ALBERT

Description: An interactive (multi-access) global identification key (OncIdent) has been developed for the pelagic marine microcopepod family Oncaeidae and made accessible online. Details of the general approach and development of the key are given in Bottger-Schnack and Schnack (J Nat Hist 49:2727-2741, 2015). After beta-testing, new additions include illustrations for all species and feature attributes considered, plus a textual summary of each species' feature states in the key. Additional taxonomic notes are given where required, highlighting morphological or molecular genetic peculiarities or problems, with links to large data bases leading directly to more comprehensive information about each species. The present paper briefly reviews the taxonomic background for key construction, summarizes the opportunities and limitations of the current online version OncIdent2.0, and provides guidance for its practical use.

Description: Marine sponges and other sessile macro-organisms were collected at a shallow water hydrothermal site in Eyjafjörður, Iceland. Bacteria were isolated from the organisms using selective media for actinomycetes, and the isolates were screened for antimicrobial activity. A total of 111 isolates revealed antimicrobial activity displaying different antimicrobial patterns which indicates production of various compounds. Known test strains were grown in the presence of ethyl acetate extracts from one selected isolate, and a clear growth inhibition of Staphylococcus aureus was observed down to 0.1 % extract concentration in the medium. Identification of isolates shows different species of Actinobacteria with Streptomyces sp. playing the largest role, but also members of Bacilli, Alphaproteobacteria and Gammaproteobacteria. Sponges have an excellent record regarding production of bioactive compounds, often involving microbial symbionts. At the hydrothermal vents, however, the majority of active isolates originated from other invertebrates such as sea anemones or algae. The results indicate that antimicrobial assays involving isolates in full growth can detect activity not visible by other methods. The macro-organisms inhabiting the Eyjafjörður hydrothermal vent area host diverse microbial species in the phylum Actinobacteria with antimicrobial activity, and the compounds responsible for the activity will be subject to further research.

Description: Bacteria use quorum sensing to orchestrate gene expression programmes that underlie collective behaviours. Quorum sensing relies on the production, release, detection and group-level response to extracellular signalling molecules, which are called autoinducers. Recent work has discovered new autoinducers in Gram-negative bacteria, shown how these molecules are recognized by cognate receptors, revealed new regulatory components that are embedded in canonical signalling circuits and identified novel regulatory network designs. In this Review we examine how, together, these features of quorum sensing signal–response systems combine to control collective behaviours in Gram-negative bacteria and we discuss the implications for host–microbial associations and antibacterial therapy.

Description: The results of study of six cores taken from different morphostructural zones in the Mendeleev Ridge area are discussed. Average contents of minerals of the illite group, chlorite, kaolinite, and smectite are about 60, 21, 12, and 5%, respectively. It was found that fluctuations of minerals along the section correlate with variations in sedimentation constraints in the Late Quaternary. Peaks of kaolinite usually coincide with increased contents of the sand fraction, probably, due to its delivery by icebergs. In contrast, illite shows good correlation with the pelite fraction, testifying to its transport mainly by ices and currents. Minerals of the chlorite and smectite groups in the studied cores are less informative.

Description: The major structural characteristics of zooplankton communities that inhabit 35 Arctic lakes in the catchment basin of the Anabar River (Yakutia) have been analyzed. The ecological state of the lakes has been evaluated. The structure-forming abiotic factors that have the greatest influence on the formation of zooplankton communities have been revealed using the indirect ordination method.

Description: Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage–CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE).

Description: Purpose: The consequential inventory modeling approach for life cycle assessment implies that an increase in the demand for a specific product is met by the marginal suppliers within the market. The identification of marginal suppliers is however complicated by difficulties in defining appropriate geographical market delimitations. In this study, an advanced system thinking approach is proposed to address this challenge in the identification of marginal supplying countries of wood products. Methods: Groups of countries which represent geographical markets are identified from trade data by using a network analysis-based clustering technique. Within these markets, marginal supplying countries are selected based on positive historical increments. The analysis covers 12 different products and all countries in the world using trade data for the period 1998–2013. Results and discussion: Global indices allow differentiating how product-specific trade networks are separated into communities and how interconnected these networks are. Large differences between products and minor differences between trade years are observed. Communities identified for each product tend to overlap with existing geographical regions and seem thus realistic. By combining this information with product-specific production increment rankings, marginal supplying countries of wood products were identified. Conclusions: The identified geographical market delimitation is a key for proper consequential life cycle assessment (LCA) inventory modeling in areas such as timber-based construction and biomass-based energy production. The method can in principle be applied to any product for which trade network data are available and ideally should be accompanied by a detailed analysis of technological constrains within the identified supplying country.

Description: Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a key enzyme of the Calvin cycle, which is responsible for most of Earth's primary production. Although research on RubisCO genes and enzymes in plants, cyanobacteria and bacteria has been ongoing for years, still little is understood about its regulation and activation in bacteria. Even more so, hardly any information exists about the function of metagenomic RubisCOs and the role of the enzymes encoded on the flanking DNA owing to the lack of available function-based screens for seeking active RubisCOs from the environment. Here we present the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. We constructed a metagenomic library from hydrothermal vent fluids and screened 1056 fosmid clones. Twelve clones exhibited RubisCO activity and the metagenomic fragments resembled genes from Thiomicrospira crunogena. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of twelve genes and two intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly characterized gene and RubisCO activity. This screen opens the door to directly investigating RubisCO genes and respective enzymes from environmental samples.