Nitrate Reduction Functional Genes and Nitrate Reduction Potentials Persist in Deeper Estuarine Sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases

Can chlorophyll fluorescence be used to estimate the rate of photosynthetic electron transport within microphytobenthic biofilms?

Chlorophyll fluorometry has frequently been used to estimate the photosynthetic electron transport rate (ETR) within oxygenic organisms, One of the requirements of this method is that the absorptivity of the photosynthetic system is known. In the specific case of microphytobenthos within biofilms, it is known that cells migrate vertically over relatively short time periods. This can radically alter the absorptivity of the photosynthetic biomass as a whole and, potentially, could result in highly inaccurate values of ETR being calculated. In this study, both modulated, integrating fluorometry and high resolution imaging of fluorescence have been used to investigate the error introduced into the calculation of ETR by the vertical migration of cells, Estimates of ETR derived from fluorescence data were compared with rates of primary production measured using a C-14-radiotracer method, The effect of fluorescence from photosystem I (PS 1) on the calculated value of ETR was also assessed. Overall, these data suggest that PS I fluorescence can introduce significant errors into the estimation of ETR from diatom cultures and in the estimation of ETR from individual cells at the biofilm surface, when using high resolution imaging of chlorophyll fluorescence. Measurements made on intact biofilms under incident light showed an extremely poor correlation between estimated ETR (derived from fluorescence data) and primary production (measured by C-14 incorporation). The simplest explanation for this result is that the downward migration of cells decreased the amount of light absorbed by the photosynthetic biomass, which led to substantial errors in the calculation of ETR. The clear implication is that conventional (integrating) fluorometers cannot be used to determine rates of ETR from intact, migratory biofilms and that any realistic estimation of ETR within intact biofilms is likely to involve high resolution imaging of fluorescence.</p

Growth form defines physiological photoprotective capacity in intertidal benthic diatoms

International audienceIn intertidal marine sediments, characterized by rapidly fluctuating and often extreme lightconditions, primary production is frequently dominated by diatoms. We performed a comparativeanalysis of photophysiological traits in 15 marine benthic diatom species belonging to the fourmajor morphological growth forms (epipelon (EPL), motile epipsammon (EPM-M) and non-motileepipsammon (EPM-NM) and tychoplankton (TYCHO)) found in these sediments. Our analysesrevealed a clear relationship between growth form and photoprotective capacity, and identified fastregulatory physiological photoprotective traits (that is, non-photochemical quenching (NPQ) and thexanthophyll cycle (XC)) as key traits defining the functional light response of these diatoms. EPMNMand motile EPL showed the highest and lowest NPQ, respectively, with EPM-M showingintermediate values. Like EPL, TYCHO had low NPQ, irrespective of whether they were grown inbenthic or planktonic conditions, reflecting an adaptation to a low light environment. Our resultsthus provide the first experimental evidence for the existence of a trade-off between behavioural(motility) and physiological photoprotective mechanisms (NPQ and the XC) in the four majorintertidal benthic diatoms growth forms using unialgal cultures. Remarkably, although motilityis restricted to the raphid pennate diatom clade, raphid pennate species, which have adopted anon-motile epipsammic or a tychoplanktonic life style, display the physiological photoprotectiveresponse typical of these growth forms. This observation underscores the importance of growthform and not phylogenetic relatedness as the prime determinant shaping the physiologicalphotoprotective capacity of benthic diatoms

Resistance and resilience of benthic biofilm communities from a temperate saltmarsh to desiccation and rewetting

Periods of desiccation and rewetting are regular, yet stressful events encountered by saltmarsh microbial communities. To examine the resistance and resilience of microbial biofilms to such stresses, sediments from saltmarsh creeks were allowed to desiccate for 23 days, followed by rewetting for 4 days, whereas control sediments were maintained under a natural tidal cycle. In the top 2 mm of the dry sediments, salinity increased steadily from 36 to 231 over 23 days, and returned to seawater salinity on rewetting. After 3 days, desiccated sediments had a lower chlorophyll a (Chl a) fluorescence signal as benthic diatoms ceased to migrate to the surface, with a recovery in cell migration and Chl a fluorescence on rewetting. Extracellular Β-glucosidase and aminopeptidase activities decreased within the first week of drying, but increased sharply on rewetting. The bacterial community in the desiccating sediment changed significantly from the controls after 14 days of desiccation (salinity 144). Rewetting did not cause a return to the original community composition, but led to a further change. Pyrosequencing analysis of 16S rRNA genes amplified from the sediment revealed diverse microbial responses, for example desiccation enabled haloversatile Marinobacter species to increase their relative abundance, and thus take advantage of rewetting to grow rapidly and dominate the community. A temporal sequence of effects of desiccation and rewetting were thus observed, but the most notable feature was the overall resistance and resilience of the microbial community