Groundwater-N pollution derives from agricultural and urban activities, and compromises water quality in shallow aquifers, putting human and environmental health at risk. Nonetheless, subsurface microbiota can transform dissolved inorganic nitrogen into N₂. In this study, we surveyed the microbial community of a shallow aquifer by sampling one well, one piezometer and a spring within an agricultural area that receives N-inputs of more than 700 kg/ha per year through irrigation with wastewater. The survey was conducted during a year with a 16S rRNA next-gen approach. In parallel, we quantified the number of gene copies and transcripts related to anaerobic ammonium oxidation (anammox, hzo), nitrite-dependent anaerobic methane oxidation (n-damo, nod and pmoA) and nitrous oxide reduction (last step of denitrification, nosZ), during the dry and rainy seasons. Our results showed that the groundwater samples had 17.7 to 22.5 mg/L of NO₃⁻-N. The bacterial and archaeal community structure was distinctive at each site, and it remained relatively stable over time. We verified the co-occurrence of N-transforming bacteria, which was correlated with the concentration of NO₂⁻/NO₃⁻ and ORP/DO values (DO: ~3.0 mg/L). Our analyses suggest that these conditions may allow the presence of nitrifying microorganisms which can couple with anammox, n-damo and denitrifying bacteria in interrelated biogeochemical pathways. Gene density (as the number of gene copies per litre) was lower in the rainy season than in the dry season, possibly due to dilution by rainwater infiltration. Yet, the numbers of hzo gene copies here found were similar to those reported in oceanic oxygen minimum zones and in a carbonate-rock aquifer. The transcript sequences showed that Candidatus Brocadia spp. (anammox), Candidatus Methylomirabilis spp. (n-damo) and autotrophic denitrifying Betaproteobacteria coexist in the groundwater environment, with the potential to attenuate the concentration of dissolved inorganic nitrogen by reducing it to N₂ rather than N₂O; delivering thus, an important ecosystem service to remove contaminants.

地下水中的氮污染源于农业和城市活动，危害了浅层含水层的水质，使人类和环境健康处于危险之中。尽管如此，地下微生物群仍可将溶解的无机氮转化为N ₂。在这项研究中，我们对一个浅水层中的微生物群落进行了调查，方法是在一个农业区内采样一口井，一个测压计和一个弹簧，该区每年通过废水灌溉获得的氮输入量超过700千克/公顷。这项调查是在一年中使用16S rRNA下一代方法进行的。同时，我们量化了与厌氧铵氧化（anammox，hzo），亚硝酸盐依赖性厌氧甲烷氧化（n-damo，nod和pmoA）和一氧化二氮的减少（反硝化的最后一步，nosZ），在干燥和雨季。我们的结果表明，地下水样品中的NO ₃ ^-- N含量为17.7至22.5 mg / L。细菌和古细菌的群落结构在每个部位都各不相同，并且随着时间的推移保持相对稳定。我们已验证的N-转化的细菌，其与NO的浓度相关的同现₂ ^- / NO ₃ ^-和ORP / DO值（DO：〜3.0 mg / L）。我们的分析表明，这些条件可能允许存在硝化微生物，这些微生物可以在相关的生物地球化学途径中与厌氧氨氧化菌，正达摩和反硝化细菌耦合。雨季的基因密度（以每升基因拷贝数计）比旱季低，这可能是由于雨水渗入造成的稀释。然而，这里发现的hzo基因拷贝数与海洋最低氧区和碳酸盐岩含水层中报道的相似。该副本序列表明，暂定Brocadia属。（厌氧菌），念珠菌甲基甲虫属 （n-damo）和自养型反硝化Betaproteobacteria并存于地下水环境中，具有通过将其还原为N ₂而不是N ₂ O来降低溶解的无机氮浓度的潜力；因此，这是去除污染物的重要生态系统服务。