The social network of microorganisms — how auxotrophies shape complex communities

Zengler, Karsten; Zaramela, Livia S.

doi:10.1038/s41579-018-0004-5

Cited by 353 publications

(309 citation statements)

References 98 publications

(140 reference statements)

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“…However, these results must be interpreted with caution as the co‐culture contains yeast extract, which contains amino acids. Some recent studies also identify coordinated cross‐feeding between organisms (Hubalek et al ., ; Liu et al ., ; Zengler and Zaramela, ), suggesting nutrient exchange may be a prevalent and critical interaction for syntrophy.…”

Section: Resultsmentioning

confidence: 99%

Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism

Hidalgo-Ahumada

Nobu

Narihiro

et al. 2018

Environmental Microbiology

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Under methanogenic conditions, short-chain fatty acids are common byproducts from degradation of organic compounds and conversion of these acids is an important component of the global carbon cycle. Due to the thermodynamic difficulty of propionate degradation, this process requires syntrophic interaction between a bacterium and partner methanogen; however, the metabolic strategies and behaviour involved are not fully understood. In this study, the first genome analysis of obligately syntrophic propionate degraders (Pelotomaculum schinkii HH and P. propionicicum MGP) and comparison with other syntrophic propionate degrader genomes elucidated novel components of energy metabolism behind Pelotomaculum propionate oxidation. Combined with transcriptomic examination of P. schinkii behaviour in co-culture with Methanospirillum hungatei, we found that formate may be the preferred electron carrier for P. schinkii syntrophy. Propionate-derived menaquinol may be primarily re-oxidized to formate, and energy was conserved during formate generation through newly proposed proton-pumping formate extrusion. P. schinkii did not overexpress conventional energy metabolism associated with a model syntrophic propionate degrader Syntrophobacter fumaroxidans MPOB (i.e., CoA transferase, Fix and Rnf). We also found that P. schinkii and the partner methanogen may also interact through flagellar contact and amino acid and fructose exchange. These findings provide new understanding of syntrophic energy acquisition and interactions.

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Section: Resultsmentioning

confidence: 99%

Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism

Hidalgo-Ahumada

Nobu

Narihiro

et al. 2018

Environmental Microbiology

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“…This observation fits well to the notion that mutualistic (or commensalistic) interactions predominantly occur between evolutionarily distant species (Valiente‐Banuet & Verdú, ). There are many examples of convolute networks involving distant microorganisms that exchange electron donors and metabolites (Zengler & Zaramela, ). This is not to say that positive interactions do not take place among close relatives, for example synchronized crosstalk‐induced gene expression (Ng & Bassler, ).…”

Section: Discussionmentioning

confidence: 99%

“…However, multiple biological interactions among bacteria have been documented in the laboratory. Evidence for positive interactions includes cell-cell communication, division of labour in biofilms, exchange of electron donors and metabolites, sharing of public goods or coordinated motility (Jousset, Eisenhauer, Materne, & Scheu, 2013;Morris, Lenski, & Zinser, 2012;Zengler & Zaramela, 2018), among others. Main negative interactions include competition by interference (e.g.…”

Section: Introductionmentioning

confidence: 99%

Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes

Goberna

Montesinos‐Navarro

Valiente‐Banuet

et al. 2019

Molecular Ecology Resources

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Co‐occurrence network analysis based on amplicon sequences is increasingly used to study microbial communities. Patterns of co‐existence or mutual exclusion between pairs of taxa are often interpreted as reflecting positive or negative biological interactions. However, other assembly processes can underlie these patterns, including species failure to reach distant areas (dispersal limitation) and tolerate local environmental conditions (habitat filtering). We provide a tool to quantify the relative contribution of community assembly processes to microbial co‐occurrence patterns, which we applied to explore soil bacterial communities in two dry ecosystems. First, we sequenced a bacterial phylogenetic marker in soils collected across multiple plots. Second, we inferred co‐occurrence networks to identify pairs of significantly associated taxa, either co‐existing more (aggregated) or less often (segregated) than expected at random. Third, we assigned assembly processes to each pair: patterns explained based on spatial or environmental distance were ascribed to dispersal limitation (2%–4%) or habitat filtering (55%–77%), and the remaining to biological interactions. Finally, we calculated the phylogenetic distance between taxon pairs to test theoretical expectations on the linkages between phylogenetic patterns and assembly processes. Aggregated pairs were more closely related than segregated pairs. Furthermore, habitat‐filtered aggregated pairs were closer relatives than those assigned to positive interactions, consistent with phylogenetic niche conservatism and cooperativism among distantly related taxa. Negative interactions resulted in equivocal phylogenetic signatures, probably because different competitive processes leave opposing signals. We show that microbial co‐occurrence networks mainly reflect environmental tolerances and propose that incorporating measures of phylogenetic relatedness to networks might help elucidate ecologically meaningful patterns.

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“…helminths) or other 'pathobionts'. [104][105][106][107] Consequently, the microbiota is dynamic. 108 An intriguing finding is the far-reaching impact that the microbiota can have on the host.…”

Section: Discussionmentioning

confidence: 99%

The interaction between invariant Natural Killer T cells and the mucosal microbiota

Hapil¹,

Wingender

2018

Immunology

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SummaryThe surface of mammalian bodies is colonized by a multitude of microbial organisms, which under normal conditions support the host and are considered beneficial commensals. This requires, however, that the composition of the commensal microbiota is tightly controlled and regulated. The host immune system plays an important role in the maintenance of this microbiota composition. Here we focus on the contribution of one particular immune cell type, invariant Natural Killer T (iNKT) cells, in this process. The iNKT cells are a unique subset of T cells characterized by two main features. First, they express an invariant T-cell receptor that recognizes glycolipid antigens presented by CD1d, a non-polymorphic major histocompatibility complex class I-like molecule. Second, iNKT cells develop as effector/memory cells and swiftly exert effector functions, like cytokine production and cytotoxicity, after activation. We outline the influence that the mucosal microbiota can have on iNKT cells, and how iNKT cells contribute to the maintenance of the microbiota composition.

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The social network of microorganisms — how auxotrophies shape complex communities

Cited by 353 publications

References 98 publications

Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism

Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism

Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes

The interaction between invariant Natural Killer T cells and the mucosal microbiota

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