Dead wood fungi in North America: an insight into research and conservation potential

DNA Barcoding for an Undergraduate Class

DNA technique is a topic mandatorily covered in a biology and biochemistry undergraduate curriculum. Inquiry-based pedagogy is proven to be the most effective way of learning, and DNA barcoding method allows to merge necessary-to-study experimental techniques such as DNA isolation and purification, PCR, and basic BLAST search into a two- or three-week inquiry-based student project. It also provides a research-based experience to the students, who, when organized in groups, can design their own DNA-barcoding project if they wish. Here, we describe how DNA barcoding can be offered in an undergraduate college or advanced high school settings. This chapter is intended to help college and high school instructors to include DNA barcoding in their classes.

MycoPins: a metabarcoding-based method to monitor fungal colonization of fine woody debris

The MycoPins method described here is a rapid and affordable protocol to monitor early colonization events in communities of wood-inhabiting fungi in fine woody debris. It includes easy to implement field sampling techniques and sample processing, followed by data processing, and analysis of the development of early dead wood fungal communities. The method is based on fieldwork from a time series experiment on standard sterilized colonization targets followed by the metabarcoding analysis and automated molecular identification of species. This new monitoring method through its simplicity, moderate costs, and scalability paves a way for a broader and scalable project pipeline. MycoPins establishes a standard routine for research stations or regularly visited field sites for monitoring of fungal colonization of woody substrates. The routine uses widely available consumables and therefore presents a unifying method for monitoring of fungi of this type.

Citizen science helps in the study of fungal diversity in New Jersey

The history of fungal diversity of the Northeastern United States is currently fragmentary and restricted to particular functional groups or limited geospatial scales. Here, we describe a unique by its size, lifespan and data originators dataset, to improve our understanding of species occurrence and distribution across the state and time. Between the years 2007 to 2019, over 30 parks and nature preserves were sampled during forays conducted by members of the New Jersey Mycological Association (USA), a nonprofit organization of fungi enthusiasts. The dataset contains over 400 000 occurrences of over 1400 species across the state, made up mostly of the phylum Basidiomycota (89%) and Ascomycota (11%), with most observations resolved at the species level (>99%). The database is georeferenced and openly accessible through the Global Biodiversity Information Facility (GBIF) repository. This dataset marks a productive endeavor to contribute to our knowledge of the biodiversity of fungi in the Northeastern United States leveraging citizen science to better resolve biodiversity of this critical and understudied kingdom.

Importance of Dead Wood in Virgin Forest Ecosystem Functioning in Southern Carpathians

Dead wood (DW) is an important component of sustainable forest management and climate change mitigation. Three research plots (each with an area of 1 ha), located in virgin forests in the Southern Carpathians (Semenic P20, Retezat–Zănoaga, and Făgăraș–Șinca), were installed in order to study the synergies between DW and climate change mitigation effects. Data on the dendrometric characteristics of standing and lying DW, the species, and the degree of decay were recorded. The aboveground biomass (AGB) and carbon stock (CS) of the DW were also determined. The DW volume was between 48 m3·ha−1 and 148 m3·ha−1, with the total volume (dead and alive) ranging between 725 m3·ha−1 and 966 m3·ha−1. The DW volume distribution shows a decreasing trend, with the most suitable theoretical distributions for describing this being the lognormal, the 2P Weibull, and the 2P-Gamma. The AGB ranged between 17 t·ha−1 and 30 t·ha−1 and showed a decreasing trend according to altitude. The CS was between 8 t·ha−1 and 14.33 t·ha−1. A slow decomposition rate for the hardwood was identified by analyzing the relationship between the surface and volume of the DW. This highlighted the capacity of DW to store carbon for a long period of time.

Exploring DNA in biochemistry lab courses: DNA barcoding and phylogenetic analysis

DNA structure has been leveraged in a variety of facets that allow scientists to perform a range of assays, including ones for identification of species, establishing evolutionary relationships between taxa, or even identifying individuals. Here, we present a DNA barcoding method as practical, hands-on approach that connects several experimental techniques in one sequence to teach the principles behind DNA isolation, purification, PCR, sequencing, and phylogeny analysis. Our set of exercises is designed for a teaching university laboratory setting. The three laboratory class assignments utilize DNA from a mushroom (can be purchased at a supermarket) and provide a pipeline to guide students through the process of identifying an unknown sample, like in many research laboratories. The third assignment can be used as a stand-alone exercise on phylogeny analysis and can be taught remotely. Students explore the theory behind the standard molecular techniques and apply it in a hands-on setting that involves experimental design, sample preparation, and use of hallmark molecular instruments.

Rare species of wood-inhabiting fungi are not local

Wood-inhabiting fungal communities are a diverse and ecologically critical part of forest ecosystems, yet the spatial structure of fungal biodiversity in these ecosystems is largely unknown. Legislation allowed harvesting of deadwood from temperate rainforests on conservation lands in New Zealand following Cyclone Ita in 2014. Harvesting guidelines specified widely spread harvesting, on the assumption that rare fungal species may be highly spatially restricted, but were not based on quantitative assessment. We sampled fungi in and on logs of Dacrydium cupressinum (Podocarpaceae) a long-lived, common, canopy tree in lowland New Zealand forests. DNA was extracted from 81 logs varying in decay state across a 40 km long region of West Coast (South Island) forests, and sequenced using general fungal primers for metabarcoding to identify OTUs (operational taxonomic units). We examined three axes of rarity: occupancy, dominance when present, and niche breadth (as spatial extent and decay state specialization). Low-occupancy fungi were common, including a group of infrequently occurring but dominant when present fungi, the majority of which were Ascomycota. Despite this, there was an overall positive relationship between occupancy and dominance. Widespread, dominant fungi were most commonly Basidiomycota. Testing all fungal OTUs, there were no more fungi with maximum range sizes < 4 km than would be expected at random. Of the 351 low-occupancy OTUs found two to four times, only 12 had maximum range sizes < 900 m, and there was no more spatial restriction at scales < 900 m than would be expected by random chance, although there was some evidence of niche breadth restriction based on decay state similarity. The results show that fungal communities in deadwood are highly diverse, and include many rare taxa. Nonetheless, the lack of fungal OTUs with spatial restriction at scales < 900 m suggests that spatially dispersed timber harvesting will not mitigate risks of harvesting to rare fungal biodiversity.

Polypores, Agrobacterium and ivy damage on Hungarian ancient trees

Ancient trees are important habitats, confer vital ecological roles and function as cultural legacies. Old trees with large girth are keystone structures in various ecosystems. We aim to present which species amongst the greatest Hungarian trees (and some other phanerophyte plants) are damaged by polypores (the most important agents of wood decay), Agrobacterium tumefaciens (usually causing root tumour) or ivy (competing against the native vegetation and causing windthrow damage) and at what extent and frequency; and whether there is a relationship between these types of damage and the origin of the species (native or adventive) or its situation (solitary or surrounded by other trees). We measured 2,000 trees, belonging to 29 native and 43 non-native species. Polypore infection could be detected in 12.2% of the observed 531 settlements, 22.8% are damaged by Agrobacterium and 29.6% by ivy, while 51.2% by other types of pests and diseases. Altogether, one third of the observed 2000 ancient or veteran trees suffered from one or more types of damage. A total of 33.5% of the native species (519 specimens out of 1550) and 28.7% of the adventives (129 trees out of 450) are damaged by any (or more than one) of the mentioned infections or ivy. Mostly, damage occurred to those old trees that stand in a park or forest, while the single (solitary) trees were usually healthy. The most infected regions are the western and south-western counties, while the Northern Hungarian Mountain Range is much less affected, despite its great sample size. Low damage was detected in the Great Hungarian Plain, but the number of sample areas and veteran trees was also low here. The damage to old trees remains without any management or healing in Hungary, since the only effective solution would be prevention.