Biology subjects

Slaby, B. M.

Publications and source records attributed to Slaby, B. M..

6 recordsLinked to original sources

bioRxiv2023

Maribacter halichondris sp. nov., isolated from the marine sponge Halichondria panicea

A new member of the family Flavobacteriaceae (termed Hal144T) was isolated from the marine breadcrumb sponge Halichondria panicea. Sponge material was collected in 2018 at Schilksee which is located in the Kiel Fjord (Baltic Sea, Germany). Phylogenetic analysis of the full-length Hal144T 16S rRNA gene sequence revealed similarities from 94.3% - 96.6% to the nearest type strains of the genus Maribacter. The phylogenetic tree depicted a cluster of strain Hal144T with its closest relatives Maribacter aestuarii GY20T (96.6%) and Maribacter thermophilus HT7-2T (96.3%). Genome comparisons of strain Hal144T with Maribacter spp. type strains exhibited average nucleotide identities in the range of 75% - 76% and digital DNA-DNA hybridization values in the range of 13.1% - 13.4%. Strain Hal144T was determined to be Gram-negative, mesophilic, strictly aerobic, flexirubin positive, resistant to aminoglycoside antibiotics, and able to utilize N-acetyl-{beta}-D-glucosamine. Optimal growth occurred at 25 - 30 {degrees}C, within a salinity range of 2 - 6% sea salt, and a pH range between 5 - 8. The major fatty acids identified were C17:0 3-OH, iso-C15:0, and iso-C15:1 G. The DNA G+C content of strain Hal144T was 41.4 mol%. Based on the polyphasic approach, strain Hal144T represents a novel species of the genus Maribacter, and we propose the name Maribacter halichondris sp. nov.. The type strain is Hal144T (= DSM 114563T = LMG 32744T).

microbiology↗

bioRxiv2021

Rethinking symbiotic metabolism: trophic strategies in the microbiomes of different sponge species

In this study we describe the major lithoheterotrophic and autotrophic processes in 21 microbial sponge-associated phyla using novel and existing genomic and transcriptomic datasets. We show that a single gene family, molybdenum-binding subunit of dehydrogenase (coxL), likely evolved to benefit both lithoheterotrophic and organoheterotrophic symbionts, through adaptation to different inorganic and organic substrates. We show the main microbial carbon fixation pathways in sponges are restricted to specialized symbiotic lineages within five phyla. We also propose that sponge symbionts, in particular Acidobacteria, are capable of assimilating carbon through anaplerotic processes. However, the presence of symbionts genomically capable of autotrophy does not inform on their actual contribution to light and dark carbon fixation. Using radioisotope assays we identified variability in the relative contributions of chemosynthesis to total carbon fixation in different sponge species. Furthermore, the symbiosis of sponges with two closely related Cyanobacteria results in outcomes that are not predictable by analysis of -omics data alone: Candidatus Synechococcus spongiarum contributes to the holobiont carbon budget by transfer of photosynthates, while Candidatus Synechococcus feldmannii does not. Our results highlight the importance of combining sequencing data with physiology to gain a broader understanding of carbon metabolism within holobionts characterized by highly diverse microbiomes.

microbiology↗

bioRxiv2020

Bacterial precursors and unsaturated long-chain fatty acids are biomarkers of North-Atlantic demosponges

Sponges produce distinct fatty acids (FAs) that (potentially) can be used as chemotaxonomic and ecological biomarkers to study endosymbiont-host interactions and the functional ecology of sponges. Here, we present FA profiles of five common habitat-building deep-sea sponges (class Demospongiae, order Tetractinellida), which are classified as high microbial abundance (HMA) species. Geodia hentscheli, G. parva, G. atlantica, G. barretti, and Stelletta rhaphidiophora were collected from boreal and Arctic sponge grounds in the North-Atlantic Ocean. Bacterial FAs dominated in all five species and particularly isomeric mixtures of mid-chain branched FAs (MBFAs, 8- and 9-Me-C16:0 and 10 and 11-Me-C18:0) were found in high abundance (together [≥] 20% of total FAs) aside more common bacterial markers. In addition, the sponges produced long-chain linear, mid- and a(i)-branched unsaturated FAs (LCFAs) with a chain length of 24-28 C atoms and had predominantly the typical {Delta}5,9 unsaturation, although also {Delta}9,19 and (yet undescribed) {Delta}11,21 unsaturations were identified. G. parva and S. rhaphidiophora each produced distinct LCFAs, while G. atlantica, G. barretti, and G. hentscheli produced similar LCFAs, but in different ratios. The different bacterial precursors varied in carbon isotopic composition ({delta}13C), with MBFAs being more enriched compared to other bacterial (linear and a(i)-branched) FAs. We propose biosynthetic pathways for different LCFAs from their bacterial precursors, that are consistent with small isotopic differences found in LCFAs. Indeed, FA profiles of deep-sea sponges can serve as chemotaxonomic markers and support the conception that sponges acquire building blocks from their endosymbiotic bacteria.

biochemistry↗

bioRxiv2020

Microbial strategies for survival in the glass sponge Vazella pourtalesii

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. ImportanceWe 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 m). 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.

microbiology↗

bioRxiv2020

Microbial diversity of the glass sponge Vazella pourtalesii in response to anthropogenic activities

Establishment of adequate conservation areas represents a challenging but crucial task in the conservation of genetic diversity and biological variability. Anthropogenic pressures on marine ecosystems and organisms are steadily increasing. Whether and to what extent these pressures influence marine genetic biodiversity is only starting to be revealed. Using 16S rRNA gene amplicon sequencing, we analysed the microbial community structure of 33 individuals of the habitat-forming glass sponge Vazella pourtalesii, as well as reference seawater, sediment, and biofilm samples. We assessed how two anthropogenic impacts, i.e. habitat destruction by trawling and artificial substrate provision (moorings made of composite plastic), correspond with in situ V. pourtalesii microbiome variability. In addition, we evaluated the role of two bottom fishery closures in preserving sponge-associated microbial diversity on the Scotian Shelf, Canada. Our results illustrate that V. pourtalesii sponges collected from pristine sites within fishery closures contained distinct and taxonomically largely novel microbial communities. At the trawled site we recorded significant quantitative differences in distinct microbial phyla, such as a reduction in Nitrospinae in sponges and environmental references. Individuals of V. pourtalesii growing on the mooring were significantly enriched in Bacteroidetes, Verrucomicrobia and Cyanobacteria in comparison to sponge individuals growing on the natural seabed. Due to a concomitant enrichment of these taxa in the mooring biofilm, we propose that biofilms on artificial substrates may prime sponge-associated microbial communities when small sponges settle on such substrates. These observations likely have relevant management implications when considering the increase of artificial substrates in the marine environment, e.g., marine litter, off-shore wind parks, and petroleum platforms.

ecology↗

bioRxiv2018

Marine sponges as Chloroflexi hot-spots: Genomic insights and high resolution visualization of an abundant and diverse symbiotic clade

Chloroflexi represent a widespread, yet enigmatic bacterial phylum. Meta-and single cell genomics were performed to shed light on the functional gene repertoire of Chloroflexi symbionts from the HMA sponge 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, and amino acid utilization as nutrient source by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding for co-factor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPRs-Cas systems, eukaryote-like repeat proteins and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by FISH-CLEM method. Chloroflexi cells were generally rod-shaped and about 1 m in length, albeit displayed different and characteristic cellular morphotypes per each class. The extensive potential for carbohydrate degradation has been reported previously for Ca. 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 also contribute to DOM re-cycling and primary productivity in reef ecosystems via a pathway termed the \"sponge loop\".

microbiology↗