Tissue-scale microbiota of the Mediterranean mussel (Mytilus galloprovincialis) and its relationship with the environment

Abstract In this study, we characterize the structural variation of the microbiota of Mytilus galloprovincialis at the tissue scale, also exploring the connection with the microbial ecosystem of the surrounding water. Mussels were sampled within a farm located in the North-Western Adriatic Sea and microbiota composition was analyzed in gills, hemolymph, digestive glands, stomach and foot by Next Generation Sequencing marker gene approach. Mussels showed a distinctive microbiota structure, with specific declinations at the tissue level. Indeed, each tissue is characterized by a distinct pattern of dominant families, reflecting a peculiar adaptation to the respective tissue niche. For instance, the microbiota of the digestive gland is characterized by Ruminococcaceae and Lachnospiraceae, being shaped to ferment complex polysaccharides of dietary origin into short-chain fatty acids, well matching the general asset of the animal gut microbiota. Conversely, the gill and hemolymph ecosystems are dominated by marine microorganisms with aerobic oxidative metabolism, consistent with the role played by these tissues as an interface with the external environment. Our findings highlight the putative importance of mussel microbiota for different aspects of host physiology, with ultimate repercussions on mussel health and productivity

Computational resources for structural and metagenomic characterization of functions in bacteria and bacterial communities. Antimicrobial resistance, pathways for xenobiotic degradation and relationship between gut microbiome and ageing.

Prokaryotic organisms are one of the most successful forms of life, they are present in all known ecosystems. The deluge diversity of bacteria reflects their ability to colonise every environment. Also, human beings host trillions of microorganisms in their body districts, including skin, mucosae, and gut. This symbiosis is active for all other terrestrial and marine animals, as well as plants. With the term holobiont we refer, with a single word, to the systems including both the host and its symbiotic microbial species. The coevolution of bacteria within their ecological niches reflects the adaptation of both host and guest species, and it is shaped by complex interactions that are pivotal for determining the host state. Nowadays, thanks to the current sequencing technologies, Next Generation Sequencing, we have unprecedented tools for investigating the bacterial life by studying the prokaryotic genome sequences. NGS revolution has been sustained by the advancements in computational performance, in terms of speed, storage capacity, algorithm development and hardware costs decreasing following the Moore’s Law. Bioinformaticians and computational biologists design and implement ad hoc tools able to analyse high-throughput data and extract valuable biological information. Metagenomics requires the integration of life and computational sciences and it is uncovering the deluge diversity of the bacterial world. The present thesis work focuses mainly on the analysis of prokaryotic genomes under different aspects. Being supervised by two groups at the University of Bologna, the Biocomputing group and the group of Microbial Ecology of Health, I investigated three different topics: i) antimicrobial resistance, particularly with respect to missense point mutations involved in the resistant phenotype, ii) bacterial mechanisms involved in xenobiotic degradation via the computational analysis of metagenomic samples, and iii) the variation of the human gut microbiota through ageing, in elderly and longevous individuals

Analysis of fecal bile acids and metabolites by high resolution mass spectrometry in farm animals and correlation with microbiota

There is a growing interest in the named "acidic sterolbiome" and in the genetic potential of the gut microbiome (GM) to modify bile acid (BA) structure. Indeed, the qualitative composition of BAs in feces correlates with the bowel microorganisms and their collective genetic material. GM is responsible for the production of BA metabolites, such as secondary and oxo-BAs. The specific BA profiles, as microbiome-host co-metabolic products, could be useful to investigate the GM-host interaction in animals under physiological conditions, as well as in specific diseases. In this context, we developed and validated an ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry method for the simultaneous analysis of up to 21 oxo-BAs and their 9 metabolic precursors. Chromatographic separation was achieved in 7 min with adequate analytical performance in terms of selectivity, sensitivity (LOQ from 0.05 to 0.1 mu g/mL), accuracy (bias% < 5%), precision (CV% < 5%) and matrix effect (ME% < 10%). A fast solvent extraction protocol has been fine-tuned, achieving recoveries > 90%. In parallel, the gut microbiota assessment in farming animals was evaluated by 16S rRNA next-generation sequencing, and the correlation with the BA composition was performed by multivariate analysis, allowing to reconstruct species-specific associations between the BA profile and specific GM components

A morphological, biological and molecular approach reveals four cryptic species of Trissolcus Ashmead (Hymenoptera, Scelionidae), egg parasitoids of Pentatomidae (Hemiptera)

Accurate identification of parasitoids is crucial for biological control of the invasive brown marmorated stink bug, Halyomrpha halys (Stål). A recent work by Talamas et al. (2017) revised the Palearctic fauna of Trissolcus Ashmead, egg-parasitoids of stink bugs, and treated numerous species as junior synonyms of T. semistriatus (Nees von Esenbeck). In the present paper, we provide a detailed taxonomic history and treatment of T. semistriatus and the species treated as its synonyms by Talamas et al. (2017) based on examination of primary types, molecular analyses and mating experiments. Trissolcus semistriatus, T. belenus (Walker), T. colemani (Crawford), and T. manteroi (Kieffer) are here recognized as valid and a key to species is provided. The identification tools provided here will facilitate the use of Trissolcus wasps as biological control agents and as the subject of ecological studies

Halyomorpha halys and its egg parasitoids Trissolcus japonicus and T. mitsukurii: the geographic dimension of the interaction

Halyomorpha halys (Stål) (Hemiptera, Pentatomidae) was accidentally introduced to North America and Europe, becoming a key pest of many important crops. In its native range, it is attacked by egg parasitoids, including Trissolcus japonicus (Ashmead), considered to be the main species, and T. mitsukurii (Ashmead) (Hymenoptera, Scelionidae). Trissolcus japonicus was detected in North America in 2014 and Europe in 2017, while T. mitsukurii was detected in Australia in the early 20th century and in Europe in 2016. Both species now appear established in the new areas. The present study used the MaxEnt algorithm to clarify the geographic dimension of the potential interaction between H. halys and these two parasitoid species, and to indicate where the release of one or the other parasitoid species is more likely to be effective. We found that the suitability for the two parasitoids overlaps the H. halys native range completely. In invaded areas, T. japonicus showed higher potential habitat suitability at the global scale, compared to T. mitsukurii, and also higher potential suitability at lower latitudes at continental and national scales. These results can substantially improve the effectiveness of biological control against H. halys, by targeting the releases of parasitoids to the areas where each species is most likely to succeed

Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient

Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions