Improving the learning experience in an undergraduate course on microbial metabolism by using an illustrated story.

In the classroom, metabolism is often approached and received as a mundane exercise in memorization. Teaching metabolism also faces the challenge of negative perceptions that can impede learning. We sought to improve the learning experience in an undergraduate lecture course on microbial metabolism by implementing an illustrated story that follows an Escherichia coli cell during a cholera outbreak.

Quorum sensing in Vibrio controls carbon metabolism to optimize growth in changing environmental conditions.

Bacteria sense population density via the cell-cell communication system called quorum sensing (QS). The evolution of QS and its maintenance or loss in mixed bacterial communities is highly relevant to understanding how cell-cell signaling impacts bacterial fitness and competition, particularly under varying environmental conditions such as nutrient availability. We uncovered a phenomenon in which Vibrio cells grown in minimal medium optimize expression of the methionine and tetrahydrofolate (THF) synthesis genes via QS.

Bacterial cross-feeding can promote gene retention by lowering gene expression costs.

Gene loss is expected in microbial communities when the benefit of obtaining a biosynthetic precursor from a neighbor via cross-feeding outweighs the cost of retaining a biosynthetic gene. However, gene cost primarily comes from expression, and many biosynthetic genes are only expressed when needed. Thus, one can conversely expect cross-feeding to repress biosynthetic gene expression and promote gene retention by lowering gene cost.

Bacterial quorum sensing controls carbon metabolism to optimize growth in changing environmental conditions.

Bacteria sense population density via the cell-cell communication system called quorum sensing (QS). Some QS-regulated phenotypes ( , secreted enzymes, chelators), are public goods exploitable by cells that stop producing them. We uncovered a phenomenon in which cells optimize expression of the methionine and tetrahydrofolate (THF) synthesis genes via QS.

Better off breathing: an explanation for the seemingly detrimental impact of aerobic respiration on .

The bacterium is best known for fermentatively producing more ethanol than yeast. However, has also puzzled researchers for decades with the counterintuitive observation that disrupting aerobic respiration benefits aerobic growth, implying that fermentation remains favorable. Retention of detrimental respiration genes seemed to defy natural selection.

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired.

Denitrification is a form of anaerobic respiration wherein nitrate (NO) is sequentially reduced via nitrite (NO), nitric oxide, and nitrous oxide (NO) to dinitrogen gas (N) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire.

A purine salvage bottleneck leads to bacterial adenine cross-feeding.

Diverse ecosystems host microbial relationships that are stabilized by nutrient cross-feeding. Cross-feeding can involve metabolites that should hold value for the producer. Externalization of such communally valuable metabolites is often unexpected and difficult to predict.

Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding.

The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding.

Complete Genome Sequence of Rhodopseudomonas palustris CGA0092 and Corrections to the R. palustris CGA009 Genome Sequence.

Rhodopseudomonas palustris CGA009 is a versatile model purple nonsulfur bacterium used for both fundamental and applied research. Here, we present a new genome sequence for the derivative strain CGA0092. We further present an improved CGA009 genome assembly that differs from the original CGA009 sequence at three positions.

Nitric oxide stimulates type IV MSHA pilus retraction in via activation of the phosphodiesterase CdpA.

Bacteria use surface appendages called type IV pili to perform diverse activities including DNA uptake, twitching motility, and attachment to surfaces. The dynamic extension and retraction of pili are often required for these activities, but the stimuli that regulate these dynamics remain poorly characterized. To address this question, we study the bacterial pathogen , which uses mannose-sensitive hemagglutinin (MSHA) pili to attach to surfaces in aquatic environments as the first step in biofilm formation.

Extracellular Metabolism Sets the Table for Microbial Cross-Feeding.

The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding.

Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community.

Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH), are communally valuable and impose a cost on the producer.

Covert Cross-Feeding Revealed by Genome-Wide Analysis of Fitness Determinants in a Synthetic Bacterial Mutualism.

Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing and , wherein provides carbon to in the form of glucose fermentation products and fixes N gas and provides nitrogen to in the form of NH The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism.

Reductive tricarboxylic acid cycle enzymes and reductive amino acid synthesis pathways contribute to electron balance in a Calvin-cycle mutant.

Purple non-sulfur bacteria (PNSB) use light for energy and organic substrates for carbon and electrons when growing photoheterotrophically. This lifestyle generates more reduced electron carriers than are required for biosynthesis, even during consumption of some of the most oxidized organic substrates like malate and fumarate. Reduced electron carriers not used in biosynthesis must still be oxidized for photoheterotrophic growth to occur.

Fermentative Escherichia coli makes a substantial contribution to H2 production in coculture with phototrophic Rhodopseudomonas palustris.

Individual species within microbial communities can combine their attributes to produce services that benefit society, such as the transformation of renewable resources into valuable chemicals. Under defined genetic and environmental conditions, fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris exchange essential carbon and nitrogen, respectively, to establish a mutualistic relationship. In this relationship, each species produces H2 biofuel as a byproduct of its metabolism.

Phototrophic Lactate Utilization by Is Stimulated by Coutilization with Additional Substrates.

The phototrophic purple nonsulfur bacterium is known for its metabolic versatility and is of interest for various industrial and environmental applications. Despite decades of research on growth under diverse conditions, patterns of growth and carbon utilization with mixtures of carbon substrates remain largely unknown. readily utilizes most short-chain organic acids but cannot readily use lactate as a sole carbon source.

Cell Aggregation and Aerobic Respiration Are Important for ZM4 Survival in an Aerobic Minimal Medium.

produces ethanol from glucose near the theoretical maximum yield, making it a potential alternative to the yeast for industrial ethanol production. A potentially useful industrial feature is the ability to form multicellular aggregates called flocs, which can settle quickly and exhibit higher resistance to harmful chemicals than single cells. While spontaneous floc-forming mutants have been described, little is known about the natural conditions that induce floc formation or about the genetic factors involved.

Restricted Localization of Photosynthetic Intracytoplasmic Membranes (ICMs) in Multiple Genera of Purple Nonsulfur Bacteria.

In bacteria and eukaryotes alike, proper cellular physiology relies on robust subcellular organization. For the phototrophic purple nonsulfur bacteria (PNSB), this organization entails the use of a light-harvesting, membrane-bound compartment known as the intracytoplasmic membrane (ICM). Here we show that ICMs are spatially and temporally localized in diverse patterns among PNSB.

Differential carbohydrate utilization and organic acid production by honey bee symbionts.

The honey bee worker gut hosts a community of bacteria that comprises 8-10 core bacterial species, along with a set of more transient environmental microbes. Collectively, these microbes break down and ferment saccharides present in the host's diet, based on analyses of metagenomes, and metatranscriptomes from this environment. As part of this metabolism, the bacteria produce short-chain fatty acids that may serve as a food source for the host bee, stimulating biological processes that may contribute to host weight gain.

An Escherichia coli Nitrogen Starvation Response Is Important for Mutualistic Coexistence with Rhodopseudomonas palustris.

Microbial mutualistic cross-feeding interactions are ubiquitous and can drive important community functions. Engaging in cross-feeding undoubtedly affects the physiology and metabolism of individual species involved. However, the nature in which an individual species' physiology is influenced by cross-feeding and the importance of those physiological changes for the mutualism have received little attention.

Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists.

Many mutualistic microbial relationships are based on nutrient cross-feeding. Traditionally, cross-feeding is viewed as being unidirectional, from the producer to the recipient. This is likely true when a producer's waste, such as a fermentation product, has value only for a recipient.