Drawing from the growing database of complex three-dimensional RNA structures, a systematic method has been developed for classifying and analyzing the variety of conformations adopted by nucleic acids. This method is based on the development of a reduced representation for nucleic acid backbone conformation, simplifying the formidable eight-dimensional problem that has long complicated nucleic acid conformational analysis. Two pseudotorsion angles (eta and theta) have been defined, based on the selection of two appropriate pivot points along the RNA backbone, P and C4'. These pseudotorsions, together with a complete library of conventional torsion angles, can be calculated for any RNA structure or all-atom model using a new program called AMIGOS. Having computed eta and theta pseudotorsions for each position on an RNA molecule, they can be represented on a two-dimensional plot similar to the phi-phi plots that have traditionally been used for protein conformational analysis. Like a Ramachandran plot, clusters of residues appear at discrete regions on an eta-theta plot. Nucleotides within these clusters share conformational properties, often belonging to the same type of structural motif such as A-platforms, sheared tandem purine-purine pairs and GNRA tetraloops. An eta-theta plot provides a two-dimensional representation of the conformational properties of an entire RNA molecule, facilitating rapid analysis of structural features. In addition to the utility of eta-theta plots for intuitive visualization of conformational space, the pseudotorsional convention described here should significantly simplify approaches to macromolecular modeling of RNA structure.
Here we provide evidence, based on prokaryote metabolic proxies and direct estimates of oxygen consumption, that the mesopelagic prokaryote assemblage in the subtropical Northeast Atlantic is an active one. It supports a high respiration (0.22 ± 0.05 μmol O 2 l −1 d −1 , corresponding to 68 ± 8 mmol CO 2 m −2 d −1 ), comparable to that of the epipelagic zone during the same period (64–97 mmol C m −2 d −1 ). Our findings suggest that mesopelagic prokaryotes in the NE subtropical Ocean, as well as in other eastern boundary regions, are important carbon sinks for organic matter advected from the highly productive coastal systems, and would play a key role in the global carbon cycle of the oceans.
<strong class="journal-contentHeaderColor">Abstract.</strong> Dark CO<sub>2</sub> fixation by bacteria is believed to be particularly important in oligotrophic ecosystems. However, only a few studies have characterized the role of bacterial dissolved inorganic carbon (DIC) fixation in global carbon dynamics. Therefore, this study quantified the primary production (PP), total bacteria dark CO<sub>2</sub> fixation (TB<sub>DIC</sub> fixation), and heterotrophic bacterial production (HBP) in the warm and oligotrophic Red Sea using stable isotope labeling and cavity ring-down spectroscopy (<sup>13</sup>C-CRDS). Additionally, we assessed the contribution of bacterial DIC fixation (TB<sub>DIC</sub> %) relative to the total DIC fixation (Total<sub>DIC</sub> fixation). Our study demonstrated that TB<sub>DIC</sub> fixation increased the Total<sub>DIC</sub> fixation from 2.03 to 60.45 µg C L<sup>−1</sup> d<sup>−1</sup> within the photic zone, contributing 13.18 % to 71.68 % with an average value of 33.95 ± 0.02 % of the photic layer Total<sub>DIC</sub> fixation. The highest TB<sub>DIC</sub> fixation values were measured at the surface and deep (400 m) water with an average value of 5.23 ± 0.45 µg µg C L<sup>−1</sup> d<sup>−1</sup>, and 4.95 ± 1.33 µg C L<sup>−1</sup> d<sup>−1</sup>, respectively. These findings suggest that the non-photosynthetic processes such as anaplerotic DIC reactions and chemo-autotrophic CO<sub>2</sub> fixation extended to the entire oxygenated water column. On the other hand, the % of TB<sub>DIC</sub> contribution to Total<sub>DIC</sub> fixation increased as primary production decreased (R<sup>2</sup> = 0.45, p <0.0001), suggesting the relevance of increased dark DIC fixation when photosynthetic production was low or absent, as observed in other systems. Therefore, when estimating the total carbon dioxide production in the ocean, dark DIC fixation must also be accounted as a crucial component of the carbon dioxide flux in addition to photosynthesis.
MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 374:75-84 (2009) - DOI: https://doi.org/10.3354/meps07715 Dissolved organic matter release in a Posidonia oceanica meadow Cristina Barrón1,2,*, Carlos M. Duarte1 1IMEDEA (CSIC-UIB), C/ Miquel Marqués 21, 07190 Esporles (Islas Baleares), Spain 2Present address: Vrije Universiteit Brussel, Analytical and Environmental Chemistry, Pleinlaan 2, 1050 Brussels, Belgium *Email: cbarron@vub.ac.be ABSTRACT: We examined annual nutrient changes (nitrate, phosphate and ammonium) and the net dissolved organic carbon (DOC), nitrogen (DON) and phosphorus (DOP) release using in situ benthic incubations in a Posidonia oceanica meadow and in unvegetated sediments of Magalluf Bay (Mallorca Island, Spain) at monthly intervals. We also examined the role of the P. oceanica meadow in the C:N:P ratio transformations by comparing the ratios between the inorganic and dissolved organic fluxes in the seagrass ecosystem and those in the plant material. Our results indicate that P. oceanica communities enhance DOC fluxes relative to adjacent unvegetated sediments. The net DOC release from the P. oceanica meadow represents 71% of the net community production. The C:N:P ratio in the flux of dissolved organic material (DOM) from the P. oceanica community (1450:69:1) exceeded the C:N:P ratio in the DOM flux of unvegetated sediment communities. The high flux of DOC release from this seagrass community might be enriched in carbon compounds, as these plants produce non-structural carbohydrates in excess. KEY WORDS: Benthic fluxes · Seagrasses · Dissolved organic carbon · Posidonia oceanica · Dissolved organic matter · Carbohydrates Full text in pdf format PreviousNextCite this article as: Barrón C, Duarte CM (2009) Dissolved organic matter release in a Posidonia oceanica meadow. Mar Ecol Prog Ser 374:75-84. https://doi.org/10.3354/meps07715 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 374. Online publication date: January 13, 2009 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2009 Inter-Research.
Abstract The introduction and establishment of exotic species often result in significant changes in recipient communities and their associated ecosystem services. However, usually the magnitude and direction of the changes are difficult to quantify because there is no pre‐introduction data. Specifically, little is known about the effect of marine exotic macrophytes on organic carbon sequestration and storage. Here, we combine dating sediment cores ( 210 Pb) with sediment eDNA fingerprinting to reconstruct the chronology of pre‐ and post‐arrival of the Red Sea seagrass Halophila stipulacea spreading into the Eastern Mediterranean native seagrass meadows. We then compare sediment organic carbon storage and burial rates before and after the arrival of H. stipulacea and between exotic ( H. stipulacea) and native ( C. nodosa and P. oceanica ) meadows since the time of arrival following a Before‐After‐Control‐Impact (BACI) approach. This analysis revealed that H. stipulacea arrived at the areas of study in Limassol (Cyprus) and West Crete (Greece) in the 1930s and 1970s, respectively. Average sediment organic carbon after the arrival of H. stipulacea to the sites increased in the exotic meadows twofold, from 8.4 ± 2.5 g C org m −2 year −1 to 14.7 ± 3.6 g C org m −2 year −1 , and, since then, burial rates in the exotic seagrass meadows were higher than in native ones of Cymodocea nodosa and Posidonia oceanica . Carbon isotopic data indicated a 50% increase of the seagrass contribution to the total sediment C org pool since the arrival of H. stipulacea . Our results demonstrate that the invasion of H. stipulacea may play an important role in maintaining the blue carbon sink capacity in the future warmer Mediterranean Sea, by developing new carbon sinks in bare sediments and colonizing areas previously occupied by the colder thermal affinity P. oceanica .
AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 60:175-191 (2010) - DOI: https://doi.org/10.3354/ame01421 Phyto- and bacterioplankton abundance and viability and their relationship with phosphorus across the Mediterranean Sea Sebastien Lasternas*, Susana Agustí, Carlos M. Duarte Department of Global Change Research, IMEDEA (CSIC-UIB), Instituto Mediterráneo de Estudios Avanzados, C/ Miquel Marqués 21, 07190 Esporles, Balearic Islands, Spain *Email: sebastien.lasternas@uib.es ABSTRACT: In a synoptic cruise performed during early summer, the composition and viability of pelagic communities of the Mediterranean Sea were studied across the different sub-basins and straits in relation to nutrient regimes and hydrological conditions. The picoplankton fraction dominated the pelagic community across the study region. Bacterioplankton was the most abundant (mean ± SE = 7.73 ± 0.39 × 105 cells ml–1) component of the plankton, reaching the highest abundance in the Marmara and Black Seas, and its abundance was positively related to phosphate concentration. Synechococcus spp. was abundant (3.70 ± 0.87 × 104 cells ml–1), and was most frequent in the surface layers of the West Basin and the Black Sea. Two populations of Synechococcus (Synechococcus sp. 1 and sp. 2) were identified, with contrasting distributions along the Mediterranean Sea. Prochlorococcus spp. was also present (3.77 ± 0.36 × 104 cells ml–1) and was associated with the deep chlorophyll maximum. Diatoms dominated the microphytoplankton except in the Black Sea, where dinoflagellates and flagellates became predominant. The percentage of living cells (%LC) of Synechococcus sp. 1 displayed a negative relationship with temperature, whereas that of Synechococcus sp. 2 increased with increasing temperature. Prochlorococcus spp. %LC was negatively related to inorganic nitrogen, but positively related to salinity. The viability of heterotrophic bacteria, dinoflagellates and Synechococcus sp. 1 increased with increasing phosphate, underlining the important role of phosphorus in the Mediterranean Sea. Our in situ observations relating survival to environmental forcing allowed the identification of competition and niche segregation within the coexisting populations. KEY WORDS: Phytoplankton · Bacterioplankton · Viability · Phosphorus · Mediterranean Sea Full text in pdf format PreviousNextCite this article as: Lasternas S, Agustí S, Duarte CM (2010) Phyto- and bacterioplankton abundance and viability and their relationship with phosphorus across the Mediterranean Sea. Aquat Microb Ecol 60:175-191. https://doi.org/10.3354/ame01421Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 60, No. 2. Online publication date: June 07, 2010 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2010 Inter-Research.
