Rapid increase in soil pH solubilises organic matter, dramatically increases denitrification potential and strongly stimulates microorganisms from the Firmicutes phylum
- Published
- Accepted
- Subject Areas
- Agricultural Science, Microbiology, Soil Science, Biogeochemistry
- Keywords
- KOH, denitrification, silt-loam soil, N2O emissions, denitrifying bacterial isolates, Clostridia, Bacillus
- Copyright
- © 2018 Anderson et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Rapid increase in soil pH solubilises organic matter, dramatically increases denitrification potential and strongly stimulates microorganisms from the Firmicutes phylum. PeerJ Preprints 6:e26903v2 https://doi.org/10.7287/peerj.preprints.26903v2
Abstract
Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 hours. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO2 respiration nor N-metabolism rates. Microbial communities became dominated by Firmicutes bacteria within 16 hours, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3000 ng N2-N g-1 h-1 in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated by Bacillus spp. and exhibited varying nitrate reductive potential.
Author Comment
This is a revised version incorporating suggested changes from 3 reviewers. The main change is a full analysis of rarefied data with documentation of the results included in the supplementary information. For this work, rarefication made absolutely no difference to the overall conclusions. Some of the original figures were also moved to the supplemental information section. The aims and structure of the work were also changed in accordance to the reviewers recommendations, namely accentuating that the study was predominantly about denitrification dynamics and the organisms contributing as pH increases under anaerobic conditions.
Significant criticism was given to our inclusion of results surrounding cultured organisms instead of providing qPCR data to determine function. Functional information was however provided in the original manuscript in the form of biogeochemical results and reflects the contribution of the whole community in those conditions rather than a subset of the community that can be targeted using current qPCR primers. The 16S rRNA information suggested that the Firmicutes have a significant functional role to play in denitrification under alkaline anaerobic soil conditions - a conclusion that definitely warrants further study using specific qPCR primers designed to target the bacteria contributing most to community change - something beyond the scope of the original work. The cultured bacteria in this study were predominantly Bacillus (Firmicutes) and accompanying biogeochemical analyses provides some supporting evidence that the Firmicutes indeed have significant denitrification abilities.
Although cause and effect can't be proven outright with the dataset available, this work attempts to make some interesting observations about common soil bacteria that might have a significant role to play in denitrification.
Supplemental Information
Supplementary figures and tables
This file contains relevant figures and tables associated with the manuscript " Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum."
OTU Input file for PRIMER 7 statistical package
Data represents raw sequence counts which were then standardised by total in PRIMER 7 prior to analysis.
OTU identification table
This data represents the OTU information with Megablast ID.