Decaying Plant Material Research Articles

Parathozetella microsperma gen. & sp. nov. from the Brazilian Amazon

A new genus and species of asexual ascomycete, Parathozetella microsperma, are described and illustrated from decaying plant material collected from three rainforest areas in Mato Grosso and Pará States. The new genus resembles Thozetella in sporodochial conidiomata, presence of microawns, and enteroblastic monophialidic conidiogenesis that produces lunate conidia, but Parathozetella can be easily distinguished by the absence of setulae.

Contribution to Chaetosphaeriaceae—Kionochaeta setosimplicia sp. nov. from Thailand

Species of Kionochaeta are saprobes commonly associated with decaying plant materials. As a part of surveys on freshwater microfungi, Kionochaeta-like taxon was found on a submerged decaying twig at a rivulet in the protected forest area of Khao Kheow Open Zoo (KKOZ), eastern Thailand. This taxon is microscopically similar to Kionochaeta, but clearly differs by its accessory lateral setiform branches and sterile setae arising beside the conidiophores. Multi-locus phylogenies inferred from four combined loci (SSU, ITS, LSU and RPB2) demonstrated that this taxon clustered as a unique clade with Kionochaeta species (Chaetosphaeriaceae, Chaetosphaeriales). Therefore, we introduce this taxon as K. setosimplicia, and it is phylogenetically close to K. castaneae, K. ramifera and K. pughii. Kionochaeta setosimplicia is separated from K. microspora and K. spissa. In Kionochaeta clade 1, K. nanophora forms a basal taxon. Kionochaeta ivoriensis forms a distinct Kionochaeta clade 2 distant from other Kionochaeta.

Natural nest substrates influence squamate embryo physiology but have little effect on hatchling phenotypes.

Vertebrate embryos require access to water; however, many species nest in terrestrial habitats that vary considerably in moisture content. Oviparous, non-avian reptiles have served as models to understand how environmental factors, like moisture availability, influence development because eggs are often exposed to prevailing environments in the absence of parental care. Though much research demonstrates the importance of water absorption by eggs, many ecological factors that influence moisture availability in natural nests have received little attention. For example, the type of substrate in which nests are constructed is understudied. We experimentally incubated eggs of the brown anole lizard (Anolis sagrei) in 2 naturally occurring nest substrates that were treated with varying amounts of water to determine how natural substrates influence development at different moisture concentrations. One substrate consisted of sand and crushed seashells and the other was mostly organic material (i.e. decayed plant material). Both are common nesting substrates at our field site. When controlling for water uptake by eggs, we found that egg survival and hatchling phenotypes were similar between substrates; however, embryos developed more quickly in the sand/shell substrate than the organic substrate, indicating substrate-specific effects on embryo physiology. These results demonstrate that different natural substrates can result in similar developmental outcomes if the water available to eggs is comparable; however, some aspects of development, like developmental rate, are affected by the type of substrate, independent of water availability. Further study is required to determine how natural substrates influence embryo physiology independent of water content.

Reflections on Menisporopsis, Multiguttulispora and Tainosphaeria Using Molecular and Morphological Data.

The genera Menisporopsis, Multiguttulispora and Tainosphaeria (Chaetosphaeriaceae) are saprobes inhabiting decaying plant material. This study is based on an integrated morpho-molecular characterisation to assess their generic concepts and explore phylogenetic relationships. Menisporopsis is revealed as polyphyletic, and species with 1-septate conidia and synnemata growing unilaterally along the seta are placed in the new segregate genus Arcuatospora. Codinaea dimorpha and C. triseptata are shown to be congeneric with Multiguttulispora sympodialis, the type species. Two new combinations are proposed: M. sympodialis is found conspecific with M. dimorpha. The Tainosphaeria complex is resolved into three genera. We found that the morphological separation of three groups within the genus is consistent with phylogenetic relationships. Tainosphaeria s. str. is accepted with five species. Tainosphaeria aseptata and T. lunata are transferred to the newly erected Phialoturbella, whereas T. obclavata is revealed as conspecific with Phialogeniculata guadalcanalensis, reducing it to a synonym. A new genus Flectospora is erected for a chloridium-like fungus nested in the Tainosphaeria clade. Based on molecular evidence, we show that asymmetrical, scolecosporous ascospores are a unique teleomorphic characteristic among family members. Therefore, we propose new combinations for Chaetosphaeria hispida in Paragaeumannomyces and Ch. spinosa in the new genus Ericiosphaeria, both exhibiting this rare morphotype.

Myxomycetes Diversity of Batman Province and Hasankeyf district

This study was conducted on samples collected from 13 different localities in the province of Batman and Hasankeyf district between 2017-2019. The samples were consisted of various leaves, bark, decayed plant material and animal waste. All of the samples collected were cultured in moisture chamber technique to develop myxomycetes sporophore. In addition, myxomycetes were collected from natural area on materials. As a result of field and moist chamber collection, 33 taxa obtained and identified belonging to 5 ordo, 7 families and 12 genera and added to mycetozoa of Turkey.

Phylogeny, Global Biogeography and Pleomorphism of Zanclospora.

Zanclospora (Chaetosphaeriaceae) is a neglected, phialidic dematiaceous hyphomycete with striking phenotypic heterogeneity among its species. Little is known about its global biogeography due to its extreme scarcity and lack of records verified by molecular data. Phylogenetic analyses of six nuclear loci, supported by phenotypic data, revealed Zanclospora as highly polyphyletic, with species distributed among three distantly related lineages in Sordariomycetes. Zanclospora is a pleomorphic genus with multiple anamorphic stages, of which phaeostalagmus-like and stanjehughesia-like are newly discovered. The associated teleomorphs were previously classified in Chaetosphaeria. The generic concept is emended, and 17 species are accepted, 12 of which have been verified with DNA sequence data. Zanclospora thrives on decaying plant matter, but it also occurs in soil or as root endophytes. Its global diversity is inferred from metabarcoding data and published records based on field observations. Phylogenies of the environmental ITS1 and ITS2 sequences derived from soil, dead wood and root samples revealed seven and 15 phylotypes. The field records verified by DNA data indicate two main diversity centres in Australasia and Caribbean/Central America. In addition, environmental ITS data have shown that Southeast Asia represents a third hotspot of Zanclospora diversity. Our data confirm that Zanclospora is a rare genus.

A review on the role of plant in pharmaceuticals and personal care products (PPCPs) removal in constructed wetlands.

Pharmaceuticals and personal care products (PPCPs) cause ongoing water pollution and consequently have attracted wide attention. Constructed wetlands (CWs) show good PPCP removal performance through combined processes of substrates, plants, and microorganisms; however, most published research focuses on the role of substrates and microorganisms. This review summarizes the direct and indirect roles of wetland plants in PPCP removal, respectively. These direct effects include PPCP precipitation on root surface iron plaque, and direct absorption and degradation by plants. Indirect effects, which appear more significant than direct effects, include enhancement of PPCP removal through improved rhizosphere microbial activities (more than twice as much as bulk soil) stimulated by radial oxygen loss and exudate secretions, and the formation of supramolecular ensembles from PPCPs and humic acids from decaying plant materials which improving PPCPs removal efficiency by up to four times. To clarify the internal mechanisms of PPCP removal by plants in CWs, factors affecting wetland plant performance were reviewed. Based on this review, future research needs have been identified.

Dynamics of Aspergillus fumigatus in Azole Fungicide-Containing Plant Waste in the Netherlands (2016-2017).

The treatment of patients suffering from Aspergillus diseases is hampered due to infections with Aspergillus fumigatus that are already resistant to medical azoles. Previous work has suggested that A. fumigatus likely gains resistance through environmental azole exposure in so-called hot spots. Here, we investigated A. fumigatus resistance dynamics over time at three sites at which farmers used azole fungicides for crop protection. Over 16 months, 114 samples were taken from stockpiles of decaying plant waste. A. fumigatus and azole fungicide residues were ubiquitously present in the plant waste. On average, 105A. fumigatus CFU/g was recovered, of which roughly half were itraconazole and tebuconazole resistant. Similar tandem repeat-mediated resistance mechanisms were found in colonies cultured from plant waste as reported in clinical azole-resistant isolates. Our results show a consistent high burden of azole-resistant A. fumigatus in azole-containing plant waste and underscores the need to further investigate resistance-reducing interventions and transmission routes.IMPORTANCEAspergillus fumigatus is consistently present independently on season at a high abundance in plant waste material throughout the sampling period. Our study confirmed that long-term storage sites of azole-containing decaying plant material can indeed be considered hot spots, which can sustain resistance development and maintenance in A. fumigatus Roughly half of individual isolates were azole resistant and carried genetic mutations that are highly similar to those found in patients with azole-resistant invasive aspergillosis. Our work suggests that environmental sources of azole resistance in A. fumigatus may be important, underscoring the need for further studies on environment-to-patient transmission routes.

Complex plant-derived organic aerosol as ice-nucleating particles – more than the sums of their parts?

Abstract. Quantifying the impact of complex organic particles on the formation of ice crystals in clouds remains challenging, mostly due to the vast number of different sources ranging from sea spray to agricultural areas. In particular, there are many open questions regarding the ice nucleation properties of organic particles released from terrestrial sources such as decaying plant material. In this work, we present results from laboratory studies investigating the immersion freezing properties of individual organic compounds commonly found in plant tissue and complex organic aerosol particles from vegetated environments, without specifically investigating the contribution from biological particles, which may contribute to the overall ice nucleation efficiency observed at high temperatures. To characterize the ice nucleation properties of plant-related aerosol samples for temperatures between 242 and 267 K, we used the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) cloud chamber and the Ice Nucleation SpEctrometer of the Karlsruhe Institute of Technology (INSEKT), which is a droplet freezing assay. Individual plant components (polysaccharides, lignin, soy and rice protein) were mostly less ice active, or similarly ice active, compared to microcrystalline cellulose, which has been suggested by recent studies to be a proxy for quantifying the primary cloud ice formation caused by particles originating from vegetation. In contrast, samples from ambient sources with a complex organic matter composition (agricultural soils and leaf litter) were either similarly ice active or up to 2 orders of magnitude more ice active than cellulose. Of all individual organic plant components, only carnauba wax (i.e., lipids) showed a similarly high ice nucleation activity as that of the samples from vegetated environments over a temperature range between 245 and 252 K. Hence, based on our experimental results, we suggest considering cellulose as being representative for the average ice nucleation activity of plant-derived particles, whereas lignin and plant proteins tend to provide a lower limit. In contrast, complex biogenic particles may exhibit ice nucleation activities which are up to 2 orders of magnitude higher than observed for cellulose, making ambient plant-derived particles a potentially important contributor to the population of ice-nucleating particles in the troposphere, even though major uncertainties regarding their transport to cloud altitude remain.

Genome-wide study of saprotrophy-related genes in the basal fungus Conidiobolus heterosporus.

Conidiobolus spp. are important saprophytic basal fungi. However, to date, no genomic-level data for decaying plant materials in the genus Conidiobolus has been reported. Here, we report that the 33.4-Mb genome of Conidiobolus heterosporus encodes 10,857 predicted genes. Conidiobolus heterosporus harbors 394 CAZyme-encoding genes belonging to 4 major modules but does not encode a polysaccharide lyase (PL). Many carbohydrate esterases (CEs) belonging to the family CE12 play crucial roles as pectin acetylesterases, and 14 genes were upregulated in the IM (fungus grown on inducing medium) among 17 expressed CE12 family genes. In addition, most of the genes in the GH132 CAZyme family showed a greater than 5-fold increase in expression in the IM compared with that in the wild type. Furthermore, 122 P450-encoding genes grouped into 11 families were detected in the fungal genome, most of which belonged to the CYP547 family (36 genes) followed by CYP548 (27 genes) and CYP5856 (25 genes). Interestingly, members of the families CYP5014 and CYP5136 were identified, the first time such enzymes have been described in a fungus. Our findings provide new insights into the genomics and genomic features of the saprophytic basal fungus C. heterosporus.Key Points• Genome of the saprobiotic basal fungus C. heterosporus was sequenced and analyzed.• 394 CAZymes but no PL family genes were found and expression levels were determined.• CE12 and GH132 proteins may play roles in the pectin and plant material degradation.• A large number of P450s but few P450 families existed in the fungus.

Genome Comparison Identifies Different Bacillus Species in a Bast Fibre-Retting Bacterial Consortium and Provides Insights into Pectin Degrading Genes

Retting of bast fibres requires removal of pectin, hemicellulose and other non-cellulosic materials from plant stem tissues by a complex microbial community. A microbial retting consortium with high-efficiency pectinolytic bacterial strains is effective in reducing retting-time and enhancing fibre quality. We report comprehensive genomic analyses of three bacterial strains (PJRB 1, 2 and 3) of the consortium and resolve their taxonomic status, genomic features, variations, and pan-genome dynamics. The genome sizes of the strains are ~3.8 Mb with 3729 to 4002 protein-coding genes. Detailed annotations of the protein-coding genes revealed different carbohydrate-degrading CAZy classes viz. PL1, PL9, GH28, CE8, and CE12. Phylogeny and structural features of pectate lyase proteins of PJRB strains divulge their functional uniqueness and evolutionary convergence with closely related Bacillus strains. Genome-wide prediction of genomic variations revealed 12461 to 67381 SNPs, and notably many unique SNPs were localized within the important pectin metabolism genes. The variations in the pectate lyase genes possibly contribute to their specialized pectinolytic function during the retting process. These findings encompass a strong foundation for fundamental and evolutionary studies on this unique microbial degradation of decaying plant material with immense industrial significance. These have preponderant implications in plant biomass research and food industry, and also posit application in the reclamation of water pollution from plant materials.

Population Structure of Fusarium graminearum Isolated from Different Sources in One Area over the Course of Three Years.

Fusarium head blight (FHB) is an important crop disease worldwide and is mainly caused by members of the Fusarium graminearum species complex. F. graminearum sensu stricto is the most common cosmopolitan and predominant FHB causal agent in Europe. Thus far, the majority of studies have focused on the primary hosts (wheat and barley) of this pathogen, while the relationships between other sources of infection remain unclear. We monitored and sampled test fields over the course of 3 years and acquired 804 F. graminearum isolates from different sources: primary hosts and other plant species included in the crop rotations, weeds from the test fields, decaying plant residue, soil samples, and crop seed. Of these isolates, 73.3% had the 15-acetyldeoxynivalenol genotype and 26.7% had the 3-acetyldeoxynivalenol genotype. F. graminearum isolation rates from weeds (>50%) were much higher than from soil (< 10%) or decaying plant matter (4%). Variable number of tandem repeat markers were used for population analysis. Noticeable genetic differentiation was detected between isolates from living plants and soil biome. In contrast, absence of any noticeable division between primary and alternative plant host communities indicates the importance of weeds and other segetal plants for FHB control and prevention.

Food/Feed and Environmental Risk Assessment of Insect Resistant Genetically Modified Maize 1507 for Cultivation, Import, Processing, Food and Feed Uses under Directive 2001/18/EC and Regulation (EC) No 1829/2003 (C/ES/01/01, C/NL/00/10, EFSA/GMO/NL/2004/02)

Food/Feed and Environmental Risk Assessment of Insect Resistant Genetically Modified Maize 1507 for Cultivation, Import, Processing, Food and Feed Uses under Directive 2001/18/EC and Regulation (EC) No 1829/2003 (C/ES/01/01, C/NL/00/10, EFSA/GMO/NL/2004/02)

Insects and other invertebrate remains from the coffin of a 17th century bishop in Lund Minster, S Sweden

An extraordinarily diverse and well-preserved material, including the remains of 47 insect taxa and 12 taxa of other invertebrates, extracted from the 17th century burial of Bishop Peder Winstrup in Lund Minster, is presented and discussed in terms of the treatment of the body, activities connected with the burial and faunal significance. The invertebrate assemblages include species from gardens, insects feeding on living plants as well as dried or decaying plant matter. Many of the species are regarded as closely associated with humans (synanthropic), and a number of these are associated with outbuildings, such as stables and cellars. The absence of species associated with cadavers (necrophilous taxa) in the studied insect material is significant. The most plausible explanation is that the bishop died, and was buried during the winter, when such species are inactive, and thus precluded from colonising the body. A number of species were recorded which are today rare or very rare in southern Sweden. This is a strong indication that they once were more common and widespread, perhaps due to a greater prevalence of their preferred habitats. Sweden’s earliest fossil bedbug is also amongst the finds.

Vertebrate Carrion in Land Snail Diets: First Observation of Amphibian (Plethodontid Salamander) Consumption by a Terrestrial Snail in Southern Appalachia

The diet of land snails that are detritivores usually consists of decaying plant material and fungi. Animal carrion is also consumed, and is usually composed of invertebrates like earthworms and other snails. However, while working at the Coweeta Hydrologic Laboratory in southwestern North Carolina in 2017, I observed a land snail (most likely Cepaea nemoralis [Grove Snail]) feeding on the carcass of a Desmognathus aeneus (Seepage Salamander), a vertebrate. This is the first report of a land snail feeding on an amphibian carcass in the United States. The Erratum for this article can be found in Southeastern Naturalist 19(3).

Food/Feed and Environmental Risk Assessment of Insect Resistant Genetically Modified Maize MON810 for Cultivation, Seed Production, Import, Processing and Feed Uses under Directive 2001/18/EC (Notification C/F/95/12/02)

Food/Feed and Environmental Risk Assessment of Insect Resistant Genetically Modified Maize MON810 for Cultivation, Seed Production, Import, Processing and Feed Uses under Directive 2001/18/EC (Notification C/F/95/12/02)

A Small Horizontally Transferred Gene Cluster Contributes to the Sporulation of Alternaria alternata.

Horizontal gene transfer (HGT) has been identified as an important source of genomic innovation in fungi. However, how HGT drove the evolution of Alternaria alternata, a necrotrophic fungus which can be ubiquitously isolated from soil and various plants and decaying plant materials is largely known. In this study, we identified 12 protein-encoding genes that are likely acquired from lineages outside Pezizomycotina. Phylogenetic trees and approximately unbiased comparative topology tests strongly supported the evolutionary origin of these genes. According to their predicted functions, these HGT candidates are involved in nitrogen and carbohydrate metabolism. Especially, five genes of them were likely transferred as a physically linked cluster from Tremellales (Basidiomycota). Functionally knocking out the five-gene cluster in an A. alternata isolate causing citrus brown spot resulted in an 80% decrease in asexual spore production in the deletion mutant. We further knocked out each of these five genes in this cluster and the resultant single-gene deletion mutants exhibited a various degree of reduction in spore production. Except for conidiation, functions of these genes associated with vegetative growth, stress tolerance, and virulence are very limited. Our results provide new evidence that HGT has played important roles over the course of the evolution of filamentous fungi.

Environmental Risk Assessment of Insect Resistant Genetically Modified Maize MON810 for Cultivation, Seed Production, Import, Processing and Feed Uses under Directive 2001/18/EC (Notification C/F/95/12/02)

Environmental Risk Assessment of Insect Resistant Genetically Modified Maize MON810 for Cultivation, Seed Production, Import, Processing and Feed Uses under Directive 2001/18/EC (Notification C/F/95/12/02)

Preliminary Environmental Risk Assessment of Insect Resistant Genetically Modified Maize MON 89034 for Cultivation (EFSA/GMO/BE/2011/90)

Preliminary Environmental Risk Assessment of Insect Resistant Genetically Modified Maize MON 89034 for Cultivation (EFSA/GMO/BE/2011/90)

Soil as A Fundamental Element of Silviculture for Sustainable Tropical Rain Forest Management

Soil is a fundamental element of a forest ecosystem. It provides physical support for plants, absorbs and retains water, retains and supplies essential nutrients and other chemical compounds for plant growth, and provides nutrients cycling services and habitats for organisms. Soils underlying tropical rainforest ecosystems have distintive characteristics. The soils are old and highly-weathered and leached, highly-acidic, lacking of weatherable minerals and nutrient reserves, and dominated by low-activity clays with poor retention capacity to nutrients. Under such conditions, rainforest productivity relies heavily on the top layer of the soils, consisting of decaying plant materials and animal remains in which most biological activities such as nutrient cycling occur. These characteristics indicate that rainforest ecosystem is very fragile. When the forest trees overlying such soils are cut down, the logged over areas lose this thick layer and then the forest will seriously degrade. Therefore maintaining vegetation on soil surface is imperative. This paper aims to discuss properties of soils in the tropical rainforests, to identify soil-related damages due to silvicultural practices, and to find preventive and currative actions in order to promote sustainable tropical rainforest management.