Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments.

IF 5.1 Q1 ECOLOGY ISME communications Pub Date : 2024-10-15 eCollection Date: 2024-01-01 DOI:10.1093/ismeco/ycae110
Kathrin B L Baumann, Alessandra Mazzoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Beat Müller, Robert Niederdorfer, Shinichi Sunagawa, Mark A Lever, Moritz F Lehmann, Helmut Bürgmann
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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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瑞士湖泊沉积物中微生物氮转化潜力和基因表达的元基因组和转录组分析。
全球氮(N)循环因人为活动而发生了巨大变化,包括水生生态系统中生物可利用氮的输入量增加。淡水沉积物是固定氮周转和消除的热点,但人们对底栖生物脱氮微生物途径的环境控制还不完全了解。在此,我们利用元基因组学和转录组学分析了瑞士 12 个湖泊沉积物中参与氮转化的微生物基因的丰度和表达,这些湖泊的沉积速率和营养系统各不相同。我们的研究结果表明,这些沉积物中的微生物氮损失主要是由硝化和反硝化耦合驱动的。氮转化基因组成显示了三类湖泊:受农业影响的湖泊,其特点是沉积物孔隙水中的氧化剂迅速耗尽;棱岩-高山湖泊,其氧气和硝酸盐的沉积渗透相对较深;大而深的湖泊,其孔隙水的水化学性质处于中等水平。沉积有机物(OM)特征与微生物氮循环群落结构的相关性最强。大多数转化途径都有表达,但表达量与基因丰度有偏差,且与底栖生物地球化学无关。即使底物含量低于检测水平,隐性氮循环也可能保持转录活性。大型深湖沉积物的原位氮基因表达量普遍低于受农业影响的湖泊和半数棱绿-高山湖泊。这意味着水体中长期的 OM 矿化可导致底栖氮基因表达受抑制。
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