First detection of thiotrophic symbiont phylotypes in the pelagic marine environment

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.

Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis

Symbioses between eukaryotes and sulfur-oxidizing (thiotrophic) bacteria have convergently evolved multiple times. Although well described in at least eight classes of metazoan animals, almost nothing is known about the evolution of thiotrophic symbioses in microbial eukaryotes (protists). In this study, we characterized the symbioses between mouthless marine ciliates of the genus Kentrophoros, and their thiotrophic bacteria, using comparative sequence analysis and fluorescence in situ hybridization. Ciliate small-subunit rRNA sequences were obtained from 17 morphospecies collected in the Mediterranean and Caribbean, and symbiont sequences from 13 of these morphospecies. We discovered a new Kentrophoros morphotype where the symbiont-bearing surface is folded into pouch-like compartments, illustrating the variability of the basic body plan. Phylogenetic analyses revealed that all investigated Kentrophoros belonged to a single clade, despite the remarkable morphological diversity of these hosts. The symbionts were also monophyletic and belonged to a new clade within the Gammaproteobacteria, with no known cultured representatives. Each host morphospecies had a distinct symbiont phylotype, and statistical analyses revealed significant support for host-symbiont codiversification. Given that these symbioses were collected from two widely separated oceans, our results indicate that symbiotic associations in unicellular hosts can be highly specific and stable over long periods of evolutionary time.

Bacterial cell biology outside the streetlight

As much as vertical transmission of microbial symbionts requires their deep integration into the host reproductive and developmental biology, symbiotic lifestyle might profoundly affect bacterial growth and proliferation. This review describes the reproductive oddities displayed by bacteria associated - more or less intimately - with multicellular eukaryotes.

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla

The level of integration between associated partners can range from ectosymbioses to extracellular and intracellular endosymbioses, and this range has been assumed to reflect a continuum from less intimate to evolutionarily highly stable associations. In this study, we examined the specificity and evolutionary history of marine symbioses in a group of closely related sulphur-oxidizing bacteria, called Candidatus Thiosymbion, that have established ecto- and endosymbioses with two distantly related animal phyla, Nematoda and Annelida. Intriguingly, in the ectosymbiotic associations of stilbonematine nematodes, we observed a high degree of congruence between symbiont and host phylogenies, based on their ribosomal RNA (rRNA) genes. In contrast, for the endosymbioses of gutless phallodriline annelids (oligochaetes), we found only a weak congruence between symbiont and host phylogenies, based on analyses of symbiont 16S rRNA genes and six host genetic markers. The much higher degree of congruence between nematodes and their ectosymbionts compared to those of annelids and their endosymbionts was confirmed by cophylogenetic analyses. These revealed 15 significant codivergence events between stilbonematine nematodes and their ectosymbionts, but only one event between gutless phallodrilines and their endosymbionts. Phylogenetic analyses of 16S rRNA gene sequences from 50 Cand. Thiosymbion species revealed seven well-supported clades that contained both stilbonematine ectosymbionts and phallodriline endosymbionts. This closely coupled evolutionary history of marine ecto- and endosymbionts suggests that switches between symbiotic lifestyles and between the two host phyla occurred multiple times during the evolution of the Cand. Thiosymbion clade, and highlights the remarkable flexibility of these symbiotic bacteria.

All the microbiology nematodes can teach us

Be it their pervasiveness, experimental tractability or their impact on human health and agriculture, nematode–bacterium associations are far-reaching research subjects. Although the omics hype did not spare them and helped reveal mechanisms of communication and exchange between the associated partners, a huge amount of knowledge still awaits to be harvested from their study. Here, I summarize and compare the kind of research that has been already performed on the model nematode Caenorhabditis elegans and on symbiotic nematodes, both marine and entomopathogenic ones. The emerging picture highlights how complementing genetic studies with ecological ones (in the case of well-established genetic model systems such as C. elegans) and vice versa (in the case of the yet uncultured Stilbonematinae) will deepen our understanding of how microbial symbioses evolved and how they impact our environment.

Nematode–bacterium associations are major research subjects. Complementing genetic studies with ecological ones is necessary to boost our understanding of how microbial symbioses evolved and how they impact the environment.

Associated bacteria of different life stages of Meloidogyne incognita using pyrosequencing-based analysis

The root knot nematode (RKN), Meloidogyne incognita, belongs to the most damaging plant pathogens worldwide, and is able to infect almost all cultivated plants, like tomato. Recent research supports the hypothesis that bacteria often associated with plant-parasitic nematodes, function as nematode parasites, symbionts, or commensal organisms etc. In this study, we explored the bacterial consortia associated with M. incognita at different developmental stages, including egg mass, adult female and second-stage juvenile using the pyrosequencing approach. The results showed that Proteobacteria, with a proportion of 71-84%, is the most abundant phylum associated with M. incognita in infected tomato roots, followed by Actinobacteria, Bacteroidetes, Firmicutes etc. Egg mass, female and second-stage juvenile of M. incognita harbored a core microbiome with minor difference in communities and diversities. Several bacteria genera identified in M. incognita are recognized cellulosic microorganisms, pathogenic bacteria, nitrogen-fixing bacteria and antagonists to M. incognita. Some genera previously identified in other plant-parasitic nematodes were also found in tomato RKNs. The potential biological control microorganisms, including the known bacterial pathogens and nematode antagonists, such as Actinomycetes and Pseudomonas, showed the largest diversity and proportion in egg mass, and dramatically decreased in second-stage juvenile and female of M. incognita. This is the first comprehensive report of bacterial flora associated with the RKN identified by pyrosequencing-based analysis. The results provide valuable information for understanding nematode-microbiota interactions and may be helpful in the development of novel nematode-control strategies.

Phylogenetic confirmation of the genus Robbea (Nematoda: Desmodoridae, Stilbonematinae) with the description of three new species

The Stilbonematinae are a monophyletic group of marine nematodes that are characterized by a coat of thiotrophic bacterial symbionts. Among the ten known genera of the Stilbonematinae, the genus Robbea Gerlach 1956 had a problematic taxonomic history of synonymizations and indications of polyphyletic origin. Here we describe three new species of the genus, R. hypermnestra sp. nov., R. ruetzleri sp. nov. and R. agricola sp. nov., using conventional light microscopy, interference contrast microscopy and SEM. We provide 18S rRNA gene sequences of all three species, together with new sequences for the genera Catanema and Leptonemella. Both our morphological analyses as well as our phylogenetic reconstructions corroborate the genus Robbea. In our phylogenetic analysis the three species of the genus Robbea form a distinct clade in the Stilbonematinae radiation and are clearly separated from the clade of the genus Catanema, which has previously been synonymized with Robbea. Surprisingly, in R. hypermnestra sp. nov. all females are intersexes exhibiting male sexual characters. Our extended dataset of Stilbonematinae 18S rRNA genes for the first time allows the identification of the different genera, e.g. in a barcoding approach. http://zoobank.org/urn:lsid:zoobank.org:pub:D37C3F5A-CF2B-40E6-8B09-3C72EEED60B0.

Size-independent symmetric division in extraordinarily long cells

Two long-standing paradigms in biology are that cells belonging to the same population exhibit little deviation from their average size and that symmetric cell division is size limited. Here, ultrastructural, morphometric and immunocytochemical analyses reveal that two Gammaproteobacteria attached to the cuticle of the marine nematodes Eubostrichus fertilis and E. dianeae reproduce by constricting a single FtsZ ring at midcell despite being 45 μm and 120 μm long, respectively. In the crescent-shaped bacteria coating E. fertilis, symmetric FtsZ-based fission occurs in cells with lengths spanning one order of magnitude. In the E. dianeae symbiont, formation of a single functional FtsZ ring makes this the longest unicellular organism in which symmetric division has ever been observed. In conclusion, the reproduction modes of two extraordinarily long bacterial cells indicate that size is not the primary trigger of division and that yet unknown mechanisms time the localization of both DNA and the septum.

Known mechanisms that determine symmetric division-plane positioning during cell division are unlikely to operate effectively over very long distances. Pende et al. show that extraordinarily long Gammaproteobacteria divide symmetrically despite reaching 120 microns in length

Origins and evolutionary flexibility of chemosynthetic symbionts from deep-sea animals

Bathymodiolin mussels dominate hydrothermal vent and cold seep communities worldwide. Symbiotic associations with chemosynthetic sulfur- and methane-oxidizing bacteria that provide for their nutrition are the key to their ecological and evolutionary success. The current paradigm is that these symbioses evolved from two free-living ancestors, one methane-oxidizing and one sulfur-oxidizing bacterium. In contrast to previous studies, our phylogenetic analyses of the bathymodiolin symbionts show that both the sulfur and the methane oxidizers fall into multiple clades interspersed with free-living bacteria, many of which were discovered recently in metagenomes from marine oxygen minimum zones. We therefore hypothesize that symbioses between bathymodiolin mussels and free-living sulfur- and methane-oxidizing bacteria evolved multiple times in convergent evolution. Furthermore, by 16S rRNA sequencing and fluorescence in situ hybridization, we show that close relatives of the bathymodiolin symbionts occur on hosts belonging to different animal phyla: Raricirrus beryli, a terebellid polychaete from a whale-fall, and a poecilosclerid sponge from a cold seep. The host range within the bathymodiolin symbionts is therefore greater than previously recognized, confirming the remarkable flexibility of these symbiotic associations.

Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age

Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.