Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Bacteria in nature often thrive in fragmented environments, like soil pores, plant roots or plant leaves, leading to smaller isolated habitats, shared with fewer species. This spatial fragmentation can significantly influence bacterial interactions, affecting overall community diversity. To investigate this, we contrast paired bacterial growth in tiny picoliter droplets (1-3 cells per 35 pL up to 3-8 cells per species in 268 pL) with larger, uniform liquid cultures (about 2 million cells per 140 µl). We test four interaction scenarios using different bacterial strains: substrate competition, substrate independence, growth inhibition, and cell killing. In fragmented environments, interaction outcomes are more variable and sometimes even reverse compared to larger uniform cultures. Both experiments and simulations show that these differences stem mostly from variation in initial cell population growth phenotypes and their sizes. These effects are most significant with the smallest starting cell populations and lessen as population size increases. Simulations suggest that slower-growing species might survive competition by increasing growth variability. Our findings reveal how microhabitat fragmentation promotes diverse bacterial interaction outcomes, contributing to greater species diversity under competitive conditions.

Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere

Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.

Comparative evaluation of the effectiveness of alcohol-based sanitizers, UV-C radiation and hot air on three-age Salmonella biofilms

Dry sanitation is recommended to control contamination and prevent microbial growth and biofilm formation in the low-moisture food manufacturing plants. The objective of this study was to evaluate the effectiveness of dry sanitation protocols on Salmonella three-age biofilms formed on stainless steel (SS) and polypropylene (PP). Biofilms were formed for 24, 48 and 96 h at 37 °C using a cocktail of six Salmonella strains (Muenster, Miami, Glostrup, Javiana, Oranienburg, Yoruba) isolated from the peanut supply chain. Then, the surfaces were exposed to UV-C radiation, hot air (90 °C), 70% ethanol and a commercial product based on isopropyl alcohol for 5, 10, 15 and 30 min. After 30min exposure, on PP the reductions ranged from 3.2 to 4.2 log CFU/cm² for UV-C, from 2.6 to 3.0 log CFU/cm² for hot air, from 1.6 to 3.2 log CFU/cm² for 70% ethanol and from 1.5 to 1.9 log CFU/cm² for the commercial product. On SS, after the same exposure time, reductions of 1.3-2.2 log CFU/cm², 2.2 to 3.3 log CFU/cm², 1.7 to 2.0 log CFU/cm² and 1.6 to 2.4 log CFU/cm² were observed for UV-C, hot air, 70% ethanol and commercial product, respectively. UV-C was the only treatment affected by the surface material (p < 0.05) whereas the biofilm age influenced the effectiveness of UV-C and hot air (p < 0.05). For most treatment, there was significant difference among the exposure times (p < 0.05). Overall, the fastest loss in the biofilm viability was noted in the first 5 min, followed by a tail phase. The time predicted by the Weibull model for the first decimal reduction ranged from 0.04 to 9.9 min on PP and from 0.7 to 8.5 min on SS. In addition, the Weibull model indicates that most of treatments (79%) required a long-term exposure time (>30 min) to achieve 3-log reductions of Salmonella biofilms. In summary, UV-C showed the best performance on PP whereas hot air was noted to be the most effective on SS.

Metabolic interaction models recapitulate leaf microbiota ecology

Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We combined synthetic community experiments with computational models to predict interaction outcomes between plant-associated bacteria. We mapped the metabolic capabilities of 224 leaf isolates from Arabidopsis thaliana by assessing the growth of each strain on 45 environmentally relevant carbon sources in vitro. We used these data to build curated genome-scale metabolic models for all strains, which we combined to simulate >17,500 interactions. The models recapitulated outcomes observed in planta with >89% accuracy, highlighting the role of carbon utilization and the contributions of niche partitioning and cross-feeding in the assembly of leaf microbiomes.

Resolving metabolic interaction mechanisms in plant microbiomes

Metabolic interactions are fundamental to the assembly and functioning of microbiomes, including those of plants. However, disentangling the molecular basis of these interactions and their specific roles remains a major challenge. Here, we review recent applications of experimental and computational methods toward the elucidation of metabolic interactions in plant-associated microbiomes. We highlight studies that span various scales of taxonomic and environmental complexity, including those that test interaction outcomes in vitro and in planta by deconstructing microbial communities. We also discuss how the continued integration of multiple methods can further reveal the general ecological characteristics of plant microbiomes, as well as provide strategies for applications in areas such as improved plant protection, bioremediation, and sustainable agriculture.

Droplet size and surface hydrophobicity enhance bacterial plasmid transfer rates in microscopic surface wetness

Conjugal plasmids constitute a major engine for horizontal gene transfer in bacteria, and are key drivers of the spread of antibiotic resistance, virulence, and metabolic functions. Bacteria in terrestrial habitats often inhabit surfaces that are not constantly water-saturated, where microscopic surface wetness (MSW), comprised of thin liquid films and microdroplets, permanently or intermittently occurs. How physical properties of microdroplets, and of the surfaces they reside on, affect plasmid transfer rates is not well understood. Here, building on microscopy-based microdroplet experiments, we examined the relation between droplet properties (size and spread) and plasmid transfer rates at single-cell and individual droplet resolution, using Pseudomonas putida as a model species. We show that transfer rates increase with droplet size, due to higher densities of cells on the surface in larger droplets, resulting from lower ratio between the area of the liquid-solid interface and droplet volumes. We further show that surface hydrophobicity promotes transfer rates via the same mechanism. Our results provide new insights into how physical properties of surfaces and MSW affect plasmid transfer rates, and more generally, microbial interactions mediated by cell-to-cell contact, with important implications for our understanding of the ecology and evolution of bacteria in unsaturated environments.

It's the Economy, Stupid: Applying (Micro)economic Principles to Microbiome Science

A key challenge in microbiome science is the scale mismatch problem, which arises when the scale at which microbial communities are sampled, interrogated, and averaged is different from the scale at which individual microorganisms within those communities interact with each other and with their environment. Profiling the microbial communities in a teaspoon of soil, from a scoop of fecal matter, or along a plant leaf surface represents a scale mismatch of multiple orders of magnitude, which may limit our ability to interpret or predict species interactions and community assembly within such samples. In this Perspective, we explore how economists, who are historically and topically split along the lines of micro- and macroeconomics, deal with the scale mismatch problem, and how taking clues from (micro)economists could benefit the field of microbiomics.

Wet-dry cycles protect surface-colonizing bacteria from major antibiotic classes

Diverse antibiotic compounds are abundant in microbial habitats undergoing recurrent wet-dry cycles, such as soil, root and leaf surfaces, and the built environment. These antibiotics play a central role in microbial warfare and competition, thus affecting population dynamics and the composition of natural microbial communities. Yet, the impact of wet-dry cycles on bacterial response to antibiotics has been scarcely explored. Using the bacterium E. coli as a model organism, we show through a combination of experiments and computational modeling, that wet-dry cycles protect bacteria from beta-lactams. This is due to the combined effect of several mechanisms including tolerance induced by high salt concentrations and slow cell-growth, which are inherently associated with microscopic surface wetness-a hydration state typical to 'dry' periods. Moreover, we find evidence for a cross-protection effect, where lethal doses of antibiotic considerably increase bacterial survival during the dry periods. This work focuses on beta-lactams, yet similar protection was observed for additional major antibiotic classes. Our findings shed new light on how we understand bacterial response to antibiotics, with broad implications for population dynamics, interspecies interactions, and the evolution of antibiotic resistance in vast terrestrial microbial habitats.

Bacterial Growth in Brines Formed by the Deliquescence of Salts Relevant to Cold Arid Worlds

Hygroscopic salts at Mars' near-surface (MgSO₄, (per)chlorates, NaCl) may form brines by absorbing moisture from the atmosphere at certain times through the process of deliquescence. We have previously shown strong bacterial growth in saturated MgSO₄ (∼67% w/v as epsomite) at room temperature, and growth was observed at the MgSO₄ eutectic point (43% w/v at -4°C). Here, we have investigated the growth of salinotolerant microbes (Halomonas, Marinococcus, Planococcus) from Hot Lake, Washington; Basque Lake, British Columbia; and Great Salt Plains, Oklahoma under deliquescing conditions. Bacterial cultures were grown to mid-log phase in SP medium supplemented with 50% MgSO₄ (as epsomite), 20% NaClO₃, or 10% NaCl (w/v), and small aliquots in cups were dried by vacuum desiccation. When the dried culture was rehydrated by the manual addition of water, the culture resumed growth in the reconstituted brine. When desiccated cultures were maintained in a sealed container with a brine reservoir of the matching growth medium controlling the humidity of the headspace, the desiccated microbial culture evaporites formed brine by deliquescence using humidity alone. Bacterial cultures resumed growth in all three salts once rehydrated by deliquescence. Cultures of Halomonas sp. str. HL12 showed robust survival and growth when subjected to several cycles of desiccation and deliquescent or manual rehydration. Our laboratory demonstrations of microbial growth in deliquescent brines are relevant to the surface and near-subsurface of cold arid worlds like Mars. When conditions become wetter, hygroscopic evaporite minerals can deliquesce to produce the earliest habitable brines. Survival after desiccation and growth in deliquescent brines increases the likelihood that microbes from Earth, carried on spacecraft, pose a contamination risk to Mars.

BioMateriOME: To understand microbe-material interactions within sustainable, living architectures

BioMateriOME evolved from a prototyping process which was informed from discussions between a team of designers, architects and microbiologists, when considering constructing with biomaterials or human cohabitation with novel living materials in the built environment. The prototype has two elements (i) BioMateriOME-Public (BMP), an interactive public materials library, and (ii) BioMateriOME-eXperimental (BMX), a replicated materials library for rigorous microbiome experimentation. The prototype was installed into the OME, a unique experimental living house, in order to (1) gain insights into society's perceptions of living materials, and (2) perform a comparative analysis of indoor surface microbiome development on novel biomaterials in contrast to conventional indoor surfaces, respectively. This review summarizes the BioMateriOME prototype and its use as a tool in combining microbiology, design, architecture and social science. The use of microbiology and biological components in the fabrication of biomaterials is provided, together with an appreciation of the microbial communities common to conventional indoor surfaces, and how these communities may change in response to the implementation of living materials in our homes. Societal perceptions of microbiomes and biomaterials, are considered within the framework of healthy architecture. Finally, features of architectural design with microbes in mind are introduced, with the possibility of codifying microbial surveillance into design and construction benchmarks, standards and regulations toward healthier buildings and their occupants.

Divergent assembly processes? A comparison of the plant and soil microbiome with plant communities in a glacier forefield

Community assembly is a result of dispersal, abiotic and biotic characteristics of the habitat as well as stochasticity. A direct comparison between the assembly of microbial and 'macrobial' organisms is hampered by the sampling of these communities in different studies, at different sites or on different scales. In a glacier forefield in the Austrian Alps, we recorded the soil and plant microbiome (bacteria and fungi) and plants that occurred in the same landscape and in close proximity in the same plots. We tested five predictions deduced from assembly processes and revealed deviating patterns of assembly in these community types. In short, microbes appeared to be less dispersal limited than plants and soil microbes, and plants strongly responded to abiotic factors whereas the leaf microbiome was plant species specific and well buffered from environmental conditions. The observed differences in community assembly processes may be attributed to the organisms' dispersal abilities, the exposure of the habitats to airborne propagules and habitat characteristics. The finding that assembly is conditional to the characteristics of the organisms, the habitat and the spatial scale under consideration is thus central for our understanding about the establishment and the maintenance of biodiversity.

Microbial anhydrobiosis

The loss of cellular water (desiccation) and the resulting low cytosolic water activity are major stress factors for life. Numerous prokaryotic and eukaryotic taxa have evolved molecular and physiological adaptions to periods of low water availability or water-limited environments that occur across the terrestrial Earth. The changes within cells during the processes of desiccation and rehydration, from the activation (and inactivation) of biosynthetic pathways to the accumulation of compatible solutes, have been studied in considerable detail. However, relatively little is known on the metabolic status of organisms in the desiccated state; that is, in the sometimes extended periods between the drying and rewetting phases. During these periods, which can extend beyond decades and which we term 'anhydrobiosis', organismal survival could be dependent on a continued supply of energy to maintain the basal metabolic processes necessary for critical functions such as macromolecular repair. Here, we review the state of knowledge relating to the function of microorganisms during the anhydrobiotic state, highlighting substantial gaps in our understanding of qualitative and quantitative aspects of molecular and biochemical processes in desiccated cells.