Conservation of isolate substrate preferences in mixed communities revealed through ribosomal marker protein profiling

Assessment of structure-function relationships is a central theme in microbial ecology. However, the degree that isolate metabolic activities are conserved in communities remains unclear. This is because tracking population dynamics and substrate partitioning in microbial communities remains technically challenging. Here, we describe the application of a mass spectrometry-based ribosomal marker protein profiling with stable isotope probing approach that allows for concurrent monitoring of community structure dynamics and resource assimilation within a five-member synthetic soil bacterial community. Using this approach, we find that isolate substrate preferences for glutamine and phenylalanine are largely conserved in the community and can be predicted using a weighted-sum model. However, time-series monitoring revealed a significant delay in phenylalanine incorporation by two of the strains, as well as enhanced growth for Variovorax paradoxus presumably due to interspecies interactions. The unique utility of this approach to temporally probe resource incorporation and community structure enables deciphering the dynamic interactions occurring within the community. Extension of this approach to other communities under various environmental perturbations is needed to reveal the generality of microbial conservation of substrate preferences.

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Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)

Microorganisms ◽

10.3390/microorganisms9071368 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1368

Author(s):

Qianqian Li ◽

Rebecca E. Cooper ◽

Carl-Eric Wegner ◽

Martin Taubert ◽

Nico Jehmlich ◽

...

Keyword(s):

Transcriptional Activity ◽

Co2 Fixation ◽

Carbon Fixation ◽

Stable Isotope Probing ◽

Acidic Lake ◽

General Role ◽

Polysaccharide Biosynthesis ◽

Iron Oxidizers ◽

Metabolic Activities ◽

Chemolithoautotrophic Bacteria

Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6–85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0–5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

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Microbial food web mapping: linking carbon cycling and community structure in soils through pyrosequencing enabled stable isotope probing

10.2172/1172474 ◽

2015 ◽

Author(s):

Daniel Buckley

Keyword(s):

Community Structure ◽

Stable Isotope ◽

Food Web ◽

Carbon Cycling ◽

Stable Isotope Probing ◽

Microbial Food Web ◽

Web Mapping

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Tracing Carbon and Nitrogen Microbial Assimilation in Suspended Particles in Freshwaters

10.21203/rs.3.rs-995821/v1 ◽

2021 ◽

Author(s):

Leonardo Mena-Rivera ◽

Charlotte E.M. Lloyd ◽

Michaela K. Reay ◽

Tim Goodall ◽

Daniel S Read ◽

...

Keyword(s):

Organic Matter ◽

Sewage Treatment ◽

Suspended Sediments ◽

Freshwater Ecosystems ◽

Stable Isotope Probing ◽

Dynamic Interactions ◽

Carbon And Nitrogen ◽

Spatial Differences ◽

Molecular Information ◽

Inorganic Substrate

Abstract The dynamic interactions between dissolved organic matter (DOM) and particulate organic matter (POM) are central in nutrient cycling in freshwater ecosystems. However, the molecular-level mechanisms of such interactions are still poorly defined. Here, we study spatial differences in the chemical and molecular composition of suspended sediments in the River Chew, UK. We then applied a compound-specific stable isotope probing (SIP) approach to test the potential assimilation of 13C,15N-glutamate (Glu) and 15N-nitrate into proteinaceous biomass by particle-associated microbial communities over a 72-h period. Our results demonstrate that the composition of suspended sediments is strongly influenced by the effluent of sewage treatment works (STW). Fluxes and percentages of assimilation of both isotopically labelled substrates into individual proteinaceous amino acids (AAs) showed contrasting dynamics in processing at each site linked to primary biosynthetic metabolic pathways. Preferential assimilation of the organic molecule glutamate and evidence of its direct assimilation into newly synthesised biomass was obtained. Our approach provides quantitative molecular information on the mechanisms by which low molecular weight DOM is mineralised in the water column compared to an inorganic substrate. This is paramount for better understanding the processing and fate of organic matter in aquatic ecosystems.

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Nanoprobe-Based Affinity Mass Spectrometry for Cancer Marker Protein Profiling

Nanotechnologies for the Life Sciences ◽

10.1002/9783527610419.ntls0080 ◽

2007 ◽

Author(s):

Li-Shing Huang ◽

Yuh-Yih Chien ◽

Shu-Hua Chen ◽

Po-Chiao Lin ◽

Kai-Yi Wang ◽

...

Keyword(s):

Mass Spectrometry ◽

Protein Profiling ◽

Marker Protein ◽

Cancer Marker

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Stable isotope probing of bacterial community structure and gene expression in the rhizosphere of Arabidopsis thaliana

FEMS Microbiology Ecology ◽

10.1111/j.1574-6941.2012.01345.x ◽

2012 ◽

Vol 81 (2) ◽

pp. 291-302 ◽

Cited By ~ 39

Author(s):

Feth el Zahar Haichar ◽

Marie-Anne Roncato ◽

Wafa Achouak

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Community Structure ◽

Stable Isotope ◽

Bacterial Community ◽

Bacterial Community Structure ◽

Stable Isotope Probing

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Temporal Patterns in Fish Community Structure: Environmental Perturbations from a Well-Mixed Tropical Estuary

Proceedings of the National Academy of Sciences India Section B Biological Sciences ◽

10.1007/s40011-015-0581-2 ◽

2015 ◽

Vol 87 (1) ◽

pp. 135-145 ◽

Cited By ~ 3

Author(s):

G. B. Sreekanth ◽

N. Manju Lekshmi ◽

Narendra Pratap Singh

Keyword(s):

Community Structure ◽

Fish Community ◽

Temporal Patterns ◽

Tropical Estuary ◽

Fish Community Structure ◽

Environmental Perturbations

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Arbuscular Mycorrhizal Fungi Co-Colonizing on A Single Plant Root System Recruit Distinct Microbiomes

10.21203/rs.3.rs-73473/v1 ◽

2020 ◽

Author(s):

Jiachao Zhou ◽

Xiaofen Chai ◽

Lin Zhang ◽

Timothy S George ◽

Gu Feng

Keyword(s):

Community Structure ◽

Arbuscular Mycorrhizal Fungi ◽

Root System ◽

Mycorrhizal Fungi ◽

Arbuscular Mycorrhizal ◽

Fungal Species ◽

Stable Isotope Probing ◽

Genetic Traits ◽

Single Root ◽

Extraradical Hyphae

Abstract Background: Plant roots are usually colonized by various arbuscular mycorrhizal (AM) fungal species which vary in morphological, physiological and genetic traits and constitute the mycorrhizal nutrient uptake pathway (MP) in addition to roots. Simultaneously, the extraradical hyphae of each AM fungus is associated with a community of bacteria. However, whether the community structure and function of microbiome on the extraradical hyphae would differ between the AM fungal species are mostly unknown. Methods: In order to understand the community structure and the predicted functions of the microbiome associated with different AM fungal species, a split-root compartmented rhizobox culturing system, which allowed us to inoculate two AM fungal species separately in two root compartments was used. We inoculated two separate AM fungal species combinations, Funneliformis mosseae ( F.m ) and Gigaspora margarita ( G.m ), Rhizophagus intraradices ( R.i ) and G. margarita, on a single root system of cotton . The hyphal exudate fed active microbiome was measured by combining 13 C-DNA stable isotope probing with Miseq sequencing. Results: We found different AM fungal species, that were simultaneously colonizing on a single root system, hosted distinct active microbiomes from one another. Moreover, the predicted potential functions of the different microbiomes were distinct. Conclusion: We conclude that the arbuscular mycorrhizal fungi component of the system is responsible for the recruitment distinct microbiomes in the hyphosphere. The potential significance of the predicted functions of the microbiome ecosystem services is discussed.

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Modeling trophic dependencies and exchanges among insects’ bacterial symbionts in a host-simulated environment

10.1101/086165 ◽

2016 ◽

Cited By ~ 1

Author(s):

Itai Opatovsky ◽

Diego Santos-Garcia ◽

Tamar Lahav ◽

Shani Ofaim ◽

Laurence Mouton ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Metabolic Networks ◽

Symbiotic Bacterium ◽

Single Species ◽

Metabolic Interactions ◽

Sap Feeding ◽

Metabolic Activities ◽

Genome Analyses ◽

Species Specific

AbstractIndividual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community structure. Metabolic interactions with bacteria have been key drivers in the evolution of sap-feeding insects, enabling complementation of their deprived nutrition. The sap-feeding whiteflyBemisia tabaci(Hemiptera: Aleyrodidae) harbors an obligatory symbiotic bacterium, as well as varying combinations of facultative symbionts. We took advantage of the well-defined bacterial community inB. tabacias a case study for a comprehensive and systematic survey of metabolic interactions within the bacterial community and their associations with documented frequency of bacterial combinations. We first reconstructed the metabolic networks of five commonB. tabacisymbionts(Portiera, Rickettsia, Hamiltonella, CardiniumandWolbachia),and then used network analysis approaches to predict: (1) species-specific metabolic capacities in a simulated bacteriocyte-like environment; (2) metabolic capacities of the corresponding species’ combinations, and (3) dependencies of each species on different media components.The automatic-based predictions for metabolic capacities of the symbionts in the host environment were in general agreement with previously reported genome analyses, each focused on the single-species level. The analysis suggested several previously un-reported routes for complementary interactions. Highly abundant symbiont combinations were found to have the potential to produce a diverse set of complementary metabolites, in comparison to un-detected combinations. No clear association was detected between metabolic codependencies and co-occurrence patterns. The findings indicate a potential key role for metabolic exchanges as key determinants shaping community structure in this system.

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Networks of energetic and metabolic interactions define dynamics in microbial communities

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1506034112 ◽

2015 ◽

Vol 112 (50) ◽

pp. 15450-15455 ◽

Cited By ~ 116

Author(s):

Mallory Embree ◽

Joanne K. Liu ◽

Mahmoud M. Al-Bassam ◽

Karsten Zengler

Keyword(s):

Microbial Communities ◽

Community Diversity ◽

Metagenomic Data ◽

Interspecies Interactions ◽

Environmental Perturbations ◽

Technological Advances ◽

Metabolic Interactions ◽

High Species Richness ◽

Species Specific ◽

And Control

Microorganisms form diverse communities that have a profound impact on the environment and human health. Recent technological advances have enabled elucidation of community diversity at high resolution. Investigation of microbial communities has revealed that they often contain multiple members with complementing and seemingly redundant metabolic capabilities. An understanding of the communal impacts of redundant metabolic capabilities is currently lacking; specifically, it is not known whether metabolic redundancy will foster competition or motivate cooperation. By investigating methanogenic populations, we identified the multidimensional interspecies interactions that define composition and dynamics within syntrophic communities that play a key role in the global carbon cycle. Species-specific genomes were extracted from metagenomic data using differential coverage binning. We used metabolic modeling leveraging metatranscriptomic information to reveal and quantify a complex intertwined system of syntrophic relationships. Our results show that amino acid auxotrophies create additional interdependencies that define community composition and control carbon and energy flux through the system while simultaneously contributing to overall community robustness. Strategic use of antimicrobials further reinforces this intricate interspecies network. Collectively, our study reveals the multidimensional interactions in syntrophic communities that promote high species richness and bolster community stability during environmental perturbations.

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