Abteilung Umweltmikrobiologie

Mikrobielle Gemeinschaften

Forschungsgebiete

Unsere Forschung fokussiert darauf generelle ökologische Prinzipien, die sich mit den Ursachen und Konsequenzen von mikrobieller Diversität befassen, abzuleiten und zu testen. Wir wollen die folgenden zwei zentralen Fragen der mikrobiellen Ökologie beantworten:

  • Wieso gibt es in mikrobiellen Gemeinschaften so viele verschiedene Zelltypen? In anderen Worten: was verhindert, dass ein paar wenige Zelltypen evolvieren, die sich durchsetzen und die anderen verdrängen?
  • Ist Diversität ein wichtiger Faktor der funktionalen Leistung von mikrobiellen Gemeinschaften? Falls ja, was sind die Mechanismen, die dafür verantwortlich sind?

Wir verwenden eine Kombination aus Laborexperimenten und der Untersuchung von Umweltsystemen um diese Fragen zu beantworten. Die Ursachen von mikrobieller Diversität untersuchen wir mittels experimenteller Systeme und fokussieren dabei insbesondere auf das Konzept der metabolischen Spezialisierung. Die zentrale Hypothese ist hierbei, dass gewisse metabolische Prozesse miteinander inkompatibel sind und deshalb am effizientesten in verschiedenen Zelltypen ausgeführt werden. Dies führt letztlich dazu, dass Diversität entsteht. Um diese Hypothese zu testen, messen wir in Laborexperimenten die Effekte von Interaktionen zwischen verschiedenen metabolischen Prozessen und verfolgen ihr Schicksal über evolutionäre Zeiträume.

Um die Konsequenzen mikrobieller Diversität zu untersuchen, untersuchen wir Umweltsysteme. Die zentrale Hypothese ist hierbei, dass mikrobielle Diversität ein wichtiger Faktor für die funktionale Leistung von Ökosystemen ist. Um dies zu testen, messen wir die Raten und das Ausmass von verschiedenen metabolischen Prozessen in Umweltsystemen und untersuchen ob es einen Zusammenhang mit dem Ausmass der Diversität in diesen Systemen gibt. Wir manipulieren dann experimentell das Ausmass der Diversität und werten die Konsequenzen für die verschiedenen metabolischen Prozesse aus. Das Ziel ist letztlich unser Verständnis darüber zu verbessern was Diversität in der Umwelt begünstigt und wieso Diversität ein wichtiger Faktor für die funktionale Leistung von Ökosystemen sein könnte.

Mehr Information finden Sie hier: www.mca-johnson.com

Gruppenleiter

Dr. David Johnson Gruppenleiter Tel. +41 58 765 5520 E-Mail senden

Team

Jelena Bitterli Bachelorstudentin Tel. E-Mail senden
Lea Caduff Technikerin Tel. +41 58 765 5714 E-Mail senden
Miao Han Gastdoktorandin Tel. +41 58 765 6479 E-Mail senden
Sahil Oza Bachelorstudent Tel. E-Mail senden
Helena Moser Bachelorstudentin Tel. E-Mail senden
Dr. Chujin Ruan Postdoktorandin Tel. +41 58 765 5537 E-Mail senden
Janis Steiner Bachelorstudent Tel. E-Mail senden
Deepthi Vinod Doktorandin Tel. +41 58 765 6441 E-Mail senden
Agustina Ziliani PhD Student Tel. +41 58 765 5446 E-Mail senden

Ausgewählte Publikationen

Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion

Plasmids are the main vector by which antibiotic resistance is transferred between bacterial cells within surface-associated communities. In this study, we ask whether there is an optimal time to administer antibiotics to minimize plasmid spread in new bacterial genotypes during community expansion across surfaces. We address this question using consortia of Pseudomonas stutzeri strains, where one is an antibiotic resistance-encoding plasmid donor and the other a potential recipient. We allowed the strains to co-expand across a surface and administered antibiotics at different times. We find that plasmid transfer and transconjugant proliferation have unimodal relationships with the timing of antibiotic administration, where they reach maxima at intermediate times. These unimodal relationships result from the interplay between the probabilities of plasmid transfer and loss. Our study provides mechanistic insights into the transfer and proliferation of antibiotic resistance-encoding plasmids within microbial communities and identifies the timing of antibiotic administration as an important determinant.
Ma, Y.; Ramoneda, J.; Johnson, D. R. (2023) Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion, Nature Communications, 14(1), 3530 (12 pp.), doi:10.1038/s41467-023-39354-z, Institutional Repository

Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion

The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains. This is true regardless of the type of interaction (competition or resource cross-feeding) imposed between the bacterial strains. We further show that the underlying cause is that flagellar motility drives bacterial dispersal along the hyphal network, which counteracts the purifying effects of ecological drift at the expansion frontier. We finally demonstrate that hyphae-mediated spatial intermixing increases the conjugation-mediated spread of plasmid-encoded antibiotic resistance. In conclusion, fungal hyphae are important regulators of bacterial diversity and promote plasmid-mediated functional novelty during range expansion in an interaction-independent manner.
Ruan, C.; Ramoneda, J.; Gogia, G.; Wang, G.; Johnson, D. R. (2022) Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion, Current Biology, 32(24), 5285-5294, doi:10.1016/j.cub.2022.11.009, Institutional Repository

Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment

Spatial self-organization is a hallmark of surface-associated microbial communities that is governed by local environmental conditions and further modified by interspecific interactions. Here, we hypothesize that spatial patterns of microbial cell-types can stabilize the composition of cross-feeding microbial communities under fluctuating environmental conditions. We tested this hypothesis by studying the growth and spatial self-organization of microbial co-cultures consisting of two metabolically interacting strains of the bacterium Pseudomonas stutzeri. We inoculated the co-cultures onto agar surfaces and allowed them to expand (i.e. range expansion) while fluctuating environmental conditions that alter the dependency between the two strains. We alternated between anoxic conditions that induce a mutualistic interaction and oxic conditions that induce a competitive interaction. We observed co-occurrence of both strains in rare and highly localized clusters (referred to as “spatial jackpot events”) that persist during environmental fluctuations. To resolve the underlying mechanisms for the emergence of spatial jackpot events, we used a mechanistic agent-based mathematical model that resolves growth and dispersal at the scale relevant to individual cells. While co-culture composition varied with the strength of the mutualistic interaction and across environmental fluctuations, the model provides insights into the formation of spatially resolved substrate landscapes with localized niches that support the co-occurrence of the two strains and secure co-culture function. This study highlights that in addition to spatial patterns that emerge in response to environmental fluctuations, localized spatial jackpot events ensure persistence of strains across dynamic conditions.
Ciccarese, D.; Micali, G.; Borer, B.; Ruan, C.; Or, D.; Johnson, D. R. (2022) Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment, ISME Journal, 16, 1453-1463, doi:10.1038/s41396-022-01189-9, Institutional Repository

Projekte

Die plasmid-vermittelte Ausbreitung von Antibiotikaresistenzen (AR) innerhalb von und zwischen mikrobiellen Gemeinschaften ist eines der drängendsten Probleme unserer Gesellschaft, doch sind die Ursachen und potenziellen Abhilfemaßnahmen nach wie vor unklar.

Antibiotikaresistenz während mikrobieller Expansion
Warum blühen giftige Cyanbakterien? ...

Cyano Bloom
Mikrobielle Interaktionen bestimmen die Distickstoffmonoxid-Produktion

Ursachen der Distickstoffmonoxid-Produktion