Morando Michael, Capone Douglas G
Marine and Environmental Biology, University of Southern California Los Angeles, CA, USA.
Front Microbiol. 2016 Dec 2;7:1932. doi: 10.3389/fmicb.2016.01932. eCollection 2016.
Nitrogen can greatly influence the structure and productivity of microbial communities through its relative availability and form. However, the roles of specific organisms in the uptake of different nitrogen species remain poorly characterized. Most studies seeking to identify agents of assimilation have been correlative, indirectly linking activity measurements (e.g., nitrate uptake) with the presence or absence of biological markers, particularly functional genes and their transcripts. Evidence is accumulating of previously underappreciated functional diversity in major microbial subpopulations, which may confer physiological advantages under certain environmental conditions leading to ecotype divergence. This microdiversity further complicates our view of genetic variation in environmental samples requiring the development of more targeted approaches. Here, next-generation tag sequencing was successfully coupled with stable isotope probing (Tag-SIP) to assess the ability of individual phylotypes to assimilate a specific N source. Our results provide the first direct evidence of nitrate utilization by organisms thought to lack the genes required for this process including the heterotrophic clades SAR11 and the Archaeal Marine Group II. Alternatively, this may suggest the existence of tightly coupled metabolisms with primary assimilators, e.g., symbiosis, or the rapid and efficient scavenging of recently released products by highly active individuals. These results may be connected with global dominance often seen with these clades, likely conferring an advantage over other clades unable to access these resources. We also provide new direct evidence of nitrate utilization by the cyanobacterium in support of recent findings. Furthermore, these results revealed widespread functional heterogeneity, i.e., different levels of nitrogen assimilation within clades, likely reflecting niche partitioning by ecotypes.
氮可通过其相对有效性和形态极大地影响微生物群落的结构和生产力。然而，特定生物体在不同氮形态吸收中的作用仍未得到充分表征。大多数旨在确定同化作用因子的研究都是相关性的，将活性测量（例如硝酸盐吸收）与生物标志物（特别是功能基因及其转录本）的存在与否间接联系起来。越来越多的证据表明，主要微生物亚群中存在以前未被充分认识的功能多样性，这可能在某些环境条件下赋予生理优势，导致生态型分化。这种微观多样性进一步使我们对环境样本中遗传变异的看法变得复杂，需要开发更具针对性的方法。在这里，下一代标签测序成功地与稳定同位素探测（标签-SIP）相结合，以评估各个系统发育型吸收特定氮源的能力。我们的结果首次直接证明了被认为缺乏该过程所需基因的生物体（包括异养类群SAR11和古菌海洋第二组）能够利用硝酸盐。或者，这可能表明存在与初级同化者紧密耦合的代谢，例如共生，或者高活性个体对最近释放的产物进行快速有效的清除。这些结果可能与这些类群经常表现出的全球优势有关，可能赋予它们相对于其他无法获取这些资源的类群的优势。我们还提供了蓝细菌利用硝酸盐的新直接证据，以支持最近的发现。此外，这些结果揭示了广泛的功能异质性，即类群内不同水平的氮同化，这可能反映了生态型的生态位划分。
