Genomic features of “Candidatus Venteria ishoeyi”, a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile

Fonseca, Alexis; Ishoey, Thomas; Espinoza, Claudia; Pérez‐Pantoja, Danilo; Manghisi, Antonio; Morabito, Marina; Salas-Burgos, Alexis; Gallardo, Víctor A.

doi:10.1371/journal.pone.0188371

Cited by 15 publications

(9 citation statements)

References 104 publications

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“…In the sulfide‐rich sediments off the coast of Chile, microscopy and metagenomic sequencing has recently identified a novel nonvacuolated filamentous sulfur bacterium, “ Candidatus Venteria ishoeyi” within the family Thiotrichaceae, a distant relative to Thioploca (Fonseca et al 2017). The draft genome indicates that it contains an abundance of sulfide/sulfur oxidation pathways (Fonseca et al 2017). However, the prevalence of “ Ca .…”

Section: Termination Of Sulfidic Events By a Succession Of Sulfide‐oxidizing Bacteriamentioning

confidence: 99%

Sulfur cycling in oceanic oxygen minimum zones

Callbeck

Canfield

Kuypers

et al. 2021

Limnology & Oceanography

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The sulfur cycle is an important, although understudied facet of today's modern oxygen minimum zones (OMZs). Sulfur cycling is most active in highly productive coastal OMZs where sulfide-rich sediments interact with the overlying water column, forming a tightly coupled benthic-pelagic sulfur cycle. In such productive coastal systems, highly eutrophic and anoxic conditions can result in the benthic release of sulfide leading to an intensification of OMZ-shelf biogeochemistry. Active blooms involving a succession of sulfide-oxidizing bacteria detoxify sulfide and reduce nitrate to N 2 , while generating nitrite and ammonium that augment anammox and nitrification. Furthermore, the abiotic interactions of sulfide with trace metals may have the potential to moderate nitrous oxide emissions. While sulfide/sulfur accumulation events were previously considered to be rare, new evidence indicates that events can develop in OMZ shelf waters over prolonged periods of anoxia. The prevalence of these events has ramifications for nitrogen loss and greenhouse gas emissions, including other linked cycles involving carbon and phosphorous. Sulfur-based metabolisms and activity also extend into the offshore OMZ as a result of particle microniches and lateral transport processes. Moreover, OMZ waters ubiquitously host a community of organosulfur-based heterotrophs that ostensibly moderate the turnover of organic sulfur, offering an exciting avenue for future research. Our synthesis highlights the widespread distribution and multifaceted nature of the sulfur cycle in oceanic OMZs.

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Section: Termination Of Sulfidic Events By a Succession Of Sulfide‐oxidizing Bacteriamentioning

confidence: 99%

Sulfur cycling in oceanic oxygen minimum zones

Callbeck

Canfield

Kuypers

et al. 2021

Limnology & Oceanography

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“…The dissolved sulfide was analyzed, according to the diamine method, with a detection limit of 1 μM. For the analysis of SO 4 2- and chloride (Cl - ) concentrations, we aliquoted 20 μL of sample into 1 mL of milli-Q water, which was then measured by ion chromatography on a Metrohm 850 [ 50 ], with a detection limit of 0.1 μM. In this study, we used the Cl - as an indicator of changing pore water salinity.…”

Section: Methodsmentioning

confidence: 99%

Attenuation of wind intensities exacerbates anoxic conditions leading to sulfur plume development off the coast of Peru

Flores,

Mendoza,

Callbeck

et al. 2023

PLoS ONE

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The release of vast quantities of sulfide from the sediment into the water column, known as a sulfidic event, has detrimental consequences on fish catches, including downstream effects on other linked element cycles. Despite being frequent occurrences in marine upwelling regions, our understanding of the factors that moderate sulfidic event formation and termination are still rudimentary. Here, we examined the biogeochemical and hydrodynamic conditions that underpinned the formation/termination of one of the largest sulfur plumes to be reported in the Peruvian upwelling zone. Consistent with previous research, we find that the sulfur-rich plume arose during the austral summer when anoxic conditions (i.e., oxygen and nitrate depletion) prevailed in waters overlying the upper shelf. Furthermore, the shelf sediments were organically charged and characterized by low iron-bound sulfur concentrations, further enabling the diffusion of benthic-generated sulfide into the water column. While these biogeochemical conditions provided a predicate to sulfidic event formation, we highlight that attenuations in local wind intensity served as an event trigger. Namely, interruptions in local wind speed constrained upwelling intensity, causing increased stratification over the upper shelf. Moreover, disturbances in local wind patterns likely placed additional constraints on wind-driven mesoscale eddy propagation, with feedback effects on coastal elemental sulfur plume (ESP) formation. We suggest ESP development occurs as a result of a complex interaction of biogeochemistry with regional hydrodynamics.

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“…In the estuarine ecosystems, the genome of Vibrio gazogenes PB1 harbors three CRISPR/Cas operons and four Cas-less CRISPR arrays [ 76 ]. Candidatus Venteria ishoeyi isolated from the hypoxic waters of the upwelling ecosystem also possesses CRISPR/Cas systems [ 77 ].…”

Section: Huge Inventory Of Crispr/cas In the Oceanmentioning

confidence: 99%

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

Li,

Wu,

Zhang

et al. 2024

Microorganisms

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Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of ‘dark’ genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

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Genomic features of “Candidatus Venteria ishoeyi”, a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile

Cited by 15 publications

References 104 publications

Sulfur cycling in oceanic oxygen minimum zones

Sulfur cycling in oceanic oxygen minimum zones

Attenuation of wind intensities exacerbates anoxic conditions leading to sulfur plume development off the coast of Peru

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

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