Mapping diversity indices: not a trivial issue

Biogeographical patterns of the soil fungal:bacterial ratio across France

Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.

Linking Land Use and Plant Functional Diversity Patterns in Sabah, Borneo, through Large-Scale Spatially Continuous Sentinel-2 Inference

Global biodiversity losses erode the functioning of our vital ecosystems. Functional diversity is increasingly recognized as a critical link between biodiversity and ecosystem functioning. Satellite earth observation was proposed to address the current absence of information on large-scale continuous patterns of plant functional diversity. This study demonstrates the inference and spatial mapping of functional diversity metrics through satellite remote sensing over a large key biodiversity region (Sabah, Malaysian Borneo, ~53,000 km2) and compares the derived estimates across a land-use gradient as an initial qualitative assessment to test the potential merits of the approach. Functional traits (leaf water content, chlorophyll-a and -b, and leaf area index) were estimated from Sentinel-2 spectral reflectance using a pre-trained neural network on radiative transfer modeling simulations. Multivariate functional diversity metrics were calculated, including functional richness, divergence, and evenness. Spatial patterns of functional diversity were related to land-use data distinguishing intact forest, logged forest, and oil palm plantations. Spatial patterns of satellite remotely sensed functional diversity are significantly related to differences in land use. Intact forests, as well as logged forests, featured consistently higher functional diversity compared to oil palm plantations. Differences were profound for functional divergence, whereas functional richness exhibited relatively large variances within land-use classes. By linking large-scale patterns of functional diversity as derived from satellite remote sensing to land-use information, this study indicated initial responsiveness to broad human disturbance gradients over large geographical and spatially contiguous extents. Despite uncertainties about the accuracy of the spatial patterns, this study provides a coherent early application of satellite-derived functional diversity toward further validation of its responsiveness across ecological gradients.

Environmental DNA effectively captures functional diversity of coastal fish communities

Robust assessments of taxonomic and functional diversity are essential components of research programmes aimed at understanding current biodiversity patterns and forecasting trajectories of ecological changes. Yet, evaluating marine biodiversity along its dimensions is challenging and dependent on the power and accuracy of the available data collection methods. Here we combine three traditional survey methodologies (underwater visual census strip transects [UVCt], baited underwater videos [BUV] and small-scale fishery catches [SSFc]), and one novel molecular technique (environmental DNA metabarcoding [eDNA]-12S rRNA and cytochrome oxidase subunit 1 [COI]) to investigate their efficiency and complementarity in assessing fish diversity. We analysed 1,716 multimethod replicates at a basin scale to measure the taxonomic and functional diversity of Mediterranean fish assemblages. Taxonomic identities were investigated at species, genus and family levels. Functional identities were assessed using combinations of morphological, behavioural and trophic traits. We show that: (a) SSFc provided the higher taxonomic diversity estimates followed by eDNA, and then UVCt and BUV; (b) eDNA was the only method able to gather the whole spectrum of considered functional traits, showing the most functionally diversified and least redundant fish assemblages; and (c) the effectiveness of eDNA in describing functional structure reflected its lack of selectivity towards any considered functional trait. Our findings suggest that the reach of eDNA analysis stretches beyond taxon detection efficiency and provides new insights into the potential of metabarcoding in ecological studies.