Electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii with a DNA-biosensor

The steady rise of observations of harmful or toxic algal blooms throughout the world in the past decades constitute a menace for coastal ecosystems and human interests. As a consequence, a number of programs have been launched to monitor the occurrence of harmful and toxic algae. However, the identification is currently done by microscopic examination, which requires a broad taxonomic knowledge, expensive equipment and is very time consuming. In order to facilitate the identification of toxic algae, an inexpensive and easy-to-handle DNA-biosensor has been adapted for the electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii. The detection of the toxic algae is based on a sandwich hybridisation, which is carried out on a disposable sensor chip. A set of two probes for the species specific identification of A. ostenfeldii was developed. The specificity of the probes could be shown in dot-blot hybridisation and with the DNA-biosensor. The sensitivity of the DNA-biosensor was optimised with respect to hybridisation temperature and NaCl-concentration and a significant increase of the sensitivity of the DNA-biosensor could be obtained by a fragmentation of the rRNA prior to the hybridisation and by adding a helper oligonucleotide, which binds in close proximity to the probes to the hybridisation

Uncovering hidden biodiversity in the Cryptophyta: New picoplanktonic clades from clone library studies at the Helgoland time series site in the southern German Bight.

Cryptophyceae are important group in marine phytoplankton, but little is known about the occurrence and distribution of individual species. Recently, with use of molecular probes and microarray technology, it has been shown that species related to Teleaulax spp. or Chroomonas spp. (clades 4 and 6) contributed most to cryptophyceam biomass in the North Sea. The probe for clades 4 and 6 cannot separate them and the single probe recognises members of both clades. Here, we increase the genetic diversity of our investigations of cryptophycean diversity in the North Sea by sequencing 18S rRNA clone libraries made from fractionated water samples to examine specifically the picoplanktonic fraction and to determine whether clade 4 or 6 were the dominant cyrptophytes. We focused on samples from the spring phytoplankton bloom in 2004 because the microarray signals were the strongest at this time. Excluding chimeric sequences, we detected nine cryptophycean OTUs, seven of which fell into the Teleaulax/ Plagioselmis branch, whereas two grouped with Geminigera spp. Our results indicate that these OTUs, affiliated with clade 4, may be an important component of cryptophyte community during spring bloom in the North Sea

Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea

The dynamics of diatoms and dinoflagellates have been monitored for many decades at the Helgoland Roads Long-Term Ecological Research site and are relatively well understood. In contrast, small-sized eukaryotic microbes and their community changes are still much more elusive, mainly due to their small size and uniform morphology, which makes them difficult to identify microscopically. By using next-generation sequencing, we wanted to shed light on the Helgoland planktonic community dynamics, including nano- and picoplankton, during a spring bloom. We took samples from March to May 2016 and sequenced the V4 region of the 18S rDNA. Our results showed that mixotrophic and heterotrophic taxa were more abundant than autotrophic diatoms. Dinoflagellates dominated the sequence assemblage, and several small-sized eukaryotic microbes like Haptophyta, Choanoflagellata, Marine Stramenopiles and Syndiniales were identified. A diverse background community including taxa from all size classes was present during the whole sampling period. Five phases with several communities were distinguished. The fastest changes in community composition took place in phase 3, while the communities from phases 1 to 5 were more similar to each other despite contrasting environmental conditions. Synergy effects of next-generation sequencing and traditional methods may be exploited in future long-term observations

Climate Change: Warming Impacts on Marine Biodiversity

In this chapter, the effects of temperature change—as a main aspect of climate change—on marine biodiversity are assessed. Starting from a general discussion of species responses to temperature, the chapter presents how species respond to warming. These responses comprise adaptation and phenotypic plasticity as well as range shifts. The observed range shifts show more rapid shifts at the poleward range edge than at the equator-near edge, which probably reflects more rapid immigration than extinction in a warming world. A third avenue of changing biodiversity is change in species interactions, which can be altered by temporal and spatial shifts in interacting species. We then compare the potential changes in biodiversity to actual trends recently addressed in empirical synthesis work on local marine biodiversity, which lead to conceptual issues in quantifying the degree of biodiversity change. Finally we assess how climate change impacts the protection of marine environments

Building capacities for ’omics’ observations in the ocean at high spatiotemporal resolution

Analyzing the distributions and activities of marine organisms with metagenomic, metatranscriptomic, and other ‘omic’ techniques holds great potential in the observation of marine biodiversity and functions. When applied to microbial communities, such approaches are able to capture the multi-faceted responses of marine microbes to natural and anthropogenic pressures and the connected impacts on element cycling including fixation of inorganic carbon and dinitrogen. Ocean time-series and regular transects have delivered a strong foundation of knowledge of marine biogeochemistry. However, the imperative of characterizing the organisms that underly elemental cycles in times of rapid global change is hindered by the low resolution of human- and ship-based observation programs. The benefit of introducing omics-based investigations into ocean observation efforts has been recognized by several institutions and projects running observing programs (e.g., PAP, HAUSGARTEN, CPR, Tara Oceans) and by international initiatives and networks in the field (e.g., GOOS, MBON, LTER, NEON, GLOMICON). In order to establish omics observations as a component of routine observation of the open ocean there is a strong need for technologies that allow for unattended sampling with autonomous platforms as well as for automated shipbased sampling that may be carried out with research vessels and ships of opportunity. Activities to build capacities for omics-based observations were carried out in the framework of the EU FP7 projects AtlantOS and EnviGuard, with a focus on unicellular planktonic organisms that are poorly – or not at all – identified by morphology-based taxonomic techniques,. These efforts focused on the development and validation of new sampling technologies, on the investigation of the performance of different preservatives available to store samples, in situ, for the period of sampler deployments, and on the application of omics methods to samples collected with off-the shelf sampling equipment. In this context, this presentation introduces the new ‘AUTOmated FIltration system for marine Microbes’ / AUTOFIM and ‘Marine Autonomous Plankton Sampler’ / MAPS samplers, informs about the approach and first outcomes of a comparison of both standard preservatives and specific agents for molecular studies, and shows some examples of omics observations carried out in Fram Strait by means of particle traps and moored water samplers as part of the FRAM observatory infrastructure in the HAUSGARTEN area

DNA Microarrays for Identifying Fishes

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products

Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

The Arctic Ocean is experiencing unprecedented changes because of climate warming, necessitating detailed analyses on the ecology and dynamics of biological communities to understand current and future ecosystem shifts. Here, we generated a four-year, high-resolution amplicon dataset along with one annual cycle of PacBio HiFi read metagenomes from the East Greenland Current (EGC), and combined this with datasets spanning different spatiotemporal scales (Tara Arctic and MOSAiC) to assess the impact of Atlantic water influx and sea-ice cover on bacterial communities in the Arctic Ocean. Densely ice-covered polar waters harboured a temporally stable, resident microbiome. Atlantic water influx and reduced sea-ice cover resulted in the dominance of seasonally fluctuating populations, resembling a process of “replacement” through advection, mixing and environmental sorting. We identified bacterial signature populations of distinct environmental regimes, including polar night and high-ice cover, and assessed their ecological roles. Dynamics of signature populations were consistent across the wider Arctic; e.g. those associated with dense ice cover and winter in the EGC were abundant in the central Arctic Ocean in winter. Population- and community-level analyses revealed metabolic distinctions between bacteria affiliated with Arctic and Atlantic conditions; the former with increased potential to use bacterial- and terrestrial-derived substrates or inorganic compounds. Our evidence on bacterial dynamics over spatiotemporal scales provides novel insights into Arctic ecology and indicates a progressing Biological Atlantification of the warming Arctic Ocean, with consequences for food webs and biogeochemical cycles

Multiomics in the central Arctic Ocean for benchmarking biodiversity change.

Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth

3 year report on activities for the Working Group on Phytoplankton and Microbial Ecology (WGPME)

The ICES Working Group on Phytoplankton and Microbial Ecology (WGPME) provides tools and expert perspectives on the sampling methods, ecology and diversity of phytoplankton and other planktonic microbes. The group set out terms of reference to improve access to data, crossdisciplinary approaches and to develop ecological interpretations of the changing phytoplankton seascape. The group published 16 papers between 2019–2021, including key tools, high-profile synthesis papers and science reports. Tools: The group has progressed efforts to collect images of commonly used Lugol’s-preserved phytoplankton, alongside live images to aid those in correctly identifying species. Members have noticed and published records of new phytoplankton species. The group aims to produce a New Records database to assist in notifying new or reoccurrence of a species. WGPME work, with other Expert Groups (EG) to improve access to molecular genetic tools and records. A multi-EG thematic session has been submitted for ICES ASC 2022 in cooperation with other EGs, whilst phytoplankton barcoding information will be incorporated into the Working Group on Integrated Morphological and Molecular Taxonomy (WGIMT) barcoding Atlas (https://metazoogene.org/atlas). Information and access: The group is gathering information on nano and picoplankton (small phytoplankton less than 10 and 2µm respectively) to incorporate into global datasets such as GLOMICON. Multiple data sources point to an increasing trend in picoplankton and few indicators exist in current EU or national legislation to measure their impact on marine ecology. Many members are involved in indicator development for governmental and pan-governmental organisations such as OSPAR. However, the number and level of indicators vary in each country. Long-term ecology: The cooperative zooplankton and phytoplankton report has been delayed but initial analysis has indicated ≥30 years of data reliably shows spatio-temporal trends in phytoplankton and the effects of temperature on key phytoplankton groups. Two research papers are being produced on climate change effects on key marine phytoplankton species with the additional aim of improving indicators of change using species-specific information