Biophysical properties at patch scale shape the metabolism of biofilm landscapes

Depetris, Anna; Tagliavini, Giorgia; Peter, Hannes; Kühl, Michael; Holzner, Markus; Battin, Tom J.

doi:10.1038/s41522-022-00269-0

Cited by 10 publications

(7 citation statements)

References 58 publications

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“…In this study, the synthetic communities were established under specific environmental condition (e.g., high nutrient concentration and specific actinic light exposure). Under another environmental filtering, community development and species succession might be therefore different 8 , 9 , 70 – 72 . The absence of flow, as is the case in our experimental system, might also lead to a potential formation of gradients of light, oxygen, pH, and nutrients within the biofilm 72 , 73 , which in turn can affect the biofilm development, extracellular matrix production, species interactions, and competition 74 , 75 .…”

Section: Resultsmentioning

confidence: 99%

“…Under another environmental filtering, community development and species succession might be therefore different 8 , 9 , 70 – 72 . The absence of flow, as is the case in our experimental system, might also lead to a potential formation of gradients of light, oxygen, pH, and nutrients within the biofilm 72 , 73 , which in turn can affect the biofilm development, extracellular matrix production, species interactions, and competition 74 , 75 . Developing the synthetic periphyton in sterile flow-through chambers 76 , would mimic to some extend conditions in streams and rivers.…”

Section: Resultsmentioning

confidence: 99%

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Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities

Lamprecht

Wagner

Derlon

et al. 2022

npj Biofilms Microbiomes

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Phototrophic biofilms, also known as periphyton, are microbial freshwater communities that drive crucial ecological processes in streams and lakes. Gaining a deep mechanistic understanding of the biological processes occurring in natural periphyton remains challenging due to the high complexity and variability of such communities. To address this challenge, we rationally developed a workflow to construct a synthetic community by co-culturing 26 phototrophic species (i.e., diatoms, green algae, and cyanobacteria) that were inoculated in a successional sequence to create a periphytic biofilm on glass slides. We show that this community is diverse, stable, and highly reproducible in terms of microbial composition, function, and 3D spatial structure of the biofilm. We also demonstrate the ability to monitor microbial dynamics at the single species level during periphyton development and how their abundances are impacted by stressors such as increased temperature and a herbicide, singly and in combination. Overall, such a synthetic periphyton, grown under controlled conditions, can be used as a model system for theory testing through targeted manipulation.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities

Lamprecht

Wagner

Derlon

et al. 2022

npj Biofilms Microbiomes

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“…These results suggest that part of the sediment microbiome is adapted to grow in low‐oxygen to anaerobic environments. One possibility is that this is due to oxygen depletion within the fine and low‐permeability sediments or even within the biofilms, particularly when they grow thick as shown in experimental phototrophic biofilms (Depetris et al 2022). However, we can also not exclude the possibility that part of the microbiome in glacier‐fed streams may originate from anoxic subglacial environments or basal ice (Ren et al 2022), and that is mobilized and transported downstream.…”

Section: Discussionmentioning

confidence: 99%

Unexpected functional diversity of stream biofilms within and across proglacial floodplains despite close spatial proximity

Michoud,

Kohler,

Peter

et al. 2023

Limnology & Oceanography

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High‐mountain streams are particularly vulnerable to climate change because they intimately interface with the cryosphere. As glaciers shrink and snowpack diminishes, proglacial streams will eventually shift from being glacier‐fed to streams fed by groundwater, snowmelt and precipitation. This shift will affect both the flow regime and physico‐chemical characteristics of streams, possibly also the structure and function of their benthic microbiome. Here, we applied genome‐resolved metagenomics to benthic biofilms from glacier‐fed streams and their groundwater‐fed tributaries within three proglacial floodplains in the Swiss Alps. Despite the close spatial proximity between both stream types, their microbiome structure differed consistently for both prokaryotes and eukaryotes. The glacier‐fed stream microbiome was taxonomically and functionally less diverse than its groundwater‐fed counterpart, and had smaller genomes, but with conservation of the central metabolic functions primarily related to nitrogen and sulfur cycling. Consequently, much higher functional variability was associated with the microbiome of tributary streams, mainly due to abundant genes involved in the transport and degradation of organic matter. Our findings suggest that glacier shrinkage will cause shifts in the functioning of benthic microbiomes of proglacial floodplains with yet unknown consequences for downstream biogeochemistry.

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“…While there is a good understanding of such structure–function relationships in many natural biofilm communities (e.g. Depetris et al, 2021 , 2022 ), the question remains how bacteria are organized in chronic infections and whether a complex 3D structural organization and derived changes of their microenvironment confer any advantage for their persistence and resilience to the immune response or antibiotic treatment.…”

Section: The Structural Organization Of Bacteria In Infectionsmentioning

confidence: 99%

The structure–function relationship ofPseudomonas aeruginosain infections and its influence on the microenvironment

Lichtenberg

Jakobsen

Kühl

et al. 2022

FEMS Microbiology Reviews

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Pseudomonas aeruginosa is a human pathogen associated with both acute and chronic infections. While intensively studied, the basic mechanisms enabling the long-term survival of P. aeruginosa in the host, despite massive immune system attack and heavy antimicrobial treatment, remain to be identified. We argue that such infections may represent niche invasions by P. aeruginosa that influence the microenvironment by depleting host-derived substrate and activating the immune response. Bacteria embedded in cell aggregates establish a microenvironmental niche, where they endure the initial host response by slowing down their metabolism. This provides stable, lasting growth conditions with a constant, albeit slow supply of substrate and electron acceptors. Under such stable conditions, P. aeruginosa exhibits distinct adaptive traits, where its gene expression pattern reflects a life exposed to continuous attack by the host immune system and antimicrobials. Here we review fundamental microenvironmental aspects of chronic P. aeruginosa infections and examine how their structural organization influences their in vivo microenvironment, which in turn affects the interaction of P. aeruginosa biofilm aggregates with the host immune system. We discuss how improving our knowledge about the microenvironmental ecology of P. aeruginosa in chronic infections can be used to combat persistent, hard-to-treat bacterial infections.

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Biophysical properties at patch scale shape the metabolism of biofilm landscapes

Cited by 10 publications

References 58 publications

Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities

Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities

Unexpected functional diversity of stream biofilms within and across proglacial floodplains despite close spatial proximity

The structure–function relationship ofPseudomonas aeruginosain infections and its influence on the microenvironment

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