Department of Biological Sciences, University of Delaware, Newark, Delaware, USA.
Sequencing and Genotyping Center, University of Delaware, Newark, Delaware, USA.
Microbiol Spectr. 2023 Aug 17;11(4):e0511222. doi: 10.1128/spectrum.05112-22. Epub 2023 Jul 5.
Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.
混凝土中存在着一个小型但多样化的微生物群落，且其随时间而变化。宏基因组测序技术能够评估混凝土中微生物群落的多样性和功能，但混凝土样本存在一些独特的挑战，使得这一技术难以实施。混凝土中二价阳离子的浓度很高，会干扰核酸提取，而混凝土中的生物量极低，这意味着来自实验室污染的 DNA 可能会占据序列数据的很大一部分。在这里，我们开发了一种从混凝土中提取 DNA 的改良方法，该方法具有更高的产量和更低的实验室污染。为了表明该方法能够提供足够质量和数量的 DNA 用于宏基因组测序，我们从一座公路桥的混凝土样本中提取了 DNA，并使用 Illumina MiSeq 系统进行了测序。该微生物群落主要由嗜盐细菌和古菌组成，富含与渗透胁迫反应相关的功能途径。尽管这是一项小规模的尝试，但我们证明了宏基因组测序可用于描述混凝土中的微生物群落，并且较旧的混凝土结构可能比最近浇筑的混凝土具有不同的微生物。 之前关于混凝土微生物群落的研究主要集中在混凝土结构的表面，如污水管或桥桩，在这些地方容易观察到和采样厚生物膜。由于混凝土内部的生物量很低，最近对混凝土内部微生物群落的分析使用了扩增子测序方法来描述这些群落。然而，为了了解混凝土中微生物的活性和生理学，或者开发具有生命力的基础设施，我们必须开发更直接的群落分析方法。这里开发的用于 DNA 提取和宏基因组测序的方法可用于分析混凝土中的微生物群落，并且可能适用于其他胶凝材料。
