Microbiotic particles in water and soil, water-soil microbiota coalescences, and antimicrobial resistance

Bacterial organisms like surfaces. Water and soil contain a multiplicity of particulated material where bacterial populations and communities might attach. Microbiotic particles refers to any type of small particles (less than 2 mm) where bacteria (and other microbes) might attach, resulting in medium- long-term colonization. In this work, the interactions of bacterial organisms with microbiotic particles of the soil and water are reviewed. These particles include bacteria-bacteria aggregates, and aggregates with particles of fungi (particularly in the rhizosphere), protozoa, phytoplankton, zooplankton, biodetritus resulting from animal and vegetal decomposition, humus, mineral particles (clay, carbonates, silicates), and anthropogenic particles (including wastewater particles or microplastics). At they turn, these particles might interact and coalesce (as in the marine snow). Natural phenomena (from river flows to tides, tsunamis, currents, or heavy winds) and anthropogenic activity (such as agriculture, waste-water management, mining, soil-mass movement) favors interaction and merging between all these soil and water particles, and consequently coalescence of their bacterial-associated populations and communities, resulting in an enhancement of mixed-recombinant communities capable of genetic exchange, including antimicrobial resistance genes, particularly in antimicrobial-polluted environments. Particles also favor compartmentalization of bacterial populations favoring diversification and acquisition of mutational resistance by random drift. In general, microbial evolution is accelerated by the aggregation of microbiotic particles. We propose that the world spread of antimicrobial resistance might relate with the environmental dynamics of microbiotic particles, and discuss possible methods to reduce this problem influencing One Health and Planetary Health.

3CAC: improving the classification of phages and plasmids from metagenomic assemblies using assembly graphs

Bacteriophages and plasmids usually coexist with their host bacteria in microbial communities and play important roles in microbial evolution. Accurately identifying sequence contigs as phages, plasmids, and bacterial chromosomes in mixed metagenomic assemblies is critical for further unraveling their functions. Many classification tools have been developed for identifying either phages or plasmids in metagenomic assemblies. However, only two classifiers, PPR-Meta and viralVerify, were proposed to simultaneously identify phages and plasmids in mixed metagenomic assemblies. Due to the very high fraction of chromosome contigs in the assemblies, both tools achieve high precision in the classification of chromosomes but perform poorly in classifying phages and plasmids. Short contigs in these assemblies are often wrongly classified or classified as uncertain. Here we present 3CAC, a new three-class classifier that improves the precision of phage and plasmid classifications. 3CAC starts with an initial three-class classification generated by existing classifiers and further improves the classification of short contigs and contigs with low confidence classification by using proximity in the assembly graph. Evaluation on simulated metagenomes and on real human gut microbiome samples showed that 3CAC outperformed PPR-Meta and viralVerify in both precision and recall, and increased F1-score by at least 10 percentage points.

Drosophila Model for Gut-Mediated Horizontal Transfer of Narrow- and Broad-Host-Range Plasmids

Microbial evolution in the gut of animals due to horizontal gene transfer (HGT) is of significant interest for microbial evolution as well as within the context of human and animal health. Microbial populations evolve within the host, and factors from the bacteria and host interact to regulate this evolution.

Energy Availability Determines Strategy of Microbial Amino Acid Synthesis in Volatile Fatty Acid–Fed Anaerobic Methanogenic Chemostats

In natural communities, microbes exchange a variety of metabolites (public goods) with each other, which drives the evolution of auxotroph and shapes interdependent patterns at community-level. However, factors that determine the strategy of public goods synthesis for a given community member still remains to be elucidated. In anaerobic methanogenic communities, energy availability of different community members is largely varied. We hypothesized that this uneven energy availability contributed to the heterogeneity of public goods synthesis ability among the members in these communities. We tested this hypothesis by analyzing the synthetic strategy of amino acids of the bacterial and archaeal members involved in four previously enriched anaerobic methanogenic communities residing in thermophilic chemostats. Our analyses indicate that most of the members in the communities did not possess ability to synthesize all the essential amino acids, suggesting they exchanged these essential public goods to establish interdependent patterns for survival. Importantly, we found that the amino acid synthesis ability of a functional group was largely determined by how much energy it could obtain from its metabolism in the given environmental condition. Moreover, members within a functional group also possessed different amino acid synthesis abilities, which are related to their features of energy metabolism. Our study reveals that energy availability is a key driver of microbial evolution in presence of metabolic specialization at community level and suggests the feasibility of managing anaerobic methanogenic communities for better performance through controlling the metabolic interactions involved.

Spatial structure affects evolutionary dynamics and drives genomic diversity in experimental populations of Pseudomonas fluorescens

Most populations live in spatially structured environments and that structure has the potential to impact the evolutionary dynamics in a number of important ways. Theoretical models tracking evolution in structured environments using a range of different approaches, suggest that local interactions and spatial heterogeneity can increase the adaptive benefits of motility, impact both the rate and extent of adaptation, and increase the probability of parallel evolution. We test these general predictions in a microbial evolution experiment tracking phenotypic and genomic changes in replicate populations of Pseudomonas fluorescens evolved in both well-mixed and spatially-structured environments, where spatial structure was generated through the addition of semi-solid agar. In contrast to the well-mixed environment, populations evolved in the spatially-structured environment adapted more slowly, retained the ability to disperse more rapidly, and had a greater putatively neutral population genomic diversity. The degree of parallel evolution measured at the gene-level, did not differ across these two types of experimental environments, perhaps because the populations had not evolved for long enough to near their fitness optima. These results confirm important general impacts of spatial structure on evolutionary dynamics at both the phenotypic and genomic level.

Core genes can have higher recombination rates than accessory genes within global microbial populations

Recombination is essential to microbial evolution, and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche. Yet quantifying the impact of homologous recombination on different gene classes, which is critical to understanding how selection acts on variation to shape species diversity and genome structure, remains challenging. This is largely due to the dynamic nature of bacterial genomes, whose high intraspecies genome content diversity and complex phylogenetic relationships present difficulties for inferring rates of recombination, particularly for rare genes. In this work, we apply a computationally efficient, non-phylogenetic approach to measure homologous recombination rates in the core and accessory genome (genes present in all strains and only a subset of strains, respectively) using >100,000 whole genome sequences from 12 microbial species. Our analysis suggests that even well-resolved sequence clusters sampled from global populations interact with overlapping gene pools, which has implications for the role of population structure in genome evolution. We show that in a majority of species, core genes have shorter coalescence times and higher recombination rates than accessory genes, and that gene frequency is often positively correlated with increased recombination. Our results provide a new line of population genomic evidence supporting the hypothesis that core genes are under strong, purifying selection, and indicate that homologous recombination may play a key role in increasing the efficiency of selection in those parts of the genome most conserved within each species.

Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales

How important is adaptive evolution to the unique diversity that we can observe for each individual human gut microbiome? How do gut microbes evolve in response to changes in their environment, and how does evolution in real time impact microbial functionality in the context of host health? My interdisciplinary research uses in vitro microcosm models to test how different abiotic and biotic factors impact microbial evolution in a community context. We complement this approach by tracking focal species as they evolve in real time and in their natural environment of the human gut.