Denise Cummings

Diurnal changes in photochemical efficiency and xanthophyll concentrations in shallow water reef corals : evidence for photoinhibition and photoprotection

Abstract Diurnal patterns of photoinhibition have been identified in seven species of shallow water reef corals from the Andaman Sea, off the west coast of Thailand, using pulse amplitude fluorometry. Photochemical efficiency (Fv/Fm) and quantum yield (ΔF/Fm∑) of symbiotic dinoflagellates within the corals declined after dawn to reach a minimum between midday and early afternoon, recovering to former dawn levels by early evening. Parallel studies on the xanthophylls diadinoxanthin (Dn) and diatoxanthin (Dt), and their inter-conversion, also revealed a strong diurnal pattern as well as inverse correlations between the xanthophyll ratio Dt/(Dn+Dt) and Fv/Fm and ΔF/Fm′. These findings suggest a photoprotective function for these pigments.

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB) and metatranscriptomes (157 MB) for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer) and including day and night samples. This is the first microbial ‘multi-omic’ study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1) Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2) Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3) Diversity is highest in winter and at night; 4) Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar), while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups) of genes; 5) Changes in key genes occur among seasons and between day and night (i.e., photosynthesis); but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan sequences underscores the need to determine the gene products of sequences with currently unknown function.

Phytoplankton pigment and absorption characteristics along meridional transects in the Atlantic Ocean

Pigment patterns and associated absorption properties of phytoplankton were investigated in the euphotic zone along two meridional transects in the Atlantic Ocean, between the UK and the Falkland Islands, and between South Africa and the UK. Total chlorophyll a (TChla=MVChla+DVChla+chlorophyllide a) concentrations and the biomarker pigments for diatoms (fucoxanthin), nanoflagellates and cyanobacteria (zeaxanthin) appeared to have similar distribution patterns in the spring and in the autumn in the temperate NE Atlantic and the northern oligotrophic gyre. Divinyl chlorophyll a levels (prochlorophytes) were greater in spring at the deep chlorophyll maximum in the oligotrophic gyre, however. Marked seasonal differences were observed in the NW African upwelling region. TChla concentrations were twice as high in the upper mixed layer in the spring, with the community dominated by diatoms and prymnesiophytes (19?-hexanoyloxyfucoxanthin). A layered structure was prevalent in the autumn where cyanobacteria, diatoms and prymnesiophytes were located in the upper water column and diatoms and mixed nanoflagellates at the sub-surface maximum. In the South Atlantic, the Benguela upwelling ecosystem and the Brazil-Falklands Current Confluence Zone (BFCCZ) were the most productive regions with the TChla levels being twice as high in the Benguela. Diatoms dominated the Benguela system, while nanoflagellates were the most ubiquitous group in the BFCCZ. Pigment concentrations were greater along the eastern boundary of the southern oligotrophic gyre and distributed at shallower depths. Deep chlorophyll maxima were a feature of the western boundary oligotrophic waters, and cyanobacteria tended to dominate the upper water column along both transects with a mixed group of nanoflagellates at the chlorophyll maximum. Absorption coefficients were estimated from spectra reconstructed from pigment data. Although absorption was greater in the productive areas, the TChla-specific coefficients were higher in oligotrophic regions. In communities that were dominated by diatoms or nanoflagellates, pigment absorption was generally uniform with depth and attenuating irradiance, with TChla being the major absorbing pigment at 440 nm and photosynthetic carotenoids (PSC) at 490 nm. Absorption by chlorophyll c and photoprotective carotenoids (PPC) was much lower. Populations where cyanobacteria were prevalent were characterized by high PPC absorption, particularly at 490 nm, throughout most of the euphotic zone. The data suggested that the effect of pigments on the variability of phytoplankton absorption was due primarily to the variations in absorption by PPC.

Pigment chemotaxonomic distributions of phytoplankton during summer in the western Mediterranean

Pigment distributions were investigated in the western Mediterranean basin during July 1993 to document the trophic status of the summer phytoplankton community. The characteristic deep chlorophyll maximum (DCM) was observed at all oceanic stations, and chlorophyll a concentrations of up to 1700 ng 1−1 were measured in the DCM in the northern regions. High chlorophyll a levels (2000–3000 ng 1−1) were determined in the lower reaches of the Rhone River, accompanied by high fucoxanthin levels. Fucoxanthin was also the dominant accessory pigment at the inshore stations influenced by the Rhone, while hexanoyloxyfucoxanthin was the major carotenoid at all other northern sites. Divinyl chlorophyll a concentrations were very low in the north (<30 ng 1−1) and only accounted for a maximum of 8% of the total chlorophyll a. Chlorophyll a levels were much lower in the southwestern Mediterranean; we estimate that divinyl chlorophyll a contributed 11–40% to the total chlorophyll a. Fucoxanthin was the prominent accessory pigment at Gibraltar, but hexanoyloxyfucoxanthin, chlorophyll b, zeaxanthin and divinyl chlorophyll a were more important at the other southern stations. The pigment data were used to estimate the contributions of prokaryotes (cyanobacteria and prochlorophytes) and eukaryotes to the total chlorophyll a at the surface and in the DCM. Overall, we determined that eukaryotes accounted for most of the chlorophyll a biomass, contributing 53–98%, and the prokaryote proportion was 2–47%. The pigment pattern revealed that the phytoplankton assemblage was not homogeneous and trophic conditions ranged from eutrophic in coastal and frontal regions where fucoxanthin containing diatoms dominated, to oligotrophic throughout most of the basin. Higher chlorophyll a biomass and dominant hexanoyloxyfucoxanthin containing prymnesiophytes were observed in the northern sector, while an increased prominence of prokaryotes in the south suggested that the southern sector was more oligotrophic.

Impact of ocean acidification on benthic and water column ammonia oxidation

Ammonia oxidation is a key microbial process within the marine N-cycle. Sediment and water column samples from two contrasting sites in the English Channel (mud and sand) were incubated (up to 14 weeks) in CO2-acidified seawater ranging from pH 8.0 to pH 6.1. Additional observations were made off the island of Ischia (Mediterranean Sea), a natural analogue site, where long-term thermogenic CO2 ebullition occurs (from pH 8.2 to pH 7.6). Water column ammonia oxidation rates in English Channel samples decreased under low pH with near-complete inhibition at pH 6.5. Water column Ischia samples showed a similar though not statistically significant trend. However, sediment ammonia oxidation rates at all three locations were not affected by reduced pH. These observations may be explained by buffering within sediments or low-pH adaptation of the microbial ammonia oxidizing communities. Our observations have implications for modeling the future impact of ocean acidification on marine ecosystems.

Marked seasonality in the concentrations and sea‐to‐air flux of volatile iodocarbon compounds in the western English Channel

[1] In the first seasonal study of volatile iodinated organic compounds (VICs) in the open sea, concentrations of five VICs were measured approximately weekly at four depths, over 20 months from July 2002 to April 2004, in the western English Channel. Seawater concentrations varied seasonally by an order of magnitude for all five compounds, with winter minima and, generally, late summer/autumn maxima. The average contribution to the dissolved VIC pool was chloroiodomethane (39%), diiodomethane (33%), iodomethane (22%), iodoethane (6%), and bromoiodomethane (4%). Total sea-to-air flux of iodine atoms carried by the VICs (15.5 mmol I m � 2 yr � 1 ) was approximately fourfold higher than that for iodomethane alone. This contrasts with previous studies that indicated that iodomethane was the main vector of iodine away from macroalgal beds. The estimated sea-to-air flux takes into account the significant airside control of the gas exchange of certain VICs, particularly diiodomethane; for which a 30% reduction in average daily flux was observed when an additional airside transfer velocity was included in the calculations. Because of their high reactivity, chloroiodomethane and diiodomethane are likely to drive the atmospheric organic iodine chemistry over these shelf seas, rather than the monohalogenated VICs.

Microplankton community structure and the impact of microzooplankton grazing during an Emiliania huxleyi bloom, off the Devon coast

Phytoplankton and microzooplankton community structure and the impact of microzooplankton grazing were investigated during a one-day study of an Emiliania huxleyi bloom off the coast of Devon during July 1999. Vertical profiles were undertaken at four stations, along a transect which crossed from a low reflectance to a high reflectance area as seen by satellite imagery. Microzooplankton dilution grazing experiments, coupled with pigment analysis to determine class specific grazing rates, were performed at two of these stations. Highest concentrations of chlorophyll-a (5.3 mg m -3 ) and accessory pigments were measured inside the area of high reflectance. Phytoplankton standing stocks ranged between 1588 and 5460 mg C m -2 and were also highest in the area of high reflectance. The phytoplankton community was dominated by coccolithophores and diatoms in low reflectance waters and by photosynthetic dinoflagellates in high reflectance areas. Microzooplankton standing stocks ranged between 905 and 2498 mg C m -2 . Protozoa dominated the microzooplankton community. The protozoan community comprised a relatively even mixture of heterotrophic dinoflagellates, non-choreotrich and choreotrich ciliates in low reflectance waters. However, non-choreotrich ciliates dominated the communities inside the high reflectance area. Of the heterotrophic ciliates, a predatory ciliate Askenasia sp. dominated both non-choreotrich abundance and biomass. Results from grazing experiments showed that 60-64% of the chlorophyll-a biomass was consumed daily by the microzooplankton. Highest grazing mortality was associated with peridinin (dinoflagellates) and alloxanthin (cryptophytes). Lower grazing rates were found on fucoxanthin (diatoms and prymnesiophytes). Our results indicate that grazing on E. huxleyi in the area of remotely sensed high reflectance was low and highest grazing was on photosynthetic dinoflagellates and cryptophytes.

Phytoplankton pigment distributions and associated fluxes in the Bellingshausen Sea during the austral spring 1992

Abstract Pigment distribution patterns were investigated in the marginal ice zone of the Bellingshausen Sea and across the Drake Passage during the austral spring of November/December 1992. Elevated chlorophyll a (chl a) and fucoxanthin levels were observed at the Sub-Antarctic and Polar Fronts in the Drake Passage and at the Southern Polar Front in the Bellingshausen Sea. Investigations at 5 stations along 85°W in the Bellingshausen Sea between 70.3°S and 67.5°S revealed high concentrations of chl a (up to 24 000 ng l−1 ice melt) and fucoxanthin in hard pack ice samples and very low levels of pigments in the underlying water column ( 70%), although prymnesiophytes (hexanoyloxyfucoxanthin) and green algae (chl b) were present in smaller proportions. Diatoms dominated at the open water stations (>60%) and were prominent in the water column under the pack ice (52–61%). However, at the ice melt stations, prymnesiophytes (40–45%), green algae (11–13%) and, to a lesser extent, cryptophytes (4–6%; alloxanthin) collectively contributed more to the chl a biomass than the diatoms (37–42%). Budgeting the proportions of chloropigments indicated an increase in chlorophyllide a and phaeopigments from the ice to the northern open water stations, with chlorophyllide a being prominent in the upper water column and in the ice. Export fluxes of phytoplankton–carbon and phytodetritus in the upper 100 m were estimated from chloropigment inventories and residence times of 210 Po radionuclide reported by Shimmield et al. (1995) [Shimmield, G.B., Ritchie, G., Fileman, T.W., 1995. The impact of marginal zone processes on the distribution of 210 Pb , 210 Po and 234 Th and implications for new production in the Bellingshausen Sea Antarctica. Deep-Sea Res. II, 42 (1995) 1313–1335], revealing very low fluxes at the ice stations and up to 29 mg phyto-C m−2 day−1 at the open water high chlorophyll locality.

Uncertainty in Ocean-Color Estimates of Chlorophyll for Phytoplankton Groups

Over the past decade, techniques have been presented to derive the community structure of phytoplankton at synoptic scales using satellite ocean-colour data. There is a growing demand from the ecosystem modelling community to use these products for model evaluation and data assimilation. Yet, from the perspective of an ecosystem modeller these products are of limited use unless: (i) the phytoplankton products provided by the remote-sensing community match those required by the ecosystem modellers; and (ii) information on per-pixel uncertainty is provided to evaluate data quality. Using a large dataset collected in the North Atlantic, we re-tune a method to estimate the chlorophyll concentration of three phytoplankton groups, partitioned according to size (pico- (20μm)). The method is modified to account for the influence of sea surface temperature, also available from satellite data, on model parameters and on the partitioning of microphytoplankton into diatoms and dinoflagellates, such that the phytoplankton groups provided match those simulated in a state of the art marine ecosystem model (the European Regional Seas Ecosystem Model, ERSEM). The method is validated using another dataset, independent of the data used to parameterise the method, of more than 800 satellite and in situ match-ups. Using fuzzy-logic techniques for deriving per-pixel uncertainty, developed within the ESA Ocean Colour Climate Change Initiative (OC-CCI), the match-up dataset is used to derive the root mean square error and the bias between in situ and satellite estimates of the chlorophyll for each phytoplankton group, for 14 different optical water types (OWT). These values are then used with satellite estimates of OWTs to map uncertainty in chlorophyll on a per pixel basis for each phytoplankton group. It is envisaged these satellite products will be useful for those working on the validation of, and assimilation of data into, marine ecosystem models that simulate different phytoplankton groups.

Potential controls of isoprene in the surface ocean

Isoprene surface ocean concentrations and vertical distribution, atmospheric mixing ratios, and calculated sea-to-air fluxes spanning approximately 125° of latitude (80°N–45°S) over the Arctic and Atlantic Oceans are reported. Oceanic isoprene concentrations were associated with a number of concurrently monitored biological variables including chlorophyll a (Chl a), photoprotective pigments, integrated primary production (intPP), and cyanobacterial cell counts, with higher isoprene concentrations relative to all respective variables found at sea surface temperatures greater than 20°C. The correlation between isoprene and the sum of photoprotective carotenoids, which is reported here for the first time, was the most consistent across all cruises. Parameterizations based on linear regression analyses of these relationships perform well for Arctic and Atlantic data, producing a better fit to observations than an existing Chl a-based parameterization. Global extrapolation of isoprene surface water concentrations using satellite-derived Chl a and intPP reproduced general trends in the in situ data and absolute values within a factor of 2 between 60% and 85%, depending on the data set and algorithm used.