Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages

Bacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novel Arthrobacter globiformis phages–Powerpuff, Lego, and YesChef–which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ, Microbacterium Cluster EH, and the former Microbacterium singleton Zeta1847 exhibited low nucleotide similarity. However, their gene content similarity was in excess of the recently adopted Microbacterium clustering parameter, which ultimately resulted in the reassignment of Zeta1847 to Cluster EH. This finding further highlights the importance of using multiple metrics to capture phage relatedness. Additionally, Clusters AZ and EH phages encode a shared integrase indicative of a lysogenic life cycle. In the first experimental verification of a Cluster AZ phage’s life cycle, we show that phage Powerpuff is a true temperate phage. It forms stable lysogens that exhibit immunity to superinfection by related phages, despite lacking identifiable repressors typically required for lysogenic maintenance and superinfection immunity. The ability of phage Powerpuff to undergo and maintain lysogeny suggests that other closely related phages may be temperate as well. Our findings provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera and demonstrate the continued need for verification and characterization of life cycles in newly isolated phages.

Introducing a Novel, Broad Host Range Temperate Phage Family Infecting Rhizobium leguminosarum and Beyond

Temperate phages play important roles in bacterial communities but have been largely overlooked, particularly in non-pathogenic bacteria. In rhizobia the presence of temperate phages has the potential to have significant ecological impacts but few examples have been described. Here we characterize a novel group of 5 Rhizobium leguminosarum prophages, capable of sustaining infections across a broad host range within their host genus. Genome comparisons identified further putative prophages infecting multiple Rhizobium species isolated globally, revealing a wider family of 10 temperate phages including one previously described lytic phage, RHEph01, which appears to have lost the ability to form lysogens. Phylogenetic discordance between prophage and host phylogenies suggests a history of active mobilization between Rhizobium lineages. Genome comparisons revealed conservation of gene content and order, with the notable exception of an approximately 5 kb region of hypervariability, containing almost exclusively hypothetical genes. Additionally, several horizontally acquired genes are present across the group, including a putative antirepressor present only in the RHEph01 genome, which may explain its apparent inability to form lysogens. In summary, both phenotypic and genomic comparisons between members of this group of phages reveals a clade of viruses with a long history of mobilization within and between Rhizobium species.

Morphology and reproduction in the Hapalocarcinus marsupialis Stimpson, 1859 species complex (Decapoda: Brachyura: Cryptochiridae)

Symbiotic relationships contribute considerably to the high biodiversity found on coral reefs. Coral-dwelling gall crabs (Cryptochiridae) represent a prime example of coral-associated invertebrates that exhibit obligate relationships with their host. The induction of a skeletal modification in the coral, used as a dwelling by the crab, is the most remarkable aspect of this close association. Here we examined Hapalocarcinus marsupialisStimpson, 1859, collected from Pocillopora and Stylophora corals in the Saudi Arabian Red Sea. Specimens were DNA barcoded, and five distinct clades were revealed, providing further evidence for the hypothesis that H. marsupialis is a species complex. Divergence (COI) between the clades ranged from 3.2 to 15.7%. The putative species were tested for differences in morphology and reproduction. Crabs were examined regarding morphometric characters (carapace length and width, pleon (abdomen), chelae, and growth patterns) and reproductive traits. The data were pooled and analysed by host genus and putative species, which revealed significant differences for most of the measured variables in female crabs. Specimens retrieved from Pocillopora were significantly larger (up to 49 %) and had higher fecundity than those inhabiting Stylophora. For reproductive output (RO) no differences at species- or host-genus level were detected. The average RO of ~70% over all specimens is high compared to other brachyurans, supporting the assumption that symbiotic brachyurans invest more energy in reproduction than their free-living counterparts. Discrepancies with published data on growth and reproduction of Hapalocarcinus are discussed. Our results demonstrate the usefulness of morphometric traits and fecundity in separating the clades in the H. marsupialis complex, and prepare the ground for further morphometric studies on the genus and other symbiotic brachyurans. Moreover, it highlights the need to check for the presence of cryptic species when studying aspects of the biology of a species.

Co-occurrence in ant primary parasitoids: a Camponotus rectangularis colony as host of two eucharitid wasp genera

Different assemblages of parasitoids may attack a given host species and non-random distribution patterns in parasitoid species assemblages have been reported on various occasions, resulting in co-occurrence at the population, colony, or even individual host levels. This is the case for different closely related species of eucharitid wasps (a family of specialized ant parasitoids) sharing similar niches and co-occurring on the same host at different levels. Here we reviewed all known associations between eucharitid wasps and the ant host genus Camponotus Mayr, 1861 and reported new ant-parasitoid associations. In addition, we report a new case of co-occurrence in eucharitid wasps, at the host colony level, involving a new undescribed species of Pseudochalcura Ashmead, 1904 and an unidentified species of Obeza Heraty, 1985, which attack the common but very poorly known neotropical arboreal ant Camponotus rectangularis Emery, 1890. Most attacks were solitary, but various cocoons were parasitized by two (16%) or three (8%) parasitoids. Globally, parasitism prevalence was very low (3.7%) but showed an important variability among samples. Low parasitism prevalence along with host exposure to parasitoid attack on host plants and overlapping reproductive periods of both parasitoid species may have allowed the evolution of co-occurrence. We also provided some additional data regarding the host ant nesting habits, the colony composition and new symbiotic associations with membracids and pseudococcids. The seemingly polydomous nesting habits of C. rectangularis could play a part in the reduction of parasitism pressure at the population level and, combined with occasionally important local parasitism rates, could also contribute to some parts of the colonies escaping from parasites, polydomy possibly representing an effective parasitism avoidance trait.

Morphology and phylogenetic analyses reveal Montagnula puerensis sp. nov. (Didymosphaeriaceae, Pleosporales) from southwest China

A dead woody sample of Acer sp. with fungal fruiting bodies was collected in Pu’er City of Yunnan Province. Multigene phylogenetic analyses of LSU, ITS, SSU, and tef1-α sequence data showed that our collection belongs to Montagnula and is well separated from all other extant species. Montagnula puerensis is compared with all extant species by morphological characteristics, culture characteristics, host, and location information and is the first report of Montagnula from the host genus Acer.

The Hidden Diversity of Diatrypaceous Fungi in China

In this study, we investigated the diversity of diatrypaceous fungi from six regions in China based on morpho-molecular analyses of combined ITS and tub2 gene regions. We accept 23 genera in Diatrypaceae with 18 genera involved in the phylogram, and the other five genera are lacking living materials with sequences data. Eleven species included in four genera (viz. Allocryptovalsa, Diatrype, Diatrypella, and Eutypella) have been isolated from seven host species, of which nine novel species (viz. Allocryptovalsa castaneae, A. castaneicola, Diatrype betulae, D. castaneicola, D. quercicola, Diatrypella betulae, Da. betulicola, Da. hubeiensis, and Da. shennongensis), a known species of Diatrypella favacea, and a new record of Eutypella citricola from the host genus Morus are included. Current results show the high diversity of Diatrypaceae which are wood-inhabiting fungi in China.

Morphology and phylogeny of a new species, Pseudocercospora haldinae (Mycosphaerellaceae) on Haldina cordifolia from India

Pseudocercospora haldinae, a new anamorphic foliicolous hyphomycetous fungus discovered on living leaves of Haldina cordifolia (Rubiaceae) is taxonomically described and illustrated. This species is compared with closely related species of Pseudocercospora and other dematiaceous cercosporoid forms reported on the same host genus. The phylogeny of this species has been inferred from partial nuclear ribosomal 28S large subunit (LSU) and complete internal transcribed spacer (ITS) rDNA sequence data. On the basis of LSU, P. haldinae represents characteristic features of Pseudocercospora s. str. and did not form red crystals when cultivated on agar media.

A new species of Echidnodella (Asterinales, Lembosiaceae) from Western Ghats of Kerala State, India

Black mildews belong to a wide range of leaf inhabiting fungal genera, which causes severe damage to the living leaves, affect photosynthetic efficiency, cause physiological imbalances, and reduces the plants’ aesthetic value. During a survey of foliicolous fungi in Vagamon hills of Kerala state’s Western Ghats region, an endemic medicinal plant Xanthophyllum arnottianum was found infected with an undescribed species of black mildew causing fungal genus Echidnodella. Their mycelia are non-appressoriate and devoid of hypostroma. Thyriothecia are oval, ellipsoidal, X or Y shaped, elongated producing eight uniseptate brown coloured ascospores in each bitunicate asci. Echidnodella was distinguished from the allied genus Echidnodes in the absence of paraphyses and from the genera Lembosia and Morenoella in the lack of appressoria (haustoria). This new species, Echidnodella vagamonensis is described and illustrated in detail to provide the consolidated account of the species known on this host genus.

Phakopsora ampelopsidis (Ampelopsis rust fungus).

As currently defined (Ono, 2000), the rust fungus P. ampelopsidis is a pathogen of hosts in the genus Ampelopsis and perhaps in related genera in the Vitaceae, but not of the cultivated grapevine species of Vitis or the ornamental species in Parthenocissus. Plants in Ampelopsis occur in Asia from Japan to Turkey as well as in North America (USDA-ARS, 2009), but the rust is not known in Europe, and has not been reported on Ampelopsis in the Americas. Only in eastern Asia, where the medicinal uses of Ampelopsis species are being investigated (Kim et al., 2007; Zhang et al., 2008), is this rust a potential problem. It is most likely to be spread by aerial dispersal of urediniospores to nearer parts of Asia, where species in the host genus are distributed.

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Background In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. Results Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host’s immune system. Conclusions This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy.