Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environments

Jenkins, Bethany D.; Zehr, Jonathan P.; Gibson, Angela H.; Campbell, Lisa

doi:10.1111/j.1462-2920.2006.01084.x

Cited by 25 publications

(31 citation statements)

References 41 publications

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“…Most of the sub-clade IV-B sequences were obtained from a near-shore station at the chlorophyll maximum. Two distinct Clade IV clusters were also observed using environmental sequences of the nitrate reductase gene (narB) from Monterey Bay, California (Jenkins et al 2006). It is likely that these Clade IV clusters are from the same Synechococcus types observed with the rpoC1 sequence phylogeny.…”

Section: Coastal To Open-ocean Transectmentioning

confidence: 74%

Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays

Tai¹,

Burton²,

Palenik

2011

Mar. Ecol. Prog. Ser.

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Marine Synechococcus diversity has been previously described using multi-locus gene sequence phylogenies and the identification of distinct clades. Synechococcus from Clades I, II, III, and IV and from sub-clades within Clades I and IV were enumerated from environmental samples by developing a hybridization assay to liquid bead-arrays (Luminex). Oligonucleotide probes targeting a gene encoding a subunit of RNA polymerase (rpoC1) were used simultaneously in multiplexed assays to track Synechococcus diversity from a Pacific Ocean coastal monitoring site and along a coastal to open-ocean transect in the Southern California Bight. The Luminex assay demonstrated that Synechococcus from Clades I and IV were the dominant types at the coastal site throughout the year. Synechococcus from Clades II and III were not detected except during the late summer or early winter. Within the dominant Clades I and IV, rpoC1-defined sub-clades of Synechococcus showed distinct spatial distributions along the coastal to open-ocean transect, coinciding with changes in the nitricline, thermocline, and fluorescence (chlorophyll) maximum depths. In coastal waters, Synechococcus targeted by 2 sub-clade IV probes were dominant at the surface, whereas 2 sub-clade I probes and a third sub-clade IV probe had increased signals in deeper water near the fluorescence maximum. In mesotrophic waters, this third sub-clade IV probe dominated at the fluorescence maximum (depth of 50 to 70 m), whereas all other sub-clade probes were below detection limits. The differing distributions of sub-clades within the dominant Synechococcus clades indicate that the subclades likely have adapted to distinct ecological niches found within the Southern California Bight. KEY WORDS: Cyanobacteria · Microbial ecology · Biogeography · Time-series · LuminexResale or republication not permitted without written consent of the publisher Mar Ecol Prog Ser 426: 133-147, 2011, Zwirglmaier et al. 2008) and off-shore oligotrophic environments (Ferris & Palenik 1998, Toledo & Palenik 2003, Ahlgren & Rocap 2006. Physiologically, differences in growth rates, in nitrogen and phosphate utilization, in pigment composition, in chromatic adaptation, and in motility have typically been used to describe isolated strains of Synechococcus (Moore et al. 1995, Collier et al. 1999, Toledo et al. 1999, Ahlgren & Rocap 2006, but, with the exception of motility (which has been found only in Clade III isolates), phenotypic traits and adaptations that uniquely characterize the genetically defined clades have yet to be identified.To understand the ecology of Synechococcus, diversity and abundance measures are fundamental. However, due to their small size, obtaining these measures is technically challenging. Traditionally, microbes are often distinguished physiologically by studying cultured isolates. But since only a small fraction of microbial diversity is represented by cultured isolates, and since the process of cultivation is labor-intensive, culture-independent and molecular methods h...

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Section: Coastal To Open-ocean Transectmentioning

confidence: 74%

Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays

Tai¹,

Burton²,

Palenik

2011

Mar. Ecol. Prog. Ser.

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“…Such waters are enriched in oxidized N compounds, mostly nitrate, and ntcA expression data show that Synechococcus populations have adapted to assimilate these compounds (150,151). Nitrate utilization is widespread among oceanic and coastal Synechococcus strains, and phylogenies based on narB sequences have revealed new clades with a distinct geographic distribution (127).…”

Section: Nutrient Acquisition Nitrogen Nutritionmentioning

confidence: 99%

Ecological Genomics of Marine Picocyanobacteria

Scanlan

Ostrowski

Mazard

et al. 2009

Microbiol Mol Biol Rev

648

824

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SUMMARY Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.

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“…Direct measurements of NO − 3 assimilation into phytoplankton (Dugdale and Goering, 1967), nitrate reductase enzyme activity (Eppley et al, 1969), and more recent nucleic acid-based methods for detecting nitrate reductase-encoding genes (Jenkins et al, 2006;Paerl et al, 2008;Ward, 2008) and gene transcripts (Paerl et al, 2012) have all shown the importance and prevalence of nitrate-reducing activity in marine phytoplankton and the potential for NO − 2 production. None of these methods, however, address how much NO − 2 is released into the water column, where it is detected in the dissolved phase, versus how much remains in the cell.…”

Section: Introductionmentioning

confidence: 99%

Measurements of nitrite production in and around the primary nitrite maximum in the central California Current

et al. 2013

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Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environments

Cited by 25 publications

References 41 publications

Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays

Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays

Ecological Genomics of Marine Picocyanobacteria

Measurements of nitrite production in and around the primary nitrite maximum in the central California Current

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