The fitness of the Brazilian damsel <Emphasis Type="Italic">Stegastes fuscus</Emphasis> is increased by sharing the territory with the dusky grouper <Emphasis Type="Italic">Epinephelus marginatus</Emphasis>

Stegastes fuscus and Epinephelus marginatus are known for co-habiting shelters. The damselfish S. fuscus uses the territory for nesting and must protect its eggs from grazers; the grouper E. marginatus is an omnivorous sit-and-wait predator. This study aims to evaluate the effect of juvenile groupers on the reproductive success of the Brazilian damsel. Twenty-five hours of underwater observations were done in São Sebastião and Ilhabela, Northern shore of São Paulo, Brazil. Fitness increase was measured by the egg-clutch area and number of contributing females in 130 nests shared by groupers and another 130 where damselfishes stood alone. An egg predator crab was placed into the damselfish territory, and behavioural responses during 2 min were recorded for nests with or without E. marginatus, 80 replicates each. Nests shared by the dusky groupers had more eggs and received eggs from more females too. While fathers who were alone in the territory had to deal with the egg predator crab, in shared nests, the grouper would take care of the intruder, sometimes feeding on it. Therefore, the Brazilian damsel may benefit from the presence of the dusky grouper by increasing the fitness and diminishing the costs of parental care.     

Genetic diversity of free-living <Emphasis Type="Italic">Symbiodinium</Emphasis> in the Caribbean: the importance of habitats and seasons

Although reef corals are dependent of the dinoflagellate Symbiodinium, the large majority of corals spawn gametes that do not contain their vital symbiont. This suggests the existence of a pool of Symbiodinium in the environment, of which surprisingly little is known. Reefs around Curaçao (Caribbean) were sampled for free-living Symbiodinium at three time periods (summer 2009, summer 2010, and winter 2010) to characterize different habitats (water column, coral rubble, sediment, the macroalgae Halimeda spp., Dictyota spp., and Lobophora variegata, and the seagrass Thalassia testudinum) that could serve as environmental sources of symbionts for corals. We detected the common clades of Symbiodinium that engage in symbiosis with Caribbean coral hosts A, B, and C using Symbiodinium-specific primers of the hypervariable region of the chloroplast 23S ribosomal DNA gene. We also discovered clade G and, for the first time in the Caribbean, the presence of free-living Symbiodinium clades F and H. Additionally, this study expands the habitat range of free-living Symbiodinium as environmental Symbiodinium was detected in T. testudinum seagrass beds. The patterns of association between free-living Symbiodinium types and habitats were shown to be complex. An interesting, strong association was seen between some clade A sequence types and sediment, suggesting that sediment could be a niche where clade A radiated from a free-living ancestor. Other interesting relationships were seen between sequence types of Symbiodinium clade C with Halimeda spp. and clades B and F with T. testudinium. These relationships highlight the importance of some macroalgae and seagrasses in hosting free-living Symbiodinium. Finally, studies spanning beyond a 1-yr cycle are needed to further expand on our results in order to better understand the variation of Symbiodinium in the environment through time. All together, results presented here showed that the great diversity of free-living Symbiodinium has a dynamic distribution across habitats and time.     

<Emphasis Type="Italic">Megaviridae</Emphasis>-like particles associated with <Emphasis Type="Italic">Symbiodinium</Emphasis> spp. from the endemic coral <Emphasis Type="Italic">Mussismilia braziliensis</Emphasis>

Coral reefs are one of the most dynamic and productive marine ecosystems. The coral holobiont consists of the coral animal and a variety of associated microorganisms that include symbiotic dinoflagellates of the genus Symbiodinium, bacteria, archaea, fungi and viruses. The interactions among these components are crucial for coral health and, consequently, to the coral reef resilience to disturbance. Environmental stressors such as elevated temperature, high irradiance and ultraviolet (UV) radiation can lead to the breakdown of the coral-Symbiodinium symbiosis in a phenomenon known as “coral bleaching”. The present study provides evidence for virus-like particles (VLPs) induced in UV-irradiated Symbiodinium spp. cultures (clades A and C) that were isolated from the coral Mussismilia braziliensis, suggesting a latent viral infection in these strains. Scanning and transmission electron microscopy images of the UV stressed cultures revealed the presence of giant (ca. 450 nm) and small (ca. 40 nm) VLPs. Morphological features link the giant VLPs to the family Megaviridae. Symbiodinium spp. Megaviridae giant viruses and other associated viruses may represent dynamic forces driving and influencing health of the coral holobiont.     

<Emphasis Type="Italic">SnRK2</Emphasis> Homologs in <Emphasis Type="Italic">Gossypium</Emphasis> and <Emphasis Type="Italic">GhSnRK2.6</Emphasis> Improved Salt Tolerance in Transgenic Upland Cotton and <Emphasis Type="Italic">Arabidopsis</Emphasis>

SnRK2s are a large family of plant-specific protein kinases, which play important roles in multiple abiotic stress responses in various plant species. But the family in Gossypium has not been well studied. Here, we identified 13, 10, and 13 members of the SnRK2 family from Gossypium raimondii, Gossypium arboreum, and Gossypium hirsutum, respectively, and analyzed the locations of SnRK2 homologs in chromosomes based on genome data of cotton species. Phylogenetic tree analysis of SnRK2 proteins showed that these families were classified into three groups. All SnRK2 genes were comprised of nine exons and eight introns, and the exon distributions and the intron phase of homolog genes among different cotton species were analogous. Moreover, GhSnRK2.6 was overexpressed in Arabidopsis and upland cotton, respectively. Under salt treatment, overexpressed Arabidopsis could maintain higher biomass accumulation than wild-type plants, and GhSnRK2.6 overexpression in cotton exhibited higher germination rate than the control. So, the gene GhSnRK2.6 could be utilized in cotton breeding for salt tolerance.     

Taxonomic hierarchy of the phylum <Emphasis Type="Italic">Firmicutes</Emphasis> and novel <Emphasis Type="Italic">Firmicutes</Emphasis> species originated from various environments in Korea

This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and Daejeon.     

Molecular evidence for hybridization between invasive <Emphasis Type="Italic">Solidago canadensis</Emphasis> and native <Emphasis Type="Italic">S</Emphasis>. <Emphasis Type="Italic">virgaurea</Emphasis>

Hybridization between alien and native species is biologically very important and could lead to genetic erosion of native taxa. Solidago × niederederi was discovered over a century ago in Austria and described by Khek as a natural hybrid between the alien (nowadays regarded also as invasive) S. canadensis and native S. virgaurea. Although interspecific hybridization in the genus Solidago is considered to be relatively common, hybrid nature of S. × niederederi has not been independently proven using molecular tools, to date. Because proper identification of the parentage for the hybrid Solidago individuals solely based on morphological features can be misleading, in this paper we report an additive polymorphism pattern expressed in the ITS sequences obtained from individuals representing S. × niederederi, and confirm the previous hypothesis that the parental species of this hybrid are S. canadensis and S. virgaurea. Additionally, based on variability at the cpDNA rpl32-trnL locus, we showed that in natural populations hybridization occurs in both directions.     

Influence of Invasive <Emphasis Type="Italic">Plants Parthenocissus</Emphasis> vitacea and <Emphasis Type="Italic">Vinca minor</Emphasis> on Biodiversity Indices of Forest Communities

The distribution and phytocenotic association of Parthenocissus vitacea and Vinca minor on the territory of the Bryansk oblast has been studied. An assessment of the distribution of invasive species is performed on a grid basis. Vinca minor is registered in 19 cells on the territory of the oblast, which is 4.9% of the total number of cells and 11.9% of the surveyed cells; Parthenocissus vitacea is registered in 50 cells, which is 12.8% of the total number of cells and 31.2% of the surveyed cells. The invasive status of Parthenocissus vitacea and Vinca minor is category 3: an adventive species whose invasions into natural and seminatural habitats in the region at the moment are rare and, as a rule, confined to the outskirts of populated areas, abandoned parks, and old plantings. The indices of successful invasion in forest communities is the formation of syntaxonomically valid variants of the communities of Corylo avellanae-Pinetum sylvestris Bulokhov et Solomeshch 2003 with depleted cenoflora. Invasive species change the phytosphere and reliably decrease the indices of α and β diversity, the structural indices of communities. The invasion of Parthenocissus vitacea and Vinca minor is successful due to active vegetative reproduction, allelopathic effects on native species, and decreasing illumination of the ground cover. The introduction of invasive species into complex pine forests blocks demutational changes of endogenous succession during the restoration of broad-leaved forests: they simplify the structure of communities and reduce the intensity of the mosaic. Parthenocissus vitacea and Vinca minor can exhibit signs of an edificator, a community builder, and a violent and transformer type. There has been only one case of a radical transformation of the natural community, registered on the territory of the Lyubin Khutor nature monument (Novozybkovskii district, Bryansk oblast).     

Revision of the <Emphasis Type="Italic">Serrulati</Emphasis> species of <Emphasis Type="Italic">Penstemon</Emphasis> section <Emphasis Type="Italic">Saccanthera</Emphasis> subsection <Emphasis Type="Italic">Serrulati</Emphasis>

A revision of Penstemon sect. Saccanthera subsect. Serrulati includes a new species (P. salmonensis), a new variety (P. triphyllus var. infernalis), and the elevation of a subspecies to species (P. curtiflorus), bringing the total number of species to eight, which are keyed and described, complete with nomenclature and type citations.     

Parasitism rates and parasitoid complexes of the wheat midges, <Emphasis Type="Italic">Sitodiplosis mosellana</Emphasis>, <Emphasis Type="Italic">Contarinia tritici</Emphasis> and <Emphasis Type="Italic">Haplodiplosis marginata</Emphasis>

Three species of cecidomyiid midges (Diptera: Cecidomyiidae), whose larvae overwinter in the soil, can cause significant yield losses on wheat in Europe: the orange wheat blossom midge, Sitodiplosis mosellana (Géhin), the yellow wheat blossom midge, Contarinia tritici (Kirby), and the saddle gall midge, Haplodiplosis marginata (von Roser). The biological control of wheat midges by their parasitoids can contribute to reduce the midge populations. Soil samples were collected in several fields in Belgium in 2012–2014 in order to characterize the parasitism rates and parasitoid complexes in overwintering larvae. The parasitism rates varied greatly between the sampled fields: 3–100, 0–100 and 2% for S. mosellana, H. marginata and C. tritici, respectively. The parasitism rate was not related to the larval density of wheat midge. The three wheat midges have totally distinct parasitoid complexes in Belgium. Eight species (Hymenoptera: Pteromalidae and Platygastridae) were found as parasitoid of S. mosellana: Macroglenes penetrans (Kirby), Amblypasis tritici (Walker), Euxestonotus error (Fitch), Euxestonutus sp. Fouts, Leptacis sp. Foerster, Platygaster gracilipes (Huggert), Platygaster nisus Walker, and Platygaster tuberosula (Kieffer). According to their abundance, M. penetrans, E. error and P. tuberosula appeared as the main parasitoids of S. mosellana in Belgium. For the two other wheat midges, only one species of the family Platygastridae was found for each midge: Platygaster equestris (Spittler) for H. marginata and Synopeas myles (Walker) for C. tritici.     

Molecular evidence for a natural diploid hybrid between <Emphasis Type="Italic">Miscanthus</Emphasis><Emphasis Type="Italic">sinensis</Emphasis> (Poaceae) and <Emphasis Type="Italic">M. sacchariflorus</Emphasis>

The hybrid origin of Miscanthus purpurascens has previously been proposed, primarily because of its intermediate morphology. In this study, phylogenies based on the DNA sequences from the internal transcribed spacer region of nuclear ribosomal DNA (nrDNA ITS), on the DNA sequences of the trnL intron and trnL-F intergenic spacer of chloroplast DNA, and on amplified fragment length polymorphism (AFLP) fingerprinting confirm that M. purpurascens originated through homoploid hybridization between M. sinensis and M. sacchariflorus. Two different types of ITS sequences were identified from almost all plants of M. purpurascens. One type was found to be closely related to M. sinensis and the other to M. sacchariflorus. Miscanthus purpurascens was found to possess many M. sinensis- and M. sacchariflorus-specific AFLP bands but no band specific to itself. Clustering with the Unweighted Pair Group Method with Arithmetic Mean and principal coordinate analysis based on the AFLP data also demonstrated that M. purpurascens is an approximate intermediate of the two species. In addition, M. purpurascens has the plastid genome of M. sinensis or M. sacchariflorus, suggesting that either species could be its maternal parent. All specimens of M. purpurascens and its coexisting parental species are identified as diploids (2n = 2x = 38). Possible mechanisms of natural hybridization, hybrid status, chloroplast DNA recombination, and evolutionary implications of this hybridization are also discussed.     

<Emphasis Type="Italic">Cantharellus</Emphasis> sect. <Emphasis Type="Italic">Amethystini</Emphasis> in Asia

In this contribution on the genus Cantharellus in Asia, C. subvaginatus is described from the Republic of Korea as a close relative to the Chinese C. vaginatus, which is here reported for the first time from India. Both species are here placed in Cantharellus subg. Cantharellus sect. Amethystini, together with the Indian C. pseudoformosus (syn.: C. umbonatus) and the Malayan C. subamethysteus. As such, Asia has suddenly become the continent with the highest diversity for Amethystini. Species delimitation in sect. Amethystini is molecularly supported by a combined phylogenetic analysis of rDNA sequences obtained for LSU and ITS and additionally suggests the existence of a still undescribed species in North America. Character variability is discussed for all known members of Amethystini, including atypical specimens of the North American C. lewisii that are morphologically more reminiscent of the South Korean C. subvaginatus.     

Complete chloroplast genome sequence of <Emphasis Type="Italic">Capsicum</Emphasis><Emphasis Type="Italic">baccatum</Emphasis> var. <Emphasis Type="Italic">baccatum</Emphasis>

Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Complete chloroplast (cp) genome sequences of Capsicum species have been reported. We herein report the complete chloroplast genome sequence of Capsicum baccatum var. baccatum, a wild Capsicum species. The total length of the chloroplast genome is 157,145 bp with 37.7 % overall GC content. One pair of inverted repeats, 25,910 bp in length, was separated by a small single-copy region (17,974 bp) and large single-copy region (87,351 bp). This region contains 86 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 11 genes contain one or two introns. Pair-wise alignments of chloroplast genome were performed for genome-wide comparison. Analysis revealed a total of 134 simple sequence repeat (SSR) motifs and 282 insertions or deletions variants in the C. baccatum var. baccatum cp genome. The types and abundances of repeat units in Capsicum species were relatively conserved, and these loci could be used in future studies to investigate and conserve the genetic diversity of the Capsicum species.     

Interseasonal and interspecies diversities of <Emphasis Type="Italic">Symbiodinium</Emphasis> density and effective photochemical efficiency in five dominant reef coral species from Luhuitou fringing reef,northern South China Sea

Although it is well established that different coral species have different susceptibilities to thermal stress, the reasons behind this variation are still unclear. In this study, 384 samples across five dominant coral species were collected seasonally between September 2013 and August 2014 at Luhuitou fringing reef in Sanya, Hainan Island, northern South China Sea, and their algal symbiont density and effective photochemical efficiency (Φ _PSII) were measured. The results indicated that both the Symbiodinium density and Φ _PSII of corals were subject to significant interspecies and seasonal variations. Stress-tolerant coral species, including massive Porites lutea and plating Pavona decussata, had higher symbiont densities but lower Φ _PSII compared to the vulnerable branching species of Acropora over the course of all four seasons. Seasonally, coral symbiont densities were the lowest during winter, while during the same period, Φ _PSII of corals was at the highest point. Further analysis suggested that dissolved inorganic nutrients and upwelling in the reef area were probably responsible for the observed seasonal variations in symbiont density. The fact that Porites lutea has the lowest Φ _PSII during all four seasons is likely related to their symbionts’ lower capacity to provide required photosynthates for calcification. These results suggest that a coral’s thermal tolerance is primarily and positively dependent on its symbiont density and is less related to its effective photochemical efficiency.     

Analysis of <Emphasis Type="Italic">Streptomyces coelicolor</Emphasis> M145 genes <Emphasis Type="Italic">SCO4164</Emphasis> and <Emphasis Type="Italic">SCO5854</Emphasis> encoding putative rhodaneses

Streptomyces coelicolor genome carries two apparently paralogous genes, SCO4164 and SCO5854, that encode putative thiosulfate sulfurtransferases (rhodaneses). These genes (and their presumed translation products) are highly conserved and widely distributed across actinobacterial genomes. The SCO4164 knockout strain was unable to grow on minimal media with either sulfate or sulfite as the sole sulfur source. The SCO5854 mutant had no growth defects in the presence of various sulfur sources; however, it produced significantly less amounts of actinorhodin. Furthermore, we discuss possible links between basic interconversions of inorganic sulfur species and secondary metabolism in S. coelicolor.     

Taxonomy and pathogenicity of <Emphasis Type="Italic">Leptographium</Emphasis> species associated with <Emphasis Type="Italic">Ips subelongatus</Emphasis> infestations of <Emphasis Type="Italic">Larix</Emphasis> spp. in northern China,including two new species

The larch bark beetle (Ips subelongatus), which occurs in larch plantations over a vast area of eastern Asia, infects both dying and fallen trees. When its population reaches a high density, the beetle may also infect healthy trees, resulting in tree decline and, eventually, death. Leptographium spp., in both their sexual and asexual states, are mainly associated with conifer-infesting bark beetles; some species are important tree pathogens. The aims of this study were to identify the Leptographium spp. associated with I. subelongatus infestations of Larix spp. in northern China and to examine their pathogenicity towards the tree. Morphological studies and phylogenetic approaches based on multilocus DNA sequence data (ITS2- partial r28S, partial β-tubulin, and EF-1α gene regions) showed that three Leptographium species occur in association with I. subelongatus in the areas investigated: Leptographium taigense, which is recorded in China for the first time, and two new species, namely L. innermongolicum sp. nov. and L. zhangii sp. nov. Leptographium innermongolicum is closely related to L. taigense, whereas L. zhangii belongs to the Grosmannia piceaperda species complex. The pathogenicity of these Leptographium species towards mature Larix spp. was tested by stem inoculation in forests. All inoculations only resulted in small lesions on the inner bark; therefore, the three Leptographium species were not considered to be pathogenic.     

Multilocus phylogeny of <Emphasis Type="Italic">Clonostachys</Emphasis> subgenus <Emphasis Type="Italic">Bionectria</Emphasis> from Brazil and description of <Emphasis Type="Italic">Clonostachys chloroleuca</Emphasis> sp. nov.

Phylogenetic analyses based on protein-encoding gene exons and introns of ATP citrate lyase (ACL1), beta tubulin (TUB), the largest subunit of RNA polymerase II (RPB1), and translation elongation factor 1-α (TEF1) are used for inferring the existence of a new Clonostachys species from the Cerrado biome in Brazil, described here as C. chloroleuca. The species produces dimorphic, primary, and secondary conidiophores that form consistently greenish conidial masses on artificial media. It resembles therefore C. rosea f. catenulata although it differs from this species by less adpressed branches in the secondary conidiophores. The new species is also phylogenetically related to C. byssicola and C. rhizophaga. Our inventory suggests that C. byssicola, C. chloroleuca, C. pseudochroleuca, C. rhizophaga, C. rogersoniana, and C. rosea commonly occur in native and agriculturally used soils of the Cerrado and Amazon Forest. Using sequences available from two genome-sequenced strains employed as biological control agents, we confirm the identity of the European strain IK726 as C. rosea and identify strain 67-1 from China as C. chloroleuca.     

<Emphasis Type="Italic">Bruguiera hainesii</Emphasis>, a critically endangered mangrove species,is a hybrid between <Emphasis Type="Italic">B. cylindrica</Emphasis> and <Emphasis Type="Italic">B. gymnorhiza</Emphasis> (Rhizophoraceae)

Bruguiera hainesii (Rhizophoraceae) is one of the two Critically Endangered mangrove species listed in the IUCN Red List of Threatened Species. Although the species is vulnerable to extinction, its genetic diversity and the evolutionary relationships with other Bruguiera species are not well understood. Also, intermediate morphological characters imply that the species might be of hybrid origin. To clarify the genetic relationship between B. hainesii and other Bruguiera species, we conducted molecular analyses including all six Bruguiera species using DNA sequences of two nuclear genes (CesA and UNK) and three chloroplast regions (intergenic spacer regions of trnL-trnF, trnS-trnG and atpB-rbcL). For nuclear DNA markers, all nine B. hainesii samples from five populations were heterozygous at both loci, with one allele was shared with B. cylindrica, and the other with B. gymnorhiza. For chloroplast DNA markers, the two haplotypes found in B. hainesii were shared only by B. cylindrica. These results suggested that B. hainesii is a hybrid between B. cylindrica as the maternal parent and B. gymnorhiza as the paternal one. Furthermore, chloroplast DNA haplotypes found in B. hainesii suggest that hybridization has occurred independently in regions where the distribution ranges of the parental species meet. As the IUCN Red List of Threatened Species currently excludes hybrids (except for apomictic plant hybrids), the conservation status of B. hainesii should be reconsidered.