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1. Active pH regulation facilitates Bacillus subtilis biofilm development in a minimally buffered environment

   https://doi.org/10.1128/mbio.03387-23  

   Tran, Peter; Lander, Stephen M; Prindle, Arthur (March 2024, mBio)

   Kline, Kimberly A (Ed.)

   ABSTRACT Biofilms provide individual bacteria with many advantages, yet dense cellular proliferation can also create intrinsic metabolic challenges including excessive acidification. Because such pH stress can be masked in buffered laboratory media—such as MSgg commonly used to studyBacillus subtilisbiofilms—it is not always clear how such biofilms cope with minimally buffered natural environments. Here, we report howB. subtilisbiofilms overcome this intrinsic metabolic challenge through an active pH regulation mechanism. Specifically, we find that these biofilms can modulate their extracellular pH to the preferred neutrophile range, even when starting from acidic and alkaline initial conditions, while planktonic cells cannot. We associate this behavior with dynamic interplay between acetate and acetoin biosynthesis and show that this mechanism is required to buffer against biofilm acidification. Furthermore, we find that buffering-deficient biofilms exhibit dysregulated biofilm development when grown in minimally buffered conditions. Our findings reveal an active pH regulation mechanism inB. subtilisbiofilms that could lead to new targets to control unwanted biofilm growth.IMPORTANCEpH is known to influence microbial growth and community dynamics in multiple bacterial species and environmental contexts. Furthermore, in many bacterial species, rapid cellular proliferation demands the use of overflow metabolism, which can often result in excessive acidification. However, in the case of bacterial communities known as biofilms, these acidification challenges can be masked when buffered laboratory media are employed to stabilize the pH environment for optimal growth. Our study reveals thatB. subtilisbiofilms use an active pH regulation mechanism to mitigate both growth-associated acidification and external pH challenges. This discovery provides new opportunities for understanding microbial communities and could lead to new methods for controlling biofilm growth outside of buffered laboratory conditions. 

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2. Resource limitation of autotrophs and heterotrophs in boreal forest headwater streams

   https://doi.org/10.1086/722256  

   Weaver, Sophie A.; Jones, Jeremy B. (December 2022, Freshwater Science)

   Autotrophic and heterotrophic microbes in stream biofilms dominate biogeochemical cycling and rely on nutrient and energy resources for growth and productivity. In the boreal forest, variation in these resources can originate from permafrost distribution and controls competition for nutrients between stream autotrophs and heterotrophs. We investigated which resources control nutrient uptake and metabolism in headwater stream biofilms of subarctic Alaska, USA, and how resource availability affects competition for inorganic nutrients. We hypothesized that the competitive outcome between autotrophs and heterotrophs for inorganic nutrients would be dependent on availability of organic C, or inorganic nutrients (N and P). To test our hypotheses, we measured resource limitation at the patch and reach scales along a permafrost gradient in interior Alaska. At the patch scale, nutrient diffusing substrata revealed that, secondary to light, N and P were colimiting to autotrophic growth, whereas C was primarily limiting to heterotrophic respiration. In the presence of labile C, heterotrophs exhibited a larger response to nutrient enrichment and outcompeted autotrophs for inorganic nutrients. At the reach scale, light availability had the largest influence on nutrient uptake, but inorganic nutrients were also important. The positive response to increased nutrient and C availability at the patch scale suggests that the predicted increase in exports into fluvial networks with permafrost degradation will alter biofilm structure and function. Ultimately, biofilm communities will shift to more heterotroph-dominated patches if heterotrophs outcompete autotrophs for inorganic nutrients. As permafrost thaws and nutrients and organic C mobilize into streams, nutrient uptake dynamics and competition within biofilms will be altered, affecting nutrient use and export. 

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3. Soil-atmosphere fluxes of CO2, CH4, and N2O across an experimentally-grown, successional gradient of biocrust community types

   https://doi.org/10.3389/fmicb.2022.979825  

   Richardson, Andrew D; Kong, Gary V; Taylor, Katrina M; Le_Moine, James M; Bowker, Matthew A; Barber, Jarrett J; Basler, David; Carbone, Mariah S; Hayer, Michaela; Koch, George W; et al (September 2022, Frontiers in Microbiology)

   Biological soil crusts (biocrusts) are critical components of dryland and other ecosystems worldwide, and are increasingly recognized as novel model ecosystems from which more general principles of ecology can be elucidated. Biocrusts are often diverse communities, comprised of both eukaryotic and prokaryotic organisms with a range of metabolic lifestyles that enable the fixation of atmospheric carbon and nitrogen. However, how the function of these biocrust communities varies with succession is incompletely characterized, especially in comparison to more familiar terrestrial ecosystem types such as forests. We conducted a greenhouse experiment to investigate how community composition and soil-atmosphere trace gas fluxes of CO₂, CH₄, and N₂O varied from early-successional light cyanobacterial biocrusts to mid-successional dark cyanobacteria biocrusts and late-successional moss-lichen biocrusts and as biocrusts of each successional stage matured. Cover type richness increased as biocrusts developed, and richness was generally highest in the late-successional moss-lichen biocrusts. Microbial community composition varied in relation to successional stage, but microbial diversity did not differ significantly among stages. Net photosynthetic uptake of CO₂by each biocrust type also increased as biocrusts developed but tended to be moderately greater (by up to ≈25%) for the mid-successional dark cyanobacteria biocrusts than the light cyanobacterial biocrusts or the moss-lichen biocrusts. Rates of soil C accumulation were highest for the dark cyanobacteria biocrusts and light cyanobacteria biocrusts, and lowest for the moss-lichen biocrusts and bare soil controls. Biocrust CH₄and N₂O fluxes were not consistently distinguishable from the same fluxes measured from bare soil controls; the measured rates were also substantially lower than have been reported in previous biocrust studies. Our experiment, which uniquely used greenhouse-grown biocrusts to manipulate community composition and accelerate biocrust development, shows how biocrust function varies along a dynamic gradient of biocrust successional stages. 

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4. Metabolic Remodeling during Biofilm Development of Bacillus subtilis

   https://doi.org/10.1128/mBio.00623-19  

   Pisithkul, Tippapha; Schroeder, Jeremy W.; Trujillo, Edna A.; Yeesin, Ponlkrit; Stevenson, David M.; Chaiamarit, Tai; Coon, Joshua J.; Wang, Jue D.; Amador-Noguez, Daniel; Ghigo, Jean-Marc; et al (June 2019, mBio)

   ABSTRACT Biofilms are structured communities of tightly associated cells that constitute the predominant state of bacterial growth in natural and human-made environments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilis has been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, we performed a time-resolved analysis of the metabolic changes associated with pellicle biofilm formation and development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. We report surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hitherto unrecognized as biofilm associated. For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was largely controlled at the transcriptional level. Our results also provide insights into the transcription factors and regulatory networks involved in this complex metabolic remodeling. Following upon these results, we demonstrated that acetoin production via acetolactate synthase is essential for robust biofilm growth and has the dual role of conserving redox balance and maintaining extracellular pH. This report represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilis biofilm development that will serve as a useful road map for future studies on biofilm physiology. IMPORTANCE Bacterial biofilms are ubiquitous in natural environments and play an important role in many clinical, industrial, and ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation in model bacteria such as Bacillus subtilis , very little is known about the role of metabolism in this complex developmental process. To address this important knowledge gap, we performed a time-resolved analysis of the metabolic changes associated with bacterial biofilm development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. Here, we report a widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. This report serves as a unique hypothesis-generating resource for future studies on bacterial biofilm physiology. Outside the biofilm research area, this work should also prove relevant to any investigators interested in microbial physiology and metabolism. 

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5. Niche partitioning of microbial communities in riverine floodplains

   https://doi.org/10.1038/s41598-019-52865-4  

   Peipoch, Marc; Miller, Scott R.; Antao, Tiago R.; Valett, H. Maurice (November 2019, Scientific Reports)

   Abstract Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H’: 2.8–4.1) nor β (Sørensen: 0.3–0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients. 

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