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1. Feedback Regulation between Aquatic Microorganisms and the Bloom-Forming Cyanobacterium Microcystis aeruginosa

   https://doi.org/10.1128/AEM.01362-19  

   Zhang, Meng; Lu, Tao; Paerl, Hans W.; Chen, Yiling; Zhang, Zhenyan; Zhou, Zhigao; Qian, Haifeng; Drake, Harold L. (November 2019, Applied and Environmental Microbiology)

   ABSTRACT The frequency and intensity of cyanobacterial blooms are increasing worldwide. Interactions between toxic cyanobacteria and aquatic microorganisms need to be critically evaluated to understand microbial drivers and modulators of the blooms. In this study, we applied 16S/18S rRNA gene sequencing and metabolomics analyses to measure the microbial community composition and metabolic responses of the cyanobacterium Microcystis aeruginosa in a coculture system receiving dissolved inorganic nitrogen and phosphorus (DIP) close to representative concentrations in Lake Taihu, China. M. aeruginosa secreted alkaline phosphatase using a DIP source produced by moribund and decaying microorganisms when the P source was insufficient. During this process, M. aeruginosa accumulated several intermediates in energy metabolism pathways to provide energy for sustained high growth rates and increased intracellular sugars to enhance its competitive capacity and ability to defend itself against microbial attack. It also produced a variety of toxic substances, including microcystins, to inhibit metabolite formation via energy metabolism pathways of aquatic microorganisms, leading to a negative effect on bacterial and eukaryotic microbial richness and diversity. Overall, compared with the monoculture system, the growth of M. aeruginosa was accelerated in coculture, while the growth of some cooccurring microorganisms was inhibited, with the diversity and richness of eukaryotic microorganisms being more negatively impacted than those of prokaryotic microorganisms. These findings provide valuable information for clarifying how M. aeruginosa can potentially modulate its associations with other microorganisms, with ramifications for its dominance in aquatic ecosystems. IMPORTANCE We measured the microbial community composition and metabolic responses of Microcystis aeruginosa in a microcosm coculture system receiving dissolved inorganic nitrogen and phosphorus (DIP) close to the average concentrations in Lake Taihu. In the coculture system, DIP is depleted and the growth and production of aquatic microorganisms can be stressed by a lack of DIP availability. M. aeruginosa could accelerate its growth via interactions with specific cooccurring microorganisms and the accumulation of several intermediates in energy metabolism-related pathways. Furthermore, M. aeruginosa can decrease the carbohydrate metabolism of cooccurring aquatic microorganisms and thus disrupt microbial activities in the coculture. This also had a negative effect on bacterial and eukaryotic microbial richness and diversity. Microcystin was capable of decreasing the biomass of total phytoplankton in aquatic microcosms. Overall, compared to the monoculture, the growth of total aquatic microorganisms is inhibited, with the diversity and richness of eukaryotic microorganisms being more negatively impacted than those of prokaryotic microorganisms. The only exception is M. aeruginosa in the coculture system, whose growth was accelerated. 

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2. Metabolic Synergy between Human Symbionts Bacteroides and Methanobrevibacter

   https://doi.org/10.1128/spectrum.01067-22  

   Catlett, Jennie L.; Carr, Sean; Cashman, Mikaela; Smith, Megan D.; Walter, Mary; Sakkaff, Zahmeeth; Kelley, Christine; Pierobon, Massimiliano; Cohen, Myra B.; Buan, Nicole R. (June 2022, Microbiology Spectrum)

   Claesen, Jan (Ed.)

   ABSTRACT Trophic interactions between microbes are postulated to determine whether a host microbiome is healthy or causes predisposition to disease. Two abundant taxa, the Gram-negative heterotrophic bacterium Bacteroides thetaiotaomicron and the methanogenic archaeon Methanobrevibacter smithii , are proposed to have a synergistic metabolic relationship. Both organisms play vital roles in human gut health; B. thetaiotaomicron assists the host by fermenting dietary polysaccharides, whereas M. smithii consumes end-stage fermentation products and is hypothesized to relieve feedback inhibition of upstream microbes such as B. thetaiotaomicron . To study their metabolic interactions, we defined and optimized a coculture system and used software testing techniques to analyze growth under a range of conditions representing the nutrient environment of the host. We verify that B. thetaiotaomicron fermentation products are sufficient for M. smithii growth and that accumulation of fermentation products alters secretion of metabolites by B. thetaiotaomicron to benefit M. smithii . Studies suggest that B. thetaiotaomicron metabolic efficiency is greater in the absence of fermentation products or in the presence of M. smithii . Under certain conditions, B. thetaiotaomicron and M. smithii form interspecies granules consistent with behavior observed for syntrophic partnerships between microbes in soil or sediment enrichments and anaerobic digesters. Furthermore, when vitamin B 12 , hematin, and hydrogen gas are abundant, coculture growth is greater than the sum of growth observed for monocultures, suggesting that both organisms benefit from a synergistic mutual metabolic relationship. IMPORTANCE The human gut functions through a complex system of interactions between the host human tissue and the microbes which inhabit it. These diverse interactions are difficult to model or examine under controlled laboratory conditions. We studied the interactions between two dominant human gut microbes, B. thetaiotaomicron and M. smithii , using a seven-component culturing approach that allows the systematic examination of the metabolic complexity of this binary microbial system. By combining high-throughput methods with machine learning techniques, we were able to investigate the interactions between two dominant genera of the gut microbiome in a wide variety of environmental conditions. Our approach can be broadly applied to studying microbial interactions and may be extended to evaluate and curate computational metabolic models. The software tools developed for this study are available as user-friendly tutorials in the Department of Energy KBase. 

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3. Expedited screening of methanotroph-microalgae cocultures for integrated biogas valorization and wastewater remediation

   https://doi.org/10.1016/j.jenvman.2025.125824  

   Murphy, Loyal P; He, Q Peter; Wang, Jin (August 2025, Journal of Environmental Management)

   Anaerobic digestion (AD) is a well-established waste-to-value technology commonly used at water resource recovery facilities (WRRFs), generating biogas from organic waste. However, the generated biogas is typically used only for heat and electricity generation due to contaminants, while the nutrient-rich AD effluent requires further treatment before environmental release. Methanotroph-microalgae cocultures have recently emerged as promising candidates for integrated biogas valorization and nutrient recovery. Although the choice of the coculture pairs is one of the most important factors that determine the performance of the application, there have not been any results on the comparison or screening of different coculture pairs for a desired application. To expedite the screening of methanotroph-microalgae cocultures for optimal performance, we developed a cost-effective screening system consisting of nine parallel bioreactors. The compact design of the system allows it to fit in a fume hood, and enables the simultaneous evaluation of multiple species with triplicates under uniformly controlled conditions. The system was applied to screen seven methanotrophs, five microalgae, and six methanotroph-microalgae coculture pairs on a diluted AD effluent from a local WRRF. To systematically assess the growth performance of different monocultures and cocultures, mathematical models that describe the microbial growth under batch cultivation were developed to determine the maximum growth rate, delay time, and carrying capacity from growth data, allowing for consistent and systematic assessment of different species, as well as the identification of the coculture pairs with synergistic and inhibitory interactions. The developed experimental system and modeling approach enabled expedited strain screening and unbiased assessment for integrated biogas valorization and nutrient recovery. Specifically, the cost of each bioreactor system in S3 is less than 5% of commercially available bioreactor system (such as Bioflo 120), while the screening throughput of S3 is 9 times that of a single bioreactor system. In addition, the identified synergistic cocultures demonstrate potential for scalable biogas valorization and nutrient recovery in wastewater treatment. 

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4. From networks to mechanisms: A cross-scale analysis of bacterial - fungal interactions in fungal necromass

   Beatty, Briana (December 2024, University of Minnesota Graduate School)

   Microbial community dynamics are dependent on interactions between the community members, yet studies of interactions across domains and with multiple experimental approaches are lacking. In this study, we explored interactions between bacteria and fungi associated with decaying fungal necromass using both field-based co-occurrence networks and laboratory-based pairwise interactions. The majority of field-derived bacterial-fungal correlations were negative, suggesting a potentially competitive environment within necromass compared to other systems. Laboratory experiments consisted of bacteria most often reducing fungal growth, while the fungal effect on bacterial growth was more varied and dependent on bacterial taxa. However, these interactions were not consistently predicted by field correlations, highlighting a disconnect between field-based and direct experimental approaches. Our findings suggest that using co-occurrence networks alone to predict BFI outcomes could be misleading, emphasizing the need for more comprehensive, multi-method studies to capture the dynamic and context-dependent nature of microbial interactions. 

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5. Data and code from an examination of growth rates of cyanobacteria co-cultured with a heterotrophic bacterium, Alteromonas, under either present-day or predicted future pCO2 conditions

   https://doi.org/10.26008/1912/bco-dmo.925841.1  

   Morris, James J; Entwistle, Elizabeth; Lu, Zhiying; Kuhl, Matthew; Durrant, Alexander (January 2024, Biological and Chemical Oceanography Data Management Office (BCO-DMO))

   The CO2 content of Earth's atmosphere is rapidly increasing due to human consumption of fossil fuels. Models based on short-term culture experiments predict that major changes will occur in marine phytoplankton communities in the future ocean, but these models rarely consider how the evolutionary potential of phytoplankton or interactions within marine microbial communities may influence these changes. Here we experimentally evolved representatives of four phytoplankton functional types (silicifiers, calcifiers, coastal cyanobacteria, and oligotrophic cyanobacteria) in co-culture with a heterotrophic bacterium, Alteromonas, under either present-day or predicted future pCO2 conditions. The data and analysis code in this dataset show that the growth rates of cyanobacteria generally increased under both conditions, and the growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution. Evolved Alteromonas were also poorer "helpers" for Prochlorococcus, supporting the assertion that the interaction between Prochlorococcus and heterotrophic bacteria is not a true mutualism but rather a competitive interaction stabilized by Black Queen processes. This work provides new insights on how phytoplankton will respond to anthropogenic change and on the evolutionary mechanisms governing the structure and function of marine microbial communities. 

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