Description: Benthic foraminifera are unicellular eukaryotes inhabiting sediments of aquatic environments. Several species were shown to store and use nitrate for complete denitrification, a unique energy metabolism among eukaryotes. The population of benthic foraminifera reaches high densities in oxygen-depleted marine habitats, where they play a key role in the marine nitrogen cycle. However, the mechanisms of denitrification in foraminifera are still unknown, and the possibility of a contribution of associated bacteria is debated. Here, we present evidence for a novel eukaryotic denitrification pathway that is encoded in foraminiferal genomes. Large-scale genome and transcriptomes analyses reveal the presence of a denitrification pathway in foraminifera species of the genus Globobulimina. This includes the enzymes nitrite reductase (NirK) and nitric oxide reductase (Nor) as well as a wide range of nitrate transporters (Nrt). A phylogenetic reconstruction of the enzymes' evolutionary history uncovers evidence for an ancient acquisition of the foraminiferal denitrification pathway from prokaryotes. We propose a model for denitrification in foraminifera, where a common electron transport chain is used for anaerobic and aerobic respiration. The evolution of hybrid respiration in foraminifera likely contributed to their ecological success, which is well documented in palaeontological records since the Cambrian period.

Description: The impact of ocean acidification and carbonation on microbial community structure was assessed during a large-scale in situ costal pelagic mesocosm study, included as part of the EPOCA 2010 Arctic campaign. The mesocosm experiment included ambient conditions (fjord) and nine mesocosms, with pCO2 range from ~145 to ~1420 μatm. Samples collected at nine time points (t-1, t1, t5, t7, t12, t14, t22, t26 to t28) in seven treatments (ambient fjord (~145), 2×~185, ~270, ~685, ~820, ~1050 μatm) were analysed for "free-living" and "particle associated" microbial community composition using 16S rRNA amplicon sequencing. This high-throughput sequencing analysis produced ~20 000 000 16S rRNA V4 reads, which comprised 7000 OTUs. The main variables structuring these communities were, sample origin (fjord or mesocosms) and the filter size fraction (free-living or particle associated). The community was significantly different between the fjord and both the control and elevated 2 mesocosms (which were not significant different) after nutrients were added to the mesocosms; suggesting that the addition of nutrients is the primary driver of the change in mesocosm community structure. The relative importance of each structuring variable depended greatly on the time at which the community was sampled in relation to the phytoplankton bloom. The size fraction was the second most important factor for community structure; separating free-living from particle-associated bacteria. When free-living and particle-associated bacteria were analysed separately at different time points, the only taxon pCO2 was found to significantly affect were the Gammaproteobacteria after nutrient addition. Finally, pCO2 treatment was found to be significantly correlated (non-linear) with 15 rare taxa, most of which increased in abundance with higher CO2.

Description: Recently it was shown that female fish injected with enriched stable isotopes maternally transmit a chemical signature to larval otoliths. Validation of this larval marking technique requires laboratory experiments to determine appropriate injection concentrations and to assess any negative effects on larval and adult condition. This study investigated the temporal profile of (137)barium assimilation and retention in tissues of adult female anemonefish Amphiprion melanopus (Pomacentridae) following intraperitoneal injection with either 2 or 4 mu g Ba-137 g(-1) body mass. Mean barium isotope ratios (Ba-138:Ba-137) in the two groups of treated fish were not significantly different from each other, but were significantly different from those in the control group up to 56 days post-injection. This pattern of Ba-137 retention was consistent across gonad, muscle, liver and bone tissues. Mean plasma cortisol concentration (an indicator of non-specific physiological stress) was not significantly different among groups and was considered to be representative of unstressed fish. Together, these results indicate that (1) A. melanopus suffer minimal physiological stress and cope well after treatment with Ba-137, (2) Ba-137 is retained in female A. melanopus for a prolonged period (at least 56 days), such that multiple clutches of offspring are likely to be marked with an isotopic signature, and (3) a lower dosage of 2 mu g Ba-137 g(-1) appears sufficient for transgenerational marking. It is concluded that Ba-137 is suitable for use as a transgenerational marker and is a powerful tool to resolve long-standing enigmas such as larval dispersal distances and the fishery benefits of marine reserves.

Description: ABSTRACT: BACKGROUND: Biogeochemical elemental cycling is driven by primary production of biomass via phototrophic phytoplankton growth, with 40% of marine productivity being assigned to diatoms. Phytoplankton growth is widely limited by the availability of iron, an essential component of the photosynthetic apparatus. The oceanic diatom Thalassiosira oceanica shows a remarkable tolerance to low-iron conditions and was chosen as a model for deciphering the cellular response upon shortage of this essential micronutrient. RESULTS: The combined efforts in genomics, transcriptomics and proteomics reveal an unexpected metabolic flexibility in response to iron availability for T. oceanica CCMP1005. The complex response comprises cellular retrenchment as well as remodeling of bioenergetic pathways, where the abundance of iron-rich photosynthetic proteins is lowered, whereas iron-rich mitochondrial proteins are preserved. As a consequence of iron deprivation, the photosynthetic machinery undergoes a remodeling to adjust the light energy utilization with the overall decrease in photosynthetic electron transfer complexes. CONCLUSIONS: Beneficial adaptations to low-iron environments include strategies to lower the cellular iron requirements and to enhance iron uptake. A novel contribution enhancing iron economy of phototrophic growth is observed with the iron-regulated substitution of three metal-containing fructose-bisphosphate aldolases involved in metabolic conversion of carbohydrates for enzymes that do not contain metals. Further, our data identify candidate components of a high-affinity iron-uptake system, with several of the involved genes and domains originating from duplication events. A high genomic plasticity, as seen from the fraction of genes acquired through horizontal gene transfer, provides the platform for these complex adaptations to a low-iron world.

Description: The increase in atmospheric carbon dioxide (CO2) results in acidification of the oceans, expected to lead to the fastest drop in ocean pH in the last 300 million years, if anthropogenic emissions are continued at present rate. Due to higher solubility of gases in cold waters and increased exposure to the atmosphere by decreasing ice cover, the Arctic Ocean will be among the areas most strongly affected by ocean acidification. Yet, the response of the plankton community of high latitudes to ocean acidification has not been studied so far. This work is part of the Arctic campaign of the European Project on Ocean Acidification (EPOCA) in 2010, employing 9 in situ mesocosms of about 45 000 l each to simulate ocean acidification in Kongsfjorden, Svalbard (78°56.2' N 11°53.6' E). In the present study, we investigated effects of elevated CO2 on the composition and richness of particle attached (PA; 〉3 μm) and free living (FL; 〈3 μm 〉0.2 μm) bacterial communities by Automated Ribosomal Intergenic Spacer Analysis (ARISA) in 6 of the mesocosms and the surrounding fjord, ranging from 185 to 1050 initial μatm pCO2. ARISA was able to resolve about 20–30 bacterial band-classes per sample and allowed for a detailed investigation of the explicit richness. Both, the PA and the FL bacterioplankton community exhibited a strong temporal development, which was driven mainly by temperature and phytoplankton development. In response to the breakdown of a picophytoplankton bloom (phase 3 of the experiment), number of ARISA-band classes in the PA-community were reduced at low and medium CO2 (∼180–600 μatm) by about 25%, while it was more or less stable at high CO2 (∼ 650–800 μatm). We hypothesise that enhanced viral lysis and enhanced availability of organic substrates at high CO2 resulted in a more diverse PA-bacterial community in the post-bloom phase. Despite lower cell numbers and extracellular enzyme activities in the post-bloom phase, bacterial protein production was enhanced in high CO2-treatments, suggesting a positive effect of community richness on this function and on carbon cycling by bacteria.

Description: Background Although the importance and widespread occurrence of iron limitation in the contemporary ocean is well documented, we still know relatively little about genetic adaptation of phytoplankton to these environments. Compared to its coastal relative Thalassiosira pseudonana, the oceanic diatom Thalassiosira oceanica is highly tolerant to iron limitation. The adaptation to low-iron conditions in T. oceanica has been attributed to a decrease in the photosynthetic components that are rich in iron. Genomic information on T. oceanica may shed light on the genetic basis of the physiological differences between the two species. Results The complete 141790 bp sequence of the T. oceanica chloroplast genome [GenBank: GU323224], assembled from massively parallel pyrosequencing (454) shotgun reads, revealed that the petF gene encoding for ferredoxin, which is localized in the chloroplast genome in T. pseudonana and other diatoms, has been transferred to the nucleus in T. oceanica. The iron-sulfur protein ferredoxin, a key element of the chloroplast electron transport chain, can be replaced by the iron-free flavodoxin under iron-limited growth conditions thereby contributing to a reduction in the cellular iron requirements. From a comparison to the genomic context of the T. pseudonana petF gene, the T. oceanica ortholog can be traced back to its chloroplast origin. The coding potential of the T. oceanica chloroplast genome is comparable to that of T. pseudonana and Phaeodactylum tricornutum, though a novel expressed ORF appears in the genomic region that has been subjected to rearrangements linked to the petF gene transfer event. Conclusions The transfer of the petF from the cp to the nuclear genome in T. oceanica represents a major difference between the two closely related species. The ability of T. oceanica to tolerate iron limitation suggests that the transfer of petF from the chloroplast to the nuclear genome might have contributed to the ecological success of this species.

Description: Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origins. However, the prevalence of denitrification genes in foraminifera remains unknown and the missing denitrification pathway components are elusive. Analysing transcriptomes and metagenomes of ten foraminifera species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer of the last common ancestor of denitrifying foraminifera, which enables us to predict further denitrifying species. Additionally, an examination of the foraminifera microbiota reveals evidence for a stable interaction with Desulfobacteracea , which harbour genes that complement the foraminifera denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera microbiome. The interaction of Foraminifera with their resident bacteria is at the basis of foraminifera adaptation to anaerobic environments that manifested in ecological success within oxygen depleted habitats.