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Metagenomic and -Transcriptomic Analyses of Microbial Nitrogen Transformation Potential, and Gene Expression in Swiss Lake Sediments

ISME COMMUNICATIONS(2024)

Swiss Fed Inst Aquat Sci & Technol | Univ Basel | Swiss Fed Inst Technol | Eawag

Cited 0|Views8
Abstract
The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes. Our results indicate that microbial N loss in these sediments is primarily driven by nitrification coupled to denitrification. N-transformation gene compositions indicated three groups of lakes: agriculture-influenced lakes characterized by rapid depletion of oxidants in the sediment porewater, pristine-alpine lakes with relatively deep sedimentary penetration of oxygen and nitrate, and large, deep lakes with intermediate porewater hydrochemical properties. Sedimentary organic matter (OM) characteristics showed the strongest correlations with the community structure of microbial N-cycling communities. Most transformation pathways were expressed, but expression deviated from gene abundance and did not correlate with benthic geochemistry. Cryptic N-cycling may maintain transcriptional activity even when substrate levels are below detection. Sediments of large, deep lakes generally showed lower in-situ N gene expression than agriculture-influenced lakes, and half of the pristine-alpine lakes. This implies that prolonged OM mineralization in the water column can lead to the suppression of benthic N gene expression.
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denitrification,nitrification,anammox,DNRA,freshwater sediment,metatranscriptomics,metagenomics
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要点】:本研究通过宏基因组学和转录组学方法,分析了瑞士12个湖泊沉积物中微生物氮转化潜力及其基因表达,揭示了微生物氮循环途径的环境控制因素。

方法】:利用宏基因组学和转录组学技术分析微生物氮转化基因的丰度和表达情况。

实验】:在12个具有不同沉积速率和营养状态的瑞士湖泊沉积物中进行,使用的数据集为这些湖泊的沉积物样本,实验结果表明沉积物中有机物特征与微生物氮循环群落结构关联性最强,且大多数转化途径均被表达,但其表达与基因丰度和底质地球化学性质不相关。大深湖的沉积物通常表现出较低的氮基因原位表达,表明长期的水柱中有机物矿化可能导致底栖氮基因表达的抑制。