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

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

Morphology of obligate ectosymbionts reveals Paralaxus gen. nov.: A new circumtropical genus of marine stilbonematine nematodes

Stilbonematinae are a subfamily of conspicuous marine nematodes, distinguished by a coat of sulphur‐oxidizing bacterial ectosymbionts on their cuticle. As most nematodes, the worm hosts have a relatively simple anatomy and few taxonomically informative characters, and this has resulted in numerous taxonomic reassignments and synonymizations. Recent studies using a combination of morphological and molecular traits have helped to improve the taxonomy of Stilbonematinae but also raised questions on the validity of several genera. Here, we describe a new circumtropically distributed genus Paralaxus (Stilbonematinae) with three species: Paralaxus cocos sp. nov., P. bermudensis sp. nov. and P. columbae sp. nov. We used single worm metagenomes to generate host 18S rRNA and cytochrome c oxidase I (COI) as well as symbiont 16S rRNA gene sequences. Intriguingly, COI alignments and primer matching analyses suggest that the COI is not suitable for PCR‐based barcoding approaches in Stilbonematinae as the genera have a highly diverse base composition and no conserved primer sites. The phylogenetic analyses of all three gene sets, however, confirm the morphological assignments and support the erection of the new genus Paralaxus as well as corroborate the status of the other stilbonematine genera. Paralaxus most closely resembles the stilbonematine genus Laxus in overlapping sets of diagnostic features but can be distinguished from Laxus by the morphology of the genus‐specific symbiont coat. Our re‐analyses of key parameters of the symbiont coat morphology as character for all Stilbonematinae genera show that with amended descriptions, including the coat, highly reliable genus assignments can be obtained

Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2

Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans(1,2). Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host(3-6). We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax sp. H2 lives in symbiosis with two intracellular bacteria. One symbiont forms an undescribed genus in the Midichloriaceae (Rickettsiales)(7,8) and has a genomic repertoire similar to that of rickettsial parasites(9,10), but does not seem to express key genes for energy parasitism. Correlative image analyses and three-dimensional electron tomography revealed that this symbiont resides in the rough endoplasmic reticulum of its host's internal fibre cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations(11-13). This symbiont lives in the ventral epithelial cells of Trichoplax, probably metabolizes algal lipids digested by its host and has the capacity to supplement the placozoan's nutrition. Our study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter

Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses

Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations

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

Connecting structure and function from organisms to molecules in small-animal symbioses through chemo-histo-tomography

Our understanding of metabolic interactions between small symbi-otic animals and bacteria or parasitic eukaryotes that reside within their bodies is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect histologi -cal changes in host tissues induced by beneficial and parasitic (micro)organisms to the underlying metabolites. We addressed this challenge and developed chemo-histo-tomography (CHEMHIST), a culture-independent approach to connect anatomic structure and metabolic function in millimeter-sized symbiotic animals. CHEMHIST combines chemical imaging of metabolites based on mass spectrom-etry imaging (MSI) and microanatomy-based micro-computed X-ray tomography (micro-CT) on the same animal. Both high-resolution MSI and micro-CT allowed us to correlate the distribution of metab-olites to the same animal's three-dimensional (3D) histology down to submicrometer resolutions. Our protocol is compatible with tissue-specific DNA sequencing and fluorescence in situ hybridiza-tion for the taxonomic identification and localization of the associ-ated micro(organisms). Building CHEMHIST upon in situ imaging, we sampled an earthworm from its natural habitat and created an in-teractive 3D model of its physical and chemical interactions with bacteria and parasitic nematodes in its tissues. Combining MSI and micro-CT, we present a methodological groundwork for connecting metabolic and anatomic phenotypes of small symbiotic animals that often represent keystone species for ecosystem functioning

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

Asynchronous division by non-ring FtsZ in the gammaproteobacterial symbiont of <em>Robbea hypermnestra</em>

The reproduction mode of uncultivable microorganisms deserves investigation as it can largely diverge from conventional transverse binary fission. Here, we show that the rod-shaped gammaproteobacterium thriving on the surface of the Robbea hypermnestra nematode divides by FtsZ-based, non-synchronous invagination of its poles-that is, the host-attached and fimbriae-rich pole invaginates earlier than the distal one. We conclude that, in a naturally occurring animal symbiont, binary fission is host-oriented and does not require native FtsZ to polymerize into a ring at any septation stage