Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on "Environmental DNA: What's behind the term?" by Pawlowski et al., (2020).

In a recent paper, "Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring," Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived.

Temporal dynamics of freshwater planktonic parasites inferred using a DNA metabarcoding time-series.

Parasites are important components of biodiversity and contributors to ecosystem functioning, but are often neglected in ecological studies. Most studies examine model parasite systems or single taxa, thus our understanding of community composition is lacking. Here, the seasonal and annual dynamics of parasites was quantified using a 5-year metabarcoding time-series of freshwater plankton, collected weekly. We first identified parasites in the dataset using literature searches of the taxonomic match and using sequence metadata from the National Center for Biotechnology Information (NCBI) nucleotide database. In total, 441 amplicon sequence variants (belonging to 18 phyla/clades) were classified as parasites. The four phyla/clades with the highest relative read abundance and richness were Chytridiomycota, Dinoflagellata, Oomycota and Perkinsozoa. Relative read abundance of total parasite taxa, Dinoflagellata and Perkinsozoa significantly varied with season and was highest in summer. Parasite richness varied significantly with season and year, and was generally lowest in spring. Each season had distinct parasite communities, and the difference between summer and winter communities was most pronounced. Combining DNA metabarcoding with searches of the literature and NCBI metadata allowed us to characterize parasite diversity and community dynamics and revealed the extent to which parasites contribute to the diversity of freshwater plankton communities.

Feeding behavior and activity budget of the southern yellow-cheeked crested gibbons (Nomascus gabriellae) in a lowland tropical forest.

The southern yellow-cheeked crested gibbon (Nomascus gabriellae), an endangered species native to Vietnam and Cambodia, lives exclusively in undisturbed tropical forests and depends primarily on ripe fruit for food. Although this species is highly threatened, its ecology and conservation status remain relatively unknown. In order to understand how this heavily frugivorous primate adapts to the seasonal fluctuation of fruit resources in the forest, we collected feeding behavior and ranging activity data on one group of southern yellow-cheeked crested gibbons in Cat Tien National Park, Vietnam, over 1-year period. We compared these data to information on phenological patterns at the site gleaned during a prior study. We found that the gibbons gathered most of their food from 69 different plant species and also consumed insects and bird eggs. Fruits were the main dietary item (43.3%), followed by leaves (38.4%), flowers (11.6%), and other plant parts (6.0%). A significant seasonal shift in diet was observed; fruit generally dominated the diet in the rainy season and leaves in the dry season. The gibbons often started daily activities very early (05:10 am) in the morning and also ended quite early (16:45 pm) in the afternoon. Socializing was concentrated in the early morning, feeding had a bimodal pattern of high activity levels in mid-morning and mid-afternoon, and resting was most intense at the earliest and latest hours of the day and at midday, with proportionally less time used for traveling at these times. Averaged over the annual cycle, the gibbons spent 45% of their time feeding, 31.9% resting, 14.1% traveling, and 9.0% socializing. The percentage of time allocated to different activities varied significantly across months and between the dry and rainy seasons. Monthly variation in the activity budget was strongly related to changes in diet. In the rainy season, when the gibbons ate a higher percentage of fruit, they decreased their feeding time, while increasing traveling time in search of food; conversely, in the dry season, when they fed on a higher percentage of leaves, they decreased traveling time. Overall, our results show that the activity budget and diet of the southern yellow-cheeked crested gibbon are associated with seasonal shifts in climate. This study provides information relevant to the conservation and management of this endangered species by identifying important habitat conditions for reintroducing captive animals into the wild and providing insight into dietary needs, which may be relevant to the maintenance of animals in rescue centers.

Amplicon sequencing dataset of soil fungi and associated environmental variables collected in karst and non-karst sites across Yunnan province, southwest China.

Fungi are among the most widely distributed organisms on Earth, performing key roles in nutrient cycling, disease, and the global carbon cycle. However, studies on regional-scale fungal assemblage patterns and the underlying drivers, are scarce. The aim of this research was to determine the relative importance of environmental heterogeneity and spatial distance on the metacommunity structure of soil fungi in Yunnan province, southwest China. This dataset is supplementary to research by [1] and presents 12,843 fungal operational taxonomic unit (OTU) sequences, OTU distribution and abundance across 220 samples, OTU taxonomic and ecological annotations, and environmental characteristics of the sites where the samples were collected. Differences in fungal alpha and beta diversity indices between karst and non-karst soils for the full dataset, six class-level (Agaricomycetes, Dothideomycetes, Sordariomycetes, Leotiomycetes, Tremellomycetes, and Eurotiomycetes) and four functional-level (symbiotrophs, pathotrophs, saprotrophs, and ectomycorrhizal fungi) datasets are presented.

Seasonal changes in the diversity and composition of the litter fauna in native forests and rubber plantations.

The litter layer of tropical forests supports a significant fraction of total arthropod diversity and decomposition of this layer is the main pathway by which nutrients are returned to the soil and CO2 to the atmosphere. Conversion of tropical forests to agriculture is the main threat to biodiversity and ecosystem services, and understanding effects on the litter layer is important for understanding and mitigating these impacts. We used high through-put DNA sequencing of the mitochondrial cytochrome c oxidase subunit I (COI) gene to assess seasonal changes in the diversity and composition of the litter fauna at five matched pairs of native forests and rubber plantations in tropical SW China every month for a year, and measured the environmental factors expected to drive intra-annual variation. Forests and rubber had very different arthropod assemblages throughout the year, with forests more species-rich than rubber in all months except February. Very high rates of intra-annual turnover in species composition in both forests and rubber were associated with seasonality in environmental variables, with the influence of particular variables differing among taxa. Tropical arthropods are very sensitive to seasonality and sampling at only one time of the year captures only a subset of the total community.