Complete genome sequence of Halorhodospira halophila SL1

Challacombe, Jean F.; Majid, Sophia; Deole, Ratnakar; Brettin, Thomas; Bruce, David; Delano, Susana F.; Detter, John C.; Gleasner, Cheryl D.; Han, Cliff; Misra, Monica; Reitenga, Krista G.; Mikhailova, Natalia; Woyke, Tanja; Pitluck, Sam; Nolan, Matt; Land, Miriam; Saunders, Elizabeth; Tapia, Roxanne; Lapidus, Alla; Ivanova, Natalia; Hoff, Wouter D.

doi:10.4056/sigs.3677284

Cited by 24 publications

(15 citation statements)

References 34 publications

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“…salexigens has been shown to have one of the widest salinity ranges for growth found in nature, and it is known for its ability to cope with thermal stress via transcriptional regulation [ 46 – 49 ]. Our results also indicate the presence of Spiribacter Salinus (7,132 reads), a newly named aerobic, heterotrophic, halophilic Gammaproteobacteria unable to grow in the absence of NaCl [ 50 ], as well as Halorhodospira halophila (3,032 reads), a recently reclassified halophilic purple bacterium, also within the family Ectothiorhodospiraceae and also known to oxidize sulfide to sulfur, which is deposited outside the cell via metabolic pathways that are not yet fully resolved [ 51 , 52 ]. While other Ectothiorhodospiraceae have been found in acidic conditions (including Acidiferrobacter thiooxidans , previously known as Thiobacillus ferrooxidans , an acidophilic iron-oxidizing bacterium first described 25 years ago [ 53 ]), our data suggests that that capacity for acid tolerance may also be held among these recently reclassified organisms, though it is not possible to entirely rule out inputs to the metagenome from the surrounding sandflats, soils, and dunes.…”

Section: Resultsmentioning

confidence: 83%

Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment

et al. 2015

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The extremely acidic brine lakes of the Yilgarn Craton of Western Australia are home to some of the most biologically challenging waters on Earth. In this study, we employed metagenomic shotgun sequencing to generate a microbial profile of the depositional environment associated with the sulfur-rich sediments of one such lake. Of the 1.5 M high-quality reads generated, 0.25 M were mapped to protein features, which in turn provide new insights into the metabolic function of this community. In particular, 45 diverse genes associated with sulfur metabolism were identified, the majority of which were linked to either the conversion of sulfate to adenylylsulfate and the subsequent production of sulfide from sulfite or the oxidation of sulfide, elemental sulfur, and thiosulfate via the sulfur oxidation (Sox) system. This is the first metagenomic study of an acidic, hypersaline depositional environment, and we present evidence for a surprisingly high level of microbial diversity. Our findings also illuminate the possibility that we may be meaningfully underestimating the effects of biology on the chemistry of these sulfur-rich sediments, thereby influencing our understanding of past geobiological conditions that may have been present on Earth as well as early Mars.

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Section: Resultsmentioning

confidence: 83%

Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment

et al. 2015

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“… 2011 ; Challacombe et al. 2013 ). The ability of these organisms to overcome nitrogen limitation through fixation, and to respire anaerobically in anoxic soils, may make this group well suited to harsh forefield environments.…”

Section: Resultsmentioning

confidence: 99%

Metagenomic insights into diazotrophic communities across Arctic glacier forefields

Nash

Anesio

Barker

et al. 2018

FEMS Microbiology Ecology

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Microbial nitrogen fixation is crucial for building labile nitrogen stocks and facilitating higher plant colonisation in oligotrophic glacier forefield soils. Here, the diazotrophic bacterial community structure across four Arctic glacier forefields was investigated using metagenomic analysis. In total, 70 soil metagenomes were used for taxonomic interpretation based on 185 nitrogenase (nif) sequences, extracted from assembled contigs. The low number of recovered genes highlights the need for deeper sequencing in some diverse samples, to uncover the complete microbial populations. A key group of forefield diazotrophs, found throughout the forefields, was identified using a nifH phylogeny, associated with nifH Cluster I and III. Sequences related most closely to groups including Alphaproteobacteria, Betaproteobacteria, Cyanobacteria and Firmicutes. Using multiple nif genes in a Last Common Ancestor analysis revealed a diverse range of diazotrophs across the forefields. Key organisms identified across the forefields included Nostoc, Geobacter, Polaromonas and Frankia. Nitrogen fixers that are symbiotic with plants were also identified, through the presence of root associated diazotrophs, which fix nitrogen in return for reduced carbon. Additional nitrogen fixers identified in forefield soils were metabolically diverse, including fermentative and sulphur cycling bacteria, halophiles and anaerobes.

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“…aand b-Proteobacteria were represented in 18 of the 29 MtrB homologs lacking an N-terminal CXXC motif, including the MtrB homologs of the Fe(II)oxidizing b-proteobacteria Dechloromonas aromatica, Gallionella capsiferriformans, and Sideroxydans lithotrophicus (Emerson & Moyer, 1997;Chakraborty et al, 2005;Hedrich et al, 2011). CXXC motifs were also missing from the N-terminus of PioB, the MtrB homolog of the Fe(II)-oxidizing a-proteobacterium Rhodopseudomonas palustris (Jiao & Newman, 2007), and from the MtrB homolog of the c-proteobacterium Halorhodospira halophila, a sulfur-oxidizing anoxygenic phototroph (Challacombe et al, 2013). Three of the 29 MtrB homologs lacking an N-terminal CXXC motif were found in metal-reducing bacteria, including the b-proteobacterium Rhodoferax ferrireducens (Finneran et al, 2003) and the d-proteobacteria Geobacter sp.…”

Section: Identification Of N-terminal Cxxc Motifs In Mtrb Homologs Oumentioning

confidence: 99%

Identification of a molecular signature unique to metal-reducingGammaproteobacteria

Wee

Burns

DiChristina

2013

FEMS Microbiol Lett

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Functional genes required for microbial (dissimilatory) metal reduction display high sequence divergence, which limits their utility as molecular biomarkers for tracking the presence and activity of metal-reducing bacteria in natural and engineered systems. In the present study, homologs of the outer membrane beta-barrel protein MtrB of metal-reducing Gammaproteobacteria were found to contain a unique N-terminal CXXC motif that was missing from MtrB homologs of nonmetal-reducing Gammaproteobacteria and metal- and nonmetal-reducing bacteria outside the Gammaproteobacteria. To determine whether the N-terminal CXXC motif of MtrB was required for dissimilatory metal reduction, each cysteine in the CXXC motif of the representative metal-reducing gammaproteobacterium Shewanella oneidensis was replaced with alanine, and the resulting site-directed mutants were tested for metal reduction activity. Anaerobic growth experiments demonstrated that the first, but not the second, conserved cysteine was required for metal reduction by S. oneidensis. The ability to predict metal reduction by Gammaproteobacteria with unknown metal reduction capability was confirmed with Vibrio parahaemolyticus, a pathogen whose genome encodes an MtrB homolog with an N-terminal CXXC motif. MtrB homologs with an N-terminal CXXC motif may thus represent a molecular signature unique to metal-reducing members of the Gammaproteobacteria.

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Complete genome sequence of Halorhodospira halophila SL1

Cited by 24 publications

References 34 publications

Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment

Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment

Metagenomic insights into diazotrophic communities across Arctic glacier forefields

Identification of a molecular signature unique to metal-reducingGammaproteobacteria

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