Adaptation, Ecology, and Evolution of the Halophilic Stromatolite ArchaeonHalococcus hamelinensisInferred through Genome Analyses

Abstract

Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia

“…Another pronounced difference within the non-lithifying mats compared to the stromatolite-forming mat types in Spaven Province was the enrichment of oxidative (e.g., nitric oxide reductases, peroxidases) and osmotic stress (e.g., glycine betaine/proline synthesis and transport) genes in the upper tidal non-lithifying mats, whereas genes typically associated with UV stress were found to be evenly represented in all of the different mat types examined. The enriched oxidative and osmotic stress genes in the non-lithifying mats corresponded to several of observed osmoadaptive genes and pathways recovered from hypersaline mat environments, including Hamelin Pool ( Goh et al, 2010 ; Goh et al, 2011 ; Gudhka et al, 2015 ; Gunde-Cimerman et al, 2018 ). As there is a pronounced desiccation gradient within the pool ( Burne and Johnson, 2012 ; Suosaari et al, 2016b ), the enrichment of genes associated with the production of osmoregulation and oxidative stress responses in the non-lithifying mats likely reflects the dynamic tidal extremes within the pool.…”

Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

“…The abundance of these genes might play a role in bacterial adaptations to the low temperature, high pressure, oligotrophic, saline and dark marine environment by ensuring protein synthesis and maintaining protein functional stability. The overrepresentation of COG category J was also observed in the genome of the halophilic archaeon Halococcus hamelinensis ( Gudhka et al, 2015 ). The abundance of COG category O was also consistent with previous research ( Kuwahara et al, 2007 ; Wang et al, 2008 ).…”

Patterns of metal distribution in hypersaline microbialites during early diagenesis: Implications for the fossil record

“…Many micro‐organisms use As(V) as electron acceptor for respiration or As(III) as donor for energy conserving systems (e.g., Oremland & Stolz, , ; Stolz et al., ; Van Lis, Nitschke, Duval, & Schoepp‐Cothenet, ). The organisms thriving on these bioenergetic pathways are not confined to polluted environments (Stolz et al., ), but can be found in a wide range of settings, notably in hypersaline environments such as Mono Lake, (California, Oremland et al., ), Searless Lake (California, Kulp et al., ), Laguna Socompa (Argentina, Farías et al., ), and Shark Bay (Gudhka, Neilan, & Burns, ). Both the detoxification mechanism and the bioenergetic pathway alter the redox state of arsenic oxyanions, influencing the As mobility.…”