Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons
Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons
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DOI：
10.1128/mbio.01318-19
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发表时间：
2019-09-01
期刊：
影响因子：
6.4
通讯作者：
Fierer, Noah
中科院分区：
文献类型：
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作者：
Brewer, Tess E.;Aronson, Emma L.;Fierer, Noah
虽然大多数生活在表层土壤中的细菌和古生菌分类群仍未被描述，但由于在地下发现的独特的寡营养条件，这个问题在更深的土壤中加剧。此外，以前对土壤微生物群落的研究几乎完全集中在表层土壤上，尽管生活在深层土壤中的微生物在广泛的生物地球化学过程中也发挥着关键作用。我们研究了从美国各地20个不同剖面收集的土壤，以表征生活在地下土壤中的细菌和古生菌群落，并确定在广泛的土壤和环境条件下，土壤微生物群落是否随深度发生一致的变化。我们发现，细菌和古生物的多样性通常随着深度的增加而减少，微生物群落与表层发现的微生物群落的相似程度也是如此。我们观察到五个门的相对丰度在我们的土壤剖面上随着深度的增加而持续增加：Chloroflei，Nitrosprae，Eurya chaeota，以及候选的GAL15门和Dormiblicaeota(以前的AD3)。利用多米细菌门在深处异常高的丰度，我们组装了代表这一候选门的基因组，并确定了可能在低营养环境中有益的特征，包括碳水化合物的合成和储存，使用一氧化碳(CO)作为补充能源的可能性，以及形成孢子的能力。综合起来，这些属性很可能允许候选的多米细菌门的成员在更深的土壤中茁壮成长，并为在营养稀少的土壤环境中茁壮成长的微生物所采用的生存和生长策略提供了洞察。资源可获得性和微生物丰度通常随着土壤深度的增加而减少，但在更深层次发现的微生物仍然是陆地生态系统的重要组成部分。通过研究美国各地的20个土壤剖面，我们记录了土壤细菌和古生物群落随深度的持续变化。更深的土壤蕴藏着不同于更常被研究的表层的群落。最值得注意的是，我们发现候选的多米细菌门(以前的AD3)经常在地下土壤中占优势，我们使用了这一组中未被耕种的成员的基因组来确定为什么这些类群能够在资源有限的环境中茁壮成长。只要更深入地挖掘土壤，就可以发现数量惊人的新微生物，它们对营养不足的地下条件具有独特的适应能力。
While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.