Pacific Northwest National Laboratory, Richland, Washington, USA.
Department of Agricultural & Biosystems Engineering, Iowa State University, Ames, Iowa, USA.
Appl Environ Microbiol. 2019 May 2;85(10). doi: 10.1128/AEM.02851-18. Print 2019 May 15.
Nitrogen (N) is a scarce nutrient commonly limiting primary productivity. Microbial decomposition of complex carbon (C) into small organic molecules (e.g., free amino acids) has been suggested to supplement biologically fixed N in northern peatlands. We evaluated the microbial (fungal, bacterial, and archaeal) genetic potential for organic N depolymerization in peatlands at Marcell Experimental Forest (MEF) in northern Minnesota. We used guided gene assembly to examine the abundance and diversity of protease genes and further compared them to those of N fixation () genes in shotgun metagenomic data collected across depths and in two distinct peatland environments (bogs and fens). Microbial protease genes greatly outnumbered genes, with the most abundant genes (archaeal M1 and bacterial trypsin [S01]) each containing more sequences than all sequences attributed to Bacterial protease gene assemblies were diverse and abundant across depth profiles, indicating a role for bacteria in releasing free amino acids from peptides through depolymerization of older organic material and contrasting with the paradigm of fungal dominance in depolymerization in forest soils. Although protease gene assemblies for fungi were much less abundant overall than those for bacteria, fungi were prevalent in surface samples and therefore may be vital in degrading large soil polymers from fresh plant inputs during the early stage of depolymerization. In total, we demonstrate that depolymerization enzymes from a diverse suite of microorganisms, including understudied bacterial and archaeal lineages, are prevalent within northern peatlands and likely to influence C and N cycling. Nitrogen (N) is a common limitation on primary productivity, and its source remains unresolved in northern peatlands that are vulnerable to environmental change. Decomposition of complex organic matter into free amino acids has been proposed as an important N source, but the genetic potential of microorganisms mediating this process has not been examined. Such information can inform possible responses of northern peatlands to environmental change. We show high genetic potential for microbial production of free amino acids across a range of microbial guilds in northern peatlands. In particular, the abundance and diversity of bacterial genes encoding proteolytic activity suggest a predominant role for bacteria in regulating productivity and contrasts with a paradigm of fungal dominance of organic N decomposition. Our results expand our current understanding of coupled carbon and nitrogen cycles in northern peatlands and indicate that understudied bacterial and archaeal lineages may be central in this ecosystem's response to environmental change.
氮（N）是一种常见的限制初级生产力的稀缺营养素。有人提出，微生物将复杂的碳（C）分解为小分子有机分子（例如游离氨基酸），以补充北方泥炭地中生物固定的 N。我们评估了明尼苏达州马塞尔实验林（MEF）北部泥炭地中微生物（真菌、细菌和古菌）有机 N 解聚的遗传潜力。我们使用有针对性的基因组装来研究蛋白酶基因的丰度和多样性，并将其与在不同深度和两个不同泥炭地环境（沼泽和湿地）中收集的鸟枪法宏基因组数据中的 N 固定（）基因进行比较。微生物蛋白酶基因的数量远远超过 基因，最丰富的基因（古菌 M1 和细菌胰蛋白酶 [S01]）每个基因的序列都多于归因于 基因的所有序列。细菌蛋白酶基因组装在深度剖面中多样且丰富，表明细菌在通过解聚较老的有机物质从肽中释放游离氨基酸方面发挥作用，与森林土壤中真菌在解聚中占主导地位的范式形成对比。尽管真菌的蛋白酶基因组装总体上比细菌的蛋白酶基因组装少得多，但真菌在表层样品中很普遍，因此在解聚的早期阶段，可能对降解新鲜植物输入的大型土壤聚合物至关重要。总的来说，我们证明了来自多种微生物（包括研究较少的细菌和古菌谱系）的解聚酶在北方泥炭地中普遍存在，并且可能会影响 C 和 N 循环。氮（N）是初级生产力的常见限制因素，其来源在易受环境变化影响的北方泥炭地中仍未得到解决。有人提出，将复杂的有机物质分解为游离氨基酸是一种重要的 N 源，但介导这一过程的微生物的遗传潜力尚未得到检验。这些信息可以为北方泥炭地对环境变化的可能反应提供信息。我们在北方泥炭地的一系列微生物类群中展示了微生物产生游离氨基酸的高遗传潜力。特别是，编码蛋白水解活性的细菌基因的丰度和多样性表明细菌在调节生产力方面发挥主要作用，这与真菌在有机 N 分解中占主导地位的范式形成对比。我们的研究结果扩展了我们对北方泥炭地中碳氮耦合循环的现有认识，并表明研究较少的细菌和古菌谱系可能是该生态系统对环境变化响应的核心。
