Sharing vitamins: Cobamides unveil microbial interactions

Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study—from individual isolates, to synthetic consortia, to complex communities—have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.

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Cofactor Selectivity in Methylmalonyl Coenzyme A Mutase, a Model Cobamide-Dependent Enzyme

mBio ◽

10.1128/mbio.01303-19 ◽

2019 ◽

Vol 10 (5) ◽

Cited By ~ 6

Author(s):

Olga M. Sokolovskaya ◽

Kenny C. Mok ◽

Jong Duk Park ◽

Jennifer L. A. Tran ◽

Kathryn A. Quanstrom ◽

...

Keyword(s):

Binding Affinity ◽

Bacterial Growth ◽

Microbial Interactions ◽

Vitamin B ◽

Content Type ◽

Domains Of Life ◽

Enzyme Cofactors ◽

Lower Ligand ◽

Enzyme Selectivity

ABSTRACT Cobamides, a uniquely diverse family of enzyme cofactors related to vitamin B12, are produced exclusively by bacteria and archaea but used in all domains of life. While it is widely accepted that cobamide-dependent organisms require specific cobamides for their metabolism, the biochemical mechanisms that make cobamides functionally distinct are largely unknown. Here, we examine the effects of cobamide structural variation on a model cobamide-dependent enzyme, methylmalonyl coenzyme A (CoA) mutase (MCM). The in vitro binding affinity of MCM for cobamides can be dramatically influenced by small changes in the structure of the lower ligand of the cobamide, and binding selectivity differs between bacterial orthologs of MCM. In contrast, variations in the lower ligand have minor effects on MCM catalysis. Bacterial growth assays demonstrate that cobamide requirements of MCM in vitro largely correlate with in vivo cobamide dependence. This result underscores the importance of enzyme selectivity in the cobamide-dependent physiology of bacteria. IMPORTANCE Cobamides, including vitamin B12, are enzyme cofactors used by organisms in all domains of life. Cobamides are structurally diverse, and microbial growth and metabolism vary based on cobamide structure. Understanding cobamide preference in microorganisms is important given that cobamides are widely used and appear to mediate microbial interactions in host-associated and aquatic environments. Until now, the biochemical basis for cobamide preferences was largely unknown. In this study, we analyzed the effects of the structural diversity of cobamides on a model cobamide-dependent enzyme, methylmalonyl-CoA mutase (MCM). We found that very small changes in cobamide structure could dramatically affect the binding affinity of cobamides to MCM. Strikingly, cobamide-dependent growth of a model bacterium, Sinorhizobium meliloti, largely correlated with the cofactor binding selectivity of S. meliloti MCM, emphasizing the importance of cobamide-dependent enzyme selectivity in bacterial growth and cobamide-mediated microbial interactions.

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Exploration of social spreading reveals behavior is prevalent among Pedobacter and P. fluorescens isolates, and shows variations in induction of phenotype

Applied and Environmental Microbiology ◽

10.1128/aem.01344-21 ◽

2021 ◽

Author(s):

Lucy M. McCully ◽

Jasmine Graslie ◽

Alana R. McGraw ◽

Adam S. Bitzer ◽

Auður M. Sigurbjörnsdóttir ◽

...

Keyword(s):

Microbial Communities ◽

Close Contact ◽

Soil Microbial Communities ◽

Group Behavior ◽

Microbial Interactions ◽

Emergent Behavior ◽

Individual Species ◽

Emergent Properties ◽

Community Function ◽

The Individual

Within soil, bacteria are found in multi-species communities, where interactions can lead to emergent community properties. Studying bacteria in a social context is critical for investigation of community-level functions. We previously showed that co-cultured Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48 engage in interspecies social spreading (ISS) on a hard agar surface, a behavior which required close contact and depended on the nutritional environment. Here, we investigate whether social spreading is widespread among P. fluorescens and Pedobacter isolates, and whether the requirements for interaction vary. We find that this phenotype is not restricted to the interaction between P. fluorescens Pf0-1 and Pedobacter sp. V48, but is a prevalent behavior found in one clade in the P. fluorescens group and two clades in the Pedobacter genus. We show that the interaction with certain Pedobacter isolates occurred without close contact, indicating induction of spreading by a putative diffusible signal. As with ISS by Pf0-1+V48, motility of interacting pairs is influenced by the environment, with no spreading behaviors (or induction of motility) observed under high nutrient conditions. While Pf0-1+V48 require low nutrient but high NaCl conditions, in the broader range of interacting pairs the high salt influence was variable. The prevalence of motility phenotypes observed here and found within the literature indicates that community-induced locomotion in general, and social spreading in particular, is likely important within the environment. It is crucial that we continue to study microbial interactions and their emergent properties to gain a fuller understanding of the functions of microbial communities. Importance Interspecies social spreading (ISS) is an emergent behavior observed when P. fluorescens Pf0-1 and Pedobacter sp. V48 interact, during which both species move together across a surface. Importantly, this environment does not permit movement of either individual species. This group behavior suggests that communities of microbes can function in ways not predictable by knowledge of the individual members. Here we have asked whether ISS is widespread and thus potentially of importance in soil microbial communities. The significance of this research is the demonstration that surface spreading behaviors are not unique to the Pf0-1-V48 interaction, but rather is a more widespread phenomenon observed among members of distinct clades of both P. fluorescens and Pedobacter isolates. Further, we identify differences in mechanism of signaling and nutritional requirements for ISS. Emergent traits resulting from bacterial interactions are widespread and their characterization is necessary for a complete understanding of microbial community function.

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A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

Biochemical Society Transactions ◽

10.1042/bst20190172 ◽

2020 ◽

Vol 48 (2) ◽

pp. 399-409

Author(s):

Baizhen Gao ◽

Rushant Sabnis ◽

Tommaso Costantini ◽

Robert Jinkerson ◽

Qing Sun

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Environmental Remediation ◽

Real Life ◽

Design Principles ◽

Microbial Interactions ◽

Potential Applications ◽

New Gene ◽

Global Biogeochemical Cycles ◽

Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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Cellulose-induced shifts in microbial communities and microbial interactions in an anoxic/aerobic membrane bioreactor

Journal of Water Process Engineering ◽

10.1016/j.jwpe.2021.102106 ◽

2021 ◽

Vol 42 ◽

pp. 102106

Author(s):

Chunli Chen ◽

Zhihao Gan ◽

Ronghua Xu ◽

Fangang Meng

Keyword(s):

Microbial Communities ◽

Membrane Bioreactor ◽

Microbial Interactions

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Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽

10.3390/ani11030865 ◽

2021 ◽

Vol 11 (3) ◽

pp. 865

Author(s):

Lantian Su ◽

Xinxin Liu ◽

Guangyao Jin ◽

Yue Ma ◽

Haoxin Tan ◽

...

Keyword(s):

Microbial Community ◽

Environmental Factors ◽

Microbial Communities ◽

Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Functional Genes ◽

Martes Zibellina ◽

Clear Cutting ◽

Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

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REPLICA PLATING TECHNIQUE FOR STUDYING MICROBIAL INTERACTIONS IN SOIL

Canadian Journal of Microbiology ◽

10.1139/m65-084 ◽

1965 ◽

Vol 11 (4) ◽

pp. 629-636 ◽

Cited By ~ 28

Author(s):

G. Stotzky

Keyword(s):

Nutritional Composition ◽

Mixed Population ◽

Microbial Interactions ◽

Individual Species ◽

Selective Inhibitors ◽

Subsequent Growth ◽

Sterile Soil ◽

Plating Technique ◽

Replica Plating ◽

Plating Method

A replica plating method was developed to study ecology of microorganisms in soil. Precise placement of inocula and amendments at desired loci in sterile soil contained in petri plates were accomplished with a template. Subsequent growth and distribution of individual species, even when part of a mixed population, was measured by periodic transfer with an easily constructed replicator to agar plates of differing nutritional composition or containing selective inhibitors. The method is rapid and reproducible, and permits the study of many variables and interactions in a single soil plate; it can also be used with non-sterile soil and other suitable microbial habitats.

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The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

Bioinformatics ◽

10.1093/bioinformatics/bty941 ◽

2018 ◽

Vol 35 (13) ◽

pp. 2332-2334 ◽

Cited By ~ 16

Author(s):

Federico Baldini ◽

Almut Heinken ◽

Laurent Heirendt ◽

Stefania Magnusdottir ◽

Ronan M T Fleming ◽

...

Keyword(s):

Microbial Communities ◽

Microbial Interactions ◽

Microbial Genome ◽

Metagenomic Data ◽

Metabolic Interactions ◽

Constraint Based Modeling ◽

Genome Scale

Abstract Motivation The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes. Results To address this gap, we created a comprehensive toolbox to model (i) microbe–microbe and host–microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox. Availability and implementation The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.

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Deciphering the evolution of microbial interactions: in silico studies of two-member microbial communities

10.1101/2022.01.14.476316 ◽

2022 ◽

Author(s):

Gayathri Sambamoorthy ◽

Karthik Raman

Keyword(s):

Microbial Communities ◽

In Silico ◽

Microbial Interactions ◽

Interaction Patterns ◽

Wild Type ◽

Community Function ◽

Evolutionary Forces ◽

In Silico Studies ◽

Wide Range ◽

In The Wild

Microbes thrive in communities, embedded in a complex web of interactions. These interactions, particularly metabolic interactions, play a crucial role in maintaining the community structure and function. As the organisms thrive and evolve, a variety of evolutionary processes alter the interactions among the organisms in the community, although the community function remains intact. In this work, we simulate the evolution of two-member microbial communities in silico to study how evolutionary forces can shape the interactions between organisms. We employ genomescale metabolic models of organisms from the human gut, which exhibit a range of interaction patterns, from mutualism to parasitism. We observe that the evolution of microbial interactions varies depending upon the starting interaction and also on the metabolic capabilities of the organisms in the community. We find that evolutionary constraints play a significant role in shaping the dependencies of organisms in the community. Evolution of microbial communities yields fitness benefits in only a small fraction of the communities, and is also dependent on the interaction type of the wild-type communities. The metabolites cross-fed in the wild-type communities appear in only less than 50% of the evolved communities. A wide range of new metabolites are cross-fed as the communities evolve. Further, the dynamics of microbial interactions are not specific to the interaction of the wild-type community but vary depending on the organisms present in the community. Our approach of evolving microbial communities in silico provides an exciting glimpse of the dynamics of microbial interactions and offers several avenues for future investigations.

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A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

10.1101/245290 ◽

2018 ◽

Author(s):

Manuel Kleiner ◽

Xiaoli Dong ◽

Tjorven Hinzke ◽

Juliane Wippler ◽

Erin Thorson ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Carbon Isotope ◽

Isotope Ratio ◽

Single Cells ◽

Stable Carbon Isotope ◽

Carbon Sources ◽

Food Sources ◽

Individual Species ◽

Stable Carbon

AbstractMeasurements of the carbon stable isotope ratio (δ13C) are widely used in biology to address major questions regarding food sources and metabolic pathways used by organisms. Measurement of these so called stable carbon isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals have led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide limited taxonomic resolution, such as with the use of lipid biomarkers, or are limited in throughput, such as NanoSIMS imaging of single cells.Here we present “direct Protein-SIF” and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we show that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis showed that direct Protein-SIF confirms previous physiological hypotheses and can provide unexpected new insights into the symbionts’ metabolism. This confirms the usefulness of this new approach to accurately determine δ13C values for different species in microbial community samples.SignificanceTo understand the roles that microorganisms play in diverse environments such as the open ocean and the human intestinal tract, we need an understanding of their metabolism and physiology. A variety of methods such as metagenomics and metaproteomics exist to assess the metabolism of environmental microorganisms based on gene content and gene expression. These methods often only provide indirect evidence for which substrates are used by a microorganism in a community. The direct Protein-SIF method that we developed allows linking microbial species in communities to the environmental carbon sources they consume by determining their stable carbon isotope signature. Direct Protein-SIF also allows assessing which carbon fixation pathway is used by autotrophic microorganisms that directly assimilate CO2.

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