Biodiversity Institute Research Articles

Mapping plant communities of the Karoo National Park, South Africa, using Sentinel-2 and topo-morphological data

AimsThis study aimed at classifying, mapping and describing the plant communities of the Karoo National Park using floristic surveys in conjunction with Sentinel-2 and topo-morphological data. Study areaKaroo National Park, Western Cape, South Africa. MethodsThe vegetation of the Karoo National Park was delineated into homogenous physiognomic-physiographic units using Sentinel-2 images. A total of 128 survey plots (100 m2 each) were surveyed within the different homogeneous units during the period 2016 to 2020. Within each survey plot, all rooted species were identified and their cover abundance estimated. Each plot was photographed and its geolocation recorded. The floristic data were captured using the Braun Blanquet Personal Computer suite and exported to the JUICE Software programme. A modified TWINSPAN classification was done to derive a first tabled synopsis of the plant communities. The different plant communities were subsequently classified and described according to their diagnostic and dominant species gleaned from the synoptic table. Species richness was determined by counting the number of different species per plant community while the Shannon–Wiener Index and Rich-Gini–Simpson Index of diversity (D) were used to derive indices of species diversity per plant community. Results12 major communities and two sub-communities that are distinctly linked to various abiotic factors were identified, described and mapped. The higher-lying rocky steep midslopes as well as the valley bottomland areas had the highest diversity and species richness. ConclusionsThis study proves the efficacy of using Sentinel-2 and topo-morphological data in classification, description and mapping vegetation of extensive natural areas. The vegetation map and classification of plant communities provide a baseline to inform management decisions.Taxonomic reference: SA-Plant Checklist-2019–2020, South African National Biodiversity Institute, 2020, Botanical Database of Southern Africa (BODATSA) (http://posa.sanbi.org/) [accessed January 2022].

Identification of ticks and tick-borne pathogens of wildlife necropsy cases submitted to the SANBI National Zoological Gardens, South Africa

Ticks are arachnid blood-feeding parasites, which infest livestock, wildlife, and humans, transmitting medically and veterinary significant pathogens. Their biodiversity and distribution in wild animals remains complex. This study analysed archived tick samples (n = 48) from the South African Biodiversity Institute (SANBI) Wildlife Biobank utilizing morphology and genetic analyses of the 16S rRNA and COI (DNA barcoding) mitochondrial genes to identify ticks collected among 13 vertebratesavian, reptilian, and mammalian host species. The specimens came from nine localities including nature reserves and captive facilities (zoological garden) in South Africa, Namibia, and Botswana. These ticks were also assessed for associated pathogens with the reverse line blot (RLB) hybridization assay. Seven tick genera, Amblyomma, Hyalomma, Haemaphysalis, Ixodes, Rhipicephalus, Rhipicentor, and Otobius were identified, with Amblyomma being the most prevalent (22.9 %) in our sample set.Obtained sequences were 95–100 % similar to published records of tick species collected from wild and domestic animals, as well as those collected from vegetation, from different southern African areas. However, tick specimens (n = 3) identified morphologically as Hyalomma truncatum, Rhipicephalus e. evertsi, and R. simus, were, on a molecularly level, more closely related to their sister taxa (H. glabrum, R. e. mimeticus, and R. gertrudae, respectively) suggesting a need for taxonomic verification. With the RLB hybridization assay, six samples reacted with the Ehrlichia/Anaplasma genus-specific probe, while two reacted with the Theileria/Babesia genus-specific probe. Sequencing of the RLB amplicons targeting the 18S rRNA gene (n = 2) indicated 100 % similarity to Hepatozoon fitzsimonsi, while one was closely related to He. ingwe with 99.39 % similarity. The results show that wildlife harbour different tick species, and pathogen detection identified novel genotypes, indicating wildlife as potential pathogens reservoirs. This study enhances our understanding of tick biodiversity, distribution and highlights wildlife's role in harbouring diverse tick species and novel pathogens.

INBio: its innovative work in the knowledge and sustainable use of biodiversity in Costa Rica

The National Institute of Biodiversity of Costa Rica (INBio), the first institution of its kind worldwide, was created in 1989 as a civil society organization, with the mission of promoting greater awareness of the value of biodiversity, to achieve its conservation and promote human development. It operated within the framework of a national biodiversity conservation strategy consisting of three types of actions: “save, know and use”, forming a public-private alliance with the National System of Conservation Areas, whose work represented the first step of “saving”. INBio focused on the generation of scientific knowledge of Costa Rican biodiversity (knowing) and the search and promotion of its intelligent use (using). This article describes the genesis of the institution and its main contributions to the knowledge and use of Costa Rican biodiversity between 1989-2015. These include the results of the protected areas biodiversity inventory process and the development of the largest systematic collection of biological specimens in the country's history, fully systematized; the development of an information management system that integrated all the information from the inventory and the specimens in its collection in digital format, allowing global access to this information or its correlation with that of other sources. The results of promoting and facilitating the use of information through five programs: Natural Sciences and Conservation Biology, for scientific purposes; Bioliteracy and Education, conceptually designed for the teaching and development of awareness about the value of biodiversity; Bioprospecting, the systematic search for economic uses of biodiversity for medicinal, agricultural and industrial purposes; Conservation for Development, the use of the information for wild areas conservation purposes, surrounding communities or nature tourism, among others; Technical Assistance and Training, program in charge of assisting public and private entities, inside and outside the country, in the development of initiatives in which Biodiversity was the central element. The main results of its work and the national and international awards that INBio received for its innovative approaches and contributions are described, as well as the financial and political reasons why INBio discontinued its activities in the period 2015-2016 are summarized. Viewing the work of INBio as a first stage, the importance and need to continue with a state program on the knowledge and use of Costa Rican biodiversity is raised, in addition to its protection, with the goal of creating awareness of its value before the serious threats to life on Earth.

Review of Plant Genetic Resources, Utilization and Conservation of Genetic Resources

According to the review, genetic resources are derived from native plant landraces and wild species. Material originating from plants is referred to as genetic resources. These genetic resources are very important for nutrition and the development of agricultural productivity. Cereals, pulses, oilseeds, and cash crops are a group of field crops grown in Ethiopia. The group of forest genetic resources includes plantations, forests, scrub, natural closed forests, and trees on farms. Ethiopia has rich plant genetic resources with its diverse agro-ecological region but faces several threats. In order to conserve plant genetic resources, the Ethiopian Biodiversity Institute uses a diverse strategy that includes gene banks, on-farm conservation, education, and policy lobbying. Genetic resources preserved by ex situ and in situ conservation. This review article was intended to discuss plant genetic resources, utilization, threats, and conservation strategies.

First report of Colletotrichum incanum causing leaf spots on common bean in Europe (Slovenia).

A Phaseolus vulgaris L. leaf showing necrotic spots was collected in an experimental bean field in central Slovenia in August 2021. The field contained diverse common bean lines sourced from genebank collections, with each line represented by 10 plants. While symptomatic leaves were seen across various lines, the reported species derived exclusively from a Huasca Huallaga Colorado plant (single-seed descent, USDA accession PI153714, doi: 10.18730/H7P9N), a Peruvian landrace. After incubating the leaf for 2 d at ambient temperature in a moist chamber, setose acervuli developed producing curved, distally tapering and proximately truncated conidia. Single-spore cultures developed equally-shaped conidia measuring 14.5-21.5 (avg. 18.5) × 3-4 (avg. 3.5) μm (n=60) on corn meal agar when mounted in lactic acid. Obtained morphological characters and sequences of the partial actin (GenBank accession, OR208162), beta-tubulin (OR208164), and histone 3 (OR208165) gene identified the isolate as Colletotrichum incanum H.-C. Yang, J.S. Haudenshield & G.L. Hartman. Sequences were identical to those from CBS 133485 (= NRRL 62592, IL6A), ex-type strain of C. incanum (KC110823, KC110814, and KC110796). Partial sequences of the chitin synthase (CHS) gene (OR208163), not available for the ex-type strain, was identical to sequences of other C. incanum strains reported from China (KP145539, ON189040, and OQ613679-OQ613686) or differed in two nucleotide positions (OL471268 and OL471269). The strain from Slovenia was deposited in the CBS biobanks of the Westerdijk Fungal Biodiversity Institute (Utrecht, The Netherlands) as CBS 150848. Pathogenicity of the strain was tested by spraying ca. 3×105 conidia as a watery spore suspension onto each leaf of 6 greenhouse-grown and 3 wk-old common bean plantlets (cv. KIS Amand). Nonsterile commercial substrate (Potgrond H, AGRO-FertiCrop) was used and natural light conditions at ambient temperatures (18-23°C) applied. Sterile water was sprayed on 6, equally grown negative control plants. Treated plants showed small brownish spots after 3 wks similar to those described by Yang et al. (2014) on soybean. Setose acervuli formed within 5 days after detached leaves were incubated in moist chambers. No acervuli formed on negative control plants. Conidia re-isolated from these acervuli and obtained cultures were morphologically identical to originally obtained conidia and cultures and those used for performing the pathogenicity test. Anthracnose is an important disease of common bean attributed to various races of C. lindemuthianum (Sacc. & Magnus) Briosi & Cavara (Nunes et al. 2021). Reporting an additional agent potentially able to cause diseases in common bean and so far not known to occur in Europe is of high relevance as the various genetic bean lines used in Europe may show alternative susceptibility levels to it. However, symptoms caused by C. incanum seem to be less severe as those caused by C. lindemuthianum and the species belongs to the C. spaethianum species complex, whose members have so far not been considered as pathogens of economic importance (Talhinhas & Baroncelli 2021). Yang et al. (2014) based C. incanum on isolates from soybean petioles (USA) and associated it with common bean by re-identifying strain ATCC 64682 obtained by Tu (1990) in Canada. Database queries revealed that it was encountered also on sugar beet (USA; Hanson et al. 2023) and on various crop hosts in China (e.g., chili; Diao et al. 2017), but not in Europe. The work was funded by the Ministry of Agriculture, Forestry and Food and conducted as part of research programs P4-0072 and P4-0431, financed by the Slovenian Research and Innovation Agency ARIS, and the Horizon 2020 project INCREASE funded by the European Union.

First Report of Globisporangium (Pythium) mastophorum causing Damping-off / Root Rot on Parsley in Slovenia.

Pythium-like species cause damping-off symptoms of various hosts, including umbelliferous crops. In April 2023, parsley plantlets (Petroselinum crispum), showing stunted growth, yellowing, decayed roots and damping-off, were obtained from a nursery in central Slovenia, where parsley was grown in polystyrene trays in a greenhouse. Nearly 30% of plants were symptomatic. Sampled roots of ten plants contained ornamented oogonia (avg. 33.3 ± 1.4 µm in diam) with conical projections (5.2 ± 0.5 µm long) (Figure S1 A, B) in microscopically analyzed squash mounts. The pathogen was isolated from root pieces treated for surface disinfection with 0.5% sodium hypochlorite for 30 s, and washed with sterile water. Four 1-2 mm root pieces were taken from each of 10 plants, plated on the selective medium P5ARP, and incubated at 21 °C. Mycelia emerging from root pieces were transferred to carrot piece agar (CPA). Twenty-two equally looking oomycetous colonies were obtained; all sampled plants were infested. Oogonia formed by all colonies were similar to those observed on decayed roots and suggested that Globisporangium (Pythium) mastophorum is the causal disease agent. Analyses of partial β-tubulin (Kroon et al. 2004) and mitochondrial cytochrome c oxidase I (COI) gene sequences (Robideau et al. 2011) confirmed the identification. Obtained COI (Genbank accession number OR725417) sequence was 100% identical to that from G. mastophorum strain CBS 375.72 (EU350523), whereas the β-tubulin sequence (OR725416) corresponded to 99.6 % pairwise identity (KJ595502). Further, pathogenicity of an obtained isolate was tested on 4 wk-old curly leaf (cv. Petra F1) parsley. Half of a 7 d-old CPA culture, consisting of mycelium and oogonia, was finely cut and mixed with ca 50 ml of nonsterile commercial substrate (Potgrond H, AGRO-FertiCrop) in each of six 400 ml pots. Pots were filled with ca 300 ml additional substrate, into which 5 parsley seedlings were planted. Control plants were treated equally but with sterile CPA. Plantlets were watered with sterile tap water and held at ambient light conditions and temperature (night 18 °C - day 23 °C). After 14 d, inoculated plants started wilting and yellowing and showed stunted growth. After 21 d, roots were severely decayed and the seedlings damped-off (Figure S1 C). Four pieces each from 10 decayed roots were plated. Thirty-one pieces revealed pythium-like colonies. Obtained isolates were morphologically identical to the strain used for inoculation and identified as G. mastophorum. Control plants developed no foliar or root symptoms and no pythium-like species was obtained. Agricultural advisors observed occurrence of parsley damping-off also in other nurseries in Slovenia what may lead to spreading the pathogen to parsley in production fields and private gardens. The case emphasizes the need for implementing phytosanitary measures in order to eliminate primary inoculum. Reports from field-infected plants showed that G. mastophorum is a pathogen of parsley in Australia (Petkowski et al. 2013) and the USA (Tsuchida et al. 2018), and celery in the Czech Republic (Šafránková and Holková 2017). Others isolated G. mastophorum from parsley in The Netherlands (online database of the Westerdijk Fungal Biodiversity Institute, strain CBS 243.86). However, the here described case is, to the best of our knowledge, one of the rare documentations of damping-off due to G. mastophorum in Europe (Šafránková and Holková 2017) and the first in Slovenia. Funding: The work was funded by the Ministry of Agriculture, Forestry and Food of Slovenia, and Slovenian Research and Innovation Agency (ARIS Programs P4-0431 and P4-0072).

Peer Review Statement

All papers published in this volume have been reviewed through processes administered by the Editors. Reviews were conducted by expert referees to the professional and scientific standards expected of a proceedings journal published by IOP Publishing.• Type of peer review: Double Anonymous• Conference submission management system: Morressier• Number of submissions received: 15• Number of submissions sent for review: 15• Number of submissions accepted: 12• Acceptance Rate (Submissions Accepted / Submissions Received × 100): 80• Average number of reviews per paper: 2• Total number of reviewers involved: 20• Contact person for queries: Name: Siti Aekbal Salleh Email: aekbal@uitm.edu.my Affiliation: Universiti Teknologi MARA - Institute for Biodiversity and Sustainable Development

Preface

The 2nd International Conference on Biodiversity and Sustainable Development 2023 - “Forging a collective and resilient path towards sustainable development for all life,” organized by the Institute of Biodiversity and Sustainable Development, was a program based on seminars/ lectures that involved Educational Institutions Public Higher Education from within and outside the country, as well as research and industry agencies that were directly involved in research work based on biodiversity and sustainable development, whether in the field of natural science, architecture, or engineering and technology.This program also aimed to improve collaboration between researchers (staff and students), UiTM with participants from all over the world, as well as with research agencies inside and outside the country. The conference was the first initiative of the newly established institute to fuel the spirit of knowledge sharing among researchers and subsequently produce indexed publications.Through this program, participants were exposed to papers where the presentation of these papers could expand and produce expert energy, especially in the field of sustainable development, who were able to realize something new with more innovation.Lastly, we would like to give a big applause and thanks to all the authors for their presentations and papers. Their contributions have generously contributed to the intellectual exchange of useful information, idea and knowledge that is so vital towards tackling the challenges the world facing now.The Editorial TeamIBIOSDG 2023List of Committee, Conference Information are availabel in this Pdf.

First Report of Diplodia intermedia Causing Canker and Dieback Diseases on Apple Trees in Canada.

A dieback of apple trees (Malus domestica (Suckow) Borkh.) associated with cankers was observed in commercial orchards in southwestern Ontario, Canada, in 2019. Fifteen 2 to 10-year-old symptomatic trees were collected from three orchards exhibiting up to 37% disease incidence. Small sections of diseased wood (1 cm long) were surface sterilized with 70% ethanol for 30 sec and 1% NaClO for 20 min, rinsed thrice in sterile water, placed on 2% PDA (Difco) amended with kanamycin (50 mg liter-1), and incubated at 22°C for 5 days in the dark (Ilyukhin et al. 2023). Fungal colonies that were consistently isolated were hyphal-tipped, transferred to individual PDA plates and incubated at 22°C for 7 days in the dark. Purified isolates with same characteristics were classed into morphotypes. One morphotype was initially white and turned dark olivaceous with dense aerial mycelium. Pycnidia were produced on pine needles on PDA (Fig. S2) after incubation at 22°C for 17 days in the dark. Conidia were brown, aseptate, ovoid, and measured 27.9 to 31.3 μm x 12.1 to 14.2 μm (mean ± S.D. of 15 conidia = 29.9 ± 0.9 μm × 13.2 ± 0.6 μm), the typical morphology of a Diplodia sp. (Phillips et al. 2012). Genomic DNA was extracted from a 7-day-old culture of a representative isolate M45-28, using the Plant/Fungi DNA Isolation Kit (Norgen Biotech, Canada). The internal transcribed spacer (ITS), translation elongation factor 1-α (EF1-α) and β-tubulin gene regions were amplified and sequenced with primers ITS1/ITS4, EF1-728F/EF1-986R and Bt2a/Bt2b and deposited in GenBank with accession numbers MZ970605, MZ995430 and MZ995431, respectively. Based on the sequence, the fungus was identified as Diplodia intermedia A.J.L. Phillips et al. and matched isolates from different hosts and countries (ITS: 100%, MG220378; EF1-α: 100%, MG220385; β-tubulin: 99.24%, MT592502). The maximum likelihood-based phylogenetic analysis of ITS, EF1-α and β-tubulin concatenated sequences was performed using IQ-Tree 2.2.2.7 (Minh et al. 2020). M45-28 was clustered with high bootstrap support values with D. intermedia isolates from the Westerdijk Fungal Biodiversity Institute collection, including the ex-holotype (CBS 124462) (Fig. S1). A living culture of M45-28 was deposited in the Canadian Collection of Fungal Cultures (DAOMC 252253). Pathogenicity assay was conducted by inoculating mycelial plugs from a 7-day-old culture of M45-28 into wounds made on the trunk of 5 eight-month-old potted healthy 'Royal Gala' apple seedlings. Five control seedlings were inoculated with sterile plugs. Canker symptoms appeared 15 days after inoculation, spread around, up and down the main stem from the inoculation point, and by 7 weeks the upper portion of the seedling was dead (Fig. S2). Diplodia intermedia was re-isolated from all inoculated seedlings and species identity was confirmed by sequencing as described above, fulfilling Koch's postulates. Control seedlings remained symptomless and the fungus was not isolated from the wood. Diplodia intermedia was reported to cause cankers on apple in Uruguay (Delgado-Cerrone et al. 2016), wild apple (Malus sylvestris) in Portugal (Phillips et al. 2012), grapevines in France (Comont et al. 2016) and forest trees in Iran (Kazemzadeh Chakusary et al. 2019). To the best of our knowledge, this is the first report of D. intermedia causing canker and dieback diseases on apple trees in Canada. Further studies are required to better understand the epidemiology involved in the dynamic spread of the disease in order to recommend an adequate phytosanitary program for its control.

Cytospora: an important genus of canker pathogens

Cytospora species have commonly been reported as important plant pathogenic fungi with wide host ranges and geographic distributions. With the increase in the number of cryptic species being described, a comprehensive global taxonomic revision of the genus Cytospora is required. The present study includes 399 isolates from 32 countries. These isolates were subjected to DNA sequence analysis for five genomic loci (ITS, act1, rpb2, tef1-α and tub2). Based on these data, it could be confirmed that Cytospora, Leucostoma, Valsa, Valsella and Valseutypella are congeneric. Furthermore, 111 species of Cytospora could also be reassessed, 44 species and four combinations newly introduced, and new typifications proposed for a further three species. Three asexual morphological groups (including 13 asexual morphological types) and three sexual morphological groups (including eight sexual morphological types) were designated. The present study explored the species diversity of Cytospora and re-evaluated the identity of all cultures in the Westerdijk Fungal Biodiversity Institute (Utrecht, The Netherlands) that were deposited as either Cytospora or as one of its related genera. This is the most comprehensive phylogenetic analysis thus far conducted on Cytospora and the results contribute to an increased understanding of the taxonomy of these important fungi. It is also hoped that the findings will lead to improved management strategies for diseases associated Cytospora species.

Records and distribution of House Crow Corvus splendens within the eThekwini Municipality from August 2019 to August 2023

House Crows Corvus splendens are originally from southern Asia and are considered one of the most invasive birds in the world (Meininger et al. 1980, Nyári et al. 2006, Ryall 2010). They are invading parts of South Africa, mostly along the coastal areas in three provinces (Western Cape, Eastern Cape, and KwaZulu-Natal) (SABAP2). Here we discuss the distribution of House Crows within the eThekwini Municipality, Durban, KwaZulu-Natal from 2019–2023 records collected by the eThekwini Municipality and South African National Biodiversity Institute (SANBI) officials. The record includes the one known roosting site within the Durban Central and most preferred areas within the city.

Phenotypic characterization and seed viability test in ex-situ conserved Ethiopian cultivated barley (Hordeum vulgare L.) landraces

BackgroundNowadays, most of the Ethiopian barley landraces had been lost from farmer’s field and exclusively found ex-situ conserved at the Ethiopian Biodiversity Institute (EBI). Those ex-situ conserved are generally believed to be representative of the original population and possess high genetic diversity and important unique genes that are useful for tackling the various biotic and abiotic stresses in the face of the current climate change. Thus, this research was aimed at testing the performance of 150 ex-situ conserved landraces that had been collected from Arsi and Bale highlands, Southeastern Ethiopia. The landraces were tested at multiple test locations over two years (2021 and 2022).ResultsAll the tested landraces showed a good germination rate regardless of their long storage duration. In addition, performance of all the qualitative traits revealed a varying frequency for each character state. For example, most of the accessions (51.3%) had six kernel row numbers (KRN). All the remaining accessions had two rows (28.7%) and irregular KRN with variable lateral florets (20%). Likewise, some of the quantitative traits considered showed a significant variation among the landraces. However, there observed a significant variation for all the interaction effects in some of the traits considered signifying the importance of considering environment effects while targeting genetic selection and improvement of ex-situ conserved germplasms. The phenotypic coefficients of variation (PCV) were considerably high to medium in most of the traits considered including seed yield per hectare (SYPH) but with no associated higher genotypic coefficients of variation (GCV). Moreover, all the traits showed a far greater phenotypic coefficient of variation (PCV) to that of genotypic coefficients of variation (GCV) once again suggesting the pronounced effect of environmental factors to the variation. This was far supported by the significantly higher absolute magnitudes in phenotypic correlation compared to their corresponding genotypic correlation in most of the traits. Low estimates of heritability and genetic advance observed in all the traits considered except seed yield per hectare indicate importance of the trait for selection in Ethiopian barley improvement programs. Clustering patterns of the accessions, in narrow sense, revealed the existence of low divergence among the samples.ConclusionEthiopian barley landraces are promising candidates for further yield improvement and conservation. However, further regular testing and screening should be conducted for the ex-situ conserved landraces because of the current erratic climate change. In addition, more robust molecular marker systems could be used to clearly reveal the extents of genetic diversity and to facilitate the breeding and conservation of Ethiopian barley landraces.

First report of Neofusicoccum parvum causing stem blight and dieback of highbush blueberry in the Czech Republic.

Neofusicoccum parvum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips is a cosmopolitan pathogen causing dieback of multiple diverse woody hosts including highbush blueberry (Vaccinium corymbosum L.). This fungus can survive inside colonized plants without causing any symptoms for several years. Once the endophytic lifestyle is switched to the parasitic one, the symptoms of dieback can rapidly occur (bronze leaves, necroses under the bark, apoplexy) and the plant usually declines within a few weeks (Slipper and Wingfield 2007). In August 2022, blueberry plants displaying symptoms described above were observed in a production orchard located in Hovorany, the Czech Republic. Around 3 % of 1000 observed plants were symptomatic. In order to identify the pathogen, leaves, stems and roots of three diseased plants were collected, sectioned into small pieces (5 × 5 mm), surface sterilized (60 s in 75% ethanol, followed by 60 s in 1% sodium hypochlorite and rinsed three times using sterile distilled water), plated on potato dextrose agar (PDA) supplemented with 0.5 g/liter of streptomycin sulfate (PDAS) (Biosynth, Staad, Switzerland) and incubated at 25°C for 2 weeks at dark. Newly developed mycelia were immediately transferred to fresh PDA plates and purified by single-spore or hyphal-tip isolation. In total 33 fungal isolates were obtained. All the 33 isolates shared similar morphology and resembled Botryosphaeriaceae spp. Colonies on PDA (7 d at 25°C) were felty, white to iron grey in the centre. Conidiomata were observed on sterile pine needles on 2 % water agar (WA) at 25°C under near-UV light after 2 wks (110-220 × 60-175 μm). Conidia (n=30) were cylindrical to ellipsoidal, hyaline, 0(-1)-septate, (3.8-8.1 × 2-3 μm). Two representative isolates were deposited at the Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands (CBS 149846 and CBS 149847). The partial internal transcribed spacer (ITS) regions, beta-tubulin gene (tub2) and translation elongation factor 1-alpha (tef) gene were amplified from genomic DNA of both isolates following primers and protocols previously described (Eichmeier et al. 2020). Newly generated sequences were deposited in NCBI GenBank (acc. nos. ITS: OQ376566, OQ376567; tub2: OQ401701, OQ401702 and tef: OQ401699, OQ401700), being >99% identical (ITS 483/484 nt, tub2 426/430 nt and tef 230/232 nt) with the ex-type ITS (AY236943), tub2 (AY236888) and tef (AY236917) sequences of N. parvum strain CMW9081. Phylogenetically, newly obtained isolates grouped with ex-type and another three cultures of N. parvum in the three gene-based phylogenetic tree with strong 98/1.0 (BP/PP) support. To confirm pathogenicity, one-year-old canes of ten two-year-old V. corymbosum plants grown in pots were wounded by a 5 mm diam cork borer, and a 5-mm mycelial plug of a 7-day-old culture of both (CBS 149846 and CBS 149847) strains (five plants per strain) was inserted into the wound. Ten plants were inoculated with sterile PDA plugs and served as controls. Wounds were covered by sterile wet cotton, sealed with Parafilm® and inoculated plants were maintained in a growth chamber at 20 °C with 12/12 h light/dark period. Within two weeks, inoculated shoots changed colour from green to dark brown and exhibited dark necroses under the bark; after one month inoculated plants declined, while controls remained symptomless. The pathogen was reisolated from the inoculated plants with 100 % re-isolation rate, and its identity confirmed by sequencing ITS region. The experiment was repeated. Neofusicoccum parvum causing dieback of highbush blueberry was already reported from Australia, California, Chile, China, Italy, Mexico, Portugal and Uruguay (Rossman et al. 2023). Pecenka et al. (2021) reported a presence of another pathogen - Lasiodiplodia theobromae (Pat.) Griffon & Maubl. from the same plantation. This suggests that stem blight and dieback of highbush blueberry is caused by more than one Botryosphaeriaceae spp. as it was previously proved by Xu et al. (2015). To the best of our knowledge, this is the first report of stem blight and dieback of highbush blueberry caused by N. parvum in the Czech Republic.

First report of Sclerotinia sclerotiorum causing Sclerotinia wilt of hop (Humulus lupulus) in Poland.

The common hop (Humulus lupulus L., Cannabaceae) is a perennial plant cultivated in the temperate climate zone and used in the brewing and pharmaceutical industry. In June 2021, symptoms of wilting and subsequent drying of shoots were observed on hop plants (cv. Lubelski) in Lubelskie Province, in Poland (50°55'30.5"N, 22°10'35.4"E). Wilted shoots showed no symptoms of chlorosis. Usually both healthy and wilted shoots were present on the same plant. Approx. 20% of the plants in the 2 hectare hop garden showed these symptoms. An inspection of the underground parts of the infected shoots revealed a brown necrosis of the tissues partly covered by white mycelium with black sclerotia. These symptoms were characteristic for Sclerotinia sclerotiorum (Lib.) de Bary (Bolton et al. 2006), but this pathogen has never been detected in hop gardens in Poland before. In order to confirm the preliminary diagnosis, shoots from five different plants with symptoms of necrosis were collected, disinfected with 1% sodium hypochlorite for 1 min, rinsed with sterile water and dried. Twelve fragments from partially necrotized tissue were placed on potato dextrose agar (PDA) amended with chlortetracycline hydrochloride. After three days of incubation at room temperature and daylight, 75% of the explants had white or light grey mycelia present. Pure cultures were obtained by transplanting mycelium to fresh PDA. Within 4 days, the mycelium has reached the diameter of Petri dishes (90 mm). On PDA at room temperature and daylight, black spherical or cylindrical sclerotia formed after 6-14 days. Sclerotial size was 1.0 to 10.0 x 1.0 to 5.0 mm (average 2.8 x 2.0 mm; n = 57 from 3 plates). Five isolates were subjected to DNA extraction. Then ITS region was amplified and sequenced using primers ITS1/ITS4 (White et al. 1990). The sequences obtained from the five fungal isolates were identical with each other and BLAST analysis revealed also 100% identity with the GenBank records of S. sclerotiorum (e.g. KT224645, Baturo-Ciesniewska et al. 2017). One representative sequence of isolate Ss5HL was deposited to GenBank (OQ998981). Pathogenicity of the isolate Ss5HL was confirmed in inoculation tests on approx. 30 cm high, young shoots of hop plants (cv. Lubelski) grown from rootstock for 4 weeks in the greenhouse. Five plants were inoculated by placing mycelial discs from a 7-day-old culture on shoots and covering them with wet sterilized cotton pads and aluminum foil. Two control plants were treated in the same way but instead of mycelial discs pure agar discs were placed on the shoots. Then plants were kept in a climate chamber (80% relative humidity, 15-h light at 22°C, 9-h dark at 18°C). All fungal inoculated shoots wilted within 3-4 days, then necrosis developed and spread from the place of inoculation up the shoot. No tissue necrosis was observed below the place of inoculation. The control plants remained asymptomatic. The inoculation test was carried out twice with the same result. Fungal cultures reisolated from the inoculated shoots were morphologically identical with the culture used as inoculum. Isolate Ss5HL was deposited in the collection of the Westerdijk Fungal Biodiversity Institute (CBS 150077).To our knowledge, this is the first case of Sclerotinia wilt of hops in Poland and also in Europe, with the exception of one, nearly 100 years old report from the United Kingdom (Salmon and Ware 1936). S. sclerotiorum rarely occurs on hop but it can cause severe yield reduction if pathogen accumulates in the soil.

The Virtual Museum: an African biodiversity database holding more than two million records

This paper describes the history of the Virtual Museum, originally developed in 2005 for the Southern African Reptile Conservation Assessment (SARCA), which was sponsored by the South African National Biodiversity Institute (SANBI). The Virtual Museum grew to have 17 sections and the associated database, in 2023, contained 2.2 million biodiversity records from Africa. We summarize the major outputs of this initiative, and discuss potential future uses of the database.

Structuring Information from Plant Morphological Descriptions using Open Information Extraction

Structuring Information from Plant Morphological Descriptions using Open Information Extraction

Connecting the Dots: Aligning human capacity through networks toward a globally interoperable Digital Extended Specimen (DES) infrastructure

Thanks to substantial support for biodiversity data mobilization in recent decades, billions of occurrence records are openly available, documenting life on Earth and enabling timely research, awareness raising, and policy-making. Initiatives across local to global scales have been separately funded to serve different, yet often overlapping audiences of data users, and have developed a variety of platforms and infrastructures to meet the needs of these audiences. The independent progress of biodiversity data providers has led to innovations as well as challenges for the community at large as we move towards connecting and linking a diversity of information from disparate sources as Digital Extended Specimens (DES). Recognizing a need for deeper and more frequent opportunities for communication and collaboration across the globe, an ad-hoc group of representatives of various international, national, and regional organizations have been meeting virtually since 2020 to provide a forum for updates, announcements, and shared progress. This group is provisionally named International Partners for the Digital Extended Specimen (IPDES), and is guided by these four concepts: Biodiversity, Connection, Knowledge and Agency. Participants in IPDES include representatives of the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), American Institute of Biological Sciences (AIBS), Biodiversity Collections Network (BCoN), Natural Science Collections Alliance (NSCA), Distributed System of Scientific Collections (DiSSCo), Atlas of Living Australia (ALA), Biodiversity Information Standards (TDWG), Society for the Preservation of Natural History Collections (SPNHC), National Specimen Information Infrastructure of China (NSII), and South African National Biodiversity Institute (SANBI), as well as individuals involved with biodiversity informatics initiatives, natural science collections, museums, herbaria, and universities. Our global partners group strives to increase representation from around the globe as we aim to enable research that contributes to novel discoveries and addresses the societal challenges leading to the biodiversity crisis. Our overarching mission is to expand on the community-driven successes to connect biodiversity data and knowledge through coordination of a globally integrated network of stakeholders to enable an extensible technical and social infrastructure of data, tools, and working practices in support of our vision. The main work of our group thus far includes publishing a paper on the Digital Extended Specimen (Hardisty et al. 2022), organizing and hosting an array of activities at conferences, and asynchronous online work and forum-based exchanges. We aim to advance discussion on topics of broad interest to our community such as social and technical capacity building, broadening participation, expanding social and data networks, improving data models and building a backbone for the DES, and identifying international funding solutions. This presentation will highlight some of these activities and detail progress towards a roadmap for the development of the human network and technical infrastructure necessary to support the DES. It provides an opportunity for feedback from and engagement by stakeholder communities such as TDWG and other initiatives with a focus on data standards and biodiversity informatics, as we solidify our plans for the future in support of integrated and interconnected biodiversity data and credit for those doing the work.

First report of Stemphylium leaf blight of onion (Allium cepa) caused by Stemphylium vesicarium in Italy.

In July 2019, severe leaf symptoms were observed on onion plants (Allium cepa L. cv. Dorata di Parma) in a commercial field located in the municipality of Medicina (Bologna, Emilia-Romagna region), in northern Italy. Diseased leaves showed yellowish-pale-brown and oval-shaped lesions, which later coalesced in larger necrotic areas, and black leaf tips. As the disease progressed, conidia developed on the necrotizing leaves, until premature desiccation of the whole plants. Disease incidence of approximately 70% was calculated in the affected field, together with yield losses that were estimated to be above 30%. Symptomatic tissue fragments excised from the leaf lesions were surface disinfested with NaOCl 1% for 2 minutes, rinsed with sterile water and transferred onto potato dextrose agar (PDA). Fungi were consistently isolated after 5 days of incubation at 27 ± 1°C in the dark. Single spore isolation was performed on PDA to obtain 7 pure cultures, whose morphological characteristics were consistent with the description of Stemphylium vesicarium (Ellis 1971). DNA from a representative single spore isolate was extracted and the internal transcribed spacer region (ITS) of ribosomal DNA (rDNA) was amplified using the universal primers P-ITS1 and P-ITS4 (White et al. 1990). The PCR product was sequenced and deposited in GenBank (Accession No. OP144057). A BLAST search in CBS-KNAW collection bank (Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands) showed 100% identity for the ITS gene with the strain of S. vesicarium under accession number CBS 124749. Moreover, the PCR assay using the primer pair KES 1999 and KES 2000 (Graf et al. 2016) for the cytochrome b gene displayed the specific fragments of 420 bp for S. vesicarium. The isolate was tested for pathogenicity on onion (potted plants cv. Texas Early Gran, fourth leaf stage) by spraying 4 ml of a conidial suspension (1 × 104 conidia/ ml) per plant. Inoculated and non-inoculated (sprayed with sterile distilled water) plants were kept at 24 ± 1°C and 90% relative humidity with a 16-h photoperiod. Seven days after inoculation, disease assessment was performed. Inoculated plants showed typical Stemphylium leaf blight (SLB) symptoms, similar to those observed in the field. No symptoms developed on the water-inoculated plants. S. vesicarium was consistently reisolated from the artificially inoculated onion plants and identified using a PCR assay, according to Graf et al. (2016). The assay was repeated twice with the same results. SLB is currently reported worldwide and it is considered a re-emerging threat and a truly challenging fungal disease, which can result in yield and quality losses of up to 90% in onion crops (Hay et al. 2021). In Italy, S. vesicarium has been reported several years ago on pear (Ponti et al. 1982) and, more recently, on radish sprouts (Belisario et al. 2008), chili pepper (Vitale et al. 2017) and spinach (Gilardi et al. 2022). To our knowledge, this is the first report of S.vesicarium on onion in Italy. Our results stress that development and implementation of innovative Integrated Pest Management (IPM) strategies are urgently needed to ensure an effective control of SLB, since only a few moderately resistant onion varieties are available (Hay et al. 2021) and no fungicides are currently registered to specifically control SLB in Italy. Further studies are underway to elucidate the pathogen geographic distribution and assess the impact of this disease on the onion crop in Italy.

A Phytogeographical Classification and Survey of the Indigenous Browse Flora of South Africa, Lesotho, and Eswatini

Rangelands in South Africa, Lesotho, and Eswatini contain a rich diversity of valuable fodder trees and shrubs. This research is the first attempt to document the regional diversity and distribution of these browse resources. Scientific publications, textbooks, databases, and published reports were accessed to compile a database of plant species that were recorded as utilised by ruminants and non-ruminants. Relevant forage attributes, such as functional traits as well as utilisation traits, were added to each species record. Thereafter, distribution records were extracted from the South African National Biodiversity Institute’s Botanical Database of South Africa and analysed with numerical techniques to establish phytogeographical patterns. A total of 613 plant species from 76 families have been recorded, which formed seven distinct phytochoria, termed the Central Arid, Eastern Subtropical, Highland Temperate, Moist Temperate, Northern Subtropical, Southern Temperate, and Western Arid browse-choria. Key families and species, as well as functional and utilisation traits, are discussed, focusing on key species present in the browse-choria. This browse database, together with the earlier compiled Leguminosae and Poaceae databases, will be used to prioritise indigenous southern African plant species/infraspecific taxa to be collected for the conservation of genetic resources and future evaluations for potential development as forage crops.

Vegetation structure and composition at different elevational intervals in the arid Tankwa Karoo National Park, South Africa

Study area: The study was conducted in the Tankwa Karoo National Park, one of the driest areas in South Africa. Historic overgrazing has resulted in the poor and often degraded state of vegetation in large parts of the Tanqua Karoo region.Aim: This study assessed the spatial variation of vegetation structure and composition in the three main vegetation types namely: Tanqua Karoo (TK), Tanqua Wash Riviere (TWR) and Tanqua Escarpment Shrubland (TES), along an elevational gradient.Method: Using the point intercept survey method, vegetation cover, plant height, species diversity, life forms, proportions of perennials and annuals were examined in 43 sites, widely distributed in these vegetation types.Results: There were 150 vascular plant species belonging to 83 genera and 29 families recorded across all sites. The most diverse vegetation type was TES with 96 species belonging to 61 genera and 26 families. The vegetation structure was comprised mainly of shrubs and dwarf shrubs with a high proportion of leaf and stem succulent species. The mean perennial vegetation cover throughout the study area was 28 and annuals covered 22%, but this cover varied significantly between the vegetation types. The most dominant life forms were chamaephytes, which comprised 64% of all species, with cryptophytes (18%), therophytes (16%) and nanophanerophytes (2%) less abundant. Surveyed sites in the TES showed a clear association with each other but there was an overlap in the species composition and environmental conditions between some TWR and TK sites. This study highlighted the important role of elevation and topography as drivers of vegetation characteristics.Conclusion: The findings from this study can be used as a vegetation baseline to identify and prioritise degraded areas for active restoration in order to limit further degradation. Considering climate change, elevational studies may provide additional insight into species dynamics across landscapes.Taxonomic reference: Plants of Southern Africa Checklist (South African National Biodiversity Institute 2016).Abbreviations: ANOVA = analysis of variance; GPS = Global Positioning System; LFA = Landscape Function Assessment; NDVI = Normalized difference vegetation index; PCA = principal component analysis; PCo-A = principal co-ordinate analysis; TES = Tanqua Escarpment Shrubland; TK = Tanqua Karoo; TKNP = Tankwa Karoo National Park; TWR = Tanqua Wash Riviere.