Temperature impacts differentially on the methanogenic food web of cellulose‐supplemented peatland soil

Abstract

The impact of temperature on the largely unresolved intermediary ecosystem metabolism and associated unknown microbiota that link cellulose degradation and methane production in soils of a moderately acidic (pH 4.5) fen was investigated. Supplemental [(13) C]cellulose stimulated the accumulation of propionate, acetate and carbon dioxide as well as initial methane production in anoxic peat soil slurries at 15°C and 5°C. Accumulation of organic acids at 15°C was twice as fast as that at 5°C. 16S rRNA [(13) C]cellulose stable isotope probing identified novel unclassified Bacteria (79% identity to the next cultured relative Fibrobacter succinogenes), unclassified Bacteroidetes (89% identity to Prolixibacter bellariivorans), Porphyromonadaceae, Acidobacteriaceae and Ruminococcaceae as main anaerobic degraders of cellulose-derived carbon at both 15°C and 5°C. Holophagaceae and Spirochaetaceae were more abundant at 15°C. Clostridiaceae dominated the degradation of cellulose-derived carbon only at 5°C. Methanosarcina was the dominant methanogenic taxa at both 15°C and 5°C. Relative abundance of Methanocella increased at 15°C whereas that of Methanoregula and Methanosaeta increased at 5°C. Thaumarchaeota closely related to Nitrosotalea (presently not known to grow anaerobically) were abundant at 5°C but absent at 15°C indicating that Nitrosotalea sp. might be capable of anaerobic growth at low temperatures in peat.

Quantitative Microbial Ecology through Stable Isotope Probing

“…These treatments were selected in order to evaluate the effects of isotope addition on the density and isotopic composition of DNA. We assessed (i) the effect of 18 O in the absence of supplemental glucose as the difference between treatments 2 and 1, (ii) the effect of 13 C in the presence of supplemental glucose as the difference between treatments 4 and 3, and (iii) the effect of 18 O with supplemental glucose as the difference between treatments 5 and 3. In each case, these comparisons isolate the effect of the presence of an isotope tracer.…”

“…Low-GC-content organisms that incorporated the isotope label may not have shifted sufficiently in density to be part of the labeled density fraction, and high-GC-content organisms that did not incorporate the label may be erroneously inferred to be part of the labeled community. This could result in incomplete coverage when discrete, noncontiguous density intervals representing heavy and light fractions (13,14) are selected for sequencing, omitting information about the microbial assemblage contained in the DNA at intermediate densities. In other cases, only the heavy fractions in both labeled and unlabeled treat-ments were sequenced and compared: any new organisms that appeared in the heavy fraction of the labeled treatment were inferred to have taken up enough of the isotope tracer to have shifted the density of their DNA (15).…”

“…Some hypotheses to explain priming invoke microbial biodiversity (22), and yet, those controls remain cryptic, in part because of the difficulty of identifying organisms that respond indirectly to the addition of substrate by increasing the decomposition of native soil organic matter. Quantitative SIP has the potential to address these phenomena, by parsing out the contributions of specific microorganisms to the decomposition of the added substrate, labeled with 13 C, and to the decomposition of native soil organic matter, which an […”

Methanogenic food web in the gut contents of methane-emitting earthwormEudrilus eugeniaefrom Brazil

“…Cloning of PCR products for mcrA, mrtA and 16S rRNA cDNA retrieved from pooled fractions 2 and 3 (representing the 'heavy' [labeled] RNA; buoyant density: 1.803±0.001-1.794±0.003 g ml À 1 ; Supplementary Figure S1) and from pooled fractions 9 and 10 (representing the 'light' [unlabeled] RNA; buoyant density: 1.743±0.003-1.735± 0.004 g ml À 1 ; Supplementary Figure S1), and also of PCR products obtained from the enrichment culture, was performed as previously described (Schmidt et al, 2014). PCR products of clones with correct inserts were selected for sequencing at Macrogen Europe (Amsterdam, the Netherlands).…”

“…The resulting alignment contained 880 aligned nucleotide positions. Chimeric 16S rRNA cDNA gene sequences were identified as described (Schmidt et al, 2014). Potential chimeric sequences were blasted (BLASTn) and corrected by removing the shorter part of the sequence at the connection point of the different fragments.…”