Late Holocene climate anomaly concurrent with fire activity and ecosystem shifts in the eastern Australian Highlands

MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.

A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples

High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol−chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.

Influence of Climatic Factors on Lightning Fires in the Primeval Forest Region of the Northern Daxing’an Mountains, China

Forest fires lead to permafrost degradation and localized drought, and regional droughts increase the probability of forest fires, leading to a positive feedback loop between climate change and fires. However, the relationship between fire occurrence and climatic factors change is unclear for boreal forests, which represent the largest land-based biome and stock of carbon. Here, we analyzed the relationship between lightning fire occurrence and meteorological and topographic factors based on the fire frequency, burned area, and meteorological data from the primeval forest region of the northern Daxing’an Mountains in China. We found that lightning fires occurred most frequently at an altitude of 600 to 700 m. From 1999 to 2019, the frequency of lightning fires showed an overall upward trend, whereas the affected area had no obvious change. It can be attributed to fire suppression efforts and greatly increased investment in fire prevention in China. Snow cover had a strong regulatory effect on the start and end dates of lightning fires for seasonal cycle. The frequency of lightning fires was positively correlated with the average temperature, maximum temperature, and surface evaporation and negatively correlated with precipitation and surface soil moisture (0–10 cm). The result will be useful in the spatially assessment of fire risk, the planning and coordination of regional efforts to identify areas at greatest risk, and in designing long-term lightning fires management strategies.