Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose

Vandera, Elpiniki; Samiotaki, Martina; Parapouli, Maria; Panayotou, George; Koukkou, Anna‐Irini

doi:10.1016/j.jprot.2014.08.018

Cited by 70 publications

(45 citation statements)

References 77 publications

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“…This lack of transcriptional induction also suggests that rhizodeposits did not trigger a massive carbon catabolite repression (CCR), which would expectedly yield lower transcription of PAH-RHD genes in planted soil. Purified sugars and root extracts have been shown to inhibit the degradation of aromatic compounds by CCR in several cultivated isolates (Keuth and Rehm, 1991 ; Dal et al, 2002 ; Kamath et al, 2004 ; Rentz et al, 2004 ; Rojo, 2010 ; Zhang and Anderson, 2013 ; Vandera et al, 2015 ). However, it has been suggested that CCR may be more significant when considering a single species of degrader rather than a diverse community (Martin et al, 2014 ).…”

Section: Discussionmentioning

confidence: 99%

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil

Thomas

Cébron

2016

Front. Microbiol.

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Over the last decades, understanding of the effects of plants on soil microbiomes has greatly advanced. However, knowledge on the assembly of rhizospheric communities in aged-contaminated industrial soils is still limited, especially with regard to transcriptionally active microbiomes and their link to the quality or quantity of carbon sources. We compared the short-term (2–10 days) dynamics of bacterial communities and potential PAH-degrading bacteria in bare or ryegrass-planted aged-contaminated soil spiked with phenanthrene, put in relation with dissolved organic carbon (DOC) sources and polycyclic aromatic hydrocarbon (PAH) pollution. Both resident and active bacterial communities (analyzed from DNA and RNA, respectively) showed higher species richness and smaller dispersion between replicates in planted soils. Root development strongly favored the activity of Pseudomonadales within the first 2 days, and of members of Actinobacteria, Caulobacterales, Rhizobiales, and Xanthomonadales within 6–10 days. Plants slowed down the dissipation of phenanthrene, while root exudation provided a cocktail of labile substrates that might preferentially fuel microbial growth. Although the abundance of PAH-degrading genes increased in planted soil, their transcription level stayed similar to bare soil. In addition, network analysis revealed that plants induced an early shift in the identity of potential phenanthrene degraders, which might influence PAH dissipation on the long-term.

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Section: Discussionmentioning

confidence: 99%

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil

Thomas

Cébron

2016

Front. Microbiol.

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“…However, a large proportion of these genes were also identified in temperate Arthrobacter spp., suggesting that these genes may be important for growth and survival in a range of soil habitats. Further investigations by transcriptomic- and proteomic-based techniques, as previously reported for A. chlorophenolicus [ 70 , 71 ] and A. phenanthrenivorans [ 72 ], are essential to reveal the expression profiles of these genes as well as identify novel traits or genes that are crucial for cold adaptation.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2015

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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.

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“…Members of the genus Arthrobacter have been associated with the degradation of compounds, such as 4-chlorophenol ( 1 ), polychlorinated biphenyls ( 2 , 3 ), pentachloronitrobenzene, ( 4 ), 2-nitrobenzoate ( 5 ), atrazine ( 6 ), 2,4-dinitrotoluene ( 7 ), para -nitrophenol ( 8 ), 4-bromophenol ( 9 ), phenanthrene, and phthalates ( 10 , 11 ). Genome sequence data indicate that several strains of Arthrobacter are capable of degrading aromatic compounds, including Arthrobacter sp.…”

Section: Genome Announcementmentioning

confidence: 99%

Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium

et al. 2015

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Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose

Cited by 70 publications

References 77 publications

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil

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

Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium

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