PHOTOSYNTHESIS AND CALCIFICATION IN THE COCCOLITHOPHORE EMILIANIA HUXLEYI AND TWO HERMATYPIC CORALS, PORITES PORITES AND ACROPORA SP.

PhDMost global calcification is carried out by organisms which are also photosynthetic. In this study, the coccolithophore Emiliania huxleyi (Lohmann) Hay and Mohler and two species of hermatypic coral were used to: examine the effect of dissolved inorganic carbon (DIC) and light on photosynthesis and calcification; and determine the extent to which these two processes interact. A novel method of producing coccolith-less (non-calcifying) cells from calcifying cells of the same strain of E huxley! was developed thus allowing photosynthesis and calcification to be studied separately. The kinetics of photosynthesis in both types of cell, and of calcification in coccolith-bearing cells, were shown to be biphasic with respect to DIC concentration. The hiatus in all three cases was located at 1 mM DIC. This unusual pattern was shown to be the product of two carbon uptake mechanisms: an anion exchanger working at all DIC concentrations and an external carbonic anhydrase active only at low DIC concentrations. In contrast to the commonly-held view, this study demonstrated that calcification did not promote photosynthesis in E. huxleyi. Nevertheless, there was clearly strong biological control of calcification in this alga since DIC uptake was mediated by an anion transporter and a dehydroxylating enzyme. This work also showed that in E huxleyi, DIC addition enhanced photosynthesis at both limiting and saturating photon flux densities and that bicarbonate affected photochemical processes directly. Photosystem II activity was stimulated and non-photochemical quenching was reduced, possibly protecting the photosynthetic apparatus from damage by light. In the two corals; Porites porites and Acropora sp., strong biological control of calcium carbonate precipitation was also evident. Again, calcification did not stimulate photosynthesis. Calcification rates of Acropora sp. were monitored in the dark and although these were lower than in the light, they still increased dramatically with bicarbonate addition. This showed that high concentrations of the bicarbonate ion can compensate for the lack of light. Hence, it seems that in hermatypic corals, light-dependence of calcification may be facultative and not obligate. It is therefore clear from the results of this study that calcification and photosynthesis are not as closely coupled as has been previously thought. In neither E. huxleyi, nor in the hermatypic corals, were photosynthetic and calcification rates saturated at the present ambient DIC concentration of seawater

Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in MicrobiologyOpen 6 (2017): e467, doi:10.1002/mbo3.467.Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3-μm prefilter and 0.2-μm collection filter. Although this approach targeted bacteria by removing comparatively large eukaryotic cells, the metagenome from the ES-5 sample (5 PSU) nevertheless contained an abundance of diatom DNA. Biogeochemical measurements and prior studies indicated that this finding resulted from the leakage of cellular material due to freshwater diatom lysis at low salinity. Relative to the other metagenomes, the bacterial fraction of ES-5 was dramatically depleted of genes annotated as Bacteroidetes and lysogenic bacteriophages, but was overrepresented in DNA of protists and Myxococcales bacterivores. We suggest the following equally plausible scenarios for the microbial response to phytoplankton lysis: (1) Bacteroidetes depletion in the free-living fraction may at least in part be caused by their attachment to fluvial diatoms as the latter are lysed upon contact with low-salinity estuarine waters; (2) diatom particle colonization is likely followed by rapid bacterial growth and lytic phage infection, resulting in depletion of lysogenic bacteriophages and host bacteria; and (3) the subsequent availability of labile organic matter attracted both grazers and predators to feed in this estuarine biogeochemical “hotspot,” which may have additionally depleted Bacteroidetes populations. These results represent the first detailed molecular analysis of the microbial response to phytoplankton lysis at the freshwater–brackish water interface in the fast-flowing Columbia River estuary.National Science Foundation Grant Numbers: OCE 0424602, MCB 064446

Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in MicrobiologyOpen 6 (2017): e00522, doi:10.1002/mbo3.522.Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production (3H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1–24 PSU), but summer non-ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free-living (0.2–3 μm) assemblages of non-ETM waters were similar to each other, indicating that particle-attached (>3 μm) non-ETM bacteria do not develop a distinct community. Brackish water type (ETM or non-ETM) is thus a major factor affecting particle-attached bacterial communities. Heterotrophic production was higher in particle-attached than free-living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM-impacted waters). However, free-living communities showed higher productivity prior to or after an ETM event (i.e., non-ETM-impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the existence of three particle types characterized by different bacterial communities in ETM, ETM-impacted, and non-ETM-impacted brackish waters. Taxonomic analysis suggests that ETM key biological function is to remineralize organic matter.National Science Foundation Grant Number: OCE-042460

Red Waters of Myrionecta rubra are Biogeochemical Hotspots for the Columbia River Estuary with Impacts on Primary/Secondary Productions and Nutrient Cycles

The localized impact of blooms of the mixotrophic ciliate Myrionecta rubra in the Columbia River estuary during 2007-2010 was evaluated with biogeochemical, light microscopy, physiological, and molecular data. M. rubra affected surrounding estuarine nutrient cycles, as indicated by high and low concentrations of organic nutrients and inorganic nitrogen, respectively, associated with red waters. M. rubra blooms also altered the energy transfer pattern in patches of the estuarine water that contain the ciliate by creating areas characterized by high primary production and elevated levels of fresh autochthonous particulate organic matter, therefore shifting the trophic status in emergent red water areas of the estuary from net heterotrophy towards autotrophy. The pelagic estuarine bacterial community structure was unaffected by M. rubra abundance, but red waters of the ciliate do offer a possible link between autotrophic and heterotrophic processes since they were associated with elevated dissolved organic matter and showed a tendency for enhanced microbial secondary production. Taken together, these findings suggest that M. rubra red waters are biogeochemical hotspots of the Columbia River estuary.Keywords: Myrionecta rubra, Biogeochemical cycles, Red waters, Mesodinium rubrum, Columbia River estuar

Co-variation of crenarchaeol and branched GDGTs in globally-distributed marine and freshwater sedimentary archives

Two major types of glycerol dialkyl glycerol tetraethers (GDGTs) are commonly used in paleoecological and paleoclimatological reconstructions: isoprenoidal and branched GDGTs. In aquatic environments, it was originally assumed that isoprenoidal GDGTs, especially crenarchaeol, derive mainly from aquatic Thaumarchaeota, whilst branched GDGTs are an allochthonous input derived from soil Bacteria. Recently, direct co-variation of crenarchaeol and branched GDGTs has been described in two marine sedimentary records, and this observation suggests in situ production of branched GDGTs is possible at least in some aquatic environments. After investigating 30 published and unpublished data sets from downcore and surface sediments as well as sediment traps from 19 distinct regions around the world, we found a widespread significant correlation between concentrations of branched GDGTs and crenarchaeol (p<0.01; r²=0.57-0.99), even when normalized against TOC, where available. These data sets include freshwater and marine environments with varying distances from the shore, varying redox conditions and different terrestrial matter input pathways. Our findings from this large-scale data set suggest that a common or mixed source for both GDGT types is actually commonplace in lacustrine and marine settings.Keywords: Branched GDGTs, Oceans, Crenarchaeol, Archaea, Isoprenoid GDGTs, Lakes, In situ production

Photosynthesis and calcification in the coccolithophore, emiliana huxleyi, and two hermatypic corals, porites porites and acropora sp

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt

Author Posting. © Inter-Research, 2009. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 55 (2009): 189-201, doi:10.3354/ame01294.Pelagic archaeal phylogenetic diversity and the potential for crenarchaeotal nitrification of Group 1.1a were determined in the rivers Rhine and Têt by 16S rRNA sequencing, catalyzed reported deposition-fluorescence in situ hybridization (CARD–FISH) and quantification of 16S rRNA and functional genes. Euryarchaeota were, for the first time, detected in temperate river water even though a net predominance of crenarchaeotal phylotypes was found. Differences in phylogenic distribution were observed between rivers and seasons. Our data suggest that a few archaeal phylotypes (Euryarchaeota Groups RC-V and LDS, Crenarchaeota Group 1.1a) are widely distributed in pelagic riverine environments whilst others (Euryarchaeota Cluster Sagma-1) may only occur seasonally in river water. Crenarchaeota Group 1.1a has recently been identified as a major nitrifier in the marine environment and phylotypes of this group were also present in both rivers, where they represented 0.3% of the total pelagic microbial community. Interestingly, a generally higher abundance of Crenarchaeota Group 1.1a was found in the Rhine than in the Têt, and crenarchaeotal ammonia monooxygenase gene (amoA) was also detected in the Rhine, with higher amoA copy numbers measured in February than in September. This suggests that some of the Crenarchaeota present in river waters have the ability to oxidize ammonia and that riverine crenarchaeotal nitrification of Group 1.1a may vary seasonally.The present study is part of the Land–Ocean Interactions in the Coastal Zone (LOICZ) project supported by the Research Council for Earth and Life Science (ALW), with financial aid from the Netherlands Organisation for Scientific Research (NWO) (grant no. 014.27.003 to J.S.S.D.)

Ubiquitous Dissolved Inorganic Carbon Assimilation by Marine Bacteria in the Pacific Northwest Coastal Ocean as Determined by Stable Isotope Probing

<div><p>In order to identify bacteria that assimilate dissolved inorganic carbon (DIC) in the northeast Pacific Ocean, stable isotope probing (SIP) experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM ¹³C-NaHCO₃, doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. <em>Alteromonadales</em> and <em>Oceanospirillales</em> contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of <em>Burkholderia</em>. DIC-assimilating bacteria among <em>Deltaproteobacteria</em> included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process.</p> </div