Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching

www.nature.com/scientificreports Correction: Author Correction OPEN Received: 15 March 2017 Accepted: 14 July 2017 Published: xx xx xxxx Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching Jiří Bárta1, Karolina Tahovská1, Hana Šantrůčková1 & Filip Oulehle2 Nitrogen leaching owing to elevated acid deposition remains the main ecosystem threat worldwide. We aimed to contribute to the understanding of the highly variable nitrate losses observed in Europe after acid deposition retreat. Our study proceeded in adjacent beech and spruce forests undergoing acidification recovery and differing in nitrate leaching. We reconstructed soil microbial functional characteristics connected with nitrogen and carbon cycling based on community composition. Our results showed that in the more acidic spruce soil with high carbon content, where Acidobacteria and Actinobacteria were abundant (Proteo:Acido = 1.3), the potential for nitrate reduction and loss via denitrification was high (denitrification: dissimilative nitrogen reduction to ammonium (DNRA) = 3). In the less acidic beech stand with low carbon content, but high nitrogen availability, Proteobacteria were more abundant (Proteo:Acido = 1.6). Proportionally less nitrate could be denitrified there (denitrification:DNRA = 1), possibly increasing its availability. Among 10 potential keystone species, microbes capable of DNRA were identified in the beech soil while instead denitrifiers dominated in the spruce soil. In spite of the former acid deposition impact, distinct microbial functional guilds developed under different vegetational dominance, resulting in different N immobilization potentials, possibly influencing the ecosystem’s nitrogen retention ability. Since the industrial period, atmospheric sulphur (S) and nitrogen (N) deposition has become one of the main drivers for changing ecosystem biogeochemistry. The main consequences of long-term S and N loading lie in soil acidification and the interlinked changes in plant productivity and diversity1–3, soil carbon and nutrient cycling4 and alteration in the soil microbial community structure5. Besides soil acidification, long-term N deposition can lead to an ecosystem’s N saturation where the excess N may be lost in the form of nitrates6. Reduced depositions in the last decades started the recovery of many European ecosystems, accompanied only in some of them by reduced nitrate leaching7,8. Apart from plants, soil microbes, as essential mediators of all assimilative and dissimilative N transformation processes, play a key role in the soil mineral N balance. Nitrates accumulate in soil either under high nitrification rates and/or low nitrate reduction rates (i.e. low microbial immobilization, denitrification or dissimilative nitrate reduction to ammonium (DNRA)). Generally, it is the heterotrophic community (usually prevailing over the autotrophic), being dependent on soil carbon (C), which regulates whether N is lost or retained in the soil9–11. Although we have now advanced ability to explore structures of soil microbial communities, there is still a need for studies focusing on specific links between microbial taxonomic and functional diversity and their participation in soil C and N transformation and eventually soil N retention12. The effect of elevated N input on soil microbial communities has been widely discussed with most studies drawing the conclusion of decreasing fungal biomass and activity, particularly mycorrhizas5,13–15. Lower fungal biomass and thus lower activity of the lignin-degrading enzymes16,17 shift microbial utilization to easily available C and after these are quickly exhausted it may lead to overall C limitation of the microbial community4,18–21. As a consequence, N mineralization and nitrate concentrations increase22–25. 1 Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic. 2Czech Geological Survey, Department of Environmental Geochemistry and Biogeochemistry, Prague, 118 21, Czech Republic. Correspondence and requests for materials should be addressed to J.B. (email: ) Scientific RepOrTs | 7: 9738 | DOI:10.1038/s41598-017-08554-1 1 www.nature.com/scientificreports/ Elevated N loading and subsequent changes in microbial utilization of organic C can change the overall structure of a soil prokaryotic community. Particularly, copiotrophic taxa (r-strategists) namely Alpha- and Gammaproteobacteria increase at elevated N input26–28. In contrast, Acidobacteria, a group which is mostly considered as oligotrophic (K-strategists), decline with increasing N loads27,29. Functional metagenomic analyses showed higher relative abundances of specific gene categories associated with DNA/RNA replication, electron transport and protein metabolism after N amendments. This indicates higher growth and metabolic activity typical for copiotrophs27. Such community shifts may lead to changes in substrate use efficiencies since copiotrophs are supposed to grow faster but with lower growth efficiency30. The Czech side of the central European area of the so-called “Black Triangle” located along the German-Polish-Czech border and belongs among the regions most affected by acid pollution31. Since the 1980’s, a considerable decline in S and N deposition has occurred (more than 90% and 40% reduction, respectively) due to the restructuring of industrial and agricultural practices31. Here we investigated the microbial community structure using DNA sequencing in the beech and spruce soils of two adjacent forests and currently differing in their nitrate leaching7. We combined molecular identification data with biogeochemical soil and microbial characteristics to explore the links among microbial community composition and N transformation processes. Our primary question was whether variations in microbial community structure could help to explain observed differences in nitrate leaching between both forests. We supposed that the microbial community structure could be different between both forests due to different vegetation type per se (i.e. differences in litter composition and input, different levels of dry deposition etc.). We hypothesized that due to historically high acid deposition, the fungal abundances would be rather similar probably with a shift to saprotrophic strategy. Furthermore, the bacterial community would be dominated by Acidobacteria in both forests due to very low soil pH. However, we also recognized that copiotrophic taxa might be favoured in the beech soils that could correspond to richer N conditions there. Materials and Methods Sampling sites. Our experimental site, Načetín, is located on the ridge of the Ore Mountains, in the north-western part of the Czech Republic (Fig. S1). This region was exposed to extremely high acid deposition in the past32 and has currently been undergoing recovery since the 1990s31 (...truncated)