Reclassification of species of the spiral-shaped phototrophic purple non-sulfur bacteria of the alpha-Proteobacteria: description of the new genera Phaeospirillum gen. nov., Rhodovibrio gen. nov., Rhodothalassium gen. nov. and Roseospira gen. nov. as well as transfer of Rhodospirillum fulvum to Phaeospirillum fulvum comb. nov., of Rhodospirillum molischianum to Phaeospirillum molischianum comb. nov., of Rhodospirillum salinarum to Rhodovibrio salexigens

The 16S rDNA sequence of Rhodospirillum mediosalinum was determined and compared with corresponding sequences from other spiral-shaped purple non-sulfur bacteria classified as or related to the genus Rhodospirillum in the α subclass of the Proteobacteria. Sequence similarities separate the currently recognized Rhodospirillum species into five different groups with no more than 91% sequence similarity, clearly indicating the necessity to recognize these groups as different genera. Major diagnostic properties of these bacteria are compared and new genera Phaeospirillum gen. nov., Roseospira gen. nov., Rhodothalassium gen. nov. and Rhodovibrio gen. nov. are described with the species Phaeospirillum fulvum comb, nov., Phaeospirillum molischianum comb. nov., Rhodovibrio salinarum comb. nov., Rhodovibrio sodomensis comb. nov., Rhodothalassium salexigens comb. nov. and Roseospira mediosalina comb. nov. The genus Rhodospirillum is represented by Rhodospirillum rubrum and Rhodospirillum photometricum and an emended description of this genus is also give

Cruise Summary Report AL528

18.-30.9.2019 The overall objective of this practical for students is to investigate the ecological role of gelatinous plankton in the Baltic Sea food webs and alongside the salinity gradient. To demonstrate the temporal as well as spatial variation of pelagic communities such as bacteria-, phyto and zooplankton as well as in the benthic food webs, different food web tracers will be used. Main focus here is therefore to obtain qualitative and quantitative sample sets of gelatinous zooplankton to investigate their distinct role on bentho-pelagic processes. Over the last several decades, a significant increase of both frequency and severity of jellyfish (JF) blooms were reported worldwide. Blooms of these organisms can extend for thousands of square kilometers, with drastic consequences and economic losses. When JF outbreak, they will not only affect the pelagic community by direct feeding on fish larvae, fish eggs or competing for the prey with bigger fishes, but only serve as organic matter source for benthic systems via sinking to the sea floor. Due to the scarcity of data on the potential role of gelatinous zooplankton from only few locations in the Baltic Sea, there is only a limited understanding on the role of JF in the bentho-pelagic food web of the Baltic Sea. A quantitative and qualitative assessment of gelatinous zooplankton in the BS systems and their functioning with regard to salinity gradient of the Baltic Sea , are now urgently needed to better account for the role of gelatinous zooplankton in the future of the system. Applicant and working group have performed this student research/educational cruise with the specific focus on jellyfish ecology every year and on a regular basis since 2013. During this two-week cruise students will perform the compulsory „Practical at Sea“. The general goal is to survey and characterize the temporal and special distribution of bacterial, phyto-, zooplankton and macroplankton specially jellyfish in Skagerrak and Baltic Se

2. Wochenbericht AL528

(23.09. – 29.09.2019

1. Wochenbericht AL528

(18.09. – 22.09.2019

Phylogenetic relationships among the Chromatiaceae, their taxonomic reclassification and description of the new genera Allochromatium, Halochromatium, Isochromatium, Marichromatium, Thiococcus, Thiohalocapsa, and Thermochromatium

Sequences of the 16S rDNA from all available type strains of Chromatium species have been determined and were compared to those of other Chromatiaceae, a few selected Ectothiorhodospiraceae and Escherichia coli. The clear separation of Ectothiorhodospiraceae and Chromatiaceae is confirmed. Most significantly the sequence comparison revealed a genetic divergence between Chromatium species originated from freshwater sources and those of truly marine and halophilic nature. Major phylogenetic branches of the Chromatiaceae contain (i) marine and halophilic species, (ii) freshwater Chromatium species together with Thiocystis species and (iii) species of the genera Thiocapsa and Amoebobacter as recently reclassified [Guyoneaud, R. & 6 other authors (1988). Int J Syst Bacteriol 48, 957-964], namely Thiocapsa roseopersicina, Thiocapsa pendens (formerly Amoebobacter pendens), Thiocapsa rosea (formerly Amoebobacter roseus), Amoebobacter purpureus and Thiolamprovum pedioforme (formerly Amoebobacter pedioformis). The genetic relationships between the species and groups are not in congruence with the current classification of the Chromatiaceae and a reclassification is proposed on the basis of 16S rDNA sequence similarity supported by selected phenotypic properties. The proposed changes include the transfers of Chromatium minus and Chromatium violascens to Thiocystis minor comb. nov. and Thiocystis violascens comb. nov., of Chromatium vinosum, Chromatium minutissimum and Chromatium warmingii to the new genus Allochromatium as Allochromatium vinosum comb. nov., Allochromatium minutissimum comb. nov., and Allochromatium warmingii comb. nov., of Chromatium tepidum to the new genus Thermochromatium as Thermochromatium tepidum comb. nov., of Chromatium salexigens and Chromatium glycolicum to the new genus Halochromatium as Halochromatium salexigens comb. nov. and Halochromatium glycolicum comb. nov., of Chromatium gracile and Chromatium purpuratum to the new genus as Marichromatium gracile comb. nov. and Marichromatium purpuratum comb. nov., of Thiocapsa pfennigii to Thiococcus pfennigii gen. nom. rev., of Thiocapsa halophila to the new genus Thiohalocapsa as Thiohalocapsa halophila comb. nov., and of Chromatium buderi to the new genus Isochromatium as Isochromatium buderi comb. nov

Presence of two phylogenetically distinct groups in the deep sea mussel Acharax (Mollusca, Bivalvia, Solemyidae)

The family Solemyidae represents ancestral protobranch bivalves with the shallow-water genus Solemya and the deep-sea genus Acharax. All known members of this family host symbiotic sulfur-oxidizing bacteria in their gill filaments. Analysis of 18S rRNA gene sequences of Acharax specimens from methane-seeps off Makran (Pakistan), Java (Indonesia), the Aleutian Trench and off the Oregon, Costa Rica, and Peru margins revealed that Solemya spp. and Acharax spp. are well-separated genetically. This supports the current systematic distinction based on morphological criteria. We found 2 clearly distinct clusters within the genus Acharax, with specimens from the Makran, Oregon and Peru (MOP) margins in one (MOP–Acharax) cluster, and those from Java, the Aleutian Trench and Costa Rica (JAC) in the other (JAC–Acharax) cluster. The separation of MOP– and JAC–Acharax clusters from each other and from Solemya (S. reidi and S. velum) is well-supported by phylogenetic calculations employing maximum likelihood and maximum parsimony. Compared to genetic distances among other protobranch groups, distances between the MOP– and JAC–Acharax clusters would justify the affiliation of these clusters to separate species. This implies that species differentiation in Acharax based on shell morphology is likely to underestimate true species diversity within this taxon. Furthermore, our results support the hypothesis that genetic separation of Solemya and Acharax is congruent with the phylogeny of their bacterial endosymbionts

How to curate and exhibit various types of physical samples using FAIR principles

In a modern research environment, physical samples are often treated as a burden, to be stored and forgotten but when their existence is digitalised and connected to the underlying metadata it becomes a great resource for present and future generations of researchers. This value is further expanded if the information is easily accessible for the research community, particular by offering intelligent search options, interconnection, extraction of data files etc. GEOMAR Helmholtz Centre for Ocean Research has accumulated thousands of biological and geological samples, collected mainly during marine expeditions but also from time series and experiments. Samples date back as far as 1964. Today, the biological collection comprises roughly 180.000 samples (mainly fish and plankton) in formaldehyde as well as a large amount of cryofrozen materials. The core and rock repository holds a collection of about 4000 sediment cores totaling 30.000 core sections and more than 5000 boxes with hard rock samples and refined sample specimens. We have set ourselves the task to curate all these materials and connect them with sufficient metadata in order to make them searchable and, more importantly, findable. The Ocean Science Information System at GEOMAR (OSIS) joins all kind of data resulting from the institute's sea-going expeditions and land-based projects. It is designed for data exchange in the context of these expeditions and experiments, and during a research project's moratorium it supports scientists in documenting provenance of their research data and ultimately their publication. OSIS also serves as a hub for detailed information, metadata and references to peer-review journal publications. The metadata in OSIS are publicly accessible and the system is interlinked to the institutional repository OceanRep as well as several other data archives and databases. It will act as a first entry point for scientists to identify samples by their metadata even before contacting the appropriate curator to inquire sample accessibility and conditions. In context with the physical specimens, OSIS provides linkage to more specific sample databases. Currently we connect biological samples collected on a research vessel via the expedition metadata to their current storage locations on land, which will be further refined to connecting single ship-based sampling stations with the storage position of individual samples. Moreover, for geological samples (sediment cores) metadata from OSIS are made available for further in-house use by the software CurationDIS from smartcube GmbH. The sediment core specific details are managed by the curation software which is also used to provide a persistent identifier (IGSN). Future plans include connecting rock samples in a similar structure as sediment cores

16S rDNA-based phylogeny of sulfur-oxidizing bacterial endosymbionts in marine bivalves from cold-seep habitats

The phylogenetic relationship of sulphur-oxidising endosymbiotic bacteria from bivalves of the families Vesicomyidae (Calyptogena sp. C1, Calyptogena sp. C3), Solemyidae (Acharax sp.) and Thyasiridae (Conchocele sp.) from cold-seep habitats were determined by 16S rDNA nucleotide sequence analyses. The endosymbiotic bacteria form distinct groups within the gamma-Proteobacteria and are well separated from each other and from free-living sulphur-oxidising bacteria of the genera Beggiatoa, Halothiobacillus and Thiomicrospira. The endosymbiotic bacteria of Acharax sp. from cold seeps off Oregon, Indonesia and Pakistan have sequences highly similar to each other but quite distinct from other thiotrophic endosymbionts. This includes endosymbionts from Solemya spp., to which they are distantly related. Symbiotic bacteria of Conchocele sp. from a cold seep in the Sea of Okhotsk are similar to those of Bathymodiolus thermophilus and related species, as shown by their overall sequence similarity and by signature sequences. The endosymbiotic bacteria of Calyptogena spp. from cold seeps off Oregon and Pakistan are closely related to those of other vesicomyids. Endosymbiont species found off Oregon corresponded to 2 different clusters of Calyptogena spp. symbionts in the same samples. The results corroborate the hypothesis of a monophyletic origin of the symbionts in vesicomyid clams, and support the existence of deeply branching groups in solemyid symbionts and of divergent lines and distribution for thyasirid symbionts. The results also indicate that certain symbiont species cluster according to the depth distribution of their hosts, and that in consequence host species together with their symbionts may have undergone depth-specific adaptation and evolution

Thiorhodospira sibirica gen. nov., and sp. nov., a new alkaliphilic purple sulfur bacterium from a Siberian soda lake

A new purple sulfur bacterium was isolated from microbial films on decaying plant mass in the near-shore area of the soda lake Malyi Kasytui (pH 9.5, 0.2% salinity) located in the steppe of the Chita region of south-east Siberia. Single cells were vibrioid- or spiral-shaped (3-4 microns wide and 7-20 microns long) and motile by means of a polar tuft of flagella. Internal photosynthetic membranes were of the lamellar type. Lamellae almost filled the whole cell, forming strands and coils. Photosynthetic pigments were bacteriochlorophyll a and carotenoids of the spirilloxanthin group. The new bacterium was strictly anaerobic. Under anoxic conditions, hydrogen sulfide and elemental sulfur were used as photosynthetic electron donors. During growth on sulfide, sulfur globules were formed as intermediate oxidation products. They were deposited outside the cytoplasm of the cells, in the peripheral periplasmic space and extracellularly. Thiosulfate was not used. Carbon dioxide, acetate, pyruvate, propionate, succinate, fumarate and malate were utilized as carbon sources. Optimum growth rates were obtained at pH 9.0 and optimum temperature was 30 degrees C. Good growth was observed in a mineral salts medium containing 5 g sodium bicarbonate l-1 without sodium chloride. The new bacterium tolerated up to 60 g sodium chloride l-1 and up to 80 g sodium carbonates l-1. Growth factors were not required. The DNA G + C composition was 56.0-57.4 mol%. Based on physiological, biochemical and genetic characteristics, the newly isolated bacterium is recognized as a new species of a new genus with the proposed name Thiorhodospira sibirica

Taxonomic rearrangements of the genera Thiocapsa and Amoebobacter on the basis of 16S rDNA sequence analyses and description of Thiolamprovum gen. nov.

Complete nucleotide sequences of the 16S rDNAs were determined from Thiocapsa and Amoebobacter species, including all available type strains and some additional isolates. The distance-matrix analysis and the dendrogram for estimating the genetic relationships revealed that the investigated strains were found in two major clusters within the Chromatiaceae. One cluster comprises all Amoebobacter species, Thiocapsa roseopersicina and several isolates related to Thiocapsa roseopersicina. Representatives of the species Amoebobacter roseus, Amoebobacter pendens and Thiocapsa roseopersicina, the so called ‘Thiocapsa roseopersicina group’, are very closely related, justifying their inclusion into one genus, Thiocapsa, for which an emended description is presented. Amoebobacter purpureus and Amoebobacter pedioformis formed two separate lines of descent with less than 93% (89·6–92·9%) similarity to strains of the ‘Thiocapsa roseopersicina group’. Therefore, they will be considered as two separate genera. As a consequence, an emended description is presented for the genus Amoebobacter, with Amoebobacter purpureus as the new type species and A. pedioformis is transferred to Thiolamprovum pedioforme gen. nov., comb. nov. Two species, Thiocapsa pfennigii and Thiocapsa halophila, which have been classified with the genus Thiocapsa because of their morphological properties, were found within another major cluster of the Chromatiaceae and are only distantly phylogenetically related to the first cluster with 88·4–90·6% and 90·4–92·2% sequence similarity, respectively