BACKGROUND Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial communities, particularly those colonizing host surfaces, can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. For a proof-of-concept, we studied a model plant-soil system and employed a non-deterministic gene-centric approach. A holistic analysis was performed using plants of two species and irrigation with water of low quality to induce host stress. Our analyses examined the genetic potential (DNA) and gene expression patterns (RNA) of plant-associated microbial communities, as well as transcriptional profiling of host plants. RESULTS Transcriptional analysis of plants irrigated with treated wastewater revealed significant enrichment of general stress-associated root transcripts relative to plants irrigated with fresh water. Metagenomic analysis of root-associated microbial communities in treated wastewater-irrigated plants, however, revealed enrichment of more specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Meta-analysis of these differentially abundant genes obtained from other metagenome studies, provided evidence of the link between environmental factors such as pH and oxygen and these genes. Analysis of microbial transcriptional response demonstrated that enriched gene content was actively expressed, which implies contemporary response to elevated levels of pH and salt. CONCLUSIONS We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms. This study is a proof-of-concept for the use of microbial communities as microsensors, with great potential for interrogation of a wide range of host systems. Video Abstract.

中文翻译：

---

微生物组作为生物传感器：功能概况阐明了宿主中隐藏的压力。

背景技术微生物群落对环境线索具有高度的响应，并且其微生物的结构和活性都可以响应于变化的条件而改变。我们假设与宿主相关的微生物群落，尤其是那些定殖在宿主表面的微生物群落，可以作为原位传感器来揭示微生物和宿主都经历的环境条件。为了进行概念验证，我们研究了植物-土壤模型系统，并采用了非确定性的以基因为中心的方法。使用两种物种的植物进行整体分析，并用劣质水灌溉以诱导宿主胁迫。我们的分析检查了植物相关微生物群落的遗传潜能（DNA）和基因表达模式（RNA），以及宿主植物的转录谱。结果对用处理过的废水灌溉的植物进行的转录分析表明，与用淡水灌溉的植物相比，与胁迫相关的根系转录本显着丰富。但是，经过处理的废水灌溉植物中与根相关的微生物群落的元基因组学分析显示，与高盐，高pH和低氧有关的与胁迫相关的基因更加丰富。对从其他元基因组研究中获得的这些差异丰富的基因进行的荟萃分析提供了环境因素（例如pH和氧气）与这些基因之间联系的证据。微生物转录反应的分析表明，活跃表达了丰富的基因含量，这意味着当代对pH和盐浓度升高的反应。结论我们在此证明，微生物谱分析可以阐明即使通过询问宿主转录组也无法观察到的应激信号，从而导致了评估宿主生物体原位条件的另一种机制。这项研究是使用微生物群落作为微传感器的概念证明，具有探究各种宿主系统的巨大潜力。录像摘要。