ALBERT

Description: Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including the causing agents of toxoplasmosis and malaria, and emergent diseases like cryptosporidiosis or babesiosis. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys, and our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of apicomplexan sequences. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.

Description: Nitrous oxide (N2O) is an important atmospheric trace gas involved in tropospheric warming and stratospheric ozone depletion. Estimates of the global ocean contribution to N2O emissions average 21% (range: 10 to 53%). Ongoing environmental changes such as warming, deoxygenation and acidification are affecting oceanic N2O cycling and emissions to the atmosphere. International activities over the last decades aimed at improving estimates of global N2O emissions, including (i) the MarinE MethanE and NiTrous Oxide database (MEMENTO) for archiving of quality-controlled data, and (ii) a recent large-scale inter-laboratory comparison by Working Group 143 of the Scientific Committee on Ocean Research (SCOR). To reduce uncertainties in oceanic N2O emission estimates and to characterize the spatial and temporal variability in N2O distributions in a changing ocean, we propose the establishment of a harmonized N2O Observation Network (N2O-ON) combining discrete and continuous data from various platforms. The network will integrate observations obtained by calibrated techniques, using time series measurements at fixed stations and repeated hydrographic sections on voluntary observing ships and research vessels. In addition to exploiting existing oceanographic infrastructure, we propose the establishment of central calibration facilities in selected international laboratories to improve accuracy, and ensure standardization and comparability of N2O measurements. Final data products will include a harmonized global N2O concentration and emission fields for use in model validation and projections of future oceanic N2O emissions, to inform the global research community and policy makers.

Description: Nowadays, most biodiversity assessments involving meiofauna are mainly carried out using very time-consuming, specimen-wise morphological identifications, which demands comprehensive taxonomic knowledge. Animals have to be examined for minor differences of setae compositions, mouthpart morphology or number of segments for various extremities. DNA-based methods such as metabarcoding as well as recently emerged rapid analyses using MALDI-TOF mass spectrometry to identify specimens based on a proteome fingerprint could vastly accelerate the process of specimen identification in biodiversity assessments. However, these techniques depend on reference libraries to connect collected data to morphologically described species. In this study the success rate of both approaches have been tested based on reference libraries constructed using part of the samples from a new study area to identify unknown samples. Using MALDI-TOF MS we found, that species which do not exist in an incomplete mass spectra reference library only have minor impact on the results, when employing a post hoc test for Random Forest classifications. This test reveals specimens that demand morphological re-examination for the final species assignment. Metabarcoding however strongly demands a rich reference library to provide correct MOTU assessments in congruence with morphological determination. Nevertheless, with a complete library and a suitable data transformation [herein log(x + 1)], the number of reads per MOTU reflects relative species abundances in metabarcoding inference. The results of this study facilitate specimen identification by using MALDI-TOF MS, which is incomparably cheap for specimen-by-specimen identification, but when it comes to sample-wise analyses, metabarcoding outperforms other techniques by far.

Description: In the autumn of 2014, nine large mesocosms were deployed in the oligotrophic subtropical North-Atlantic coastal waters off Gran Canaria (Spain). Their deployment was designed to address the acidification effects of CO2 levels from 400 to 1,400 mu atm, on a plankton community experiencing upwelling of nutrient-rich deep water. Among other parameters, chlorophyll a (chl-a), potential respiration (Phi), and biomass in terms of particulate protein (B) were measured in the microplankton community (0.7-50.0 mu m) during an oligotrophic phase (Phase I), a phytoplankton-bloom phase (Phase II), and a post-bloom phase (Phase III). Here, we explore the use of the Phi/chl-a ratio in monitoring shifts in the microplankton community composition and its metabolism. Phi/chl-a values below 2.5 mu L O-2 h(-1) (mu g chl-a)(-1) indicated a community dominated by photoautotrophs. When Phi/chl-a ranged higher, between 2.5 and 7.0 mu L O-2 h(-1) (pg chl-a)(-1) , it indicated a mixed community of phytoplankton, microzooplankton and heterotrophic prokaryotes. When Phi/chl-a rose above 7.0 mu L O-2 h(-1) (mu g chl-a)(-1), it indicated a community where microzooplankton proliferated (〉10.0 mu L O-2 h(-1) (mu g chl-a)(-1)), because heterotrophic dinoflagellates bloomed. The first derivative of B, as a function of time (dB/dt), indicates the rate of protein build-up when positive and the rate of protein loss, when negative. It revealed that the maximum increase in particulate protein (biomass) occurred between 1 and 2 days before the chl-a peak. A day after this peak, the trough revealed the maximum net biomass loss. This analysis did not detect significant changes in particulate protein, neither in Phase I nor in Phase III. Integral analysis of Phi/chl-a and B, over the duration of each phase, for each mesocosm, reflected a positive relationship between 4) and pCO(2) during Phase II [alpha = 230.10-5 mu L O-2 h(-1) L-1 (patm CO2)(-1) (phase-day)(-1), R-2 = 0.30] and between chl-a and pCO(2) during Phase III [alpha = 100.10(-5) Ag chl-a L-1 (mu atmCO(2))(-1) (phase-day)(-1), R-2 = 0.84]. At the end of Phase II, a harmful algal species (HAS), Vicicitus globosus, bloomed in the high pCO(2) mesocosms. In these mesocosms, microzooplankton did not proliferate, and chl-a retention time in the water column increased. In these V globosus-disrupted communities, the (Phi/chl-a ratio [4.1 +/- 1.5 /mu L O-2 h(-1) (mu g chl-a)(-1)] was more similar to the Phi/chl-a ratio in a mixed plankton community than to a photoautotroph-dominated one.

Description: The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3–V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 × 104 cells ml–1. This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.

Description: Oxygen minimum zones (OMZs) have been suggested as a suitable niche for the oxygen-sensitive process of biological fixation of dinitrogen (N2) gas. However, most N2 fixation rates reported from such waters are low. This low N2 fixation activity has been proposed to result from the unusual community of N2 fixers, in which cyanobacteria were typically underrepresented. The Northern Benguela Upwelling System (North BUS) is part of one of the most productive marine ecosystems and hosts a well-developed OMZ. Although previous observations indicated low to absent N2 fixation rates, the community composition of diazotrophs needed to understand the North BUS has not been described. Here, we present a first detailed analysis of the diazotrophic diversity in the North BUS OMZ and the Angola tropical zone (ATZ), based on genetic data and isotope speciation. Consistent with a previous study, we detected a slight N deficit in the OMZ, but isotope data did not indicate any active or past N2 fixation. The diazotroph community in the North BUS was dominated by non-cyanobacterial microbes clustering with members of gamma-proteobacteria, as is typical for other OMZ regions. However, we found a strikingly high diversity of Cluster III diazotrophs not yet described in other OMZs. In contrast to previous observations, we could also identify cyanobacteria of the clades Trichodesmium sp., UCYN-A and Cyanothece sp., in surface waters connected to or above the OMZ, which were potentially active as shown by the presence of genes and transcripts of the key functional marker gene for N2 fixation, nifH. While the detection of diazotrophs and the absence of active N2 fixation (based on isotopic speciation) are consistent with other OMZ observations, the detected regional variation in the diversity and presence of cyanobacteria indicate that we still are far from understanding the role of diazotrophs in OMZs, which, however, is relevant for understanding the N cycle in OMZ waters, as well for predicting the future development of OMZ biogeochemistry in a changing ocean.

Description: Biomass is defined as organic matter from living organisms represented in all kingdoms. It is recognized to be an excellent source of proteins, polysaccharides and lipids and, as such, embodies a tailored feedstock for new products and processes to apply in green industries. The industrial processes focused on the valorization of terrestrial biomass are well established, but marine sources still represent an untapped resource. Oceans and seas occupy over 70% of the Earth’s surface and are used intensively in worldwide economies through the fishery industry, as logistical routes, for mining ores and exploitation of fossil fuels, among others. All these activities produce waste. The other source of unused biomass derives from the beach wrack or washed-ashore organic material, especially in highly eutrophicated marine ecosystems. The development of high-added-value products from these side streams has been given priority in recent years due to the detection of a broad range of biopolymers, multiple nutrients and functional compounds that could find applications for human consumption or use in livestock/pet food, pharmaceutical and other industries. This review comprises a broad thematic approach in marine waste valorization, addressing the main achievements in marine biotechnology for advancing the circular economy, ranging from bioremediation applications for pollution treatment to energy and valorization for biomedical applications. It also includes a broad overview of the valorization of side streams in three selected case study areas: Norway, Scotland, and the Baltic Sea.

Description: From 2008 through 2019, a comprehensive research project, SFB 754, Climate - Biogeochemistry Interactions in the Tropical Ocean, was funded by the German Research Foundation to investigate the climate-biogeochemistry interactions in the tropical ocean with a particular emphasis on the processes determining the oxygen distribution. During three 4-year long funding phases, a consortium of more than 150 scientists conducted or participated in 34 major research cruises and collected a wealth of physical, biological, chemical, and meteorological data. A common data policy agreed upon at the initiation of the project provided the basis for the open publication of all data. Here we provide an inventory of this unique data set and briefly summarize the various data acquisition and processing methods used.

Description: Deep-sea mining in the Pacific Clarion-Clipperton Fracture Zone (CCZ), a low-energy sedimentary habitat with polymetallic nodules, is expected to have considerable and long-lasting environmental impact. The CCZ hosts extraordinarily high species diversity across representatives from all Domains of Life. Data on species biology and ecology remain scarce, however. The current study describes the reproductive biology of Ophiosphalma glabrum (Ophiosphalmidae) and Ophiacantha cosmica (Ophiacanthidae), two ophiuroids frequently found in the CCZ. Specimens collected in Spring 2015 and 2019 in four contract areas were examined morphologically and histologically. Size-class frequencies (disc diameter and oocytes feret diameters), sex ratios, gametogenic status, putative reproductive mode, and a simple proxy for fecundity are presented. Habitat use differs in each. While O. glabrum is epibenthic, occurring as single individuals, O. cosmica often forms size-stratified groups living on stalked sponges, suggesting gregarious settlement or retention of offspring (though no brooding individuals were found). Further molecular analyses are needed to establish whether O. cosmica groups are familial. In O. glabrum, for which sample sizes were larger, sex ratios approximated a 1:1 ratio with no size-structuring. In both species, individuals were at various stages of gametogenic maturity, but no ripe females were identified. Based on this, O. glabrum is most probably gonochoric. Reproductive mode remains inconclusive for O. cosmica. Both species are presumptively lecithotrophic, with vitellogenic-oocyte feret diameters exceeding 250 μm. Oocyte feret diameters at times exceeded 400 μm in O. glabrum, indicating substantial yolk reserves. Estimates of instantaneous fecundity (vitellogenic specimens of O. glabrum only) were confounded by interindividual variability in gonad characteristics. The well-furnished lecithotrophic larvae of O. glabrum would be capable of dispersing even under food-impoverished conditions. The current study examines ophiuroid reproductive biology over multiple localities in the CCZ concurrently for the first time, at sites characterised by differing productivity regimes. The reproductive biology of each species is thus discussed with reference to past evolutionary (habitat stability), contemporary (food supply), and future environmental drivers (potential impacts of deep-sea mining).

Description: The Clarion Clipperton Zone (CCZ) in the Northeast Pacific Ocean holds the largest deposits of polymetallic nodules at abyssal depths. These nodules are rock formations containing valuable metals and minerals targeted for mining. They further provide diverse habitat for a range of deep-sea species. Little is known so far on the taxonomy, natural history and biogeography of these deep-sea animals which is vital for accurate assessment of the risk of species extinctions from large-scale mining. One of the most abundant megafaunal groups in the CCZ is the Ophiuroidea (brittle stars), of which Ophiotholia is one of the more abundant genera found in the area. The genus Ophiotholia has a world-wide distribution and currently holds six species.