Biology subjects

Siebert, J.

Publications and source records attributed to Siebert, J..

5 recordsLinked to original sources

bioRxiv2023

Sustainable land management enhances ecological and economic multifunctionality under ambient and future climate

1.Anthropogenic activity is threatening ecosystem multifunctionality, i.e. the ability of ecosystems to provide multiple functions and services which are vital for human well-being. Here we assess how multifunctionality of agroecosystems in Central Germany depends on land-use type and climate change. Our analysis included 13 ecosystem functions in a large-scale field experiment with five different land-use types (three grassland and two farmland types either sustainably or intensively managed) under two different climate scenarios (ambient and future climate). We consider ecological measures of multifunctionality using averaging approaches with different weights, i.a. reflecting preferences of farmers and environmentalists, and assess an economic multifunctionality measure based on the total value of ecosystem services. Results show that intensive management and future climate decrease ecological multifunctionality for multiple weighting scenarios in both grassland and farmland. Only under a weighting according to farmers preferences, intensively-managed grassland shows higher multifunctionality as compared to sustainably-managed grassland. The economic multifunctionality measure, which includes economic benefits for society at large, reveals a multifunctionality about [~]1.7 times higher for sustainable compared to intensive management for both grassland and farmland. Above-belowground biodiversity correlates positively with ecosystem multifunctionality and is expected to be one of its main drivers. Based on these findings, we suggest to promote and economically incentivise sustainable land management that enhances both ecological and economic multifunctionality, also under future climatic conditions.

ecology↗

bioRxiv2020

Climate change and intensive land use reduce soil animal biomass through dissimilar pathways

Global change drivers, such as climate and land use, may profoundly influence body size, density, and biomass of organisms. It is still poorly understood how these concurrent drivers interact in affecting ecological communities. We present results of an experimental field study assessing the interactive effects of climate change and land-use intensification on body size, density, and biomass of soil microarthropods. We found that both climate change and intensive land use decreased their total biomass. Strikingly, this reduction was realized via two dissimilar pathways: climate change reduced mean body size, while intensive land use decreased population size. These findings highlight that two of the most pervasive global change drivers operate via different pathways when decreasing soil animal biomass. These shifts in soil communities may threaten essential ecosystem functions like organic matter turnover and nutrient cycling in future ecosystems. SignificanceMany important ecosystem functions are determined by the biomass of soil animal, however, how their biomass may respond to climate change and land-use intensification still remains unknown. We conducted a large field study to investigate the potential interaction between these two pervasive global change drivers, and disentangle the pathways where they contribute to the changes in soil animal biomass. Our findings are exceptionally novel by showing detrimental, but largely independent, effects of climate change and land-use intensity on soil animal biomass, and that these independent effects can be explained by two dissimilar pathways: climate change reduced mean body size, while intensive land use decreased population size. Notably, consistent climate change effects under different land-use regimes suggest that (1) the identified pathways may apply to a wide range of environmental conditions, and (2) current extensive land-use regimes do not mitigate detrimental climate change effects on ecosystems.

ecology↗

bioRxiv2019

Complete genome sequence of Escherichia coli C - an old model organism with a new application in biofilm research

Escherichia coli C forms more robust biofilms than the other laboratory strains. Biofilm formation and cell aggregation under a high shear force depends on temperature and salt concentrations. It is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43, waaSBOJYZUL for LPS synthesis, and cpsB for curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the -35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of the csgD gene, which may drive its overexpression in biofilm. And finally, E. coli C encodes an additional sigma70 subunit overexpressed in biofilm and driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions and total expression profiles using RNA-seq analyses comparing planktonic and biofilm envirovars provided insights into understanding this regulatory pathway in E. coli. IMPORTANCEBiofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains of E. coli grown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain of E. coli C produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence as well as gene expression profiles of both the biofilm and planktonic envirovars of this classic strain, which provide for a base level of characterization and make it useful for many biofilm-based applications.

microbiology↗

bioRxiv2018

VOLARE: Visual analysis of disease-associated microbiome-immune system interplay

BackgroundRelationships between specific microbes and proper immune system development, composition, and function have been reported in a number of studies. However, researchers have discovered only a fraction of the likely relationships. High-dimensional \"omic\" methodologies such as 16S ribosomal RNA (rRNA) sequencing and Time-of-flight mass cytometry (CyTOF) immunophenotyping generate data that support generation of hypotheses, with the potential to identify additional relationships at a level of granularity ripe for further experimentation. Pairwise linear regressions between microbial and host immune features is one approach for quantifying relationships between \"omes\", and the differences in these relationships across study cohorts or arms. This approach yields a top table of candidate results. However, the top table alone lacks the detail that domain experts need to vet candidate results for follow-up experiments.\n\nResultsTo support this vetting, we developed VOLARE (Visualization Of LineAr Regression Elements), a web application that integrates a searchable top table, small in-line graphs illustrating the fitted models, a network summarizing the top table, and on-demand detailed regression plots showing full sample-level detail. We applied VOLARE to three case studies--microbiome:cytokine data from fecal samples in HIV, microbiome:cytokine data in inflammatory bowel disease and spondyloarthritis, and microbiome:immune cell data from gut biopsies in HIV. We present both patient-specific phenomena and relationships that differ by disease state. We also analyzed interaction data from system logs to characterize usage scenarios. This log analysis revealed that, in using VOLARE, domain experts frequently generated detailed regression plots, suggesting that this detail aids the vetting of results.\n\nConclusionsSystematically integrating microbe:immune cell readouts through pairwise linear regressions and presenting the top table in an interactive environment supports the vetting of results for scientific relevance. VOLARE allows domain experts to control the analysis of their results, screening dozens of candidate relationships with ease. This interactive environment transcends the limitations of a static top table.

bioinformatics↗

bioRxiv2018

The effects of drought and nutrient addition on soil organisms vary across taxonomic groups, but are constant across seasons

Anthropogenic global change alters the activity and functional composition of soil communities that are responsible for crucial ecosystem functions and services. Two of the most pervasive global change drivers are drought and nutrient enrichment. However, the responses of soil organisms to interacting global change drivers remain widely unknown. We tested the interactive effects of extreme drought and fertilization on soil biota ranging from microbes to invertebrates across seasons. We expected drought to reduce the activity of soil organisms and fertilization to induce positive bottom-up effects via increased plant productivity. Furthermore, we hypothesized fertilization to reinforce drought effects through enhanced plant growth, resulting in even dryer soil conditions. Our results revealed that drought had detrimental effects on soil invertebrate feeding activity and simplified nematode community structure, whereas soil microbial activity and biomass were unaffected. Microbial biomass increased in response to fertilization, whereas invertebrate feeding activity substantially declined. Notably, these effects were consistent across seasons. The dissimilar responses suggest that soil biota differ vastly in their vulnerability to global change drivers. As decomposition and nutrient cycling are driven by the interdependent concurrence of microbial and faunal activity, this may imply far-reaching consequences for crucial ecosystem processes in a changing world.

ecology↗