A Global Survey of Mycobacterial Diversity in Soil

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.

16S and 23S rRNA Gene Mutation Independent Multidrug Resistance of Non-Tuberculous Mycobacteria Isolated from South Korean Soil

“…Additionally, M. kansasii and M. abscessus, which are frequently isolated from clinical samples, were not isolated. The distribution of NTM species can be affected by environmental factors such as nutrients, acidity and the aridity of soil [51]. In this context, the absence of several clinically relevant NTM species in the current study might be related to the characteristics of the soil samples and sampling sites.…”

“…Antibiotic resistance of NTM has been described in previous studies [54][55][56][57]. Several studies reported evidence of the transmission of NTM infection from environmental sources [51,58]. Therefore, the antibiotic resistance profile of NTM in environmental sources is key to establishing a treatment and control strategy for NTM infection.…”

Novel hydrocarbon-utilizing soil mycobacteria synthesize unique mycocerosic acids at a Sicilian everlasting fire

“…The assessment of soil bacterial diversity has mainly relied on 16S ribosomal RNA (rRNA) gene sequencing and has indicated that the most abundant bacterial phylotypes in global soils include Alphaproteobacteria, Gammaproteobac-teria, Betaproteobacteria, Actinobacteria, Acidobacteria and Planctomycetes (Fierer et al, 2012;Delgado-Baquerizo et al, 2018). Besides the use of DNA-based techniques, lipid biomarkers offer an additional tool to investigate soil bacterial communities, such as branched glycerol dialky glycerol tetraether (brGDGTs) believed to derive from soil acidobacteria (Weijers et al, 2009;Peterse et al, 2010;Sinninghe Damsté et al, 2018) or lipids derived from methanotrophic bacteria like certain fatty acids (Bull et al, 2000;Bodelier et al, 2009), specific bacteriohopanepolyols (van Winden et al, 2012;Talbot et al, 2016) or 13 C-depleted hopanoids (Inglis et al, 2019;van Winden et al, 2020).…”

Assessment of Soil Features on the Growth of Environmental Nontuberculous Mycobacterial Isolates from Hawai'i

“…The NTM species responsible for human lung infections are thought to be influenced by the specific environmental source exposures and the NTM species diversity within these environmental niches. While water-associated biofilms contain potentially disease-causing NTM, a variety of NTM species have also been discovered in soil (2)(3)(4). Prior studies have shown that potting soil can be a reservoir for clinically relevant mycobacteria (4).…”