Dominant nitrogen metabolisms of a tropical monomictic lake identified using genome resolved metatranscriptomics

<strong>Dataset for manuscript entitled "Dominant nitrogen metabolisms of a tropical monomictic lake identified using genome resolved metatranscriptomics"</strong> <strong>Abstract: </strong>Reactive nitrogen (N) is one of the principal drivers of primary productivity across aquatic ecosystems. However, N cycling in tropical inland waters is less well understood relative to temperate ecosystems. In particular, N cycling in monomictic tropical lakes may be distinct from that of their temperate counterparts due to the warm (&gt;20 °C) temperatures of their anoxic hypolimnions (deepest portion of a stratified water column). These warm anoxic conditions have the potential to dramatically alter ecosystem biogeochemistry by releasing anaerobic metabolic pathways from temperature limitations that are present in anoxic strata of lake ecosystems at higher latitudes. To explore dominant N transformation pathways under warm anoxic conditions, we combined measurements of geochemistry and water column thermophysical structure with genome resolved metatranscriptomic analyses of the water column microbiome in Lake Yojoa, Honduras. Lake Yojoa is characterized by a pronounced accumulation of ammonium in the hypolimnions during stratification, beginning in May, and an annual mixing event that releases reactive N to the photic zone, in November. We sampled Lake Yojoa both above (1m) and below (16m) the thermocline at three locations, in June 2021, when the water column was stratified, and again at the same depths and locations in January 2022, when the water column was mixed. We identified 335 different lineages and significantly different microbiome membership between seasons and, in June, between depths. Expression of genes associated with N metabolic pathways was highest in June below the thermocline. In particular, we found <em>nrfA</em>, along with other respiratory NO₂^- reductases, was upregulated relative to other N metabolism genes in the June hypolimnions, suggesting that dissimilatory nitrate reduction to ammonium (DNRA) was partially responsible for the previously observed ammonium accumulation. DNRA is infrequently identified as a dominant N transformation pathway in natural aquatic ecosystems. This work highlights the need to better define N biogeochemistry in the poorly understood warm anoxic hypolimnions of tropical lake ecosystems. Defining the dominant anaerobic pathways when temperature is not limiting is one key to providing a more complete understanding of how rapidly occurring global change is altering tropical inland waters. <strong>Files described below: </strong> <em>Yojoa_572_MAGs_scaffolds.fna.zip </em>scaffolds for 572 dereplicated MAGs <em>Yojoa_572_MAGs_annotations.tsv.zip</em> DRAM annotations for 572 dereplicated MAGs <em>bipartitionsBranchLabels.nxr_nar_for_tree_aligned.fasta_mode_low.renamed </em>phylogenetic tree for nar/nxr genes <em>bipartitionsBranchLabels.amo_pmo_fortree_aligned.fasta_mode_low.renamed </em>phylogenetic tree for amo/pmo genes <em>YojoaMasterSheet_final.xls</em> MAG inventory with accession numbers and quality stats <em>MetaT_norm.counts.rpk_edger.bins_mean.csv </em>mean geTMM values per bin expressed in metatranscriptomic data <em>MetaT_geTMM_norm.counts.rpk_edger_genes.csv</em> geTMM values per gene expressed in metranscriptomic data <em>geochem_data_Yojoa.csv</em> geochemical data from each location including NH₄⁺, NO₃^-, total phosphorus (TP), and dissolved organic carbon (DOC) <em>profile_data_Yojoa.csv</em> depth profile data at each location including temperature and dissolved oxygen measurements## 研究论文配套数据集 **题为《利用基因组解析宏转录组学（genome resolved metatranscriptomics）鉴定热带单环流湖的主导氮代谢途径》** ## 摘要 活性氮（Reactive nitrogen, N）是水生生态系统初级生产力的核心驱动因子之一。相较于温带生态系统，人们对热带内陆水域的氮循环机制认知仍较为匮乏。尤其值得注意的是，热带单环流湖的缺氧下层滞水带（anoxic hypolimnions，即分层水体的最深区域）水温常年高于20℃，其缺氧温暖环境可使厌氧代谢途径摆脱高纬度湖泊缺氧层所受的温度限制，从而显著改变生态系统生物地球化学过程。 为探究温暖缺氧条件下的主导氮转化途径，本研究结合地球化学与水柱热物理结构测量数据，对洪都拉斯约霍阿湖（Lake Yojoa）水柱微生物组开展基因组解析宏转录组学分析。约霍阿湖的典型特征为：每年5月进入分层期后，下层滞水带会出现显著的铵离子积累；并于每年11月发生全湖混合事件，将活性氮释放至透光带（photic zone）。 本研究于2021年6月（水体分层期）在3个采样点分别采集温跃层（thermocline）上方1米与下方16米的水样，并于2022年1月（水体混合期）在相同点位与深度重复采样。研究共鉴定出335个不同演化支，且不同季节间、6月采样点的不同深度间微生物组组成均存在显著差异。氮代谢相关基因的表达量在6月下层滞水带中最高；其中，nrfA基因与其他呼吸型亚硝酸盐（NO₂⁻）还原酶基因在6月下层滞水带的表达量相较于其他氮代谢基因显著上调，表明异化硝酸盐还原产铵（dissimilatory nitrate reduction to ammonium, DNRA）是此前观测到的铵离子积累的部分成因。在自然水生生态系统中，异化硝酸盐还原产铵极少被认定为主导氮转化途径。 本研究凸显了深化热带湖泊缺氧下层滞水带氮生物地球化学研究的必要性——这类环境的研究长期以来存在认知空白。明确不受温度限制的厌氧代谢主导途径，是全面理解快速发生的全球变化如何改变热带内陆水域的关键一环。 ## 数据集文件说明 1. `Yojoa_572_MAGs_scaffolds.fna.zip`：572个去重复化宏基因组组装基因组（Metagenome-Assembled Genomes, MAGs）的支架序列文件 2. `Yojoa_572_MAGs_annotations.tsv.zip`：572个去重复化宏基因组组装基因组的DRAM注释结果文件 3. `bipartitionsBranchLabels.nxr_nar_for_tree_aligned.fasta_mode_low.renamed`：nar/nxr基因的系统发育树文件 4. `bipartitionsBranchLabels.amo_pmo_fortree_aligned.fasta_mode_low.renamed`：amo/pmo基因的系统发育树文件 5. `YojoaMasterSheet_final.xls`：包含登录号与质量统计信息的宏基因组组装基因组总表 6. `MetaT_norm.counts.rpk_edger.bins_mean.csv`：宏转录组数据中每个宏基因组组装基因组的平均geTMM标准化表达值文件 7. `MetaT_geTMM_norm.counts.rpk_edger_genes.csv`：宏转录组数据中每个基因的geTMM标准化表达值文件 8. `geochem_data_Yojoa.csv`：各采样点地球化学数据文件，包含铵根离子（NH₄⁺）、硝酸根离子（NO₃⁻）、总磷（TP）与溶解性有机碳（DOC） 9. `profile_data_Yojoa.csv`：各采样点深度剖面数据文件，包含温度与溶解氧测量值