Yu Baohong, Zeng Quanchao, Li Jinlin, Li Jun, Tan Xun, Gao Xin, Mao Ziqiang, Huang Ping, Wu Shengjun
Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China.
Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China.
Sci Total Environ. 2023 Dec 20;905:167055. doi: 10.1016/j.scitotenv.2023.167055. Epub 2023 Sep 12.
The recent discovery of comammox Nitrospira as complete ammonia-oxidizing microorganism has fundamentally revolutionized our understanding of nitrogen cycling in sediment environments. However, knowledge regarding their abundance, biodiversity, community structure, and interactions is predominantly limited to the upper layers (0-20 cm). To address this gap, we collected sediment samples along profiles ranging from 0 to 300 cm in depth at three locations within the middle segment of the Three Gorges Reservoir (TGR), China. Quantitative real-time PCR (qPCR) analyses suggested that comammox bacteria were not only ubiquitous in deep sediments but also more abundant than ammonia-oxidizing bacteria (AOB). Ammonia monooxygenases subunit A (amoA) gene amplicon sequencing illuminated that comammox bacteria were more sensitive to sedimental depth compared to AOB and ammonia-oxidizing archaea (AOA), as evidenced by a more significant decline in community diversity and similarity over distance along sediment vertical profiles. Notably, we discovered that the amoA gene abundance, alpha- and beta-diversity of comammox bacteria exerted an essential contribution to potential nitrification rates according to random forest model. Phylogenetic analysis indicted that most comammox bacteria within sediment samples belonged to clade A.2. Intriguingly, the average relative abundance of comammox clade A.2 displayed a noteworthy rise with sediment depth, whereas clade A.1 demonstrated a converse pattern, unveiling distinct ecological niche adaptations of these two clades along the sediment profile. Ecological network analysis further revealed closer interactions between comammox bacteria and canonical ammonia oxidizers in the superficial layer (0-40 cm), with the network structure gradually simplifying from superficial to deep sediment (200-300 cm). Overall, these findings broaden the current recognition of the geographic distribution and niche segregation of comammox bacteria at the fine scale of the sediments ecosystems and provide insights into sediment depth-related variations of their coexistence network patterns in large freshwater reservoirs.
最近发现的完全氨氧化微生物——硝化螺旋菌属（Comammox Nitrospira），从根本上改变了我们对沉积物环境中氮循环的理解。然而，关于它们的丰度、生物多样性、群落结构和相互作用的知识主要局限于上层（0 - 20厘米）。为了填补这一空白，我们在中国三峡水库（TGR）中段的三个地点，沿着深度从0到300厘米的剖面采集了沉积物样本。定量实时PCR（qPCR）分析表明，完全氨氧化细菌不仅在深层沉积物中普遍存在，而且比氨氧化细菌（AOB）更丰富。氨单加氧酶亚基A（amoA）基因扩增子测序表明，与AOB和氨氧化古菌（AOA）相比，完全氨氧化细菌对沉积物深度更敏感，这一点从沿沉积物垂直剖面距离上群落多样性和相似性更显著的下降中得到证明。值得注意的是，根据随机森林模型，我们发现完全氨氧化细菌的amoA基因丰度、α - 和β - 多样性对潜在硝化速率有重要贡献。系统发育分析表明，沉积物样本中的大多数完全氨氧化细菌属于A.2进化枝。有趣的是，完全氨氧化A.2进化枝的平均相对丰度随沉积物深度呈现出显著上升，而A.1进化枝则呈现相反的模式，揭示了这两个进化枝在沉积物剖面上不同的生态位适应性。生态网络分析进一步揭示，完全氨氧化细菌与表层（0 - 40厘米）中的典型氨氧化菌之间的相互作用更为密切，网络结构从表层到深层沉积物（200 - 300厘米）逐渐简化。总体而言，这些发现拓宽了目前对沉积物生态系统精细尺度上完全氨氧化细菌地理分布和生态位分离的认识，并为大型淡水水库中其共存网络模式与沉积物深度相关的变化提供了见解。
