1,721,036 research outputs found
Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits
No full textThe genus Paracoccu s capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus -type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa , and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus , known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Göttingen UniversityOpen-Access-Publikationsfonds 202
Microbial epibiotic community of the deep-sea galatheid squat lobster Munidopsis alvisca
No full textAbstract Life at hydrothermal vent sites is based on chemosynthetic primary producers that supply heterotrophic microorganisms with substrates and generate biomass for higher trophic levels. Often, chemoautotrophs associate with the hydrothermal vent megafauna. To investigate attached bacterial and archaeal communities on deep-sea squat lobsters, we collected ten specimens from a hydrothermal vent in the Guaymas Basin (Gulf of California). All animals were identified as Munidopsis alvisca via morphological and molecular classification, and intraspecific divergence was determined. Amplicon sequencing of microbial DNA and cDNA revealed significant differences between microbial communities on the carapaces of M. alvisca and those in ambient sea water. Major epibiotic bacterial taxa were chemoautotrophic Gammaproteobacteria , such as Thiotrichaceae and Methylococcaceae , while archaea were almost exclusively represented by sequences affiliated with Ca. Nitrosopumilus . In sea water samples, Marine Group II and III archaea and organoheterotrophic Alphaproteobacteria , Flavobacteriia and Planctomycetacia were more dominant. Based on the identified taxa, we assume that main metabolic processes, carried out by M. alvisca epibiota, include ammonia, methane and sulphide oxidation. Considering that M. alvisca could benefit from sulphide detoxification by its epibiota, and that attached microbes are supplied with a stable habitat in proximity to substrate-rich hydrothermal fluids, a mutualistic host-microbe relationship appears likely
Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle
No full textMacroalgae harbour specific microbial communities on their surface that have functions related to host health and defence. In this study, the bacterial biofilm of the marine brown alga Fucus spiralis was investigated using 16S rRNA gene amplicon-based analysis and isolation of bacteria. Rhodobacteraceae (Alphaproteobacteria) were the predominant family constituting 23% of the epibacterial community. At the genus level, Sulfitobacter, Loktanella, Octadecabacter and a previously undescribed cluster were most abundant, and together they comprised 89% of the Rhodobacteraceae. Supported by a specific PCR approach, 23 different Rhodobacteraceae-affiliated strains were isolated from the surface of F. spiralis, which belonged to 12 established and three new genera. For seven strains, closely related sequences were detected in the 16S rRNA gene dataset. Growth experiments with substrates known to be produced by Fucus spp. showed that all of them were consumed by at least three strains, and vitamin B12 was produced by 70% of the isolates. Since growth of F. spiralis depends on B12 supplementation, bacteria may provide the alga with this vitamin. Most strains produced siderophores, which can enhance algal growth under iron-deficient conditions. Inhibiting properties against other bacteria were only observed when F. spiralis material was present in the medium. Thus, the physiological properties of the isolates indicated adaption to an epiphytic lifestyle
Genetic Analysis of the Upper Phenylacetate Catabolic Pathway in the Production of Tropodithietic Acid by Phaeobacter gallaeciensis
No full textProduction of the antibiotic tropodithietic acid (TDA) depends on the central phenylacetate catabolic pathway, specifically on the oxygenase PaaABCDE, which catalyzes epoxidation of phenylacetyl-coenzyme A (CoA). Our study was focused on genes of the upper part of this pathway leading to phenylacetyl-CoA as precursor for TDA. Phaeobacter gallaeciensis DSM 17395 encodes two genes with homology to phenylacetyl-CoA ligases (paaK1 and paaK2), which were shown to be essential for phenylacetate catabolism but not for TDA biosynthesis and phenylalanine degradation. Thus, in P. gallaeciensis another enzyme must produce phenylacetyl-CoA from phenylalanine. Using random transposon insertion mutagenesis of a paaK1-paaK2 double mutant we identified a gene (ion) with similarity to iorA and iorB in archaea, encoding an indolepyruvate:ferredoxin oxidoreductase (IOR). The ion l mutant was unable to grow on phenylalanine, and production of TDA was significantly reduced compared to the wildtype level (60%). Nuclear magnetic resonance (NMR) spectroscopic investigations using C-13-labeled phenylalanine isotopomers demonstrated that phenylalanine is transformed into phenylacetyl-CoA by Ion. Using quantitative real-time PCR, we could show that expression of ion l depends on the adjacent regulator IorR. Growth on phenylalanine promotes production of TDA, induces expression of ion 1 (27-fold) and paaK1 (61-fold), and regulates the production of TDA. Phylogenetic analysis showed that the aerobic type of IOR as found in many roseobacters is common within a number of different phylogenetic groups of aerobic bacteria such as Burkholderia, Cupriavidis, and Rhizobia, where it may also contribute to the degradation of phenylalanine
Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans
No full textThe bacterial degradation of polysaccharides is central to marine carbon cycling, but little is known about the bacterial taxa that degrade specific marine polysaccharides. Here, bacterial growth and community dynamics were studied during the degradation of the polysaccharides chitin, alginate and agarose in microcosm experiments at four contrasting locations in the Southern and Atlantic Oceans. At the Southern polar front, chitin-supplemented microcosms were characterized by higher fractions of actively growing cells and a community shift from Alphaproteobacteria to Gammaproteobacteria and Bacteroidetes. At the Antarctic ice shelf, chitin degradation was associated with growth of Bacteroidetes, with 24% higher cell numbers compared with the control. At the Patagonian continental shelf, alginate and agarose degradation covaried with growth of different Alteromonadaceae populations, each with specific temporal growth patterns. At the Mauritanian upwelling, only the alginate hydrolysis product guluronate was consumed, coincident with increasing abundances of Alteromonadaceae and possibly cross-feeding SAR11. 16S rRNA gene amplicon libraries indicated that growth of the Bacteroidetes-affiliated genus Reichenbachiella was stimulated by chitin at all cold and temperate water stations, suggesting comparable ecological roles over wide geographical scales. Overall, the predominance of location-specific patterns showed that bacterial communities from contrasting oceanic biomes have members with different potentials to hydrolyse polysaccharides.German Research Foundation, DFG [WI3888/1-1, NI1366/1-1, TRR51
Genome sequence of Planktotalea frisia type strain (SH6-1T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom
No full textAbstract Planktotalea frisia SH6-1T Hahnke et al. (Int J Syst Evol Microbiol 62:1619–24, 2012) is a planktonic marine bacterium isolated during a phytoplankton bloom from the southern North Sea. It belongs to the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Here we describe the draft genome sequence and annotation of the type strain SH6-1T. The genome comprises 4,106,736 bp and contains 4128 protein-coding and 38 RNA genes. The draft genome sequence provides evidence for at least three extrachromosomal elements, encodes genes for DMSP utilization, quorum sensing, photoheterotrophy and a type IV secretion system. This indicates not only adaptation to a free-living lifestyle of P. frisia but points also to interactions with prokaryotic or eukaryotic organisms
Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle
Get PDFThe genus Pseudooceanicola from the alphaproteobacterial Roseobacter group currently includes ten validated species. We herein describe strain Lw-13eT, the first Pseudooceanicola species from marine macroalgae, isolated from the brown alga Fucus spiralis abundant at European and North American coasts. Physiological and pangenome analyses of Lw-13eT showed corresponding adaptive features. Adaptations to the tidal environment include a broad salinity tolerance, degradation of macroalgae-derived substrates (mannitol, mannose, proline), and resistance to several antibiotics and heavy metals. Notably, Lw-13eT can degrade oligomeric alginate via PL15 alginate lyase encoded in a polysaccharide utilization locus (PUL), rarely described for roseobacters to date. Plasmid localization of the PUL strengthens the importance of mobile genetic elements for evolutionary adaptations within the Roseobacter group. PL15 homologs were primarily detected in marine plant-associated metagenomes from coastal environments but not in the open ocean, corroborating its adaptive role in algae-rich habitats. Exceptional is the tolerance of Lw-13eT against the broad-spectrum antibiotic tropodithietic acid, produced by Phaeobacter spp. co-occurring in coastal habitats. Furthermore, Lw-13eT exhibits features resembling terrestrial plant-bacteria associations, i.e. biosynthesis of siderophores, terpenes and volatiles, which may contribute to mutual bacteria-algae interactions. Closest described relative of Lw-13eT is Pseudopuniceibacterium sediminis CY03T with 98.4% 16S rRNA gene sequence similarity. However, protein sequence-based core genome phylogeny and average nucleotide identity indicate affiliation of Lw-13eT with the genus Pseudooceanicola. Based on phylogenetic, physiological and (chemo)taxonomic distinctions, we propose strain Lw-13eT (=DSM 29013T = LMG 30557T) as a novel species with the name Pseudooceanicola algae
Production of a Blue Pigment (Glaukothalin) by Marine Rheinheimera spp.
Get PDFTwo γ-Proteobacteria strains, that is, HP1 and HP9, which both produce a diffusible deep blue pigment, were isolated from the German Wadden Sea and from the Øresund, Denmark, respectively. Both strains affiliate with the genus Rheinheimera. Small amounts of the pigment could be extracted from HP1 grown in a 50 L fermenter and were purified chromatographically. Chemical analysis of the pigment including NMR and mass spectrometry led to a molecular formula of C34H56N4O4 (m.w. 584.85) which has not yet been reported in literature. The molecule is highly symmetrically and consists of two heterocyclic halves to which aliphatic side chains are attached. The pigment has been named glaukothalin due to its blue color and its marine origin (glaukos, gr.=blue, thalatta, gr.=sea). Production of glaukothalin on MB2216 agar plates by our Rheinheimera strains is affected in the presence of other bacterial strains either increasing or decreasing pigment production. The addition of a single amino acid, arginine (5 gl−1), greatly increases pigment production by our Rheinheimera strains. Even though the production of glaukothalin leads to inhibitory activity against three bacterial strains from marine particles, our Rheinheimera isolates are inhibited by various bacteria of different phylogenetic groups. The ecological role of glaukothalin production by Rheinheimera strains, however, remains largely unknown
Nischen von häufigen heterotrophen Bakterien während der Algenblüten in der Nordsee
No full textThe remineralization of algal biomass by heterotrophic bacteria during spring phytoplankton blooms is a globally important process in carbon cycling. Yet, the ecophysiology of environmentally relevant bacteria occurring during these events is largely unknown. In this thesis, I investigated the niches of the gammaproteobacterial genus Reinekea and the flavobacterial genera Polaribacter and Formosa, which are recurrently abundant during the 2009-2012 North Sea spring algal blooms off Helgoland. Firstly, I studied a Reinekea forsetiia , the representative of North Sea Reinekea clade, using genomic and physiological analyses. The results suggested a versatile opportunistic lifestyle comprising (i) utilization of relevant algal polysaccharides, (ii) potential toxin production, and (iii) strategies to deal with phosphorus limitation. Secondly, temporal dynamics and large niche space of diverse North Sea Polaribacter spp. was investigated using fluorescence in situ hybridization with novel oligonucleotide probes, binning of time-series metagenomes and re-analysis of in situ expression data. These analyses showed the succession of four major Polaribacter clades with varying degradation capacity for high molecular weight compounds and suggested a polysaccharide-driven niche partitioning between these closely-related bacteria. Finally, the polysaccharide niche of North Sea Formosa clade was examined using metaa omic approaches and complementary physiological and biochemical experiments. An efficient laminarin uptake and degradation mechanism, which is coupled to peptide utilization, was revealed. This thesis demonstrated how heterotrophic bacteria employ different ecological strategies to utilize diverse high molecular weight compounds released during spring algal blooms and increased our knowledge on microbially mediated carbon turnover in the surface ocean
Untersuchung von Kieselalgen-Bakterien-Interaktionen mit dem Modellorganismus Thalassiosira rotula
No full textMarine microalgae are key primary producers responsible for more than 45% of global net primary production, fixing billions of tons of inorganic carbon each year. Diatoms constitute one of the most diverse and ecologically important group of microalgae. While diatom productivity and health are likely to be strongly governed by the structure and function of the diatom microbiome, we have little understanding which factors contribute to the microbiome assembly. In order to investigate the microbiome establishment on diatoms, an in vitro model system for reproducible laboratory studies was developed with the marine diatom Thalassiosira rotula. Thus, this thesis describes the isolation of diatoms and bacteria from the environment and the development of an in vitro model system for reproducible laboratory studies followed by the investigation of the microbiome assembling on the diatom T. rotula using co-culture experiments. In Chapter 2 diatoms and bacteria were co-isolated from a spring bloom in the German Bight of the North Sea. The isolation resulted in four different diatom species and 200 morphological different bacteria in culture. The marine diatom Thalassiosira rotula was selected as the model organism for the in vitro studies with diatoms and bacteria. Chapter 3 focused on the development of a co-culture to study mutualistic interactions between the diatom T. rotula and bacteria as well as the generation of an axenic (bacteria-free) culture of the diatom T. rotula. The experiments revealed that the diatom T. rotula is auxotroph for B-vitamins and that the bacterial community of T. rotula is able to maintain the growth of the vitamin-free diatom with the provision of vitamins. In Chapter 4 and 5 the microbiome assembling was investigated by exposing the vitamin-free and axenic diatom T. rotula to several bacterial source communities obtained from different diatom species. The co-culture experiments revealed that each of the newly established microbiomes on the T. rotula acceptor supports the growth of the diatom under vitamin absence, indicating that all microbiomes comprise bacteria capable for B-vitamin synthesis. To investigate the factors that contribute to the microbiome assembling, the bacterial community compositions of the different inoculated bacterial source communities and newly assembled acceptor microbiomes were analysed. The analysis revealed that the different inoculated bacterial source communities were highly different in their bacterial community composition and contained up to 4406 different operational taxonomic units (OTUs). On the contrary, the analysis of the newly established acceptor microbiomes revealed that all acceptor microbiomes were similar to each other in respect to their bacterial community composition and that they were more similar to the original T. rotula bacterial source community than to the donor cultures where the bacterial source communities were obtained from. The similarity of the acceptor microbiomes was most likely caused by 10 OTUs, which constituted for more than 80% of the total relative abundance of all acceptor microbiomes. Furthermore, these 10 OTUs were shown to be most responsible for the differences between acceptor microbiomes and bacterial source communities and were thus described as the core microbiome of the diatom T. rotula. Consequently, it was shown for the first time that the ecologically relevant diatom T. rotula establishes a robust and reproducible bacterial core microbiome of 10 OTUs if it is offered highly diverse and compositionally different bacterial source communities with up to 4406 OTUs. The results of the robust and reproducible microbiome composition on the diatom T. rotula suggest that host factors contribute more than the bacterial diversity in the environment to the shaping of the microbiome composition
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