Data from: Distinct N-cycling microbial communities contribute to microtopographic variation in soil N2O emissions

Climate change is increasing the frequency and intensity of large
precipitation events that flood soils and establish anoxic conditions that
promote microbial denitrification, a predominant source of atmospheric
nitrous oxide (N2O, a strong greenhouse gas). Denitrification may be
favored within topographic depressions in otherwise flat fields that are
prone to ponding, establishing “hotspots” of N2O emissions. The location
of N2O hotspots may also depend on the distribution of soil microbial
communities that are responsible for the production and consumption of N2O
in soils. Yet, relating soil microbial community composition to N2O
emissions remains challenging. To assess how spatial variation in soil
microbial communities affects N2O emissions, we measured the community
composition of active microorganisms using amplicon-based sequencing of
cDNA generated from mRNA transcripts associated with N-cycling processes
in response to experimentally flooding and draining soils in the lab. We
also used stable isotope tracers to relate microbial communities to
process rates. Consistent with the hypothesis that denitrifying microbial
communities are not functionally redundant, we found that the diversity of
microbial taxa expressing nitrite reduction genes (nirK) and N2O reduction
genes (Clade I nosZ) were correlated with denitrifier-derived N2O
emissions. Depressional soils had more diverse active N2O consuming
communities (assessed using Clade I nosZ) under flooded conditions,
limiting net N2O emissions compared to upslope soils. Furthermore,
non-flooded depressional soils maintained higher rates of dissimilatory
nitrate reduction to ammonia (DNRA), limiting nitrate available to
denitrifiers. Our results show that depressional soils maintain distinct
microbial communities that likely promote higher rates of N2O reduction
and DNRA compared to upslope soils. Soil microtopography can, therefore,
select for distinct microbial communities that emit different amount of
N2O in response to large precipitation events.

气候变化正加剧强降水事件的发生频率与强度，此类事件会导致土壤被淹并形成缺氧环境，进而促进微生物反硝化作用——这是大气中一氧化二氮（N₂O，一种强效温室气体）的主要来源。在原本平坦但易积水的农田中，地形低洼区域或更利于反硝化作用发生，从而形成N₂O排放的“热点区域”。N₂O排放热点的位置还可能取决于土壤微生物群落的分布——这些群落负责土壤中N₂O的产生与消耗。然而，将土壤微生物群落组成与N₂O排放关联起来仍具挑战性。为评估土壤微生物群落的空间变异对N₂O排放的影响，我们在实验室模拟土壤淹水与排水的条件下，针对参与氮循环过程的mRNA转录本生成的cDNA进行扩增子测序，以此测定活性微生物的群落组成。我们还利用稳定同位素示踪剂，将微生物群落与过程速率关联起来。与反硝化微生物群落不具备功能冗余性的假设一致，我们发现表达亚硝酸盐还原基因（nirK）和N₂O还原基因（Clade I nosZ）的微生物类群多样性，与反硝化菌产生的N₂O排放存在相关性。在淹水条件下，低洼区域土壤中具有更丰富的活性N₂O消耗群落（通过Clade I nosZ评估），与上坡土壤相比，其净N₂O排放量受到限制。此外，未淹水的低洼区域土壤维持着更高的异化硝酸盐还原成铵（DNRA）速率，从而限制了反硝化菌可利用的硝酸盐含量。我们的研究结果表明，与上坡土壤相比，低洼区域土壤维持着独特的微生物群落，这些群落可能促进更高的N₂O还原速率与DNRA速率。因此，土壤微地形可筛选出独特的微生物群落，这些群落在应对强降水事件时会排放不同量的N₂O。