Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

Background

Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium.

Results

Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments.

Conclusions

This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02370-4.

Welcome biological breakthroughs, supply psychosocial insights

Human behaviour, emotions, and cognition are complex to understand and explain. It is even more difficult to understand the basis for abnormal behaviour, disturbed emotions, and impaired cognitions, something mental health professionals are trying for long. In these pursuits, psychiatry has traversed through eras of humours, witchcraft, spirits, psychoanalysis, and gradually deviated from other medical specialities. Now, with recent biological breakthroughs like advances in psychopharmacology, neuroimaging and genetics, increasingly more emphasis is being given to the biological model of psychiatric disorders. These new biological models have given a more scientific appearance to the speciality. It has also revolutionised the management strategies and outcome of many psychiatric disorders. However, this rapid development in biological understanding of psychiatry also leads to a new wave of reductionism. In an attempt to deduce everything in terms of neurons, neurochemicals, and genes, can we neglect psychosocial aspects of mental health? Patients' personality, expectations, motives, family background, sociocultural backgrounds continue to affect mental health no matter how much 'biological' psychiatry gets. Biological and psychosocial approaches are not mutually exclusive but complementary. Integrating them harmoniously is the skill psychiatry demands for comprehensive understanding of mental and behavioural disorders.