Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia; Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia.
Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia.
Sci Total Environ. 2021 Aug 10;781:146526. doi: 10.1016/j.scitotenv.2021.146526. Epub 2021 Mar 18.
Traditional environmental monitoring techniques are well suited to resolving acute exposure effects but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s). Surveillance with sensitive omics-based technologies could bridge this gap but, to date, most omics-based environmental studies have focused on previously degraded environments, identifying key metabolic differences resulting from anthropogenic perturbations. Here, we apply omics-based approaches to pristine environments to establish blueprints of microbial functionality within healthy estuarine sediment communities. We collected surface sediments (n = 50) from four pristine estuaries along the Western Cape York Peninsula of Far North Queensland, Australia. Sediment microbiomes were analyzed for 16S rRNA amplicon sequences, central carbon metabolism metabolites and associated secondary metabolites via targeted and untargeted metabolic profiling methods. Multivariate statistical analyses indicated heterogeneity among all the sampled estuaries, however, taxa-function relationships could be established that predicted community metabolism potential. Twenty-four correlated gene-metabolite pathways were identified and used to establish sediment microbial blueprints of essential carbon metabolism and amino acid biosynthesis that were positively correlated with community metabolic function outputs (2-oxisocapraote, tryptophan, histidine citrulline and succinic acid). In addition, an increase in the 125 KEGG genes related to metal homeostasis and metal resistance was observed, although, none of the detected metabolites related to these specific genes upon integration. However, there was a correlation between metal abundance and functional genes related to Fe and Zn metabolism. Our results establish a baseline microbial blueprint for the pristine sediment microbiome, one that drives important ecosystem services and to which future ecosurveillance monitoring can be compared.
传统的环境监测技术非常适合解决急性暴露效应，但在确定慢性暴露导致的生态系统功能微妙变化方面缺乏分辨率。基于敏感组学技术的监测可以弥补这一差距，但迄今为止，大多数基于组学的环境研究都集中在以前退化的环境中，确定了人为干扰导致的关键代谢差异。在这里，我们将基于组学的方法应用于原始环境，以建立健康港湾沉积物群落中微生物功能的蓝图。我们从澳大利亚远北昆士兰州约克角半岛西部的四个原始河口采集了表层沉积物（n = 50）。通过靶向和非靶向代谢谱分析方法，对沉积物微生物组进行了 16S rRNA 扩增子序列、中心碳代谢代谢物和相关次生代谢物的分析。多元统计分析表明，所有采样的河口都存在异质性，但可以建立与群落代谢潜力相关的分类群-功能关系。确定了 24 个相关的基因-代谢物途径，并用于建立与群落代谢功能输出呈正相关的基本碳代谢和氨基酸生物合成的沉积物微生物蓝图（2-氧代异己酸、色氨酸、组氨酸瓜氨酸和琥珀酸）。此外，还观察到与金属稳态和金属抗性相关的 125 个 KEGG 基因增加，尽管在整合后，没有检测到与这些特定基因相关的代谢物。然而，金属丰度与与 Fe 和 Zn 代谢相关的功能基因之间存在相关性。我们的研究结果为原始沉积物微生物组建立了一个基线微生物蓝图，这是一个推动重要生态系统服务的蓝图，未来的生态监测可以与之进行比较。
