Co-occurrence patterns and the large-scale spatial structure of benthic communities in seagrass meadows and bare sand.

Background: Species distribution models are commonly used tools to describe diversity patterns and support conservation measures. There is a wide range of approaches to developing SDMs, each highlighting different characteristics of both the data and the ecology of the species or assemblages represented by the data. Yet, signals of species co-occurrences in community data are usually ignored, due to the assumption that such structuring roles of species co-occurrences are limited to small spatial scales and require experimental studies to be detected.

Diverse interactions and ecosystem engineering can stabilize community assembly.

The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact directly with each other and indirectly through environmental effects, however to our knowledge the role of these ecosystem engineers has not been considered in ecological network models. Here we explore the dynamics of ecosystem assembly, where species colonization and extinction depends on the constraints imposed by trophic, service, and engineering dependencies.

Uncovering the intricacies of microbial community dynamics at Helgoland Roads at the end of a spring bloom using automated sampling and 18S meta-barcoding.

In May 2016, the remote-controlled Automated Filtration System for Marine Microbes (AUTOFIM) was implemented in parallel to the Long Term Ecological Research (LTER) observatory Helgoland Roads in the German Bight. We collected samples for characterization of dynamics within the eukaryotic microbial communities at the end of a phytoplankton bloom via 18S meta-barcoding. Understanding consequences of environmental change for key marine ecosystem processes, such as phytoplankton bloom dynamics requires information on biodiversity and species occurrences with adequate temporal and taxonomic resolution via time series observations.

Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida).

In the present study, we profiled bacterial and archaeal communities from 13 phylogenetically diverse deep-sea sponge species (Demospongiae and Hexactinellida) from the South Pacific by 16S rRNA-gene amplicon sequencing. Additionally, the associated bacteria and archaea were quantified by real-time qPCR. Our results show that bacterial communities from the deep-sea sponges are mostly host-species specific similar to what has been observed for shallow-water demosponges.

Nitric oxide mediates metabolic functions in the bivalve Arctica islandica under hypoxia.

The free radical nitric oxide (NO) is a powerful metabolic regulator in vertebrates and invertebrates. At cellular concentrations in the nanomolar range, and simultaneously reduced internal oxygen partial pressures (pO2), NO completely inhibits cytochrome-c-oxidase (CytOx) activity and hence mitochondrial- and whole-tissue respiration. The infaunal clam Arctica islandica regulates pO2 of hemolymph and mantle cavity water to mean values of <5 kPa, even in a completely oxygen-saturated environment of 21 kPa.

Anti-Fouling Effects of Saponin-Containing Crude Extracts from Tropical Indo-Pacific Sea Cucumbers.

Sea cucumbers are bottom dwelling invertebrates, which are mostly found on subtropical and tropical sea grass beds, sandy reef flats, or reef slopes. Although constantly exposed to fouling communities in these habitats, many species are surprisingly free of invertebrate epibionts and microfouling algae such as diatoms. In our study, we investigated the anti-fouling (AF) activities of different crude extracts of tropical Indo-Pacific sea cucumber species against the fouling diatom .

Deciphering Patterns of Adaptation and Acclimation in the Transcriptome of Phaeocystis antarctica to Changing Iron Conditions.

The haptophyte Phaeocystis antarctica is endemic to the Southern Ocean, where iron supply is sporadic and its availability limits primary production. In iron fertilization experiments, P. antarctica showed a prompt and steady increase in cell abundance compared to heavily silicified diatoms along with enhanced colony formation.

Impact of UV radiation on DOM transformation on molecular level using FT-ICR-MS and PARAFAC.

Dissolved organic matter (DOM) is an omnipresent constituent of natural water bodies. Reuse and transformation of DOM compounds in the water column is driven by physicochemical and biological processes leading to the production of refractory DOM. Typically, breakdown of DOM chemical compounds into smaller or more condensed fragments is triggered by ultraviolet (UV) radiation.

Meta-analysis on pulse disturbances reveals differences in functional and compositional recovery across ecosystems.

Most ecosystems are affected by anthropogenic or natural pulse disturbances, which alter the community composition and functioning for a limited period of time. Whether and how quickly communities recover from such pulses is central to our understanding of biodiversity dynamics and ecosystem organisation, but also to nature conservation and management. Here, we present a meta-analysis of 508 (semi-)natural field experiments globally distributed across marine, terrestrial and freshwater ecosystems.

Improved Mass Accuracy and Isotope Confirmation through Alignment of Ultrahigh-Resolution Mass Spectra of Complex Natural Mixtures.

Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is one of the state-of-the-art methods to analyze complex natural organic mixtures. The precision of detected masses is crucial for molecular formula attribution. Random errors can be reduced by averaging multiple measurements of the same mass, but because of limited availability of ultrahigh-resolution mass spectrometers, most studies cannot afford analyzing each sample multiple times.

Long-term stability of marine dissolved organic carbon emerges from a neutral network of compounds and microbes.

Dissolved organic carbon (DOC) is the main energy source for marine heterotrophic microorganisms, but a small fraction of DOC resists microbial degradation and accumulates in the ocean. The reason behind this recalcitrance is unknown. We test whether the long-term stability of DOC requires the existence of structurally refractory molecules, using a mechanistic model comprising a diverse network of microbe-substrate interactions.

Author Correction: The importance of Antarctic krill in biogeochemical cycles.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Biotechnological Potential of Bacteria Isolated from the Sea Cucumber and from Lampung, Indonesia.

In order to minimize re-discovery of already known anti-infective compounds, we focused our screening approach on understudied, almost untapped marine environments including marine invertebrates and their associated bacteria. Therefore, two sea cucumber species, and , were collected from Lampung (Indonesia), and 127 bacterial strains were identified by partial 16S rRNA-gene sequencing analysis and compared with the NCBI database. In addition, the overall bacterial diversity from tissue samples of the sea cucumbers and was analyzed using the cultivation-independent Illumina MiSEQ analysis.

The importance of Antarctic krill in biogeochemical cycles.

Antarctic krill (Euphausia superba) are swarming, oceanic crustaceans, up to two inches long, and best known as prey for whales and penguins - but they have another important role. With their large size, high biomass and daily vertical migrations they transport and transform essential nutrients, stimulate primary productivity and influence the carbon sink. Antarctic krill are also fished by the Southern Ocean's largest fishery.

Marked isotopic variability within and between the Amazon River and marine dissolved black carbon pools.

Riverine dissolved organic carbon (DOC) contains charcoal byproducts, termed black carbon (BC). To determine the significance of BC as a sink of atmospheric CO and reconcile budgets, the sources and fate of this large, slow-cycling and elusive carbon pool must be constrained. The Amazon River is a significant part of global BC cycling because it exports an order of magnitude more DOC, and thus dissolved BC (DBC), than any other river.

Publisher Correction: Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Global change drives modern plankton communities away from the pre-industrial state.

The ocean-the Earth's largest ecosystem-is increasingly affected by anthropogenic climate change. Large and globally consistent shifts have been detected in species phenology, range extension and community composition in marine ecosystems. However, despite evidence for ongoing change, it remains unknown whether marine ecosystems have entered an Anthropocene state beyond the natural decadal to centennial variability.

Contrasting responses of the coral Acropora tenuis to moderate and strong light limitation in coastal waters.

Coastal water quality and light attenuation can detrimentally affect coral health. This study investigated the effects of light limitation and reduced water quality on the physiological performance of the coral Acropora tenuis. Branches of individual colonies were collected in 2 m water depth at six inshore reefs at increasing distances from major river sources in the Great Barrier Reef, along a strong water quality gradient in the Burdekin and a weak gradient in the Whitsunday region.

Precipitation and temperature drive continental-scale patterns in stream invertebrate production.

Secondary production, the growth of new heterotrophic biomass, is a key process in aquatic and terrestrial ecosystems that has been carefully measured in many flowing water ecosystems. We combine structural equation modeling with the first worldwide dataset on annual secondary production of stream invertebrate communities to reveal core pathways linking air temperature and precipitation to secondary production. In the United States, where the most extensive set of secondary production estimates and covariate data were available, we show that precipitation-mediated, low-stream flow events have a strong negative effect on secondary production.

What's the Difference? 2D DIGE Image Analysis by DeCyderTM versus SameSpotsTM.

The efficiency and reproducibility of two-dimensional difference gel electrophoresis (2D DIGE) depends on several crucial steps: (i) adequate number of replicate gels, (ii) accurate image acquisition, and (iii) statistically confident protein abundance analysis. The latter is inherently determined by the image analysis system. Available software solutions apply different strategies for consecutive image alignment and protein spot detection.

Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes.

We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico, in vitro, and in situ.

The marine bacterium Phaeobacter inhibens secures external ammonium by rapid buildup of intracellular nitrogen stocks.

Reduced nitrogen species are key nutrients for biological productivity in the oceans. Ammonium is often present in low and growth-limiting concentrations, albeit peaks occur during collapse of algal blooms or via input from deep sea upwelling and riverine inflow. Autotrophic phytoplankton exploit ammonium peaks by storing nitrogen intracellularly.

Universal molecular structures in natural dissolved organic matter.

Natural dissolved organic matter (DOM) comprises a broad range of dissolved organic molecules in aquatic systems and is among the most complex molecular mixtures known. Here we show, by comparing detailed structural fingerprints of individual molecular formulae in DOM from a set of four marine and one freshwater environments, that a major component of DOM is molecularly indistinguishable in these diverse samples. Molecular conformity was not only apparent by the co-occurrence of thousands of identical molecular formulae, but also by identical structural features of those isomers that collectively represent a molecular formula.

Sponge chemical defenses are a possible mechanism for increasing sponge abundance on reefs in Zanzibar.

Coral reefs are experiencing increasing anthropogenic impacts that result in substantial declines of reef-building corals and a change of community structure towards other benthic invertebrates or macroalgae. Reefs around Zanzibar are exposed to untreated sewage and runoff from the main city Stonetown. At many of these sites, sponge cover has increased over the last years.