The Application of NIRS to Determine Animal Physiological Traits for Wildlife Management and Conservation

Comparison of DNA quantity and quality from fecal samples of mammals transported in ethanol or lysis buffer

Using fecal microbial community profiles through sequencing approaches helps to unravel the intimate interplay between health, wellness, and diet in wild animals with their environment. Ensuring the proper preservation of fecal samples before processing is crucial to ensure reliable results. In this study, we evaluated the efficiency of two different preservation methods, considering the following criteria: DNA yield, quality and integrity, and microbial community structure based on Oxford Nanopore amplicon sequencing of the V3-V4 region of bacterial 16S rRNA and protozoa 18S rRNA genes. Eighteen matched pairs of mammalian fecal samples were collected and transported in 99.8% ethanol and lysis buffer; processing occurred between 55 and 461 days post-collection. Wilcoxon signed-rank tests were used to analyze quantitative measurements for paired samples. The A260/280 ratio, a measure of nucleic acid purity, was assessed descriptively for each media, and the Bartlett test evaluated dispersion of this ratio. A Fisher test was performed to compare the number of positive reactions for DNA extraction or PCR amplification of the 16S and 18S rRNA genes between both media. The concentration of total DNA and amplicons, as well as the number of reads obtained in sequencing, was significantly higher in the samples preserved with lysis buffer compared to ethanol, with magnitudes up to three times higher. Electrophoretic analysis of total DNA and amplicons further confirmed superior DNA integrity in lysis buffer preserved samples. The A260/280 values  obtained using the lysis buffer were of optimal purity (mean: 1.92) and with little dispersion (SD: 0.27); on the other hand, the ethanol samples also presented an excellent average quality (mean: 1.94), but they were dispersed (SD: 1.10). For molecular studies using mammalian feces, the lysis buffer reagent proved to be a reliable solution for their collection, conservation, and storage.

Remote Sensing of Geomorphodiversity Linked to Biodiversity—Part III: Traits, Processes and Remote Sensing Characteristics

Remote sensing (RS) enables a cost-effective, extensive, continuous and standardized monitoring of traits and trait variations of geomorphology and its processes, from the local to the continental scale. To implement and better understand RS techniques and the spectral indicators derived from them in the monitoring of geomorphology, this paper presents a new perspective for the definition and recording of five characteristics of geomorphodiversity with RS, namely: geomorphic genesis diversity, geomorphic trait diversity, geomorphic structural diversity, geomorphic taxonomic diversity, and geomorphic functional diversity. In this respect, geomorphic trait diversity is the cornerstone and is essential for recording the other four characteristics using RS technologies. All five characteristics are discussed in detail in this paper and reinforced with numerous examples from various RS technologies. Methods for classifying the five characteristics of geomorphodiversity using RS, as well as the constraints of monitoring the diversity of geomorphology using RS, are discussed. RS-aided techniques that can be used for monitoring geomorphodiversity in regimes with changing land-use intensity are presented. Further, new approaches of geomorphic traits that enable the monitoring of geomorphodiversity through the valorisation of RS data from multiple missions are discussed as well as the ecosystem integrity approach. Likewise, the approach of monitoring the five characteristics of geomorphodiversity recording with RS is discussed, as are existing approaches for recording spectral geomorhic traits/ trait variation approach and indicators, along with approaches for assessing geomorphodiversity. It is shown that there is no comparable approach with which to define and record the five characteristics of geomorphodiversity using only RS data in the literature. Finally, the importance of the digitization process and the use of data science for research in the field of geomorphology in the 21st century is elucidated and discussed.

Near-Infrared Spectroscopy and Mode Cloning (NIR-MC) for In-Situ Analysis of Crude Protein in Bamboo

This study develops Near-Infrared Spectroscopy (NIRS) and Mode-Cloning (MC) for the rapid assessment of the nutritional quality of bamboo leaves, the primary diet of giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens). To test the NIR-MC approach, we evaluated three species of bamboo (Phyllostachys bissetii, Phyllostachys rubromarginata, Phyllostachys aureosulcata). Mode-Cloning incorporated a Slope and Bias Correction (SBC) transform to crude protein prediction models built with NIR spectra taken from Fine–Ground leaves (master mode). The modified models were then applied to spectra from leaves in the satellite minimal processing modes (Course–Ground, Dry–Whole, and Fresh–Whole). The NIR-MC using the SBC yielded a residual prediction deviation (RPD) = 2.73 and 1.84 for Course–Ground and Dry–Whole sample modes, respectively, indicating a good quantitative prediction of crude protein for minimally processed samples that could be easily acquired under field conditions using a portable drier and grinder. The NIR-MC approach also improved the model of crude protein for spectra collected from Fresh–Whole bamboo leaves in the field. Thus, NIR-MC has the potential to provide a real-time prediction of the macronutrient distribution in bamboo in situ, which affects the foraging behavior and dispersion of giant and red pandas in their natural habitats.