Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.

中文翻译：

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选择性碳源影响微生物硝酸盐呼吸的最终产物。


呼吸和分解代谢基因在微生物基因组中的分布存在差异。因此，特定的碳源可能有利于不同的呼吸过程。我们分析了 94 种碳源对来自不同陆地环境的微生物富集培养物中硝酸盐呼吸最终产物的影响。我们发现一些碳源始终有利于硝酸盐异化还原为铵（DNRA/硝酸盐氨化），而其他碳源则有利于亚硝酸盐积累或反硝化。对于水生沉积物的富集培养，我们对最丰富菌株的基因组进行了测序，将这些基因组与 16S rDNA 精确序列变体 (ESV) 进行匹配，并使用 16S rDNA 扩增子测序来跟踪功能不同的 ESV 在不同碳源上的差异富集。我们发现，具有不同亚硝酸盐积累、DNRA 或反硝化遗传潜力的菌株丰度的变化与在不同碳源上回收的富集培养物中的亚硝酸盐或铵浓度相关。具体来说，我们发现L-山梨糖或D-纤维二糖富集了亚硝酸盐克雷伯菌，其他糖富集了硝酸盐氨化剂，柠檬酸盐或甲酸盐富集了假单胞菌反硝化剂和硫螺菌硝酸盐氨化剂。我们的结果为当前的范式添加了重要的细微差别，即较高浓度的碳总是有利于 DNRA 而不是反硝化或亚硝酸盐积累，并且我们提出，在某些情况下，在确定硝酸盐呼吸终产物时，碳组成与碳浓度一样重要。 此外，我们的方法可以扩展到其他环境和新陈代谢，以表征选择性参数如何影响微生物群落组成、基因内容和功能。