ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)

<p>Abstract</p> <p>Background</p> <p>Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the '<it>Hydrodictyon</it>' and the '<it>Scenedesmus</it>' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the '<it>Sphaeroplea</it>' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the '<it>Sphaeroplea</it>' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment.</p> <p>Results</p> <p>The newly obtained ITS2 sequences of <it>Ankyra judayi, Atractomorpha porcata </it>and <it>Sphaeroplea annulina </it>of the '<it>Sphaeroplea</it>' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the '<it>Sphaeroplea</it>' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae.</p> <p>Conclusion</p> <p>In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the '<it>Sphaeroplea</it>' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics.</p

Seabed methane emissions and the habitat of frenulate tubeworms on the Captain Arutyunov mud volcano (Gulf of Cadiz)

Submarine mud volcanism represents an important. pathway for methane from deeper reservoirs to the surface, where it enters the benthic carbon cycle. To quantify overall methane release from the Captain Arutyunov mud volcano (CAMV) and to assess the contribution of macrobenthic seep organisms to the regulation of the benthic methane flux, we linked water column methane concentrations, seabed methane emission and pore water geochemistry to the spatial distribution of seep biota. Prominent organisms of the CAMV seep biota were 3 different species of frenulate tubeworms. Seabed methane emission ranged from 0.001 to 0.66 mmol m(-2) d(-1). Dense patches of tubeworms were associated with the lowest seabed methane emission. Elevated methane emission was associated with a sporadic distribution of tubeworms and the occurrence of numerous mud clasts. Despite the presence of a large subsurface methane reservoir, the estimated total methane release from CAMV was low (0.006 x 10(6) mol yr(-1)). In addition to direct methane consumption by Siboglinum poseidoni, the tubeworms likely contribute to the retention of methane carbon in the sediment by affecting bacterial communities in the proximity of the tubes. The siboglinids create new meso-scale habitats on the sediment Surface, increasing habitat heterogeneity and introducing niches for bacterial communities

The ITS2 Database III—sequences and structures for phylogeny

The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps.biozentrum.uni-wuerzburg.de) which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version, we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline. This allowed the identification of more than 160 000 correct full length and more than 50 000 partial structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses

Informing epidemic (research) responses in a timely fashion by knowledge management - a Zika virus use case

The response of pathophysiological research to emerging epidemics often occurs after the epidemic and, as a consequence, has little to no impact on improving patient outcomes or on developing high-quality evidence to inform clinical management strategies during the epidemic. Rapid and informed guidance of epidemic (research) responses to severe infectious disease outbreaks requires quick compilation and integration of existing pathophysiological knowledge. As a case study we chose the Zika virus (ZIKV) outbreak that started in 2015 to develop a proof-of-concept knowledge repository. To extract data from available sources and build a computationally tractable and comprehensive molecular interaction map we applied generic knowledge management software for literature mining, expert knowledge curation, data integration, reporting and visualization. A multi-disciplinary team of experts, including clinicians, virologists, bioinformaticians and knowledge management specialists, followed a pre-defined workflow for rapid integration and evaluation of available evidence. While conventional approaches usually require months to comb through the existing literature, the initial ZIKV KnowledgeBase (ZIKA KB) was completed within a few weeks. Recently we updated the ZIKA KB with additional curated data from the large amount of literature published since 2016 and made it publicly available through a web interface together with a step-by-step guide to ensure reproducibility of the described use case. In addition, a detailed online user manual is provided to enable the ZIKV research community to generate hypotheses, share knowledge, identify knowledge gaps, and interactively explore and interpret data. A workflow for rapid response during outbreaks was generated, validated and refined and is also made available. The process described here can be used for timely structuring of pathophysiological knowledge for future threats. The resulting structured biological knowledge is a helpful tool for computational data analysis and generation of predictive models and opens new avenues for infectious disease research. ZIKV Knowledgebase is available at www.zikaknowledgebase.eu

Quantification of methane emission from bacterial mat sites at Quepos Slide offshore Costa Rica

Seafloormethane emission from the Quepos Slide on the submarine segment of the Costa Rica fore-arc margin was estimated by extrapolating flux measurements from individual seeps to the total area covered by bacterial mats. This approach is based on the combination of detailed mapping to determine the abundance of seeps and the application of a numerical model to estimate the amount of benthic methane fluxes. Model results suggest that the majority of the studied seeps transport rather limited amount of methane (on average: *177 lmol cm-2 a-1) into the water column due to moderate upward advection, allowing for intense anaerobic oxidation of methane (AOM; on average: 53 % of the methane flux is consumed). Depth-integrated AOM rates (56–1,538 lmol CH4 cm-2 a-1) are comparable with values reported from other active seep sites. The overall amount of dissolved methane released into the water column from the entire area covered by bacterial mats on the Quepos Slide is estimated to be about 0.28 9 106 mol a-1. This conservative estimate which relies on rather accurate determinations of seafloor methane fluxes emphasizes the potential importance of submarine slides as sites of natural methane seepage; however, at present the global extent of methane seepage from submarine slides is largely unknown

Seepage of methane at Jaco Scar, a slide caused by seamount subduction offshore Costa Rica

Methane (CH4) concentrations and CH4 stable carbon isotopic composition (d13CCH4 ) were investigated in the water column within Jaco Scar. It is one of several scars formed by massive slides resulting from the subduction of seamounts offshore Costa Rica, a process that can open up structural and stratigraphical pathways for migrating CH4. The release of large amounts of CH4 into the adjacent water column was discovered at the outcropping lowermost sedimentary sequence of the hanging wall in the northwest corner of Jaco Scar, where concentrations reached up to 1,500 nmol L-1. There CH4-rich fluids seeping from the sedimentary sequence stimulate both growth and activity of a dense chemosynthetic community. Additional point sources supplying CH4 at lower concentrations were identified in density layers above and below the main plume from light carbon isotope ratios. The injected CH4 is most likely a mixture of microbial and thermogenic CH4 as suggested by d13CCH4 values between -50 and -62 % Vienna Pee Dee Belemnite. This CH4 spreads along isopycnal surfaces throughout the whole area of the scar, and the concentrations decrease due to mixing with ocean water and microbial oxidation. The supply of CH4 appears to be persistent as repeatedly high CH4 concentrations were found within the scar over 6 years. The maximum CH4 concentration and average excess CH4 concentration at Jaco Scar indicate that CH4 seepage from scars might be as significant as seepage from other tectonic structures in the marine realm. Hence, taking into account the global abundance of scars, such structures might constitute a substantial, hitherto unconsidered contribution to natural CH4 sources at the seafloor

Oceanographic data, oxygen and methane concentrations, and C-CH4 isotope ratios measured at Jaco Scar

Methane (CH4) concentrations and CH4 stable carbon isotopic composition (d13CCH4) were investigated in the water column within Jaco Scar. It is one of several scars formed by massive slides resulting from the subduction of seamounts offshore Costa Rica, a process that can open up structural and stratigraphical pathways for migrating CH4. The release of large amounts of CH4 into the adjacent water column was discovered at the outcropping lowermost sedimentary sequence of the hanging wall in the northwest corner of Jaco Scar, where concentrations reached up to 1,500 nmol L**-1. There CH4-rich fluids seeping from the sedimentary sequence stimulate both growth and activity of a dense chemosynthetic community. Additional point sources supplying CH4 at lower concentrations were identified in density layers above and below the main plume from light carbon isotope ratios. The injected CH4 is most likely a mixture of microbial and thermogenic CH4 as suggested by d13CCH4 values between -50 and -62 per mil Vienna Pee Dee Belemnite. This CH4 spreads along isopycnal surfaces throughout the whole area of the scar, and the concentrations decrease due to mixing with ocean water and microbial oxidation. The supply of CH4 appears to be persistent as repeatedly high CH4 concentrations were found within the scar over 6 years. The maximum CH4 concentration and average excess CH4 concentration at Jaco Scar indicate that CH4 seepage from scars might be as significant as seepage from other tectonic structures in the marine realm. Hence, taking into account the global abundance of scars, such structures might constitute a substantial, hitherto unconsidered contribution to natural CH4 sources at the seafloor