Ecosystems biology of the hidden sulfur cycle in rice paddy soil - phylogenetic, functional, and proteogenomic analysis of key players with focus on sulfate reducers
Final Report Abstract
Rice agriculture provides food for more than 50% of the world’s human population. At the same time, rice paddies are major sources of the greenhouse gas methane, contributing 5-15% of its annual emission to the atmosphere. Cryptic sulfur cycling occurs at high rates in these water-submerged soils and controls methane production, an effect that is increased by sulfatecontaining fertilizers or soil amendments. In this project, we grew rice plants in a greenhouse setting until their late vegetative phase with and without gypsum (CaSO4·2H2O) amendment. Gypsum was applied in amounts relevant for rice agriculture (0.15% w/w) to stimulate microorganisms involved in sulfate reduction as the driving process of cryptic sulfur cycling. Sulfate reducing microorganisms (SRM) were identified by 16S rRNA gene amplicon sequencing and a metaproteogenomic approach. Gypsum amendment decreased methane emissions by up to 99% but had no major impact on the general phylogenetic composition of the bacterial community. It rather selectively stimulated or repressed a small number of 129 and 27 species-level operational taxonomic units (OTUs) (out of 1,883–2,287 observed) in the rhizosphere and bulk soil, respectively. Gypsum-stimulated OTUs were affiliated with several potential sulfate-reducing (Syntrophobacter, Desulfovibrio, unclassified Desulfobulbaceae, unclassified Desulfobacteraceae) and sulfur-oxidizing taxa (Thiobacillus, unclassified Rhodocyclaceae), while gypsum-repressed OTUs were dominated by aerobic methanotrophs (Methylococcaceae). Abundance correlation networks suggested that two abundant (>1%) OTUs (Desulfobulbaceae, Rhodocyclaceae) were central to the reductive and oxidative parts of the sulfur cycle. Molecular screenings of rice paddy soil with the functional marker genes dsrAB (encoding subunit A and B of dissimilatory sulfite reductase), which are present in all known SRM, indicated the presence of novel yet undescribed sulfate reducers. Using a metaproteogenomic approach, we identified Nitrospirae bacterium Nbg-4 encoding dsrAB most closely related to uncultured dsrAB family-level lineage 13. Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression thereof in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics. In addition, Nbg-4 encoded the full pathway of dissimilatory nitrate reduction to ammonia (DNRA) with expression of its first step being detected in bulk soil without gypsum amendment. A subsequent phylogenomic approach identified Nbg-4 as a representative species of a novel genus. Considering the widespread occurrence of this novel genus in environments of medium temperature, we proposed for Nbg-4 the name Candidatus Sulfobium mesophilum, gen. nov., spec. nov. The experience gained during the large scale analysis of the metagenomics data sets of rice paddy soil enabled us to identify in a parallel approach dsrAB-carrying Acidobacteria in peatlands. These novel Acidobacteria encoded the full pathway of dissimilatory sulfate reduction as well and showed expression thereof in peat soil microcosms as revealed by parallel metatranscriptomics. In addition, a dsrB amplicon sequencing approach could be established in this project and successfully applied to littoral lake sediment, where members of the Desulfobacteraceae and Syntrophobacteraceae were identified as the numerically dominant and transcriptionally most active SRM. In summary, we have deepened our knowledge on the identity and ecophysiology of SRM not only in rice paddy fields but also in natural low-sulfate environments such as peatlands and lake sediments. We further provided a showcase approach for not only identifying but also genomically and transcriptionally characterizing putatively novel SRM encoding dsrAB so far only found in PCR-based screenings of environmental samples.
Publications
- (2015) Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases. ISME J. 9: 1152–1165
Müller, A.B., Kjeldsen, K.U., Rattei, T., Pester, M., Loy, A.
(See online at https://doi.org/10.1038/ismej.2014.208) - (2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. ISME J. 10: 2365–2375
Hausmann, B., Knorr, K.-H., Schreck, K., Tringe, S.G., Glavina del Rio, T., Loy, A., Pester, M.
(See online at https://doi.org/10.1038/ismej.2016.42) - (2016) Gypsum amendment to rice paddy soil stimulates bacteria involved in sulfur cycling but largely preserves the phylogenetic composition of the total bacterial community. Environ. Microbiol. 8: 413–423
Wörner, S., Zecchin, S., Dan, J., Todorova, N. H., Loy, A., Conrad, R., Pester, M.
(See online at https://doi.org/10.1111/1758-2229.12413) - (2018) Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium. Appl Environ Microbiol. 84: e02224-17
Zecchin, S., Mueller, R.C., Seifert, J., Stingl, U., Anantharaman, K., von Bergen, M., Cavalca, L., Pester, M.
(See online at https://doi.org/10.1101/196774) - (2018). Peatland Acidobacteria with a dissimilatory sulfur metabolism. ISME J. 12: 1729–1742
Hausmann, B., Pelikan, C., Herbold, C.W., Koestlbacher, S., Albertsen, M., Eichorst, S.A., Glavina del Rio, T., Huemer, M., Nielsen, P.H., Rattei, T., Stingl, U., Tringe, S.G., Trojan, D., Wentrup, C., Woebken, D., Pester, M., Loy, A.
(See online at https://doi.org/10.1038/s41396-018-0077-1) - (2019) Long-term transcriptional activity at zero growth by a cosmopolitan rare biosphere member. mBio. 10: e02189-02118
Hausmann, B., Pelikan, C., Rattei, T., Loy, A., Pester, M.
(See online at https://doi.org/10.1128/mBio.02189-18) - (2019) The active sulfate-reducing microbial community in littoral sediment of oligotrophic Lake Constance. Front Microbiol 10: 247
Wörner, S., and Pester, M.
(See online at https://doi.org/10.3389/fmicb.2019.00247)
