Diversity and Transcriptional Levels of RuBisCO Form II of Sulfur-Oxidizing γ-Proteobacteria in Coastal-Upwelling Waters with Seasonal Anoxia

Léniz, Bárbara; Murillo, Alejandro A.; Ramírez-Flandes, Salvador; Ulloa, Osvaldo

doi:10.3389/fmars.2017.00213

Cited by 5 publications

(13 citation statements)

References 70 publications

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“…Sulfur plumes can also be transported into the offshore OMZ (> 200 m water depth) due to lateral transport processes (e.g., mesoscale eddies). (A,B) Remote sensing images of sulfur plumes using the water-leaving reflectance wavelength of 560 nm (optimal waveband for sulfur plume detection; Ohde et al 2007;Ohde and Dadou 2018) Léniz et al 2017. Shown are the maximum ccbM copy numbers of the three sampled depths by Léniz et al 2017.…”

Section: Sulfidic Events and Sulfur Cycling Associated With The Upper Shelfmentioning

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: Sulfidic Events and Sulfur Cycling Associated With The Upper Shelfmentioning

confidence: 99%

Sulfur cycling in oceanic oxygen minimum zones

Callbeck

Canfield

Kuypers

et al. 2021

Limnology & Oceanography

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“…In fact, closely related sequences to Ca . Nitromaritima were numerically dominant in OMZ metagenomes in the ETSP off northern Chile as well as in metatranscriptomes in the subtropical ESP off Concepción (Léniz et al., ).…”

Section: Discussionmentioning

confidence: 99%

“…Two mechanisms could explain a potentially fish-stimulated response in the number of Nitrospina transcripts. The ammonia excretion from fish can favor the first reaction of nitrification (Eikebrokk & Piedrahita, 1997 (Léniz et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…Two recent studies described sequences affiliated only with Nitrospina in connected oceanographic areas off the Chilean coast, namely, the ESP off Concepcion (Bristow et al, 2016) and eastern tropical South Pacific (ETSP) off Iquique (~20° S, northern Chile) (Pachiadaki et al, 2017). Therefore, other ubiquitous NOB in marine ecosystems such as members of genera Nitrospira (Hawley, Brewer, Norbeck, Pasa-Tolic, & Hallam, 2014;Lüke, Speth, Kox, Villanueva, & Jetten, 2016) and Nitrococcus (Füssel et al, 2012(Füssel et al, , 2017 appear to be absent or occur at very low abundance in Chilean waters (Léniz, Murillo, Ramírez-Flandes, & Ulloa, 2017;Ngugi et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Nitrospina bacteria in a rocky intertidal habitat (Quintay Bay, central Chile)

2018

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Nitrospina bacteria are among the most important nitrite oxidizers in coastal and open-ocean environments, but the relevance of the genus contrasts with the scarceness of information on their ecophysiology and habitat range. Thus far, Nitrospina bacteria have been the only nitrite oxidizers detected at high abundance in Chilean coastal waters. These levels are often higher than at other latitudes. In this study, the abundance of 16S-rRNA gene transcripts of Nitrospina (hereafter just transcripts) was measured by reverse transcription quantitative PCR in a rocky intertidal gradient and compared with the nearshore counterpart off central Chile (~33°S). Rocky pond transcripts were also compared with the taxonomic composition of the macrobiota and bacterioplankton (by 16S-rRNA gene-based T-RFLP) in the intertidal gradient. Transcripts increased from warmer, saltier, and low-nitrite ponds in the upper intertidal zone (19.5 ± 1.6°C, 39.0 ± 1.0 psu, 0.98 ± 0.17 μmol/L) toward cooler, less salty, and high-nitrite ponds (17.8 ± 2.6°C, 37.7 ± 0.82 psu, 1.23 ± 0.21 μmol/L) from middle and low zones. These varied from ~1,000 up to 62,800 transcripts. This increasing trend in the number of transcripts toward the lower zone was positively associated with the Shannon's diversity index for the macrobiota (r = .81, p < .01). Moreover, an important increase in the average number of transcripts was observed in ponds with a greater number of fish in the upper (7,846 transcripts during 2013) and lower zones (62,800 transcripts during 2015). Altogether, intertidal and nearshore transcripts were significantly correlated with nitrite concentrations (r = .804, p ˂ .01); rocky pond transcripts outnumbered nearshore ones by almost two orders of magnitude. In summary, rocky ponds favored both the presence and activity of Nitrospina bacteria that are tolerant to environmental stress. This in turn was positively influenced by the presence of ammonia- or urea-producing macrobiota.

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“…Among them, the CBB cycle of photosynthesizers contributes most to the global synthesis of organic matter (Hügler and Sievert, ). Nevertheless, many microorganisms, including the anammox (anaerobic ammonium oxidation) bacteria (Woebken et al ., ) and the abundant sulfur oxidisers (Walsh et al ., ; Schunck et al ., ; Léniz et al ., ) in AMZs, have the genetic potential for carrying out autotrophic carbon fixation in dark marine ecosystems (Swan et al ., ). Previous studies that have measured carbon fixation rates in the ETSP AMZ have reported a peak of values ranging from 9 to 130 nmol C L −1 d −1 below the photic zone (100–500 m), which has been attributed to the dark autotrophic carbon fixation (Löscher et al ., ; Callbeck et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Autotrophic carbon fixation pathways along the redox gradient in oxygen‐depleted oceanic waters

Ruiz-Fernández

Ramírez-Flandes

Rodríguez-León

et al. 2020

Environ Microbiol Rep

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Anoxic marine zones (AMZs), also known as 'oxygendeficient zones', contribute to the loss of fixed nitrogen from the ocean by anaerobic microbial processes. While these microbial processes associated with the nitrogen cycle have been extensively studied, those linked to the carbon cycle in AMZs have received much less attention, particularly the autotrophic carbon fixationa crucial component of the carbon cycle. Using metagenomic and metatranscriptomic data from major AMZs, we report an explicit partitioning of the marker genes associated with different autotrophic carbon fixation pathways along the redox gradient (from oxic to anoxic conditions) present in the water column of AMZs. Sequences related to the Calvin-Benson-Bassham cycle were found along the entire gradient, while those related to the reductive Acetyl-CoA pathway were restricted to suboxic and anoxic waters. Sequences putatively associated with the 3-hydroxypropionate/4-hydroxybutyrate cycle dominated in the upper and lower oxyclines. Genes related to the reductive tricarboxylic acid cycle were represented from dysoxic to anoxic waters. The taxonomic affiliation of the sequences is consistent with the presence of microorganisms involved in crucial steps of biogeochemical cycles in AMZs, such as the gamma-proteobacteria sulfur oxidisers, the anammox bacteria Candidatus Scalindua and the thaumarcheota ammonia oxidisers of the Marine Group I.

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Diversity and Transcriptional Levels of RuBisCO Form II of Sulfur-Oxidizing γ-Proteobacteria in Coastal-Upwelling Waters with Seasonal Anoxia

Cited by 5 publications

References 70 publications

Sulfur cycling in oceanic oxygen minimum zones

Sulfur cycling in oceanic oxygen minimum zones

Nitrospina bacteria in a rocky intertidal habitat (Quintay Bay, central Chile)

Autotrophic carbon fixation pathways along the redox gradient in oxygen‐depleted oceanic waters

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