Spatiotemporal Distribution of Key Pelagic Microbes in a Seasonal Oxygen-Deficient Coastal Upwelling System of the Eastern South Pacific Ocean

Molina, Verónica; Belmar, Lucy; Levipan, Héctor A.; Ramírez-Flandes, Salvador; Anguita, C.; Galán, Alexander; Montès, Ivonne; Ulloa, Osvaldo

doi:10.3389/fmars.2020.561597

Cited by 14 publications

(10 citation statements)

References 114 publications

(175 reference statements)

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“…Our results revealed that the WCA and WCB ecotypes also exhibited significant seasonal changes in the marine environments where they were dominant (Figure 4A,B, D,E). Unexpectedly, the variation in the NP clade between spring and summer was not significant in the study area (Figures 4C and 5B), which differed from previous observations reported in coastal waters (Liu et al, 2018;Molina et al, 2020;Parada & Fuhrman, 2017;Tolar et al, 2020). Given that the NP clade, with relatively low diversity (Figures 2 and S6), has a similar level of transcriptional activity in both seasons (Figures 5B and 6), the environmental determinants of the NP clade in oligotrophic conditions may be different from that of the WCA and WCB ecotypes and remain to be identified.…”

Section: Seasonal Variations In Thaumarchaeal Ecotypescontrasting

confidence: 97%

Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea

Liu

et al. 2022

Environmental Microbiology

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Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.

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Section: Seasonal Variations In Thaumarchaeal Ecotypescontrasting

confidence: 97%

Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea

Liu

et al. 2022

Environmental Microbiology

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“…In addition, Nitrososphaeria archaeal sequences involved in the aerobic oxidation of NH 4 + were retrieved at different depths in the slope stations during both ENSO phases, with Nitrosopumilales (0.65% of the total sequences) dominating in the base of the oxycline, whereas Marine Benthic Group A (0.26%) and Group 1.1c (0.01%) dominated in the anoxic OMZ core (amplicon sequence data taken during La Niña) and bottom. This supports a high potential for niche partitioning among different ammoniaoxidizing archaea in this and other OMZs (Beman et al, 2008;Bertagnolli & Ulloa, 2017;Molina et al, 2020).…”

Section: Distribution Patterns Of N Gene Abundancessupporting

confidence: 76%

Prokaryotic community dynamics and nitrogen‐cycling genes in an oxygen‐deficient upwelling system during La Niña and El Niño conditions

Pajares

Merino–Ibarra

2023

Environmental Microbiology

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Dissolved oxygen regulates microbial distribution and nitrogen cycling and, therefore, ocean productivity and Earth's climate. To date, the assembly of microbial communities in relation to oceanographic changes due to El Niño Southern Oscillation (ENSO) remains poorly understood in oxygen minimum zones (OMZ). The Mexican Pacific upwelling system supports high productivity and a permanent OMZ. Here, the spatiotemporal distribution of the prokaryotic community and nitrogen-cycling genes was investigated along a repeated transect subjected to varying oceanographic conditions associated with La Niña in 2018 and El Niño in 2019. The community was more diverse during La Niña and in the aphotic OMZ, dominated by the Subtropical Subsurface water mass, where the highest abundances of nitrogen-cycling genes were found. The largest proportion of the Gulf of California water mass during El Niño provided warmer, more oxygenated, and nutrient-poor waters towards the coast, leading to a significant increase of Synechococcus in the euphotic layer compared with the opposite conditions during La Niña. These findings suggest that prokaryotic assemblages and nitrogen genes are linked to local physicochemical conditions (e.g. light, oxygen, nutrients), but also to oceanographic fluctuations associated with ENSO phases, indicating the crucial role of climate variability in microbial community dynamics in this OMZ.

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“…High abundance, diversity, and activity of microorganisms in marine sediments play vital roles in global biogeochemical cycles ( Prokopenko et al, 2013 ; Hoshino et al, 2020 ), partially because they are involved in the transforming and degrading organic matter ( Koho et al, 2013 ), these processes, release nitrogen and phosphorus nutrients into the water column, thus facilitating the growth of primary producers and contributing to climate regulation ( Cavicchioli et al, 2019 ). However, most previous studies that consider the composition and spatial distribution of microbial communities in coastal areas both worldwide ( Jayakumar et al, 2012 ; Glass et al, 2015 ) and in Chile have focused on the water column (e.g., Molina et al, 2010 , 2020 , 2021 ; Stewart et al, 2012 ; Ulloa et al, 2012 ) and little is known about benthic microbial structure, activity and interactions in marine sediments that experience fluctuating redox conditions due to the oxygen-depleted waters and trace metal (TM) gradients ( Farías et al, 2004 ; Broman et al, 2017 ; Rasigraf et al, 2017 ; Miranda et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline

et al. 2023

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Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach’s to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages’ features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.

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Spatiotemporal Distribution of Key Pelagic Microbes in a Seasonal Oxygen-Deficient Coastal Upwelling System of the Eastern South Pacific Ocean

Cited by 14 publications

References 114 publications

Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea

Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea

Prokaryotic community dynamics and nitrogen‐cycling genes in an oxygen‐deficient upwelling system during La Niña and El Niño conditions

Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline

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