Drying and Rainfall Shape the Structure and Functioning of Nitrifying Microbial Communities in Riverbed Sediments

Abstract

Non-flow periods in fluvial ecosystems are a global phenomenon. Streambed drying and rewetting by sporadic rainfalls could drive considerable changes in the microbial communities that govern stream nitrogen (N) availability at different temporal and spatial scales. We performed a microcosm-based experiment to investigate how dry period duration (DPD) (0, 3, 6, and 9 weeks) and magnitude of sporadic rewetting by rainfall (0, 4, and 21 mm applied at end of dry period) affected stocks of N in riverbed sediments, ammonia-oxidizing bacteria (AOB) and archaea (AOA) and rates of ammonia oxidation (AO), and emissions of nitrous oxide (N2O) to the atmosphere. While ammonium (NH4+) pool size decreased, nitrate (NO3−) pool size increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of AOB and, especially, AOA (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes) increased, despite an apparent decrease of AO rates with drying. An increase of N2O emissions occurred at early drying before substantially dropping until the end of the experiment. Strong rainfall of 21 mm increased AO rates and NH4+ in sediments, whereas modest rainfall of 4 mm triggered a notable increase of N2O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Our findings are particularly relevant for N processing and transport in rivers with alternating dry and wet phases – a hydrological scenario expected to become more important in the future.

Global CO2 emissions from dry inland waters share common drivers across ecosystems

“…While desiccation and subsequent oxygenation of the sediment might minimise emissions of CH 4 from dry sediments 44 , there are nevertheless reports of high CH 4 emissions immediately after drying 3,42 . In addition, we expect desiccation to have a major impact on nitrogen cycling with consequences for N 2 O emissions; that is lower denitrification but higher nitrification, with both processes contributing to N 2 O production 45 . Further research is necessary to improve our understanding of the magnitude and drivers of the emissions of these GHGs from dry inland waters.…”

Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures

“…The efficiency of qPCR assays ranged between 80 and 99% with R 2 ≥ 0.99. Archaeal amoA genes were quantified in 20 μL reactions containing 10 μL GoTaq ® qPCR Master Mix 2x (Promega), 0.2 mg mL-1 BSA, 2 μL DNA template, and 1 μM of each of the primers CamoA-19F (5′-ATGGTCTGGYTWAGACG-3′) (Tourna et al, 2008; Pester et al, 2012) and the new primer TamoA-629R (5′-TGGCANTAYMGATGGATGGC-3′) (Arce et al, 2018), which was designed for improved coverage of archaeal amoA genes, particularly from Ca . Nitrosocosmicus spp.…”

“…PCR amplification of archaeal amoA gene fragments (595 bp excluding primers) was performed in 50 μL reactions containing: 1.25 U of GoTaq® Flexi DNA Polymerase, 1 x Green GoTaq® Flexi Buffer (Promega, Madison, WI, USA), 2 mM MgCl 2 , 0.2 mM dNTPs and 1 μM of each primer CamoA-19F (5′-ATGGTCTGGYTWAGACG-3′) (Tourna et al, 2008; Pester et al, 2012) and TamoA-629R (5′-TGGCANTAYMGATGGATGGC-3′) (Arce et al, 2018). Thermal conditions were as follows: 5 min initial denaturing step at 95°C, followed by 35 cycles of 45 s denaturing at 95°C, 45 s annealing at 58°C and 45 s extension at 72°C, with a final extension step of 10 min at 72°C.…”

Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands

“…However, some modifications were made. The ASVs involved in nitrification were further verified by blasting against NCBI database according to a previous study [48]. The anaerobic methanotrophic groups ANME were excluded from methanogenesis.…”