Microbial Population Dynamics Research Articles

Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic.

The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.

Effect of Corm and Soil Treatments with Organic Liquid Formulations on Performance of Elephant Foot Yam in Jharkhand, India

A field experiment was carried out at the farm of Divyayan Krishi Vigyan Kendra, Ramakrishna Mission Ashrama, Morabadi, Ranchi during kharif season of 2022 with 10 treatments (T1: control or no treatment, T2: Corm treatment with Beej Sanjeevani, T3: Corm treatment with Beejamrit, T4: Soil application of Jiwamrit, T5: Soil application of Panchagavya, T6: Soil application of Jiwamrit + Panchagavya, T7: Corm treatment with Beej Sanjeevani + soil application of Jiwamrit, T8: Corm treatment with Beej Sanjeevani + soil application of Panchagavya, T9: Corm treatment with Beejamrit + soil application of Jiwamrit, T10: Corm treatment with Beejamrit + soil application of Panchagavya) placed in three times replicated randomized block design to study the growth, yield and production economics of elephant foot yam under uses of organic corm and soil treatments. Results revealed that corm treatment with Beejamrit + soil application of Jiwamrit resulted in higher growth attributes, corm length (23.3 cm), dimeter (26.9 cm) and yield (32.8 t/ha). This corm + soil treatment also recorded the highest gross return (INR.2,62,400/ha), net return (INR.1,69,189/ha) and B:C (2.82). It also increased soil microbial population dynamics especially total bacteria (69.7 CFU × 106/g of soil).

Survey of Domestic Refrigerator Storage Temperatures in Poland for Use as a QMRA Tool for Exposure Assessment

In the framework of Quantitative Microbiological Risk Assessment, the estimation of the ingested dose of a hazard by the consumer is of paramount importance. This may be calculated by means of predictive modeling of growth/inactivation of the pathogen studied. For products that spend the majority of their shelf life in the domestic refrigerator, storage temperature will significantly impact the microbial population dynamics. To describe the variability of domestic storage temperatures in Poland, a survey including 77 participants, was carried out in Lodz, Poland. Participants were provided with temperature data loggers, which measured their refrigerator temperature for 24 h in 5-min intervals. The temperature-time profiles were used to calculate the mean working temperature, standard deviation, minimum and maximum values, and the data were statistically analyzed to find the best fitting probability distribution using R programming language. Out of the tested refrigerators, 49.35% had a mean working temperature of over 5 °C and 3.9% exceeded 10 °C. Distribution fitting scenarios were tested for goodness of fit, and the final selected distribution was a truncated normal distribution. This study can prove useful in Monte Carlo simulation analysis for stochastic quantitative food risk assessment in Poland.

Efficacy of Herbicides on Nutrient Uptake of Crop, Weed and Its Impact on Soil Microflora of Irrigated Maize (Zea mays L.)

Aim: Field experiment was conducted to study the suitable weed management methods to check the nutrient depletion by weeds, check the dynamics of microbial population and in relation to improve the biomass stover yield of maize (Zea mays L.).
 Study Design: This experiment laid out in a randomized block design and 8 different weed management treatments with three replications.
 Place and Duration of Study: Field experiment was conducted at Agricultural College and Research Institute, Madurai, Tamil Nadu Agricultural University, Tamil Nadu in kharif 2019.
 Methodology: TNAU maize hybrid CO-6 was used for this experiment. Treatments were application of pre-emergence herbicide atrazine at 0.25 kg/ha or pendimethalin 1 kg/ha applied singly on 3 days after sowing and in combination with post-emergence herbicide tembotrione 120 g/ha or halosulfuron methyl 90 g/ha on 25 DAS, weed free check, unweeded check in maize crop. Weed nutrient depletion and microbial population was analysed in laboratory.
 Results: The application of pre-emergence atrazine 0.25 kg/ha followed by post-emergence tembotrione 120 g/ha effective in controlling of grasses and BLW and enhance the nutrient uptake of maize. The stover maize yield increased with application of herbicides and sequential application of herbicides achieved 88% improved stover yield over unweeded check. Sequential application of herbicides initially reduce the population of soil microflora but the population gradually build up in all the herbicide applied plots at 60 days after application.
 Conclusion: Based on the results of the experiment, it was concluded that pre-emergence atrazine 0.25 kg/ha followed by post emergence tembotrione 120 g/ha effective in controlling of weeds and enhance the nutrient uptake and stover yield of maize without much adverse impact on soil microbial population.

Gut Dysbiosis in Experimental Kidney Disease: A Meta-Analysis of Rodent Repository Data.

Alterations in gut microbiota contribute to the pathophysiology of a diverse range of diseases, leading to suggestions that chronic uremia may cause intestinal dysbiosis that contributes to the pathophysiology of CKD. Various small, single-cohort rodent studies have supported this hypothesis. In this meta-analysis of publicly available repository data from studies of models of kidney disease in rodents, cohort variation far outweighed any effect of experimental kidney disease on the gut microbiota. No reproducible changes in animals with kidney disease were seen across all cohorts, although a few trends observed in most experiments may be attributable to kidney disease. The findings suggest that rodent studies do not provide evidence for the existence of "uremic dysbiosis" and that single-cohort studies are unsuitable for producing generalizable results in microbiome research. Rodent studies have popularized the notion that uremia may induce pathological changes in the gut microbiota that contribute to kidney disease progression. Although single-cohort rodent studies have yielded insights into host-microbiota relationships in various disease processes, their relevance is limited by cohort and other effects. We previously reported finding metabolomic evidence that batch-to-batch variations in the microbiome of experimental animals are significant confounders in an experimental study. To attempt to identify common microbial signatures that transcend batch variability and that may be attributed to the effect of kidney disease, we downloaded all data describing the molecular characterization of the gut microbiota in rodents with and without experimental kidney disease from two online repositories comprising 127 rodents across ten experimental cohorts. We reanalyzed these data using the DADA2 and Phyloseq packages in R, a statistical computing and graphics system, and analyzed data both in a combined dataset of all samples and at the level of individual experimental cohorts. Cohort effects accounted for 69% of total sample variance ( P <0.001), substantially outweighing the effect of kidney disease (1.9% of variance, P =0.026). We found no universal trends in microbial population dynamics in animals with kidney disease, but observed some differences (increased alpha diversity, a measure of within-sample bacterial diversity; relative decreases in Lachnospiraceae and Lactobacillus ; and increases in some Clostridia and opportunistic taxa) in many cohorts that might represent effects of kidney disease on the gut microbiota . These findings suggest that current evidence that kidney disease causes reproducible patterns of dysbiosis is inadequate. We advocate meta-analysis of repository data as a way of identifying broad themes that transcend experimental variation.

Pengaruh Aplikasi Bioarang dan Zeolit pada Fluks CO2, Populasi Mikrob, dan Aktivitas Enzim Mikrob pada Gambut

Oil palm plantation on peatlands is considered to contribute to increasing global warming by releasing CO2 as one of the greenhouse gases that cause global warming. The addition of ameliorants, such as biochar and zeolite, can absorb CO2 from soil respiration and store and filter it in their molecular pores. This research aimed to study the effect of ameliorant application on the CO2 flux, water content, microbial population, and enzyme activities. Ameliorant was applied to peat soil with two factors. The first factor was an ameliorant combination with 6 treatment levels: control (A0); zeolite (A1); biochar (A2); zeolite:biochar 75:25; zeolite:biochar 25:75; zeolite:biochar 50:50, and the second factor was 3 levels dose of treatment (% w/w): 1.5%, 3%, and 4.5%. Peat flux CO2 and water content were measured monthly for four months in the laboratory. Without mixing with biochar (A1), the results showed that zeolite suppressed CO2 flux and suppressed the decrease of water content better than other ameliorant combinations. However, different ameliorant dosage percentages did not show any significant results. Ameliorant application and incubation affected the microbial population and enzyme activities, and the results were varied. Chemical characteristics changed after 4 months of incubation. In conclusion, our results indicate that only zeolite amendment can suppress CO2 flux and decrease water content but did not affect microbial population dynamics and enzyme activities.&#x0D; &#x0D; Keywords: ameliorant, CO2 flux, enzyme activities, lignocellulolytic microbes, peat

Microbial population dynamics decouple growth response from environmental nutrient concentration

How the growth rate of a microbial population responds to the environmental availability of chemical nutrients and other resources is a fundamental question in microbiology. Models of this response, such as the widely used Monod model, are generally characterized by a maximum growth rate and a half-saturation concentration of the resource. What values should we expect for these half-saturation concentrations, and how should they depend on the environmental concentration of the resource? We survey growth response data across a wide range of organisms and resources. We find that the half-saturation concentrations vary across orders of magnitude, even for the same organism and resource. To explain this variation, we develop an evolutionary model to show that demographic fluctuations (genetic drift) can constrain the adaptation of half-saturation concentrations. We find that this effect fundamentally differs depending on the type of population dynamics: Populations undergoing periodic bottlenecks of fixed size will adapt their half-saturation concentrations in proportion to the environmental resource concentrations, but populations undergoing periodic dilutions of fixed size will evolve half-saturation concentrations that are largely decoupled from the environmental concentrations. Our model not only provides testable predictions for laboratory evolution experiments, but it also reveals how an evolved half-saturation concentration may not reflect the organism's environment. In particular, this explains how organisms in resource-rich environments can still evolve fast growth at low resource concentrations. Altogether, our results demonstrate the critical role of population dynamics in shaping fundamental ecological traits.

Avoiding the All-or-None Response in Gene Expression During E. coli Continuous Cultivation Based on the On-Line Monitoring of Cell Phenotypic Switching Dynamics.

Different expression vectors are available for the effective production of recombinant proteins by bacterial populations. However, the productivity of such systems is limited by the inherent noise of the gene circuits used for the synthesis of recombinant products. An extreme case of cell-to-cell heterogeneity that has been previously reported for the ara- and lac-based expression systems in E. coli is the all-or-none response. According to this mode of response, two subpopulations of cells are generated, i.e., a "low-" subpopulation exhibiting a shallow expression level and a "high-" subpopulation exhibiting a high-expression level. The "low-" subpopulation can be considered as a cluster of non-producing cells contributing to the loss of productivity. Here we describe the setup, design, and operation of a continuous culture where inducer addition is operated based on microbial population dynamics. The determination of population dynamics is done based on an automated flow cytometry (FC) procedure previously denoted as segregostat. We illustrate how this setup can be used to control the activation of an ara-based expression system and avoid phenotypic diversification leading to an all-or-none response. Upon the determination of the natural frequency of the gene circuit used as an expression system, our current protocol can be set up without the requirement of a feedback controller.

Microbial Population Dynamics in Lemnaceae (Duckweed)-Based Wastewater Treatment System.

The dynamic microflora associated within, and in the surrounding aquatic environment, has been found to be responsible for the functional properties of many aquatic plants. The aim of the current work was to evaluate the effectiveness of Lemnaceae-based wastewater treatment system under tropical conditions and investigate the changes in the aquatic microflora upon plant growth. A biological wastewater treatment system was designed and investigated using mixed Lemnaceae culture comprising Lemna minor and Spirodela polyrhiza in a batch mode. A significant reduction in total solids (31.8%), biochemical oxygen demand (93.5%), and chemical oxygen demand (73.2%) was observed after seven days of duckweed growth using a low inoculum. A preliminary study on the change in the microbial population diversity and functionality, in the wastewater before and after treatment, revealed an increase in the denitrifying microflora in wastewater post-Lemnaceae treatment. Dominance of 10 bacterial phyla, contributing for 98.3% of the total bacterial communities, was recorded, and ~ 50.6% loss of diversity post-treatment of wastewater was revealed by the Shannon Index. Among 16 bacterial families showing relative abundance of ≥ 1% in untreated wastewater, Methylobacteriaceae, Pseudomonadaceae, Brucellaceae, Rhodobacteraceae, and Acetobacteraceae prevailed in the water post-treatment by duckweeds. This is a novel work done on the dynamics of aquatic microflora associated with Lemnaceae under tropical Indian conditions. It confirms the application of Lemnaceae-based wastewater treatment system as effective biofilter and calls for further studies on the active involvement of the endophytic and aquatic microflora in the functions of these plant.

Microbial population dynamics and meta-proteomic evaluation for functional insight into an anaerobic membrane bioreactor during startup

Startup of an anaerobic membrane reactor (AnMBR) involves a significant concentration of active and functioning microbial communities participating in the process. Here, we monitored the physical, microbial, and functional performance during the first 90 days of AnMBR operation. The results indicate initiation of anaerobic digestion on days 31–60 (transitional stage) and its stabilization on days 61–90 (stable stage), with an average COD removal efficiency of 93.14 ± 1.41% and biogas production of 0.82 ± 0.15 L/d. Moreover, the microbial population and its associated proteome were studied using 16s rDNA-based PCR-DGGE and SDS-PAGE-LC/MS/MS techniques to acquire a detailed understanding of reactor startup conditions. Later, a conventional library was created through the UniprotKB protein database using the observed community of all organisms identified with 16s rDNA sequencing. The results clearly depicted Gammaproteobacteria as the dominant fermentative during the initial and transitional stages. Firmicutes predominated over Gammaproteobacteria during the stabilization stage. During the transitional stage, methanobacteriales and metheanosarcinales coexisted. In the two-step reaction, a combination of syntrophic acetate oxidation and hydrogenotrophic methanogenesis was observed. During the stabilization stage, diverse metheanosarcinales were detected. The methanogenic pathway seemed to shift to acetoclastic methanogenesis, as indicated by detection of acetyl-coenzyme A synthetase, aminomethyltransferase, and methyl-coenzyme M reductase. Thus, by linking microbial community dynamics with the meta-proteomic functions of AnMBR during startup, a stable reactor performance with up-regulated acetoclastic methanogenesis was observed in 90 days.

Neural Network Modelling of Phenolic Content, Antioxidant Capacity and Microbial Population Dynamics of a Household Scale Spontaneous Fermentation of Carica Papaya Leaf

Neural Network Modelling of Phenolic Content, Antioxidant Capacity and Microbial Population Dynamics of a Household Scale Spontaneous Fermentation of Carica Papaya Leaf

Individual-Based Modeling of Spatial Dynamics of Chemotactic Microbial Populations.

One important direction of synthetic biology is to establish desired spatial structures from microbial populations. Underlying this structural development process are different driving factors, among which bacterial motility and chemotaxis serve as a major force. Here, we present an individual-based, biophysical computational framework for mechanistic and multiscale simulation of the spatiotemporal dynamics of motile and chemotactic microbial populations. The framework integrates cellular movement with spatial population growth, mechanical and chemical cellular interactions, and intracellular molecular kinetics. It is validated by a statistical comparison of single-cell chemotaxis simulations with reported experiments. The framework successfully captures colony range expansion of growing isogenic populations and also reveals chemotaxis-modulated, spatial patterns of a two-species amensal community. Partial differential equation-based models subsequently validate these simulation findings. This study provides a versatile computational tool to uncover the fundamentals of microbial spatial ecology as well as to facilitate the design of synthetic consortia for desired spatial patterns.

Dynamics of microbial populations and metabolites of fermenting saps throughout tapping process of ron and oil palm trees in Côte d'Ivoire.

Palm wine fermentation is a complex microbial process that evolves with tapping times. The dynamics in microbiota and metabolites throughout palm wine tapping days is still not established, which are critical for the distinctive characteristics of palm wine taste and quality, and thus the mastery of the daily quality fluctuation during tapping. We analyzed the changes in microbial community structure by amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region, and metabolite profile changes using mass spectrometry in palm wine collected over 25-30 days tapping of ron (Borassus aethiopum) and oil palms (Elaeis guineensis) from Côte d'Ivoire. The stage-wise collected palm wine samples showed distinct changes in microbial diversity and pH, supporting microbial community dynamics during palm wine tapping. Results highlighted the dominance of Saccharomyces cerevisiae in early stages and the emergence of non-Saccharomyces yeasts, particularly Hanseniaspora spp. in the later stages of oil palm wine tapping, vice versa in the case of ron palm wine tapping, with a unique presence of Saccharomycodes in the later stages (15-30 days). Fructophilic lactic acid bacteria (FLAB), mainly Fructobacillus and Leuconostoc, encountered in both types of palm wine tapping showed a decline at later stages of oil palm wine tapping. In this type of palm wine, acetic acid bacteria with genera Acetobacter and Glucanoacetobacter, by surpassing Lactobacillus in the last stage become dominant, whereas Lactobacillus remained dominant in ron palm wine throughout tapping days. The decline in the relative abundance of gevotroline and essential amino acids during the later stages of palm wine tapping (15-25 days) supports the difference in the health benefits of the palm wine obtained from different days of tapping, indicating that early stages of tapping is more nutritional and healthy than the later stages. The microbial dynamics may be a potential indicator of metabolite changes during palm sap fermentation, thus contributing to establish particular features of palm wines in different stages of tapping. This understanding of microbial ecology and chemical composition changes during palm wine tapping can be used as biomarkers to assess palm wine's quality and help to design an optimum starter culture.

Enhancing resource recovery via cranberry syrup waste at the Wisconsin Rapids WRRF: An experimental and modeling study

The Wisconsin Rapids Wastewater Treatment Plant (WRWWTP) is faced with a more stringent effluent phosphorus requirement that will drive capital investment between 2020 and 2025. The facility will need to achieve a monthly average value of 0.36 mg L−1 of total phosphorus (TP). While the facility has sufficient influent carbon to drive a conventional enhanced biological phosphorus removal (EBPR) configuration, the existing infrastructure makes the addition of influent selector zones cost prohibitive. Underutilized aeration basin capacity was repurposed for testing return activated sludge (RAS) fermentation. The WRWWTP began pilot testing of RAS fermentation in April 2021. The facility moved through a series of operational setpoints to optimize phosphorus removal in a sidestream RAS (SSR) configuration, including RAS diversion, decrease of DO in aeration basins and chemical dosing shutoff. One of the key implementations was the addition of cranberry syrup waste to provide additional carbon for RAS fermentation, converting the process to a SSR plus carbon (SSRC) configuration. By the end of the testing period, effluent total phosphorus was averaging less than 0.4 mg L−1 with no chemical addition. A model was developed in the SUMO platform and was used to capture orthophosphate trends during the testing period. The model investigated microbial population dynamics and found that the operational changes including RAS diversion, chemical dosing shutoff and cranberry syrup waste addition impacted the enrichment of phosphorus accumulating organisms (PAO). After performing a sensitivity analysis on hydrolysis parameters, the predicted hydrolysis rate around 1.8–1.9 mg COD g VSS−1 hr−1 was found to match the batch rate testing data. This is the first study where cranberry syrup waste was used to successfully enhance EBPR performance, resulting in 90% TP removal. While further research is needed regarding the composition of the waste matrix and the microbial community composition, this expands the routes for resource recovery in the field of wastewater treatment.

Application of soil amendments to enhance soil carbon and biological properties in a paddy field under elevated CO2 conditions

ABSTRACT A field experiment was carried out to elucidate the effect of elevated carbon dioxide (eCO2 – 550 ± 30 ppm) on soil enzymes (dehydrogenase, β-glucosidase, fluorescein diacetate, urease, acid and alkaline phosphatase), soil carbon pool (Soil Organic Carbon (SOC), Microbial Biomass Carbon (MBC), oxidizable carbon, humic acid (HA), fulvic acid (FA) fractions), microbial population dynamics (heterotrophs, fungi, actinobacteria, diazotrophs, methanotrophs, and total anaerobes), carbon sequestration and yield in a flooded paddy soil in open top chambers (OTCs) in relation to rhizospheric and bulk soil. Responses of most of the observed parameters to eCO2 with biochar application in rhizosphere soil were significantly higher. The carbon (C) sequestration potential was found higher in the biochar applied plot under eCO2 with 0.59 Mg C sequestered ha−1. The same recorded the highest biomass yield and grain yield which is 12.8 and 30.8% higher than the control. Principal Component Analysis (PCA) recognized soil dehydrogenase, β – glucosidase, SOC, FA, Substrate Induced Respiration (SIR), metabolic quotient (qCO2) and counts of heterotrophs as key drivers of variability. The current study thus provides some dependable biological indicators to assess the paddy ecosystems, vis-à-vis anticipatory climate change.

Absolute quantification and genome-centric analyses elucidate the dynamics of microbial populations in anaerobic digesters

Anaerobic digestion (AD) relies on myriads of functions performed by complex microbial communities in customized settings, thus, a comprehensive investigation on the AD microbiome is central to the fine-tuned control. Most current AD microbiome studies are based on relative abundance, which hinders the interpretation of microbes’ dynamics and inter-sample comparisons. Here, we developed an absolute quantification (AQ) approach that integrated cellular spike-ins with metagenomic sequencing to elucidate microbial community variations and population dynamics in four anaerobic digesters. Using this method, 253 microbes were defined as decaying populations with decay rates ranging from -0.05 to -5.85 d−1, wherein, a population from Flavobacteriaceae family decayed at the highest rates of -3.87 to -5.85 d−1 in four digesters. Meanwhile, 25 microbes demonstrated the growing trend in the AD processes with growth rates ranging from 0.11 to 1.77 d−1, and genome-centric analysis assigned some of the populations to the functional niches of hydrolysis, short-chain fatty acids metabolism, and methane generation. Additionally, we observed that the specific activity of methanogens was lower in the prolonged digestion stage, and redundancy analysis revealed that the feedstock composition and the digestion duration were the two key parameters in governing the AD microbial compositions.

Mapping mineralogical heterogeneities at the nm-scale by scanning electron microscopy in modern Sardinian stromatolites: Deciphering the origin of their laminations

Stromatolites are found throughout the geological record and have received strong attention because they provide precious information about paleoenvironments and microbial paleobiodiversity. However, while this information is interpreted based on our knowledge about modern analogs, the latter remains incomplete. Here, we investigated the environmental and biological information recorded by modern stromatolites in Mari Ermi, a coastal pond in Western Sardinia that experiences severe seasonal evaporation and large salinity variations. For this purpose, we combined a variety of analytical tools, allowing to characterize the mineralogical composition of these stromatolites from the bulk, centimeter-scale to the nanometer-scale and assess the spatial distribution of the mineral phases. In particular, we used quantified x-ray elemental maps provided by energy dispersive x-ray spectrometry analyses coupled with scanning electron microscopy (SEM-EDXS). These maps were processed using an innovative data treatment allowing (i) mineral phase recognition, (ii) assessment of the mineral formula of each phase and (iii) mapping of their spatial distribution with a spatial resolution down to a hundred nanometers. Overall, this proved as an efficient approach to unravel mineralogical heterogeneities and detect informative mineral phases overlooked by bulk analyses. Mari Ermi stromatolites were mostly composed of magnesian calcite with an average Mg/Ca of ~0.1–0.2 as indicated by bulk analyses. However, microscopy observations revealed variable Mg-contents of calcite with a specific distribution, the most Mg-enriched calcites (Mg/Ca up to ~0.5) being systematically distributed around microbial remnants. Moreover, Mari Ermi stromatolites comprised an alternation of Mg-richer and Mg-poorer laminae, which paralleled the varying enrichment in microbial remnants of alternating laminae. The combination of SEM-EDXS, focused ion beam milling and transmission electron microscopy allowed to detect several minor phases, hardly or not detected at all by bulk analyses, such as aragonite, a variety of clay minerals as well as a gypsum-like phase. An additional calcium sulfate phase, best interpreted as S-apatite (cesanite), was detected by SEM-EDXS. Overall, this mineral assemblage and its definite spatial distribution record only discrete stages of the evaporation of Mari Ermi lagoon. Moreover, microorganisms seem to have a major control on Mg substitution in calcite. As a result, the dynamics of microbial populations, influenced by the salinity variations induced by evaporation in the lagoons, generates the formation of laminae in Mari Ermi stromatolites.

Microbial Populations Are Shaped by Dispersal and Recombination in a Low Biomass Subseafloor Habitat.

ABSTRACTThe subseafloor is a vast habitat that supports microorganisms that have a global scale impact on geochemical cycles. Many of the endemic microbial communities inhabiting the subseafloor consist of small populations under growth-limited conditions. For small populations, stochastic evolutionary events can have large impacts on intraspecific population dynamics and allele frequencies. These conditions are fundamentally different from those experienced by most microorganisms in surface environments, and it is unknown how small population sizes and growth-limiting conditions influence evolution and population structure in the subsurface. Using a 2-year, high-resolution environmental time series, we examine the dynamics of microbial populations from cold, oxic crustal fluids collected from the subseafloor site North Pond, located near the mid-Atlantic ridge. Our results reveal rapid shifts in overall abundance, allele frequency, and strain abundance across the time points observed, with evidence for homologous recombination between coexisting lineages. We show that the subseafloor aquifer is a dynamic habitat that hosts microbial metapopulations that disperse frequently through the crustal fluids, enabling gene flow and recombination between microbial populations. The dynamism and stochasticity of microbial population dynamics in North Pond suggest that these forces are important drivers in the evolution of microbial populations in the vast subseafloor habitat.

Mutation in the Two-Component System Regulator YycH Leads to Daptomycin Tolerance in Methicillin-Resistant Staphylococcus aureus upon Evolution with a Population Bottleneck.

ABSTRACTAdaptive laboratory evolution (ALE) is a useful tool to study the evolution of antibiotic tolerance in bacterial populations under diverse environmental conditions. The role of population bottlenecks in the evolution of tolerance has been investigated in Escherichia coli, but not in a more clinically relevant pathogen, methicillin-resistant Staphylococcus aureus (MRSA). In this study, we used ALE to evolve MRSA under repetitive daptomycin treatment and incorporated population bottlenecks following antibiotic exposure. We observed that the populations finally attained a tolerance mutation in the yycH gene after 2 weeks of evolution with population bottlenecks, and additional mutations in yycI and several other genes further increased the tolerance level. The tolerant populations also became resistant to another glycopeptide antibiotic, vancomycin. Through proteomics, we showed that yycH and yycI mutations led to the loss of function of the proteins and downregulated the WalKR two-component system and the downstream players, including the autolysin Atl and amidase Sle1, which are important for cell wall metabolism. Overall, our study offers new insights into the evolution of daptomycin tolerance under population bottlenecking conditions, which are commonly faced by pathogens during infection; the study also identified new mutations conferring daptomycin tolerance and revealed the proteome alterations in the evolved tolerant populations.IMPORTANCE Although population bottlenecks are known to influence the evolutionary dynamics of microbial populations, how such bottlenecks affect the evolution of tolerance to antibiotics in a clinically relevant methicillin-resistant S. aureus (MRSA) pathogen are still unclear. Here, we performed in vitro evolution of MRSA under cyclic daptomycin treatment and applied population bottlenecks following the treatment. We showed that under these experimental conditions, MRSA populations finally attained mutations in yycH, yycI, and several other genes that led to daptomycin tolerance. The discovered yycH and yycI mutations caused early termination of the genes and loss of function of the proteins, and they subsequently downregulated the expression of proteins controlled by the WalKR two-component system, such as Atl and Sle1. In addition, we compared our proteomics data with multiple studies on distinct daptomycin-tolerant MRSA mutants to identify proteins with a consistent expression pattern that could serve as biological markers for daptomycin tolerance in MRSA.

Deciphering the Virus Signal Within the Marine Dissolved Organic Matter Pool.

Viruses are ubiquitously distributed in the marine environment, influencing microbial population dynamics and biogeochemical cycles on a large scale. Due to their small size, they fall into the oceanographic size-class definition of dissolved organic matter (DOM; <0.7 μm). The purpose of our study was to investigate if there is a detectable imprint of virus particles in natural DOM following standard sample preparation and molecular analysis routines using ultrahigh-resolution mass spectrometry (FT-ICR-MS). Therefore, we tested if a molecular signature deriving from virus particles can be detected in the DOM fingerprint of a bacterial culture upon prophage induction and of seawater containing the natural microbial community. Interestingly, the virus-mediated lysate of the infected bacterial culture differed from the cell material of a physically disrupted control culture in its molecular composition. Overall, a small subset of DOM compounds correlated significantly with virus abundances in the bacterial culture setup, accounting for <1% of the detected molecular formulae and <2% of the total signal intensity of the DOM dataset. These were phosphorus- and nitrogen-containing compounds and they were partially also detected in DOM samples from other studies that included high virus abundances. While some of these formulae matched with typical biomolecules that are constituents of viruses, others matched with bacterial cell wall components. Thus, the identified DOM molecular formulae were probably not solely derived from virus particles but were partially also derived from processes such as the virus-mediated bacterial cell lysis. Our results indicate that a virus-derived DOM signature is part of the natural DOM and barely detectable within the analytical window of ultrahigh-resolution mass spectrometry when a high natural background is present.