Distribution of anaerobic methane-oxidizing and sulfate-reducing communities in the G11 Nyegga pockmark,Norwegian Sea

Pockmarks are seabed geological structures sustaining methane seepage in cold seeps. Based on RNA-derived sequences the active fraction of the archaeal community was analysed in sediments associated with the G11 pockmark, in the Nyegga region of the Norwegian Sea. The anaerobic methanotrophic Archaea (ANME) and sulfate-reducing bacteria (SRB) communities were studied as well. The vertical distribution of the archaeal community assessed by PCR-DGGE highlighted the presence of ANME-2 in surface sediments, and ANME-1 in deeper sediments. Enrichments of methanogens showed the presence of hydrogenotrophic methanogens of the Methanogenium genus in surface sediment layers as well. The active fraction of the archaeal community was uniquely composed of ANME-2 in the shallow sulfate-rich sediments. Functional methyl coenzyme M reductase gene libraries showed that sequences affiliated with the ANME-1 and ANME-3 groups appeared in the deeper sediments but ANME-2 dominated both surface and deeper layers. Finally, dissimilatory sulfite reductase gene libraries revealed a high SRB diversity (i.e. Desulfobacteraceae, Desulfobulbaceae, Syntrophobacteraceae and Firmicutes) in the shallow sulfate-rich sediments. The SRB diversity was much lower in the deeper section. Overall, these results show that the microbial community in sediments associated with a pockmark harbour classical cold seep ANME and SRB communities.     

Isolation of sulfate‐reducing bacteria from deep sediment layers of the pacific ocean

Bacterial populations exist at great depths in marine sediments, but little is known about the type and characteristics of organisms in this unique bacterial environment. Cascadia Margin sediments from the Pacific Ocean have deep bacterial activity and bacterial populations, which are stimulated around a gas hydrate zone (215–225 m below sea floor [mbsf]). Bacterial sulfate reduction is the dominant anaerobic process within these sediments, and the depth distribution of sulfate‐reducing activity corresponds with distributions of viable sulfate‐reducing bacteria (SRB). Anaerobically stored sediments from this site were used to isolate sulfate‐reducing bacteria using a temperature‐gradient system, elevated pressure and temperatures, different media, and a range of growth substrates. A variety of enrichments on lactate were obtained from 0.5 and 222 mbsf, with surprisingly more rapid growth from the deeper sediments. The temperature range of enrichments producing strong growth from 222 mbsf was markedly wider than those from the near surface sediment (15–45°C and 9–19°C, respectively). This presumably reflects a temperature increase in deeper sediments. Only a few of these enrichments were successfully isolated due to very slow or no growth on subculture, despite the use of a wide range of different media and growth conditions. Psychrophilic and mesophilic sulfate‐reducing isolates were obtained from 0.5 m depth. As the minimum growth temperature of the mesophile (probably a Desulfotomaculum sp.) was above the in situ temperature of 3°C, it must have been present in the sediment as spores. A larger number of isolates (23) was obtained from 222 mbsf, and these barophilic SRB were closely related (based on 16S rRNA gene analysis), but not identical to, Desulfovibrio profundus, recently isolated from deep sediments from the Japan Sea. Bacteria related to D. profundus may be widespread in deep marine sediments.     

Phylogenetic diversity in sulphate-reducing bacterial communities from oxidised and reduced bottom sediments of the Barents Sea

In the bottom sediments from a number of the Barents Sea sites, including coastal areas of the Novaya Zemlya, Franz Josef Land, and Svalbard archipelagos, sulphate reduction rates were measured and the phylogenetic composition of sulphate-reducing bacterial (SRB) communities was analysed for the first time. Molecular genetic analysis of the sequences of the 16S rRNA and dsrB genes (the latter encodes the β-subunit of dissimilatory (bi)sulphite reductase) revealed significant differences in the composition of bacterial communities in different sampling stations and sediment horizons of the Barents Sea depending on the physicochemical conditions. The major bacteria involved in reduction of sulphur compounds in Arctic marine bottom sediments belonged to Desulfobulbaceae, Desulfobacteraceae, Desulfovibrionaceae, Desulfuromonadaceae, and Desulfarculaceae families, as well as to uncultured clades SAR324 and Sva0485. Desulfobulbaceae and Desulfuromonadaceae predominated in the oxidised (E_h = 154–226 mV) upper layers of the sediments (up to 9% and 5.9% from all reads of the 16S rRNA gene sequences in the sample, correspondingly), while in deeper, more reduced layers (E_h = ?210 to ?105 mV) the share of Desulfobacteraceae in the SRB community was also significant (up to 5%). The highest relative abundance of members of Desulfarculaceae family (3.1%) was revealed in reduced layers of sandy-clayey sediments from the Barents Sea area affected by currents of transformed (mixed, with changed physicochemical characteristics) Atlantic waters.

     

Detection of anaerobic sulfate-reducing bacteria in oxygen-containing upper water layers of the Black and Baltic Seas

Fluorescent in situ hybridization (FISH) and PCR were used for analysis of phylogenetic structure of anaerobic sulfate-reducing bacterial communities in oxygen-containing upper water layers of meromictic basins: the Black Sea and the Gdansk Deep of the Baltic Sea. In the Black Sea (continental slope at depths 30–70 m), cells of sulfate-reducing bacteria (SRB) hybridizing with 16S rRNA-specific FISH-probes for Desulfotomaculum, Desulfobacter, and Desulfovibrio genera were revealed, whereas Desulfomicrobium-related bacteria were prevalent in the chemocline zone at a 150-m depth. Besides Desulfotomaculum (SRB subgroup 1), Desulfobacter (SRB subgroup 4), and Desulfovibrio-Desulfomicrobium (SRB subgroup 6), nested PCR with the use of 16S rRNA gene-specific primers detected the presence of Desulfococcus–Desulfonema–Desulfosarcina (SRB subgroup 5) in the oxygen-containing water column of the Black and Baltic seas. Active enrichment SRB culture that contained bacterium Desulfosporosinus sp. as a major component was obtained from the Black Sea water sample collected at a 70-m depth.     

Phylogenetic Diversity of the Sulfur Cycle Bacteria in the Bottom Sediments of the Chersonesus Bay

The Black Sea is the largest meromictic basin, in the bottom sediments of which a powerful biogenic process of sulfide production occurs. The goal of the present work was to obtain data on phylogenetic diversity of the sulfur cycle microorganisms (sulfate-reducing and sulfur-oxidizing bacteria) in the Black Sea coastal gas-saturated bottom sediments. The samples were collected in the Chersonesus (Blue) Bay near Sevastopol from whitish bacterial mats of sulfurettes, and from the upper layer of the nearby seabed. Using DNA isolated from the native samples and obtained enrichment cultures, PCR analysis was performed with oligonucleotide primers specific to the fragments of the 16S rRNA genes of the main subgroups of sulfatereducing bacteria (SRB) and to the fragments of the dsrB gene (both reductive and oxidative types), encoding the β-subunit of dissimilatory (bi)sulfite reductase, the key enzyme in the sulfur cycle, inherent in both sulfate- reducing and sulfur-oxidizing microorganisms. The presence of 16S rRNA gene fragments specific to the genera Desulfobacterium, Desulfobacter, Desulfococcus–Desulfonema–Desulfosarcina, and Desulfovibrio–Desulfomicrobium was detected in the DNA samples isolated from coastal bottom bacterial mats. Usage of denaturing gradient gel electrophoresis (DGGE) with subsequent sequencing of reamplified dsrB gene fragments revealed that according to deduced amino acid sequences encoded by the dsrB gene (reductive type), SRB from the coastal gas-saturated bottom sediments of the Black Sea had the highest homology (92?99%) with the dsrB gene of cultured SRB belonging to the genera Desulfovibrio, Desulfatitalea, Desulfobacter, and Desulfobacterium, as well as with uncultured SRB strains from various marine habitats, such as bottom sediments of the Northern and Japanese seas. Deduced amino acid sequences encoded by the oxidative dsrB gene had the highest homology (90?99%) with the relevant sequences of the genera Thiocapsa, Thiobaca, Thioflavicoccus, and Thiorhodococcus.     

Diversity of dimethylsulfide-degrading methanogens and sulfate-reducing bacteria in anoxic sediments along the Medway Estuary,UK

Methane is a powerful greenhouse gas but the microbial diversity mediating methylotrophic methanogenesis is not well-characterized. One overlooked route to methane is via the degradation of dimethylsulfide (DMS), an abundant organosulfur compound in the environment. Methanogens and sulfate-reducing bacteria (SRB) can degrade DMS in anoxic sediments depending on sulfate availability. However, we know little about the underlying microbial community and how sulfate availability affects DMS degradation in anoxic sediments. We studied DMS-dependent methane production along the salinity gradient of the Medway Estuary (UK) and characterized, for the first time, the DMS-degrading methanogens and SRB using cultivation-independent tools. DMS metabolism resulted in high methane yield (39%–42% of the theoretical methane yield) in anoxic sediments regardless of their sulfate content. Methanomethylovorans, Methanolobus and Methanococcoides were dominant methanogens in freshwater, brackish and marine incubations respectively, suggesting niche-partitioning of the methanogens likely driven by DMS amendment and sulfate concentrations. Adding DMS also led to significant changes in SRB composition and abundance in the sediments. Increases in the abundance of Sulfurimonas and SRB suggest cryptic sulfur cycling coupled to DMS degradation. Our study highlights a potentially important pathway to methane production in sediments with contrasting sulfate content and sheds light on the diversity of DMS degraders.     

Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon

Hydrogenotrophic microbiota have a significant impact on colonic health; however, little is known about their diversity and ecology in situ. Here, molecular-based methods and multivariate analyses were used to examine the abundance and diversity of mucosa-associated hydrogenotrophic microbes in 90 biopsies collected from right colon, left colon and rectum of 25 healthy subjects. Functional genes of all three hydrogenotrophic groups were detected in at least one colonic region of all subjects. Methanogenic archaea (MA) constituted approximately one half of the hydrogenotrophic microbiota in each colonic region. Sulfate-reducing bacteria (SRB) were more abundant than acetogens in right colon, while acetogens were more abundant than SRB in left colon and rectum. MA genotypes exhibited low diversity, whereas SRB genotypes were diverse and generally similar across the three regions within subject but significantly variable among subjects. Multivariate cluster analysis defined subject-specific patterns for the diversity of SRB genotypes; however, neither subject- nor region-specific clusters were observed for the abundance of hydrogenotrophic functional genes. Sequence analyses of functional gene clones revealed that mucosa-associated SRB were phylogenetically related to Desulfovibrio piger, Desulfovibrio desulfuricans and Bilophila wadsworthia; whereas MA were related to Methanobrevibacter spp., Mb. smithii and the order Methanomicrobiales. Together these data demonstrate for the first time that the human colonic mucosa is persistently colonized by all three groups of hydrogenotrophic microbes, which exhibit segmental and interindividual variation in abundance and diversity.     

Fish growth enhances microbial sulfur cycling in aquaculture pond sediments

Microbial sulfate reduction and sulfur oxidation are vital processes to enhance organic matter degradation in sediments. However, the diversity and composition of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) and their environmental driving factors are still poorly understood in aquaculture ponds, which received mounting of organic matter. In this study, bacterial communities, SRB and SOB from sediments of aquaculture ponds with different sizes of grass carp (Ctenopharyngodon idellus) were analysed using high-throughput sequencing and quantitative real-time PCR (qPCR). The results indicated that microbial communities in aquaculture pond sediments of large juvenile fish showed the highest richness and abundance of SRB and SOB, potentially further enhancing microbial sulfur cycling. Specifically, SRB were dominated by Desulfobulbus and Desulfovibrio, whereas SOB were dominated by Dechloromonas and Leptothrix. Although large juvenile fish ponds had relatively lower concentrations of sulfur compounds (i.e. total sulfur, acid-volatile sulfide and elemental sulfur) than those of larval fish ponds, more abundant SRB and SOB were found in the large juvenile fish ponds. Further redundancy analysis (RDA) and linear regression indicated that sulfur compounds and sediment suspension are the major environmental factors shaping the abundance and community structure of SRB and SOB in aquaculture pond sediments. Findings of this study expand our current understanding of microbial driving sulfur cycling in aquaculture ecosystems and also provide novel insights for ecological and green aquaculture managements.     

Seasonal abundance estimates of cetaceans in the southern Black Sea (Sinop), Türkiye

The availability of reliable information on the abundance and distribution of threatened species is fundamental to evaluating their conservation status and taking the necessary measures to implement effective management. The seasonal abundance and distribution of cetaceans in the Sinop region, one of the essential fishing areas of the Black Sea, were estimated with line-transect data. Dedicated boat-based visual observations were conducted in four seasons between May 2019 and March 2020. Average estimates of abundance in the region over all seasons were 1,058 individuals for Black Sea harbor porpoises (Phocoena phocoena relicta; CV = 19.25%, 95% CI[725, 1,542]), 188 individuals for Black Sea bottlenose dolphins (Tursiops truncatus ponticus; CV = 21.67%, 95% CI[123, 289]), and 311 individuals for Black Sea common dolphin (Delphinus delphis ponticus; CV = 16.77%, 95% CI[123, 427]). The highest estimates for all three species were obtained in the spring. Harbor porpoises and bottlenose dolphins were present in the study area throughout the year, while common dolphins left the region in winter. These findings offer valuable insights that can guide and inform future conservation strategies, aligning with national and international frameworks for the protection of these cetacean species.     

Diversity and Distribution of Methanotrophic Archaea at Cold Seeps

In this study we investigated by using 16S rRNA-based methods the distribution and biomass of archaea in samples from (i) sediments above outcropping methane hydrate at Hydrate Ridge (Cascadia margin off Oregon) and (ii) massive microbial mats enclosing carbonate reefs (Crimea area, Black Sea). The archaeal diversity was low in both locations; there were only four (Hydrate Ridge) and five (Black Sea) different phylogenetic clusters of sequences, most of which belonged to the methanotrophic archaea (ANME). ANME group 2 (ANME-2) sequences were the most abundant and diverse sequences at Hydrate Ridge, whereas ANME-1 sequences dominated the Black Sea mats. Other seep-specific sequences belonged to the newly defined group ANME-3 (related to Methanococcoides spp.) and to the Crenarchaeota of marine benthic group B. Quantitative analysis of the samples by fluorescence in situ hybridization (FISH) showed that ANME-1 and ANME-2 co-occurred at the cold seep sites investigated. At Hydrate Ridge the surface sediments were dominated by aggregates consisting of ANME-2 and members of the Desulfosarcina-Desulfococcus branch (DSS) (ANME-2/DSS aggregates), which accounted for >90% of the total cell biomass. The numbers of ANME-1 cells increased strongly with depth; these cells accounted 1% of all single cells at the surface and more than 30% of all single cells (5% of the total cells) in 7- to 10-cm sediment horizons that were directly above layers of gas hydrate. In the Black Sea microbial mats ANME-1 accounted for about 50% of all cells. ANME-2/DSS aggregates occurred in microenvironments within the mat but accounted for only 1% of the total cells. FISH probes for the ANME-2a and ANME-2c subclusters were designed based on a comparative 16S rRNA analysis. In Hydrate Ridge sediments ANME-2a/DSS and ANME-2c/DSS aggregates differed significantly in morphology and abundance. The relative abundance values for these subgroups were remarkably different at Beggiatoa sites (80% ANME-2a, 20% ANME-2c) and Calyptogena sites (20% ANME-2a, 80% ANME-2c), indicating that there was preferential selection of the groups in the two habitats. These variations in the distribution, diversity, and morphology of methanotrophic consortia are discussed with respect to the presence of microbial ecotypes, niche formation, and biogeography.     

Comparison of the diversity of sulfate-reducing bacterial communities in the water column and the surface sediments of a Japanese meromictic lake

The diversity and abundance of sulfate-reducing bacteria (SRB) were investigated in Lake Suigetsu, a meromictic lake in Japan characterized by a permanent oxycline at a depth between 3 and 8 m separating the aerobic freshwater epilimnion from the anaerobic, saline, sulfidogenic hypolimnion. A quantitative competitive PCR targeting the gene coding for a portion of the α-subunit of dissimilatory sulfite reductase (dsrA) was used to assess the distribution of the SRB in the stratified water column and the surface sediments. The diversity of the SRB communities was assessed using a sequence analysis of the differing dsrA isomers. The dsrA gene copy numbers of SRB in the hypolimnic waters were from 9.6 × 10³ to 7.5 × 10⁵ copies ml⁻¹, whereas higher dsrA copy numbers of SRB were observed in surface sediments, ranging from 1.8–8.1 × 10⁷ copies ml⁻¹ as estimated by competitive PCR. Phylogenetic analysis of the dsrA sequences retrieved from the surface sediments shows most belong to a deeply branching lineage of diverse dsrA sequences not related to any cultured SRB group. In contrast, dsrA sequences found in the oxycline waters were related to sequences of members of the genera Desulfonema, Desulfosarcina, and Dusulfococcus and to sequences of the incomplete oxidizers from the Desulfobulbaceae family. Diversity and abundance of dsrA genes significantly differed between the samples from the oxycline waters and the surface sediments of Lake Suigetsu, indicating habitat-specific SRB communities may contribute to the biogeochemical cycling of carbon and sulfur.     

Fouling mussels (Dreissena spp.) colonize soft sediments in Lake Erie and facilitate benthic invertebrates

• 1 We conducted survey and transplant studies to determine whether colonization and residency on soft sediments by introduced, fouling mussels (Dreissena polymorpha and D. bugensis) were affected by physical disturbance, and whether Dreissena presence in turn influenced the diversity and population densities of other benthic invertebrates. Surveys revealed that colony density was typically higher at moderate depths than at shallower and greater ones. However, the largest, midsummer colonies and greatest coverage of sediments by mussels occurred at deeper sites.
• 2 Disturbance of transplanted colonies varied by depth and colony size, with deeper and larger colonies experiencing the lowest destruction rates. Colony destruction rate was positively correlated with current velocity adjacent to the lakebed.
• 3 Absence of mussel colonies at shallow sites was not determined by recruitment or substrate limitation, as recruit density was higher and sediment characteristics more suitable for postveliger settlement at shallow than at deeper sites. Rather, seasonal storms have much stronger effects in shallow than in deep water.
• 4 Mussel residency on soft sediment has profound effects on invertebrate biodiversity. Invertebrate species (taxon) richness and total abundance were positively correlated with mussel colony area. Mussel‐sediment habitat supported between 462 and 703% more taxa, and between 202 and 335% more individuals (exclusive of Dreissena) than adjacent soft‐sediment lacking mussels.
• 5 Results from this study illustrate that physical disturbance directly limits the distribution of mussels on soft sediments, and the diversity and abundance of other benthic invertebrates in consequence.

     

Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis

The identity and abundance of potentially active sulfate-reducing bacteria (SRB) in several metre deep sediments of a tidal sand flat in the German Wadden Sea were assessed by directed cultivation and cultivation-independent CARD-FISH analysis (catalysed reporter deposition fluorescence in situ hybridization). Presumably abundant SRB from different sediment layers between 0.5 and 4 m depth were selectively enriched in up to million-fold diluted cultures supplemented with lactate, acetate or hydrogen. Partial 16S rRNA gene sequences obtained from highest dilution steps showing sulfide formation indicated growth of deltaproteobacterial SRB belonging to the Desulfobulbaceae and the Desulfobacteraceae as well as of members of the Firmicutes. Subsequent isolation resulted in 10 novel phylotypes of both litho- and organotrophic sulfate-reducing Deltaproteobacteria. Molecular pre-screening identified six isolates as members of the Desulfobulbaceae, sharing highest identities with either candidatus 'Desulfobacterium corrodens' (95-97%) or Desulfobacterium catecholicum (98%), and four isolates as members of Desulfobacteraceae, being related to either Desulfobacter psychrotolerans (98%) or Desulfobacula phenolica (95-97%). Relatives of D. phenolica were exlusively isolated from 50 and 100 cm deep sediments with 10 and 2 mM of pore water sulfate respectively. In contrast, relatives of D. corrodens, D. psychrotolerans and D. catecholicum were also obtained from layers deeper than 100 cm and with less than 2 mM sulfate. The high in situ abundance of members of both families in sediment layers beneath 50 cm could be confirmed via CARD-FISH analysis performed with a set of six SRB-specific oligonucleotide probes. Moreover, SRB represented a numerically significant fraction of the microbial community throughout the sediment (up to 7%) and reached even higher cell numbers in deep, sulfate-poor layers than in the sulfate-rich surface sediment. This relatively large community size of potentially active SRB in deep sandy sediments might on the one hand be a result of their syntrophic association with other anaerobes. Our results furthermore support the hypothesis that enhanced advective pore water transport might supply nutrients to microbial communities in deep sandy sediments and point to their so far unrecognized contribution to biogeochemical processes in Wadden Sea sediments.     

Distribution of Sprattus sprattus phalericus (Risso, 1827) and zooplankton near the Black Sea redoxcline

Understanding what environmental drivers influence marine predator–prey relationships can be key to managing and protecting ecosystems, especially in the face of future climate change risks. This is especially important in environments such as the Black Sea, where strong biogeochemical gradients can drive marine habitat partitioning and ecological interactions. We used underwater video recordings in the north-eastern Black Sea in November 2013 to observe the distribution and behaviour of the Black Sea sprat (Sprattus sprattus phalericus, Risso 1827) and its zooplankton prey. Video recordings have shown that the Black Sea sprat S. sprattus phalericus tolerates severely hypoxic waters near the redoxcline. The school was distributed in the 33–96 m layer [oxygen concentration (O₂) 277–84 μmol L⁻¹]. Some individuals were observed to leave the school and descended 20 m deeper for foraging on copepods in the 119–123 m layer (O₂ 12–10 μmol L⁻¹). Zooplankton appeared concentrated on the upper boundary of the suboxic zone (O₂ < 10 μmol L⁻¹). No zooplankton were observed below O₂ 6–7 μmol L⁻¹ (128 m). Understanding the ability of this species to tolerate low oxygen waters is crucial to predicting future responses to natural and anthropogenic changes in hypoxia.     

Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

Simultaneous production of sulfide and methane by anaerobic sewer biofilms has recently been observed, suggesting that sulfate-reducing bacteria (SRB) and methanogenic archaea (MA), microorganisms known to compete for the same substrates, can coexist in this environment. This study investigated the community structures and activities of SRB and MA in anaerobic sewer biofilms (average thickness of 800 μm) using a combination of microelectrode measurements, molecular techniques, and mathematical modeling. It was seen that sulfide was mainly produced in the outer layer of the biofilm, between the depths of 0 and 300 μm, which is in good agreement with the distribution of SRB population as revealed by cryosection-fluorescence in situ hybridization (FISH). SRB had a higher relative abundance of 20% on the surface layer, which decreased gradually to below 3% at a depth of 400 μm. In contrast, MA mainly inhabited the inner layer of the biofilm. Their relative abundances increased from 10% to 75% at depths of 200 μm and 700 μm, respectively, from the biofilm surface layer. High-throughput pyrosequencing of 16S rRNA amplicons showed that SRB in the biofilm were mainly affiliated with five genera, Desulfobulbus, Desulfomicrobium, Desulfovibrio, Desulfatiferula, and Desulforegula, while about 90% of the MA population belonged to the genus Methanosaeta. The spatial organizations of SRB and MA revealed by pyrosequencing were consistent with the FISH results. A biofilm model was constructed to simulate the SRB and MA distributions in the anaerobic sewer biofilm. The good fit between model predictions and the experimental data indicate that the coexistence and spatial structure of SRB and MA in the biofilm resulted from the microbial types and their metabolic transformations and interactions with substrates.     

Biodiversity of Zoobenthos in the Coastal Zone of the South Coast of Crimea (Laspi Bay Area)

Based on data of a1996 benthos survey, the structure of soft bottom zoobenthos of Laspi Bay (South Coast of Crimea, the Black Sea) was examined. One hundred thirty-one species of macrozoobenthos, including 44 molluscan species, 43 annelids, 31 crustaceans and 13 species representing other groups, were recorded. Two biocenoses were distinguished: Chamelea gallina and Mytilus galloprovincialis within the depths 5–52 m. The first biocenosis was presented by two biocenosic complexes. Their structure was characterized using Shannon, Simpson, and Pielou indices. The representativeness of the basic taxonomic groups of the benthos was analyzed. The conclusion of the high species abundance of benthos in Laspi Bay was made. There were recorded changes in structure of the biocenoses, which were manifested in the development of sestonophage filterers (first of all, the mollusc Chamelea gallina) with increasing organic pollution of the coastal water areas of Black sea.     

Populations of the red tide forming dinoflagellate Noctiluca scintillans (Macartney): A comparison between the Black Sea and the northern Adriatic Sea

Populations of Noctiluca scintillans (hereafter Noctiluca) were compared from two regions: the northeastern-central Black Sea and the northern Adriatic Sea. In both seas samples were collected in near-shore waters 2–3 times per month during 2004–2012. For analysis of feeding activities and seasonal dynamics additional cruise data on the open waters of the Black Sea were used. Comparison between the two populations shows similarity in size structure with two classes 401–500 μm and 501–600 μm being the most numerous. Seasonal changes in cell abundance in both seas demonstrated a regular annual maximum with the peak period of high abundances in May–June with additional sporadic peaks in other seasons. In spring the average number of food vacuoles in the cell (1.78) and the proportion of feeding cells in populations (79%) in the Adriatic Sea were similar to those in the Black Sea (1.58 and 76%). In September–October, these parameters were lower both in the Adriatic Sea (0.69 and 49%) and in the Black Sea (1.46 and 65%) demonstrating that Noctiluca was better provided with food in spring. Among biotic parameters (wet phytoplankton biomass, chlorophyll biomass and zooplankton species) only the concentration of the eggs of Calanus euxinus was significantly positively correlated with abundance of Noctiluca. The possible effect of a high concentration of copepod eggs on the growth of Noctiluca in the peak period is discussed. An obvious negative relationship was observed between Noctiluca cell numbers in the peak period and wind velocity in both seas. The most significant negative correlation was observed between the number of windy hours per month (velocity more than 5–6 m s⁻¹) and cell concentrations in the Black Sea (r = −0.92) and in the northern Adriatic Sea (r = −0.67). On this basis, a new hypothesis has been proposed and discussed: in connection with features of the food behavior of Noctiluca, its outbursts during the peak period are controlled by the wind. An evident positive relationship was observed between the number of Noctiluca in the peak period and its quantity in the preceding months in both seas. Thus, we suggest that abundance data during early spring and weather forecasts (winds) may be used for medium-term prediction of Noctiluca outbursts and red tides.     

Large-Scale Distribution and Activity of Prokaryotes in Deep-Sea Surface Sediments of the Mediterranean Sea and the Adjacent Atlantic Ocean

The deep-sea represents a substantial portion of the biosphere and has a major influence on carbon cycling and global biogeochemistry. Benthic deep-sea prokaryotes have crucial roles in this ecosystem, with their recycling of organic matter from the photic zone. Despite this, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments. To assess the influence of environmental and trophic variables on the large-scale distribution of prokaryotes, we investigated the prokaryotic assemblage composition (Bacteria to Archaea and Euryarchaeota to Crenarchaeota ratio) and activity in the surface deep-sea sediments of the Mediterranean Sea and the adjacent North Atlantic Ocean. Prokaryotic abundance and biomass did not vary significantly across the Mediterranean Sea; however, there were depth-related trends in all areas. The abundance of prokaryotes was positively correlated with the sedimentary concentration of protein, an indicator of the quality and bioavailability of organic matter. Moving eastwards, the Bacteria contribution to the total prokaryotes decreased, which appears to be linked to the more oligotrophic conditions of the Eastern Mediterranean basins. Despite the increased importance of Archaea, the contributions of Crenarchaeota Marine Group I to the total pool was relatively constant across the investigated stations, with the exception of Matapan-Vavilov Deep, in which Euryarchaeota Marine Group II dominated. Overall, our data suggest that deeper areas of the Mediterranean Sea share more similar communities with each other than with shallower sites. Freshness and quality of sedimentary organic matter were identified through Generalized Additive Model analysis as the major factors for describing the variation in the prokaryotic community structure and activity in the surface deep-sea sediments. Longitude was also important in explaining the observed variability, which suggests that the overlying water masses might have a critical role in shaping the benthic communities.     

Resource utilization by deep-sea sharks at the Le Danois Bank, Cantabrian Sea, north-east Atlantic Ocean

The feeding habits of birdbeak dogfish Deania calcea, velvet belly lantern shark Etmopterus spinax and blackmouth catshark Galeus melastomus at Le Danois Bank, Cantabrian Sea, south Bay of Biscay were studied in relation to their bathymetric distribution. Deep‐sea sharks were collected during two multidisciplinary surveys carried out in October 2003 and April 2004 at the Le Danois Bank. Two different habitats were defined: (1) the top of the bank, ranging from 454 to 642 m depth and covered by fine‐sand sediments with a low percentage of organic matter, and (2) the inner basin located between the bank and the Cantabrian Sea's continental shelf, at depths of 810–1048 m, which was characterized by a high proportion of silt and organic matter. Deania calcea was not present at the top of the bank but was abundant below 642 m, while E. spinax was abundant in the shallower top of the bank but was not found in the deeper inner basin. There was almost no bathymetric overlap between these two deep‐sea shark species. Galeus melastomus was found over the whole depth range. There seemed to be an ontogenetic segregation with depth for this species, however, since 80% of the specimens collected at the top of the bank were < 600 mm total length (L_T) (mean 510 mm L_T), whereas larger individuals (mean 620 mm L_T) inhabited deeper zones. Galeus melastomus exhibited a significantly higher feeding intensity than both E. spinax at the top of the bank and D. calcea in the inner basin. Little dietary overlap between D. calcea and G. melastomus in the inner basin was found, with D. calcea being an ichthyophagous predator while the diet of G. melastomus at these depths was composed of a variety of meso‐bathypelagic shrimps (e.g. Acantephyra pelagica, Pasiphaea spp. and Sergia robusta), cephalopods and fishes. The diets of E. spinax and G. melastomus at the top of the bank showed a high dietary overlap of euphausiids, which represented the main prey taxa for both species. Euphausiids declined in abundance with depth which was reflected in the diet of G. melastomus. The cluster analysis of prey affinities among hauls depicted two major groups, corresponding to the two different habitats (top of the bank and inner basin). Redundancy analysis also indicated top–basin segregation, with euphausiids representing the main prey taxa at the top of the bank and bathypelagic shrimps in the inner basin. Euphausiids and Micromesistius poutassou were key prey within the Le Danois Bank ecosystem since they were positively selected by the three deep‐sea shark species. These results show that the feeding ecology of these predators in Le Danois Bank ecosystem is highly influenced by depth‐related variables, as a result of changes in prey availability. Overall results were analysed in relation to the deep‐sea Le Danois ecosystem structure and functioning.     

Sulphur‐oxidizing and sulphate‐reducing communities in Brazilian mangrove sediments

Mangrove soils are anaerobic environments rich in sulphate and organic matter. Although the sulphur cycle is one of the major actors in this ecosystem, little is known regarding the sulphur bacteria communities in mangrove soils. We investigated the abundance, composition and diversity of sulphur‐oxidizing (SOB) and sulphate‐reducing (SRB) bacteria in sediments from three Brazilian mangrove communities: two contaminated, one with oil (OilMgv) and one with urban waste and sludge (AntMgv), and one pristine (PrsMgv). The community structures were assessed using quantitative real‐time polymerase chain reaction (qPCR), polymerase chain reaction‐denaturing gradient gel electrophoresis (PCR‐DGGE) and clone libraries, using genes for the enzymes adenosine‐5′‐phosphosulphate reductase (aprA) and sulphite reductase (Dsr) (dsrB). The abundance for qPCR showed the ratio dsrB/aprA to be variable among mangroves and higher according to the gradient observed for oil contamination in the OilMgv. The PCR‐DGGE patterns analysed by Nonmetric Multidimensional Scaling revealed differences among the structures of the three mangrove communities. The clone libraries showed that Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria were the most abundant groups associated with sulphur cycling in mangrove sediments. We conclude that the microbial SOB and SRB communities in mangrove soils are different in each mangrove forest and that such microbial communities could possibly be used as a proxy for contamination in mangrove forests.