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:e26903v1 https://doi.org/10.7287/peerj.preprints.26903v1
Abstract
We used potassium hydroxide (KOH) to induce rapid soil pH changes and then observed microbial community change over 48 hours in anaerobic conditions before measuring denitrification enzyme activity (DEA). Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, straddling the range of localized pH changes likely to be observed in soil after deposition of livestock urine or urea fertiliser. Up to 240-fold higher dissolved organic matter (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 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 (N2O-R) was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded of 3000 ng N2-N g-1 h-1 in the presence of native DOM. Evidence for DNRA and/or organic matter mineralisation was observed with ammonium (NH4+) increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate (NO3-) were utilised. Pure isolates from the microcosms were predominantly Bacillus spp. and exhibited varying NO3- reductive potential.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
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.
Raw data included in table 1, figure 2 and supplemental figure 1
Summary of data included in table 1, figure 2 and supplemental figure 1
Raw data included in table 1, figure 2 and supplemental figure 1
Raw data included in table 1, figure 2 and supplemental figure 1
Raw data included in table 1, figure 2 and supplemental figure 1
Chemical change in microcosms during the DEA assays
Mineral N-chemistry, DOC and DON presenting changes during the 4 hour DEA period. Numbers in square brackets beside pH values are the cmolc kg-1 KOH additions.
DOC/DON correlation
Correlation of DOC and DON for each treatment irrespective of incubation time. Error bars represent standard deviation of the mean.
Summary of bacterial isolates grown from the microcosms
Bacterial isolates were either grown on full strength TSB-nitrate media (ST2A) or 1/10 diluted TSB-nitrate media (ST2B). Nitrate (NO3-) utilisation, ammonium (NH4+) production and nitrous oxide (N2O) emission data represents N-chemistry from isolates grown for a period of 48 hours in liquid TSB-nitrate media compared to uninoculated controls. Those isolates selected for genome sequencing are presented in ST2C. For samples identified via Blastn search of the 16S rRNA gene, the NCBI GenBank accessions numbers are presented in column 8. All accession numbers are prefixed by MH211 as indicated by the first number in the series and are in order of the Isolate Accessions presented in column 1. Possible N metabolism is inferred based on the changes in N-chemistry observed. Data is not curated for the isolates selected for genome sequencing, therefore these results are not presented in this paper.