A new wood-decaying basidiomycete species associated with esca of grapevine: Fomitiporia mediterranea (Hymenochaetales)

Fomitiporia mediterranea is described as a new wood-decaying basidiomycete species associated with esca of grapevine in European wine-growing countries. Characters of the fruit body are essentially identical with those of the closely related species, Fomitiporia punctata. Fomitiporia mediterranea is distinct by the sequences of the ribosomal ITS1-5.8S-ITS2 region and by larger mycelial growth rates at temperatures between 15 °C and 35 °C. While F. punctata is confirmed as a homothallic species, F. mediterranea is shown to be outcrossing, exhibiting a unifactorial mating behaviour with a multiple allelism of the mating type factor, A; single spore isolates of F. mediterranea are intersterile in pairing tests with F. punctata. In southern Europe, F. mediterranea not only occurs on Vitis vinifera, but also on a number of other hardwood genera; it seems restricted to Vitis vinifera elsewhere in Europe.     

Functional richness, functional evenness and functional divergence: the primary components of functional diversity

Functional diversity is hypothesised as being beneficial for ecosystem functions, such as productivity and resistance to invasion. However, a precise definition of functional diversity, and hence a framework for its quantification, have proved elusive. We present a definition based on the analogy of the components of species diversity – richness, evenness and divergence. These concepts are applied to functional characters to give three components of functional diversity – functional richness, functional evenness and functional divergence. We demonstrate how each of these components may be calculated. It is hoped that our definition of functional diversity and its components will aid in elucidation of the mechanisms behind diversity/ecosystem-function relationships.     

Biscogniauxia mediterranea associated with cork oak (Quercus suber) in Tunisia: Relationships between phenotypic variation,genetic diversity and ecological factors

Biscogniauxia mediterranea is a xylariaceous ascomycete responsible for ‘charcoal disease’, the most frequent disease of cork oak in the Mediterranean basin. However, little is known regarding this fungus in North Africa. This is the first report on the morphological and genetic diversity of B. mediterranea populations in Tunisia.A total of forty-eight isolates from cork oak trees, corresponding to three different sites and three tree parts, were identified as B. mediterranea based on morphological and molecular diagnosis. Variability among the isolates was evaluated using morphological traits and microsatellite-primed PCR (MSP-PCR). B. mediterranea isolates showed high variability in culture, specifically in colony color. A high level of genetic diversity within populations and within tree parts was detected (H = 0.417, I = 0.605, and H = 0.415, I = 0.601 respectively). Significant genetic differentiation among populations (G_ST = 0.116 and Φ_ST = 0.137; p < 0.001) was determined. However, a low genetic differentiation among tree parts (G_ST = 0.066 and Φ_ST = 0.018; p = 0.07) was observed. Principal coordinate analysis showed that genetic divergence was partially related to the geographical origin. Cluster analysis based on morphological traits showed that the grouping of the isolates occurs independently of the geographic location and the tree part. The effective number of alleles (Ne), the Nei's gene diversity index (H), the Shannon's information index (I), the colony color and the presence of exudates were significantly correlated with the altitude and the rainfall. The number of alleles (Na), the percentage of polymorphic loci (PPL), the texture and the density of the mycelium were significantly correlated with the temperature. These results provide a deeper understanding of population genetics of B. mediterranea and its adaptation to environmental conditions which could help to develop control strategies against charcoal canker disease.     

Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter

The relative abundance of bacteria in the mucus and crushed tissue of the Mediterranean coral Oculina patagonica was determined by analyses of the 16S rRNA genes of isolated colonies and from a 16S rRNA clone library of extracted DNA. By SYBR gold staining, the numbers of bacteria in mucus and tissue samples were 6.2 x 10(7) and 8.3 x 10(8)/cm2 of coral surface, respectively, 99.8% of which failed to produce colonies on Marine Agar. From analysis of mucus DNA, the most-abundant bacterium was Vibrio splendidus, representing 68% and 50% of the clones from the winter and summer, respectively. After removal of mucus from coral by centrifugation, analyses of DNA from the crushed tissue revealed a large diversity of bacteria, with Vibrio species representing less than 5% of the clones. The most-abundant culturable bacteria were a Pseudomonas sp. (8 to 14%) and two different alpha-proteobacteria (6 to 18%). Out of a total 1,088 16S rRNA genes sequenced, 400 different operational taxonomic units were identified (> 99.5% identity). Of these, 295 were novel (< 99% identical to any sequences in the GenBank database). This study provides a comprehensive database for future examinations of changes in the bacterial community during bleaching events.     

Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization

Microbial and functional diversity were assessed, from a serpentinization‐driven subterrestrial alkaline aquifer – Cabeço de Vide Aquifer (CVA) in Portugal. DGGE analyses revealed the presence of a stable microbial community. By 16S rRNA gene libraries and pyrosequencing analyses, a diverse bacterial composition was determined, contrasting with low archaeal diversity. Within Bacteria the majority of the populations were related to organisms or sequences affiliated to class Clostridia, but members of classes Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Deinococci, Gammaproteobacteria and of the phyla Bacteroidetes, Chloroflexi and Nitrospira were also detected. Domain Archaea encompassed mainly sequences affiliated to Euryarchaeota. Only form I RuBisCO – cbbL was detected. Autotrophic carbon fixation via the rTCA, 3‐HP and 3‐HP/4H‐B cycles could not be confirmed. The detected APS reductase alpha subunit – aprA sequences were phylogenetically related to sequences of sulfate‐reducing bacteria belonging to Clostridia, and also to sequences of chemolithoautothrophic sulfur‐oxidizing bacteria belonging to Betaproteobacteria. Sequences of methyl coenzyme M reductase – mcrA were phylogenetically affiliated to sequences belonging to Anaerobic Methanotroph group 1 (ANME‐1). The populations found and the functional key markers detected in CVA suggest that metabolisms related to H₂, methane and/or sulfur may be the major driving forces in this environment.     

Extra carbohydrate binding module contributes to the processivity and catalytic activity of a non-modular hydrolase family 5 endoglucanase from Fomitiporia mediterranea MF3/22

FmEG from Fomitiporia mediterranea is a non-modular endoglucanase composed of a 24-amino acids extension and 13-amino acids linker-like peptide at the N-terminus and a 312-amino acids GH5 catalytic domain (CD) at the C-terminus. In this study, six FmEG derivatives with deletion of N-terminal fragments or fusion with an extra family 1 carbohydrate-binding module (CBM1) was constructed in order to evaluate the contribution of CBM1 to FmEG processivity and catalytic activity. FmEG showed a weak processivity and released cellobiose (G2) and cellotriose (G3) as main end products, and cellotriose (G4) as minor end product from filter paper (FP), but more amount of G4 was released from regenerated amorphous cellulose (RAC). All derivatives had similar activity on carboxymethylcellulose (CMC) with the same optimal pH (7.0) and temperature (50 °C). However, fusing an extra CBM1 to FmEG△24 or FmEG△37 with flexible peptide significantly improved its processivity and catalytic activity to FP and RAC. Overall, 1.79- and 1.84-fold increases in the soluble/insoluble product ratio on FP, and 1.38- and 1.39-fold increases on RAC, compared to FmEG△24, were recorded for CBM1-FmEG△24 and CBM1-linker-FmEG△24, respectively. Meanwhile, they displayed 2.64- and 2.67-fold more activity on RAC, and 1.68- and 1.77-fold on FP, respectively. Similar improvement was also obtained for CBM1-linker-FmEG△37 as compared with FmEG△37. Interestingly, fusion of an extra CBM1 with FmEG also caused an alteration of cleavage pattern on insoluble celluloses. Our results suggest that such improvements in processivity and catalytic activity may arise from CBM1 binding affinity. The N-terminal 24- or 37-amino acids may serve as linker for sufficient spatial separation of the two domains required for processivity and catalytic activity. In addition, deletion of the N-terminal 24- or 37-amino acids led to significant reduction in thermostability but not the enzymatic activity.     

Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how ‘Candidatus Liberibacter asiaticus'' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that ‘Ca. L. asiaticus'' infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in ‘Ca. L. asiaticus''-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of ‘Ca. L. asiaticus'' infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the ‘Ca. L. asiaticus''-infected citrus rhizosphere. Our results showed that the microbial community of the ‘Ca. L. asiaticus''-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by ‘Ca. L. asiaticus'' infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability of citrus-producing agro-ecosystems.     

Relationships between taxonomic and functional components of diversity: implications for conservation of tropical freshwater fishes

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Osteoarthritic tissues modulate functional properties of sensory neurons associated with symptomatic OA pain

Osteoarthritis (OA) is an age-related degenerative disease of cartilaginous tissues that is accompanied by hyperalgesia. Molecular cause and effect relationships between OA and pain remain to be elucidated. In this study, we have developed an experimental ex vivo organ co-culture system with dorsal root ganglia (DRGs) and knee synovial tissues from OA patients or unaffected human subjects. Our results suggest that tissues may generate symptomatic pain by altering the functional properties of sensory neurons. Specifically, we find that the expression levels of genes associated with neuronal pathways (e.g., SP, NK1, NK2, NPYR1, NPYR2, α2δ1) or inflammation (COX2/PTGS2 and IL6/interferon β2) are clearly elevated in DRG explants cultured in the presence of OA derived synovial tissues. These findings are consistent with a model in which cytokines and pain molecules produced by knee synovium sensitize nociceptive neurons in tissues peripheral to joint cartilage.     

Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines

The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. In this work, we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analysed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. Using a model‐based approach implemented in the software structure , we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars.     

Shifts in mollusc traits following floodplain reconnection: Testing the response of functional diversity components

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湿地土壤微生物功能多样性及碳氮组分对长期氮输入的响应

氮输入对湿地生态系统碳氮循环具有重要影响,研究湿地土壤微生物功能多样性及碳氮组分对氮输入的响应,对于明确湿地土壤碳氮循环微生物驱动机制具有重要意义。依托长期野外氮输入模拟试验,利用Biolog-ECO微平板技术,分析不同浓度氮输入:N1(6 g N m^-2 a^-1)、N2(12 g N m^-2 a^-1)和N3(24 g N m^-2 a^-1)对湿地土壤表层(0-15 cm)和亚表层(15-30 cm)微生物碳源代谢活性、功能多样性和碳氮组分的影响。结果表明:N2处理显著提高了亚表层土壤微生物碳源代谢活性和McIntosh指数,N3处理显著降低了表层土壤微生物Shannon指数和Shannon-evenness指数。随氮输入浓度增加湿地表层土壤微生物对糖类的利用率显著降低,N3处理表层土壤微生物对胺类的利用率以及亚表层土壤微生物对醇类的利用率显著提高。N1处理显著提高了湿地表层土壤全氮和微生物量碳含量;N2、N3处理显著提高了土壤铵态氮、硝态氮含量;N3处理显著降低了土壤pH值。湿地土壤pH、总碳、溶解性有机碳含量是影响微生物碳源代谢活性和功能多样性的重要因素,土壤溶解性有机碳、铵态氮、全氮含量、含水率是影响微生物碳源利用变化的主要因子。     

Wood anatomy of Polygonaceae: analysis of a family with exceptional wood diversity

Quantitative and qualitative data are presented for woods of 30 species of woody Polygonaceae. Wood features that ally Polygonaceae with Plumbaginaceae include nonbordered perforation plates, storeying in narrow vessels and axial parenchyma, septate or nucleate fibres, vasicentric parenchyma, pith bundles that undergo secondary growth, silica bodies, and ability to form successive cambia. These features are consistent with pairing of Plumbaginaceae and Polygonaceae as sister families. Wood features that ally Polygonaceae with Rhabdodendraceae include nonbordered perforation plates, presence of vestured pits in vessels, presence of silica bodies and dark-staining compounds in ray cells, and ability to form successive cambia. Of the features listed above, nonbordered perforation plates and ability to form successive cambia may be symplesiomorphies basic to Caryophyllales sensu lato . The other features are more likely to be synapomorphies. Wood data thus support molecular cladograms that show the three families near the base of Caryophyllales s.l. Chambered crystals are common to three genera of the family and may indicate relationship. Ray histology suggests secondary woodiness in Antigonon, Atraphaxis, Bilderdykia, Dedeckera, Eriogonum, Harfordia, Muehlenbeckia, Polygonum , and Rumex . Other genera of the family show little or no evidence of secondary woodiness. Molecular data are needed to confirm this interpretation and to clarify the controversial systematic groupings within the family proposed by various authors. Vessel features of Polygonaceae (lumen diameter, element length, density, degree of grouping) show an extraordinary range from xeromorphy to mesomorphy, indicating that wood has played a key role in ecological and habital shifts within the family; the diversity in ecology and habit are correlated with quantitative wood data.  © 2003 The Linnean Society of London. Botanical Journal of the Linnean Society , 2003, 141 , 25−51.     

Ascomycetes associated with ectomycorrhizas: molecular diversity and ecology with particular reference to the Helotiales

Mycorrhizosphere microbes enhance functioning of the plant–soil interface, but little is known of their ecology. This study aims to characterize the ascomycete communities associated with ectomycorrhizas in two Tasmanian wet sclerophyll forests. We hypothesize that both the phyto‐ and mycobiont, mantle type, soil microbiotope and geographical distance affect the diversity and occurrence of the associated ascomycetes. Using the culture‐independent rDNA sequence analysis, we demonstrate a high diversity of these fungi on different hosts and habitats. Plant host has the strongest effect on the occurrence of the dominant species and community composition of ectomycorrhiza‐associated fungi. Root endophytes, soil saprobes, myco‐, phyto‐ and entomopathogens contribute to the ectomycorrhiza‐associated ascomycete community. Taxonomically these Ascomycota mostly belong to the orders Helotiales, Hypocreales, Chaetothyriales and Sordariales. Members of Helotiales from both Tasmania and the Northern Hemisphere are phylogenetically closely related to root endophytes and ericoid mycorrhizal fungi, suggesting their strong ecological and evolutionary links. Ectomycorrhizal mycobionts from Australia and the Northern Hemisphere are taxonomically unrelated to each other and phylogenetically distant to other helotialean root‐associated fungi, indicating independent evolution. The ubiquity and diversity of the secondary root‐associated fungi should be considered in studies of mycorrhizal communities to avoid overestimating the richness of true symbionts.     

Isolation and characterization of different plant associated bacteria and their potential to degrade polychlorinated biphenyls

In our experiments the effect of different plants on microbial activities resulting in degradation and PCB removal from long-term contaminated soil was evaluated. Total bacteria and bacteria representing the dominating microflora within rhizosphere of individual plant species – tobacco (Nicotiana tabacum), black nightshade (Solanum nigrum), horseradish (Armoracia rusticana) and goat willow (Salix caprea) planted in PCB contaminated soil as well as from the same, but non-vegetated PCBs soil, were isolated and biochemically characterized. PCB bacterial degraders, stimulated by root exudates of individual plants, were detected after isolation from rhizosphere soil and precultivation on minimal medium with biphenyl as the sole carbon source. Detection of BphA1 gene (first gene of bacterial aerobic PCB degradative pathway) in genomes of rhizosphere microorganisms was performed by nested PCR technique using previously designed specific primers. Rhizosphere of individual plants contained different bacterial species, mostly gram-negative non-fermenting bacteria of Pseudomonas, Agrobacterium, Ochrobactrum and other species. Gene BphA1 was identified in genome of only several of them. From tested species, S. caprea and A. rusticana have shown to be promising candidates for rhizoremediation purposes.     

Multi-gene analysis and morphology reveal novel Ilyonectria species associated with black foot disease of grapevines

Black foot is an important disease of grapevines, which has in recent years been recorded with increased incidence and severity throughout the world, affecting grapevines both in nurseries and young vineyards. In the past the disease has been associated with infections by Ilyonectria macrodidyma, Ilyonectria liriodendri, Campylocarpon fasciculare, and Campylocarpon pseudofasciculare. Based on published data, a high level of genetic diversity was detected among isolates of I. macrodidyma. To resolve this issue, we employed a multigene analysis strategy (based on the β-tubulin, histone H3, translation elongation factor 1-α, and the internal transcribed spacers on both sides of the 5.8S nuclear ribosomal RNA gene) along with morphological characterisation to study a collection of 81 I. macrodidyma-like isolates from grapevine and other hosts. Morphological characters (particularly conidial size) and molecular data (highest resolution achieved with histone H3 nucleotide sequence) enabled the distinction of six monophyletic species within the I. macrodidyma complex, four of which (Ilyonectria alcacerensis, Ilyonectria estremocensis, Ilyonectria novozelandica, and Ilyonectria torresensis) are described here. This work forms part of an effort by the International Council on Grapevine Trunk Diseases to resolve the species associated with black foot disease, which we believe will clarify their taxonomy, and therefore help researchers to devise control strategies to reduce the devastating impact of this disease.     

The generalized replication principle and the partitioning of functional diversity into independent alpha and beta components

The replication principle was first proposed by Hill (1973, Ecology 54: 247– 432) as an advantageous property of his family of diversity indices. Later Jost (2007, Ecology 88: 2427– 2439) discovered that diversity measures satisfying this principle allow partitioning of gamma diversity into independent alpha and beta components by simple multiplicative partitioning. Despite the emerging agreement on measuring taxonomic beta‐diversity by multiplicative partitioning of Hill diversity, there is no consensus on how to measure functional beta diversity. Two different generalizations of Hill numbers for measuring functional diversity were proposed by Leinster and Cobbold (2011, Ecology 93: 477– 489) and Chiu and Chao (2014, PLoS One 9: e1000014). Both generalizations attempted to satisfy the generalized replication principle, but they formulate it in different ways. The aims of this paper are 1) to review approaches for measuring functional diversity in units of equivalent numbers without explicit reference to replication principle; 2) to compare the two proposed replication principle and to point out some important differences in the behavior of diversity families derived from the two principles; 3) to explore the conditions necessary for partitioning functional diversity of Leinster and Cobbold into meaningful alpha and beta components; 4) and, finally, to explore how transformation of among‐species distances into similarities influences the sensitivity of functional diversity to the scale parameter.     

Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis

The coral reef benthos is primarily colonized by corals and algae, which are often in direct competition with one another for space. Numerous studies have shown that coral-associated Bacteria are different from the surrounding seawater and are at least partially species specific (i.e. the same bacterial species on the same coral species). Here we extend these microbial studies to four of the major ecological functional groups of algae found on coral reefs: upright and encrusting calcifying algae, fleshy algae, and turf algae, and compare the results to the communities found on the reef-building coral Montastraea annularis. It was found using 16S rDNA tag pyrosequencing that the different algal genera harbour characteristic bacterial communities, and these communities were generally more diverse than those found on corals. While the majority of coral-associated Bacteria were related to known heterotrophs, primarily consuming carbon-rich coral mucus, algal-associated communities harboured a high percentage of autotrophs. The majority of algal-associated autotrophic Bacteria were Cyanobacteria and may be important for nitrogen cycling on the algae. There was also a rich diversity of photosynthetic eukaryotes associated with the algae, including protists, diatoms, and other groups of microalgae. Together, these observations support the hypothesis that coral reefs are a vast landscape of distinctive microbial communities and extend the holobiont concept to benthic algae.