Abstract
“Candidatus Micrarchaeota” are widely distributed in acidic environments; however, their cultivability and our understanding of their interactions with potential hosts are very limited. Their habitats were so far attributed with acidic sites, soils, peats, freshwater systems, and hypersaline mats. Using cultivation and culture-independent approaches (16S rRNA gene clonal libraries, high-throughput amplicon sequencing of V3-V4 region of 16S rRNA genes), we surveyed the occurrence of these archaea in geothermal areas on Kamchatka Peninsula and Kunashir Island and assessed their taxonomic diversity in relation with another type of low-pH environment, acid mine drainage stream (Wales, UK). We detected “Ca. Micrarchaeota” in thermophilic heterotrophic enrichment cultures of Kunashir and Kamchatka that appeared as two different phylotypes, namely “Ca. Mancarchaeum acidiphilum”-, and ARMAN-2-related, alongside their potential hosts, Cuniculiplasma spp. and other Thermoplasmatales archaea without defined taxonomic position. These clusters of “Ca. Micrarchaeota” together with three other groups were also present in mesophilic acid mine drainage community. Present work expands our knowledge on the diversity of “Ca. Micrarchaeota” in thermophilic and mesophilic acidic environments, suggests cultivability patterns of acidophilic archaea and establishes potential links between low-abundance species of thermophilic “Ca. Micrarchaeota” and certain Thermoplasmatales, such as Cuniculiplasma spp. in situ.
Highlights
Archaeal lineages represented in relatively low abundance in communities are still largely underexplored, which leaves many gaps in our knowledge regarding their distribution patterns, specific roles in the environment and interconnection with other community members
Among archaea in this particular variant, we identified sequences related to Acidiplasma aeolicum, 100% identity (35.8% reads) and sequences only distantly related to Acidiplasma aeolicum (81% identity), sequences of the last lineage were not detectable earlier by clonal libraries approach
We revealed the presence of “Ca. Micrarchaeota” in geothermal areas of Kunashir and Kamchatka
Summary
Archaeal lineages represented in relatively low abundance in communities are still largely underexplored, which leaves many gaps in our knowledge regarding their distribution patterns, specific roles in the environment and interconnection with other community members. One example of these organisms, often referred to as microbial “dark matter”, is a group of Archaeal Richmond Mine. “Ca. Micrarchaeota” were shown to cluster with “Ca. Diapherotrites” and “Ca. Parvarchaeota” to be associated with Nanoarchaeota [9]. Both groups are included into a tentative
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