Specificity and transmission in two shallow water thiotrophic symbioses

Die ‚Domestikation‘ von chemosynthetischen mit chemoautotrophen schwefeloxidierenden Bakterien ist von Mitgliedern aus sechs eukaryoten Stämmen bekannt. Die Symbionten von meiofauna Wirtsgruppen aus subtidalen Flachwassersanden - Nematoden sowie darmlose Oligochaeten - formen eine Clade von Gammaproteobakterien. Die Ektosymbionten der Nematoden werden wahrscheinlich aus der Umwelt übertragen und ich zeige erstmals freilebende Verwandte aus küstenfernen Oberflächenwassern. Die Symbionten von Stilbonematinen wie Laxus oneistus sind in eine Schleimschichte eingebettet, die das an der Anheftung der Symbionten beteiligte Wirtslektin Mermaid enthält. Ich zeige, dass Stilbonema majum – ein mit L. oneistus gemeinsam vorkommender Stilbonematinae – von verwandten aber eigenständigen Symbionten besiedelt ist. Die Selektionsmechanismen für einen monospezifischen bakteriellen Überzug, der für Laxus oneistus und andere Stilbonematinae typisch ist, werden anhand von Mermaid-Transkripten beider Wirtsarten untersucht. Mehrere gefundene Isoformen, bei denen nur eine bis drei von 105 Aminosäuren im Zuckerbindungszentrum variieren, zeigen höhere Bindungsaktivitäten zu den Symbionten des Wirtes, bei dem sie gefunden wurden und wirken in der Anheftung und der spezifischen Selektion von Symbionten mit. Die Partner in thiotrophen Symbiosen schienen bisher nur aus zwei Klassen zu stammen – den Gamma- und Epsilonproteobakterien. Gemeinsam mit den darmlosen Oligochaeten und Nematoden findet man oft mund- und darmlose catenulide Plattwürmer der Gattung Paracatenula. Ich beschreibe die größte und häufigste Paracatenula Art aus dem Barriere Riff von Belize und zeige, dass die intrazellulären Symbionten der Paracatenula Plattwürmer eine neue Familie von thiotrophen Alphaproteobakterien darstellen. Die kongruenten Stammbäume der Wirte und Symbionten in dieser 500 Millionen Jahre alten Assoziation weisen auf eine vertikale Weitergabe Symbionten von einer Wirtsgeneration zu nächsten hin.Harnessing chemosynthetic bacteria is a recurring evolutionary strategy with six eukaryote phyla harboring chemoautotrophic sulfur-oxidizing symbionts. Meiofaunal host groups occurring in subtidal sands - nematodes and gutless oligochaetes - harbor thiotrophic Gammaproteobacteria that form a phylogenetic clade. For the nematode ectosymbionts environmental transmission is likely and I for the first time find closely related members of this clade in offshore surface seawater. The symbionts of stilbonematin species such as Laxus oneistus are embedded in host mucus containing the lectin Mermaid, which mediates symbiont attachment. I show that Stilbonema majum—another co-occurring stilbonematine nematode—is covered by related but phylogenetically distinct bacteria. The selection mechanisms that lead to single phylotypes specifically covering each host are investigated by transcriptome analyses of both hosts. I found several Mermaid isoforms that are differing in only one to three of 105 aa positions in the carbohydrate recognition domain and show higher affinities to the symbionts of the host they were found in, indicating that variation of isoforms plays a role in the attachment and specific selection of symbionts. In contrast to the broad host diversity, all thiotrophic symbionts apparently belong to two classes– the Gamma- and Epsilonproteobacteria. The mouthless catenulid flatworm genus Paracatenula co-occurs with nematode and gutless oligochaete hosts. I describe the largest and most abundant species from the Belize Barrier reef and show that the intracellular endosymbionts of all studied species form a novel clade of thiotrophic Alphaproteobacteria. In this ancient association host and symbiont phylogenies match indicating vertical transmission of the symbionts

Secure Full-Duplex Device-to-Device Communication

This paper considers full-duplex (FD) device-to-device (D2D) communications in a downlink MISO cellular system in the presence of multiple eavesdroppers. The D2D pair communicate sharing the same frequency band allocated to the cellular users (CUs). Since the D2D users share the same frequency as the CUs, both the base station (BS) and D2D transmissions interfere each other. In addition, due to limited processing capability, D2D users are susceptible to external attacks. Our aim is to design optimal beamforming and power control mechanism to guarantee secure communication while delivering the required quality-of-service (QoS) for the D2D link. In order to improve security, artificial noise (AN) is transmitted by the BS. We design robust beamforming for secure message as well as the AN in the worst-case sense for minimizing total transmit power with imperfect channel state information (CSI) of all links available at the BS. The problem is strictly non-convex with infinitely many constraints. By discovering the hidden convexity of the problem, we derive a rank-one optimal solution for the power minimization problem.Comment: Accepted in IEEE GLOBECOM 2017, Singapore, 4-8 Dec. 201

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium

Background: Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species. Results: In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted. Conclusions: We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources

Rotational Subgroup Voting and Pose Clustering for Robust 3D Object Recognition

It is possible to associate a highly constrained subset of relative 6 DoF poses between two 3D shapes, as long as the local surface orientation, the normal vector, is available at every surface point. Local shape features can be used to find putative point correspondences between the models due to their ability to handle noisy and incomplete data. However, this correspondence set is usually contaminated by outliers in practical scenarios, which has led to many past contributions based on robust detectors such as the Hough transform or RANSAC. The key insight of our work is that a single correspondence between oriented points on the two models is constrained to cast votes in a 1 DoF rotational subgroup of the full group of poses, SE(3). Kernel density estimation allows combining the set of votes efficiently to determine a full 6 DoF candidate pose between the models. This modal pose with the highest density is stable under challenging conditions, such as noise, clutter, and occlusions, and provides the output estimate of our method. We first analyze the robustness of our method in relation to noise and show that it handles high outlier rates much better than RANSAC for the task of 6 DoF pose estimation. We then apply our method to four state of the art data sets for 3D object recognition that contain occluded and cluttered scenes. Our method achieves perfect recall on two LIDAR data sets and outperforms competing methods on two RGB-D data sets, thus setting a new standard for general 3D object recognition using point cloud data.Comment: Accepted for International Conference on Computer Vision (ICCV), 201

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias.

The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria as seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that support for the Cnidaria + Bilateria clade can be assigned to this source of systematic error. In interpreting these results, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).

Assie A, Leisch N, Meier DV, et al. Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria). The ISME journal. 2019;14(1):104-122.Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cyclegenes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment

Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria

Members of the gammaproteobacterial clade SUP05 couple water column sulfide oxidation to nitrate reduction in sulfidic oxygen minimum zones (OMZs). Their abundance in offshore OMZ waters devoid of detectable sulfide has led to the suggestion that local sulfate reduction fuels SUP05-mediated sulfide oxidation in a so-called “cryptic sulfur cycle”. We examined the distribution and metabolic capacity of SUP05 in Peru Upwelling waters, using a combination of oceanographic, molecular, biogeochemical and single-cell techniques. A single SUP05 species, UThioglobus perditus, was found to be abundant and active in both sulfidic shelf and sulfide-free offshore OMZ waters. Our combined data indicated that mesoscale eddy-driven transport led to the dispersal of UT. perditus and elemental sulfur from the sulfidic shelf waters into the offshore OMZ region. This offshore transport of shelf waters provides an alternative explanation for the abundance and activity of sulfide-oxidizing denitrifying bacteria in sulfide-poor offshore OMZ waters

Microanatomy of the trophosome region of Paracatenula cf. polyhymnia (Catenulida, Platyhelminthes) and its intracellular symbionts

Marine catenulid platyhelminths of the genus Paracatenula lack mouth, pharynx and gut. They live in a symbiosis with intracellular bacteria which are restricted to the body region posterior to the brain. The symbiont-housing cells (bacteriocytes) collectively form the trophosome tissue, which functionally replaces the digestive tract. It constitutes the largest part of the body and is the most important synapomorphy of this group. While some other features of the Paracatenula anatomy have already been analyzed, an in-depth analysis of the trophosome region was missing. Here, we identify and characterize the composition of the trophosome and its surrounding tissue by analyzing series of ultra-thin cross-sections of the species Paracatenula cf. polyhymnia. For the first time, a protonephridium is detected in a Paracatenula species, but it is morphologically reduced and most likely not functional. Cells containing needle-like inclusions in the reference species Paracatenula polyhymnia Sterrer and Rieger, 1974 were thought to be sperm, and the inclusions interpreted as the sperm nucleus. Our analysis of similar cells and their inclusions by EDX and Raman microspectroscopy documents an inorganic spicule consisting of a unique magnesium–phosphate compound. Furthermore, we identify the neoblast stem cells located underneath the epidermis. Except for the modifications due to the symbiotic lifestyle and the enigmatic spicule cells, the organization of Paracatenula cf. polyhymnia conforms to that of the Catenulida in all studied aspects. Therefore, this species represents an excellent model system for further studies of host adaptation to an obligate symbiotic lifestyle

Bacterial Symbiosis Maintenance in the Asexually Reproducing and Regenerating Flatworm Paracatenula galateia

Bacteriocytes set the stage for some of the most intimate interactions between animal and bacterial cells. In all bacteriocyte possessing systems studied so far, de novo formation of bacteriocytes occurs only once in the host development, at the time of symbiosis establishment. Here, we present the free-living symbiotic flatworm Paracatenula galateia and its intracellular, sulfur-oxidizing bacteria as a system with previously undescribed strategies of bacteriocyte formation and bacterial symbiont transmission. Using thymidine analogue S-phase labeling and immunohistochemistry, we show that all somatic cells in adult worms – including bacteriocytes – originate exclusively from aposymbiotic stem cells (neoblasts). The continued bacteriocyte formation from aposymbiotic stem cells in adult animals represents a previously undescribed strategy of symbiosis maintenance and makes P. galateia a unique system to study bacteriocyte differentiation and development. We also provide morphological and immunohistochemical evidence that P. galateia reproduces by asexual fragmentation and regeneration (paratomy) and, thereby, vertically transmits numerous symbiont-containing bacteriocytes to its asexual progeny. Our data support the earlier reported hypothesis that the symbiont population is subjected to reduced bottleneck effects. This would justify both the codiversification between Paracatenula hosts and their Candidatus Riegeria symbionts, and the slow evolutionary rates observed for several symbiont genes

gbtools: Interactive Visualization of Metagenome Bins in R

Improvements in DNA sequencing technology have increased the amount and quality of sequences that can be obtained from metagenomic samples, making it practical to extract individual microbial genomes from metagenomic assemblies (binning). However, while many tools and methods exist for unsupervised binning with various statistical algorithms, there are few options for visualizing the results, even though visualization is vital to exploratory data analysis. We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of annotations, including taxonomic assignments from conserved marker genes or SSU rRNA genes, can be imported simultaneously; users can choose which annotations to plot. Bins can be manually defined from plots, or be imported from third-party binning tools and overlaid onto plots, such that results from different methods can be compared side-by-side. gbtools reports summary statistics of bins including marker gene completeness, and allows the user to add or subtract bins with each other. We illustrate some of the functions available in gbtools with two examples: the metagenome of Olavius algarvensis, a marine oligochaete worm that has up to five bacterial symbionts, and the metagenome of a synthetic mock community comprising 64 bacterial and archaeal strains. We show how instances of poor automated binning, sequencer GC% bias, and variation between samples can be quickly diagnosed by visualization, and demonstrate how the results from different binning tools can be combined and refined to yield manually-curated bins with higher completeness. gbtools is open-source and written in R. The software package, documentation, and example data are available freely online at https://github.com/kbseah/genome-bin-tools