Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils

Abstract

BackgroundMembers of the bacterial genus Arthrobacter are both readily cultured and commonly identified in Antarctic soil communities. Currently, relatively little is known about the physiological traits that allow these bacteria to survive in the harsh Antarctic soil environment. The aim of this study is to investigate if Antarctic strains of Arthrobacter owe their resilience to substantial genomic changes compared to Arthrobacter spp. isolated from temperate soil environments.ResultsQuantitative PCR-based analysis revealed that up to 4% of the soil bacterial communities were comprised of Arthrobacter spp. at four locations in the Ross Sea Region. Genome analysis of the seven Antarctic Arthrobacter isolates revealed several features that are commonly observed in psychrophilic/psychrotolerant bacteria. These include genes primarily associated with sigma factors, signal transduction pathways, the carotenoid biosynthesis pathway and genes induced by cold-shock, oxidative and osmotic stresses. However, these genes were also identified in genomes of seven temperate Arthrobacter spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. Phenotypic characterisation revealed that Antarctic Arthrobacter isolates demonstrate significantly lower metabolic versatility and a narrower salinity tolerance range compared to temperate Arthrobacter species. Comparative analyses also revealed fewer protein-coding sequences and a significant decrease in genes associated with transcription and carbohydrate transport and metabolism in four of the seven Antarctic Arthrobacter isolates. Notwithstanding genome incompleteness, these differences together with the decreased metabolic versatility are indicative of genome content scaling.ConclusionsThe genomes of the seven Antarctic Arthrobacter isolates contained several features that may be beneficial for growth and survival in the Antarctic soil environment, although these features were not unique to the Antarctic isolates. These genome sequences allow further investigations into the expression of physiological traits that enable survival under extreme conditions and, more importantly, into the ability of these bacteria to respond to future perturbations including climate change and human impacts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1220-2) contains supplementary material, which is available to authorized users.

Surviving in hot and cold: psychrophiles and thermophiles from Deception Island volcano, Antarctica

“…Pseudomonas and Flavobacterium were previously isolated from Deception samples associated with lakes and cold marine sediments (Stanley and Rose 1967;Carrión et al 2011). Arthrobacter, Psychrobacter, and Sphingomonas have been described in several Antarctic ecosystems, such as soils, marine sediments, and sea ice (e.g., Bowman et al 1997;Turkiewicz et al 1999;Reddy et al 2000;Prabagaran et al 2007;Baraniecki et al 2002;Dsouza et al 2015), showing their cosmopolitan nature in cold ecosystems. Culturable cells related to psychrophilic groups are poorly described in hot environments and the majority of studies have detected these microorganisms through culture-independent genomic methods, which do not allow us to know if they were in fact Kaur et al (2018) obtained sequences related to Arthrobacter from hot spring soil in India with temperatures from 50 to 90 °C through metagenomics.…”

A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7

“…Prokaryotic organisms that produce carotenoids have been summarized by Takano and colleagues [48]. However, since 2006 several carotenoid-producing bacterial species were discovered in cold environments [49]. Carotenoids are detected in the membrane of psychrophilic [49], psychrotrophic [27], and mesophilic [50] bacterial species.…”

“…However, since 2006 several carotenoid-producing bacterial species were discovered in cold environments [49]. Carotenoids are detected in the membrane of psychrophilic [49], psychrotrophic [27], and mesophilic [50] bacterial species. The high frequency of pigment production in strains isolated from cold environments suggests that these pigments play an important role in the adaptation to this ecological niche [51].…”

“…In addition, carotenoids protect free-living bacteria from high levels of UV radiation and promote resistance to cellular oxidative stress [49]. Several genes involved in carotenoid biosynthesis, such as idi , crtE , crtB , crtI , crtEB , crtYe , and crtYf , were described in bacterial species of the Arthrobacter genus isolated from Antarctic soils [49].…”

Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin, China

“…Recently, based on the intrageneric phylogeny and chemotaxonomic characteristics, the description of the genus Arthrobacter sensu lato was emended by Busse, and the genus Arthrobacter sensu stricto was restricted to A. globiformis , A. pascens , A. oryzae and A. humicola [2]. Due to their nutritional versatility and tolerance to various environmental stressors [3–7], Arthrobacter species are widely present in soils and the environments contaminated with chemicals and heavy metal [8–13], as well as extreme environments, such as Antarctic and radioactive sediments [14, 15]. …”