Microbial population dynamics on leaves.

Microbial communities thrive in virtually every habitat on Earth and are essential to the function of diverse ecosystems. Most microbial habitats are not spatially continuous and well-mixed, but rather composed, at the microscale, of many isolated or semi-isolated local patches of different sizes, resulting in partitioning of microbial populations into discrete local populations. The impact of this spatial fragmentation on population dynamics is not well-understood. Here, we study how such variably sized micro-habitat patches affect the growth dynamics of clonal microbial populations and how dynamics in individual patches dictate those of the metapopulation. To investigate this, we developed the μ-SPLASH, an ecology-on-a-chip platform, enabling the culture of microbes in microscopic landscapes comprised of thousands of microdroplets, with a wide range of sizes. Using the μ-SPLASH, we cultured the model bacteria Escherichia coli and based on time-lapse microscopy, analyzed the population dynamics within thousands of individual droplets. Our results reveal that growth curves substantially vary with droplet size. Although growth rates generally increase with drop size, reproductive success and the time to approach carrying capacity, display non-monotonic patterns. Combining μ-SPLASH experiments with computational modeling, we show that these patterns result from both stochastic and deterministic processes, and demonstrate the roles of initial population density, patchiness, and patch size distribution in dictating the local and metapopulation dynamics. This study reveals basic principles that elucidate the effects of habitat fragmentation and population partitioning on microbial population dynamics. These insights deepen our understanding of natural microbial communities and have significant implications for microbiome engineering.

Abstract. Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet they are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the present-day sulfur cycle in the natural environment and the present-day nitrogen cycle in eutrophic terrestrial environments. These shifts may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

Although there is a long history of conjecture regarding the role and significance of bacterial chemotaxis in microbial ecology, only recently has a significant body of work appeared attempting to address this issue. The purpose of this paper is to provide a concise overview of this work, which combined mathematical modeling of bacterial population migration and experimental measurement of the model parameters with modeling of competitive microbial population dynamics in a nonmixed environment. Predictions from the population dynamics models, based on experimental estimates of the various motility and growth parameter values, are related to the small number of experimental observations available to date dealing with the effects of bacterial motility on competition in a nonmixed environment. Current results indicate that cell motility and chemotaxis properties can be as important to population dynamics as cell growth kinetic properties, so that greater attention to this aspect of microbial behavior is warranted in future studies of microbial ecology.

Microbial population dynamics were investigated during start-up and during periods of overload conditions in anaerobic co-digesters treating municipal solid waste and sewage sludge. Changes in community structure were monitored using ribosomal RNA-based oligonucleotide probe hybridization to measure the abundance of syntrophic propionate-oxidizing bacteria (SPOB), saturated fatty acid-beta-oxidizing syntrophs (SFAS), and methanogens. These changes were linked to traditional performance parameters such as biogas production and volatile fatty acid (VFA) concentrations. Digesters with high levels of Archaea started up successfully. Methanosaeta concilii was the dominant aceticlastic methanogen in these systems. In contrast, digesters that experienced a difficult start-up period had lower levels of Archaea with proportionally more abundant Methanosarcina spp. Syntrophic propionate-oxidizing bacteria and saturated fatty acid-beta-oxidizing syntrophs were present at low levels in all digesters, and SPOB appeared to play a role in stabilizing propionate levels during start-up of one digester. Digesters with a history of poor performance tolerated a severe organic overload event better than digesters that had previously performed well. It is hypothesized that higher levels of SPOB and SFAS and their methanogenic partners in previously unstable digesters are responsible for this behavior.

Division synchrony and the dynamics of microbial populations: A size-specific model

Using anaerobic/aerobic sequencing batch reactors (SBRs) it was found that pre-fermentation of influent glucose resulted in a microbial population capable of enhanced biological phosphorus removal (EBPR). Batch tests indicated the C1-C5 carboxylic acids, except propionate, typically improved phosphorus removal. Branched molecules were superior to their linear isomers. The C1-C5 alcohols did not affect removal. Glucose, propionate, and an amino-acid rich substrate were detrimental. Using NMR spectroscopy it was observed that intracellular forms and locations of phosphorus did not change regardless of the substrate received. Polyphosphate (polyP) was present throughout the cells at the end of aerobiosis. It then degraded to inorganic phosphate via a zero-order enzymatic reaction concentrated at the cell membrane. An anaerobic/aerobic SBR receiving starch, rather than glucose fermentation products, showed only marginal EBPR and did not respond to carboxylic acids or other substrates in batch tests. Pseudomonas and Bacillus were numerous in the glucose system but were not isolated from the starch system. Aeromonas were dominant in the starch system. Although the glucose system showed better phosphorus removal than the starch system, it also showed greater variability. Phosphorus removal varied in a chaotic, but bounded, manner, probably due to population dynamics.

Uninoculated wines are regarded as having improved mouthfeel and texture and more complex flavor profiles when compared to wines inoculated with commercial S. cerevisiae strains. Uninoculated fermentation involves a complex microbial succession of yeasts and bacteria during fermentation. Microbial population dynamics are affected by several factors that can ultimately determine if a particular species or strain contributes to wine aroma and flavor. In this work, we have studied the effect of aeration, a common winemaking practice, on the yeast microbiota during uninoculated Chardonnay wine fermentation. The timing of aeration and then aeration intensity were evaluated across two successive vintages. While the timing of aeration significantly impacted fermentation efficiency across oxygen treatments, different levels of aeration intensity only differed when compared to the non-aerated control ferments. Air addition increased the viable cell population size of yeast from the genera Hanseniaspora, Lachancea, Metschnikowia and Torulaspora in both vintages. While in 2019, a high relative abundance was found for Hanseniaspora species in aerated ferments, in 2020, T. delbrueckii was visibly more abundant than other species in response to aeration. Accompanying the observed differences in yeast community structure, the chemical profile of the finished wines was also different across the various aeration treatments. However, excessive aeration resulted in elevated concentrations of ethyl acetate and acetic acid, which would likely have a detrimental effect on wine quality. This work demonstrates the role of aeration in shaping yeast population dynamics and modulating a volatile profile in uninoculated wines, and highlights the need for careful air addition to avoid a negative sensory impact on wine flavor and aroma.

Microbial communities abound with examples of complex social interactions that shape microbial ecosystems. One particularly striking example is microbial cooperation via the secretion of public goods. It has been suggested by theory, and recently demonstrated experimentally, that microbial population dynamics and the evolutionary dynamics of cooperative social genes take place with similar timescales, and are linked to each other via an eco-evolutionary feedback loop. We overview this recent evidence, and discuss the possibility that a third process may be also part of this loop: phenotypic dynamics. Complex social strategies may be implemented at the single-cell level by means of gene regulatory networks. Thus gene expression plasticity or stochastic gene expression, both of which may occur with a timescale of one to a few generations, can potentially lead to a three-way coupling between behavioral dynamics, population dynamics, and evolutionary dynamics

SummaryThe microbial population dynamics on apples cv. Golden Delicious were analysed every 15 days between bud and harvest in a fully replicated experiment in northern Spain in 1994 and 1995. The total microbial populations varied with developmental stage, and with prevailing climatic conditions. The predominant mycroflora were the filamentous fungiCladosporiumandAlternariaspp. and white and pink yeasts. Other genera isolated included mainly species ofEpicoccum, FusariumandAcremonium.However, the most important post‐harvest pathogensPenicillium expansumandBotrytis cinereawere seldom isolated from ripening apples. Maximum total filamentous fungal populations occurred after fruit set and during early ripening [2 × 104cfu (colony‐forming units) g‐1approximately] while those of bacteria were maximum at bud stage (3.5 × 105and 3.0 × 104cfu g‐1in 1994 and 1995 respectively). White yeasts were more numerous than pink yeasts. Endophytic infection of apple buds byAlternariaspp., responsible for core rot, was found in almost all bud tissue. By contrast,Cladosporiumspp. were initially isolated later from 12.5–50% of tissue samples during blooming and fruit set. The impact of a four‐spray fungicide regime during apple development significantly decreased the total filamentous fungal populations in both years, and that ofCladosporiumspp. in 1994. However, bacterial populations were often higher on apples from fungicide‐treated plots. Fungicide sprays decreased populations ofCladosporium, Alternariaand white yeasts for a maximum of up to 15–30 days after application. Fungicide application had little effect on endophytic infection of apples byAlternariaspp. between bud and harvest.

In a sulfate reducing process, increasing loading rates and sulfide accumulation may induce population changes resulting in decreasing effectiveness of the process. Thus, the relationship between microbial metabolism changes and population dynamics was studied. An upflow anaerobic sludge blanket reactor was operated at different sulfate loading rates (SLR), from 290 to 981 mg SO4-S/L d at a constant carbon/sulfur ratio of 0.75. When the SLR was increased, the total organic carbon and sulfate consumption efficiencies decreased to nearly 30% and 25%, respectively. The acetate and propionate yields increased with increasing SLR and 385±7 mg sulfide-S/L d was reached. The ecological indices, determined by random amplified polymorphic DNA and denaturing gradient gel electrophoresis techniques, diversity and evenness were found to be constant, and similarity coefficient values remained higher than 76%. The results suggest that the microbial population changes were negligible compared with metabolic changes when SLR was increased. The sulfide accumulation did not modify the microbial diversity. The sequencing of 16S rRNA genes showed strains related to sulfate reducing, fermentation, and methanogenesis processes. The results indicated that the decreasing of effectiveness, under the experimental conditions tested, was dependent more on operational parameters than microbial changes.

The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for "fraction of read abundance times cells"), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio, Desulfobacter, and Desulfobacterium, increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community.IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes.

The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for a better understanding of nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points during 1 year from two depths (0 to 5 and 20 to 30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty loam) with similar cropping histories. Although the microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural aquatic ecosystems. For example, among the 69 population genomes assembled from the metagenomes, 75% showed a less than 2-fold change in abundance between any two sampling points. Interestingly, six deep-branching Thaumarchaeota and three complete ammonia oxidizer (comammox) Nitrospira populations increased up to 5-fold in abundance upon the addition of N fertilizer. These results indicated that indigenous archaeal ammonia oxidizers may respond faster (are more copiotrophic) to N fertilization than previously thought. None of 29 recovered putative denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collection of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations in agricultural soils that should facilitate future monitoring efforts and N-related studies.IMPORTANCE Even though the impact of agricultural management on the microbial community structure has been recognized, an understanding of the dynamics of individual microbial populations and what functions each population carries are limited. Yet, this information is important for a better understanding of nutrient cycling, with potentially important implications for preserving nitrogen in soils and sustainability. Here, we show that reconstructed metagenome-assembled genomes (MAGs) are relatively stable in their abundance and functional gene content year round, and seasonal nitrogen fertilization has selected for novel Thaumarchaeota and comammox Nitrospira nitrifiers that are potentially less oligotrophic than their marine counterparts previously studied.

Studies have shown that microbial community structure is influenced by tree species identity thus the objective of this study was to determine microbial community structure in the rhizosphere of five selected tropical trees. This research was conducted at the Forestry Arboretum of the Faculty of Agriculture, University of Port Harcourt. Random sampling was used to collect soil samples from the rhizosphere of selected trees at a depth of 0-30cm for microbial analysis and identification in the laboratory using standard procedures. Results showed significant difference in microbial population across all trees with the highest microbial population observed under Tectona grandis (4.6x106 cfu/g) and the lowest microbial population recorded under Irvingia gabonensis. Ranges of microbial population were, total heterotrophic bacteria 0.88x106cfu/g – 4.6x106 cfu/g, and total heterotrophic fungi 3.0x103 cfu/g – 15.0 x103 cfu/g. Microbial diversity showed variation across all tree species, a total of 11 Bacteria and 9 fungi species were isolated and identified. Bacillus spp was the most predominant bacterium; Aspergillus spp was the most predominant fungus, highest microbial diversity was observed under Tectona grandis and Gmelina arborea, and lowest microbial diversity was found under Nauclea diderrichii. All five selected tropical tree species had effect on the microbial community structure but Tectona grandis exerted the most effect. This tree can therefore be utilized in agroforestry to boast nutrient availability and sustainable agriculture.

High elevation talus soils are extreme environments for life. They are pertinent to the hydrology and biochemical cycling of high elevation ecosystems that supply drinking water to major metropolitan areas, and are undergoing change as a result of N deposition. As biological systems, they are virtually unstudied. In order to gain a basic understanding of these important systems, we studied the seasonal timing of C inputs and microclimate, and how they corresponded to microbial biomass dynamics, in vegetated and unvegetated soils from a high altitude talus slope at 3750 m in the Colorado Front Range. The soil microclimate was described by soil moisture and temperature measurements; C inputs were estimated with measures of eolian dust inputs and photosynthetically active radiation (PAR). The biomass of different microbial functional groups (glutamate and salicylate mineralizers adapted to different temperatures) was estimated seasonally over 3 years. We found that the soil microclimate can be divided into three distinct seasons: Winter, with free water and temperature between −2.9 and 0 °C; spring, characterized by wet isothermal soils (0 °C); and summer, characterized by hot (mean 10.3 °C; range 0–29.3 °C) dry soils occasionally wetted by precipitation. The highest OM inputs to unvegetated soils occurred in spring; PAR only reached soils in the summer. In unvegetated soils, the biomass of glutamate mineralizers (GM) was highest in spring and summer. In contrast, the GM of vegetated soils had highest biomass in the winter when plants were senesced. In both unvegetated and vegetated soils, salicylate mineralizers (SM) had greater biomass levels in the summer when temperatures were highest.

Enhanced microbial hydrocarbon biodegradation as stimulated during field-scale landfarming of crude oil-impacted soil