Ichnodiversity and ichnodisparity: significance and caveats

Ichnodiversity has been used as a proxy for environmental stress and stability in facies interpretations and to reconstruct evolutionary radiations and colonization histories in evolutionary palaeoecology. The three components of global diversity are exported from ecology and adapted for ichnology. Alpha ichnodiversity is used for palaeoenvironmental characterization, being assessed for individual facies. Beta ichnodiversity is commonly overlooked, although it may provide information about degree of similarity between ichnofaunas formed along environmental gradients. Gamma ichnodiversity may provide clues to detect ichnofossil provincialism. The concept of disparity may also prove to be significant in ichnological studies. Whereas ichnodiversity refers to ichnotaxonomic richness, ichnodisparity provides a measure of the variability of morphological plans in biogenic structures. Changes in global ichnodiversity do not necessarily parallel changes in ichnodisparity. For example, while the Cambrian explosion involved a dramatic increase in both, the Ordovician radiation essentially reflects an increase only in the former. Ichnodiversity and ichnodisparity should be used with caution because they are both affected by taphonomic processes. High diversity of superficial to shallow‐tier trace fossils may result from enhanced preservation due a poorly developed mixed layer, rather than a true reflection of ecosystem performance, as shown by underexploited infaunal ecospace after biotic crises (e.g. end‐Permian mass extinction).     

Role of ethylene and related gene expression in the interaction between strawberry plants and the plant growth‐promoting bacterium Azospirillum brasilense

• Induced systemic resistance (ISR) is one of the indirect mechanisms of growth promotion exerted by plant growth‐promoting bacteria, and can be mediated by ethylene (ET). We assessed ET production and the expression of related genes in the Azospirillum–strawberry plant interaction.
• Ethylene production was evaluated by gas chromatography in plants inoculated or not with A. brasilense REC3. Also, plants were treated with AgNO₃, an inhibitor of ET biosynthesis; with 1‐aminocyclopropane‐1‐carboxylic acid (ACC), a precursor of ET biosynthesis; and with indole acetic acid (IAA). Plant dry biomass and the growth index were determined to assess the growth‐promoting effect of A. brasilense REC3 in strawberry plants. Quantitative real time PCR (qRT‐PCR) was performed to analyse relative expression of the genes Faetr1, Faers1 and Faein4, which encode ET receptors; Factr1 and Faein2, involved in the ET signalling pathway; Faacs1 encoding ACC synthase; Faaco1 encoding ACC oxidase; and Faaux1 and Faami1 for IAA synthesis enzymes.
• Results showed that ET acts as a rapid and transient signal in the first 12 h post‐treatment. A. brasilense REC3‐inoculated plants had a significantly higher growth index compared to control plants. Modulation of the genes Faetr1, Faers1, Faein4, Factr1, Faein2 and Faaco1 indicated activation of ET synthesis and signalling pathways. The up‐regulation of Faaux1 and Faami1 involved in IAA synthesis suggested that inoculation with A. brasilense REC3 induces production of this auxin, modulating ET signalling.
• Ethylene production and up‐regulation of genes associated with ET signalling in strawberry plants inoculated with A. brasilense REC3 support the priming activation characteristic of ISR. This type of resistance and the activation of systemic acquired resistance previously observed in this interaction indicate that both are present in strawberry plants, could act synergistically and increase protection against pathogens.

     

Interactions Between Rhizoctonia Root Rot and the Foliar Common Bean Diseases Anthracnose and Rust

The effects of co‐inoculation of Rhizoctonia solani and Colletotrichum lindemuthianum or Uromyces appendiculatus at different inoculum levels were studied on the disease dynamics and on the growth of bean plants under greenhouse conditions. Bean seeds were sown in R. solani‐infested soil. Additional experiments in which seedlings were transplanted to infested soil were also carried out. Conidial suspensions of C. lindemuthianum or uredospores of U. appendiculatus were inoculated onto leaves at plant developmental stages V2 and V3, respectively. Interactions between root rot and the aerial diseases were observed depending on the inoculum levels and on the timing of R. solani inoculation. Anthracnose severity tended to be higher on R. solani‐infected plants. Conversely, R. solani infection significantly reduced diameter of pustules and rust severity. When seedlings were transplanted to soil infested with low levels of R. solani, root rot severity and density of R. solani in the soil were magnified at high levels of C. lindemuthianum or U. appendiculatus. In these experiments, a synergistic interaction between root rot and anthracnose was observed to affect the plant dry weight. Antagonistic effects on the plant dry weight were found for the combination root rot/rust only when seeds were sown in infested soil.     

Validation of a cheap and simple nondestructive method for obtaining AFLPs and DNA sequences (mitochondrial and nuclear) in amphibians

The use of nondestructive methods for obtaining DNA from amphibians (e.g. buccal swabs) allows genetic studies to be performed without affecting the survival of the studied individuals. In this study, we compared two methods of nondestructive DNA sampling, buccal swabs and interdigital membrane or toe‐clipping, in several amphibian species of different size: Rhinella spinulosa, R. atacamensis, six species of the genus Telmatobius and Pleurodema thaul. We evaluated the integrity of the DNA extracted by sequencing fragments of mitochondrial and nuclear genes and by generating amplified fragment length polymorphisms markers (AFLPs). In all cases, we obtained an adequate amount of DNA (mean range 55–298 ng/μL). We obtained identical DNA sequences from buccal swab and interdigital membrane/toe‐clip for all individuals. The differences in the coding of AFLP markers between the tissues were similar to those reported for replicas of the same type of sample in similar analyses in other species of amphibians. In conclusion, the use of buccal swabs is a trustworthy and inexpensive method to obtain DNA for mitochondrial and nuclear sequencing and AFLP analyses. Given the types of markers evaluated, buccal swabs may be used for phylogenetic, phylogeographic and population genetic studies, even in small amphibians (<33 mm).     

Balamuthia mandrillaris: In Vitro Interactions with Selected Protozoa and Algae

Although Balamuthia mandrillaris was identified more than two decades ago as an agent of fatal granulomatous encephalitis in humans and other animals, little is known about its ecological niche, biological behavior in the environment, food preferences and predators, if any. When infecting humans or other animals, Balamuthia feeds on tissues; and in vitro culture, it feeds on mammalian cells (monkey kidney cells, human lung fibroblasts, and human microvascular endothelial cells). According to recent reports, it is believed that Balamuthia feeds on small amebae, for example, Acanthamoeba that are present in its ecological niche. To test this hypothesis, we associated Balamuthia on a one‐on‐one basis with selected protozoa and algae. We videotaped the behavior of Balamuthia in the presence of a potential prey, its ability to hunt and attack its food, and the time required to eat and cause damage to the target cell by direct contact. We found that B. mandrillaris ingested trophozoites of Naegleria fowleri, Naegleria gruberi, Acanthamoeba spp., Trypanosoma cruzi epimastigotes, Toxoplasma gondii tachyzoites, and Giardia. However, it did not feed on Acanthamoeba cysts or algae. Balamuthia caused cytolysis of T. cruzi epimastigotes and T. gondii tachyzoites by direct contact. Balamuthia trophozoites and cysts were, however, eaten by Paramecium sp.     

Wheat's wild relatives vary in their response to nitrogen and ozone

The wild relatives of bread wheat ( Triticum aestivum ) are valued by plant breeders for their genetic diversity. However, increasing levels of nitrogen (N) deposition and ground‐level ozone (O₃) threaten plant biodiversity in the Mediterranean and Near‐East, a hotspot for many crop wild relatives. Knowledge of the effect of these air pollutants in combination is still limited, but early indications are that effects vary depending on the level of pollutants, and on the sensitivity of the species to N and O₃. This study examined the responses of four important wheat wild relatives ( Aegilops tauschii , Aegilops speltoides , Triticum dicoccoides and Triticum monococcum ) and one modern wheat cultivar ( T. aestivum ‘Cadenza’) to treatments of N (equivalent to 50 kg ha^?1 year^?1 ammonium nitrate) and O₃ (100 ppb for 21 days), alone and in combination. Measurements included root, shoot and seed biomass, and electrolyte ratios. The O₃ sensitivity of A. tauschii and T. aestivum ‘Cadenza’ were exacerbated by the addition of N, while A. speltoides was found to be nitrophilous, with N ameliorating the negative effect of O_3. Both T. aestivum ‘Cadenza’ and T. dicoccoides produced immature seed heads, with the cultivar's seed head biomass reduced in response to O₃ and N + O₃ while that of T. dicoccoides was largely unaffected. These data suggest that all four wild relatives are likely to be affected when N and O₃ air pollutants co‐occur, and there in situ populations may therefore be at risk. Equally, the results of this study can inform use of their beneficial traits by wheat breeders, and alert them to the inadvertent inclusion of N and O₃ sensitivity.     

Nematodes associated with Ips cembrae (Coleoptera: Curculionidae): comparison of generations,sexes and sampling methods

A study of nematodes associated with the large larch bark beetle Ips cembrae (Heer 1836) was carried out at three locations in the Czech Republic. The proportion of beetles infested by endoparasitic nematodes (representatives of genera Contortylenchus, Parasitylenchus, Cryptaphelenchus and Parasitorhabditis) ranged from 29.9 to 50.9%. Significant differences were determined in nematode infestation levels among locations, generations and sampling methods. No differences were found in infestation rates between males and females. The percentage of bark beetles with phoretic nematodes ranged from 18 to 42.9%. Phoretic nematodes directly found under elytra, on wings and between body segments of the bark beetles belong to the genus Micoletzkya. However, adults and juveniles of other two phoretic species Laimaphelenchus penardi and Bursaphelenchus sp. were found in the gallery frass of I. cembrae. Infestation by phoretic nematodes positively correlated with the presence of mites under elytra.     

Bulb and Root Rot in Lily (Lilium longiflorum) and Onion (Allium cepa) in Israel

In the past 10 years, there has been a substantial increase in reports, from growers and extension personnel, on bulb and root rots in lily (Lilium longiflorum) in Israel. Rot in these plants, when grown as cut flowers, caused serious economic damage expressed in reduction in yield and quality. In lily, the fungal pathogens involved in the rot were characterized as binucleate Rhizoctonia AG‐A, Rhizoctonia solani, Pythium oligandrum, Fusarium proliferatum (white and purple isolates) and F. oxysporum, using morphological and molecular criteria. These fungi were the prevalent pathogens in diseased plants collected from commercial greenhouses. Pathogenicity trials were conducted on lily bulbs and onion seedlings under controlled conditions in a greenhouse to complete Koch's postulates. Disease symptoms on lily were most severe in treatments inoculated with binucleate Rhizoctonia AG‐A, P. oligandrum and F. proliferatum. Plant height was lower in the above treatments compared with the control plants. The least aggressive fungus was R. solani. In artificial inoculations of onion, seedling survival was significantly affected by all fungi. The most pathogenic fungus was F. proliferatum w and the least were isolates of F. oxysporum (II and III). All fungi were successfully re‐isolated from the inoculated plants.     

VIP and CRF reduce ADAMTS expression and function in osteoarthritis synovial fibroblasts

ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) family is known to play an important role in the pathogenesis of osteoarthritis (OA), working on aggrecan degradation or altering the integrity of extracellular matrix (ECM). Thus, the main purpose of our study was to define the role of vasoactive intestinal peptide (VIP) and corticotrophin‐releasing factor (CRF), as immunoregulatory neuropeptides, on ADAMTS production in synovial fibroblasts (SF) from OA patients and healthy donors (HD). OA‐ and HD‐SF were stimulated with pro‐inflammatory mediators and treated with VIP or CRF. Both neuropeptides decreased ADAMTS‐4, ‐5, ‐7 and ‐12 expressions, aggrecanase activity, glycosaminoglycans (GAG), and cartilage oligomeric matrix protein (COMP) degradation after stimulation with fibronectin fragments (Fn‐fs) in OA‐SF. After stimulation with interleukin‐1β, VIP reduced ADAMTS‐4 and ‐5, and both neuropeptides decreased ADAMTS‐7 production and COMP degradation. Moreover, VIP and CRF reduced Runx2 and β‐catenin activation in OA‐SF. Our data suggest that the role of VIP and CRF on ADAMTS expression and cartilage degradation could be related to the OA pathology since scarce effects were produced in HD‐SF. In addition, their effects might be greater when a degradation loop has been established, given that they were higher after stimulation with Fn‐fs. Our results point to novel OA therapies based on the use of neuropeptides, since VIP and CRF are able to stop the first critical step, the loss of cartilage aggrecan and the ECM destabilization during joint degradation.     

Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids

• Orchidaceae is a widely distributed plant family with very diverse vegetative and floral morphology, and such variability is also reflected in their karyotypes. However, since only a low proportion of Orchidaceae has been analysed for chromosome data, greater diversity may await to be unveiled. Here we analyse both genome size (GS) and karyotype in two subtribes recently included in the broadened Maxillariinea to detect how much chromosome and GS variation there is in these groups and to evaluate which genome rearrangements are involved in the species evolution.
• To do so, the GS (14 species), the karyotype – based on chromosome number, heterochromatic banding and 5S and 45S rDNA localisation (18 species) – was characterised and analysed along with published data using phylogenetic approaches.
• The GS presented a high phylogenetic correlation and it was related to morphological groups in Bifrenaria (larger plants – higher GS). The two largest GS found among genera were caused by different mechanisms: polyploidy in Bifrenaria tyrianthina and accumulation of repetitive DNA in Scuticaria hadwenii. The chromosome number variability was caused mainly through descending dysploidy, and x=20 was estimated as the base chromosome number.
• Combining GS and karyotype data with molecular phylogeny, our data provide a more complete scenario of the karyotype evolution in Maxillariinae orchids, allowing us to suggest, besides dysploidy, that inversions and transposable elements as two mechanisms involved in the karyotype evolution. Such karyotype modifications could be associated with niche changes that occurred during species evolution.

     

Bud phenology and growth are subject to divergent selection across a latitudinal gradient in Populus angustifolia and impact adaptation across the distributional range and associated arthropods

Temperate forest tree species that span large geographical areas and climatic gradients often have high levels of genetic variation. Such species are ideal for testing how neutral demographic factors and climate‐driven selection structure genetic variation within species, and how this genetic variation can affect ecological communities. Here, we quantified genetic variation in vegetative phenology and growth traits in narrowleaf cottonwood, Populus angustifolia, using three common gardens planted with genotypes originating from source populations spanning the species' range along the Rocky Mountains of North America (ca. 1700 km). We present three main findings. First, we found strong evidence of divergent selection (Q_ST > F_ST) on fall phenology (bud set) with adaptive consequences for frost avoidance. We also found evidence for selection on bud flush duration, tree height, and basal diameter, resulting in population differentiation. Second, we found strong associations with climate variables that were strongly correlated with latitude of origin. More strongly differentiated traits also showed stronger climate correlations, which emphasizes the role that climate has played in divergent selection throughout the range. We found population × garden interaction effects; for some traits, this accounted for more of the variance than either factor alone. Tree height was influenced by the difference in climate of the source and garden locations and declined with increasing transfer distance. Third, growth traits were correlated with dependent arthropod community diversity metrics. Synthesis. Overall, we conclude that climate has influenced genetic variation and structure in phenology and growth traits and leads to local adaptation in P. angustifolia, which can then impact dependent arthropod species. Importantly, relocation of genotypes far northward or southward often resulted in poor growth, likely due to a phenological mismatch with photoperiod, the proximate cue for fall growth cessation. Genotypes moved too far southward suffer from early growth cessation, whereas those moved too far northward are prone to fall frost and winter dieback. In the face of current and forecasted climate change, habitat restoration, forestry, and tree breeding efforts should utilize these findings to better match latitudinal and climatic source environments with management locations for optimal future outcomes.     

Identification and Pathogenicity of Lasiodiplodia Species from Eucalyptus urophylla × grandis,Polyscias balfouriana and Bougainvillea spectabilis in Southern China

Species of Lasiodiplodia are important pathogens of a wide variety of plants covering a wide geographical distribution. These fungi can be associated with different symptoms such as stem cankers, shoot blights, fruit rots, dieback and gummosis. Diseases caused by Lasiodiplodia were surveyed on Eucalyptus urophylla × grandis, Polyscias balfouriana and Bougainvillea spectabilis in a nursery in southern China. Based on morphology characteristics and phylogenetic analyses of ITS rDNA sequences and translation elongation factor 1‐alpha (TEF‐1α) gene regions, four species of Lasiodiplodia were identified. Lasiodiplodia theobromae was identified from E. urophylla × grandis, P. balfouriana and B. spectabilis. L. hormozganensis, L. iraniensis and L. pseudotheobromae were identified from B. spectabilis. To our knowledge, with the exception of L. theobromae on E. urophylla × grandis, this study represents the first report of these fungi on the host plants. Pathogenicity tests showed that all Lasiodiplodia spp. obtained in this study are virulent to E. urophylla × grandis and B. spectabilis, and L. theobromae was virulent to P. balfouriana.     

Species concept and nomenclatural changes within the genera Elliptochloris and Pseudochlorella (Trebouxiophyceae) based on an integrative approach

The genera Elliptochloris and Pseudochlorella were erected for Chlorella‐like green algae producing two types of autospores and cell packages, respectively. Both genera are widely distributed in different soil habitats, either as free living or as photobionts of lichens. The species of these genera are often difficult to identify because of the high phenotypic plasticity and occasional lack of characteristic features. The taxonomic and nomenclatural status of these species, therefore, remains unclear. In this study, 34 strains were investigated using an integrative approach. Phylogenetic analyses demonstrated that the isolates belong to two independent lineages of the Trebouxiophyceae (Elliptochloris and Prasiola clades) and confirmed that the genera are not closely related. The comparison of morphology, molecular phylogeny, and analyses of secondary structures of SSU and ITS rDNA sequences revealed that all of the strains belong to three genera: Elliptochloris, Pseudochlorella, and Edaphochlorella. As a consequence of the taxonomic revisions, we propose two new combinations (Elliptochloris antarctica and Pseudochlorella signiensis) and validate Elliptochloris reniformis, which is invalidly described according to the International Code for Nomenclature (ICN), by designating a holotype. To reflect the high phenotypic plasticity of P. signiensis, two new varieties were described: P. signiensis var. magna and P. signiensis var. communis. Chlorella mirabilis was not closely related to any of these genera and was, therefore, transferred to the new genus Edaphochlorella. All of the taxonomic changes were highly supported by all phylogenetic analyses and were confirmed by the ITS‐2 Barcodes using the ITS‐2/CBC approach.     

Phylogenetic inference and peristome evolution in haplolepideous mosses,focusing on Pseudoditrichaceae and Ditrichaceae s. l.

Pseudoditrichum mirabile, the only species of Pseudoditrichaceae, has been known for a long time from a single collection from the Canadian Arctic. Its systematic position remained enigmatic due to similarity in gametophyte structure with Ditrichaceae, a family that has simple peristomes, whereas the peristome in Pseudoditrichum is double. Due to this difference, Pseudoditrichum was classified in either Funariales or Bryales. A recent discovery of this species in the Anabar Plateau in northern Siberia has allowed its phylogenetic position to be tested based on plastid rps4 and rbcL and mitochondrial nad5 sequences. The results of this research reject the earlier hypotheses. Instead, the molecular analysis resolves Pseudoditrichum in a clade with Chrysoblastella chilensis (formerly Ditrichaceae) in the haplolepideous lineage. The peristome of Pseudoditrichum is of a previously unknown type with a fully developed exostome and hyaline endostome elements opposite the exostome teeth, based not on the 4:2:4 peristomial formula, but on 4:2:3. Double peristomes of the same type, albeit rather strongly reduced, occur in Catoscopium, Chrysoblastella, Distichium and Ditrichum flexicaule. The polyphyly of Ditrichaceae is confirmed by molecular phylogenetic analysis, and Ditrichum flexicaule and D. gracile are segregated into the new genus Flexitrichum and family Flexitrichaceae. An independent status of the recently resurrected family Distichiaceae is supported, and segregation of Chrysoblastella and Saelania into new monospecific families is proposed.