Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil
Soil and litter samplingMineral soil (0–15 cm) was collected at the Elizabeth Woods site, a 120-year-old deciduous forest in West Virginia, US (39° 32′ 50.6″ N, − 80° 00′ 00.4″ W). Soils were collected from four 20 × 20 m plots dominated by either AM-associated trees (i.e. Liriodendron tulipifera and Acer saccharum), or ECM-associated trees (i.e. Quercus rubra, Quercus velutina and Carya ovata). These sites have been characterized previously as Culleoka-Westmoreland silt loam soils at the AM sites and Dormont and Guernsey silt loams at the ECM sites40. Soils were also characterized by C:N ratios 11.7 and 14.1 for the AM and ECM soils respectively, with a pH of 6.8 for both soils. Soils with the same mycorrhizal status were pooled and homogenized, air-dried at room temperature for ~ 24 h and sieved through 2.0 mm mesh before the initiation of the experiment. Uniformly 13C labeled litter ( > 97 atom % 13C) from Quercus robur (i.e., ECM substrate) and Liriodendron tulipifera (i.e. AM substrate) leaves (Isolife BV, Wageningen, NL) were incubated in soil mesocosms in a factorial design with five replicates for each treatment combination (2 soil types × 2 substrate types), along with five replicate controls (no 13C substrate addition) for each soil type. The 13C enriched substrates were dried and ground to a powder and added in a suspension of 0.5 ml sterile water to 20 g of soil at a concentration of 400 ug 13C g−1 soil. The control soils received 0.5 ml sterile water additions. These incubations were well mixed and kept at 60% water-holding capacity for the 21-day period at room-temperature18. Chemical characteristics of soils and plant substrates are provided in Table S1.DNA processing and qSIPFor quantitative stable isotope probing, DNA was extracted, quantified, ultracentrifuged, fractionated and sequenced as described in18,26. DNA was extracted using a MoBio PowerSoil HTP Kit following the manufacturer’s instructions. For stable isotope probing, 5 ug of DNA was loaded into a 5-ml ultracentrifuge tube with ~ 3.5 ml of a saturated cesium chloride (CsCl) solution and ~ 900 ml gradient buffer (200 mM Tris, 200 mM KCl, 2 mM EDTA). DNA was separated via ultracentrifugation at 127,000g for 72 h using a TLN-100 rotor in an Optima Max bench top ultracentrifuge (Beckman Coulter, Fullerton, CA, USA). Tubes were fractionated into ~ 25 fractions of 150 µl each, and the density of each fraction was measured with a Raichart AR200 digital refractometer. DNA was purified using an isopropanol precipitation method. The 16S rRNA gene was subsequently quantified and sequenced in samples containing DNA, within the density range 1.660–1.735 gml−1 (~ 10 fractions per sample). To quantify the 16S rRNA gene, quantitative PCR was performed in triplicate using a QuantStudio 5 applied biosystems (Thermo Fisher Scientific) and primers 515F (5′-GTGCCAGCMGCCGCGGTAA-3′) and 806R (5′-GGACTACVSGGGTATCTAAT-3′)41. The PCR program used was as follows: 95 °C for 2 min followed by 45 cycles of 95 °C for 30 s, 64.5 °C for 30 s and 72 °C for 1 min. Libraries were sequenced on an Illumina MiSeq instrument (Illumina, Inc., San Diego, CA, USA) using a 300-cycle v2 reagent kit. Fungal 18S rRNA gene copies in each fraction were also quantified using primers 1380F (5′-CCCTGCCHTTTGTACACAC-3′) and 1510R (5′-CCTTCYGCAGGTTCACCTAC-3′). The PCR program used was as follows: 98 °C for 3 min followed by 40 cycles of 98 °C for 45 s, 60 °C for 45 s and 72 °C for 30 s. DNA fractions were amplified for fungal ITS rRNA genes using primers ITS4F (5′-AGCCTCCGCTTATTGATATGCTTAART-3′) and 5.8SF (5′-AACTTTYRRCAAYGGATCWCT-3′)42 and 300-bp paired-end read chemistry on an IlluminaMiSeq (Illumina, Inc., San Diego, CA, USA). The PCR program used was as follows: 95 °C for 6 min followed by 35 cycles of 95 °C for 15 s, 55 °C for 30 s, and 72 °C for 1 min. DNA fractions were then sequenced using a 500 cycle v2 reagent kit.Files came pre-split and joined multiple paired ends that we combined to pick operational taxonomic units (OTU). Open reference OTUs were picked at 97% identity using SILVA 128 release database for Bacteria and RDP database for Fungi. Taxa were analyzed at the ‘OTU’ level from the QIIME L7 table. Calculation of 13C excess atom fraction (EAF) was performed for each taxon as described previously18,19. Briefly, using the CsCl density gradient data, a weighted average density (WAD) was computed for each taxon’s DNA extracted from control soils that did not receive an isotopically enriched substrate. This natural abundance WAD was then compared to the taxon’s WAD following incubation with the 13C enriched material. The change in WAD can be used to quantify the amount of isotope incorporated into the DNA17,18. Preliminary data analysis revealed an effect of ultracentrifuge tube on estimation of phylotype weighted average density, probably a consequence of slight differences in CsCl density gradients between tubes. This technical error was corrected as previously described18,19. In addition to the samples subjected to qSIP analysis we also extracted and analyzed fungal and bacterial OTU’s from control soils where the DNA was extracted prior to incubation.FTICR-MS and lipidomic analysesSoil from substrate-incubated and controls mesocosms were processed and analyzed with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), using a 12 T Bruker SolariX FTICR mass spectrometer at the Environmental Molecular Sciences Laboratory in Richland, WA, as described in Fudyma et al.43. Briefly, 100 mg of dried soil or litter substrate was extracted using an adjusted Folch extraction44. Extraction was performed on each sample by sequentially adding 2 ml MeOH, followed by a 5 s vortex; 4 ml CHCl3, followed by a 5 s vortex; sonication at 25 °C for 1 h (CPX3800 Ultrasonic Bath, Fisherbrand); addition of 1.25 ml of H2O, followed by a slight mix to achieve bi‐layer separation; and incubated at 4 °C overnight. The top, aqueous layer (metabolite—polar) was pipetted off into 1 ml glass vials and stored at − 80 °C until FTICR‐MS. The bottom, chloroform layer was dried down and stored in 50:50 methanol:chloroform until lipidomics analysis.A standard Bruker electrospray ionization (ESI) source was used to generate negatively charged molecular ions in the metabolite fraction. Samples were then introduced directly to the ESI source. The instrument settings were optimized by tuning on a Suwannee River fulvic acid (SRFA) standard, purchased from International Humic Substances Society (IHCC). Blanks (HPLC grade methanol) were analyzed at the beginning and end of the day to monitor potential carry over from one sample to another. The instrument was flushed between samples using a mixture of water and methanol. One hundred and forty‐four individual scans were averaged for each sample and internally calibrated using an organic matter homologous series separated by 14 Da (CH2 groups). The mass measurement accuracy was less than 1 ppm for singly charged ions across a broad m/z range (m/z 300– 800). Data analysis software (Bruker Daltonik version 4.2) was used to convert raw spectra to a list of m/z values, applying the FTMS peak picker module with a signal-to noise ratio (S/N) threshold set to 7 and absolute intensity threshold set to the default value of 100. Chemical formulae were then assigned using in-house software following the compound identification algorithm that was described in Tolić et al.45. Peaks below 200 and above 800 were dropped to select only for calibrated and assigned peaks. Chemical formulae were assigned based on the following criteria: S/N > 7 and mass measurement error 800 were not detected in our samples. The m/z values represent the molecular mass (in Dalton) of the detected ions since all detected ions were singly charged ions. While our results do not represent a quantitative characterization of OM, the values presented are relative differences and should be representative of the samples. Finally, we would like to acknowledge that we were not able to see any clear evidence of 13C label in our FTICR-MS analysis of the soil samples. The lack of 13C label in our FTICR-MS analysis of the soil samples even though they received labeled substrate could be either due to the fact that most of the labeled substrates produced by microbial activities were of low molecular weight, which cannot be detected by FTICR-MS and/or the leftover labeled substrate was of low abundance compared to the organic compounds previously present in the soil matrix. As such, we used the FTCIR-MS data to identify shifts in the overall composition of the chemical compounds in each soil.Lipids in the chloroform fraction were analyzed by LC‐MS/MS in both positive and negative ESI modes using a linear trap quadropole (LTQ) Orbitrap Velos mass spectrometer (Thermo Fisher Scientific), as described in detail previously46. Lipid species were identified using the LIQUID tool46 followed by manual data inspection. Confidently identified lipid species were quantified using MZmine47 and the peak intensities were normalized by linear regression and central tendency (i.e., identifying a central or typical value for a probability distribution) using InfernoRDN.Statistical analysisAll data analyses were performed using R 3.2.048. To examine the effects of soil type, substrate type and their interaction in the bacterial, fungal and chemical composition of DOM and the lipid pool; Bray–Curtis distance matrices were compared with permutational multivariate analysis of variance (PerMANOVA) and visualized with Principle Coordinate Analysis (PCoA) using vegan package49. PerMANOVA analysis were run on the relative abundance and on the 13C EAF of individual microbial taxa, separately for both bacterial and fungal communities.The analyses for FTICR-MS were performed separately for control and incubated soils using all assigned molecular formulae remaining after quality filtering31. In all cases, we applied a Z-score standardization before calculating Bray–Curtis distance matrices49. We analyzed the results from FTICR-MS as resulting from the decomposition of the added substrates for two reasons. First, this is a fully factorial design where individual soil samples were split to either receive AM poplar or ECM oak litter substrate. Thus, each soil sample starts with the same characteristics and the changes at the end of the incubation period should reflect the processing of litter. Second, we excluded molecular formulae present in the litters and thus, the differences we report in each soil type are derived from this processing (or the lack of it).We calculated aggregated indices that characterize both the composition and the physicochemical properties of the microbial (both bacteria and fungi) and the SOM and lipid pool34,36. For bacterial and fungal communities, we quantified Shannon–Weaver diversity index for each sample H′ = (-{sum }_{i=1}^{S} pi ln(pi)) (where pi is the proportion of species I) using the relative abundance of individual microbial taxa50. To find the percent of substrate assimilation by individual taxa, we calculated the proportion of C assimilated by each group as previously described18,51 as a percent. For SOM and lipid molecular formulae, we separately calculated weighted means of formula-based characteristics (i.e. m/z, Aromaticity Index—AI; H/C, O/C, and Nominal Oxidation State of Carbon-NOSC) as the sum of the product of the single-formula information (i.e. m/zi, AIi, H/Ci and NOSCi) and the relative intensity (Ii) divided by the sum of all intensities (e.g., m/z sample1 = ({sum }_{i=1}^{S})(m/zi ·Ii)/Σ(Ii)). With these metrics we obtained sample-level information related to the molecular size (i.e. m/z), the molecular bioavailability (i.e. higher H/C ratio), the molecular reactiveness (i.e. lower AI) and the energetic rewards from molecular oxidative degradation (i.e. higher NOSC) of the SOM, which allows to infer the potential of decomposition products to form stable SOM12,31,35. Detailed information of the calculated indices can be found in the literature31,35,36.We further tested the effects of soil type, substrate type and their interaction on each index using the “lm” function from the “stats” package. In these analyses, P values were approximated by an F test using Type II ANOVA tests with Kenward-Roger Degrees of Freedom52. When interactions between soil and substrate type were found at P More
