The green ribbon: Multiscale physical control of phytoplankton productivity and community structure over a narrow continental shelf

Lucas, Andrew J.; Dupont, Christopher L.; Tai, Vera; Largier, John L.; Palenik, Brian; Franks, Peter J. S.

doi:10.4319/lo.2011.56.2.0611

Cited by 63 publications

(78 citation statements)

References 55 publications

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“…It is generally well accepted that Prochlorococcus dominates in the open ocean or stratified nutrient-poor waters, along with Synechococcus clades II and III (65). Clades I and IV are often found in mesotrophic waters with intermediate nutrient concentrations (30,57). In contrast, the sodBcontaining strains of Synechococcus are numerically dominant in upwelling systems (20,41), where mixing delivers nitrate, phosphate, and Fe to the euphotic zone.…”

Section: Influence Of Ni Deprivation On Gene Expression In Wh8102mentioning

confidence: 99%

Genetic Identification of a High-Affinity Ni Transporter and the Transcriptional Response to Ni Deprivation in Synechococcus sp. Strain WH8102

Dupont

Johnson

Phillippy

et al. 2012

Appl Environ Microbiol

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dOne biological need for Ni in marine cyanobacteria stems from the utilization of the Ni metalloenzyme urease for the assimilation of urea as a nitrogen source. In many of the same cyanobacteria, including Synechococcus sp. strain WH8102, an additional and obligate nutrient requirement for Ni results from usage of a Ni superoxide dismutase (Ni-SOD), which is encoded by sodN. To better understand the effects of Ni deprivation on WH8102, parallel microarray-based analysis of gene expression and gene knockout experiments were conducted. The global transcriptional response to Ni deprivation depends upon the nitrogen source provided for growth; fewer than 1% of differentially expressed genes for Ni deprivation on ammonium or urea were concordantly expressed. Surprisingly, genes for putative Ni transporters, including one colocalized on the genome with sodN, sodT, were not induced despite an increase in Ni transport. Knockouts of the putative Ni transporter gene sodT appeared to be lethal in WH8102, so the genes for sodT and sodN in WH8102 were interrupted with the gene for Fe-SOD, sodB, and its promoter from Synechococcus sp. strain WH7803. The sodT::sodB exconjugants were unable to grow at low Ni concentrations, confirming that SodT is a Ni transporter. The sodN::sodB exconjugants displayed higher growth rates at low Ni concentrations than did the wild type, presumably due to a relaxed competition between urease and Ni-SOD for Ni. Both sodT::sodB and sodN::sodB lines exhibited an impaired ability to grow at low Fe concentrations. We propose a posttranslational allosteric SodT regulation involving the binding of Ni to a histidine-rich intracellular protein loop.

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Section: Influence Of Ni Deprivation On Gene Expression In Wh8102mentioning

confidence: 99%

Genetic Identification of a High-Affinity Ni Transporter and the Transcriptional Response to Ni Deprivation in Synechococcus sp. Strain WH8102

Dupont

Johnson

Phillippy

et al. 2012

Appl Environ Microbiol

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“…Synechococcus-specific PCR primers that flank a variable region of the rpoC1 gene were designed (RPOC493F: 5'-biotin-CTN ACN GAR GAY GAR TGG YT-3'; SAC-1039R: 5'-CYT GYT TNC CYT CDA TDA TRT C-3'; Bioneer, Integrated DNA Technologies). RPOC493F was biotinylated on the 5' end for detection using streptavidin-phycoerythrin (strep-PE) WH8016 071101H CC9617 071101J 081106maxQ 081106maxH 071101L CC9311 WH8020 022801E 050901M 050901L 050901Q 083001H 051205V 081106maxF 022801L 050901I 050901P 050901Z 050901C 081106maxL 022801M 050901Y 083001A 051205K 051205X 051205P 051205W 050901G 050901K 050901D 022801D 022801I 050901V 071101C 022801B 022801G 081106maxD 051205D 051205H 083001B 083001C 071101K 051205C 051205L 022801A 051205A 081106maxE 022801K 050901R 051205E 050901B 051205Z 050901T 050901X 051205M 083001D 050901U 071101B 081106maxM 051205J 051205Y 051205Q 071101D 051205B (Lucas et al 2011). CB-1 is a cultured strain isolated from surface waters at the end of the SIO pier in 1999.…”

Section: Methodsmentioning

confidence: 99%

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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“…Although kelp growth appears not to be influenced by water temperature per se (North and Zimmerman 1984), local sea surface temperature (SST) and nutrients (specifically nitrate þ nitrite) show a strong negative linear relationship in southern California (Fram et al 2008, Lucas et al 2011. Therefore, we used satellite observations of local SST as a proxy for nitrate/nitrite levels.…”

Section: Environmental Datamentioning

confidence: 99%

Synchrony in dynamics of giant kelp forests is driven by both local recruitment and regional environmental controls

Cavanaugh

Kendall

Siegel

et al. 2013

Ecology

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Populations of many species display spatially synchronous fluctuations in abundance. Synchrony is most commonly attributed to three processes: factors that influence recruitment (e.g., dispersal, early survival), large‐scale environmental variability, and spatially autocorrelated trophic interactions. However it is often difficult to link population synchrony to a specific dominant process, particularly when multiple synchronizing forces are operating. We utilized a new satellite‐based data set of giant kelp (Macrocystis pyrifera) canopy biomass to examine population synchrony in southern California kelp forests on spatial scales ranging from 50 m to 300 km and temporal scales ranging from 1 to 11 years. We examined the relationship between synchrony and distance for adult kelp populations, kelp recruits, sea urchin abundance (a major grazer of kelp), and environmental variables known to influence kelp population dynamics. Population synchrony in giant kelp decreased with distance between populations: an initial rapid exponential decrease between 50 m and 1.3 km was followed by a second, large‐scale decrease between distances of 1.3 km and 172 km. The 50‐m to 1.3‐km spatial scale corresponded to the scales of synchrony in the abundance of sea urchins and young kelp recruits, suggesting that local drivers of predation and recruitment influence small‐scale synchrony in kelp populations. The spatial correlation patterns of environmental variables, particularly wave height, were similar to the synchrony–distance relationship of kelp populations from 1.3 km to 172 km, suggesting that regional environmental variability, i.e., the Moran effect, was the dominant process affecting synchrony at larger spatial scales. This two‐step pattern in the relationship between kelp biomass synchrony and distance was apparent in each of the 11 years of our study. Our results highlight the potential for synthesizing approaches from both landscape and population ecology in order to identify the multiple processes that generate synchrony in population dynamics.

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The green ribbon: Multiscale physical control of phytoplankton productivity and community structure over a narrow continental shelf

Cited by 63 publications

References 55 publications

Genetic Identification of a High-Affinity Ni Transporter and the Transcriptional Response to Ni Deprivation in Synechococcus sp. Strain WH8102

Genetic Identification of a High-Affinity Ni Transporter and the Transcriptional Response to Ni Deprivation in Synechococcus sp. Strain WH8102

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

Synchrony in dynamics of giant kelp forests is driven by both local recruitment and regional environmental controls

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