scholarly journals Characterization of the Fe Metalloproteome of a Ubiquitous Marine Heterotroph, Pseudoalteromonas (BB2-AT2): Multiple Bacterioferritin Copies Enable Significant Fe Storage

2020 ◽  
Author(s):  
Michael Mazzotta ◽  
Matthew R. McIlvin ◽  
Mak A. Saito
Keyword(s):  
Heterotrophic Bacteria ◽  
Deep Ocean ◽  
The Pacific ◽  
Subsequent Degradation ◽  
Associated Proteins ◽  
Marine Heterotrophic Bacteria ◽  
Fe Complex ◽  
Value Decomposition ◽  
Fe Storage ◽  
Fe Acquisition

<p>Fe is a critical nutrient to the marine biological pump, which is the process that exports photosynthetically fixed carbon in<br>the upper ocean to the deep ocean. Fe limitation controls photosynthetic activity in large regions of the oceans, and the subsequent degradation of exported photosynthetic material is facilitated particularly by marine heterotrophic bacteria. Despite their importance in the carbon cycle and the scarcity of Fe in seawater, the Fe requirements, storage and cytosolic utilization of these marine heterotrophs has been less studied. Here, we characterized the Fe metallome of Pseudoalteromonas (BB2-AT2). We found that with two copies of bacterioferritin (Bfr), Pseudoalteromonas possesses substantial capacity for luxury uptake of Fe. Fe:C in the whole cell metallome was estimated (assuming C:P stoichiometry ~51:1) to be between ~83 μmol:mol Fe:C, ~11 fold higher than prior marine bacteria surveys, that could support growth for at least 2.6 divisions in the absence of further Fe acquisition. Under these replete conditions, other major cytosolic Fe associated proteins were observed including superoxide dismutase (SodA; with other metal SOD isoforms absent under Fe replete conditions) and catalase (KatG) involved in reactive oxygen stress mitigation and aconitase (AcnB), succinate dehydrogenase (FrdB) and cytochromes (QcrA and Cyt1) involved in respiration. With the aid of singular value decomposition (SVD), we were able to computationally attribute peaks within the metallome to specific metalloproteins contributors. An Fe complex TonB transporter associated with the closely related Alteromonas bacterium was found to be abundant within the Pacific Ocean mesopelagic environment. Despite the extreme scarcity of Fe in seawater, the marine heterotroph, Pseudoalteromonas, has expansive Fe storage capacity and utilization strategies, implying that, within detritus and sinking particle environments, there is significant opportunity for Fe acquisition. Together these results imply an evolved dedication of marine Pseudoalteromonas to maintaining an Fe metalloproteome, likely due to its dependence on Fe-based respiratory metabolism.<br></p>

scholarly journals Characterization of the Fe Metalloproteome of a Ubiquitous Marine Heterotroph, Pseudoalteromonas (BB2-AT2): Multiple Bacterioferritin Copies Enable Significant Fe Storage

2020 ◽  
Author(s):  
Michael Mazzotta ◽  
Matthew R. McIlvin ◽  
Mak A. Saito
Keyword(s):  
Heterotrophic Bacteria ◽  
Deep Ocean ◽  
The Pacific ◽  
Subsequent Degradation ◽  
Associated Proteins ◽  
Marine Heterotrophic Bacteria ◽  
Fe Complex ◽  
Value Decomposition ◽  
Fe Storage ◽  
Fe Acquisition

<p>Fe is a critical nutrient to the marine biological pump, which is the process that exports photosynthetically fixed carbon in<br>the upper ocean to the deep ocean. Fe limitation controls photosynthetic activity in large regions of the oceans, and the subsequent degradation of exported photosynthetic material is facilitated particularly by marine heterotrophic bacteria. Despite their importance in the carbon cycle and the scarcity of Fe in seawater, the Fe requirements, storage and cytosolic utilization of these marine heterotrophs has been less studied. Here, we characterized the Fe metallome of Pseudoalteromonas (BB2-AT2). We found that with two copies of bacterioferritin (Bfr), Pseudoalteromonas possesses substantial capacity for luxury uptake of Fe. Fe:C in the whole cell metallome was estimated (assuming C:P stoichiometry ~51:1) to be between ~83 μmol:mol Fe:C, ~11 fold higher than prior marine bacteria surveys, that could support growth for at least 2.6 divisions in the absence of further Fe acquisition. Under these replete conditions, other major cytosolic Fe associated proteins were observed including superoxide dismutase (SodA; with other metal SOD isoforms absent under Fe replete conditions) and catalase (KatG) involved in reactive oxygen stress mitigation and aconitase (AcnB), succinate dehydrogenase (FrdB) and cytochromes (QcrA and Cyt1) involved in respiration. With the aid of singular value decomposition (SVD), we were able to computationally attribute peaks within the metallome to specific metalloproteins contributors. An Fe complex TonB transporter associated with the closely related Alteromonas bacterium was found to be abundant within the Pacific Ocean mesopelagic environment. Despite the extreme scarcity of Fe in seawater, the marine heterotroph, Pseudoalteromonas, has expansive Fe storage capacity and utilization strategies, implying that, within detritus and sinking particle environments, there is significant opportunity for Fe acquisition. Together these results imply an evolved dedication of marine Pseudoalteromonas to maintaining an Fe metalloproteome, likely due to its dependence on Fe-based respiratory metabolism.<br></p>

scholarly journals The evolving response of mesopelagic fishes to declining midwater oxygen concentrations in the southern and central California Current

2018 ◽  
Vol 76 (3) ◽  
pp. 626-638 ◽  
Author(s):  
J Anthony Koslow ◽  
Pete Davison ◽  
Erica Ferrer ◽  
S Patricia A Jiménez Rosenberg ◽  
Gerardo Aceves-Medina ◽  
...  
Keyword(s):  
Baja California ◽  
Southern Oscillation ◽  
Global Climate ◽  
California Current ◽  
Deep Ocean ◽  
Near Surface ◽  
Oxygen Minimum Zones ◽  
The North ◽  
The Pacific ◽  
Oxygen Concentrations

Abstract Declining oxygen concentrations in the deep ocean, particularly in areas with pronounced oxygen minimum zones (OMZs), are a growing global concern related to global climate change. Its potential impacts on marine life remain poorly understood. A previous study suggested that the abundance of a diverse suite of mesopelagic fishes off southern California was closely linked to trends in midwater oxygen concentration. This study expands the spatial and temporal scale of that analysis to examine how mesopelagic fishes are responding to declining oxygen levels in the California Current (CC) off central, southern, and Baja California. Several warm-water mesopelagic species, apparently adapted to the shallower, more intense OMZ off Baja California, are shown to be increasing despite declining midwater oxygen concentrations and becoming increasingly dominant, initially off Baja California and subsequently in the CC region to the north. Their increased abundance is associated with warming near-surface ocean temperature, the warm phase of the Pacific Decadal oscillation and Multivariate El Niño-Southern Oscillation Index, and the increased flux of Pacific Equatorial Water into the southern CC.

Seismically Derived Ground Tilts Related to the 2010 Chilean Tsunami

2021 ◽  
Author(s):  
Jui-Chun Freya Chen ◽  
Wu-Cheng Chi ◽  
Chu-Fang Yang
Keyword(s):  
Deep Ocean ◽  
Propagation Model ◽  
Ocean Bottom ◽  
Ocean Bottom Seismometer ◽  
Tsunami Propagation ◽  
Ground Tilt ◽  
Tsunami Waves ◽  
The Pacific ◽  
Seismic Networks ◽  
Back Azimuth

Abstract Developing new ways to observe tsunami contributes to tsunami research. Tidal and deep-ocean gauges are typically used for coastal and offshore observations. Recently, tsunami-induced ground tilts offer a new possibility. The ground tilt signal accompanied by 2010 Mw 8.8 Chilean earthquake were observed at a tiltmeter network in Japan. However, tiltmeter stations are usually not as widely installed as broadband seismometers in other countries. Here, we studied broadband seismic records from Japan’s F-net and found ground tilt signals consistent with previously published tiltmeter dataset for this particular tsunamic event. Similar waveforms can also be found in broadband seismic networks in other countries, such as Taiwan, as well as an ocean-bottom seismometer. We documented a consistent time sequence of evolving back-azimuth directions of the tsunami waves at different stages of tsunami propagation through beamforming-frequency–wavenumber analysis and particle-motion analysis; the outcomes are consistent with the tsunami propagation model provided by the Pacific Tsunami Warning Center. These results shown that dense broadband seismic networks can provide a useful complementary dataset, in addition to tiltmeter arrays and other networks, to study or even monitor tsunami propagation using arrayed methods.

scholarly journals Structure-Function Analysis Indicates that an Active-Site Water Molecule Participates in Dimethylsulfoniopropionate Cleavage by DddK

2019 ◽  
Vol 85 (8) ◽  
Author(s):  
Ming Peng ◽  
Xiu-Lan Chen ◽  
Dian Zhang ◽  
Xiu-Juan Wang ◽  
Ning Wang ◽  
...  
Keyword(s):  
Water Molecule ◽  
Active Site ◽  
Dimethyl Sulfide ◽  
Catalytic Mechanism ◽  
Heterotrophic Bacteria ◽  
Function Analysis ◽  
Cloud Condensation Nuclei ◽  
Oxidation Products ◽  
Condensation Nuclei ◽  
Marine Heterotrophic Bacteria

ABSTRACT The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram quantities in marine environments and has important roles in global sulfur and carbon cycling. Many marine microorganisms catabolize DMSP via DMSP lyases, generating the climate-active gas dimethyl sulfide (DMS). DMS oxidation products participate in forming cloud condensation nuclei and, thus, may influence weather and climate. SAR11 bacteria are the most abundant marine heterotrophic bacteria; many of them contain the DMSP lyase DddK, and their dddK transcripts are relatively abundant in seawater. In a recently described catalytic mechanism for DddK, Tyr64 is predicted to act as the catalytic base initiating the β-elimination reaction of DMSP. Tyr64 was proposed to be deprotonated by coordination to the metal cofactor or its neighboring His96. To further probe this mechanism, we purified and characterized the DddK protein from Pelagibacter ubique strain HTCC1062 and determined the crystal structures of wild-type DddK and its Y64A and Y122A mutants (bearing a change of Y to A at position 64 or 122, respectively), where the Y122A mutant is complexed with DMSP. The structural and mutational analyses largely support the catalytic role of Tyr64, but not the method of its deprotonation. Our data indicate that an active water molecule in the active site of DddK plays an important role in the deprotonation of Tyr64 and that this is far more likely than coordination to the metal or His96. Sequence alignment and phylogenetic analysis suggest that the proposed catalytic mechanism of DddK has universal significance. Our results provide new mechanistic insights into DddK and enrich our understanding of DMS generation by SAR11 bacteria. IMPORTANCE The climate-active gas dimethyl sulfide (DMS) plays an important role in global sulfur cycling and atmospheric chemistry. DMS is mainly produced through the bacterial cleavage of marine dimethylsulfoniopropionate (DMSP). When released into the atmosphere from the oceans, DMS can be photochemically oxidized into DMSO or sulfate aerosols, which form cloud condensation nuclei that influence the reflectivity of clouds and, thereby, global temperature. SAR11 bacteria are the most abundant marine heterotrophic bacteria, and many of them contain DMSP lyase DddK to cleave DMSP, generating DMS. In this study, based on structural analyses and mutational assays, we revealed the catalytic mechanism of DddK, which has universal significance in SAR11 bacteria. This study provides new insights into the catalytic mechanism of DddK, leading to a better understanding of how SAR11 bacteria generate DMS.

scholarly journals Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacteriumZobellia galactanivoransDsijT

2016 ◽  
Vol 18 (12) ◽  
pp. 4610-4627 ◽  
Author(s):  
Tristan Barbeyron ◽  
François Thomas ◽  
Valérie Barbe ◽  
Hanno Teeling ◽  
Chantal Schenowitz ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Driving Forces ◽  
Marine Heterotrophic Bacteria ◽  
Carbohydrate Catabolism

scholarly journals Facilitation of Robust Growth of Prochlorococcus Colonies and Dilute Liquid Cultures by “Helper” Heterotrophic Bacteria

2008 ◽  
Vol 74 (14) ◽  
pp. 4530-4534 ◽  
Author(s):  
J. Jeffrey Morris ◽  
Robin Kirkegaard ◽  
Martin J. Szul ◽  
Zackary I. Johnson ◽  
Erik R. Zinser
Keyword(s):  
Solid Medium ◽  
Heterotrophic Bacteria ◽  
Cell Concentration ◽  
Preliminary Evidence ◽  
Critical Threshold ◽  
Semisolid Medium ◽  
Marine Heterotrophic Bacteria ◽  
Pure Cultures ◽  
Novel Method ◽  
Axenic Cultures

ABSTRACT Axenic (pure) cultures of marine unicellular cyanobacteria of the Prochlorococcus genus grow efficiently only if the inoculation concentration is large; colonies form on semisolid medium at low efficiencies. In this work, we describe a novel method for growing Prochlorococcus colonies on semisolid agar that improves the level of recovery to approximately 100%. Prochlorococcus grows robustly at low cell concentrations, in liquid or on solid medium, when cocultured with marine heterotrophic bacteria. Once the Prochlorococcus cell concentration surpasses a critical threshold, the “helper” heterotrophs can be eliminated with antibiotics to produce axenic cultures. Our preliminary evidence suggests that one mechanism by which the heterotrophs help Prochlorococcus is the reduction of oxidative stress.

scholarly journals Isolation of Tellurite- and Selenite-Resistant Bacteria from Hydrothermal Vents of the Juan de Fuca Ridge in the Pacific Ocean

2002 ◽  
Vol 68 (9) ◽  
pp. 4613-4622 ◽  
Author(s):  
Christopher Rathgeber ◽  
Natalia Yurkova ◽  
Erko Stackebrandt ◽  
J. Thomas Beatty ◽  
Vladimir Yurkov
Keyword(s):  
Hydrothermal Vents ◽  
Deep Ocean ◽  
Juan De Fuca Ridge ◽  
Resistant Bacteria ◽  
Ocean Water ◽  
Bacterial Films ◽  
The Pacific ◽  
Juan De Fuca ◽  
The Pacific Ocean ◽  
Reducing Bacteria

ABSTRACT Deep-ocean hydrothermal-vent environments are rich in heavy metals and metalloids and present excellent sites for the isolation of metal-resistant microorganisms. Both metalloid-oxide-resistant and metalloid-oxide-reducing bacteria were found. Tellurite- and selenite-reducing strains were isolated in high numbers from ocean water near hydrothermal vents, bacterial films, and sulfide-rich rocks. Growth of these isolates in media containing K2TeO3 or Na2SeO3 resulted in the accumulation of metallic tellurium or selenium. The MIC of K2TeO3 ranged from 1,500 to greater than 2,500 μg/ml, and the MIC of Na2SeO3 ranged from 6,000 to greater than 7,000 μg/ml for 10 strains. Phylogenetic analysis of 4 of these 10 strains revealed that they form a branch closely related to members of the genus Pseudoalteromonas, within the γ-3 subclass of the Proteobacteria. All 10 strains were found to be salt tolerant, pH tolerant, and thermotolerant. The metalloid resistance and morphological, physiological, and phylogenetic characteristics of newly isolated strains are described.

scholarly journals The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans

2014 ◽  
Vol 81 (5) ◽  
pp. 1799-1812 ◽  
Author(s):  
Agnès Groisillier ◽  
Aurore Labourel ◽  
Gurvan Michel ◽  
Thierry Tonon
Keyword(s):  
Abc Transporter ◽  
Biochemical Characterization ◽  
Heterotrophic Bacteria ◽  
Dry Weight ◽  
Sole Source ◽  
Content Type ◽  
Wide Range ◽  
Marine Heterotrophic Bacteria ◽  
Operon Gene ◽  
Living Organisms

ABSTRACTMannitol is a polyol that occurs in a wide range of living organisms, where it fulfills different physiological roles. In particular, mannitol can account for as much as 20 to 30% of the dry weight of brown algae and is likely to be an important source of carbon for marine heterotrophic bacteria.Zobellia galactanivorans(Flavobacteriia) is a model for the study of pathways involved in the degradation of seaweed carbohydrates. Annotation of its genome revealed the presence of genes potentially involved in mannitol catabolism, and we describe here the biochemical characterization of a recombinant mannitol-2-dehydrogenase (M2DH) and a fructokinase (FK). Among the observations, the M2DH ofZ. galactanivoranswas active as a monomer, did not require metal ions for catalysis, and featured a narrow substrate specificity. The FK characterized was active on fructose and mannose in the presence of a monocation, preferentially K+. Furthermore, the genes coding for these two proteins were adjacent in the genome and were located directly downstream of three loci likely to encode an ATP binding cassette (ABC) transporter complex, suggesting organization into an operon. Gene expression analysis supported this hypothesis and showed the induction of these five genes after culture ofZ. galactanivoransin the presence of mannitol as the sole source of carbon. This operon for mannitol catabolism was identified in only 6 genomes ofFlavobacteriaceaeamong the 76 publicly available at the time of the analysis. It is not conserved in allBacteroidetes; some species contain a predicted mannitol permease instead of a putative ABC transporter complex upstream of M2DH and FK ortholog genes.

scholarly journals Rhodothermus profundi sp. nov., a thermophilic bacterium isolated from a deep-sea hydrothermal vent in the Pacific Ocean

2010 ◽  
Vol 60 (12) ◽  
pp. 2729-2734 ◽  
Author(s):  
Viggó Thór Marteinsson ◽  
Snaedis H. Bjornsdottir ◽  
Nadège Bienvenu ◽  
Jakob K. Kristjansson ◽  
Jean-Louis Birrien
Keyword(s):  
Deep Sea ◽  
Heterotrophic Bacteria ◽  
Optimal Growth ◽  
Maximum Growth ◽  
Thermophilic Bacterium ◽  
Rrna Gene ◽  
The Novel ◽  
The Pacific ◽  
Pressure Maximum ◽  
Gene Similarity

Nine thermophilic strains of aerobic, non-sporulating, heterotrophic bacteria were isolated after enrichment of chimney material sampled from a deep-sea hydrothermal field at a depth of 2634 m on the East-Pacific Rise (1 °N). The bacteria stained Gram-negative. They were rod-shaped and measured approximately 0.5 μm in width and 1.5–3.5 μm in length. They grew at 55–80 °C, pH 6–8 and 1–6 % NaCl. Optimal growth was observed at 70–75 °C, pH 7.0 and 1–3 % NaCl. The organisms were identified as members of the genus Rhodothermus, having a 16S rRNA gene similarity of 98.1 % with Rhodothermus marinus DSM 4252T. The novel isolates differed morphologically, physiologically and chemotaxonomically from R. marinus, e.g. in lack of pigmentation, response to hydrostatic pressure, maximum growth temperature and DNA G+C content. DNA–DNA hybridization revealed a reassociation value of 37.2 % between strain PRI 2902T and R. marinus DSM 4252T, which strongly suggested that they represent different species. Furthermore, AFLP fingerprinting separated the novel strains from R. marinus reference strains. It is therefore concluded that the strains described here should be classified as representatives of a novel species for which the name Rhodothermus profundi sp. nov. is proposed; the type strain is PRI 2902T (=DSM 22212T =JCM 15944T).

scholarly journals Deep-ocean origin of the freshwater eels

2010 ◽  
Vol 6 (3) ◽  
pp. 363-366 ◽  
Author(s):  
Jun G. Inoue ◽  
Masaki Miya ◽  
Michael J. Miller ◽  
Tetsuya Sado ◽  
Reinhold Hanel ◽  
...  
Keyword(s):  
Deep Ocean ◽  
Evolutionary Origin ◽  
Phylogenetic Position ◽  
Genome Sequences ◽  
Apical Position ◽  
Mature Adults ◽  
Spawning Areas ◽  
The Pacific ◽  
Recent Collection ◽  
Freshwater Eels

Of more than 800 species of eels of the order Anguilliformes, only freshwater eels (genus Anguilla with 16 species plus three subspecies) spend most of their lives in freshwater during their catadromous life cycle. Nevertheless, because their spawning areas are located offshore in the open ocean, they migrate back to their specific breeding places in the ocean, often located thousands of kilometres away. The evolutionary origin of such enigmatic behaviour, however, remains elusive because of the uncertain phylogenetic position of freshwater eels within the principally marine anguilliforms. Here, we show strong evidence for a deep oceanic origin of the freshwater eels, based on the phylogenetic analysis of whole mitochondrial genome sequences from 56 species representing all of the 19 anguilliform families. The freshwater eels occupy an apical position within the anguilliforms, forming a highly supported monophyletic group with various oceanic midwater eel species. Moreover, reconstruction of the growth habitats on the resulting tree unequivocally indicates an origination of the freshwater eels from the midwater of the deep ocean. This shows significant concordance with the recent collection of mature adults of the Japanese eel in the upper midwater of the Pacific, suggesting that they have retained their evolutionary origin as a behavioural trait in their spawning areas.

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