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  • 1
    Publication Date: 2024-02-05
    Description: Non-technical summary Scenarios compatible with the Paris agreement's temperature goal of 1.5 °C involve carbon dioxide removal measures - measures that actively remove CO2 from the atmosphere - on a massive scale. Such large-scale implementations raise significant ethical problems. Van Vuuren et al. (2018), as well as the current IPCC scenarios, show that reduction in energy and or food demand could reduce the need for such activities. There is some reluctance to discuss such societal changes. However, we argue that policy measures enabling societal changes are not necessarily ethically problematic. Therefore, they should be discussed alongside techno-optimistic approaches in any kind of discussions about how to respond to climate change. Technical summary The 1.5 °C goal has given impetus to carbon dioxide removal (CDR) measures, such as bioenergy combined with carbon capture and storage, or afforestation. However, land-based CDR options compete with food production and biodiversity protection. Van Vuuren et al. (2018) looked at alternative pathways including lifestyle changes, low-population projections, or non-CO2 greenhouse gas mitigation, to reach the 1.5 °C temperature objective. Underlined by the recently published IPCC AR6 WGIII report, they show that demand-side management measures are likely to reduce the need for CDR. Yet, policy measures entailed in these scenarios could be associated with ethical problems themselves. In this paper, we therefore investigate ethical implications of four alternative pathways as proposed by Van Vuuren et al. (2018). We find that emission reduction options such as lifestyle changes and reducing population, which are typically perceived as ethically problematic, might be less so on further inspection. In contrast, options associated with less societal transformation and more techno-optimistic approaches turn out to be in need of further scrutiny. The vast majority of emission reduction options considered are not intrinsically ethically problematic; rather everything rests on the precise implementation. Explicitly addressing ethical considerations when developing, advancing, and using integrated assessment scenarios could reignite debates about previously overlooked topics and thereby support necessary societal discourse. Social media summary Policy measures enabling societal changes are not necessarily as ethically problematic as commonly presumed and reduce the need for large-scale CDR
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  • 2
    Publication Date: 2024-03-08
    Description: The Falkland Shelf is a highly productive ecosystem in the Southwest Atlantic Ocean. It is characterized by upwelling oceanographic dynamics and displays a wasp-waist structure, with few intermediate trophic-level species and many top predators that migrate on the shelf for feeding. One of these resident intermediate trophic-level species, the Patagonian longfin-squid Doryteuthis gahi, is abundant and plays an important role in the ecosystem. We used two methods to estimate the trophic structure of the Falkland Shelf food web, focusing on the trophic niche of D. gahi and its impacts on other species and functional groups to highlight the importance of D. gahi in the ecosystem. First, stable isotope measurements served to calculate trophic levels based on an established nitrogen baseline. Second, an Ecopath model was built to corroborate trophic levels derived from stable isotopes and inform about trophic interactions of D. gahi with other functional groups. The results of both methods placed D. gahi in the centre of the ecosystem with a trophic level of ∼ 3. The Ecopath model predicted high impacts and therefore a high keystoneness for both seasonal cohorts of D. gahi. Our results show that the Falkland Shelf is not only controlled by species feeding at the top and the bottom of the trophic chain. The importance of species feeding at the third trophic level (e.g. D. gahi and Patagonotothen ramsayi) and observed architecture of energy flows confirm the ecosystem's wasp-waist structure with middle-out control mechanisms at play.
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  • 3
    Publication Date: 2023-06-15
    Description: Increases in ocean temperatures in the Filchner Ronne region of Antarctica are likely to result in increased ice mass loss and sea level rise. We constrain projections of the 21st century sea level contribution of this region using process-based ice-sheet modeling, with model parameters controlling ice dynamics calibrated using observed surface speeds and Markov-chain Monte Carlo sampling. We use climate forcing from Representative Concentration Pathway (RCP) scenarios as well as a set of hypothetical scenarios of deep ocean warming to evaluate the sensitivity of this region to ocean temperatures. Projected changes in regional ice mass correspond to a decrease in global mean sea level of 24±7 mm over 2015–2100 under RCP 2.6 and 28±9 mm under RCP 8.5. Increased regional inland surface accumulation related to higher warming levels in RCP 8.5 leads to more ice above flotation, offsetting increased ice shelf basal melt. The tests involving step changes in ocean temperatures with constant surface forcing show that one degree of ocean warming from present results in an additional +11 mm contribution to sea level by 2100 and 1% of the ice-covered area in the domain becomes ungrounded (23 200 km2). The rate of mass loss with temperature increases at higher temperatures.
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  • 4
    Publication Date: 2024-01-08
    Description: Radiocarbon (14C) concentrations in the oceans are different from those in the atmosphere. Understanding these ocean-atmospheric 14C differences is important both to estimate the calendar ages of samples which obtained their 14C in the marine environment, and to investigate the carbon cycle. The Marine20 radiocarbon age calibration curve is created to address these dual aims by providing a global-scale surface ocean record of radiocarbon from 55,000–0 cal yr BP that accounts for the smoothed response of the ocean to variations in atmospheric 14C production rates and factors out the effect of known changes in global-scale palaeoclimatic variables. The curve also serves as a baseline to study regional oceanic 14C variation. Marine20 offers substantial improvements over the previous Marine13 curve. In response to community questions, we provide a short intuitive guide, intended for the lay-reader, on the construction and use of the Marine20 calibration curve. We describe the choices behind the making of Marine20, as well as the similarities and differences compared with the earlier Marine calibration curves. We also describe how to use the Marine20 curve for calibration and how to estimate ΔR—the localized variation in the oceanic 14C levels due to regional factors which are not incorporated in the global-scale Marine20 curve. To aid understanding, illustrative worked examples are provided.
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  • 5
    Publication Date: 2024-01-08
    Description: The Marine20 radiocarbon (14C) age calibration curve, and all earlier marine 14C calibration curves from the IntCal group, must be used extremely cautiously for the calibration of marine 14C samples from polar regions (outside ∼ 40ºS–40ºN) during glacial periods. Calibrating polar 14C marine samples from glacial periods against any Marine calibration curve (Marine20 or any earlier product) using an estimate of , the regional 14C depletion adjustment, that has been obtained from samples in the recent (non-glacial) past is likely to lead to bias and overconfidence in the calibrated age. We propose an approach to calibration that aims to address this by accounting for the possibility of additional, localized, glacial 14C depletion in polar oceans. We suggest, for a specific polar location, bounds on the value of during a glacial period. The lower bound may be based on 14C samples from the recent non-glacial (Holocene) past and corresponds to a low-depletion glacial scenario. The upper bound, , representing a high-depletion scenario is found by increasing according to the latitude of the 14C sample to be calibrated. The suggested increases to obtain are based upon simulations of the Hamburg Large Scale Geostrophic Ocean General Circulation Model (LSG OGCM). Calibrating against the Marine20 curve using the upper and lower bounds provide estimates of calibrated ages for glacial 14C samples in high- and low-depletion scenarios which should bracket the true calendar age of the sample. In some circumstances, users may be able to determine which depletion scenario is more appropriate using independent paleoclimatic or proxy evidence.
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  • 6
    Publication Date: 2024-01-24
    Description: Spatially variable basal conditions are thought to govern how ice sheets behave at glacial time scales (〉1000 years) and responsible for changes in dynamics between the core and peripheral regions of the Laurentide and Fennoscandian ice sheets. Basal motion is accomplished via the deformation of unconsolidated sediments, or via sliding of the ice over an undeformable bed. We present an ice sheet sliding module for the Parallel Ice Sheet Model (PISM) that takes into account changes in sediment cover and incorporates surface meltwater. This model routes meltwater, produced at the surface and base of the ice sheet, toward the margin of the ice sheet. Basal sliding is accomplished through the deformation of water saturated sediments, or sliding at the ice-bed interface. In areas with continuous, water saturated sediments, sliding is almost always accomplished through sediment deformation. In areas with incomplete cover, sliding has a stronger dependence on the supply of water. We find that the addition of surface meltwater to the base is a more important factor for ice sheet evolution than the style of sliding. In a glacial cycle simulation, our model causes a more rapid buildup of the Laurentide Ice Sheet.
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  • 7
    Publication Date: 2023-06-29
    Type: Report , NonPeerReviewed
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  • 8
    Publication Date: 2023-06-29
    Type: Book chapter , NonPeerReviewed
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  • 9
    Publication Date: 2024-02-07
    Description: For the abundant marine Alphaproteobacterium Pelagibacter (SARI 1), and other bacteria, phages are powerful forces of mortality. However, little is known about the most abundant Pelagiphages in nature, such as the widespread HTVC023P-type, which is currently represented by two cultured phages. Using viral metagenomic data sets and fluorescence-activated cell sorting, we recovered 80 complete, undescribed Podoviridae genomes that form 10 phylogenomically distinct clades (herein, named Clades I to X) related to the HTVC023P-type. These expanded the HTVC023P-type pangenome by 15-fold and revealed 41 previously unknown auxiliary metabolic genes (AMGs) in this viral lineage. Numerous instances of partner-AMGs (colocated and involved in related functions) were observed, including partners in nucleotide metabolism, DNA hypermodification, and Curli biogenesis. The Type VIII secretion system (T8SS) responsible for Curli biogenesis was identified in nine genomes and expanded the repertoire of T8SS proteins reported thus far in viruses. Additionally, the identified T8SS gene cluster contained an iron-dependent regulator (FecR), as well as a histidine kinase and adenylate cyclase that can be implicated in T8SS function but are not within T8SS operons in bacteria. While T8SS are lacking in known Pelagibacter, they contribute to aggregation and biofilm formation in other bacteria. Phylogenetic reconstructions of partner-AMGs indicate derivation from cellular lineages with a more recent transfer between viral families. For example, homologs of all T8SS genes are present in syntenic regions of distant Myoviridae Pelagiphages, and they appear to have alphaproteobacterial origins with a later transfer between viral families. The results point to an unprecedented multipartner-AMG transfer between marine Myoviridae and Podoviridae. Together with the expansion of known metabolic functions, our studies provide new prospects for understanding the ecology and evolution of marine phages and their hosts. IMPORTANCE One of the most abundant and diverse marine bacterial groups is Pelagibacter. Phages have roles in shaping Pelagibacter ecology; however, several Pelagiphage lineages are represented by only a few genomes. This paucity of data from even the most widespread lineages has imposed limits on the understanding of the diversity of Pelagiphages and their impacts on hosts. Here, we report 80 complete genomes, assembled directly from environmental data, which are from undescribed Pelagiphages and render new insights into the manipulation of host metabolism during infection. Notably, the viruses have functionally related partner genes that appear to be transferred between distant viruses, including a suite that encode a secretion system which both brings a new functional capability to the host and is abundant in phages across the ocean. Together, these functions have important implications for phage evolution and for how Pelagiphage infection influences host biology in manners extending beyond canonical viral lysis and mortality.
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  • 10
    Publication Date: 2024-02-07
    Description: Membrane transport proteins perform crucial roles in cell physiology. The obligate intracellular parasite Plasmodium falciparum, an agent of human malaria, relies on membrane transport proteins for the uptake of nutrients from the host, disposal of metabolic waste, exchange of metabolites between organelles, and generation and maintenance of transmembrane electrochemical gradients for its growth and replication within human erythrocytes. Despite their importance for Plasmodium cellular physiology, the functional roles of a number of membrane transport proteins remain unclear, which is particularly true for orphan membrane transporters that have no or limited sequence homology to transporter proteins in other evolutionary lineages. Therefore, in the current study, we applied endogenous tagging, targeted gene disruption, conditional knockdown, and knockout approaches to investigate the subcellular localization and essentiality of six membrane transporters during intraerythrocytic development of P. falciparum parasites. They are localized at different subcellular structures—the food vacuole, the apicoplast, and the parasite plasma membrane—and four out of the six membrane transporters are essential during asexual development. Additionally, the plasma membrane resident transporter 1 (PMRT1; PF3D7_1135300), a unique Plasmodium-specific plasma membrane transporter, was shown to be essential for gametocytogenesis and functionally conserved within the genus Plasmodium. Overall, we reveal the importance of four orphan transporters to blood stage P. falciparum development, which have diverse intracellular localizations and putative functions. IMPORTANCE: Plasmodium falciparum-infected erythrocytes possess multiple compartments with designated membranes. Transporter proteins embedded in these membranes not only facilitate movement of nutrients, metabolites, and other molecules between these compartments, but also are common therapeutic targets and can confer antimalarial drug resistance. Orphan membrane transporters in P. falciparum without sequence homology to transporters in other evolutionary lineages and divergent from host transporters may constitute attractive targets for novel intervention approaches. Here, we localized six of these putative transporters at different subcellular compartments and probed their importance during asexual parasite growth by using reverse genetic approaches. In total, only two candidates turned out to be dispensable for the parasite, highlighting four candidates as putative targets for therapeutic interventions. This study reveals the importance of several orphan transporters to blood stage P. falciparum development.
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  • 11
    Publication Date: 2024-02-07
    Description: Although it is generally known that a combination of abiotic and biotic drivers shapes the distribution and abundance of parasites, our understanding of the interplay of these factors remains to be assessed for most marine host species. The present field survey investigated spatial patterns of richness, prevalence and abundance of parasites in Mytilus galloprovincialis along the coast of the northern Adriatic Sea. Herein, the relationships between biotic (host size, density and local parasite richness of mussel population) and abiotic (eutrophication and salinity) drivers and parasite richness of mussel individuals, prevalence and abundance were analysed. Local parasite richness was the most relevant factor driving parasite species richness in mussel individuals. Prevalence was mainly driven by eutrophication levels in 3 out of 4 parasite species analysed. Similarly, abundance was driven mainly by eutrophication in two parasite species. Mussel size, density and salinity had only minor contributions to the best fitting models. This study highlights that the influence of abiotic and biotic drivers on parasite infections in mussels can be differentially conveyed, depending on the infection measure applied, i.e., parasite richness, prevalence or abundance. Furthermore, it stresses the importance of eutrophication as a major factor influencing parasite prevalence and abundance in mussels in the Adriatic Sea
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  • 12
    Publication Date: 2024-02-07
    Description: The genome of the wheat-pathogenic fungus Zymoseptoria tritici represents extensive presence-absence variation in gene content. Here, we addressed variation in biosynthetic gene cluster (BGC) content and biochemical profiles among three isolates. We analyzed secondary metabolite properties based on genome, transcriptome, and metabolome data. The isolates represent highly distinct genome architecture but harbor similar repertoires of BGCs. Expression profiles for most BGCs show comparable patterns of regulation among the isolates, suggesting a conserved biochemical infection program. For all three isolates, we observed a strong upregulation of a putative abscisic acid (ABA) gene cluster during biotrophic host colonization, indicating that Z. tritici interferes with host defenses by the biosynthesis of this phytohormone. Further, during in vitro growth, the isolates show similar metabolomes congruent with the predicted BGC content. We assessed if secondary metabolite production is regulated by histone methylation using a mutant impaired in formation of facultative heterochromatin (H3K27me3). In contrast to other ascomycete fungi, chromatin modifications play a less prominent role in regulation of secondary metabolites. In summary, we show that Z. tritici has a conserved program of secondary metabolite production, contrasting with the immense variation in effector expression, and some of these metabolites might play a key role during host colonization. IMPORTANCE Zymoseptoria tritici is one of the most devastating pathogens of wheat. So far the molecular determinants of virulence and their regulation are poorly understood. Previous studies have focused on proteinaceous virulence factors and their extensive diversity. In this study, we focus on secondary metabolites produced by Z. tritici. Using a comparative framework, we characterize core and noncore metabolites produced by Z. tritici by combining genome, transcriptome, and metabolome data sets. Our findings indicate highly conserved biochemical profiles with contrasting genetic and phenotypic diversity of the field isolates investigated here. This discovery has relevance for future crop protection strategies.
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  • 13
    Publication Date: 2023-06-29
    Type: Report , NonPeerReviewed
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  • 14
    Publication Date: 2024-02-07
    Description: The marine bone biome is a complex assemblage of macro- and microorganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic collagen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of microbial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia contained the most diverse gene repertoires. We postulate that demineralization of inorganic bone components is achieved by a timely succession of a closed sulfur biogeochemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone surface communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia.
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  • 15
    Publication Date: 2024-02-07
    Description: A considerable fraction of organic matter derived from photosynthesis in the euphotic zone settles into the ocean’s interior and, as it progresses, is degraded by diverse microbial consortia that utilize a suite of extracellular enzymes and membrane transporters. Still, the molecular details that regulate carbon cycling across depths remain little explored. As stratification in fjords has made them attractive models to explore patterns in biological oceanography, we here analyzed bacterial and archaeal transcription in samples from five depth layers in the Gullmar Fjord, Sweden. Transcriptional variation over depth correlated with gradients in chlorophyll a and nutrient concentrations. Differences in transcription between sampling dates (summer and early autumn) were strongly correlated with ammonium concentrations, which potentially was linked with a stronger influence of (micro-)zooplankton grazing in summer. Transcriptional investment in carbohydrate-active enzymes (CAZymes) decreased with depth and shifted toward peptidases, partly a result of elevated CAZyme transcription by Flavobacteriales, Cellvibrionales, and Synechococcales at 2 to 25 m and a dominance of peptidase transcription by Alteromonadales and Rhodobacterales from 50 m down. In particular, CAZymes for chitin, laminarin, and glycogen were important. High levels of transcription of ammonium transporter genes by Thaumarchaeota at depth (up to 18% of total transcription), along with the genes for ammonia oxidation and CO2 fixation, indicated that chemolithoautotrophy contributed to the carbon flux in the fjord. The taxon-specific expression of functional genes for processing of the marine pool of dissolved organic matter and inorganic nutrients across depths emphasizes the importance of different microbial foraging mechanisms over spatiotemporal scales for shaping biogeochemical cycles. IMPORTANCE It is generally recognized that stratification in the ocean strongly influences both the community composition and the distribution of ecological functions of microbial communities, which in turn are expected to shape the biogeochemical cycling of essential elements over depth. Here, we used metatranscriptomics analysis to infer molecular detail on the distribution of gene systems central to the utilization of organic matter in a stratified marine system. We thereby uncovered that pronounced shifts in the transcription of genes encoding CAZymes, peptidases, and membrane transporters occurred over depth among key prokaryotic orders. This implies that sequential utilization and transformation of organic matter through the water column is a key feature that ultimately influences the efficiency of the biological carbon pump.
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  • 16
    Publication Date: 2024-02-07
    Description: Trematode prevalence and abundance in hosts are known to be affected by biotic drivers as well as by abiotic drivers. In this study, we used the unique salinity gradient found in the south-western Baltic Sea to: (i) investigate patterns of trematode infections in the first intermediate host, the periwinkle Littorina littorea and in the downstream host, the mussel Mytilus edulis, along a regional salinity gradient (from 13 to 22) and (ii) evaluate the effects of first intermediate host (periwinkle) density, host size and salinity on trematode infections in mussels. Two species dominated the trematode community, Renicola roscovita and Himasthla elongata. Salinity, mussel size and density of infected periwinkles were significantly correlated with R. roscovita, and salinity and density correlated with H. elongata abundance. These results suggest that salinity, first intermediate host density and host size play an important role in determining infection levels in mussels, with salinity being the main major driver. Under expected global change scenarios, the predicted freshening of the Baltic Sea might lead to reduced trematode transmission, which may be further enhanced by a potential decrease in periwinkle density and mussel size.
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  • 17
    Publication Date: 2024-02-07
    Description: Coral reefs are possible sinks for microbes; however, the removal mechanisms at play are not well understood. Here, we characterize pelagic microbial groups at the CARMABI reef (Curaçao) and examine microbial consumption by three coral species: Madracis mirabilis, Porites astreoides, and Stephanocoenia intersepta. Flow cytometry analyses of water samples collected from a depth of 10 m identified 6 microbial groups: Prochlorococcus, three groups of Synechococcus, photosynthetic eukaryotes, and heterotrophic bacteria. Minimum growth rates (µ) for Prochlorococcus, all Synechococcus groups, and photosynthetic eukaryotes were 0.55, 0.29, and 0.45µ day-1, respectively, and suggest relatively high rates of productivity despite low nutrient conditions on the reef. During a series of 5-h incubations with reef corals performed just after sunset or prior to sunrise, reductions in the abundance of photosynthetic picoeukaryotes, Prochlorococcus and Synechococcus cells, were observed. Of the three Synechococcus groups, one decreased significantly during incubations with each coral and the other two only with M. mirabilis. Removal of carbon from the water column is based on coral consumption rates of phytoplankton and averaged between 138 ng h-1and 387 ng h-1, depending on the coral species. A lack of coral-dependent reduction in heterotrophic bacteria, differences in Synechococcus reductions, and diurnal variation in reductions of Synechococcus and Prochlorococcus, coinciding with peak cell division, point to selective feeding by corals. Our study indicates that bentho-pelagic coupling via selective grazing of microbial groups influences carbon flow and supports heterogeneity of microbial communities overlying coral reefs. Importance We identify interactions between coral grazing behavior and the growth rates and cell abundances of pelagic microbial groups found surrounding a Caribbean reef. During incubation experiments with three reef corals, reductions in microbial cell abundance differed according to coral species and suggest specific coral or microbial mechanisms are at play. Peaks in removal rates of Prochlorococcus and Synechococcus cyanobacteria appear highest during postsunset incubations and coincide with microbial cell division. Grazing rates and effort vary across coral species and picoplankton groups, possibly influencing overall microbial composition and abundance over coral reefs. For reef corals, use of such a numerically abundant source of nutrition may be advantageous, especially under environmentally stressful conditions when symbioses with dinoflagellate algae break down.
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  • 18
    Publication Date: 2024-02-07
    Description: The last 85,000 years were characterized by high climate and environmental variability on the Yucatán Peninsula. Heinrich stadials are examples of abrupt climate transitions that involved shifts in regional temperatures and moisture availability. Thus, they serve as natural experiments to evaluate the contrasting responses of aquatic and terrestrial ecosystems. We used ostracodes and pollen preserved in a 75.9-m-long sediment core (PI-6, ~85 ka) recovered from Lake Petén Itzá, Guatemala, to assess the magnitude and velocity of community responses. Ostracodes are sensitive to changes in water temperature and conductivity. Vegetation responds to shifts in temperature and the ratio of evaporation to precipitation. Ostracodes display larger and more rapid community changes than does vegetation. Heinrich Stadial 5-1 (HS5-1) was cold and dry and is associated with lower ostracode and vegetation species richness and diversity. In contrast, the slightly warmer and dry conditions during HS6 and HS5a are reflected in higher ostracode species richness and diversity. Our paleoecological study revealed the greatest ecological turnover for ostracodes occurred from 62.5 to 51.0 ka; for pollen, it was at the Pleistocene/Holocene transition. Future studies should use various climate and environmental indicators from lake and marine sediment records to further explore late glacial paleoclimate causes and effects in the northern neotropics.
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  • 19
    Publication Date: 2024-02-07
    Description: During the symptomatic human blood phase, malaria parasites replicate within red blood cells. Parasite proliferation relies on the uptake of nutrients, such as amino acids, from the host cell and blood plasma, requiring transport across multiple membranes. Amino acids are delivered to the parasite through the parasite-surrounding vacuolar compartment by specialized nutrient-permeable channels of the erythrocyte membrane and the parasitophorous vacuole membrane (PVM). However, further transport of amino acids across the parasite plasma membrane (PPM) is currently not well characterized. In this study, we focused on a family of Apicomplexan amino acid transporters (ApiATs) that comprises five members in Plasmodium falciparum. First, we localized four of the P. falciparum ApiATs (PfApiATs) at the PPM using endogenous green fluorescent protein (GFP) tagging. Next, we applied reverse genetic approaches to probe into their essentiality during asexual replication and gametocytogenesis. Upon inducible knockdown and targeted gene disruption, a reduced asexual parasite proliferation was detected for PfApiAT2 and PfApiAT4. Functional inactivation of individual PfApiATs targeted in this study had no effect on gametocyte development. Our data suggest that individual PfApiATs are partially redundant during asexual in vitro proliferation and fully redundant during gametocytogenesis of P. falciparum parasites. IMPORTANCE Malaria parasites live and multiply inside cells. To facilitate their extremely fast intracellular proliferation, they hijack and transform their host cells. This also requires the active uptake of nutrients, such as amino acids, from the host cell and the surrounding environment through various membranes that are the consequence of the parasite’s intracellular lifestyle. In this paper, we focus on a family of putative amino acid transporters termed ApiAT. We show expression and localization of four transporters in the parasite plasma membrane of Plasmodium falciparum-infected erythrocytes that represent one interface of the pathogen to its host cell. We probed into the impact of functional inactivation of individual transporters on parasite growth in asexual and sexual blood stages of P. falciparum and reveal that only two of them show a modest but significant reduction in parasite proliferation but no impact on gametocytogenesis, pointing toward dispensability within this transporter family.
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  • 20
    Publication Date: 2024-02-07
    Description: The Andvord fjord in the West Antarctic Peninsula (WAP) is known for its productivity and abundant megafauna. Nevertheless, seasonal patterns of the molecular diversity and abundance of protistan community members underpinning WAP productivity remain poorly resolved. We performed spring and fall expeditions pursuing protistan diversity, abundance of photosynthetic taxa, and the connection to changing conditions. 18S rRNA amplicon sequence variant (ASV) profiles revealed diverse predatory protists spanning multiple eukaryotic supergroups, alongside enigmatic heterotrophs like the Picozoa. Among photosynthetic protists, cryptophyte contributions were notable. Analysis of plastid-derived 16S rRNA ASVs supported 18S ASV results, including a dichotomy between cryptophytes and diatom contributions previously reported in other Antarctic regions. We demonstrate that stramenopile and cryptophyte community structures have distinct attributes. Photosynthetic stramenopiles exhibit high diversity, with the polar diatom Fragilariopsis cylindrus, unidentified Chaetoceros species, and others being prominent. Conversely, ASV analyses followed by environmental full-length rRNA gene sequencing, electron microscopy, and flow cytometry revealed that a novel alga dominates the cryptophytes. Phylogenetic analyses established that TPG clade VII, as named here, is evolutionarily distinct from cultivated cryptophyte lineages. Additionally, cryptophyte cell abundance correlated with increased water temperature. Analyses of global data sets showed that clade VII dominates cryptophyte ASVs at Southern Ocean sites and appears to be endemic, whereas in the Arctic and elsewhere, Teleaulax amphioxeia and Plagioselmis prolonga dominate, although both were undetected in Antarctic waters. Collectively, our studies provide baseline data against which future change can be assessed, identify different diversification patterns between stramenopiles and cryptophytes, and highlight an evolutionarily distinct cryptophyte clade that thrives under conditions enhanced by warming. IMPORTANCE The climate-sensitive waters of the West Antarctic Peninsula (WAP), including its many fjords, are hot spots of productivity that support multiple marine mammal species. Here, we profiled protistan molecular diversity in a WAP fjord known for high productivity and found distinct spatiotemporal patterns across protistan groups. Alongside first insights to seasonal changes in community structure, we discovered a novel phytoplankton species with proliferation patterns linked to temperature shifts. We then examined evolutionary relationships between this novel lineage and other algae and their patterns in global ocean survey data. This established that Arctic and Antarctic cryptophyte communities have different species composition, with the newly identified lineage being endemic to Antarctic waters. Our research provides critical knowledge on how specific phytoplankton at the base of Antarctic food webs respond to warming, as well as information on overall diversity and community structure in this changing polar environment
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  • 21
    Publication Date: 2021-01-08
    Description: Radiocarbon (14C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric 14C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international 14C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable 14C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the 14C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine 14C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.
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  • 22
    Publication Date: 2021-01-08
    Description: The concentration of radiocarbon (14C) differs between ocean and atmosphere. Radiocarbon determinations from samples which obtained their 14C in the marine environment therefore need a marine-specific calibration curve and cannot be calibrated directly against the atmospheric-based IntCal20 curve. This paper presents Marine20, an update to the internationally agreed marine radiocarbon age calibration curve that provides a non-polar global-average marine record of radiocarbon from 0–55 cal kBP and serves as a baseline for regional oceanic variation. Marine20 is intended for calibration of marine radiocarbon samples from non-polar regions; it is not suitable for calibration in polar regions where variability in sea ice extent, ocean upwelling and air-sea gas exchange may have caused larger changes to concentrations of marine radiocarbon. The Marine20 curve is based upon 500 simulations with an ocean/atmosphere/biosphere box-model of the global carbon cycle that has been forced by posterior realizations of our Northern Hemispheric atmospheric IntCal20 14C curve and reconstructed changes in CO2 obtained from ice core data. These forcings enable us to incorporate carbon cycle dynamics and temporal changes in the atmospheric 14C level. The box-model simulations of the global-average marine radiocarbon reservoir age are similar to those of a more complex three-dimensional ocean general circulation model. However, simplicity and speed of the box model allow us to use a Monte Carlo approach to rigorously propagate the uncertainty in both the historic concentration of atmospheric 14C and other key parameters of the carbon cycle through to our final Marine20 calibration curve. This robust propagation of uncertainty is fundamental to providing reliable precision for the radiocarbon age calibration of marine based samples. We make a first step towards deconvolving the contributions of different processes to the total uncertainty; discuss the main differences of Marine20 from the previous age calibration curve Marine13; and identify the limitations of our approach together with key areas for further work. The updated values for ΔR, the regional marine radiocarbon reservoir age corrections required to calibrate against Marine20, can be found at the data base http://calib.org/marine/.
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  • 23
    Publication Date: 2023-02-08
    Description: All multicellular organisms are associated with microbial communities, ultimately forming a metaorganism. Several studies conducted on well-established model organisms point to immunological, metabolic, and behavioral benefits of the associated microbiota for the host. Consequently, a microbiome can influence the physiology of a host; moreover, microbial community shifts can affect host health and fitness. The present study aimed to evaluate the significance and functional role of the native microbiota for life cycle transitions and fitness of the cnidarian moon jellyfish Aurelia aurita. A comprehensive host fitness experiment was conducted studying the polyp life stage and integrating 12 combinations of treatments with microbiota modification (sterile conditions, foreign food bacteria, and potential pathogens). Asexual reproduction, e.g., generation of daughter polyps, and the formation and release of ephyrae were highly affected in the absence of the native microbiota, ultimately resulting in a halt of strobilation and ephyra release. Assessment of further fitness traits showed that health, growth, and feeding rate were decreased in the absence and upon community changes of the native microbiota, e.g., when challenged with selected bacteria. Moreover, changes in microbial community patterns were detected by 16S rRNA amplicon sequencing during the course of the experiment. This demonstrated that six operational taxonomic units (OTUs) significantly correlated and explained up to 97% of fitness data variability, strongly supporting the association of impaired fitness with the absence/presence of specific bacteria. Conclusively, our study provides new insights into the importance and function of the microbiome for asexual reproduction, health, and fitness of the basal metazoan A. aurita.
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  • 24
    Publication Date: 2023-02-08
    Description: We report the draft genome sequence of Pseudomonas sp. strain LD120, which was isolated from a brown macroalga in the Baltic Sea. The genome of this marine Pseudomonas protegens subgroup bacterium harbors biosynthetic gene clusters for toxic metabolites typically produced by members of this Pseudomonas subgroup, including 2,4-diacetylphloroglucinol, pyoluteorin, and rhizoxin analogs.
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  • 25
    Publication Date: 2023-02-08
    Description: Organisms and their resident microbial communities form a complex and mostly stable ecosystem. It is known that the specific composition and abundance of certain bacterial species affect host health and fitness, but the processes that lead to these microbial patterns are unknown. We investigate this by deconstructing the simple microbiome of the freshwater polyp Hydra. We contrast the performance of its two main bacterial associates, Curvibacter and Duganella, on germfree hosts with two in vitro environments over time. We show that interactions within the microbiome but also the host environment lead to the observed species frequencies and abundances. More specifically, we find that both microbial species can only stably coexist in the host environment, whereas Duganella outcompetes Curvibacter in both in vitro environments irrespective of initial starting frequencies. While Duganella seems to benefit through secretions of Curvibacter, its competitive effect on Curvibacter depends upon direct contact. The competition might potentially be mitigated through the spatial distribution of the two microbial species on the host, which would explain why both species stably coexist on the host. Interestingly, the relative abundances of both species on the host do not match the relative abundances reported previously nor the overall microbiome carrying capacity as reported in this study. Both observations indicate that rare microbial community members might be relevant for achieving the native community composition and carrying capacity. Our study highlights that for dissecting microbial interactions the specific environmental conditions need to be replicated, a goal difficult to achieve with in vitro systems.
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  • 26
    Publication Date: 2023-02-09
    Description: Few studies have thus far explored the microbiomes of glass sponges (Hexactinellida). The present study seeks to elucidate the composition of the microbiota associated with the glass sponge Vazella pourtalesii and the functional strategies of the main symbionts. We combined microscopic approaches with metagenome-guided microbial genome reconstruction and amplicon community profiling towards this goal. Microscopic imaging revealed that the host and microbial cells appeared within dense biomass patches that are presumably syncytial tissue aggregates. Based on abundances in amplicon libraries and metagenomic data, SAR324 bacteria, Crenarchaeota, Patescibacteria and Nanoarchaeota were identified as abundant members of the V. pourtalesii microbiome and their genomic potentials were thus analyzed in detail. A general pattern emerged in that the V. pourtalesii symbionts had very small genome sizes in the range of 0.5-2.2 Mb and low GC contents, even below those of seawater relatives. Based on functional analyses of metagenome-assembled genomes (MAGs), we propose two major microbial strategies: the “givers”, namely Crenarchaeota and SAR324, heterotrophs and facultative anaerobes, produce and partly secrete all required amino acids and vitamins. The “takers”, Nanoarchaeota and Patescibacteria, are anaerobes with reduced genomes that tap into the microbial community for resources, e.g., lipids and DNA, likely using pili-like structures. We posit that the existence of microbial cells in sponge syncytia together with the low-oxygen conditions in the seawater environment are factors that shape the unique compositional and functional properties of the microbial community associated with V. pourtalesii . Importance: We investigated the microbial community of V. pourtalesii that forms globally unique, monospecific sponge grounds under low-oxygen conditions on the Scotian Shelf, where it plays a key role for its vulnerable ecosystem. The microbial community was found to be concentrated within biomass patches and is dominated by small cells (〈1 μm). MAG analyses showed consistently small genome sizes and low GC contents, which is unusual in comparison to known sponge symbionts. These properties as well as the (facultatively) anaerobic metabolism and a high degree of interdependence between the dominant symbionts regarding amino acid and vitamin synthesis are likely adaptations to the unique conditions within the syncytial tissue of their hexactinellid host and the low-oxygen environment.
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  • 27
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    Cambridge University Press
    In:  New Directions in Sustainability and Society
    Publication Date: 2023-07-18
    Description: In this Open Access book, Sander van der Leeuw examines how the modern world has been caught in a socioeconomic dynamic that has generated the conundrum of sustainability. Combining the methods of social science and complex systems science, he explores how western, developed nations have globalized their world view and how that view has led to the sustainability challenges we are now facing. Its central theme is the coevolution of cognition, demography, social organization, technology, and environmental impact. Beginning with the earliest human societies, van der Leeuw links the distant past with the present in order to demonstrate how the information and communications technology revolution is undermining many of the institutional pillars on which contemporary societies have been constructed. An original view of social evolution as the history of human information-processing, his book shows how the past offers insight into the present and can help us deal with the future.
    Language: English
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  • 28
    Publication Date: 2021-01-08
    Description: A new carbon isotope record for two high-latitude sedimentary successions that span the Jurassic–Cretaceous boundary interval in the Sverdrup Basin of Arctic Canada is presented. This study, combined with other published Arctic data, shows a large negative isotopic excursion of organic carbon (δ13Corg) of 4‰ (V-PDB) and to a minimum of −30.7‰ in the probable middle Volgian Stage. This is followed by a return to less negative values of c. −27‰. A smaller positive excursion in the Valanginian Stage of c. 2‰, reaching maximum values of −24.6‰, is related to the Weissert Event. The Volgian isotopic trends are consistent with other high-latitude records but do not appear in δ13Ccarb records of Tethyan Tithonian strata. In the absence of any obvious definitive cause for the depleted δ13Corg anomaly, we suggest several possible contributing factors. The Sverdrup Basin and other Arctic areas may have experienced compositional evolution away from open-marine δ13C values during the Volgian Age due to low global or large-scale regional sea levels, and later become effectively coupled to global oceans by Valanginian time when sea level rose. A geologically sudden increase in volcanism may have caused the large negative δ13Corg values seen in the Arctic Volgian records but the lack of precise geochronological age control for the Jurassic–Cretaceous boundary precludes direct comparison with potentially coincident events, such as the Shatsky Rise. This study offers improved correlation constraints and a refined C-isotope curve for the Boreal region throughout latest Jurassic and earliest Cretaceous time.
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  • 29
    Publication Date: 2022-01-31
    Description: The deep-sea tubeworm Riftia pachyptila lacks a digestive system but completely relies on bacterial endosymbionts for nutrition. Although the symbiont has been studied in detail on the molecular level, such analyses were unavailable for the animal host, because sequence information was lacking. To identify host-symbiont interaction mechanisms, we therefore sequenced the Riftia transcriptome, which served as a basis for comparative metaproteomic analyses of symbiont-containing versus symbiont-free tissues, both under energy-rich and energy-limited conditions. Our results suggest that metabolic interactions include nutrient allocation from symbiont to host by symbiont digestion and substrate transfer to the symbiont by abundant host proteins. We furthermore propose that Riftia maintains its symbiont by protecting the bacteria from oxidative damage while also exerting symbiont population control. Eukaryote-like symbiont proteins might facilitate intracellular symbiont persistence. Energy limitation apparently leads to reduced symbiont biomass and increased symbiont digestion. Our study provides unprecedented insights into host-microbe interactions that shape this highly efficient symbiosis.
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  • 30
    Publication Date: 2022-01-31
    Description: During its intraerythrocytic development, the malaria parasite Plasmodium falciparum exposes variant surface antigens (VSAs) on infected erythrocytes to establish and maintain an infection. One family of small VSAs is the polymorphic STEVOR proteins, which are marked for export to the host cell surface through their PEXEL signal peptide. Interestingly, some STEVORs have also been reported to localize to the parasite plasma membrane and apical organelles, pointing toward a putative function in host cell egress or invasion. Using deep RNA sequencing analysis, we characterized P. falciparum stevor gene expression across the intraerythrocytic development cycle, including free merozoites, in detail and used the resulting stevor expression profiles for hierarchical clustering. We found that most stevor genes show biphasic expression oscillation, with maximum expression during trophozoite stages and a second peak in late schizonts. We selected four STEVOR variants, confirmed the expected export of these proteins to the host cell membrane, and tracked them to a secondary location, either to the parasite plasma membrane or the secretory organelles of merozoites in late schizont stages. We investigated the function of a particular STEVOR that showed rhoptry localization and demonstrated its role at the parasite-host interface during host cell invasion by specific antisera and targeted gene disruption. Experimentally determined membrane topology of this STEVOR revealed a single transmembrane domain exposing the semiconserved as well as variable protein regions to the cell surface.
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  • 31
    Publication Date: 2021-03-19
    Description: Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for “Candidatus Poribacteria” and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCE Chloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.
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  • 32
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    American Society for Microbiology
    In:  Genome Announcements, 5 (17). e00268-17.
    Publication Date: 2020-02-06
    Description: We report here four draft genome sequences belonging to clade F of the cyanobacterium “Candidatus Synechococcus spongiarum” of the marine sponge Aplysina aerophoba, which were collected from two nearby locations in the northern Adriatic Sea. The sequences provide the basis for within-clade comparisons between members of this widespread group of cyanobacterial sponge symbionts.
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  • 33
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    American Society for Microbiology
    In:  Genome Announcements, 5 (48). e01368.
    Publication Date: 2020-02-06
    Description: Here, we present the draft genome sequence of Vibrio splendidus type strain DSM 19640. V. splendidus is an abundant species among coastal vibrioplankton. The assembly resulted in a 5,729,362-bp draft genome with 5,032 proteincoding sequences, 6 rRNAs, and 117 tRNAs.
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  • 34
    Publication Date: 2020-01-02
    Description: Vitamin B1 (thiamin) is a cofactor for critical enzymatic processes and is scarce in surface oceans. Several eukaryotic marine algal species thought to rely on exogenous thiamin are now known to grow equally well on the precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), including the haptophyte Emiliania huxleyi. Because the thiamin biosynthetic capacities of the diverse and ecologically important haptophyte lineage are otherwise unknown, we investigated the pathway in transcriptomes and two genomes from 30 species representing six taxonomic orders. HMP synthase is missing in data from all studied taxa, but the pathway is otherwise complete, with some enzymatic variations. Experiments on axenic species from three orders demonstrated that equivalent growth rates were supported by 1 μM HMP or thiamin amendment. Cellular thiamin quotas were quantified in the oceanic phytoplankter E. huxleyi using the thiochrome assay. E. huxleyi exhibited luxury storage in standard algal medium (1.16 ± 0.18) ☓ 10-6 pmol thiamin cell-1, whereas quotas in cultures grown under more environmentally relevant thiamin and HMP supplies (2.22 ± 0.07) ☓ 10-7 or (1.58 ± 0.14) ☓ 10-7 pmol thiamin cell-1, respectively were significantly lower than luxury values and prior estimates. HMP and its salvage-related analog 4-amino-5-aminomethyl-2-methylpyrimidine (AmMP) supported higher growth than thiamin under environmentally relevant supply levels. These compounds also sustained growth of the stramenopile alga Pelago-monas calceolata. Together with identification of a salvage protein subfamily (TENA_E) in multiple phytoplankton, the results indicate that salvaged AmMP and exogenously acquired HMP are used by several groups for thiamin production. Our studies highlight the potential importance of thiamin pathway intermediates and their analogs in shaping phytoplankton community structure. IMPORTANCE The concept that vitamin B1 (thiamin) availability in seawater controls the productivity and structure of eukaryotic phytoplankton communities has been discussed for half a century. We examined B1 biosynthesis and salvage pathways in diverse phytoplankton species. These comparative genomic analyses as well as experiments show that phytoplankton thought to require exogenous B1 not only utilize intermediate compounds to meet this need but also exhibit stronger growth on these compounds than on thiamin. Furthermore, oceanic phytoplankton have lower cellular thiamin quotas than previously reported, and salvage of intermediate compounds is likely a key mechanism for meeting B1 requirements under environmentally relevant scenarios. Thus, several lines of evidence now suggest that availability of specific precursor molecules could be more important in structuring phytoplankton communities than the vitamin itself. This understanding of preferential compound utilization and thiamin quotas will improve biogeochemical model pa-rameterization and highlights interaction networks among ocean microbes. © 2017 Gutowska et al.
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  • 35
    Publication Date: 2021-05-25
    Description: Recent rapid retreat of glacial front lines and the loss of land ice along the Antarctic margins may play an important role in exporting suspended particulate matter (SPM) potentially rich in bioavailable (defined as ascorbate leachable) iron (FeA) to coastal areas of the Southern Ocean. Sediment ablation is an additional source of iron for this high-nutrient low-chlorophyll region. In Potter Cove, King George Island, meltwater streams discharge up to 18 000 mg l-1 (average 283 mg l-1) of slightly weathered, finely ground bedrock particles into coastal waters during the summer. Approximately 15% of this SPM is exported within a low-salinity surface plume into Bransfield Strait. Based on our data, an estimated 12 mg m-2 yr-1 of FeA is exported from the South Shetland Island land surface (ice-free and subglacial areas) to the surrounding coastal waters. Extrapolated to an area of 2.5x104 km2, this FeA input is comparable to the contribution from icebergs and c. 240-fold higher than aeolian input via dust. An observed rise in local sediment accumulation rates suggests that glacial erosion has been increasing over recent decades and that (sub-)glacially derived SPM is becoming more important as a source of iron to the Southern Ocean.
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  • 36
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    Cambridge University Press
    In:  Nonlinear and Stochastic Climate Dynamics
    Publication Date: 2022-03-21
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  • 37
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    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 82 (18). pp. 5542-5552.
    Publication Date: 2019-02-01
    Description: Crown gall disease of grapevine is caused by virulent Agrobacterium strains and establishes a suitable habitat for agrobacteria and, potentially, other bacteria. The microbial community associated with grapevine plants has not been investigated with respect to this disease, which frequently results in monetary losses. This study compares the endophytic microbiota of organs from grapevine plants with or without crown gall disease and the surrounding vineyard soil over the growing seasons of 1 year. Amplicon-based community profiling revealed that the dominating factor causing differences between the grapevine microbiota is the sample site, not the crown gall disease. The soil showed the highest microbial diversity, which decreased with the distance from the soil over the root and the graft union of the trunk to the cane. Only the graft union microbiota was significantly affected by crown gall disease. The bacterial community of graft unions without a crown gall hosted transient microbiota, with the three most abundant bacterial species changing from season to season. In contrast, graft unions with a crown gall had a higher species richness, which in every season was dominated by the same three bacteria (Pseudomonas sp., Enterobacteriaceae sp., and Agrobacterium vitis). For in vitro-cultivated grapevine plantlets, A. vitis infection alone was sufficient to cause crown gall disease. Our data show that microbiota in crown galls is more stable over time than microbiota in healthy graft unions and that the microbial community is not essential for crown gall disease outbreak.
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  • 38
    Publication Date: 2019-03-05
    Description: Eukaryotic algae within the picoplankton size class (〈 2 μmin diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus, during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 × 105 and 3.37 × 105 cells · ml-1, respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 × 105 cells · ml-1 in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368±327 18S rRNA gene copies · ml-1. Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos) and BII. These share 82±6 nucleotide identity across homologs, while the Ostreococcus spp. share 75±8. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO3 - and low-affinity NH4 + transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in the open ocean, where dissolved iron concentrations were low (0.08 nM), there appeared to be a shift to the use of nickel superoxide dismutases (SODs) from Mn/Fe/Cu SODs closer inshore. Our study documents the distribution of picophytoplankton along a North Pacific ecological gradient and offers new concepts and techniques for investigating their biogeography. © 2016, American Society for Microbiology. All Rights Reserved.
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  • 39
    Publication Date: 2019-06-11
    Description: Since the Last Glacial Maximum, ice has retreated through the fjords of the South Shetland Islands leaving a valuable record of submarine landforms behind. In this study, glacial landforms and sub-bottom characteristics have been mapped to investigate the late Holocene retreat behaviour of the Fourcade Glacier and to delineate past environmental processes in Potter Cove, King George Island. The comprehensive datasets include high-resolution swath bathymetry, shallow seismic profiling and one sediment core. Moraines, moraine incisions and glacial lineations were mapped on the sea floor in the inner part of the cove, whereas pockmarks, ice scour marks and channel structures were identified in the outer part. Sub-bottom characteristics have been assigned to different acoustic facies types indicating different depositional settings. The results reveal glacial recessions as well as stillstands and potential readvances during the late Holocene. Furthermore, the sediment record indicates that the Fourcade Glacier was situated inside the inner cove during the Little Ice Age (500–100 cal yr bp).
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  • 40
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    American Society for Microbiology
    In:  Journal of Bacteriology, 198 (8). pp. 1260-1267.
    Publication Date: 2019-02-01
    Description: Sulfurimonas denitrificans is a sulfur-oxidizing epsilonproteobacterium. It has been reported to grow with sulfide and to harbor genes that encode sulfide-quinone reductases (SQRs) (catalyze sulfide oxidation). However, the actual sulfide concentrations at which S. denitrificans grows and whether its SQRs are functional remain enigmatic. Here, we illustrate the sulfide concentrations at which S. denitrificans exhibits good growth, namely, 0.18 mM to roughly 1.7 mM. Around 2.23 mM, sulfide appears to inhibit growth. S. denitrificans harbors three SQR homolog genes on its genome (Suden_2082 for type II SQR, Suden_1879 for type III SQR, and Suden_619 for type IV SQR). They are all transcribed in S. denitrificans. According to our experiments, they appear to be loosely bound to the membrane. Each individual S. denitrificans SQR was heterologously expressed in the Rhodobacter capsulatus SB1003 sqr deletion mutant, and all exhibited SQR activities individually. This suggests that all of these three genes encode functional SQRs. This study also provides the first experimental evidence of a functional bacterial type III SQR.
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  • 41
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    Cambridge University Press
    In:  In: Climate Change Geoengineering Philosophical Perspectives, Legal Issues. Cambridge University Press, Cambridge, UK, pp. 242-262. ISBN 9781107502635
    Publication Date: 2019-09-23
    Description: Introduction. Today, most countries have accepted a 2 degrees Celsius temperature increase above preindustrial levels as the maximum tolerable limit for global warming. An exceedance probability of below 20 percent for this limit implies an emission budget of less than 250 GtC from 2000 until 2049, however, extrapolating from current global CO2 emissions, this budget will only last until 2024. This sobering math should wake us up to the reality that all options, including climate engineering, need to be considered to address climate change. Climate engineering options can be classified broadly into two categories: solar radiation management and carbon dioxide removal measures. Solar radiation management schemes seek to decrease the incoming solar radiation or to increase the reflection of incoming solar radiation. These approaches can generate fast climate responses, but do not immediately address the cause of the problem. Carbon dioxide removal measures seek to decrease atmospheric carbon concentrations by enhancing or substituting natural carbon sinks. The terrestrial carbon sink can be enhanced by means of forestation; the oceanic sink may, in some regions, be enhanced by means of fertilization, for example by artificially enhanced upwelling of macronutrients or by purposeful addition of the micronutrient iron; the mineral carbon sink can be enhanced by means of chemically accelerated weathering. Some analysts have expressed doubts about the potential of mitigating climate change by sink enhancement, because of concerns about whether carbon can be stored permanently. Nevertheless, terrestrial vegetation sinks have entered the Kyoto Protocol (KP) as offsets for anthropogenic greenhouse gas emissions, but ocean sinks have not.
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  • 42
    Publication Date: 2020-04-20
    Description: The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a “Ca. Synechococcus spongiarum” group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, “Ca. Synechococcus spongiarum” includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of “Ca. Synechococcus spongiarum,” each from a different clade. By comparing all four symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of “Ca. Synechococcus spongiarum” members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the “Ca. Synechococcus spongiarum” group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack.
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  • 43
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    American Society for Microbiology
    In:  Genome Announcements, 3 (5). e01106-15.
    Publication Date: 2019-01-22
    Description: Here, we report the draft genome sequences of three actinobacterial isolates, Micromonospora sp. RV43, Rubrobacter sp. RV113, and Nocardiopsis sp. RV163 that had previously been isolated from Mediterranean sponges. The draft genomes were analyzed for the presence of gene clusters indicative of secondary metabolism using antiSMASH 3.0 and NapDos pipelines. Our findings demonstrated the chemical richness of sponge-associated actinomycetes and the efficacy of genome mining in exploring the genomic potential of sponge-derived actinomycetes.
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  • 44
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    Cambridge University Press
    In:  Journal of The Marine Biological Association of The United Kingdom, 95 (08). pp. 1613-1620.
    Publication Date: 2020-07-17
    Description: Density distribution of the common infaunal bivalves, Macoma balthica and Cerastoderma edule, was studied along the Murman Coast of the Barents Sea during 2002–2010. In both species, abundance was generally higher in West Murman in contrast to East Murman. Highest density of Macoma balthica reaching 1535 ind. m−2 was observed in the Kola Inlet. Cerastoderma edule was less abundant; its density rarely exceeded 10 ind. m−2 in all but one site, where 282 ind. m−2 was registered. Reconstruction of abundance distribution across the European geographic range of Macoma balthica revealed that it does not match an ‘abundant-centre’ pattern, having features of ramped north. On the other hand, distribution of Cerastoderma edule abundance across the range generally follows an ‘abundant-centre’ pattern but southern edge populations show relatively higher abundances as compared with those at the north edge (the Barents Sea).
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  • 45
    Publication Date: 2019-03-05
    Description: The functional diversity of eukaryotic viruses infecting a single host strain from seawater samples originating from distant marine locations is unknown. To estimate this diversity, we used lysis plaque assays to detect viruses that infect the widespread species Ostreococcus lucimarinus, which is found in coastal and mesotrophic systems, and O. tauri, which was isolated from coastal and lagoon sites from the northwest Mediterranean Sea. Detection of viral lytic activities against O. tauri was not observed using seawater from most sites, except those close to the area where the host strain was isolated. In contrast, the more cosmopolitan O. lucimarinus species recovered viruses from locations in the Atlantic and Pacific Oceans and the Mediterranean Sea. Six new O. lucimarinus viruses (OlVs) then were characterized and their genomes sequenced. Two subgroups of OlVs were distinguished based on their genetic distances and on the inversion of a central 32-kb-long DNA fragment, but overall their genomes displayed a high level of synteny. The two groups did not correspond to proximity of isolation sites, and the phylogenetic distance between these subgroups was higher than the distances observed among viruses infecting O. tauri. Our study demonstrates that viruses originating from very distant sites are able to infect the same algal host strain and can be more diverse than those infecting different species of the same genus. Finally, distinctive features and evolutionary distances between these different viral subgroups does not appear to be linked to biogeography of the viral isolates. © 2015, American Society for Microbiology.
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  • 46
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    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 80 (20). pp. 6403-6412.
    Publication Date: 2017-05-09
    Description: Methane is a potent greenhouse gas that is generated and consumed in anaerobic environments through the energy metabolism of methanogens and anaerobic methanotrophic archaea (ANME), respectively. Coenzyme F430 is essential for methanogenesis, and a structural variant of F430, 172-methylthio-F430 (F430-2), is found in ANME and is presumably essential for the anaerobic oxidation of methane. Here we use liquid chromatography–high-resolution mass spectrometry to identify several new structural variants of F430 in the cell extracts of selected methanogens and ANME. Methanocaldococcus jannaschii and Methanococcus maripaludis contain an F430 variant (denoted F430-3) that has an M+ of 1,009.2781. This mass increase of 103.9913 over that of F430 corresponds to C3H4O2S and is consistent with the addition of a 3-mercaptopropionate moiety bound as a thioether followed by a cyclization. The UV absorbance spectrum of F430-3 was different from that of F430 and instead matched that of an F430 derivative where the 173 keto moiety had been reduced. This is the first report of a modified F430 in methanogens. In a search for F430-2 and F430-3 in other methanogens and ANME, we have identified a total of nine modified F430 structures. One of these compounds may be an abiotic oxidative product of F430, but the others represent naturally modified versions of F430. This work indicates that F430-related molecules have additional functions in nature and will inspire further research to determine the biochemical role(s) of these variants and the pathways involved in their biosynthesis.
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  • 47
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    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 81 (4). pp. 1426-1441.
    Publication Date: 2018-05-04
    Description: The zonation of anaerobic methane-cycling Archaea in hydrothermal sediment of Guaymas Basin was studied by general primer pairs (mcrI, ME1/ME2, mcrIRD) targeting the alpha subunit of methyl coenzyme M reductase gene (mcrA) and by new group-specific mcrA and 16S rRNA gene primer pairs. The mcrIRD primer pair outperformed the other general mcrA primer pairs in detection sensitivity and phylogenetic coverage. Methanotrophic ANME-1 Archaea were the only group detected with group-specific primers only. The detection of 14 mcrA lineages surpasses the diversity previously found in this location. Most phylotypes have high sequence similarities to hydrogenotrophs, methylotrophs, and anaerobic methanotrophs previously detected at Guaymas Basin or at hydrothermal vents, cold seeps, and oil reservoirs worldwide. Additionally, five mcrA phylotypes belonging to newly defined lineages are detected. Two of these belong to deeply branching new orders, while the others are new species or genera of Methanopyraceae and Methermicoccaceae. Downcore diversity decreases from all groups detected in the upper 6 cm (∼2 to 40°C, sulfate measurable to 4 cm) to only two groups below 6 cm (〉40°C). Despite the presence of hyperthermophilic genera (Methanopyrus, Methanocaldococcus) in cooler surface strata, no genes were detected below 10 cm (≥60°C). While mcrA-based and 16S rRNA gene-based community compositions are generally congruent, the deeply branching mcrA cannot be assigned to specific 16S rRNA gene lineages. Our study indicates that even among well-studied metabolic groups and in previously characterized model environments, major evolutionary branches are overlooked. Detecting these groups by improved molecular biological methods is a crucial first step toward understanding their roles in nature.
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  • 48
    Publication Date: 2020-07-31
    Description: The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.
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  • 49
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    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 80 (12). pp. 3721-3728.
    Publication Date: 2019-09-23
    Description: Analyzing the dynamics of biofilm formation helps to deepen our understanding of surface colonization in natural environments. While methods for screening biofilm formation in the laboratory are well established, studies in marine environments have so far been based upon destructive analysis of individual samples and provide only discontinuous snapshots of biofilm establishment. In order to explore the development of biofilm over time and under various biotic and abiotic conditions, we applied a recently developed optical biofilm sensor to quasicontinuously analyze marine biofilm dynamics in situ. Using this technique in combination with microscope-assisted imaging, we investigated biofilm formation from its beginning to mature multispecies biofilms. In contrast to laboratory studies on biofilm formation, a smooth transition from initial attachment to colony formation and exponential growth could not be observed in the marine environment. Instead, initial attachment was followed by an adaptation phase of low growth and homogeneously distributed solitary bacterial cells. Moreover, we observed a diurnal variation of biofilm signal intensity, suggesting a transient state of biofilm formation of bacteria. Overall, the biofilm formation dynamics could be modeled by three consecutive development stages attributed to initial bacterial attachment, bacterial growth, and attachment and growth of unicellular eukaryotic microorganisms. Additional experiments showed that the presence of seaweed considerably shortened the adaptation phase in comparison with that on control surfaces but yielded similar growth rates. The outlined examples highlight the advantages of a quasicontinuous in situ detection that enabled, for the first time, the exploration of the initial attachment phase and the diurnal variation during biofilm formation in natural ecosystems
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  • 50
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    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 80 (15). pp. 4585-4598.
    Publication Date: 2018-07-18
    Description: The active venting Sisters Peak (SP) chimney on the Mid-Atlantic Ridge holds the current temperature record for the hottest ever measured hydrothermal fluids (400 degrees C, accompanied by sudden temperature bursts reaching 464 degrees C). Given the unprecedented temperature regime, we investigated the biome of this chimney with a focus on special microbial adaptations for thermal tolerance. The SP metagenome reveals considerable differences in the taxonomic composition from those of other hydrothermal vent and subsurface samples; these could be better explained by temperature than by other available abiotic parameters. The most common species to which SP genes were assigned were thermophilic Aciduliprofundum sp. strain MAR08-339 (11.8%), Hippea maritima (3.8%), Caldisericum exile (1.5%), and Caminibacter mediatlanticus (1.4%) as well as to the mesophilic Niastella koreensis (2.8%). A statistical analysis of associations between taxonomic and functional gene assignments revealed specific overrepresented functional categories: for Aciduliprofundum, protein biosynthesis, nucleotide metabolism, and energy metabolism genes; for Hippea and Caminibacter, cell motility and/or DNA replication and repair system genes; and for Niastella, cell wall and membrane biogenesis genes. Cultured representatives of these organisms inhabit different thermal niches; i.e., Aciduliprofundum has an optimal growth temperature of 70 degrees C, Hippea and Caminibacter have optimal growth temperatures around 55 degrees C, and Niastella grows between 10 and 37 degrees C. Therefore, we posit that the different enrichment profiles of functional categories reflect distinct microbial strategies to deal with the different impacts of the local sudden temperature bursts in disparate regions of the chimney.
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  • 51
    Publication Date: 2019-01-21
    Description: No published information is available on the foraging ecology and choice of feeding habitat of New Zealand’s rarest breeding bird: the New Zealand Fairy Tern (NZFT) Sternula nereis davisae. To address this gap, we conducted an assessment of the largest remaining breeding population at Mangawhai Harbour, Northland, New Zealand, during the chick-rearing period of the 2010/2011 breeding season. We combined visual tracking of birds with prey surveys and stable isotope analyses, and we present the first quantitative assessment of NZFT foraging. We recorded 405 foraging dives that show NZFT foraging habitat includes the water edges, shallow channels, and pools on the tidal flats of mangrove-lined (Avicennia marina var. resinifera) parts of the estuary; tidal pools on mud- and sandflats in the mid-estuary and lower harbour; the shallow margins of the dredged main channel in the lower harbour; the oxbow lagoons on the sand spit; and coastal shallows. Our study identifies the mangrove-lined highly tidal and shallow mid-estuary and the lagoon on the sand spit as foraging hotspots for the Mangawhai breeding population of the NZFT. The prey survey employed a seine-net sampling method at identified NZFT foraging sites and yielded 4,367 prey-sized fish of 11 species, two of which had not previously been reported in Mangawhai Harbour, as well as numerous shrimps. The most abundant fish were gobies of the genus Favonigobius. Our stable isotope results highlight gobies as the most important prey for NZFT chick rearing, also indicating that flounder Rhombosolea sp. contribute to NZFT diet. We raise the possibility that shrimps may also constitute a substantial diet component for NZFT, potentially providing up to 21% of diet mass for adult birds. While our results provide a first basis to understanding the feeding ecology of NZFT during their breeding season in order to facilitate conservation planning, further research is required to address inter-annual variation and to identify key foraging grounds for this Critically Endangered bird at other breeding sites.
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  • 52
    Publication Date: 2022-03-21
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    Publication Date: 2022-03-21
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    Publication Date: 2022-03-21
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    Publication Date: 2022-03-21
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    Cambridge University Press
    In:  Climate Change 2014: Impacts, Adaptation, and Vulnerability. [Part A: Global and Sectoral Aspects]
    Publication Date: 2022-03-21
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    Publication Date: 2022-03-21
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  • 58
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    Cambridge University Press
    Publication Date: 2022-03-21
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  • 59
    Publication Date: 2022-03-21
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  • 60
    Publication Date: 2022-03-21
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  • 61
    Publication Date: 2019-10-10
    Description: Plastid establishment involves the transfer of endosymbiotic genes to the host nucleus, a process known as endosymbiotic gene transfer (EGT). Large amounts of EGT have been shown in several photosynthetic lineages but also in present-day plastid-lacking organisms, supporting the notion that endosymbiotic genes leave a substantial genetic footprint in the host nucleus. Yet the extent of this genetic relocation remains debated, largely because the long period that has passed since most plastids originated has erased many of the clues to how this process unfolded. Among the dinoflagellates, however, the ancestral peridinin-containing plastid has been replaced by tertiary plastids on several more recent occasions, giving us a less ancient window to examine plastid origins. In this study, we evaluated the endosymbiotic contribution to the host genome in two dinoflagellate lineages with tertiary plastids. We generated the first nuclear transcriptome data sets for the “dinotoms,” which harbor diatom-derived plastids, and analyzed these data in combination with the available transcriptomes for kareniaceans, which harbor haptophyte-derived plastids. We found low level of detectable EGT in both dinoflagellate lineages, with only 9 genes and 90 genes of possible tertiary endosymbiotic origin in dinotoms and kareniaceans, respectively, suggesting that tertiary endosymbioses did not heavily impact the host dinoflagellate genomes.
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  • 62
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    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 93 (2). pp. 285-290.
    Publication Date: 2021-09-06
    Description: The feeding habits of the pelagic stingray ( Pteroplatytrygon violacea ) were studied using 84 stomachs of specimens caught in the northern Adriatic Sea in the period from April 2004 to October 2005. Percentage of empty stomachs found was overall very low, being a bit bigger in smaller specimens. The diet consisted of two main taxonomic groups such as teleost fish and cephalopods, but few specimens of crustaceans were recorded as well. The main food item was represented by anchovy, while cuttlefish and red band fish represented the alternative preys. Prey size was positively correlated with the size of predator. The proportion of anchovies in the diet grew with size of predator, while the one for red band fish decreased. The stingray was confirmed to be a top predator of pelagic fish species, although the presence of benthic prey shows that it feeds also at the bottom.
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  • 63
    Publication Date: 2021-08-24
    Description: The schooling behaviour of the oval squid Sepioteuthis lessoniana was observed over 4 summers at 3 observation sites in the coastal waters of Okinawa Island, Ryukyu Archipelago, Japan. During this field study, 3 static appearances (belt, ball and sheet shape) and 2 transitional appearances (high and low density) were noted, recorded and described. In addition to formations, a member of S. lessoniana schools also displayed particular and repeated behavioural patterns such as vanguard and intimidating display. The 3 observation sites were tropical coral reefs near the coastline at a depth of 1 to 15 m on an average. All participating observers snorkelled and were equipped with various underwater digital video and photographic cameras. The schools observed consisted of 8 to over 100 members with a wide range of body sizes. Despite these biological and locational differences, both static and transitional appearances were consistently observed with equally consistent individual behavioural patterns. There have been studies on related species, Sepioteuthis sepioidea, at the San Blas Islands along the Caribbean coast of eastern Panama, and the same species, S. lessoniana, at a different geographical location, Casuarina Beach on Lizard Island, Australia. The findings of this study are consistent with those reported previously, with some notable differences.
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  • 64
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    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 93 (2). pp. 557-565.
    Publication Date: 2021-08-20
    Description: Age structure and hatchling dates of the squid Illex argentinus collected by bottom-trawl fishery in southern Brazilian waters were assessed by the analysis of statolith growth increments. Catches occurred between 2001 and 2002, from 23° to 32°S at depths of 100–700 m. Squid from juvenile to post-spawning stages were collected year round, with age estimated from 98 to 320 days and mantle lengths ranging from 112 to 376 mm. Duration of life cycle events based on statolith growth zones revealed that squids can spend about 14% of their lifespan as paralarva (~30 days), 70% as juvenile (~130 days), leaving maturity and spawning condition to the terminal 10–20% (~30–60 days). The results suggest that, unlike estimates available for Patagonian populations, a general 0.5 year lifespan is predicted for I. argentinus off Brazil. The wide range of size-at-ages implied that catches of shortfin squid off southern Brazil probably include squid hatched throughout the year. Mature and spawning squid caught in summer months hatched in winter and spring, while winter catches revealed mature-spawning individuals hatched both in summer/autumn (~6 months of age) and winter/spring periods (~10–11 months of age). It has been argued that such groups may combine both squid resident of Brazilian outer shelf and slope (22°–34°S) with a six months' lifespan and migrating squid originated from the northern Patagonian shelf (~42°S) with 10–11 months' lifespan.
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  • 65
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    Cambridge University Press
    In:  Natural Disasters and Adaptation to Climate Change
    Publication Date: 2022-03-21
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  • 66
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    Cambridge University Press
    In:  Natural Disasters and Adaptation to Climate Change
    Publication Date: 2022-03-21
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  • 67
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    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 78 (9). pp. 3387-3399.
    Publication Date: 2019-03-05
    Description: Marine stramenopiles (MASTs) are a diverse suite of eukaryotic microbes found in marine environments. Several MAST lineages are thought to contain heterotrophic nanoflagellates. However, MASTs remain uncultured and data on distributions and trophic modes are limited. We investigated MASTs in provinces on the west and east sides of the North Pacific Subtropical Gyre, specifically the East China Sea (ECS) and the California Current system (CALC). For each province, DNA was sampled from three zones: coastal, mesotrophic transitional, and more oligotrophic euphotic waters. Along with diatoms, chrysophytes, and other stramenopiles, sequences were recovered from nine MAST lineages in the six ECS and four CALC 18S rRNA gene clone libraries. All but one of these libraries were from surface samples. MAST clusters 1, 3, 7, 8, and 11 were identified in both provinces, with MAST cluster 3 (MAST-3) being found the most frequently. Additionally, MAST-2 was detected in the ECS and MAST-4, -9, and -12 were detected in the CALC. Phylogenetic analysis indicated that some subclades within these lineages differ along latitudinal gradients. MAST-1A, -1B, and -1C and MAST-4 size and abundance estimates obtained using fluorescence in situ hybridization on 79 spring and summer ECS samples showed a negative correlation between size of MAST-1B and MAST-4 cells and temperature. MAST-1A was rarely detected, but MAST-1B and -1C and MAST-4 were abundant in summer and MAST-1C and MAST-4 were more so at the coast, with maximum abundances of 543 and 1,896 cells ml-1, respectively. MAST-4 and Synechococcus abundances were correlated, and experimental work showed that MAST-4 ingests Synechococcus. Together with previous studies, this study helps refine hypotheses on distribution and trophic modes of MAST lineages. © 2012, American Society for Microbiology.
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  • 68
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    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 92 (2). pp. 361-366.
    Publication Date: 2021-08-18
    Description: Intraspecific variation in characters such as arm sucker and gill lamellae counts in octopodids is yet to be thoroughly investigated, potentially hampering our ability to recognize species. In this study, data from 13 specimens of Muusoctopus hydrothermalis collected at four hydrothermal vents on the East Pacific Rise between 8°38′N and 12°48′N are considered. Although the northern and southern octopuses differ minimally in size, mean sucker count by arm in the northern group is 11.7 to 22.8% higher than it is in the southern group; in addition these octopuses typically have an additional gill lamella and bulkier funnel organs. The arms of each individual carry a different number of suckers. The difference is significant on nonadjacent arms, a pattern that merits examination in a broader taxonomic context. Why these differences exist among conspecifics remains unknown, the incidence of parasitic copepods is not different between the groups and the between-group variation in arm suckers seen here compares well with a previous report of variation among 18 specimens from the type locality. Increases in meristic characters (counts) in fish are attributed to lower temperatures during embryonic development following Jordan's rule. Northern and southern vents offer the octopuses a wide temperature range, but vent fluid chemistry differs. Northern vent fluids may be more toxic; if so, developing octopus embryos may survive only minimal vent fluid exposure and therefore develop at low temperatures. At the less toxic southern vents, eggs may survive greater exposure to vent fluids and thus develop at higher temperatures.
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  • 69
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    Cambridge University Press
    In:  Renewable Energy Sources and Climate Change Mitigation. Special Report of the Intergovernmental Panel on Climate Change
    Publication Date: 2022-03-21
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    Cambridge University Press
    In:  Renewable Energy Sources and Climate Change Mitigation. Special Report of the Intergovernmental Panel on Climate Change
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  • 71
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    Cambridge University Press
    In:  Renewable Energy Sources and Climate Change Mitigation. Special Report of the Intergovernmental Panel on Climate Change
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    Cambridge University Press
    In:  Renewable Energy Sources and Climate Change Mitigation. Special Report of the Intergovernmental Panel on Climate Change
    Publication Date: 2022-03-21
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  • 73
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    Cambridge University Press
    In:  Renewable Energy Sources and Climate Change Mitigation. Special Report of the Intergovernmental Panel on Climate Change
    Publication Date: 2022-03-21
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    Cambridge University Press
    In:  Renewable Energy Sources and Climate Change Mitigation. Special Report of the Intergovernmental Panel on Climate Change
    Publication Date: 2022-03-21
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    Cambridge University Press
    In:  Renewable Energy Sources and Climate Change Mitigation. Special Report of the Intergovernmental Panel on Climate Change
    Publication Date: 2022-03-21
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  • 76
    Publication Date: 2022-03-21
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    Cambridge University Press
    In:  Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation. Special Report of the Intergovernmental Panel on Climate Change | Special Report of the IPCC
    Publication Date: 2022-03-21
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    Cambridge University Press
    In:  Renewable Energy Sources and Climate Change Mitigation. Special Report of the Intergovernmental Panel on Climate Change
    Publication Date: 2022-03-21
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    Cambridge University Press
    In:  Renewable Energy Sources and Climate Change Mitigation. Special Report of the Intergovernmental Panel on Climate Change
    Publication Date: 2022-03-21
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  • 80
    Publication Date: 2020-07-31
    Description: The Cycladic blueschist belt, Greece, is mostly submerged below sea level and regional correlations are difficult to establish. Marbles are widespread within the belt and locally used as marker horizons to subdivide monotonous schist sequences. However, owing to the lack of distinctive petrographic characteristics, the marbles have not been used for island-to-island correlations. This study aims to investigate the potential of Sr-, C- and O-isotope compositions of marbles as a tool for unravelling the litho- and/or tectonostratigraphic relationships across the Cycladic islands, and as a proxy for the time of sediment formation. For this purpose, we have studied metamorphic carbonate rocks from the islands of Tinos, Andros, Syros, Sifnos and Naxos. Identical 87Sr/86Sr values for certain marble horizons occurring on Tinos, Andros and Sifnos are interpreted to document coeval regional carbonate precipitation. The 87Sr/86Sr values of the apparently least altered samples intersect the seawater curve multiple times within the most likely time interval of original carbonate precipitation (〈 240 Ma; as indicated by previously published ion probe U–Pb zircon data) and thus an unequivocal age assignment is not possible. Very broad temporal correlations are possible, but more subtle distinctions are not feasible. On Andros, the overlapping Sr-isotope values of marbles representing the lowest and highest parts of the metamorphic succession are in accordance with a model suggesting isoclinal folding or thrusting of a single horizon, or very fast sedimentation. In contrast, distinct 87Sr/86Sr values for samples from Tinos, representing different levels of the metamorphic succession, suggest that these rocks represent a temporal succession and not the tectonic repetition of a single horizon. Based on Sr-,O- and C-isotope characteristics alone the time equivalence ofmarbles occurring on different islands could not be documented unambiguously. However, by using various combinations of these parameters, some occurrences can be discriminated from the overall sample population. The new data further accentuate the general potential of coupled Sr-, C- and O-isotope characteristics for identification of archaeological provenance and complement existing datasets for Aegean marbles.
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  • 81
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    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 77 (19). pp. 6780-6787.
    Publication Date: 2015-11-17
    Description: Methane release from seafloor sediments is moderated, in part, by the anaerobic oxidation of methane (AOM) performed by consortia of archaea and bacteria. These consortia occur as isolated cells and aggregates within the sulfate-methane transition (SMT) of diffusion and seep-dominant environments. Here we report on a new SMT setting where the AOM consortium occurs as macroscopic pink to orange biofilms within subseafloor fractures. Biofilm samples recovered from the Indian and northeast Pacific Oceans had a cellular abundance of 107 to 108 cells cm−3. This cell density is 2 to 3 orders of magnitude greater than that in the surrounding sediments. Sequencing of bacterial 16S rRNA genes indicated that the bacterial component is dominated by Deltaproteobacteria, candidate division WS3, and Chloroflexi, representing 46%, 15%, and 10% of clones, respectively. In addition, major archaeal taxa found in the biofilm were related to the ANME-1 clade, Thermoplasmatales, and Desulfurococcales, representing 73%, 11%, and 10% of archaeal clones, respectively. The sequences of all major taxa were similar to sequences previously reported from cold seep environments. PhyloChip microarray analysis detected all bacterial phyla identified by the clone library plus an additional 44 phyla. However, sequencing detected more archaea than the PhyloChip within the phyla of Methanosarcinales and Desulfurococcales. The stable carbon isotope composition of the biofilm from the SMT (−35 to −43‰) suggests that the production of the biofilm is associated with AOM. These biofilms are a novel, but apparently widespread, aggregation of cells represented by the ANME-1 clade that occur in methane-rich marine sediments.
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  • 82
    Publication Date: 2019-09-23
    Description: Bacillus subtilis is an aerobic spore-forming Gram-positive bacterium that is a model organism and of great industrial significance as the source of diverse novel functional molecules. Here we present, to our knowledge, the first genome sequence of Bacillus subtilis strain gtP20b isolated from the marine environment. A subset of candidate genes and gene clusters were identified, which are potentially involved in production of diverse functional molecules, like novel ribosomal and nonribosomal antimicrobial peptides. The genome sequence described in this paper is due to its high strain specificity of great importance for basic as well as applied researches on marine organisms
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  • 83
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    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 77 (11). pp. 3726-3733.
    Publication Date: 2020-06-11
    Description: The bacterial community in the sea surface microlayer (SML) (bacterioneuston) is exposed to unique physicochemical properties and stronger meteorological influences than the bacterial community in the underlying water (ULW) (bacterioplankton). Despite extensive research, however, the structuring factors of the bacterioneuston remain enigmatic. The aim of this study was to examine the effect of meteorological conditions on bacterioneuston and bacterioplankton community structures and to identify distinct, abundant, active bacterioneuston members. Nineteen bacterial assemblages from the SML and ULW of the southern Baltic Sea, sampled from 2006 to 2008, were compared. Single-strand conformation polymorphism (SSCP) fingerprints were analyzed to distinguish total (based on the 16S rRNA gene) and active (based on 16S rRNA) as well as nonattached and particle-attached bacterial assemblages. The nonattached communities of the SML and ULW were very similar overall (similarity: 47 to 99%; mean: 88%). As an exception, during low wind speeds and high radiation levels, the active bacterioneuston community increasingly differed from the active bacterioplankton community. In contrast, the particle-attached assemblages in the two compartments were generally less similar (similarity: 8 to 98%; mean: 62%), with a strong variability in the active communities that was solely related to wind speed. Both nonattached and particle-attached active members of the bacterioneuston, which were found exclusively in the SML, were related to environmental clones belonging to the Cyanobacteria, Bacteroidetes, and Alpha-, Beta-, and Gammaproteobacteria originally found in diverse habitats, but especially in water columns. These results suggest that bacterioneuston communities are strongly influenced by the ULW but that specific meteorological conditions favor the development of distinctive populations in the air-water interface.
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  • 84
    Publication Date: 2017-07-03
    Description: Streptomyces, a branch of aerobic Gram-positive bacteria represents the largest genus of actinobacteria. The streptomycetes are characterized by a complex secondary metabolism and produce over two-thirds of the clinically used natural antibiotics today. Here we report the draft genome sequence of a Streptomyces strain PP-C42 isolated from the marine environment. A subset of unique genes and gene clusters for diverse secondary metabolites as well as antimicrobial peptides (AMPs) could be identified from the genome, showing great promise as a source for novel bioactive compounds
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  • 85
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    Cambridge University Press
    In:  In: The European Nitrogen Assessment: Sources, Effects and Policy Perspectives. , ed. by Sutton, M. Cambridge University Press, New York, USA, pp. 147-176. ISBN 978-1-107-00612-6
    Publication Date: 2015-11-26
    Type: Book chapter , NonPeerReviewed
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  • 86
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    Cambridge University Press
    In:  In: Ecosystem Approaches to Fisheries: A Global Perspective. , ed. by Christensen, V. and Maclean, J. Cambridge University Press, Cambridge, pp. 47-52.
    Publication Date: 2012-07-06
    Type: Book chapter , NonPeerReviewed
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  • 87
    Publication Date: 2019-10-09
    Description: The midwater scorpionfish Ectreposebastes imus (Scorpaeniformes: Setarchidae) is distributed in tropical and subtropical waters of the worldwide oceans, at depths of 150–800 m. It has previously been recorded from the Gulf of Guinea in the eastern Atlantic. The present work extends the northern limit for the distribution of E. imus in the Atlantic Ocean to the area of the Canary Islands.
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  • 88
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    Cambridge University Press
    In:  Journal of Paleontology, 85 (2). pp. 234-249.
    Publication Date: 2021-08-26
    Description: Morphologic analyses of a large collection of coleoid cephalopods from the Lebanese Upper Cretaceous yielded a much higher diversity than previously assumed and revealed numerous extraordinarily well-preserved, soft-part characters. An analysis of the Prototeuthidina, a gladius-bearing group with a slender torpedo-shaped body, revealed two species: Dorateuthis syriaca and Boreopeltis smithi n. sp. Previously unknown soft-part characters, such as the digestive tract, the gills, and the cephalic cartilage considerably improved our knowledge of D. syriaca. Since none of the investigated specimens show more than eight arms, similarities with modern squids are regarded as superficial. Boreopeltis smithi n. sp. is erected on the basis of its comparatively wide Paraplesioteuthis- like gladius. The latter species represents the first unambiguous record of this genus in Upper Cretaceous deposits. Phylogenetic analyses indicate that the prototeuthidid clade consists of two lineages. The plesioteuthidid lineage originates from early Jurassic Paraplesioteuthis and leads to Plesioteuthis and Dorateuthis. The other lineage is morphologically more conservative and leads to Boreopeltis.
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  • 89
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    Cambridge University Press
    In:  The European Nitrogen Assessment
    Publication Date: 2022-03-21
    Type: info:eu-repo/semantics/bookPart
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  • 90
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    Cambridge University Press
    In:  Climate Change: Global Risks, Challenges and Decisions
    Publication Date: 2022-03-21
    Type: info:eu-repo/semantics/bookPart
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  • 91
    Publication Date: 2022-03-21
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  • 92
    Publication Date: 2022-03-21
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  • 93
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    Cambridge University Press
    In:  Climate Change: Global risks, Challenges and Decisions
    Publication Date: 2022-03-21
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  • 94
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    Cambridge University Press
    In:  Climate Change: Global Risks, Challenges and Decisions
    Publication Date: 2022-03-21
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  • 95
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    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 76 (11). pp. 3702-3714.
    Publication Date: 2019-09-23
    Description: Representatives of Actinobacteria were isolated from the marine sponge Halichondria panicea collected from the Baltic Sea (Germany). For the first time, a comprehensive investigation was performed with regard to phylogenetic strain identification, secondary metabolite profiling, bioactivity determination, and genetic exploration of biosynthetic genes, especially concerning the relationships of the abundance of biosynthesis gene fragments to the number and diversity of produced secondary metabolites. All strains were phylogenetically identified by 16S rRNA gene sequence analyses and were found to belong to the genera Actinoalloteichus, Micrococcus, Micromonospora, Nocardiopsis, and Streptomyces. Secondary metabolite profiles of 46 actinobacterial strains were evaluated, 122 different substances were identified, and 88 so far unidentified compounds were detected. The extracts from most of the cultures showed biological activities. In addition, the presence of biosynthesis genes encoding polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) in 30 strains was established. It was shown that strains in which either PKS or NRPS genes were identified produced a significantly higher number of metabolites and exhibited a larger number of unidentified, possibly new metabolites than other strains. Therefore, the presence of PKS and NRPS genes is a good indicator for the selection of strains to isolate new natural products.
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  • 96
    Publication Date: 2019-10-09
    Description: The scorpionfish Setarches guentheri (Scorpaeniformes: Setarchidae) usually dwells offshore, in soft bottom deep areas at depths of about 150 to 780 m and at bottom temperature range of 5.5°C–12.5°C. This species has the widest distribution of any known scorpaenid, although this is a rare bathydemersal scorpaenid. Setarches guentheri has a large distribution, occurring from the Indo-West Pacific (Tanzania to South Africa, India and Sri Lanka to the Bay of Bengal, Andaman Sea, north to Japan, Fiji and Hawaii, south to the Philippines, Indonesia and Western Australia), from the eastern Pacific (Chile) and from the Atlantic Ocean (in the western Atlantic, USA to Brazil, and in the eastern Atlantic). In the eastern Atlantic, it has been recorded from Morocco, Madeira and Cape Verde to South Africa and, in the Iberian Peninsula, there was only one previous record from the Algarve coast, Portugal. The present record constitutes a new extended northern limit for the distribution of S. guentheri in this area.
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  • 97
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    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 90 (2). pp. 367-390.
    Publication Date: 2021-08-25
    Description: Two species of the bobtail squid Heteroteuthis are reported from the Atlantic Ocean, H. dispar in the North Atlantic Ocean and H. dagamensis in the South Atlantic Ocean. In total 58 individuals were examined, 23 belonging to the species Heteroteuthis dispar and 35 belonging to the species H. dagamensis . All specimens were captured during the Walther Herwig Expeditions 1966, 1968, 1976 and 1982. A full description of both sexes of H. dispar and H. dagamensis is provided. These two species can only be distinguished by means of the male's enlarged suckers on arm pair III. Females are not useful for taxonomic identifications and are morphologically identical in both species. The results do not support the definition of subgenera in this genus. This is the first report for Heteroteuthis dagamensis in the South-West Atlantic Ocean.
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  • 98
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    Cambridge University Press
    In:  Making Climate Change Work for Us
    Publication Date: 2022-03-21
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  • 99
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    Cambridge University Press
    In:  Making Climate Change Work for Us
    Publication Date: 2022-03-21
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  • 100
    Publication Date: 2022-03-21
    Type: info:eu-repo/semantics/bookPart
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