Friends or Foes-Microbial Interactions in Nature

Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell-cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications

First record of the non-indigenous jellyfish Blackfordia virginica (Mayer, 1910) in the Baltic Sea

Marine invasions are of increasing concern for biodiversity conservation worldwide. Gelatinous macrozooplankton contain members, which have become globally invasive, for example the ctenophore Mnemiopsis leidyi or the hydromedusae Blackfordia virginica. B. virginica is characterised by a large salinity tolerance, with a brackish-water habitat preference, and by a metagenic life history strategy with an alternation between sexually reproducing planktonic medusae and asexually reproducing benthic polyps to complete the life cycle. In this study we analysed 8 years of ichthyoplankton survey data (2010–2017) from the Kiel Canal and 14 ichthyoplankton summer surveys in the central Baltic Sea (2008–2017). We report the first presence of B. virginica in northern Europe, namely from the southwestern Baltic Sea and the Kiel Canal. In the Kiel Canal, B. virginica was first sporadically sighted in 2014 and 2015 and has developed persistent populations since summer 2016. Changes in size-frequency distributions during summer 2016 indicate active recruitment in the Kiel Canal at salinities between 7 and 13 and temperatures > 14 °C. Close vicinity to and direct connection with the southwestern Baltic Sea, where B. virginica was observed during 2017, indicate that the Baltic Sea and other brackish-water habitats of Northern Europe are at risk for colonisation of this non-indigenous species. Our results highlight that monitoring activities should consider gelatinous macrozooplankton for standard assessments to allow for the detection of non-indigenous species at an early stage of their colonisation

First insights into the Aurelia aurita transcriptome response upon manipulation of its microbiome

IntroductionThe associated diverse microbiome contributes to the overall fitness of Aurelia aurita, particularly to asexual reproduction. However, how A. aurita maintains this specific microbiome or reacts to manipulations is unknown.MethodsIn this report, the response of A. aurita to manipulations of its native microbiome was studied by a transcriptomics approach. Microbiome-manipulated polyps were generated by antibiotic treatment and challenging polyps with a non-native, native, and potentially pathogenic bacterium. Total RNA extraction followed by RNAseq resulted in over 155 million reads used for a de novo assembly.ResultsThe transcriptome analysis showed that the antibiotic-induced change and resulting reduction of the microbiome significantly affected the host transcriptome, e.g., genes involved in processes related to immune response and defense mechanisms were highly upregulated. Similarly, manipulating the microbiome by challenging the polyp with a high load of bacteria (2 × 107 cells/polyp) resulted in induced transcription of apoptosis-, defense-, and immune response genes. A second focus was on host-derived quorum sensing interference as a potential defense strategy. Quorum Quenching (QQ) activities and the respective encoding QQ-ORFs of A. aurita were identified by functional screening a cDNA-based expression library generated in Escherichia coli. Corresponding sequences were identified in the transcriptome assembly. Moreover, gene expression analysis revealed differential expression of QQ genes depending on the treatment, strongly suggesting QQ as an additional defense strategy.DiscussionOverall, this study allows first insights into A. aurita’s response to manipulating its microbiome, thus paving the way for an in-depth analysis of the basal immune system and additional fundamental defense strategies

Cultivable microbiota associated with Aurelia aurita and Mnemiopsis leidyi

The associated microbiota of marine invertebrates plays an important role to the host in relation to fitness, health, and homeostasis. Cooperative and competitive interactions between bacteria, due to release of, for example, antibacterial substances and quorum sensing (QS)/quorum quenching (QQ) molecules, ultimately affect the establishment and dynamics of the associated microbial community. Aiming to address interspecies competition of cultivable microbes associated with emerging model species of the basal animal phyla Cnidaria (Aurelia aurita) and Ctenophora (Mnemiopsis leidyi), we performed a classical isolation approach. Overall, 84 bacteria were isolated from A. aurita medusae and polyps, 64 bacteria from M. leidyi, and 83 bacteria from ambient seawater, followed by taxonomically classification by 16S rRNA gene analysis. The results show that A. aurita and M. leidyi harbor a cultivable core microbiome consisting of typical marine ubiquitous bacteria also found in the ambient seawater. However, several bacteria were restricted to one host suggesting host-specific microbial community patterns. Interbacterial interactions were assessed by (a) a growth inhibition assay and (b) QS interference screening assay. Out of 231 isolates, 4 bacterial isolates inhibited growth of 17 isolates on agar plates. Moreover, 121 of the 231 isolates showed QS-interfering activities. They interfered with the acyl-homoserine lactone (AHL)-based communication, of which 21 showed simultaneous interference with autoinducer 2. Overall, this study provides insights into the cultivable part of the microbiota associated with two environmentally important marine non-model organisms and into interbacterial interactions, which are most likely considerably involved in shaping a healthy and resilient microbiota

Differences in the microbiota of native and non-indigenous gelatinous zooplankton organisms in a low saline environment

Highlights: • Non-indigenous species (NIS) are increasingly recognized as a matter of concern. • The microbiome of native and NIS gelatinous zooplankton organisms are compared. • Next generation sequencing confirms sign. Species specific microbiome differences. • Indicator OTUs include bacteria which contain known pathogenic strains. • Microbiome monitoring of NIS should be considered for aquaculture risk assessments. Abstract: The translocation of non-indigenous species (NIS) around the world, especially in marine systems, is increasingly being recognized as a matter of concern. Species translocations have been shown to lead to wide ranging changes in food web structure and functioning. In addition to the direct effects of NIS, they could facilitate the accumulation or translocation of bacteria as part of their microbiomes. The Baltic Sea harbours many non-indigenous species, with most recent detection of the jellyfish Blackfordia virginica and the comb jelly Mnemiopsis leidyi in the low saline southwestern Baltic Sea. In this study, we used a multidisciplinary approach and investigated three gelatinous zooplankton species that co-occur in the same environment and feed on similar zooplankton food sources but show different histories of origin. The aim was to conduct a comparative microbiome analysis of indigenous and non-indigenous gelatinous zooplankton species in the low-saline southwestern Baltic Sea. Next-generation 16S rRNA marker gene sequencing of the V1/V2 region was employed to study the bacterial microbiome compositions. All tested species showed significant differences in their microbiome compositions (one way ANOSIM, R = 1, P < 0.008) with dissimilarities ranging from 85 to 92%. The indigenous jellyfish Aurelia aurita showed the highest bacterial operational taxonomic unit (OTU) richness. The overall differentiation between microbiomes was driven by eight indicator OTUs, which included Mycoplasma and Vibrio species. These bacteria can be problematic, as they include known pathogenic strains that are relevant to human health and aquaculture activities. Our results suggest that the impact assessment of NIS should consider potential pathogenic bacteria, enriched in the environment due to invasion, as potential risks to aquaculture activities

Micro-biota differences of the comb jelly Mnemiopsis leidyi in native and invasive sub-populations

The translocation of non-indigenous species around the world, especially in marine systems, is a matter of concern for biodiversity conservation and ecosystem functioning. While specific traits are often recognized to influence establishment success of non-indigenous species, the impact of the associated microbial community for the fitness, performance and invasion success of basal marine metazoans remains vastly unknown. In this study we compared the microbiota community composition of the invasive ctenophore Mnemiopsis leidyi in different native and invasive sub-populations along with characterization of the genetic structure of the host. By 16S rRNA gene amplicon sequencing we showed that the sister group to all metazoans, namely ctenophores, harbored a distinct microbiota on the animal host, which significantly differed across two major tissues, namely epidermis and gastrodermis. Additionally, we identified significant differences between native and invasive sub-populations of M. leidyi, which indicate, that the microbiota community is likely influenced by the genotypic background of the ctenophore. To test the hypothesis that the microbiota is genotypically selected for by the ctenophore host, experiments under controlled environments are required

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

Background The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as “metaorganisms.” The goal of the Collaborative Research Center “Origin and Function of Metaorganisms” is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants. Methods In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample. Conclusion While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition

Metagenomic quorum quenching enzymes affect biofilm formation of Candida albicans and Staphylococcus epidermidis.

Biofilm formation in the clinical environment is of increasing concern since a significant part of human infections is associated, and caused by biofilm establishment of (opportunistic) pathogens, for instance Candida albicans and Staphylococcus epidermidis. The rapidly increasing number of antibiotic-resistant biofilms urgently requires the development of novel and effective strategies to prevent biofilm formation ideally targeting a wide range of infectious microorganisms. Both, synthesis of extracellular polymeric substances and quorum sensing are crucial for biofilm formation, and thus potential attractive targets to combat undesirable biofilms.We evaluated the ability of numerous recently identified metagenome-derived bacterial quorum quenching (QQ) proteins to inhibit biofilm formation of C. albicans and S. epidermidis. Here, proteins QQ-5 and QQ-7 interfered with the morphogenesis of C. albicans by inhibiting the yeast-to-hyphae transition, ultimately leading to impaired biofilm formation. Moreover, QQ5 and QQ-7 inhibited biofilm formation of S. epidermidis; in case of QQ7 most likely due to induced expression of the icaR gene encoding the repressor for polysaccharide intercellular adhesin (PIA) synthesis, the main determinant for staphylococcal biofilm formation. Our results indicate that QQ-5 and QQ-7 are attractive potential anti-biofilm agents in the prevention and treatment of C. albicans and S. epidermidis mono-species biofilms, and potentially promising anti-biofilm drugs in also combating multi-species infections

Occurence data for the non-indigenous jellyfish species Blackfordia virginica in NW Europe from 2010-2017

Positions, sampling times and occurence data for the non-indigenous jellyfish species Blackfordia virginica in NW Europe