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Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites.Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host interactions thus far remain unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable,Chlamydiaerelative abundances of up to 18.7% of bacteria. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these,CandidatusSororchlamydiaceae shares a common ancestor withChlamydiaceaeanimal pathogens, suggesting long-term co-evolution with animals. Based on gene content, sponge-associated chlamydiae resemble members from the same family more than sponge-associated chlamydiae of other families, and have greater metabolic versatility than known chlamydial animal pathogens. Sponge-associated chlamydiae are also enriched in genes for degrading diverse compounds found in sponges. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis acrossChlamydiae, which may represent an unexplored source of novel natural products. This finding suggests that Chlamydiaemembers may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of theChlamydiaephylum on marine ecosystems.

Natural product discovery by isolation and structure elucidation is a laborious task often requiring ample quantities of biological starting material and frequently resulting in the rediscovery of previously known compounds. However, peptides are a compound class amenable to an alternative genomic, transcriptomic, and in silico discovery route by similarity searches of known peptide sequences against sequencing data. Based on the sequences of barrettides A and B, we identified five new barrettide sequences (barrettides C–G) predicted from the North Atlantic deep-sea demosponge Geodia barretti (Geodiidae). We synthesized, folded, and investigated one of the newly described barrettides, barrettide C (NVVPCFCVEDETSGAKTCIPDNCDASRGTNP, disulfide connectivity I–IV, II–III). Co-elution experiments of synthetic and sponge-derived barrettide C confirmed its native conformation. NMR spectroscopy and the anti-biofouling activity on larval settlement of the bay barnacle Amphibalanus improvisus (IC50 0.64 μM) show that barrettide C is highly similar to barrettides A and B in both structure and function. Several lines of evidence suggest that barrettides are produced by the sponge itself and not one of its microbial symbionts.

Cyclotides are cyclic peptides produced by plants. Due to their insecticidal properties, they are thought to be involved in host defense. Violets produce complex mixtures of cyclotides, that are characteristic for each species and variable in different environments. Herein, we utilized mass spectrometry (LC–MS, MALDI-MS), transcriptomics and biological assays to investigate the diversity, differences in cyclotide expression based on species and different environment, and antimicrobial activity of cyclotides found in violets from the Canary Islands. A wide range of different habitats can be found on these islands, from subtropical forests to dry volcano peaks at high altitudes. The islands are inhabited by the endemic Viola palmensis, V. cheiranthifolia, V. anagae and the common V. odorata. The number of cyclotides produced by a given species varied in plants from different environments. The highest diversity was noted in V. anagae which resides in subtropical forest and the lowest in V. cheiranthifolia from the Teide volcano. Transcriptome sequencing and LC–MS were used to identify 23 cyclotide sequences from V. anagae. Cyclotide extracts exhibited antifungal activities with the lowest minimal inhibitory concentrations noted for V. anagae (15.62 μg/ml against Fusarium culmorum). The analysis of the relative abundance of 30 selected cyclotides revealed patterns characteristic to both species and populations, which can be the result of genetic variability or environmental conditions in different habitats. The current study exemplifies how plants tailor their host defense peptides for various habitats, and the usefulness of cyclotides as markers for chemosystematics.

Natural product discovery by isolation and structure elucidation is a laborious task often requiring ample quantities of biological starting material and frequently resulting in the rediscovery of previously known compounds. However, peptides are a compound class amenable to an alternative genomic, transcriptomic, and in silico discovery route by similarity searches of known peptide sequences against sequencing data. Based on the sequences of barrettides A and B, we identified five new barrettide sequences (barrettides C−G) predicted from the North Atlantic deep-sea demosponge Geodia barretti (Geodiidae). We synthesized, folded, and investigated one of the newly described barrettides, barrettide (NVVPCFCVEDETSGAKTCIPDNCDASRGTNP, disulfide connectivity I−IV, II−III). Co-elution experiments of synthetic and sponge-derived barrettide C confirmed its native conformation. NMR spectroscopy and the anti-biofouling activity on larval settlement of the bay barnacle Amphibalanus improvisus (IC50 0.64 μM) show that barrettide C is highly similar to barrettides A and B in both structure and function. Several lines of evidence suggest that barrettides are produced by the sponge itself and not one of its microbial symbionts., K.S. thanks the Swedish pharmaceutical society (Apotekarsocieteten) for funds provided to purchase reagents for SPPS. K.S., A.R., and P.C. acknowledge SponGES; SponGES has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 679849.

The tropical ginger genus Amomum (Zingiberaceae) has always posed challenges for classification based on morphological characters. Previous molecular phylogenetic studies showed Amomum to be paraphyletic but limited sampling and absence of the data of the type Amomum subulatum made it impossible to resolve the paraphyly and make nomenclatural changes. Here, Amomum is further investigated in a multi-marker phylogenetic framework using matK and nrITS including multiple accessions of the type, the genus Elettaria and additional accessions of Amomum, Alpinia, Elettariopsis, Geocharis, Geostachys and Hornstedtia. Amomum is shown to consist of nine clades and Alpinia of six. The genera Elettaria, Elettariopsis, Plagiostachys, and species in Hornstedtia are nested within these clades. Morphological studies of species previously subsumed in Amomum support recognition of new genera that correspond to well-delimited clades in the phylogenetic framework presented here. Recircumscription of the paraphyletic genus Amomum facilitates identification and creates nomenclatural stability. Three genera, Conamomum, Meistera and Wurfbainia, are resurrected, and three new genera Epiamomum, Lanxangia and Sundamomum are described, together with a key to the genera and a nomenclatural synopsis placing 384 specific names (incl. all synonyms) into the new generic framework. Of these 129 represent new combinations and 3 are replacement names. Types of Geocharis and Geostachys are designated. Further studies and specific sampling will be needed to resolve other branches of Alpinioideae containing other polyphyletic genera. © International Association for Plant Taxonomy (IAPT) 2018, all rights reserved.

Aim: The Cucurbitaceae genus Trichosanthes is widespread in Asia and Australia, and previous studies have shown that the genus originated in Asia, and that three independent lineages dispersed through the Sunda archipelago to Australasia. The timing and routes of these three dispersals, as well as the dispersal of two widespread species found in Australia and New Guinea, were investigated. Location: Sunda–Sahul dispersals with a focus on New Guinea and Australia. Methods: A combined dataset of nuclear ribosomal (ITS1–5.8S–ITS2) and plastid DNA (matK, ndhF, rpl20–rps12, rps16) was used for maximum likelihood and Bayesian phylogenetic analysis to infer the relationships of the studied taxa. A fossil-calibrated molecular dating was used to time the dispersal events, and a biogeographical analysis was used to study the origin and dispersal of the genus. Results: The two widespread species, T. pilosa and T. cucumerina, form monophyletic groups in Australia, suggesting single dispersals. Molecular dating analysis dates four of the dispersal events to the Miocene, and two to the Oligo-Miocene boundary and the initial Sahul shelf collision with the Philippine plate. Most known Sahul–Philippine dispersals concern species that migrated from the Sahul shelf, whereas dispersals south are fewer. Southward Miocene dispersals include species that were present on the Sunda shelf before the tectonic formation of the Makassar Straits. All lineages that dispersed to Australasia have undergone extensive diversification following dispersal. Lineages adapted to wet tropical climates have speciated mostly in New Guinea, and lineages adapted to monsoon tropical climates have speciated mostly in northern Australia. Main conclusions: Dispersals in Trichosanthes pre-date human colonization of Australasia, suggesting natural long-distance dispersal and establishment of all lineages. Diversification within lineages found in both Australia and New Guinea is limited, corroborating frequent land connections between these areas during the Pleistocene. Sunda–Sahul dispersals are likely to have been more common through time than previously suggested, especially in genera with floating fruit such as Trichosanthes.