A molecular-based identification resource for the arthropods of Finland

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.

Environmental DNA assessment of airborne plant and fungal seasonal diversity

Environmental DNA (eDNA) metabarcoding and metagenomics analyses can improve taxonomic resolution in biodiversity studies. Only recently, these techniques have been applied in aerobiology, to target bacteria, fungi and plants in airborne samples. Here, we present a nine-month aerobiological study applying eDNA metabarcoding in which we analyzed simultaneously airborne diversity and variation of fungi and plants across five locations in North and Central Italy. We correlated species composition with the ecological characteristics of the sites and the seasons. The most abundant taxa among all sites and seasons were the fungal genera Cladosporium, Alternaria, and Epicoccum and the plant genera Brassica, Corylus, Cupressus and Linum, the latter being much more variable among sites. PERMANOVA and indicator species analyses showed that the plant diversity from air samples is significantly correlated with seasons, while that of fungi varied according to the interaction between seasons and sites. The results consolidate the performance of a new eDNA metabarcoding pipeline for the simultaneous amplification and analysis of airborne plant and fungal particles. They also highlight the promising complementarity of this approach with more traditional biomonitoring frameworks and routine reports of air quality provided by environmental agencies.

Characterization of the microbiome associated with in situ earthen materials

BACKGROUND

The current increase in public awareness of environmental risks is giving rise to a growth of interest in the microbiological safety of buildings. In particular, microbial proliferation on construction materials can be responsible for the degradation of indoor air quality that can increase health-risk to occupants. Raw earth materials are still widely used throughout the world and, in some cases, are linked to heritage habitats, as in the southwest of France. Moreover, these building materials are currently the subject of renewed interest for ecological and economic reasons. However, the microbial status of earthen materials raises major concerns: could the microbiome associated with such natural materials cause disease in building occupants? Very few analyses have been performed on the microbial communities present on these supports. Characterizing the raw earth material microbiome is also important for a better evaluation and understanding of the susceptibility of such materials to microbial development. This study presents the distribution of in situ bacterial and fungal communities on different raw earth materials used in construction. Various buildings were sampled in France and the microbial communities present were characterized by amplicon high-throughput sequencing (bacterial 16S rRNA gene and fungal ITS1 region). Bacterial culture isolates were identified at the species level by MALDI-TOF mass spectrometry.

RESULTS

The major fungal and bacterial genera identified were mainly associated with conventional outdoor and indoor environmental communities, and no specific harmful bacterial species were detected on earthen materials. However, contrary to expectations, few human-associated genera were detected in dwellings. We found lower microbial alpha-diversity in earthen material than is usually found in soil, suggesting a loss of diversity during the use of these materials in buildings. Interestingly enough, the main features influencing microbial communities were building history and room use, rather than material composition.

CONCLUSIONS

These results constitute a first in-depth analysis of microbial communities present on earthen materials in situ and may be considered as a first referential to investigate microbial communities on such materials according to environmental conditions and their potential health impact. The bacterial and fungal flora detected were similar to those found in conventional habitats and are thought to be mainly impacted by specific events in the building's life, such as water damage.

Fungal DNA barcoding

Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.