Degraded concrete road bridge metagenome. concrete metagenome

Surveys of microbial life in and on concrete have thus far relied on 16S amplicon sequencing or cultured organisms, biasing understanding of these communities toward previously characterized and more readily cultured microbes, while leaving functional and metabolic questions unanswered. Metagenomic analysis can resolve these biases and provide greater taxonomic resolution, as well as functional profiles. We improved DNA extraction from a sample of concrete obtained from a road bridge, and show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing. The microbial community was dominated by halophilic bacteria and archaea, with enriched functional pathways related to osmotic stress responses. Prior work found that halophilic bacteria were relatively rare in younger concrete samples, which had abundant oligotrophic taxa. This work suggests that as concrete ages and weathers, nutrient limitation may be alleviated, but salt and/or osmotic stress may become a more important selective pressure.

迄今为止，针对混凝土内部及表面微生物群落的调查研究，多依赖16S扩增子测序（16S amplicon sequencing）或纯培养菌株，这使得学界对这类群落的认知偏向于已被表征且更易培养的微生物类群，同时遗留了诸多功能与代谢层面的未解问题。宏基因组学分析（Metagenomic analysis）可规避此类偏差，同时提供更精细的分类学分辨率与功能谱信息。本研究针对从公路桥梁获取的混凝土样本优化了DNA提取流程，结果表明该方法可获得质量与浓度均满足鸟枪法宏基因组测序（shotgun metagenomic sequencing）要求的DNA。该混凝土样本的微生物群落以嗜盐细菌与古菌（archaea）为优势类群，且富集了与渗透应激响应相关的功能通路。已有研究表明，在较新的混凝土样本中嗜盐细菌相对罕见，这类样本中富含贫营养类群。本研究结果提示，随着混凝土的老化与风化，其营养限制状况或得到缓解，但盐胁迫与/或渗透应激可能成为更关键的选择压力。