Kinetics and Identities of Extracellular Peptidases in Subsurface Sediments of the White Oak River Estuary, North Carolina
Kinetics and Identities of Extracellular Peptidases in Subsurface Sediments of the White Oak River Estuary, North Carolina
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DOI：
10.1128/aem.00102-19
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发表时间：
2019-07
影响因子：
4.4
通讯作者：
A. D. Steen;R. Kevorkian;J. Bird;Nina Dombrowski;B. Baker;Shane M. Hagen;Katherine H. Mulligan;Jenna M. Schmidt;Austen T. Webber;T. Royalty;M. Alperin
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文献类型：
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作者：
A. D. Steen;R. Kevorkian;J. Bird;Nina Dombrowski;B. Baker;Shane M. Hagen;Katherine H. Mulligan;Jenna M. Schmidt;Austen T. Webber;T. Royalty;M. Alperin
海洋和河口沉积物中有机碳的埋藏代表着大气二氧化碳的长期汇。在全球范围内，∼40%的有机碳埋藏发生在缺氧河口和三角洲体系中。然而，对埋藏在沉积物中的有机质数量的最终控制，而不是被氧化成二氧化碳，受到的限制很少。在这项研究中，我们使用酶分析和元基因组分析相结合的方法来确定地下微生物群落如何催化蛋白质类有机碳降解的第一步。我们的结果表明，深层沉积物中的微生物群落适应了降解有机物特有的分子，这表明这些异养生物适应了地下的生活。摘要缺氧的地下沉积物中含有异养微生物群落，它们以极低的速率代谢有机碳。为了评估地下微生物获取碎屑沉积有机质的机制，我们测量了北卡罗来纳州白橡河河口缺氧沉积物中一系列胞外肽酶的动力学。九种不同的肽酶底物在所有深度都被酶解。潜在的多肽酶活性(Vmax)随着沉积物深度的增加而降低，尽管在所有深度每个细胞上表达的Vmax大致相同。半饱和常数(Km)随深度的增加而减小，表明在底物浓度较低时，多肽酶的功能更有效。相对于作用于L-苯丙氨酸的酶，富含降解有机物的分子(d-苯丙氨酸和L-鸟氨酸)上的胞外肽酶的潜在活性增加，进一步表明微生物群落适应于获取降解有机物。从同一地点的基因组数据中鉴定出19类预测的、输出的肽酶，其中C25类(牙龈痛样肽酶)的基因在每个深度都占40%以上。参与单链DNA修复的蛋氨酸氨基肽酶、锌羧肽酶和类S24多肽酶也很丰富。这些结果表明，地下异养微生物群落主要通过一套适应良好的胞外酶来获取低质量的碎屑有机物。重要的是，海洋和河口沉积物中有机碳的埋藏是大气二氧化碳的长期汇。在全球范围内，∼40%的有机碳埋藏发生在缺氧河口和三角洲体系中。然而，对埋藏在沉积物中的有机质数量的最终控制，而不是被氧化成二氧化碳，受到的限制很少。在这项研究中，我们使用酶分析和元基因组分析相结合的方法来确定地下微生物群落如何催化蛋白质类有机碳降解的第一步。我们的结果表明，深层沉积物中的微生物群落适应了降解有机物特有的分子，这表明这些异养生物适应了地下的生活。
Burial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO2, are poorly constrained. In this study, we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface. ABSTRACT Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily low rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River Estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmax expressed on a per-cell basis was approximately the same at all depths. Half-saturation constants (Km) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (d-phenylalanine and l-ornithine) increased relative to enzymes that act on l-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded-DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes. IMPORTANCE Burial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO2, are poorly constrained. In this study, we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface.