Opening Pandora's Box: Neglected Biochemical Potential of Permafrost-Associated Fungal Communities in a Warming Climate

Permafrost, a vast storage reservoir of frozen organic matter, is rapidly thawing due to climate change, releasing previously preserved carbon into the environment. This phenomenon has significant consequences for microbial communities, including fungi, inhabiting permafrost-associated regions. In this review, we delve into the intricate interplay between permafrost thawing and fungal diversity and functionality with an emphasis on thermokarst lakes. We explore how the release of organic carbon from thawing permafrost alters the composition and activities of fungal communities, emphasizing the potential for shifts in taxonomic diversity and functional gene expression. We discuss the formation of thermokarst lakes, as an example of permafrost thaw-induced ecological disruptions and their impact on fungal communities. Furthermore, we analyze the repercussions of these changes, including effects on nutrient cycling, plant productivity, and greenhouse gas (GHG) emissions. By elucidating the multifaceted relationship between permafrost thaw and aquatic fungi, this review provides valuable insights into the ecological consequences of ongoing climate change in permafrost-affected regions.

Defense Mechanisms Induced by Celery Seed Essential Oil against Powdery Mildew Incited by Podosphaera fusca in Cucumber

This study aimed to evaluate the effectiveness of essential oil extracted from celery (Apium graveolens) seeds (CSEO) for the control of powdery mildew of cucumber (Cucumis sativus) incited by Podosphaera fusca and to investigate the metabolic and genetic defense mechanisms triggered by the treatment with this essential oil in cucumber seedlings. The main compounds in the CSEO as determined by gas chromatography-mass spectrometry (GC-MS) analysis were d-limonene, 3-butyl phthalide, β-selinene, and mandelic acid. The treatment with CSEO led to an increase in the content of both chlorophyll and phenolic/flavonoid compounds in cucumber leaves. In greenhouse tests, the application of CSEO reduced by 60% the disease severity on leaves of cucumber plants and stimulated the activity of defense-related enzymes such as β-1,3-glucanase, chitinase, phenylalanine ammonia-lyase, peroxidase, and polyphenol oxidase. Moreover, treatment with CSEO induced overexpression of β-1,3-glucanase, chitinase, and phenylalanine ammonia-lyase genes. A highly significant correlation was found between the β-1,3-glucanase, chitinase, and phenylalanine ammonia-lyase enzymatic activities and the relative expression of the corresponding encoding genes in both inoculated and non-inoculated cucumber seedlings treated with the essential oil. Overall, this study showed that CSEO is a promising eco-friendly candidate fungicide that can be exploited to control cucumber powdery mildew.

Genetic Variation of Puccinia triticina Populations in Iran from 2010 to 2017 as Revealed by SSR and ISSR Markers

Puccinia triticina is a major wheat pathogen worldwide. Although Iran is within the Fertile Crescent, which is supposed to be the center of origin of both wheat and P. triticina, the knowledge of the genetic variability of local populations of this basidiomycete is limited. We analyzed 12 inter simple sequence repeats (ISSRs) and 18 simple sequence repeats (SSRs) of 175 P. triticina isolates sampled between 2010 and 2017 from wheat and other Poaceae in 14 provinces of Iran. SSRs revealed more polymorphisms than ISSRs, indicating they were more effective in differentiating P. triticina populations. Based on a dissimilarity matrix with a variable mutation rate for SSRs and a Dice coefficient for ISSRs, the isolates were separated into three large groups, each including isolates from diverse geographic origins and hosts. The grouping of SSR genotypes in UPGMA dendrograms was consistent with the grouping inferred from the Bayesian approach. However, isolates with a common origin clustered into separate subgroups within each group. The high proportion of heterozygous alleles suggests that in Iran clonal reproduction prevails over sexual reproduction of the pathogen. A significant correlation was found between SSR and ISSR genotypes and the virulence phenotypes of the isolates, as determined in a previous study.

Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy

Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.

Globisporangium coniferarum sp. nov., associated with conifers and Quercus spp

During a survey of gardens in Shiraz County, Iran, aimed at identifying oomycetes associated with roots of ornamental trees, a species of Globisporangium with distinctive morphological characters separating it from other known species in this genus was recovered from conifers and occasionally from a Quercus sp. Five isolates of this species were characterised. Phylogenetic analyses of nuclear (ITS and βtub) and mitochondrial (cox1 and cox2) loci using Bayesian inference and maximum likelihood analyses as well as their distinct morphological and cultural characteristics (e.g., abundant production of chlamydospores; globose, ellipsoid to ovoid sporangia; amorphous oogonia with a smooth wall; paragynous to rarely hypogynous antheridia and 1-5 antheridia per oogonium; mostly plerotic oospores) revealed that these isolates belong to a new Globisporangium species grouping in the phylogenetic clade G of Pythium sensu lato. This paper formally describes Globisporangium coniferarum sp. nov. as a new species and compares it with other phylogenetically related and already known Globisporangium species, including G. nagaii, G. violae, G. paddicum, G. okanoganense, G. iwayamae and G. canariense. Citation: Salmaninezhad F, Aloi F, Pane A, Mostowfizadeh-Ghalamfarsa R, Cacciola SO (2022). Globisporangium coniferarum sp. nov., associated with conifers and Quercus spp. Fungal Systematics and Evolution 10: 127-137. doi: 10.3114/fuse.2022.10.05.

Fusarium and Neocosmospora Species Associated with Rot of Cactaceae and Other Succulent Plants

Infections by Fusarium and Fusarium-like species on cacti and other succulent plants cause the syndrome known as Fusarium dry rot and soft rot. There are only few records of Fusarium species as pathogens of cacti and other succulent plants from Iran. The objective of this study was the identification and characterization of fusarioid species recovered from ornamental succulents in Shiraz County, Iran. Three fusarioid species, including F. oxysporum, F. proliferatum, and Neocosmospora falciformis (formerly F. falciforme), were recovered from 29 diverse species of cacti and other succulents with symptoms of Fusarium dry rot and soft rot. The three fungal species were identified on the basis of morphological characters and the phylogenetic analysis of the translation elongation factor1-α (tef1) nuclear gene. The F. oxysporum isolates were identified as F. oxysporum f. sp. opuntiarum. The pathogenicity of the three fusarioid species was tested on a range of economically important ornamental succulents, mostly in the Cactaceae family. The three species showed a broad host spectrum and induced different types of symptoms on inoculated plants, including soft and dry rot, chlorosis, necrotic spots, wilt, drying, root and crown rot. This is the first report of N. falciformis as a pathogen of succulent plants worldwide.

Current status of Phytophthora in Australia

Among the most economically relevant and environmentally devastating diseases globally are those caused by Phytophthora species. In Australia, production losses in agriculture and forestry result from several well-known cosmopolitan Phytophthora species and infestation of natural ecosystems by Phytophthora cinnamomi have caused irretrievable loss to biodiversity especially in proteaceous dominated heathlands. For this review, all available records of Phytophthora in Australia were collated and curated, resulting in a database of 7 869 records, of which 2 957 have associated molecular data. Australian databases hold records for 99 species, of which 20 are undescribed. Eight species have no records linked to molecular data, and their presence in Australia is considered doubtful. The 99 species reside in 10 of the 12 clades recognised within the complete phylogeny of Phytophthora. The review includes discussion on each of these species' status and additional information provided for another 29 species of concern. The first species reported in Australia in 1900 was Phytophthora infestans. By 2000, 27 species were known, predominantly from agriculture. The significant increase in species reported in the subsequent 20 years has coincided with extensive surveys in natural ecosystems coupled with molecular taxonomy and the recognition of numerous new phylogenetically distinct but morphologically similar species. Routine and targeted surveys within Australian natural ecosystems have resulted in the description of 27 species since 2009. Due to the new species descriptions over the last 20 years, many older records have been reclassified based on molecular identification. The distribution of records is skewed toward regions with considerable activity in high productivity agriculture, horticulture and forestry, and native vegetation at risk from P. cinnamomi. Native and exotic hosts of different Phytophthora species are found throughout the phylogeny; however, species from clades 1, 7 and 8 are more likely to be associated with exotic hosts. One of the most difficult challenges to overcome when establishing a pest status is a lack of reliable data on the current state of a species in any given country or location. The database compiled here for Australia and the information provided for each species overcomes this challenge. This review will aid federal and state governments in risk assessments and trade negotiations by providing a comprehensive resource on the current status of Phytophthora species in Australia. Citation: Burgess TI, Edwards J, Drenth A, et al. 2021. Current status of Phytophthora in Australia. Persoonia 47: 151-177. https://doi.org/10.3767/persoonia.2021.47.05.

Phylogenetic and Functional Diversity of Saprolegniales and Fungi Isolated from Temperate Lakes in Northeast Germany

The contribution of fungi to the degradation of plant litter and transformation of dissolved organic matter (humic substances, in particular) in freshwater ecosystems has received increasing attention recently. However, the role of Saprolegniales as one of the most common eukaryotic organisms is rarely studied. In this study, we isolated and phylogenetically placed 51 fungal and 62 Saprolegniales strains from 12 German lakes. We studied the cellulo-, lignino-, and chitinolytic activity of the strains using plate assays. Furthermore, we determined the capacity of 10 selected strains to utilize 95 different labile compounds, using Biolog FF MicroPlates™. Finally, the ability of three selected strains to utilize maltose and degrade/produce humic substances was measured. Cladosporium and Penicillium were amongst the most prevalent fungal strains, while Saprolegnia, Achlya, and Leptolegnia were the most frequent Saprolegniales strains. Although the isolated strains assigned to genera were phylogenetically similar, their enzymatic activity and physiological profiling were quite diverse. Our results indicate that Saprolegniales, in contrast to fungi, lack ligninolytic activity and are not involved in the production/transformation of humic substances. We hypothesize that Saprolegniales and fungi might have complementary roles in interacting with dissolved organic matter, which has ecological implications for carbon cycling in freshwater ecosystems.

Current status of Phytophthora in Australia

Among the most economically relevant and environmentally devastating diseases globally are those caused by Phytophthora species. In Australia, production losses in agriculture and forestry result from several well-known cosmopolitan Phytophthora species and infestation of natural ecosystems by Phytophthora cinnamomi have caused irretrievable loss to biodiversity especially in proteaceous dominated heathlands. For this review, all available records of Phytophthora in Australia were collated and curated, resulting in a database of 7 869 records, of which 2 957 have associated molecular data. Australian databases hold records for 99 species, of which 20 are undescribed. Eight species have no records linked to molecular data, and their presence in Australia is considered doubtful. The 99 species reside in 10 of the 12 clades recognised within the complete phylogeny of Phytophthora. The review includes discussion on each of these species' status and additional information provided for another 29 species of concern. The first species reported in Australia in 1900 was Phytophthora infestans. By 2000, 27 species were known, predominantly from agriculture. The significant increase in species reported in the subsequent 20 years has coincided with extensive surveys in natural ecosystems coupled with molecular taxonomy and the recognition of numerous new phylogenetically distinct but morphologically similar species. Routine and targeted surveys within Australian natural ecosystems have resulted in the description of 27 species since 2009. Due to the new species descriptions over the last 20 years, many older records have been reclassified based on molecular identification. The distribution of records is skewed toward regions with considerable activity in high productivity agriculture, horticulture and forestry, and native vegetation at risk from P. cinnamomi. Native and exotic hosts of different Phytophthora species are found throughout the phylogeny; however, species from clades 1, 7 and 8 are more likely to be associated with exotic hosts. One of the most difficult challenges to overcome when establishing a pest status is a lack of reliable data on the current state of a species in any given country or location. The database compiled here for Australia and the information provided for each species overcomes this challenge. This review will aid federal and state governments in risk assessments and trade negotiations by providing a comprehensive resource on the current status of Phytophthora species in Australia. Citation: Burgess TI, Edwards J, Drenth A, et al. 2021. Current status of Phytophthora in Australia. Persoonia 47: 151-177. https://doi.org/10.3767/persoonia.2021.47.05.

Investigation of factors affecting phytoremediation of multi-elements polluted calcareous soil using Taguchi optimization

Growing environmental concern regarding multi elements-contaminated soils reveals the necessity of paying more attention to environmentally friendly remediation techniques such as phytoremediation. A large number of factors influences phytoremediation of potentially toxic elements (PTEs) and investigation on a variety of these factors need appropriate statistical approaches such as "Taguchi optimization" which effectively decreases time and cost of experiments. In the present study, based on the Taguchi optimization method, the effects of several biological (plant type and mycorrhizal fungi (AMF)) and chemical (chelating agents, surfactants and organic acids) factors, on the phytoremediation of soils contaminated with zinc (Zn), lead (Pb), cadmium (Cd) and nickel (Ni) were investigated. The goal was to find out the most effective factors as well as the best level for each factor. The values of dry weights in roots and aerial parts of the studied plants were in orders of maize > sorghum > sunflower and sorghum > maize > sunflower, respectively. AMF was the main factor in increasing dry weight of shoots. Inoculation of AMF caused increases in root and shoot uptake of some PTEs. RESULTS: showed that phytoremediation of PTEs is element-dependent; as Zn showed the highest translocation factor (TF) and bioconcentration factor (BCF) values, while Ni showed the lowest ones and the intermediate values belonged to Pb and Cd. These results show the diverse distribution of elements in plant parts, as Zn and Ni were mostly accumulated in shoot and root, respectively. Although different factors caused impacts on phytoremediation criteria, the role of plant type in the phytoremediation of PTEs was at the first rank. Mean TF of PTEs in sunflower was 6.3 times that of maize. Sunflower showed high TF value for the four elements and translocated most of the PTEs from root to the aerial parts demonstrating phytoextraction as the main mechanism in this plant. Maize and sorghum, however, showed low TF and accumulated most of PTEs in their roots revealing phytostabilization as the main mechanism. In general, it can be concluded that plant type was the most influential factor in the phytoremediation of PTEs followed by EDTA and AMF. Taguchi optimization revealed the appropriateness and significance of different chemical and biological treatments on phytoremediation criteria of different elements.

Virulence of Leaf Rust Physiological Races in Iran From 2010 to 2017

The wheat leaf rust fungus, Puccinia triticina, has widespread geographical distribution in Iran within the Fertile Crescent region of the Middle East where wheat was domesticated and P. triticina originated. Therefore, it is of great importance to identify the prevalence and distribution of P. triticina pathotypes in this area. From 2010 to 2017, 241 single-uredinium isolates of P. triticina were purified from 175 collections of P. triticina made from various hosts in 14 provinces of Iran, and they were tested on 20 Thatcher near-isogenic lines carrying single-leaf rust resistance genes. In total, 86 pathotypes were identified, of which the pathotypes FDTTQ, FDKPQ, FDKTQ, and FDTNQ were most prevalent. No virulence for Lr2a was detected, whereas virulence for Lr1 was found only on bread wheat in a few provinces in 2016. Only isolates from durum wheat and wild barley were virulent to Lr28. Although virulence for Lr9, Lr20, and Lr26 was observed in some years, the virulence frequency for these genes was lower than that of the other Lr genes. P. triticina collections from host plants with different ploidy levels or genetically dissimilar backgrounds were grouped individually according to genetic distance. Based on these results, collections from barley, durum wheat, oat, triticale, and wild barley were different from those of bread wheat.

Three new Pythium species from rice paddy fields

In an investigation of the oomyceteous flora in rice paddy fields of Fars Province, Iran, three new Pythium species were isolated and identified on the basis of morphological features and molecular phylogenetic characteristics. Their unique morphological traits, including sexual and asexual structural characteristics (i.e., sporangial type; oogonial type and ornamentations; type and the number of antheridia per oogonium; and oospore type), cardinal temperatures, and colony morphology on various media, separated them from other known species. Using nuclear and mitochondrial genes, each species formed discrete lineages in phylogenetic analyses based on Bayesian inference and maximum likelihood methods. This paper describes these three new Pythium species, P. heteroogonium, P. longipapillum, and P. oryzicollum, and compares them with their related taxa via morphological features and molecular characteristics. Pathogenicity tests revealed the ability of P. oryzicollum to cause pre- and post-emergence damping-off, seed rot, crown rot, and reduced growth rate on rice.

Microsatellite markers for the Triticum timopheevi-derived leaf rust resistance gene Lr18 on wheat 5BL chromosome

Leaf rust, caused by Puccinia triticina, is a common wheat disease worldwide. Developing resistant cultivars through deploying new or pyramiding resistance genes in a suitable line, is the most effective approach to control this disease. However, to stack genes in a genotype, efficient and reliable markers are required. In the present study, F₂ plants and their corresponding F₃ families from a cross between the resistant line; Thatcher (Tc) Lr18, and the susceptible cultivar 'Boolani' were used to map rust resistance gene, Lr18 using SSR markers on chromosome 5BL of hexaploid wheat. The P. triticina pathotype no 15 was used to inoculate plants. Out of 20 primers tested, eight showed polymorphism between the two parents and were subsequently genotyped in the entire F₂ population. The markers Xgpw7425 and Xwmc75 flanked the locus at a distance of 0.3 and 1.2 cM, respectively. Analysis of 81 genotypes from different backgrounds with these two markers confirmed their usefulness in screening absence or presence of Lr18. Therefore, these markers can be used for gene postulation and marker-assisted selection (MAS) of this gene in wheat breeding programs in future.