Choosing And Using Diversity Indices: Insights For Ecological Applications From The German Biodiversity Exploratories

Biodiversity, a multidimensional property of natural systems, is difficult to quantify partly because of the multitude of indices proposed for this purpose. Indices aim to describe general properties of communities that allow us to compare different regions, taxa, and trophic levels. Therefore, they are of fundamental importance for environmental monitoring and conservation, although there is no consensus about which indices are more appropriate and informative. We tested several common diversity indices in a range of simple to complex statistical analyses in order to determine whether some were better suited for certain analyses than others. We used data collected around the focal plant Plantago lanceolata on 60 temperate grassland plots embedded in an agricultural landscape to explore relationships between the common diversity indices of species richness (S), Shannon\u27s diversity (H\u27), Simpson\u27s diversity (D1), Simpson\u27s dominance (D2), Simpson\u27s evenness (E), and Berger-Parker dominance (BP). We calculated each of these indices for herbaceous plants, arbuscular mycorrhizal fungi, aboveground arthropods, belowground insect larvae, and P. lanceolata molecular and chemical diversity. Including these trait-based measures of diversity allowed us to test whether or not they behaved similarly to the better studied species diversity. We used path analysis to determine whether compound indices detected more relationships between diversities of different organisms and traits than more basic indices. In the path models, more paths were significant when using H\u27, even though all models except that with E were equally reliable. This demonstrates that while common diversity indices may appear interchangeable in simple analyses, when considering complex interactions, the choice of index can profoundly alter the interpretation of results. Data mining in order to identify the index producing the most significant results should be avoided, but simultaneously considering analyses using multiple indices can provide greater insight into the interactions in a system

Molecular screening of microorganisms associated with discolored wood in dead European beech trees suffered from extreme drought event using next generation sequencing

Drought events weaken trees and make them vulnerable to attacks by diverse plant pathogens. Here, we propose a molecular method for fast screening of microorganisms associated with European beech decline after an extreme drought period (2018) in a forest of Thuringia, Germany. We used Illumina sequencing with a recent bioinformatics approach based on DADA2 to identify archaeal, bacterial, and fungal ASVs (amplicon sequence variants) based on bacterial and archaeal 16S and fungal ITS genes. We show that symptomatic beech trees are associated with both bacterial and fungal plant pathogens. Although the plant pathogen sequences were detected in both discolored and non-discolored wood areas, they were highly enriched in the discolored wood areas. We show that almost each individual tree was associated with a different combination of pathogens. Cytospora spp. and Neonectria coccinea were among the most frequently detected fungal pathogens, whereas Erwinia spp. and Pseudomonas spp. were the dominant bacterial plant pathogens. We demonstrate that bacterial plant pathogens may be of major importance in beech decline

Water Deficit History Selects Plant Beneficial Soil Bacteria Differently Under Conventional and Organic Farming

Water deficit tolerance is critical for plant fitness and survival, especially when successive drought events happen. Specific soil microorganisms are however able to improve plant tolerance to stresses, such as those displaying a 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Microorganisms adapted to dry conditions can be selected by plants over time because of properties such as sporulation, substrate preference, or cell-wall thickness. However, the complexity and interconnection between abiotic factors, like drought or soil management, and biotic factors, like plant species identity, make it difficult to elucidate the general selection processes of such microorganisms. Using a pot experiment in which wheat and barley were grown on conventional and organic farming soils, we determined the effect of water deficit history on soil microorganisms by comparing single and successive events of water limitation. The analysis showed that water deficit strongly impacts the composition of both the total microbial community (16S rRNA genes) and one of ACC deaminase-positive (acdS(+)) microorganisms in the rhizosphere. In contrast, successive dry conditions moderately influence the abundance and diversity of both communities compared to a single dry event. We revealed interactive effects of the farming soil type and the water deficit conditioning treatment. Indeed, possibly due to better nutrient status, plants grown on soils from conventional farming showed higher growth and were able to select more adapted microbial taxa. Some of them are already known for their plant-beneficial properties like the Actinobacteria Streptomyces, but interestingly, some Proteobacteria were also enriched after a water deficit history under conventional farming. Our approach allowed us to identify key microbial taxa promoting drought adaptation of cereals, thus improving our understanding of drought effects on plant-microbe interactions

Analysis of microbial populations in plastic-soil systems after exposure to high poly(butylene succinate-co-adipate) load using high-resolution molecular technique

BACKGROUND: Bio-based and biodegradable plastics are considered as plastics of the future owing to their ability to decompose under various environmental conditions. However, their effects on the soil microbiome are poorly characterised. In this study, we aimed to investigate the effects of an important bio-based and biodegradable plastic, polybutylene succinate-co-adipate (PBSA), on soil microbial diversity and community composition using high-resolution molecular technique (Illumina sequencing) targeting all three microbial domains: archaea, bacteria, and fungi. RESULTS: Adding high load of PBSA to soil (6% (w/w)) caused a significant decline in archaeal (13%) and fungal (45%) richness and substantial changes in both bacterial (Proteobacteria, Actinobacteria, and Acidobacteria) and fungal (Eurotiomycetes, Sordariomycetes, Leotiomycetes, and Dothideomycetes) community composition compared with no PBSA addition to soil. The combined effects of PBSA and (NH₄)₂SO₄ fertilisation on the soil microbiome were much greater than the effects of PBSA alone. We only detected opportunistic human pathogens in low abundance on PBSA and in the surrounding soil. However, some plant pathogenic fungi were detected and/or enriched on the PBSA films and in surrounding soil. Apart from plant pathogens, many potential microbial control agents and plant growth-promoting microorganisms were also detected/enriched owing to PBSA addition. Adding high load of PBSA together with (NH₄)₂SO₄ fertilisation can either eliminate some plant pathogens or enrich specific pathogens, especially Fusarium solani, which is economically important. CONCLUSIONS: We conclude that high load of bio-based and biodegradable PBSA plastic may negatively affect soil microbiome

Archaeal Diversity and CO 2

Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of 13CO2 stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO2, while archaeal autotrophy seems to be limited in the groundwater