-absence and Gower similarity for soil chemical data.
Multivariate test of significance for the effects of field age or location on the microbial community structure was carried out using db-RDA (Legendre and Anderson, 1999). First, the relative intensity matrices coming from image analyses were transformed using principal coordinate analysis (PCoA), based on the appropriate distance/similarity as above. All resulting axes (representing 100% of the variation in the dataset) were then used as “species” data in redundancy analysis (RDA)in Canoco 4.5 (ter Braak and Šmilauer, 2002), with treatment variables being the only environmental variable included in the analysis. The significances of each treatment were tested with 999 permutations.
Microbial community structure was related to soil factors using canonical correspondence analyses (CCA) in Canoco. Relative OTU intensity was used as “species” data while soil and environmental data were included in the analysis as “environmental” variables. Since this analysis is sensitive to rare species, only OTUs that were present in more than 4 different samples were used in the analyses. Variables having the most significant influence on the bacterial community structure were chosen by forward selection with a 0.10 baseline. The variable selected this way were then included in a model of which significance was tested with 999 permutations. Phylum relative abundance data was added as “supplementary” variables, not involved in the calculations.
ANOVA was carried out in Statistica 7.1, following normalising transformations when required (mostly log, square or cubic root transformation). Factorial ANOVA was used to test the effects of restoration type (Wrakelberg vs Gerendal), succession stage (arable field to permanent chalk grassland) and their interaction. When transformation failed to normalise data, Kruskal-Wallis ANOVA was used instead of parametric ANOVA. Results were considered to be significant at P<0.05. For some data, Tukey-HSD post-hoc tests were also carried out following ANOVA to identify significantly different groups. All correlation analyses (Spearman rs) were carried out in Statistica 7.0 (StatSoft Inc., Tulsa, OK). Results were considered significant at a P<0.05 baseline and to be nearly significant at 0.05<P<0.10.
Supplementary References
Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL et al (2006). Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol72: 6288-6298.
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