Niche Filtering of Bacteria in Soil and Rock Habitats of the Colorado Plateau Desert, Utah, USA

Abstract

A common feature of microbial colonization in deserts is biological soil crusts (BSCs), and these comprise a complex community dominated by Cyanobacteria. Rock substrates, particularly sandstone, are also colonized by microbial communities. These are separated by bare sandy soil that also supports microbial colonization. Here we report a high-throughput sequencing study of BSC and cryptoendolith plus adjacent bare soil communities in the Colorado Plateau Desert, Utah, USA. Bare soils supported a community with low levels of recoverable DNA and high evenness, whilst BSC yielded relatively high recoverable DNA, and reduced evenness compared to bare soil due to specialized crust taxa. The cryptoendolithic community displayed the greatest evenness but the lowest diversity, reflecting the highly specialized nature of these communities. A strong substrate-dependent pattern of community assembly was observed, and in particular cyanobacterial taxa were distinct. Soils were virtually devoid of photoautotrophic signatures, BSC was dominated by a closely related group of Microcoleus/Phormidium taxa, whilst cryptoendolithic colonization in sandstone supported almost exclusively a single genus, Chroococcidiopsis. We interpret this as strong evidence for niche filtering of taxa in communities. Local inter-niche recruitment of photoautotrophs may therefore be limited and so communities likely depend significantly on cyanobacterial recruitment from distant sources of similar substrate. We discuss the implication of this finding in terms of conservation and management of desert microbiota.

Core bacterial community composition of a cryptoendolithic ecosystem in the Grand Staircase‐Escalante National Monument, Utah

“…The sequencing data affirm that Cyanobacteria is the dominant phylum in cryptoendolithic habitats (Hammes et al, 2013;Kurtz & Netoff, 2001;Kurtz et al, 2005;Lee et al, 2016). Previous studies have reported Chroococcidiopsis to be the predominant cyanobacteria observed in arid lithic systems based on morphological characterization (Bell, 1993;Bhatnagar & Bhatnagar, 2005;Büdel & Wessels, 1991;Casamatta et al, 2002;Friedmann, 1980;Pointing & Belnap, 2012;Wessels & Büdel, 1995).…”

“…In comparison with the community structure of local desert soils, we find that the overall structure is comparable, with Cyanobacteria and Proteobacteria numbers being higher on a relative basis (Garcia-Pichel, Johnson, Youngkin, & Belnap, 2003;Garcia-Pichel, Lopez-Cortes, & Nubel, 2001;Lee et al, 2016). However, we also note that while the structure is similar, the presence of certain phyla such as the Acidobacteria, Verrucomicrobia, and Planctomycetes is more pronounced in the soil environments (Gundlapally & Garcia-Pichel, 2006;Nagy, Pérez, & Garcia-Pichel, 2005).…”

“…Comparing these communities to other desert communities, we see that with only a few exceptions, namely the Negev Desert and the Atacama Desert (Bell, ; Connon, Lester, Shafaat, Obenhuber, & Ponce, ; Crits‐Christoph et al., ; Friedmann, Lipkin, & Ocampo‐Paus, ; Wierzchos et al., ), the microbial diversity is quite similar (Antony et al., ; Bell, Athey, & Sommerfeld, ; de la Torre et al., ; Friedmann, ; Lacap‐Bugler et al., ). In comparison with the community structure of local desert soils, we find that the overall structure is comparable, with Cyanobacteria and Proteobacteria numbers being higher on a relative basis (Garcia‐Pichel, Johnson, Youngkin, & Belnap, ; Garcia‐Pichel, Lopez‐Cortes, & Nubel, ; Lee et al., ). However, we also note that while the structure is similar, the presence of certain phyla such as the Acidobacteria, Verrucomicrobia, and Planctomycetes is more pronounced in the soil environments (Gundlapally & Garcia‐Pichel, ; Nagy, Pérez, & Garcia‐Pichel, ).…”

Fundamental drivers for endolithic microbial community assemblies in the hyperarid Atacama Desert

“…This partitioning at the OTU phylogenetic level was not recapitulated at higher taxonomic ranks suggesting differential adaptation of close relatives to the substrate's physical and chemical properties. Substrate‐dependent patterns of community structure have been reported for hypolithic quartz and endolithic sandstone communities from the Dry Valleys, Antarctica (Pointing et al ., ) and for sandstone communities from the Colorado Plateau, USA (Lee et al ., ). In all cases, while the hypolithic communities were recruited from the surrounding soils, habitat filtering shaped the assembly of the rock communities (Pointing et al ., ; Makhalanyane et al ., ; Lee et al ., ).…”

“…Substrate‐dependent patterns of community structure have been reported for hypolithic quartz and endolithic sandstone communities from the Dry Valleys, Antarctica (Pointing et al ., ) and for sandstone communities from the Colorado Plateau, USA (Lee et al ., ). In all cases, while the hypolithic communities were recruited from the surrounding soils, habitat filtering shaped the assembly of the rock communities (Pointing et al ., ; Makhalanyane et al ., ; Lee et al ., ). Community assembly controlled by the substrate was also observed for the hypolithic colonization of meteorites found in Nullarbor Plain, Australia (Tait et al ., ).…”