publications

2023

1. One-time freeze-thawing or carbon input events have long-term legacies in soil microbial communities

   Gorka, Stefan, Ranits, Christian, Zhang, Shasha, Imai, Bruna, Guseva, Ksenia, and Kaiser, Christina

   Geoderma Apr 2023

   Abs

   Soil microbial communities are regularly exposed to sudden changes in environmental conditions, such as root exudation pulses or freeze-thaw events. As microbial communities have a high potential to adapt to changing conditions, they are expected to be resilient towards this kind of short-term perturbations and return to their pre-perturbed state quickly. Here, we conducted a lab incubation experiment to evaluate the resilience of soil microbial communities to single-pulse perturbations. We incubated temperate forest soil at constant temperature (20 °C) and water content, and exposed it to strong single-pulse perturbations, which nonetheless mimic common pulse-events in temperate soils (glucose addition at 4 mg g−1 soil, or freeze-thawing overnight at −20 °C). We subsequently measured microbial community composition and microbial storage compounds via phospho- and neutral lipid fatty acid (PLFA and NLFA) profiling, as well as C/N stoichiometry of microbial biomass and dissolved organic carbon and nitrogen in the soil solution shortly after (0.4, 1, 4, and 6 days) and after longer time periods (84 and 160 days) following the perturbations. Transferring the soils from their natural environment to the laboratory and incubating them under controlled conditions led to a continuous change of microbial community structure over time, along with an increase in microbial biomass and dissolved N in both perturbed and control soils over the time of the experiment. Against the background of this ‘press-disturbance’, caused by the permanently changed conditions, we see immediate and long-lasting effects of the single pulse events on microbial community composition, C storage and C/N stoichiometry. Both perturbations significantly influenced the microbial community structure (based on PLFA profiles), microbial biomass N and dissolved N up to 160 days, as well as fungal and bacterial biomass and storage (based on absolute PLFA and NLFA concentrations) up to 84 days. Both perturbations increased microbial N (+59.6 µg g−1 dw) and decreased dissolved N (−40.3 µg g−1 dw) after 160 days, and significantly altered C/N ratios in microbial and dissolved pools (particularly in the first 6 days of the experiment). Our results demonstrate that single-pulse perturbations can have long-term legacies in soil microbial ecosystems. In our experiment they led to alternative system states which differed from the unperturbed control in multiple parameters even after 160 days. This indicates that soil microbial communities exhibit a low resistance and resilience towards single-pulse perturbations, and may easily be pushed on alternative trajectories by short but strong environmental pulses.

2022

1. From diversity to complexity: Microbial networks in soils

   Guseva, Ksenia, Darcy, Sean, Simon, Eva, Alteio, Lauren V., Montesinos-Navarro, Alicia, and Kaiser, Christina

   Soil Biology and Biochemistry Apr 2022

2021

1. A critical perspective on interpreting amplicon sequencing data in soil ecological research

   Alteio, Lauren V., Séneca, Joana, Canarini, Alberto, Angel, Roey, Jansa, Jan, Guseva, Ksenia, Kaiser, Christina, Richter, Andreas, and Schmidt, Hannes

   Soil Biology and Biochemistry Sep 2021

   Abs

   Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation, and availability to improve the rigor of future studies.

2020

1. Numerical modelling of the effect of intermittent upwelling events on plankton blooms

   Guseva, Ksenia, and Feudel, Ulrike

   Journal of The Royal Society Interface Apr 2020

   Abs

   In the marine environment, biological processes are strongly affected by oceanic currents, particularly by eddies (vortices) formed by the hydrodynamic flow field. Employing a kinematic flow field coupled to a population dynamical model for plankton growth, we study the impact of an intermittent upwelling of nutrients on triggering harmful algal blooms (HABs). Though it is widely believed that additional nutrients boost the formation of HABs or algal blooms in general, we show that the response of the plankton to nutrient plumes depends crucially on the mesoscale hydrodynamic flow structure. In general, nutrients can either be quickly washed out from the observation area, or can be captured by the vortices in the flow. The occurrence of either scenario depends on the relation between the time scales of the vortex formation and nutrient upwelling as well as the time instants at which upwelling pulses occur and how long they last. We show that these two scenarios result in very different responses in plankton dynamics which makes it very difficult to predict whether nutrient upwelling will lead to a HAB or not. This may in part explain why observational data are sometimes inconclusive in establishing a connection between upwelling events and plankton blooms.

2019

1. The effect of intermittent upwelling events on plankton blooms

   Guseva, Ksenia, and Feudel, Ulrike

   arXiv:1905.02064 [nlin, q-bio] May 2019

   Abs

   In the marine environment biological processes are strongly affected by oceanic currents, particularly by eddies (vortices) formed by the hydrodynamic flow field. Employing a kinematic flow field coupled to a population dynamical model for plankton growth, we study the impact of an intermittent upwelling of nutrients on triggering harmful algal blooms (HABs). Though it is widely believed that additional nutrients boost the formation of HABs or algal blooms in general, we show that the response of the plankton to nutrient plumes depends crucially on the mesoscale hydrodynamic flow structure. In general nutrients can either be quickly washed out from the observation area, or can be captured by the vortices in the flow. The occurrence of either scenario depends on the relation between the time scales of the vortex formation and nutrient upwelling as well as the time instants at which upwelling pulse occurs and how long do they last. We show that these two scenarios result in very different responses in plankton dynamics which makes it very difficult to predict, whether nutrient upwelling will lead to a HAB or not. This explains, why observational data are sometimes inconclusive establishing a correlation between upwelling events and plankton blooms.

2017

1. A snapshot attractor view of the advection of inertial particles in the presence of history force

   Guseva, Ksenia, Daitche, Anton, and Tél, Tamás

   The European Physical Journal Special Topics Jun 2017
2. Aggregation and fragmentation dynamics in random flows: From tracers to inertial aggregates

   Guseva, Ksenia, and Feudel, Ulrike

   Physical Review E Jun 2017
3. Cooperative response and clustering: Consequences of membrane-mediated interactions among mechanosensitive channels

   Fernandes, Lucas D., Guseva, Ksenia, and Moura, Alessandro P. S.

   Physical Review E Aug 2017

   Abs

   Mechanosensitive channels are ion channels which act as cells’ safety valves, opening when the osmotic pressure becomes too high and making cells avoid damage by releasing ions. They are found on the cellular membrane of a large number of organisms. They interact with each other by means of deformations they induce in the membrane. We show that collective dynamics arising from the interchannel interactions lead to first- and second-order phase transitions in the fraction of open channels in equilibrium relating to the formation of channel clusters. We show that this results in a considerable delay of the response of cells to osmotic shocks, and to an extreme cell-to-cell stochastic variations in their response times, despite the large numbers of channels present in each cell. We discuss how our results are relevant for E. coli.

2016

1. History effects in the sedimentation of light aerosols in turbulence: The case of marine snow

   Guseva, Ksenia, Daitche, Anton, Feudel, Ulrike, and Tél, Tamás

   Physical Review Fluids Nov 2016

2015

1. Numerical simulations of aggregate breakup in bounded and unbounded turbulent flows

   Babler, Matthaus U., Biferale, Luca, Brandt, Luca, Feudel, Ulrike, Guseva, Ksenia, Lanotte, Alessandra S., Marchioli, Cristian, Picano, Francesco, Sardina, Gaetano, Soldati, Alfredo, and Toschi, Federico

   Journal of Fluid Mechanics Mar 2015

2013

1. Influence of the history force on inertial particle advection: Gravitational effects and horizontal diffusion

   Guseva, Ksenia, Feudel, Ulrike, and Tél, Tamás

   Physical Review E Oct 2013

2012

1. Formation and Cooperative Behaviour of Protein Complexes on the Cell Membrane

   Guseva, Ksenia

   Springer-Verlag Oct 2012

   Abs

   With the aim of providing a deeper insight into possible mechanisms of biological self-organization, this thesis presents new approaches to describe the process of self-assembly and the impact of spatial organization on the function of membrane proteins, from a statistical physics point of view. It focuses on three important scenarios: the assembly of membrane proteins, the collective response of mechanosensitive channels and the function of the twin arginine translocation (Tat) system. Using methods from equilibrium and non-equilibrium statistical mechanics, general conclusions were drawn that demonstrate the importance of the protein-protein interactions. Namely, in the first part a general aggregation dynamics model is formulated, and used to show that fragmentation crucially affects the efficiency of the self-assembly process of proteins. In the second part, by mapping the membrane-mediated forces into a simplified many-body system, the dynamic and equilibrium behaviour of interacting mechanosensitive channels is derived, showing that protein agglomeration strongly impacts its desired function. The final part develops a model that incorporates both the agglomeration and transport function of the Tat system, thereby providing a comprehensive description of this self-organizing process.

2011

1. Collective response of self-organized clusters of mechanosensitive channels

   Guseva, Ksenia, Thiel, Marco, Booth, Ian, Miller, Samantha, Grebogi, Celso, and Moura, Alessandro

   Physical Review E Feb 2011

   Abs

   Mechanosensitive channels are ion channels activated by membrane tension. We investigate the influence of the spatial distribution of bacterial mechanosensitive channels on activation (gating). Based on elastic short-range interactions we map this physical process onto an Ising-like model, which enables us to predict the clustering of channels and the effects of clustering on their gating. We conclude that the aggregation of channels and the consequent interactions among them leads to a global cooperative gating behavior with potentially dramatic consequences for the cell.