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Illmer, P.

Publications and source records attributed to Illmer, P..

3 recordsLinked to original sources

Year-round rhythms: alpine plant species modulate soil and microbial dynamics during the growing season and under the snow.

O_LISoil-plant-microbe interactions are integral throughout most terrestrial ecosystems, yet the importance of plant phenology and seasonal dynamism upon these relationships remains unknown. Given the pronounced seasonality of alpine environments, we sampled 8 plant species occurring in two habitats (alpine meadow and subnival zone) across four seasons (including snow-covered winter) in the Central Eastern Alps to determine the plant growth strategies and plant nutrient parameters which closely couple with rhizosphere microbial parameters. C_LIO_LIIn subnival locations, plants exhibited stronger seasonal changes among leaf and root tissue nutrient concentrations and non-structural carbohydrates (NSCs) compared to those in lower elevation alpine meadows. However, rhizosphere microbial parameters (microbial biomass (MBC), extracellular enzymes, and community composition) demonstrated more seasonal changes in the alpine meadow locations. C_LIO_LIA phenological delay was observed in bacterial and fungal communities of the subnival zone, with peak plant rhizosphere differentiation occurring later in the season than in alpine meadows. Therefore, the prolonged cold conditions and shorter growing season in higher elevations likely add a temporal aspect to the commonly used elevational gradient approach, which is not often considered. C_LIO_LIMBC and enzymatic potential within the rhizosphere were high across all plant species in the alpine meadow during the winter sampling, despite notable differences in microbial community composition. In contrast, winter rhizosphere communities did not differ between plant species in subnival locations, although one species, Oxyria digyna, demonstrated much higher microbial activity along with higher NSCs and root N, suggesting some alpine plant species may acquire nutrients through microbial interactions during snow-covered winter periods. C_LIO_LISynthesis: This study provides the first look at the annual phenology of multiple alpine plant species and their associated rhizosphere microbiome. Our results demonstrate that seasonal microbial dynamics are highly influenced by abiotic factors (soil and microclimatic conditions), but plants are able to modulate these conditions through growth and nutrient acquisition strategies. Taken together, seasonality and independent plant species effects cannot be overlooked when assessing habitat nutrient cycling and ecosystem stability. C_LI

microbiology↗

Biodiversity in mountain soils above the treeline

Despite the importance of healthy soils for human livelihood, wellbeing, and safety, current gaps in our knowledge and understanding of biodiversity in soil are numerous, undermining conservation efforts. These gaps are particularly wide in mountain regions where healthy soils are especially important for human safety and yet evidence is accumulating of ongoing degradation, posing significant threats to ecosystem functioning and human settlements. To analyse these gaps in detail, we synthesise current research on the global diversity of microorganisms, cryptogams, and invertebrates in mountain soils above the treeline. This synthesis is based on a semi-quantitative survey of the literature and an expert-based analysis. Our work reveals not only deficiencies in geographic cover but also significant gaps in taxonomic coverage, particularly among soil protists and invertebrates, and a lack of (functional and ecological) description of the uncultivated majority of prokaryotes, fungi, and protists. We subsequently build on this overview to highlight opportunities for research on mountain soils as systems of co-occurring species that interact in complex environmental matrices to fulfil critical functions and make essential contributions to life on land. Closing gaps in biodiversity research in mountain soil is crucial to enhance our understanding and to promote laws and guidelines advancing international soil biodiversity conservation targets in mountains. Addressing sparse and biased data, recognizing the impact of environmental changes on mountain ecosystems, and advocating dedicated policies are essential strategies to safeguard mountain soils and their biodiversity. GLOSSARY O_TBL View this table: org.highwire.dtl.DTLVardef@16682fdorg.highwire.dtl.DTLVardef@121b9feorg.highwire.dtl.DTLVardef@139eadeorg.highwire.dtl.DTLVardef@16abd74org.highwire.dtl.DTLVardef@bc3da9_HPS_FORMAT_FIGEXP M_TBL C_TBL

ecology↗

Comparison of microbial communities from diverse biological matrices using mock community as an in situ positive control

Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Understanding the interactions between the microbiotas within the same ecosystem is essential for fully understanding the role of microorganisms in evolutionary and ecological processes; however, such comparative studies across diverse biological samples are rare. In particular, currently available protocols assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. The addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases, but the impact of MC on diversity estimates is unknown. Here, standardized aliquots of bovine faecal samples with high or low biomass were extracted with high or low doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We showed that a MC was an informative in situ positive control provided an estimate of 16S rRNA sample gene copies (which allowed a more direct measure of community size), and detected sample outliers. However, we also demonstrated that if the recommended dose of MC is added to a sample with low biomass, diversity estimates were distorted. Using our results, we recommend MC doses for a range of sample types, including rhizosphere soil, whole invertebrates, and vertebrate faecal samples. ImportanceThe simultaneous processing of the sample microbiota with a known number of readily identifiable MC cells (co-extracted with the sample cells) or SNA (co-amplified with the sample DNAs) can be a valuable in situ positive control. However, guidelines regarding their application are very limited and do not consider the effect of these controls on sample diversity estimates. We demonstrate that a MC co-extracted with the study sample provides several advantages, such as highlighting bias in DNA extraction of gram positive, identifying potential sample outliers and inferring the number of 16S rRNA gene copies in the sample. However, the incorporation of a MC requires prior knowledge of sample biomass, as high ratios of MC to sample microbiota lead to biased sample diversity estimates. Practical advice on determining the appropriate MC dose for a wide range of sample types, including rhizosphere soil, whole invertebrates and mammalian faecal samples are provided.

ecology↗