Microbial Population Dynamics Research Articles

Time Series Analysis in Financial Markets and Biological Phenomena

This paper discusses the application of time series analysis in financial markets and biological phenomena. It expounds the basic theory of time series analysis, including the concepts and characteristics of time series and commonly used time series models. It also provides an in-depth analysis of its application in financial markets, covering the characteristics of financial time series and specific applications in stock markets and foreign exchange markets, such as stock price forecasting, risk measurement, foreign exchange rate forecasting and volatility analysis. It also discusses the application of time series analysis in biological phenomena, including the characteristics of biological time series and its application in biological growth and development, such as modeling the growth curves of animals and plants, and studying the dynamics of microbial populations. The application of time series analysis in these two fields is summarized, providing a valuable reference for related research and practice.

Impact of micro-habitat fragmentation on microbial population growth dynamics.

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 E. 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.

Honeysuckle branches and lactobacillus enhance quality by changing the composition and diversity of microorganisms in alfalfa silage fermentation

The incorporation of honeysuckle as a silage additive in alfalfa production has yielded promising results; however, the underlying microbial mechanisms during fermentation remain poorly understood. This study leveraged high-throughput sequencing and nutrient profiling to elucidate microbial population dynamics over 45 days of anaerobic fermentation within a vacuum-assisted co-culture system comprising varying fresh weight ratios of honeysuckle branches, Lactobacillus, and alfalfa. The experimental design encompassed a Lactobacillus-supplemented treatment (M group) and an unsupplemented control (R group), each with five honeysuckle percentages (5 %, 10 %, 15 %, 20 %, 25 %) and respective negative controls. Our findings reveal that the combined use of honeysuckle branches and Lactobacillus significantly impacts microbial community composition and diversity during alfalfa silage fermentation. The Mantel test underscores Lactobacillus's absence-dependent correlation of bacterial communities with pH and lactic acid, whereas its presence redirects these correlations towards total nitrogen, NH4+-N, neutral detergent fiber, and crude protein as key bacterial population drivers. Fungal populations exhibited analogous trends. Moreover, the combined additives reshaped microbial populations during anaerobic fermentation, altering interaction networks and intensifying microbial interplay. Notably, Lactobacillus introduction on a honeysuckle branch base diminished fungal core OTUs, thereby mitigating fungal contamination risks. This study also identified biomarkers unique to each treatment condition. Collectively, our research provides a molecular framework for employing honeysuckle branches and Lactobacillus as innovative silage additives in alfalfa production, fostering the development of eco-friendly and hygienic feed and farming industries.

179 Charting the evolution of rumen microbial models from past to present

Abstract This review delves into the intricate realm of ruminal microbes, shedding light on their complexity beyond previously recognized dimensions. Existing publications have probed the essential facets of these microorganisms on a finer scale than previously acknowledged. Mathematical models have emerged to simulate the behavior of approximately 200 distinct bacterial species, 25 genera of ciliate protozoa, and five genera of anaerobic fungi, constituting about 10% of the total viable bacteria in the rumen. However, the expansive diversity and density of rumen microbes challenge the complete characterization of species or genera in relation to substrates or end products. Consequently, continuous revision and re-engineering of mathematical models become imperative. In the context of ruminants, prevalent models often categorize bacteria into fiber-fermenting and nonfiber-fermenting groups. An additional subgroup featuring hyper-ammonia-producing bacteria has been proposed, but its explicit integration into nutrition models remains unexplored. Furthermore, incorporating a more mechanistic evaluation of protozoa and fungal growth may be warranted to improve nutrition models. The time horizon and intervals at which models are constructed present another critical consideration, with feed efficiency variations among ruminants believed to be closely tied to differences in the ruminal microbiota. Addressing immediate concerns, this review underscores the need for a comprehensive exploration of factors influencing microbial growth in the rumen. Several indices have been suggested and adopted to predict microbial efficiencies, but they may provide simplification for practical application. Thus, a mechanistic approach should be considered to remove dependencies between estimates and improve predictive accuracy and precision. While artificial intelligence holds promise in elucidating gaps within empirical and mechanistic models, the generation of accurate, vetted datasets is paramount. Furthermore, this review posits that factors such as recycled nitrogen, endotoxins, and microbial population dynamics (i.e., cross-feeding and competition) may be limiting our understanding of microbial growth, suggesting the necessity of modeling these intricacies concurrently to achieve a more nuanced comprehension. This multifaceted approach aims to propel the understanding of ruminal microbial dynamics into new frontiers, paving the way for more informed and effective modeling in the future.

Understanding the transitional phase of nitrate removal in three different specialty adsorbents for stormwater treatment

Excess nitrogen input from nonpoint sources driven by hydrologic and anthropogenic disturbances has become a significant ecological challenge in receiving water bodies. Moreover, nitrate removal by cost-effective filtration media has still not performed up to expectation because of the knowledge gap in the transitional phase from physicochemical to microbiological processes. This study developed three cost-effective, sustainable, and adaptable green sorption media (GSM), namely CPS (clay–perlite with sand sorption media), ZIPGEM (zero-valent iron and perlite green environmental media), and BIPGEM (biochar, zero-valent iron, and perlite-based green environmental media), made of readily available and recyclable materials, to compare nitrate removal methods for stormwater treatment and elucidate the transitional phase. The primary adsorption mechanism was chemisorption, and subsequent biofilm growth sustained removal efficiency for a long-lasting period. Adsorption kinetics, adsorption equilibrium, material characterization, and fixed-bed column experiments with a 2-stage cultivation approach were undertaken to characterize the transitional phase in these GSM, based on breakthrough curves, maximum adsorption capacity, and microbial population dynamics for nitrification and denitrification. As shown in the column study, BIPGEM had the highest adsorption capacity (7.637 mg∙g−1), followed by ZIPGEM (2.16 mg∙g−1), and CPS (0.1798mg∙g−1). The biochar in BIPGEM provides a better cultivation environment for nitrifying and denitrifying bacteria, contributing sufficient electron donors. Biofilm production and maturation enabled the BIPGEM to maintain 30 % nitrate removal in a steady state even after 2000 h of operation in the first stage. When the biofilm reached maturation, BIPGEM’s nitrate removal percentage was up to 70 % via denitrification in the second stage.

Microbial Community Dynamics and Metabolite Changes during Wheat Starch Slurry Fermentation.

Wheat starch fermentation slurry is the main substrate for producing Ganmianpi, a traditional Chinese fermented wheat starch-based noodle. In the present work, the microbial population dynamics and metabolite changes in wheat starch fermentation slurry at different fermentation times (0, 1, 2, 3, and 4 days) were measured by using high-throughput sequencing analysis and headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME/GC-MS) methods. The texture and sensory properties of Ganmianpi made from fermented starch slurry are also evaluated. The results showed that Latilactobacillus curvatus and Leuconostoc citreum were the dominant bacteria in wheat starch fermentation slurry, while Saccharomyces cerevisiae and Kazachstania wufongensis were identified as the main species of fungi. With the extension of fermentation time, the reducing sugar content first increased and then decreased, when the titratable acidity content showed an increasing trend, and the nonvolatile acid was significantly higher than the volatile acid. A total of 62 volatile flavor compounds were identified, and the highest content is alcohols, followed by acids. Fermentation significantly reduced the hardness and chewiness of Ganmianpi, and increased its resilience and cohesiveness. Ganmianpi made from fermented starch slurry for two and three days showed a higher sensory score than other samples. The present study is expected to provide a theoretical basis for exploiting the strains with potential for commercial application as starter cultures and quality improvement of Ganmianpi.

Extremely halophilic brine community manipulation shows higher robustness of microbiomes inhabiting human-driven solar saltern than naturally driven lake.

Viruses greatly influence succession and diversification of their hosts, yet the effects of viral infection on the ecological dynamics of natural microbial populations remain poorly understood, especially at finer scales of diversity. By manipulating the viral predation pressure by autochthonous and allochthonous viruses, we uncovered potential phage-host interaction, and their important role in structuring the prokaryote community at an ecotype level.

Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity

BackgroundFecal microbiota transplantation (FMT) is a therapeutic intervention used to treat diseases associated with the gut microbiome. In the human gut microbiome, phages have been implicated in influencing human health, with successful engraftment of donor phages correlated with FMT treatment efficacy. The impact that gastrointestinal phages exert on human health has primarily been connected to their ability to modulate the bacterial communities in the gut. Nonetheless, how FMT affects recipients’ phage populations, and in turn, how this influences the gut environment, is not yet fully understood. In this study, we investigated the effects of FMT on the phageome composition of participants within the Gut Bugs Trial (GBT), a double-blind, randomized, placebo-controlled trial that investigated the efficacy of FMT in treating obesity and comorbidities in adolescents. Stool samples collected from donors at the time of treatment and recipients at four time points (i.e., baseline and 6 weeks, 12 weeks, and 26 weeks post-intervention), underwent shotgun metagenomic sequencing. Phage sequences were identified and characterized in silico to examine evidence of phage engraftment and to assess the extent of FMT-induced alterations in the recipients’ phageome composition.ResultsDonor phages engrafted stably in recipients following FMT, composing a significant proportion of their phageome for the entire course of the study (33.8 ± 1.2% in females and 33.9 ± 3.7% in males). Phage engraftment varied between donors and donor engraftment efficacy was positively correlated with their phageome alpha diversity. FMT caused a shift in recipients’ phageome toward the donors’ composition and increased phageome alpha diversity and variability over time.ConclusionsFMT significantly altered recipients' phage and, overall, microbial populations. The increase in microbial diversity and variability is consistent with a shift in microbial population dynamics. This proposes that phages play a critical role in modulating the gut environment and suggests novel approaches to understanding the efficacy of FMT in altering the recipient’s microbiome.Trial registrationThe Gut Bugs Trial was registered with the Australian New Zealand Clinical Trials Registry (ACTR N12615001351505). Trial protocol: the trial protocol is available at https://bmjopen.bmj.com/content/9/4/e026174.A4HmAXiKAUhp3nsywzn7_QVideo

Linking Pattern Shifts of Dissolved Organic Nitrogen Fractional Removal with Microbial Species Richness in a Cascade Upflow Biofiltration Process

Nutrient pollution has become an important issue to solve in stormwater runoff due to the fast population growth and urbanization that impacts water quality and triggers harmful algal blooms. There is an acute need to link the dissolved organic nitrogen (DON) decomposition with the coupled nitrification and denitrification pathways to realize the pattern shifts in the nitrogen cycle. This paper presented a lab-scale cascade upflow biofiltration system for comparison of nitrate and phosphate removal from stormwater matrices through two specialty adsorbents at three influent conditions. The two specialty adsorbents are denoted as biochar iron and perlite integrated green environmental media (BIPGEM) and zero-valent iron and perlite-based green environmental media (ZIPGEM). An initial condition with stormwater runoff, a second condition with spiked nitrate, and a third condition with spiked nitrate and phosphate were used in this study. To differentiate nitrifier and denitrifier population dynamics associated with the decomposition of DON, integrative analysis of quantitative polymerase chain reaction (qPCR) and 21 tesla Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were performed in association with nitrate removal efficiencies for both media with or without the presence of phosphate. While the qPCR may detect one gene for a single microbe or pathogen and realize the microbial population dynamics in the bioreactors, the 21 T FT-ICR MS can separate and assign elemental compositions to identify organic compounds of DON. Results indicated that ZIPGEM obtained a higher potential for nutrient removal than BIPGEM when the influent was spiked with nitrate and phosphate simultaneously. The sustainable, scalable, and adaptable upflow bioreactors operated in sequence (in a cascade mode) can be expanded flexibly on an as-needed basis to meet the local water quality standards showing process reliability, resilience, and sustainability simultaneously.

Carbon redirection pathway, energy recovery potential, and microbial population dynamics in high-rate activated sludge

High-rate activated sludge (HRAS) is wastewater treatment focusing on reducing greenhouse gas emissions via energy recovery from sludge. However, the effect of hydraulic retention time (HRT) on HRAS performance and redirection pathways has seldom been investigated. Also, the fractionation of extracellular polymeric substance (EPS) as loosely-bound (LB) and tightly-bound (TB) in HRAS sludge have not reported yet. This study aimed to comprehensively investigate the carbon redirection pathways and biogas recovery potential of the HRAS system, examining the separate effects of HRT and SRT. An HRT of 1.5 h and an SRT of 2 d, HRAS achieved the highest COD recovery, with 64.8 % removed and 60.5 % redirected as waste activated sludge (WAS) as the pseudo-steady average values. And WAS exhibited notably high LB-EPS, reaching 366.2 mg/g volatile suspended solids (VSS). Furthermore, the metabolism pathway for redirection resulted in biosorption 54.9 %, LB-EPS 34.0 %, TB-EPS 7.2 %, and cell growth 3.9 % based VSS. The biochemical methane potential of WAS was measured at 234.0 mL CH4/g COD, equivalent to 40.5 % of influent at HRT 1.5 h and SRT 2 d as optimal conditions. Notably, Family Carnobacteriaceae and Genus Trichococcus were emerged dominantly in HRAS. This study would be useful in the design and operation of HRAS for sustainable wastewater treatment and climate change mitigation.

Linking microbial population dynamics in anaerobic bioreactors to food waste type and decomposition stage

A key question in anaerobic microbial ecology is how microbial communities develop over different stages of waste decomposition and whether these changes are specific to waste types. We destructively sampled over time 26 replicate bioreactors cultivated on fruit/vegetable waste (FVW) and meat waste (MW) based on pre-defined waste components and composition. To characterize community shifts, we examined 16S rRNA genes from both the leachate and solid fractions of the waste. Waste decomposition occurred faster in FVW than MW, as accumulation of ammonia in MW reactors led to inhibition of methanogenesis. We identified population succession during different stages of waste decomposition and linked specific populations to different waste types. Community analyses revealed underrepresentation of methanogens in the leachate fractions, emphasizing the importance of consistent and representative sampling when characterizing microbial communities in solid waste.

Soil and Mineral Nutrients in Plant Health: A Prospective Study of Iron and Phosphorus in the Growth and Development of Plants.

Plants being sessile are exposed to different environmental challenges and consequent stresses associated with them. With the prerequisite of minerals for growth and development, they coordinate their mobilization from the soil through their roots. Phosphorus (P) and iron (Fe) are macro- and micronutrient; P serves as an important component of biological macromolecules, besides driving major cellular processes, including photosynthesis and respiration, and Fe performs the function as a cofactor for enzymes of vital metabolic pathways. These minerals help in maintaining plant vigor via alterations in the pH, nutrient content, release of exudates at the root surface, changing dynamics of root microbial population, and modulation of the activity of redox enzymes. Despite this, their low solubility and relative immobilization in soil make them inaccessible for utilization by plants. Moreover, plants have evolved distinct mechanisms to cope with these stresses and coregulate the levels of minerals (Fe, P, etc.) toward the maintenance of homeostasis. The present study aims at examining the uptake mechanisms of Fe and P, and their translocation, storage, and role in executing different cellular processes in plants. It also summarizes the toxicological aspects of these minerals in terms of their effects on germination, nutrient uptake, plant-water relationship, and overall yield. Considered as an important and indispensable component of sustainable agriculture, a separate section covers the current knowledge on the cross-talk between Fe and P and integrates complete and balanced information of their effect on plant hormone levels.

Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system

The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.

Modelling the dynamics of microbial populations and Salmonella spp. in milk kefir

Kefir is a fermented dairy product based on the fermentation of milk by bacteria and yeasts. It is produced by adding kefir grains, consisting of a consortium of microorganisms, to milk in order to start a natural fermentation (Garofalo et al., 2020). Kefir is well recognized for its potential health value as a source of probiotics, however, there have been concerns about the potential growth of pathogenic microorganisms in kefir and the potential health hazards associated (Leite et al., 2013) A mathematical model was developed to describe the evolution of microbes present during kefir fermentation and the potential growth of Salmonella spp. as one example of a potential food safety hazard. For this, equations previously described in the scientific literature were combined and adapted to the milk kefir matrix. To assess the safety of the product, the growth of Salmonella was predicted considering its interaction with the medium and the other species. The drop in pH; generation of yeasts metabolites such as ethanol; and buffer capacity was described and considered when modelling Salmonellas’ kinetics. Interaction between the pathogenic species and the background microflora was included in the model. Parameters of some well-described systems were taken from literature. Alongside, some other parameters describing specific assets from the system were estimated using experimental data of microbial population kinetics during kefir fermentation. The growth of yeasts, lactic acid bacteria, Salmonella together with the pH were experimentally collected at critical processing times and fitted to the mathematical model by minimizing the residual sum of squares (RSS). Confidence intervals of 95 % were calculated. For further validation, the output of the model was contrasted with an independent data set. It was concluded that Salmonella is able to increase its population during the first hours of the kefir fermentation process. Inactivation can be apportioned to the drop of pH as a consequence of the LAB metabolism, once the pH reaches values below 4. After this no growth of Salmonella seems to be found in milk kefir as confirmed by the model. No residual population of the pathogen is observed. This suggests that by controlling the growth and metabolism of the background microflora, safety can be assured in milk kefir. This process was successfully described by a novel mathematical model and the estimation of its´parameters.

Impact of diverse weed management strategies on soil microbial population dynamics in maize

Impact of diverse weed management strategies on soil microbial population dynamics in maize

Optimization of Fermentation and Sensory Quality of Mango Yogurt Using Various Sucrose Concentration Fermented by Lacticaseibaciluus paracasei Strain Shirota

This research explores the optimization of mango yogurt production, leveraging mango as the primary fermentation ingredient and Lacticaseibacillus paracasei strain Shirota (LcS) as the probiotic inoculum. Traditional yogurt, typically derived from animal milk, faces competition from plant-based alternatives. The research objective is to investigate the impact of inoculum ratios and sucrose concentrations on LcS density and sensory attributes, with a focus on the Substrate to Inoculum Ratio (S/I) as a critical parameter influencing microbial metabolism and population dynamics. Various inoculum ratios (1:1, 1:2, 1:4, 1:8 v/v) and sucrose concentrations (0%, 2.5%, 5%, 7.5%) were applied in mango yogurt production. Results from ANOVA analysis indicated significant differences in LcS density among inoculum ratios (F3,16 = 37.01, P = 0.000) and sucrose concentrations (F3,16 = 19.07, P = 0.000). The 1:2 inoculum ratio and 7.5% sucrose concentration emerged as optimal, as evidenced by stable pH conditions and lactic acid profiles within recommended standards. Sensory analysis, employing a 5-point hedonic scale for color, odor, taste, and texture evaluation, revealed moderate acceptance. In conclusion, this study introduces an innovative approach to mango yogurt production, highlighting the potential of specific inoculum ratios and sucrose concentrations for optimal results. The findings contribute to the broader landscape of plant-based yogurt alternatives, underscoring the need for ongoing refinement to meet commercial standards and ensure consumer satisfaction.

Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.

Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.IMPORTANCEThe transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.

Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils.

Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.

Comparative microbiome analysis of beef cattle, the feedyard environment, and airborne particulate matter as a function of probiotic and antibiotic use, and change in pen environment.

Intensive beef cattle production systems are frequently implicated as a source of bacteria that can be transferred to nearby humans and animals via effluent water, manure used as fertilizer, or airborne particulate matter. It is crucial to understand microbial population dynamics due to manure pack desiccation, antibiotic usage, and antibiotic alternatives within beef cattle and their associated feedyard environment. Understanding how bacterial communities change in the presence of antibiotics can also improve management practices for reducing the spread of foodborne bacteria. In this study, we aimed to compare the microbiomes within cattle feces, the feedyard environment and artificially produced airborne particulate matter as a function of pen change and treatment with tylosin or probiotics. We utilized 16S rRNA sequencing to compare bacterial communities among sample types, study days, and treatment groups. Bacterial community diversity varied as a function of sampling day and pen change (old or new) within fecal and manure pack samples. Manure pack samples from old pens and new pens contained diverse communities of bacteria on days 0 and 84; however, by day 119 of the study these taxonomic differences were less evident. Particulate matter samples exhibited significant differences in community diversity and predominant bacterial taxa compared to the manure pack they originated from. Treatment with tylosin did not meaningfully impact bacterial communities among fecal, environmental, or particulate matter samples; however, minor differences in bacterial community structure were observed in feces from cattle treated with probiotics. This study was the first to characterize and compare microbial communities within feces, manure pack, and airborne particulate matter from the same location and as a function of tylosin and probiotic treatment, and pen change. Although fecal and environmental samples are commonly used in research studies and other monitoring programs to infer public health risk of bacteria and antimicrobial resistance determinants from feedyard environments, our study suggests that these samples may not be appropriate to infer public health risk associated with airborne particulate matter.

A Monte‐Carlo approach for the simulation of microbial population dynamics in an heterogeneous scale‐down bioreactor

AbstractPopulation heterogeneity is due to intrinsic and extrinsic noises; cell to cell variability is related to cell partitioning at division and external forcing by the environment. In this article, a Monte‐Carlo calculation of integral source terms is coupled to a compartment approach. The biological phase is represented by an ensemble of discrete particles which are equipped with a coarse‐grained model that describes the intracellular response to extracellular conditions. The redistribution of cell properties at division generates unbalanced cells and introduces additional time scales into the population dynamics. Using this fully two‐way coupled approach, the consequences of repeated exposure to feast and famine events on both the reactor and the population heterogenities are investigated in a CSTR+PFR scale‐down bioreactor. It is shown that the integration of intrinsic noise due to cell division continuously produces cells that are not at equilibrium with their environment and this contributes to population heterogeneity, even in homogeneous environments.