Review
Microbiology
Ryan K. Fritts, Alexandra L. McCully, James B. McKinlay
Summary: The transfer of nutrients between cells, known as cross-feeding, is a crucial aspect of microbial communities that impacts health and global biogeochemical cycles. Externalized molecules play a diverse role in promoting cross-feeding relationships, which can be characterized by a mix of cooperation and competition. The interplay between microbial physiology, environmental factors, and extracellular molecules shape the dynamics of cross-feeding interactions.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2021)
Article
Ecology
Jake N. Barber, Luke C. Nicholson, Laura C. Woods, Louise M. Judd, Aysha L. Sezmis, Jane Hawkey, Kathryn E. Holt, Michael J. McDonald
Summary: Species loss within a microbial community can increase resource availability and spur adaptive evolution. However, coevolution within a community can prevent destabilizing evolution in individual species, thereby preserving ecological diversity and stability.
Article
Multidisciplinary Sciences
Akihiko Mougi
Summary: Microbes interact with their environment by modifying it and reacting to these modifications, and recent research has shown that the ecological consequences of these interactions can be predicted from their effects on pH. Adaptation of pH niche can affect microbial coexistence, but the mechanisms underlying this effect are not yet understood. This study demonstrates that ecological theory may have difficulty in accurately predicting ecological consequences when there are adaptive changes in pH niche.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Samir Giri, Leonardo Ona, Silvio Waschina, Shraddha Shitut, Ghada Yousif, Christoph Kaleta, Christian Kost
Summary: The study reveals that metabolic dissimilarity between bacterial genotypes is a key factor determining the establishment of metabolic cross-feeding interactions in microbial communities. Results showed that a greater phylogenetic distance and metabolic network dissimilarity between donor and recipient were associated with better growth of auxotrophic recipients, indicating that interacting with metabolically dissimilar partners benefits recipient genotypes.
Article
Biology
Jaime G. Lopez, Ned S. Wingreen
Summary: This study introduces a novel theory called noise-averaging cooperation (NAC) to explain the emergence of cross-feeding between species. The research shows that metabolite leakage can significantly increase the growth rate of microbial communities. Using single-cell protein abundance data, it is predicted that bacteria may benefit from NAC due to noise-driven growth inefficiencies.
Review
Microbiology
Sankhadeep Mondal, Jigyasa Somani, Somnath Roy, Azariah Babu, Abhay K. Pandey
Summary: The presence of bacterial species inside the guts of insect pests provides several advantages to the insects, including food digestion, phytotoxin breakdown, and pesticide detoxification. Despite hindering insecticide management programs, these gut bacteria have biotechnological uses and can adapt to diverse ecological niches.
Article
Ecology
Rinke J. van Tatenhove-Pel, Daan H. de Groot, Anjani S. Bisseswar, Bas Teusink, Herwig Bachmann
Summary: The study reveals the evolution of costly cooperation between microorganisms through spatial structure and exchange of molecules. Experimental results show that cooperators outcompete cheaters when the growth of cheaters depends completely on cooperators, but cheaters outcompete cooperators when they can independently grow to only ten percent of the consortium carrying capacity.
Article
Multidisciplinary Sciences
Gabriele Micali, Alyson M. Hockenberry, Alma Dal Co, Martin Ackermann, Dianne Newman
Summary: Microbial communities are essential for life on Earth, but their metabolic dependencies can be detrimental when external conditions change rapidly. We found that the spatial arrangement of a microbial community plays a crucial role in maintaining metabolic interactions and growth after an environmental shift.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Environmental Sciences
Shengjie Li, Muhe Diao, Yinhao Liao, Guodong Ji
Summary: Iron addition improved the efficiency of nitrogen removal in freshwaters by promoting microbial growth and establishing syntrophic interactions among microorganisms. Metagenomic analysis revealed that the majority of the community in the iron-based system consisted of fast-growing organisms. These findings provide new insights into the iron-dependent denitrification process and its implications for freshwater remediation.
ENVIRONMENT INTERNATIONAL
(2023)
Review
Biotechnology & Applied Microbiology
Yijing Shi, David C. Queller, Yuehui Tian, Siyi Zhang, Qingyun Yan, Zhili He, Zhenzhen He, Chenyuan Wu, Cheng Wang, Longfei Shu
Summary: This study explores the complex symbiotic relationships between amoebae and bacteria, highlighting their contributions to predation, symbiosis, pathogenesis, and human health. It emphasizes the ecological and evolutionary significance of understanding these interactions and discusses their implications for human health, gene transfer, water safety, and symbiotic evolution. The study calls for future research to utilize advanced techniques to address research gaps and explore the impacts of amoeba predation on the microbiome.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Editorial Material
Ecology
Akos T. Kovacs
Summary: Experimental evolution allows researchers to explore the genetic and phenotypic changes that occur in response to specific conditions. By simplifying the environment to represent certain aspects of a complex natural niche, researchers can study the factors that drive selection, including temperature, oxygen availability, and nutrients. In this study, the authors used cross-kingdom interaction in a cheese microbiome succession experiment to investigate the distinct evolution of Staphylococcus xylosus, a bacterium associated with both food and animals. They discovered a global regulator-dependent adaptation that resulted in evolved derivatives with reduced pigment production, altered colony morphologies, and modified differentiation phenotypes, potentially enhancing their fitness.
Article
Ecology
Elena Kozlova, Shivanand Hegde, Christopher M. Roundy, George Golovko, Miguel A. Saldana, Charles E. Hart, Enyia R. Anderson, Emily A. Hornett, Kamil Khanipov, Vsevolod L. Popov, Maria Pimenova, Yiyang Zhou, Yuriy Fovanov, Scott C. Weaver, Andrew L. Routh, Eva Heinz, Grant L. Hughes
Summary: The interactions between microbes in the mosquito gut are complex and can influence mosquito behavior and the parasitic habits of the microbes.
Article
Environmental Sciences
Enze Li, Tongchu Deng, Lei Yan, Jizhong Zhou, Zhili He, Ye Deng, Meiying Xu
Summary: The study found that nitrate pollution led to functional and taxonomic convergence in microbial communities in sulfide-rich river sediments, resulting in a loss of biodiversity, community stability, and other functions. Thiobacillus and Luteimonas became dominant denitrifiers after nitrate amendment, while keystone taxa were more likely to be native auxotrophs rather than dominant denitrifiers.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Engineering, Environmental
Depeng Wang, Qi Luo, Kailong Huang, Xu-Xiang Zhang
Summary: This study investigated the assembly processes and interactions of functional bacteria in anammox and denitrification coupling systems using lab-scale up-flow bioreactors. The results showed that the community composition of functional bacteria differed between the systems, and the community assembly was mainly governed by stochastic processes and homogeneous selection. Moreover, the network structures of anammox and denitrifying bacteria varied between the systems.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Microbiology
Hiroaki Fujita, Masayuki Ushio, Kenta Suzuki, Masato S. Abe, Masato Yamamichi, Yusuke Okazaki, Alberto Canarini, Ibuki Hayashi, Keitaro Fukushima, Shinji Fukuda, E. Toby Kiers, Hirokazu Toju
Summary: By analyzing the shotgun metagenomic sequencing data of an experimental microbial community, we discovered that the network structure of facilitative interactions in microbial ecosystems can change over time. By using metabolic modeling, we inferred the potential facilitative interaction networks at 13 time points during the 110-day monitoring of the microbiomes. We found that positive feedback loops, which can lead to ecological cascade breakdown, existed in the metabolic interaction networks before the drastic community compositional shift.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Stefan Achermann, Cresten B. Mansfeldt, Marcel Mueller, David R. Johnson, Kathrin Fenner
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2020)
Article
Biology
Davide Ciccarese, Anita Zuidema, Valeria Merlo, David R. Johnson
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Biochemical Research Methods
Martin Carballo-Pacheco, Michael D. Nicholson, Elin E. Lilja, Rosalind J. Allen, Bartlomiej Waclaw
PLOS COMPUTATIONAL BIOLOGY
(2020)
Review
Microbiology
David R. Johnson, Francesco Pomati
ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Biology
Benedict Borer, Davide Ciccarese, David Johnson, Dani Or
COMMUNICATIONS BIOLOGY
(2020)
Article
Ecology
Felix Goldschmidt, Lea Caduff, David R. Johnson
Summary: Surface-attached microbial communities exhibit different patterns of spatial self-organization, known as pattern diversification, which is not influenced by initial environmental heterogeneity or genetic heterogeneity within populations. Instead, pattern diversification is caused by nongenetic heterogeneity within populations, specifically local differences in the initial spatial positionings of individuals. These different patterns also lead to varying community-level properties, such as expansion speeds.
Article
Biology
Manupriyam Dubey, Noushin Hadadi, Serge Pelet, Nicolas Carraro, David R. Johnson, Jan R. van der Meer
Summary: The study investigated the effects of environmental connectivity on natural soil microbial communities and found that while overall community growth was similar in high and low connectivity environments, low connectivity led to reduced microbial diversity due to increased negative interspecific interactions. This suggests the importance of environmental connectivity for microbial community dynamics and has implications for future interventions and restoration efforts.
COMMUNICATIONS BIOLOGY
(2021)
Article
Ecology
Davide Ciccarese, Gabriele Micali, Benedict Borer, Chujin Ruan, Dani Or, David R. Johnson
Summary: This study explores the growth and spatial self-organization of microbial co-cultures and reveals the emergence of rare and highly localized clusters, referred to as spatial jackpot events, that help stabilize the composition of the microbial community under fluctuating environmental conditions. A mechanistic agent-based mathematical model is used to understand the underlying mechanisms for the formation of these spatial jackpot events.
Article
Biochemistry & Molecular Biology
Chujin Ruan, Josep Ramoneda, Guram Gogia, Gang Wang, David R. Johnson
Summary: Fungal hyphae-mediated dispersal plays an important role in regulating bacterial diversity during range expansion.
Article
Multidisciplinary Sciences
Yinyin Ma, Josep Ramoneda, David R. Johnson
Summary: In this study, the researchers used consortia of Pseudomonas stutzeri strains to investigate the optimal timing of antibiotic administration to minimize the spread of antibiotic resistance-encoding plasmids within microbial communities. They found that plasmid transfer and transconjugant proliferation peaked at intermediate antibiotic administration times when the mixing between plasmid donors and potential recipients was maximal.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
Zhan-Biao Ge, Zhi-Qiang Zhai, Wan-Ying Xie, Jun Dai, Ke Huang, David R. Johnson, Fang-Jie Zhao, Peng Wang
Summary: In this study, a two-tiered mutualism between soil bacteria Bacillus sp. BP-3 and Delftia sp. DT-2 was identified. These bacteria cooperate to ensure their metabolic activity and competitive advantage against other soil microbes, and they use arsenic as a weapon. These findings provide insights into the complexity of bacterial interactions and their roles in ecosystem functioning.
Article
Biotechnology & Applied Microbiology
Chujin Ruan, Benedict Borer, Josep Ramoneda, Gang Wang, David R. Johnson
Summary: Droplet evaporation is a common process in unsaturated environments that affects the spatial distribution of microbial cells on surfaces. The initial deposition patterns of microbial cells, influenced by evaporation-induced hydrodynamic processes, control the spread of plasmids during surface-associated growth. The coffee ring effect and Marangoni convection determine the different deposition patterns, which in turn affect the extent of plasmid transfer. This study highlights the importance of evaporation-induced hydrodynamic processes in shaping microbial communities and controlling the spread of plasmid-encoded traits.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Environmental Sciences
Kohei Takahashi, Mamoru Oshiki, Chujin Ruan, Kana Morinaga, Masanori Toyofuku, Nobuhiko Nomura, David R. Johnson
Summary: Denitrification in low oxic environments can increase the accumulation of nitrite and nitric oxide intermediates, which have negative effects on growth, especially at low pH. This process also increases the number of individuals contributing to surface-associated growth, resulting in higher genetic diversity and evolutionary potentials for denitrifying microorganisms.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Engineering, Environmental
Sema Karakurt-Fischer, David R. Johnson, Kathrin Fenner, Jasmin Hafner
Summary: Biodegradation is a promising method for removing synthetic chemical pollutants, but rational engineering in this area remains a challenge. To overcome this, a high-throughput bio-chem-informatics pipeline is proposed to link chemicals with their predicted biotransformation pathways, enzymes, and bacterial strains. This approach can help in the design and study of fit-for-purpose bacterial communities for enhancing pollutant biodegradation.
Article
Ecology
Jiyun Li, Zheng-Shuang Hua, Tao Liu, Chengwen Wang, Jie Li, Ge Bai, Sebastian Lucker, Mike S. M. Jetten, Min Zheng, Jianhua Guo
Summary: Evaporation-induced water flows can significantly increase plasmid conjugation and reduce cell-cell distances, despite causing lower expression levels of conjugation-related genes.
ISME COMMUNICATIONS
(2021)
