Low connectivity and declining genetic variability along a depth gradient in Corallium rubrum populations

This study examines the possible effect of depth on the connectivity and genetic variability in red coral (Corallium rubrum; Octocorallia: Alcyonacea) populations. Patterns of genetic structuring along a depth gradient (from 20 to 70 m) were investigated in two locations of the western Mediterranean coast (northern Catalan and eastern Ligurian Seas) using 10 microsatellite loci. Strong patterns of genetic structuring among the samples were found both within and between the two study sites. In both locations, consistent patterns of reduction in genetic variability along the depth gradient were also observed, suggesting that depth has an important role in determining the patterns of genetic structure in Corallium rubrum. Moreover, a threshold in connectivity was observed among the samples collected across 40–50 m depth, supporting the hypothesis that discrete shallow- and deep-water red coral populations occur. This finding has major implications for management strategies and the conservation of commercially exploited deep red coral populations.     

Death of submerged macrophytes—Actual field observations and some implications

Using a photographic sampling method, the spatial distribution of dead submerged macrophytes was investigated in lakes Tyrifjord and Steinsfjord, in South Norway. Death incidents were observed in less than 5% of the samples (N = 3257). Distributed sites with unstable sediments had dead plants occuring at all depths, whereas at normal sites, the incidence of dead plants was higher towards deeper waters. In this case, the estimated mortality rose sharply, close to the lower limits of depth extension for the annual Najas flexilis (Willd.) R.&S. and the perennial Isoëtes lacustris L.The statistical analysis of death incidence for the predominant macrophyte Isoëtes lacustris showed that neither depth nor light intensity accounted adequately for the observed deep-water mortality increase. However, probit-transformed mortality correlated significantly (P < 0.001) to a hazard function, derived from light threshold statistics. Mortality magnitude was sufficient to explain the observed steep deep-water decline of I. lacustris. It is concluded that the commonly-observed double-exponential depth decline of submerged macrophytes could well be invoked by light-induced mortality.     

Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres

Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.     

Cynaroside protects the blue light-induced retinal degeneration through alleviating apoptosis and inducing autophagy in vitro and in vivo

BackgroundBlue light can directly penetrate the lens and reach the retina to induce retinal damage, causing dry age-related macular degeneration (dAMD). Cynaroside (Cyn), a flavonoid glycoside, was proved to alleviate the oxidative damage of retinal cells in vitro. However, whether or not Cyn also exerts protective effect on blue light-induced retinal degeneration and its mechanisms of action are unclear.PurposeThis study aims to evaluate the protective effects of Cyn against blue-light induced retinal degeneration and its underlying mechanisms in vitro and in vivo.Study design/methodsBlue light-induced N-retinylidene-N-retinylethanolamine (A2E)-laden adult retinal pigment epithelial-19 (ARPE-19) cell damage and retinal damage in SD rats were respectively used to evaluate the protective effects of Cyn on retinal degeneration in vitro and in vivo. MTT assay and AnnexinV-PI double staining assay were used to evaluate the in vitro efficacy. Histological analysis, TUNEL assay, and fundus imaging were conducted to evaluate the in vivo efficacy. ELISA assay, western blot, and immunostaining were performed to investigate the mechanisms of action of Cyn.ResultsCyn decreased the blue light-induced A2E-laden ARPE-19 cell damage and oxidative stress. Intravitreal injection of Cyn (2, 4 μg/eye) reversed the retinal degeneration induced by blue light in SD rats. Furthermore, Cyn inhibited the nuclear translocation of NF-κB and induced autophagy, which led to the clearance of overactivated pyrin domain containing 3 (NLRP3) inflammasome in vitro and in vivo.ConclusionCyn protects against blue light-induced retinal degeneration by modulating autophagy and decreasing the NLRP3 inflammasome.     

Population dynamics of a tropical intertidal and deep-water population of Sargassum polyceratium (Phaeophyceae)

Plant numbers, plant size, number and length of primary laterals, reproduction, growth rates and turnover rates were recorded for an intertidal and a deep-water (30 m depth) population of Sargassum polyceratium Montagne at Curaçao, Netherlands Antilles, for 1.5 years. Both populations showed distinct seasonal variations in biomass and growth rates, with maxima in late summer-early autumn and minima in winter. The observed fluctuations were probably amplified by a severe autumn storm that significantly reduced biomass in both populations at the end of the first year. The main differences between the populations were a more compact growth form and higher growth rates and turnover rates of primary laterals in the intertidal population.     

Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter–spring (that is, the 0 ^oC slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer—autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC−1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC−1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC−1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments.     

Ammonia-Oxidizing Archaea Dominate Ammonia-Oxidizing Communities within Alkaline Cave Sediments

Nitrification represents one of the key steps in the global nitrogen cycle. While originally considered an exclusive metabolic capability of bacteria, the identification of the Thaumarchaeota revealed that ammonia-oxidizing archaea (AOA) are also important contributors to this process, particularly in acidic environments. Nonetheless, the relative contribution of AOA to global nitrification remains difficult to ascertain, particularly in underexplored neutrophilic and alkalinophilic terrestrial systems. In this study we examined the contribution of AOA to nitrification within alkaline (pH 8.3–8.7) cave environments using quantitative PCR, crenarchaeol lipid identification and measurement of potential nitrification rates. Our results showed that AOA outnumber ammonia-oxidizing bacteria (AOB) by up to four orders of magnitude in cave sediments. The dominance of Thaumarchaeota in the archaeal communities was confirmed by both archaeal 16S rRNA gene clone library and membrane lipid analyses, while potential nitrification rates suggest that Thaumarchaeota may contribute up to 100% of ammonia oxidation in these sediments. Phylogenetic analysis of Thaumarchaeota amoA gene sequences demonstrated similarity to amoA clones across a range of terrestrial habitats, including acidic ecosystems. These data suggest that despite the alkaline conditions within the cave, the low NH₃ concentrations measured continue to favor growth of AOA over AOB populations. In addition to providing important information regarding niche differentiation within Thaumarchaeota, these data may provide important clues as to the factors that have historically led to nitrate accumulation within cave sediments.     

Evolutionary increases in defense during a biological invasion

Invasive plants generally escape from specialist herbivores of their native ranges but may experience serious damage from generalists. As a result, invasive plants may evolve increased resistance to generalists and tolerance to damage. To test these hypotheses, we carried out a common garden experiment comparing 15 invasive populations with 13 native populations of Chromolaena odorata, including putative source populations identified with molecular methods and binary choice feeding experiments using three generalist herbivores. Plants from invasive populations of C. odorata had both higher resistance to three generalists and higher tolerance to simulated herbivory (shoot removal) than plants from native populations. The higher resistance of plants from invasive populations was associated with higher leaf C content and densities of leaf trichomes and glandular scales, and lower leaf N and water contents. Growth costs were detected for tolerance but not for resistance, and plants from invasive populations of C. odorata showed lower growth costs of tolerance. Our results suggest that invasive plants may evolve to increase both resistance to generalists and tolerance to damage in introduced ranges, especially when the defense traits have low or no fitness costs. Greater defenses in invasive populations may facilitate invasion by C. odorata by reducing generalist impacts and increasing compensatory growth after damage has occurred.     

Niche partitioning of marine group I Crenarchaeota in the euphotic and upper mesopelagic zones of the East China Sea

Marine group I Crenarchaeota (MGI) represents a ubiquitous and numerically predominant microbial population in marine environments. An understanding of the spatial dynamics of MGI and its controlling mechanisms is essential for an understanding of the role of MGI in energy and element cycling in the ocean. In the present study, we investigated the diversity and abundance of MGI in the East China Sea (ECS) by analysis of crenarchaeal 16S rRNA gene, the ammonia monooxygenase gene amoA, and the biotin carboxylase gene accA. Quantitative PCR analyses revealed that these genes were higher in abundance in the mesopelagic than in the euphotic zone. In addition, the crenarchaeal amoA gene was positively correlated with the copy number of the MGI 16S rRNA gene, suggesting that most of the MGI in the ECS are nitrifiers. Furthermore, the ratios of crenarchaeal accA to amoA or to MGI 16S rRNA genes increased from the euphotic to the mesopelagic zone, suggesting that the role of MGI in carbon cycling may change from the epipelagic to the mesopelagic zones. Denaturing gradient gel electrophoretic profiling of the 16S rRNA genes revealed depth partitioning in MGI community structures. Clone libraries of the crenarchaeal amoA and accA genes showed both "shallow" and "deep" groups, and their relative abundances varied in the water column. Ecotype simulation analysis revealed that MGI in the upper ocean could diverge into special ecotypes associated with depth to adapt to the light gradient across the water column. Overall, our results showed niche partitioning of the MGI population and suggested a shift in their ecological functions between the euphotic and mesopelagic zones of the ECS.     

Foraminiferal taphofacies in the Mississippian rocks of the Guadiato area, SW Spain

Summary Microfacies analysis of over 1800 standard thin-sections of upper Viséan and Pendleian-aged platform limestones from southwestern Spain (Guadiato area) shows that foraminiferal assemblages contain many allochthonous specimens. The analysis of the cementation, recrystallization, abrasion, bioerosion, encrustation, dissolution, taphonomic distortion, orientation and sorting allow the recognition of eight taphofacies. They are based on the taphonomic features observed within the foraminiferal assemblages, which reflect the environmental conditions in which foraminifera were sedimented as well as about early diagenesis. The environmental conditions may be ascertained from the analysis of the biostratinomic processes, which comprise the energy, waves, tides, redox conditions, etc. The mechanisms of taphonomic alteration may be quantified, and thus the appearance or absence of these alterations may be used to define taphofacies of shallow- and deep-water environments, such as those from tidal flat, shoal, outer platform, microbial mound or slope. Moreover, the relationship among these taphofacies also helps to define depositional mechanisms and products, such as debris flows or olistolites.     

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.     

Habitat use and ecological specialization within lake Daphnia populations

Many species of planktonic cladocerans display substantial variation in habitat use (mean depth and diel vertical migration), both among and within populations. We examined whether clonal segregation and specialization contributes to such behavioral variation within several lake populations of the cladoceran, Daphnia pulicaria. Electrophoretic and quantitative genetic analysis of clonal lines isolated from different depths at night revealed that clonal habitat specialization was common. Clones that utilized shallow water at night were genetically smaller at maturity and lower fecundity under standard laboratory conditions than the deep-water clones. The magnitude of this clonal habitat specialization varied among lakes: populations displaying broad use of depth habitats contained greater genetic variance than populations with more constrained habitat use. These results are consistent with known differences in selective factors in different depth habitats and suggest that substantial clonal specialization can occur within single populations. Since previous work has discovered a heritable basis to habitat selection in several Daphnia species, including D. pulicaria in our study lakes, it is likely that clonal/depth specialization is an important factor affecting the trophic ecology of Daphnia. Received: 18 April 1996 / Accepted: 25 September 1996     

The distribution of Mysidacea in the open ocean and near-bottom over slope regions in the northern North-east Atlantic Ocean during 1979

The vertical distribution of Mysidacea at one deep-water stationin the Rockall Trough and at one deep-water station in the PorcupineSeabight is discussed together with near-bottom distributionsof Mysidacea at two slope sites in the Seabight. Comparisonsare made to investigate the effect of the shallowing of thesea-floor on mesopelagic and upper bathypelagic species. Ofthe 14 species in the survey area only six were relatively abundant.In one slope area which was intensively sampled the numericalabundance of some species tended to increase erratically withincreased proximity to the bottom but other species seemed tobe unaffected. It is thought that increased food availabilitynear the bottom may be an important factor in causing increasedabundance.     

Marine foraging ecology influences mercury bioaccumulation in deep-diving northern elephant seals

Mercury contamination of oceans is prevalent worldwide and methylmercury concentrations in the mesopelagic zone (200–1000 m) are increasing more rapidly than in surface waters. Yet mercury bioaccumulation in mesopelagic predators has been understudied. Northern elephant seals (Mirounga angustirostris) biannually travel thousands of kilometres to forage within coastal and open-ocean regions of the northeast Pacific Ocean. We coupled satellite telemetry, diving behaviour and stable isotopes (carbon and nitrogen) from 77 adult females, and showed that variability among individuals in foraging location, diving depth and δ¹³C values were correlated with mercury concentrations in blood and muscle. We identified three clusters of foraging strategies, and these resulted in substantially different mercury concentrations: (i) deeper-diving and offshore-foraging seals had the greatest mercury concentrations, (ii) shallower-diving and offshore-foraging seals had intermediate levels, and (iii) coastal and more northerly foraging seals had the lowest mercury concentrations. Additionally, mercury concentrations were lower at the end of the seven-month-long foraging trip (n = 31) than after the two-month- long post-breeding trip (n = 46). Our results indicate that foraging behaviour influences mercury exposure and mesopelagic predators foraging in the northeast Pacific Ocean may be at high risk for mercury bioaccumulation.     

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre

Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0–1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology‐based studies in the region (4,024 OTUs, 10‐fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic–upper mesopelagic depths (100–300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth‐stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2–0.5 mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones.     

Light-induced disulfide dimerization of recoverin under ex vivo and in vivo conditions

Despite vast knowledge of the molecular mechanisms underlying photochemical damage of photoreceptors, linked to progression of age-related macular degeneration, information on specific protein targets of the light-induced oxidative stress is scarce. Here, we demonstrate that prolonged intense illumination (halogen bulb, 1500 lx, 1–5 h) of mammalian eyes under ex vivo (cow) or in vivo (rabbit) conditions induces disulfide dimerization of recoverin, a Ca²⁺-dependent inhibitor of rhodopsin kinase. Western blotting and mass spectrometry analysis of retinal extracts reveals illumination time-dependent accumulation of disulfide homodimers of recoverin and its higher order disulfide cross-linked species, including a minor fraction of mixed disulfides with intracellular proteins (tubulins, etc.). Meanwhile, monomeric bovine recoverin remains mostly reduced. These effects are accompanied by accumulation of disulfide homodimers of visual arrestin. Histological studies demonstrate that the light-induced oxidation of recoverin and arrestin occurs in intact retina (illumination for 2 h), while illumination for 5 h is associated with damage of the photoreceptor layer. A comparison of ex vivo levels of disulfide homodimers of bovine recoverin with redox dependence of its in vitro thiol–disulfide equilibrium (glutathione redox pair) gives the lowest estimate of redox potential in rod outer segments under illumination from −160 to −155  mV. Chemical crosslinking and dynamic light scattering data demonstrate an increased propensity of disulfide dimer of bovine recoverin to multimerization/aggregation. Overall, the oxidative stress caused by the prolonged intense illumination of retina might affect rhodopsin desensitization via concerted disulfide dimerization of recoverin and arrestin. The developed herein models of eye illumination are useful for studies of the light-induced thiol oxidation of visual proteins.     

Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean

Fluorescence in situ hybridization (FISH) in combination with polynucleotide probes revealed that the two major groups of planktonic Archaea (Crenarchaeota and Euryarchaeota) exhibit a different distribution pattern in the water column of the Pacific subtropical gyre and in the Antarctic Circumpolar Current system. While Euryarchaeota were found to be more dominant in nearsurface waters, Crenarchaeota were relatively more abundant in the mesopelagic and bathypelagic waters. We determined the abundance of archaea in the mesopelagic and bathypelagic North Atlantic along a south-north transect of more than 4,000 km. Using an improved catalyzed reporter deposition-FISH (CARD-FISH) method and specific oligonucleotide probes, we found that archaea were consistently more abundant than bacteria below a 100-m depth. Combining microautoradiography with CARD-FISH revealed a high fraction of metabolically active cells in the deep ocean. Even at a 3,000-m depth, about 16% of the bacteria were taking up leucine. The percentage of Euryarchaeota and Crenarchaeaota taking up leucine did not follow a specific trend, with depths ranging from 6 to 35% and 3 to 18%, respectively. The fraction of Crenarchaeota taking up inorganic carbon increased with depth, while Euryarchaeota taking up inorganic carbon decreased from 200 m to 3,000 m in depth. The ability of archaea to take up inorganic carbon was used as a proxy to estimate archaeal cell production and to compare this archaeal production with total prokaryotic production measured via leucine incorporation. We estimate that archaeal production in the mesopelagic and bathypelagic North Atlantic contributes between 13 to 27% to the total prokaryotic production in the oxygen minimum layer and 41 to 84% in the Labrador Sea Water, declining to 10 to 20% in the North Atlantic Deep Water. Thus, planktonic archaea are actively growing in the dark ocean although at lower growth rates than bacteria and might play a significant role in the oceanic carbon cycle.