Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea

Marine sponges are excellent examples of invertebrate–microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.

Host species determine symbiotic community composition in Antarctic sponges (Porifera: Demospongiae)

The microbiota of four Antarctic sponges, Dendrilla antarctica, Sphaerotylus antarcticus, Mycale acerata, and Hemigellius pilosus, collected at two South Shetland Islands and at two locations in the Antarctic Peninsula separated by ca. 670 km, were analyzed together with surrounding seawater. We used high throughput sequencing of the V4 region of the 16S rRNA gene common to Bacteria and Archaea to investigate the microbial diversity and community composition. Our study reveals that sponge-associated prokaryote communities are consistently detected within a particular sponge species regardless of the collection site. Their community structure and composition are typical of low microbial abundance (LMA) sponges. We conclude that prokaryote communities from Antarctic sponges are less diverse and differ in their composition compared to those in the water column. Microbiome analysis indicates that Antarctic sponges harbor a strict core consisting of seven OTUs, and a small variable community comprising several tens of OTUs. Two abundant prokaryotes from the variable microbiota that are affiliated to the archaeal and bacterial phyla Thaumarchaeota and Nitrospirae may be involved in the sponge nitrification process and might be relevant components of the nitrogen cycling in Antarctica. The likely generalist nature of dominant microbes and the host-specific structure of symbiont communities suggest that these Antarctic sponges represent different ecological niches for particular microbial enrichments.

Mechanism Design for Multi-Type Housing Markets with Acceptable Bundles

We extend the Top-Trading-Cycles (TTC) mechanism to select strict core allocations for housing markets with multiple types of items, where each agent may be endowed and allocated with multiple items of each type. In doing so, we advance the state of the art in mechanism design for housing markets along two dimensions: First, our setting is more general than multi-type housing markets (Moulin 1995; Sikdar, Adali, and Xia 2017) and the setting of Fujita et al. (2015). Further, we introduce housing markets with acceptable bundles (HMABs) as a more general setting where each agent may have arbitrary sets of acceptable bundles. Second, our extension of TTC is strict core selecting under the weaker restriction on preferences of CMI-trees, which we introduce as a new domain restriction on preferences that generalizes commonly-studied languages in previous works.

Core Stability in Hedonic Games among Friends and Enemies: Impact of Neutrals

We investigate hedonic games under enemies aversion and friends appreciation, where every agent considers other agents as either a friend or an enemy. We extend these simple preferences by allowing each agent to also consider other agents to be neutral. Neutrals have no impact on her preference, as in a graphical hedonic game.Surprisingly, we discover that neutral agents do not simplify matters, but cause complexity. We prove that the core can be empty under enemies aversion and the strict core can be empty under friends appreciation. Furthermore, we show that under both preferences, deciding whether the strict core is non-empty, is NP^NP-complete. This complexity extends to the core under enemies aversion. We also show that under friends appreciation, we can always find a core stable coalition structure in polynomial time.

The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

ABSTRACT Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives. IMPORTANCE A comparative analysis of 1,130 Burkholderia genomes identified unique markers for many named species, including the human pathogens B. pseudomallei and B. mallei . Due to core genome reduction and signature erosion, only 38 targets specific to B. pseudomallei /mallei were identified. By using only public genomes, a larger number of markers were identified, due to undersampling, and this larger number represents the potential for false positives. This analysis has implications for the design of diagnostics for other species where the genomic space of the target and/or closely related species is not well defined.

A Solution for General Exchange Markets with Indivisible Goods when Indifferences are Allowed

It is well known that the core of an exchange market with indivisible goods is always non empty, although it may contain Pareto inefficient allocations. The strict core solves this shortcoming when indifferences are not allowed, but when agents' preferences are weak orders the strict core may be empty. On the other hand, when indifferences are allowed, the core or the strict core may fail to be stable sets, in the von Neumann and Morgenstern sense.We introduce a new solution concept that improves the behaviour of the strict core, in the sense that it solves the emptiness problem of the strict core when indifferences are allowed in the individuals' preferences and whenever the strict core is non-empty, our solution is included in it. We define our proposal, the MS-set, by using a stability property (m-stability) that the strict core fulfills. Finally, we provide a min-max interpretation for this new solution.