A Global Survey of Mycobacterial Diversity in Soil
A Global Survey of Mycobacterial Diversity in Soil
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DOI：
10.1128/aem.01180-19
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发表时间：
2019-02
影响因子：
4.4
通讯作者：
Corinne M. Walsh;Matthew J. Gebert;M. Delgado‐Baquerizo;F. Maestre;N. Fierer
中科院分区：
文献类型：
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作者：
Corinne M. Walsh;Matthew J. Gebert;M. Delgado‐Baquerizo;F. Maestre;N. Fierer
分枝杆菌是土壤中的常见居民，虽然该细菌群的大多数成员都是无害的，但一些分枝杆菌可以引起人类和其他动物的环境获得性感染。人类非结核分枝杆菌 (NTM) 感染在全球范围内日益普遍，一些地区似乎是 NTM 疾病的“热点”。虽然接触土壤经常被认为是 NTM 传播的重要模式，但土壤分枝杆菌的多样性、分布和生态偏好仍然知之甚少。我们分析了来自一系列生态系统的 143 种土壤，发现该群体内的分枝杆菌和谱系通常表现出对特定环境条件的可预测偏好。土壤中含有大量以前未被描述的分枝杆菌多样性，并且在土壤中很少检测到包括已知病原体的谱系。总之，这些发现表明土壤不太可能是许多分枝杆菌感染的来源。我们记录的生物地理模式有助于深入了解这一重要的土壤栖息细菌的生态学。摘要 分枝杆菌是一种多样化的细菌群，普遍存在于许多土壤和水生环境中。该群体的成员与人类和其他动物疾病有关，包括非结核分枝杆菌 (NTM)，它们与全球公共卫生的关系日益密切。尽管土壤通常被认为是环境获得性 NTM 感染的重要来源，但在不同的气候和生态系统类型中，土壤分枝杆菌的生物多样性和生态偏好在很大程度上仍未得到探索。我们采用独立于培养物的方法，将 16S rRNA 标记基因测序与分枝杆菌特异性 hsp65 基因测序相结合，分析了从各种生态系统类型收集的 143 个土壤样本中土壤分枝杆菌的多样性、分布和环境偏好。调查的土壤含有高度多样化的分枝杆菌群落，涵盖了已知分枝杆菌系统发育的全部范围，大多数土壤分枝杆菌（97％的分枝杆菌进化枝）属于以前未描述的谱系。虽然分枝杆菌在凉爽、潮湿和酸性土壤环境中往往具有较高的相对丰度，但几个分枝杆菌分支具有不同的环境偏好。我们确定了许多分枝杆菌分支的环境偏好，包括临床相关的鸟分枝杆菌复合体，该复合体在潮湿和酸性土壤中更常见。然而，检测到的大多数土壤分枝杆菌与已知病原体并不密切相关，这对之前关于土壤作为 NTM 感染源的普遍重要性的假设提出了质疑。总之，这项工作为土壤分枝杆菌的多样性、分布和生态偏好提供了新的见解，并为未来将分枝杆菌表型与其分布联系起来奠定了基础。重要性 分枝杆菌是土壤中的常见居民，虽然该细菌群的大多数成员是无害的，但某些分枝杆菌可引起人类和其他动物的环境获得性感染。人类非结核分枝杆菌 (NTM) 感染在全球范围内日益普遍，一些地区似乎是 NTM 疾病的“热点”。虽然接触土壤经常被认为是 NTM 传播的重要模式，但土壤分枝杆菌的多样性、分布和生态偏好仍然知之甚少。我们分析了来自一系列生态系统的 143 种土壤，发现该群体内的分枝杆菌和谱系通常表现出对特定环境条件的可预测偏好。土壤中含有大量以前未被描述的分枝杆菌多样性，并且在土壤中很少检测到包括已知病原体的谱系。总之，这些发现表明土壤不太可能是许多分枝杆菌感染的来源。我们记录的生物地理模式有助于深入了解这一重要的土壤栖息细菌的生态学。
Mycobacteria are common inhabitants of soil, and while most members of this bacterial group are innocuous, some mycobacteria can cause environmentally acquired infections of humans and other animals. Human infections from nontuberculous mycobacteria (NTM) are increasingly prevalent worldwide, and some areas appear to be “hotspots” for NTM disease. While exposure to soil is frequently implicated as an important mode of NTM transmission, the diversity, distributions, and ecological preferences of soil mycobacteria remain poorly understood. We analyzed 143 soils from a range of ecosystems and found that mycobacteria and lineages within the group often exhibited predictable preferences for specific environmental conditions. Soils harbor large amounts of previously undescribed mycobacterial diversity, and lineages that include known pathogens were rarely detected in soil. Together, these findings suggest that soil is an unlikely source of many mycobacterial infections. The biogeographical patterns we documented lend insight into the ecology of this important group of soil-dwelling bacteria. ABSTRACT Mycobacteria are a diverse bacterial group ubiquitous in many soil and aquatic environments. Members of this group have been associated with human and other animal diseases, including the nontuberculous mycobacteria (NTM), which are of growing relevance to public health worldwide. Although soils are often considered an important source of environmentally acquired NTM infections, the biodiversity and ecological preferences of soil mycobacteria remain largely unexplored across contrasting climates and ecosystem types. Using a culture-independent approach by combining 16S rRNA marker gene sequencing with mycobacterium-specific hsp65 gene sequencing, we analyzed the diversity, distributions, and environmental preferences of soil-dwelling mycobacteria in 143 soil samples collected from a broad range of ecosystem types. The surveyed soils harbored highly diverse mycobacterial communities that span the full extent of the known mycobacterial phylogeny, with most soil mycobacteria (97% of mycobacterial clades) belonging to previously undescribed lineages. While mycobacteria tended to have higher relative abundances in cool, wet, and acidic soil environments, several individual mycobacterial clades had contrasting environmental preferences. We identified the environmental preferences of many mycobacterial clades, including the clinically relevant Mycobacterium avium complex that was more commonly detected in wet and acidic soils. However, most of the soil mycobacteria detected were not closely related to known pathogens, calling into question previous assumptions about the general importance of soil as a source of NTM infections. Together, this work provides novel insights into the diversity, distributions, and ecological preferences of soil mycobacteria and lays the foundation for future efforts to link mycobacterial phenotypes to their distributions. IMPORTANCE Mycobacteria are common inhabitants of soil, and while most members of this bacterial group are innocuous, some mycobacteria can cause environmentally acquired infections of humans and other animals. Human infections from nontuberculous mycobacteria (NTM) are increasingly prevalent worldwide, and some areas appear to be “hotspots” for NTM disease. While exposure to soil is frequently implicated as an important mode of NTM transmission, the diversity, distributions, and ecological preferences of soil mycobacteria remain poorly understood. We analyzed 143 soils from a range of ecosystems and found that mycobacteria and lineages within the group often exhibited predictable preferences for specific environmental conditions. Soils harbor large amounts of previously undescribed mycobacterial diversity, and lineages that include known pathogens were rarely detected in soil. Together, these findings suggest that soil is an unlikely source of many mycobacterial infections. The biogeographical patterns we documented lend insight into the ecology of this important group of soil-dwelling bacteria.