Variability in Host Specificity and Functional Potential of Antarctic Sponge-Associated Bacterial Communities

Sponge-associated microorganisms are essential for sponge survival. They play an important role in recycling nutrients and, therefore, in the maintenance of the ecosystem. These microorganisms are diverse, species-specific, and different from those in the surrounding seawater. Bacterial sponge symbionts have been extensively studied in the tropics; however, little is known about these microorganisms in sponges from high-latitude environments. Sponges can cover up to 80% of the benthos in Antarctica and are crucial architects for the marine food web. In this study, we present analyses of the bacterial symbionts of three sponges: Haliclona (Rhizoniera) sp., Hymeniacidon torquata, and Isodictya kerguelenensis from the Western Antarctic Peninsula (WAP) with the aim to determine variations on the specificity of the bacteria–sponge interactions and potential signatures on their predicted functional profiles. We use high-throughput 16S rRNA gene sequencing of 30 sponge individuals inhabiting South Bay (Palmer Archipelago, WAP) to describe their microbiome taxonomy and diversity and predict potential functional profiles based on this marker gene. Our work shows similar bacterial community composition profiles among the same sponge species, although the symbiotic relationship is not equally conserved among the three Antarctic sponges. The number of species-specific core operational taxonomic units (OTUs) of these Antarctic sponges was low, with important differences between the total abundance accounted for these OTUs. Only eight OTUs were shared between the three sponge species. Analyses of the functional potential revealed that despite the high host–symbiont specificity, the inferred functions are conserved among these microbiomes, although with differences in the abundance of specific functions. H. torquata showed the highest level of intra-specificity and a higher potential of pathways related to energy metabolism, metabolisms of terpenoids and polyketides, and biosynthesis of other secondary metabolites. Overall, this work shows variations in the specificity of the sponge-associated bacterial communities, differences in how hosts and symbionts establish their relations, and in their potential functional capabilities.

Genetic functional potential displays minor importance in explaining spatial variability of methane fluxes within a Eriophorum vaginatum dominated Swedish peatland

Microbial communities of methane (CH4) producing methanogens and consuming methanotrophs play an important role for Earth's atmospheric CH4 budget. Despite their global significance, knowledge on how much they control the spatial variation in CH4 fluxes from peatlands is poorly understood. We studied variation in CH4 producing and consuming communities in a natural peatland dominated by Eriophorum vaginatum, via a metagenomics approach using custom designed hybridization-based oligonucleotide probes to focus on taxa and functions associated with methane cycling. We hypothesized that sites with different magnitudes of methane flux are occupied by structurally and functionally different microbial communities, despite the dominance of a single vascular plant species. To investigate this, nine plant-peat mesocosms dominated by the sedge Eriophorum vaginatum, with varying vegetation coverage, were collected from a temperate natural wetland and subjected to a simulated growing season. During the simulated growing season, measurements of CH4 emission, carbon dioxide (CO2) exchange and δ13C signature of emitted CH4 were made. Mesocosms 1 through 9 were classified into three categories according to the magnitude of CH4 flux. Gross primary production and ecosystem respiration followed the same pattern as CH4 fluxes, but this trend was not observed in net ecosystem exchange. We observed that genetic functional potential was of minor importance in explaining spatial variability of CH4 fluxes with only small shifts in taxonomic community and functional genes. In addition, a higher β-diversity was observed in samples with high CH4 emission. Among methanogens, Methanoregula, made up over 50 % of the community composition. This, in combination with the remaining hydrogenotrophic methanogens matched the δ13C isotopic signature of emitted CH4. However, the presence of acetoclastic and methylotrophic taxa and type I, II and Verrucomicrobia methanotrophs indicates that the microbial community holds the ability to produce and consume CH4 in multiple ways. This is important in terms of future climate scenarios, where peatlands are expected to alter in nutrient status, hydrology, and peat biochemistry. Due to the high functional potential, we expect the community to be highly adaptive to future climate scenarios.

Units of Military Fortification Complex as Phenomenon Elements of the Czech Borderlands Landscape

This paper is focused on selected units of casemates with enhanced fortification in the military fortification complex of the Czech borderlands landscape as specific forms of brownfields. They represent a functional system that interacts with surrounding nature, landscape character, and human society. Four approaches were chosen to study the function and potential of selected individual abandoned casemates with enhanced fortification, where each of them corresponds to one of the four landscape layers: genius loci, socio-economic sphere, functional relationship (between human and the landscape), and natural conditions. There is a corresponding research method for each of the landscape layers (guided interview with respondents, data analysis on abandoned casemates with enhanced fortifications as brownfields, analysis of their landscape functions, and zoological survey of interior). The main results could show that abandoned casemates with enhanced fortifications can play important roles in all landscape layers: stories and genius loci, abandoned casemates with enhanced fortification as a special type of military brownfield but also as a semi-natural ecosystem, and the same time as a habitat for invertebrates. The analyses and surveys conducted clearly demonstrate that abandoned casemates with enhanced fortification as units of military fortification complex of the Czech borderlands landscape perform several hidden important functions in the landscape for which they cannot be viewed as brownfields. This hidden functional potential is most likely best described by the concept of hidden singularity, which offers itself for integration into basic approaches to brownfields.

Bacterial Communities and Prediction of Microbial Metabolic Pathway in Rice Wine Koji From Different Regions in China

Rice wine koji, a traditional homemade starter culture in China, is nutritious and delicious. The final quality of rice wine koji is closely related to the structure of its microbial community. However, the diversity of natural microorganisms in rice wine koji from different regions has not been evaluated. In this study, the microbial population of 92 naturally fermented rice koji samples collected from Hubei, Guangxi, and Sichuan was systematically analyzed by high-throughput sequencing. From all the rice wine koji samples, 22 phyla and 479 bacterial genera were identified. Weissella, Pediococcus, Lactobacillus, Enterobacter, Lactococcus, Pantoea, Bacillus, Staphylococcus, and Leuconostoc were the dominant genera in rice wine koji. The bacterial community structure of rice wine koji samples from different regions was significantly different (p < 0.05). The bacterial community composition of the samples from Hubei and Guangxi was similar, but significantly different from that of SC samples (p < 0.05). These differences may be caused by variations in geography, environment, or manufacturing. In addition, the results of microbial phenotype prediction by BugBase and bacterial functional potential prediction by PICRUSt showed that eight of the nine predicted phenotypic functions of rice wine koji samples from different regions were significantly different (p < 0.05) and that vigorous bacterial metabolism occurred in rice wine koji samples.

Variation and transmission of the human gut microbiota across multiple familial generations

Although the composition and functional potential of the human gut microbiota evolve over the lifespan, kinship has been identified as a key covariate of microbial community diversification. However, to date, sharing of microbiota features within families has mostly been assessed between parents and their direct offspring. Here we investigate the potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (n = 102) spanning 3 to 5 generations over the same female bloodline. We observe microbiome community composition associated with kinship, with seven low abundant genera displaying familial distribution patterns. While kinship and current cohabitation emerge as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother–daughter pairs, decreasing with increasing daughter’s age and being higher among cohabiting pairs than those living apart. Although rare, we detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.

Limited, but potentially functional translation of non-coding transcripts in the HEK293T cellular cytosol

Ribosome profiling has revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream ORFs, long non-coding RNAs, overlapping ORFs, ORFs in UTRs or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling and CRISPR-based screens showed that hundreds of ORFs derived from non-coding transcripts produce (micro)proteins, while other studies failed to find evidence for such types of non-canonical translation products. Here, we attempted to discover translation products from non-coding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. Theoretically, we show that our strategy facilitates the detection of translation events of transcripts from non-coding regions, but experimentally only find 19 peptides (less than 1% of all identified peptides) that might originate from such translation events. Virotrap based interactome analysis of two N-terminal proteoforms originating from non-coding regions finally showed the functional potential of these novel proteins.

Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome

Background and Objectives:Little is known of the functional potential of the gut microbiome in pediatric-onset multiple sclerosis (MS). We performed metagenomic analyses using stool samples from individuals with pediatric-onset MS and unaffected controls.Methods:Persons ≤21 years old enrolled in the Canadian Pediatric Demyelinating Disease Network providing a stool sample were eligible. Twenty MS patients (McDonald criteria) with symptom onset <18 years were matched to 20 controls by sex, age (±3 years), stool consistency, and race. Microbial taxonomy and functional potentials were estimated from stool sample-derived metagenomic reads and compared by disease status (MS vs controls) and disease-modifying drug (DMD) exposure using alpha-diversity, relative abundance, and prevalence using Wilcoxon rank-sum, ALDEx2 and Fisher’s exact tests, respectively.Results:Individuals with MS were aged 13.6 years (mean) at symptom onset and 8 were DMD naïve. Mean ages at stool sample were 16.1 and 15.4 years for MS and control participants, respectively; 80% were girls. Alpha-diversity of enzymes and proteins did not differ by disease or DMD status (p>0.20), but metabolic pathways, gene annotations and microbial taxonomy did. Individuals with MS (vs controls) exhibited higher methanogenesis prevalence (odds ratio=10, p=0.044), and Methanobrevibacter abundance (log2 fold-change[LFC]=1.7, p=0.0014), but lower homolactic fermentation abundance (LFC=-0.48, p=0.039). Differences by DMD status included lower phosphate butyryltransferase for DMD-naïve vs exposed MS patients (LFC=-1.0, p=0.033).Discussion:The gut microbiome’s functional potential and taxonomy differed between individuals with pediatric-onset MS versus controls, including higher prevalence of a methane-producing pathway from Archaea and depletion of the lactate fermentation pathway. DMD exposure was associated with butyrate-producing enzyme enrichment. Together these findings indicate that the gut microbiome of individuals with MS may have a disturbed functional potential.

Functional Potential of the Activity of the NGO Ukrainian Library Association for the Development of Library Studies

The article is devoted to disclosing the functional potential of the Ukrainian Library Association (UBA) as an open professional organization that focuses its efforts on developing librarianship in Ukraine and strengthening the democratic foundations of social development in the country. The use of a set of research methods, the main of which were socio-communicative, systemic and functional methods, as well as empirical methods of inclusive and external observation, led to consideration of ULA and its activities from the standpoint of fulfilling its obligations, its compliance with library community expectations. Implementing certain functions of the ULA and its activities is revealed as a system of interconnected forms and tools that complement each other, enhancing the final effect. The creation of the ULA is considered as a response of the professional community to the need to solve certain tasks and implement a number of functions in relation to the development of the national library business and society as a whole. For the first time, the functioning of UBA as an open adaptive leadership organization that implements organizational, mobilization-motivating, communication-coordination, information, educational, scientific-methodical, consolidating, representative, advocacy, compensatory functions is substantiated. The content of these functions is revealed. The purpose of the compensatory function is to provide libraries with the necessary theoretical and practical basis for the effective implementation of promising areas of activity in the absence of relevant approved guidelines at the national level. It was found that from the beginning of the ULA the statutory documents of the organization did not provide for the implementation of the compensatory function. Still, during the development of the association and expressing its focus on prompt and effective solutions to current problems in library development, its implementation became an important vector of the ULA.

The Role of Rhythm and Metre in the Style and Genre Formation in B. Rachmanin’s Prose

The issues of rhythm and metre in prose of 1960-1970s reflect the experiments of young writers not only within the form. The search for new genres and ways of expressing new content are diverse. The article deals with literary works by Boris Leonidovich Rachmanin, the author of poetry collections, stories, screenwriter, who boldly created a new internal form of his works using both possibilities of meter and rhythm in his prose, which was different from the works of his predecessors in the Silver Age or those who worked in the Russian diaspora. The analysis of works A Letter, The Action Takes Place on the Other Planet and others shows the functional potential of special rhythm and melody of prose in the individual style of the writer and also outlines semasiological approaches in the analysis of a literary work in general. Comparison of literary works by B. Rachmanin with the works by A. Bely or I.A. Bunin as his predecessors and Yustinas Martsinkevichus as his contemporary author gives an idea of the tradition Rachmanin inherited and the cultural style of the epoch in which the writer worked.