Ganesh Sangita, Bristow Laura A, Larsen Morten, Sarode Neha, Thamdrup Bo, Stewart Frank J
School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.
Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark.
ISME J. 2015 Dec;9(12):2682-96. doi: 10.1038/ismej.2015.44. Epub 2015 Apr 7.
The genetic composition of marine microbial communities varies at the microscale between particle-associated (PA; >1.6 μm) and free-living (FL; 0.2-1.6 μm) niches. It remains unclear, however, how metabolic activities differ between PA and FL fractions. We combined rate measurements with metatranscriptomics to quantify PA and FL microbial activity in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, focusing on dissimilatory processes of the nitrogen (N) cycle. Bacterial gene counts were 8- to 15-fold higher in the FL compared with the PA fraction. However, rates of all measured N cycle processes, excluding ammonia oxidation, declined significantly following particle (>1.6 μm) removal. Without particles, rates of nitrate reduction to nitrite (1.5-9.4nMNd(-1)) fell to zero and N2 production by denitrification (0.5-1.7nMNd(-1)) and anammox (0.3-1.9nMNd(-1)) declined by 53-85%. The proportional representation of major microbial taxa and N cycle gene transcripts in metatranscriptomes followed fraction-specific trends. Transcripts encoding nitrate reductase were uniform among PA and FL fractions, whereas anammox-associated transcripts were proportionately enriched up to 15-fold in the FL fraction. In contrast, transcripts encoding enzymes for N2O and N2 production by denitrification were enriched up to 28-fold in PA samples. These patterns suggest that the majority of N cycle activity, excluding N2O and N2 production by denitrification, is confined to a FL majority that is critically dependent on access to particles, likely as a source of organic carbon and inorganic N. Variable particle distributions may drive heterogeneity in N cycle activity and gene expression in OMZs.
海洋微生物群落的遗传组成在微观尺度上因与颗粒相关（PA；>1.6μm）和自由生活（FL；0.2 - 1.6μm）的生态位而异。然而，PA和FL组分之间的代谢活动差异仍不清楚。我们将速率测量与宏转录组学相结合，以量化东热带北太平洋缺氧区（OMZ）中PA和FL微生物的活性，重点关注氮（N）循环的异化过程。与PA组分相比，FL中的细菌基因计数高8至15倍。然而，除氨氧化外，所有测量的N循环过程的速率在去除颗粒（>1.6μm）后均显著下降。没有颗粒时，硝酸盐还原为亚硝酸盐的速率（1.5 - 9.4nM Nd⁻¹）降至零，反硝化作用产生N₂的速率（0.5 - 1.7nM Nd⁻¹）和厌氧氨氧化的速率（0.3 - 1.9nM Nd⁻¹）下降了53 - 85%。宏转录组中主要微生物类群和N循环基因转录本的比例呈现出特定组分的趋势。编码硝酸盐还原酶的转录本在PA和FL组分中是一致的，而与厌氧氨氧化相关的转录本在FL组分中富集程度高达15倍。相比之下，编码反硝化作用产生N₂O和N₂的酶的转录本在PA样本中富集程度高达28倍。这些模式表明，除反硝化作用产生N₂O和N₂外，大多数N循环活动局限于以自由生活为主的群体，该群体严重依赖于获取颗粒，颗粒可能作为有机碳和无机氮的来源。可变的颗粒分布可能驱动缺氧区N循环活动和基因表达的异质性。
