The architecture of benthic biofilms - Linking hydraulics to spatially structured processes

Biofilms are spatially structured ecosystems, characterized by patterns and architectural features determined by the interplay between endogenous and exogenous processes. As in many other structured ecosystems, the characterization of spatial interactions is pivotal to infer ecological functions. To date, the majority of studies have focused on pattern formation and morphology of single-species biofilm in microfluidics devices, drawing important conclusions about the physiological mechanisms mediating this phenomenon. However, the study of spatial organization of multi-species biofilms growing under conditions that resemble the native habitat has not been conducted extensively yet. The aim of this PhD thesis is the systematic investigation of spatial patterns formation in freshwater phototrophic benthic biofilms, under quasi-natural conditions. Benthic biofilms are a type of microbial community of global importance, for instance, for carbon cycling within streams. They are characterized by close metabolic interactions between autotrophic and heterotrophic microorganisms, and they are tightly shaped by the hydrodynamics of the surrounding water. We will research the formation of spatial organization in benthic biofilms with a special focus on the link between hydrodynamics, biofilm architecture, metabolism and biodiversity. We expect that this comprehensive view will permit an enhanced mechanistic understanding of the emergence of spatial organization in phototrophic benthic biofilms, as well as its ecological consequences.

Attached biofilms and suspended aggregates are distinct microbial lifestyles emanating from differing hydraulics

Tom Ian Battin, Hannes Markus Peter

Small-scale hydraulics affects microbial behaviour at the cell level1, trophic interactions in marine aggregates2 and the physical structure and function of stream biofilms3,4. However, it remains unclear how hydraulics, predictably changing from small streams to large rivers, impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we present experimental evidence unveiling hydraulics as a hitherto poorly recognized control of microbial lifestyle differentiation in fluvial ecosystems. Exposing planktonic source communities from stream and floodplain ecosystems to different hydraulic environments revealed strong selective hydraulic pressures but only minor founder effects on the differentiation of attached biofilms and suspended aggregates and their biodiversity dynamics. Key taxa with a coherent phylogenetic underpinning drove this differentiation. Only a few resident and phylogenetically related taxa formed the backbone of biofilm communities, whereas numerous resident taxa characterized aggregate communities. Our findings unveil fundamental differences between biofilms and aggregates and build the basis for a mechanistic understanding of how hydraulics drives the distribution of microbial diversity along the fluvial continuum5,6,7.

Nature Publishing Group2016

Scaling as a key conceptual tool for the interpretation of empirical and experimental patterns in ecology and biology

Silvia Zaoli

This thesis is concerned with regular patterns found in ecology and biology, their linkages and the statistical description of their fluctuations around average trends. Among such patterns, often conforming to power laws, well-known examples include the Species-Area relationship (SAR), quantifying the increase of the number of species S inhabiting an ecosystem with ecosystem area, and the scale-invariant body size spectrum, routinely observed, e.g., in aquatic ecosystems. In biology, Kleiber's law is an allometric relationship describing how metabolic rates scale with an organism's body size. While ecological laws have often been studied independently, simple heuristic reasonings show that they are linked. The need for a unifying effort in ecology, coherently synthesizing the vast and diverse set of empirical observations across scales, has been often voiced. However, a theoretical framework answering this need was still lacking. Furthermore, ecological variables are the result of the interplay between several stochastic ecological processes, and are therefore stochastic variables fluctuating around average values. Ecological and biological scaling laws typically make predictions for such averages, but the issue of fluctuations received scarce attention in the literature. Similarly, biological fluctuations have been typically neglected in the study of the size-scaling of metabolic rates, even though body sizes and metabolic rates may have a significant variability within a species. Fluctuations may be relevant to interpret empirical observations, judge the reliability of predictions and understand ecosystem dynamics. An hypothesis for the distribution of abundances and body sizes of species inhabiting an ecosystem of finite area is proposed here. The hypothesis is inspired by finite-size scaling and is used to derive macroecological patterns and their linkages within a coherent theoretical framework. Stochastic models of community dynamics are used to support the hypothesis, and the derived linkages are tested on empirical datasets. Several stochastic models of community dynamics are also used here to study the fluctuations of S and how they scale with the average S. The intra-specific variability of metabolic rates and body sizes is investigated experimentally using freshwater phytoplankton species by nanoscale secondary ion mass spectrometry (NanoSIMS). The linkages among ecological scaling laws predicted by the theoretical framework are verified in several empirical datasets. Theoretical generalizations including deviations from pure power-law behavior and heavy-tailed intra-specific size distributions are also addressed. The theoretical study of the relative scaling of the fluctuations of S with the mean

\langle S \rangle

in various community dynamics models shows that different ecological processes predict radically different fluctuations scalings, highlighting the need of empirical investigations to sort out which scenario applies to real ecosystems. Experiments on phytoplankton metabolic rate scaling with body size suggest that intra-specific metabolic rate distributions are described by a universal scaling form across different taxa and over three orders of magnitude in body size. This thesis, along with previous works, suggests that scaling concepts derived for inanimate systems can provide new insights into the dynamics of ecosystems and help unraveling regularities across scales of biological complexity.

EPFL2018

Scaling as a key conceptual tool for the interpretation of empirical and experimental patterns in ecology and biology

Silvia Zaoli

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EPFL2018