University of Tennessee, Knoxville, Tennessee, USA
University of Tennessee, Knoxville, Tennessee, USA.
Appl Environ Microbiol. 2020 Sep 17;86(19). doi: 10.1128/AEM.00877-20.
Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily metabolized organic compounds and total microbial cell abundance decrease. However, it is unknown whether some microbial clades increase with depth. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often associated with one or more of the following: anaerobes, uncultured, or common in deep marine sediments relative to those that decreased. Maximum doubling times ( steady-state growth rates could be faster to balance cell decay) were estimated as 2 to 25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the fraction read abundance of 16S rRNA genes and total cell counts (FRAxC). Doubling times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28% ± 19%). qPCR and FRAxC in sediment cores and laboratory enrichments produced similar doubling times for key deep subsurface uncultured clades (8.7 ± 1.9 years) and /MBG-D (4.1 ± 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for selection of long-term subsistence traits after resuspension events. Many studies show that the uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments; rather, they exist in a sort of prolonged torpor for thousands of years. This is because, although studies have shown biomass turnover in these clades, no evidence has ever been found that deeper sediments have larger populations for specific clades than shallower layers. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This suggests that marine sediments may be a vast repository of mostly nongrowing microbes with a thin and relatively rapid area of cell abundance increase in the upper 10 cm, offering a chance for subsurface organisms to undergo natural selection.
全球海洋沉积物中蕴藏着一个庞大而高度多样化的微生物区系，但在沉积物埋藏过程中这个区系是如何建立的，在很大程度上还不清楚。在海洋沉积物埋藏过程中，易代谢有机化合物的浓度和总微生物细胞丰度会降低。然而，目前还不清楚某些微生物类群是否会随深度增加。我们发现，在白橡河（WOR）河口沉积物上层 7.5 厘米内的 3 厘米深的沉积物中，38 个微生物家族的总种群数量增加。随着深度增加的类群与以下一个或多个因素更为相关：厌氧菌、未培养菌或在深海沉积物中比减少的类群更为常见。通过将沉降速率与定量 PCR（qPCR）或 16S rRNA 基因和总细胞计数的分数读取丰度的乘积（FRAxC）相结合，估计最大倍增时间（稳态生长速率可能更快以平衡细胞衰减）为 2 至 25 年。在两个相邻的岩芯中，以及在北卡罗来纳州海角光滩（CLB）沉积物的两个实验室富集物中，倍增时间彼此相差一个数量级（平均差异为 28%±19%）。qPCR 和 FRAxC 在沉积物岩芯和实验室富集物中为关键的深地下未培养类群（8.7±1.9 年）和/MBG-D（4.1±0.7 年）产生了相似的倍增时间。我们的结论是，常见的深地下微生物类群在浅层沉积物中经历了一个狭窄的生长带，为重新悬浮事件后长期生存特征的选择提供了机会。许多研究表明，在海洋沉积物中占主导地位的未培养微生物实际上并没有随着它们在海洋沉积物中的埋藏而增加种群规模；相反，它们在几千年的时间里处于一种延长的休眠状态。这是因为，尽管研究表明这些类群的生物量发生了周转，但从未有证据表明深层沉积物中特定类群的种群比浅层沉积物更大。我们发现，它们实际上在埋藏过程中确实增加了种群规模，但仅在最上面的几厘米。这表明海洋沉积物可能是一个巨大的储存库，其中大部分是非生长微生物，在 10 厘米的上层有一个相对较薄且快速的细胞丰度增加区域，为地下生物提供了自然选择的机会。
