High‐quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep‐branching lineages of the phylum Actinobacteria

Abstract

Gaiella occulta strain F2‐233T (=CECT 7815 = LMG 26412), isolated from a 150 meter deep mineral water aquifer, was deemed a candidate for high‐quality draft genome sequencing because of the rare environment from which it was isolated. The draft genome sequence (QQZY00000000) of strain F2‐233T is composed of approximately 3 Mb, predicted 3,119 protein‐coding genes of which 2,545 were assigned putative functions. Genome analysis was done by comparison with the other deep‐branching Actinobacteria neighbors Rubrobacter radiotolerans, Solirubrobacter soli and Thermoleophilum album. The genes for the tricarboxylic acid cycle, gluconeogenesis and pentose phosphate pathway, were identified in G. occulta, R. radiotolerans, S. soli and T. album genomes. Genes of the Embden–Meyerhof–Parnas pathway and nitrate reduction were identified in G. occulta, R. radiotolerans and S. soli, but not in the T. album genome. Alkane degradation is precluded by genome analysis in G. occulta. Genes involved in myo‐inositol metabolism were found in both S. soli and G. occulta genomes. A Calvin–Benson–Bassham (CBB) cycle with a type I RuBisCO was identified in G. occulta genome, as well. However, experimental growth under several conditions was negative and CO2 fixation could not be proven in G. occulta.

The Composition and Assembly of Bacterial Communities across the Rhizosphere and Phyllosphere Compartments of Phragmites Australis

“…Their findings are consistent with our speculation, indicating that Lactococcus is enriched in phyllosphere for the purpose of helping plants resist such adverse external factors [73]. Gaiella (Actinobacteria) can carry out nitrate reduction, helping plants to assimilate carbohydrates, organic acids, and amino acids [74][75][76] ( Figure S3), so it accumulates in the rhizosphere to support the plant's ability to absorb nutrients from soil. In addition, Halomonas (Gammaproteobacteria) was reported to be a kind of halophilic (salt-tolerating) bacteria growing in the range of 5-25% salinity [77].…”

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

“…Rokubacteriales belongs to Candidatus Rokubacteria , whose genomes are large, with high G+C content and the potential for nitrogen respiration (Becraft et al, 2017). Gaiellales is a deep-branching lineage of Actinobacteria , and its metabolic potential is only represented by a single cultured species, Gaiella occulta ; it is predicted to reduce nitrate and to perform CO 2 fixation (Severino et al, 2019). Members of Gaiellales were also found in other subterranean environment such as volcanic caves (Riquelme et al, 2015), supporting their general existence in dark cave systems.…”

Microbial Communities in Vermiculation Deposits from an Alpine Cave

“…Distinctive characteristics are the presence of internally branched iso-fatty acids found in no other bacterium and the utilization of organic compounds (Albuquerque et al, 2011). The genome was studied by Severino et al (2019) identifying genes of nitrate reduction. This genus was also found in volcanic caves (Riquelme et al, 2015a;Gonzalez-Pimentel et al, 2018).…”