Article
Biochemical Research Methods
Philipp Wendering, Zoran Nikoloski
Summary: The composition and functions of microbial communities have significant effects on important traits in various hosts. However, understanding how individual microbe metabolism is influenced by community composition and metabolite leakage is lacking. This study presents a consensus-based approach for improving the quality of draft metabolic reconstructions and proposes a method called COMMIT for gap filling in microbial communities. By applying COMMIT to soil communities, the researchers were able to reduce the gap-filling solution without affecting genomic support. The metabolic interactions identified in the soil communities allowed for the identification of microbes with community roles of helpers and beneficiaries. Therefore, COMMIT offers a versatile and fully automated solution for modeling microbial communities in different biotechnological applications.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Jessica A. Lee, Alyssa C. Baugh, Nicholas J. Shevalier, Brandi Strand, Sergey Stolyar, Christopher J. Marx
Summary: The research team developed a model microbial consortium for studying lignocellulose degradation with the specific goal of reducing formaldehyde production, by including various bacteria to simulate ecological dynamics and metabolite exchange. Experimental results suggest that this study lays the foundation for future eco-evolutionary research and optimization of biomass transformation efficiency.
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
Engineering, Environmental
Qian Fu, Jin-long Lai, Xiao-hui Ji, Zhong-xu Luo, Guo Wu, Xue-gang Luo
Summary: This study evaluated the impact of different molecular weight polyethylene-particles (PE-particles) on soil metabolism, microbial community structure, and crop growth using a potted microcosmic simulation system. The results showed that PE-particles with varying molecular weights had distinct effects on the soil-plant system, potentially leading to adverse effects.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Steven A. Wilbert, Dianne K. Newman
Summary: Microbial communities are widely distributed in the biosphere and exhibit reproducible spatial patterns. This study demonstrates the important role of redox-active metabolites in shaping microbial communities and shows how oxygen availability can tune metabolic cross-feeding and fitness outcomes in these communities.
Article
Environmental Sciences
Jing Ding, Hongwei Sun, Aiping Liang, Jin Liu, Lehui Song, Min Lv, Dong Zhu
Summary: The exposure to testosterone significantly altered the bacterial community structure and metabolic profiles in soils in Ningbo and Kunming, China. This resulted in a decrease in the abundance of bacterial taxa associated with nutrient cycling and downregulation of metabolites related to amino acid metabolism. The close connection between bacterial taxa and specific metabolites was confirmed by Procrustes tests and a co-occurrence network analysis.
ENVIRONMENTAL POLLUTION
(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
Multidisciplinary Sciences
Alan R. Pacheco, Melisa L. Osborne, Daniel Segre
Summary: The study investigates how microbial community properties change with increasing complexity of resource combinations. Results show that environmental composition plays a major role in determining microbiome dynamics, and growth yield may not increase additively with environmental complexity. Factors like species similarity, degree of specialization, and metabolic interactions influence the non-additive behavior of communities in response to combinations of resource pools.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Feilun Wu, Yuanchi Ha, Andrea Weiss, Meidi Wang, Jeffrey Letourneau, Shangying Wang, Nan Luo, Shuquan Huang, Charlotte T. Lee, Lawrence A. David, Lingchong You
Summary: Spatial partitioning modulates the dynamics of microbial communities, promoting the persistence of populations with negative interactions and suppressing those with positive interactions. An intermediate level of partitioning maximizes the overall diversity of the community.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Miao-Miao Le, Li-Wen Zhong, Zhi-Wei Ren, Mao-Qiang An, Yan-Hua Long, Tie-Jun Ling
Summary: In the pile fermentation process of Fuzhuan brick tea, changes in the microbial community occur before changes in the metabolite profile. Bacterial metabolism and the heat generated by it contribute significantly to the overall changes observed in the metabolite profile.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Ye Wang, Yao Teng, Jianli Zhang, Zixiong Zhang, Chen Wang, Xiukun Wu, Xiuqin Long
Summary: This study analyzed the variation of microbial communities in passion fruit cultivated soil and its rhizosphere soil under continuous cropping. The results showed that continuous cropping increased the richness but reduced the diversity of soil fungi, while it dramatically increased the richness and diversity of soil bacteria. Grafting different scions in the same rootstock also influenced the differential rhizosphere microbial communities. The rhizosphere of yellow passion fruit may be beneficial for the enrichment of disease-resistant microbes, such as Trichoderma.
Article
Green & Sustainable Science & Technology
Xiaoyu He, Chunyuan Wu, Huadong Tan, Xiao Deng, Yi Li
Summary: The combined exposure of glyphosate and diquat had significant effects on microbial diversity and community structure in paddy soil. Actinobacteria and Proteobacteria were the most sensitive phyla to the combined exposure. The combined use of these herbicides did not significantly affect microbial richness and diversity compared to their separate exposure.
Article
Microbiology
Guiliang Tan, Min Hu, Xiangli Li, Xueyan Li, Ziqiang Pan, Mei Li, Lin Li, Yi Wang, Ziyi Zheng
Summary: This study provides valuable information for understanding the microbial-associated mechanisms of flavor formation during koji making through analyzing the microbial communities, metabolite profiles, and their relationships during the process.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Mengdie Geng, Weizhen Zhang, Ting Hu, Rong Wang, Xiaoying Cheng, Jianjun Wang
Summary: This study investigated the effects of eutrophication on microbial community structure in shallow lakes in the Yangtze-Huaihe River basin in China. The results showed that eutrophication led to the homogenization of bacterial and fungal communities in both water and sediments. Physicochemical factors such as water temperature, pH, and heavy metals were found to influence the community structure. Importantly, generalist species were found to play a dominant role in explaining the variations in beta diversity along the trophic gradient.
Article
Environmental Sciences
Kun Guo, Naicheng Wu, Wei Li, Annette Baattrup-Pedersen, Tenna Riis
Summary: Stream biofilms are complex aggregates of diverse organism groups that are essential for global carbon and nitrogen cycles. The study found that specific phyla dominated the prokaryotic and eukaryotic communities at most sites, with diversity peaking in July and January. Hydrological and physicochemical variables were significant factors in explaining community composition, but a large portion of variation remained unexplained, likely due to unmeasured factors such as light intensity and biological interactions. A multitrophic level perspective is suggested for future biofilm studies to capture the complexity of trophic and non-trophic interactions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Ecology
Feng Ju, Karin Beck, Xiaole Yin, Andreas Maccagnan, Christa S. McArdell, Heinz P. Singer, David R. Johnson, Tong Zhang, Helmut Burgmann
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)
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)