Centre for Integrative Biology, University of Trento, 38123, Trento, Italy.
Istituto G.B. Mattei, Stenico, Italy.
Microbiome. 2019 Jan 23;7(1):8. doi: 10.1186/s40168-019-0625-6.
Water springs provide important ecosystem services including drinking water supply, recreation, and balneotherapy, but their microbial communities remain largely unknown. In this study, we characterized the spring water microbiome of Comano Terme (Italy) at four sampling points of the thermal spa, including natural (spring and well) and human-built (storage tank, bathtubs) environments. We integrated large-scale culturing and metagenomic approaches, with the aim of comprehensively determining the spring water taxonomic composition and functional potential.
The groundwater feeding the spring hosted the most atypical microbiome, including many taxa known to be recalcitrant to cultivation. The core microbiome included the orders Sphingomonadales, Rhizobiales, and Caulobacterales, and the families Bradyrhizobiaceae and Moraxellaceae. A comparative genomic analysis of 72 isolates and 30 metagenome-assembled genomes (MAGs) revealed that most isolates and MAGs belonged to new species or higher taxonomic ranks widely distributed in the microbial tree of life. Average nucleotide identity (ANI) values calculated for each isolated or assembled genome showed that 10 genomes belonged to known bacterial species (> 95% ANI), 36 genomes (including 1 MAG) had ANI values ranging 85-92.5% and could be assigned as undescribed species belonging to known genera, while the remaining 55 genomes had lower ANI values (< 85%). A number of functional features were significantly over- or underrepresented in genomes derived from the four sampling sites. Functional specialization was found between sites, with for example methanogenesis being unique to groundwater whereas methanotrophy was found in all samples.
Current knowledge on aquatic microbiomes is essentially based on surface or human-associated environments. We started uncovering the spring water microbiome, highlighting an unexpected diversity that should be further investigated. This study confirms that groundwater environments host highly adapted, stable microbial communities composed of many unknown taxa, even among the culturable fraction.
泉水提供了重要的生态系统服务，包括饮用水供应、娱乐和水疗，但它们的微生物群落仍然知之甚少。在这项研究中，我们对意大利科马诺温泉浴场的泉水微生物组进行了研究，在温泉浴场的四个采样点进行了采样，包括自然（泉水和水井）和人工（储水罐、浴缸）环境。我们整合了大规模培养和宏基因组学方法，旨在全面确定泉水的分类组成和功能潜力。
为泉水提供地下水的地下水层拥有最典型的微生物群落，包括许多已知难以培养的类群。核心微生物群落包括鞘氨醇单胞菌目、根瘤菌目和柄杆菌目，以及布拉德氏菌科和莫拉氏菌科。对 72 株分离株和 30 个宏基因组组装基因组（MAG）的比较基因组分析表明，大多数分离株和 MAG 属于新的种或广泛分布在微生物生命之树中的更高分类等级。为每个分离或组装的基因组计算的平均核苷酸同一性（ANI）值表明，10 个基因组属于已知细菌种（>95%ANI），36 个基因组（包括 1 个 MAG）的 ANI 值在 85-92.5%之间，可以归类为属于已知属的未描述种，而其余 55 个基因组的 ANI 值较低（<85%）。四个采样点的基因组中存在大量显著过表达或低表达的功能特征。不同采样点之间存在功能特化，例如地下水特有的产甲烷作用，而所有样本中都存在甲烷氧化作用。
目前对水生微生物组的了解主要基于地表水或与人类相关的环境。我们开始揭示泉水微生物组，突出了意想不到的多样性，这应该进一步研究。本研究证实，地下水环境中存在由许多未知类群组成的高度适应、稳定的微生物群落，即使在可培养的部分中也是如此。
