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Oxide Respiring Bacteria Is Associated with Tube Worms in the Vicinity of the Juan De Fuca Ridge Black Smoker Field

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Oxide Respiring Bacteria Is Associated with Tube Worms in the Vicinity of the Juan De Fuca Ridge Black Smoker Field RESEARCH ARTICLE A Diverse Community of Metal(loid) Oxide Respiring Bacteria Is Associated with Tube Worms in the Vicinity of the Juan de Fuca Ridge Black Smoker Field Chris Maltman, Graham Walter, Vladimir Yurkov* Department of Microbiology, University of Manitoba, Winnipeg, Canada * [email protected] Abstract Epibiotic bacteria associated with tube worms living in the vicinity of deep sea hydrothermal vents of the Juan de Fuca Ridge in the Pacific Ocean were investigated for the ability to OPEN ACCESS respire anaerobically on tellurite, tellurate, selenite, selenate, metavanadate and orthovana- date as terminal electron acceptors. Out of 107 isolates tested, 106 were capable of respira- Citation: Maltman C, Walter G, Yurkov V (2016) A Diverse Community of Metal(loid) Oxide Respiring tion on one or more of these oxides, indicating that metal(loid) oxide based respiration is not Bacteria Is Associated with Tube Worms in the only much more prevalent in nature than is generally believed, but also is an important Vicinity of the Juan de Fuca Ridge Black Smoker mode of energy generation in the habitat. Partial 16S rRNA gene sequencing revealed the Field. PLoS ONE 11(2): e0149812. doi:10.1371/ journal.pone.0149812 bacterial community to be rich and highly diverse, containing many potentially new species. Furthermore, it appears that the worms not only possess a close symbiotic relationship with Editor: Sébastien Duperron, Universite Pierre et Marie Curie, FRANCE chemolithotrophic sulfide-oxidizing bacteria, but also with the metal(loid) oxide transform- ers. Possibly they protect the worms through reduction of the toxic compounds that would Received: July 29, 2015 otherwise be harmful to the host. Accepted: February 4, 2016 Published: February 25, 2016 Copyright: © 2016 Maltman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits Introduction unrestricted use, distribution, and reproduction in any medium, provided the original author and source are Bacterial respiration on oxyanions of metal(loid)s is known [1], however, it was not believed to credited. be widespread. Due to the high toxicity, especially of tellurium oxides, it has long been believed they have no significant (if any, in the case of Te) role in biological processes. However, Data Availability Statement: All sequence files are available from the Genbank database (accession microbes have adapted and evolved to incorporate oxyanions of Te, Se, and V into metabolic numbers KT277103-KT277205). processes, especially in metal(loid) rich environments [2]. In regards to dissimilatory electron transport to metal(loid)s, strong support comes from the physical/chemical features of the Funding: This work was supported by a NSERC 2- 2- 2- Discovery grant and a University of Manitoba GETS redox couples for Te, Se, and V oxides (TeO3 /Te = 0.827 V; TeO4 /TeO3 = 0.885 V; 2- + 2+ grant. The funders had no role in study design, data SeO3 /Se = 0.885 V; VO2 /VO = 1.000 V). Although highly toxic, they are more favorable 2- - collection and analysis, decision to publish, or for anaerobic respiration than that of SO4 /HS (-0.217 V) couple widely used by sulfate reduc- preparation of the manuscript. ers [3]. No dissimilatory anaerobic reduction of Te oxyanions was known until 2006, when Competing Interests: The authors have declared strain ER-Te-48 from a deep sea hydrothermal vent tube worm was found to be capable of that no competing interests exist. anaerobic tellurate based respiration [4]. Since then, four other bacteria have been shown to PLOS ONE | DOI:10.1371/journal.pone.0149812 February 25, 2016 1/14 Metal(loid) Oxide Respiring Bacteria Associated with Tube Worms respire on Te oxides [5–7]. The dissimilatory use of Se and V oxides has been known for some time, however, it is limited to only a select few species [4–19]. The majority are halophiles from locales lacking any detectable metal(loid)s, suggesting the ability to respire on oxides was not directly evolved for survival. Deep sea hydrothermal vents, so-called Black Smokers, are geological formations, which release subterranean seawater that has been superheated to more than 400°C by magma pock- ets beneath the sea floor. Through this process, metal(loid)s are mobilized from the crustal basalts, highly enriching the vent plumes [20, 21]. The harsh environment suggests life there should be scarce, however, numerous unique organisms call this ecological niche home. The sulfide and tube worms surrounding vents are of particular interest with regards to bacterial- metal(loid) interactions. Due to the proximity to the plume waters, they and their associated symbiotic microbes are in close contact with elevated levels of metal(loid)s [22]. These animals harbor a community of metal resistant bacteria [23], indicating that the microbial population does experience, and has adapted to metal(loid) exposure. Such conditions offer the perfect environment for the evolution of biological processes dependant on metal(loid)s. Another fea- ture of these worms providing selective pressure in favor of bacteria capable of metal(loid) resistance/respiration is their vanadium enriched blood [24]. Since these creatures possess con- ditions ideal for dissimilatory metal(loid) reduction, it is not surprising their epibionts gave us not only the first example of anaerobic respiration on Te oxides [4], but also on metavanadate [17], and orthovanadate [4]. As mentioned prior, there are very few known examples of microbes utilizing Te, Se, or V oxides as terminal electron acceptors during anaerobic growth. They are spread out among dif- ferent genera [4–19], suggesting metal(loid) oxide respiring microbes are phylogenetically diverse and not limited to a single taxonomic group. In this study, we investigated 107 epibiotic isolates from the vent tube worms Paralvinella sulfincola and Ridgea piscesae of the Axial Vol- cano (AV) caldera and Explorer Ridge (ER) vent field of the Juan de Fuca Ridge [4] for the ability to respire anaerobically on tellurite, tellurate, selenite, selenate, metavanadate, and orthovanadate. Partial sequencing of the 16S rRNA gene was then carried out to determine their phylogenetic diversity. Materials and Methods Growth and respiration with metal(loid) oxides Sampling and collection of sulfide tube worms (R. piscesae) and tube worms (P. sulfincola) from Axial Volcano (Hell Vent: 45°56’00”N, 130°00’51”W; 1,543 m) and Explorer Ridge (Lucky Find: 49°45’38”N, 130°15’23”W; 1,791 m) of the Juan de Fuca Ridge in the Pacific Ocean in 2003 was as previously published [4]. Tissue from the worms was rinsed, homoge- nized, and used for inoculation of enrichment cultures. 107 metal(loid) reducing epibiotic bac- terial strains were isolated as described [4]. Each was grown aerobically at 28°C in the dark on rich organic (RO) [25] plates containing 2% NaCl and used to inoculate Balch tubes of anaero- bic metal(loid) respiration (AMR) liquid medium, containing (g/l): KH2PO4, 0.5; NH4Cl, 0.5; CaCl2, 0.1; yeast extract, 1.0; lactate, 1.0; and MgSO4, traces. Vitamin and trace microelements solutions [25] were added at 2 ml/l. Medium was amended with one of tellurite, tellurate, sele- nite, selenate (100 μg/ml), or metavanadate, orthovanadate (500 μg/ml) with a headspace of N2. Tubes were incubated at 28°C in the dark and monitored for respiration over two weeks. A representative strain was chosen for each oxide reducing group. Aerobically grown cells of ER-Te-40B, ER-Te-57, AV-Te-18, ER-V-8, AV-V-4, and ER-Te-41 were used to inoculate 120 ml crimp-sealed bottles containing 100 ml of AMR medium with one of tellurite, tellurate, sele- nite, selenate, metavanadate or orthovanadate at the concentrations listed above, under a PLOS ONE | DOI:10.1371/journal.pone.0149812 February 25, 2016 2/14 Metal(loid) Oxide Respiring Bacteria Associated with Tube Worms headspace of N2. Control tubes were not supplemented with any of these oxides. Protein yield was measured by Bradford assay [26]. ATP was measured using an ATP Bioluminescence Kit from Sigma-Aldrich. All experiments were performed in triplicate. Phylogenetic analysis Genomic DNA was extracted from pure cultures of each isolate as published [27]. Partial 16S rRNA gene amplification by PCR was carried out using universal bacterial primers [28], in 50 μl reaction volumes containing: 25 μl DreamTaq PCR Master Mix, 0.25 μM of each primer, and between 10 and 50 ng of DNA. The amplification cycle was as follows: Initial denaturing at 95°C for 5 min, denaturing at 95°C for 30 sec, annealing at 46°C for 30 sec, extension at 72°C for 1.5 min for 35 cycles with a final extension at 72°C for 10 min, ending with a hold at 7°C. Preparation of the PCR products was as described [29]. Samples were sequenced by the Mani- toba Institute of Cell Biology. The nucleotide sequences were edited and phylogenetic related- ness determined as reported [29]. All sequences were deposited in Genbank under the accession numbers provided in S1 Table. Maximum likelihood phylogenetic trees were created using Phylogeny.fr [30]. Results and Discussion Growth and reduction with metal(loid) oxides Upon visual investigation for change of colorless water soluble oxides to colored elemental forms (black for Te, red for Se, and grey/black/brownish for V [4]) due to microbial activity, we found that under anaerobic conditions, all isolates but ER-V-1 were capable of reducing at least one (Fig 1), and many could use more than one of the oxides tested (Tables 1 and 2). While the color transformation obviously indicated the possibility of anaerobic respiration, experimental proof was required. For each oxide reduction group, one representative strain was chosen and protein levels with and without the oxide added to the growth medium were analyzed.
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