Gilles Vétion

Biochemical characteristics of settling particulate organic matter at two north-western Mediterranean sites : a seasonal comparison

Abstract Gross sedimentation rates (GSR) and the main biochemical characteristics of settling particulate matter were monitored at two NW Mediterranean sites (the Bay of Banyuls-sur-Mer, France, and the Medes Islands, Spain) throughout a year to assess possible differences in particulate organic matter (POM) availability to the benthic community. A similar seasonal pattern was observed at both sites with higher organic contents and lower GSR during the spring–summer than during the autumn–winter period. At both sites, there was a negative correlation between GSR and sediment trap organic contents, which is indicative of the importance of resuspension in driving GSR. Along the same line, GSR in Medes correlated positively with wave height. The principal component analysis based on GSR and biochemical characteristics of sediment trap material always segregated samples from the two studied sites mostly due to the occurrence of higher lipid and lower carbohydrate contents in Medes. These differences were indicative of the presence of more labile settling POM in the Medes Islands. They were more pronounced during the spring–summer than during the autumn–winter period. Such a pattern may reflect differences in the sensitivity of the two studied sites to resuspension. According to this interpretation, between-sites differences would be high when resuspension is low (i.e. during the spring–summer period when resuspension would mainly affect Banyuls) and become low when resuspension is high (autumn–winter period when resuspension would affect both sites).

Growth rates and RNA: DNA ratios in Paracentrotus lividus (Echinodermata: Echinoidea) fed on benthic macrophytes

We measured growth rates and RNA: DNA ratios of young sea urchins Paracentrotus lividus cultured for 6 months in the laboratory where they were fed on 12 macrophytes (Rissoella verruculosa, Cystoseira mediterranea, Corallina elongata, Stypocaulon scoparium, Padina pavonica, Ulva rigida, Cystoseira compressa, Colpomenia sinuosa, Posidonia oceanica, Codium vermilara, Asparagopsis armata, and Dilophus spiralis). Average increases in test diamter ranged from 0.3 mm · month dash1 for urchins fed on Dilophus spiralis to 1.9 mm · month 1 for urchins fed on Rissoella verruculosa. Average increases in wet mass ranged from 0.10 g wet mass · month 1 for urchins fed on Dilophus spiralis and Asparagopsis armata to 1.20 g wet mass · month 1 for urchins fed on Rissoella verruculosa. In terms of proteins, average growth rates ranged from 0.23 mg protein · month−1 for urchins fed on Codium vermilara to 3.08 mg protein · month−1 for urchins fed on Cystoseira mediterranea. In all three cases, growth rates were significantly (p = 0.0001) affected by the nature of the offered macrophytes. There was a high correlation between increase in test diameter and (1) increase in wet mass and (2) increase in proteins (r = 0.98 and 0.83, respectively). RNA: DNA ratios of Paracentrotus lividus (0.47 < r < 2.02) were within the range of what has previously been reported for larval fishes, bivalves, cephalopods, and crustaceans. Average RNA: DNA ratios were significantly affected by the food regime. However, results of a posteriori LSD tests were different for growth rates and RNA: DNA ratios. There were significantly (p = 0.0001, 0.0001, and 0.0004, respectively) positive correlations between growth rate (in terms of diameter, wet mass, and proteins) and RNA : DNA ratio. However these relationships accounted for only 23.8, 23.6, and 19.4%, respectively, of the variance of RNA : DNA ratios. These results suggest that the use of RNA : DNA ratios would be inefficient in predicting growth rates of field collected Paracentrotus lividus.

Nutrients, algal biomass and communities in land-fast ice and seawater off Adélie Land (Antarctica)

Land-fast ice in the vicinity of Adélie Land was sampled during spring 1995. The ice was annual, thin, with no consistent snow cover, and exposed to oceanic conditions. Temporal and spatial variations of the vertical pigment distribution were studied in relation to environmental factors, during the break up of the ice. Different levels were sampled in the congelation ice and the platelet ice-like layer (PLI). Under-ice water and open water masses were also sampled. The algal biomass was greater in the PLI (24 ±14 μg chl a l−1 offshore and up to 9 mg chl a l−1 near-shore), than in the under-ice water, and fell to 0.9 ± 0.64 μg chl al−1 in open water masses. Homogenous low pigment concentrations were detected in the upper levels of congelation ice. A gradient was identified along a 7 km seaward transect, sampled in November, with the lowest biomass offshore. The integrated pigment concentrations in fast ice reached very high levels 500 mg chl a m−2 near the coast and 0.8 mg m−2 offshore), with apparently no relationship with either the ice thickness or snow cover. In the congelation ice nutrient concentrations were low and their distribution homogenous, whereas in the PLI high concentrations of nitrate (up to 100–300 μM NO3) and silicic acid [30–100 μM Si(OH)4] were detected, often related to high pigment concentrations and proximity to islands. The sea ice algae communities were diverse, but mostly composed of chain-forming and tube-dwelling pennate diatoms (Amphiprora, Berkeleya, Nitzschia and Navicula). Cell densities in PLI reached up to 1010 cells l−1. At very low biomass and cell densities 2 104 cells l−1) the phytoplankton also had a low diversity; some species were similar to those of the PLI, such as Navicula glaciei, but other were typically planktonic (Chaetoceros). At sea ice break-up it is estimated that a significant proportion of particulate matter (up to 0.5 g chl a m−2 near-shore) was transferred to the underlying water masses (on an average 15 t POC km−1 shoreline).

Microphyte pigments and resting spores at the water-sediment interface in the Subantarctic deep sea (Indian sector of the Southern Ocean)

During the ANTARES I cruise (April–May 1993) in the Indian Sector of the Southern Ocean, deep-sea sediments were collected using a multiple gravity corer in the Polar Frontal Zone (PFZ) and “frontal zone” (between Crozet and Kerguelen Islands) and in the Permanently Open Ocean Zone (POOZ, south-west of Kerguelen and Heard Islands). Microphyte biomass indicators (Chl a, b, c and related phaeopigments measured by spectrofluorometry, tests on natural fluorescence, and detection of encysted diatoms observed by scanning electron microscopy SEM) were carried out on both sediment and overlying “fluff”, whenever present. Evaluation of the phytoplankton biomass in the overlying surface water masses also was performed at each sampling station. The phytoplankton biomass was, on the whole, very low and decreased from north to south (0.25− 0.10 μg 1−1 Chl a, with a maximum on the “frontal zone”), whereas the sediment-water interface of the southern sampling stations (POOZ) was pigment-enriched. A consistent bioclastic “fluffy” layer was only present in the POOZ stations (up to 13 μg 1−1 Chl a, 157 μg 1−1 Phaeo a). Biodeposition of this type was very thin or absent north of the PF (Polar Front), illustrating stronger advection in the northern part of the study area. Hydrodynamic studies of the Crozet Basin and the presence of benthic pennate coastal diatoms at the sediment interface of these northern stations further suggest increased advective activity in the north. Surficial sediments (first 5 mm) also were enriched with pigments in the POOZ (up to 0.15 μg g−1 DW Chl a, 3.5 μg g−1 DW Phaeo a), whereas in the PFZ the Chl a concentrations were insignificant. Pigment gradients in the sediments, particularly well marked in the POOZ, indicate the absence of a secondary intense reworking such as bioturbation or resuspension. Nevertheless, also in the POOZ, an unusual and well preserved megafaunal faecal cast was sampled and analysed. Sediments at southern stations (50–55°S, 56–75°E; 3600–4700 m depth) were the most enriched with encysted microphytic cells (mainly diatoms belonging to the genus Chaetoceros). This was related primarily to the presence of a “fluffy” layer, composed mainly of well preserved detritic frustules of various diatom genera, including robust Nitzschia and Thalassiosira as well as chains of delicate Chaetoceros, Corethron and Rhizosolenia. Well preserved coccoliths and silicoflagellates also were noticeable in the fluffs. Revival tests (cultures on F2 medium, initiated with samples from the water-sediment interface) were positive for the southern stations, leading to low diversity diatom assemblages dominated by the genera Chaetoceros and Nitzschia.

River organic matter shapes microbial communities in the sediment of the Rhône prodelta

Microbial-driven organic matter (OM) degradation is a cornerstone of benthic community functioning, but little is known about the relation between OM and community composition. Here we use Rhône prodelta sediments to test the hypothesis that OM quality and source are fundamental structuring factors for bacterial communities in benthic environments. Sampling was performed on four occasions corresponding to contrasting river-flow regimes, and bacterial communities from seven different depths were analyzed by pyrosequencing of 16S rRNA gene amplicons. The sediment matrix was characterized using over 20 environmental variables including bulk parameters (for example, total nitrogen, carbon, OM, porosity and particle size), as well as parameters describing the OM quality and source (for example, pigments, total lipids and amino acids and δ13C), and molecular-level biomarkers like fatty acids. Our results show that the variance of the microbial community was best explained by δ13C values, indicative of the OM source, and the proportion of saturated or polyunsaturated fatty acids, describing OM lability. These parameters were traced back to seasonal differences in the river flow, delivering OM of different quality and origin, and were directly associated with several frequent bacterial operational taxonomic units. However, the contextual parameters, which explained at most 17% of the variance, were not always the key for understanding the community assembly. Co-occurrence and phylogenetic diversity analysis indicated that bacteria–bacteria interactions were also significant. In conclusion, the drivers structuring the microbial community changed with time but remain closely linked with the river OM input.

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater

Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.

Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular- mass polycyclic aromatic hydrocarbons

A Gram-negative, rod-shaped, halotolerant bacterium, designated strain CEE_131(T), which degraded high-molecular-mass polycyclic aromatic hydrocarbons of four and five rings, was isolated from intertidal sediment of Corcubion Ria in Cee, A Coruña, Spain. Direct sequencing showed ambiguities and suggested heterogeneity. Cloned 16S rRNA gene sequence PCR products yielded five different sequences varying at five positions. Strain CEE_131(T) showed rather distant relationships to its phylogenetically closest neighbours, including the genera Rheinheimera and Serratia , exhibiting 91 % sequence similarity with Rheinheimera perlucida BA131(T) and Serratia proteamaculans subsp. quinovora DSM 4597(T). The major fatty acids were C(16 : 1 )omega7c, C(16 : 0) and C(18 : 1)omega7c. The DNA G+C content was 41.7 mol%. On the basis of these distinct phenotypic and genotypic characteristics, strain CEE_131(T) is considered to represent a novel species in a new genus in the class Gammaproteobacteria, for which the name Gallaecimonas pentaromativorans gen. nov., sp. nov. is proposed. The type strain is CEE_131(T) (=DSM 21945(T)=CECT 7479(T)).

Disturbance Increases Microbial Community Diversity and Production in Marine Sediments

Disturbance strongly impacts patterns of community diversity, yet the shape of the diversity-disturbance relationship remains a matter of debate. The topic has been of interest in theoretical ecology for decades as it has practical implications for the understanding of ecosystem services in nature. One of these processes is the remineralization of organic matter by microorganisms in coastal marine sediments, which are periodically impacted by disturbances across the sediment-water interface. Here we set up an experiment to test the hypothesis that disturbance impacts microbial diversity and function during the anaerobic degradation of organic matter in coastal sediments. We show that during the first 3 weeks of the experiment, disturbance increased both microbial production, derived from the increase in microbial abundance, and diversity of the active fraction of the community. Both community diversity and phylogenetic diversity increased, which suggests that disturbance promoted the cohabitation of ecologically different microorganisms. Metagenome analysis also showed that disturbance increased the relative abundance of genes diagnostic of metabolism associated with the sequential anaerobic degradation of organic matter. However, community composition was not impacted in a systematic way and changed over time. In nature, we can hypothesize that moderate storm disturbances, which impact coastal sediments, promote diverse, and productive communities. These events, rather than altering the decomposition of organic matter, may increase the substrate turnover and, ultimately, remineralization rates.

Can UV radiation affect benthic deposit-feeders through biochemical alteration of food resources? An experimental study with juveniles of the benthic polychaete Eupolymnia nebulosa.

The growth, tentacle development and feeding activity of the benthic polychaete Eupolymnia nebulosa were examined to determine whether UV might affect marine deposit-feeders indirectly through the modification of the nutritional quality of their resources. Since marine invertebrates have higher nutritional requirements during the period following settlement, we tested the effect of UV-altered phytodetritus on freshly settled juveniles of E. nebulosa. Phytodetritus was prepared from cultures of the diatom Skeletonema costatum either grown under or sheltered from UVB radiation. Sterol content of phytodetritus was unmodified by UV radiation. Conversely, phytodetritus was noticeably depleted in polyunsaturated fatty acids. Growth and tentacle development of juveniles fed on altered phytodetritus were reduced by 35% and 15% respectively, suggesting potential deficiencies in essential nutrients. In response to the lower quality of the phytodetritus, juveniles explored a wider area as they search for food, a strategy that could compensate for low food quality.