Natural Microbial Populations Research Articles

Soil tillage and compost amendment promote bioremediation and biofertility of polluted area

Abstract The risk for human health and environment due to the presence in agricultural soils of organic and inorganic contaminants derived from illegal waste disposal, posed the need to develop a sustainable strategy for the restoration of soils with high agricultural potential. In this study an eco-compatible method as soil tillage and compost amendment was applied in two sites of a National Interest Priority Site of Campania Region (Italy) known as “Terra dei Fuochi”. After one year, the concentration of heavy hydrocarbons (C > 12) significantly reduced in a range from 84 to 95%, probably due to the aeration causing photo-oxidation processes and an improvement of microbial activity able to degrade organic pollutants. Although a reduction trend was observed, the potentially toxic elements (PTEs) concentration in soils was unmodified indicating a potential risk of plant uptake. The high-throughput sequencing approach used to explore the response of native microbial populations following in situ treatments showed that microbiota dynamic was differently affected in the two sites. Therefore, the characteristics of the sites could differently interact with compost determining a different microbial response. Alphaproteobacteria (incidence range of 14–18%), Actinobacteria (incidence range of 10–22%) and Sordariomycetes (incidence range of 23–57%) were the dominant autochthonous populations in all soils indicating their high adaptability to different environments and high resistance to environmental stress as well as their high potential in degradation of organic xenobiotic compounds. The remediation practices based on soil tillage and compost amendment promoted the restoration of the microbial biofertility of soils affected by spotted multi-contamination, to bring them back to agricultural use.

Evaluation of a contact sterilant as a niche-clearing method to enhance the colonization of apple flowers and efficacy of Aureobasidium pullulans in the biological control of fire blight

Due to rapid expansion of organic apple production and issues with antibiotic resistance in conventional production, there is a need for novel strategies to protect orchards from outbreaks of fire blight caused by the bacterial pathogen Erwinia amylovora. The biological control material, Blossom Protect (consisting of two strains of the fungus Aureobasidium pullulans), has shown promising results in some apple growing regions but has shown reduced efficacy in humid apple-growing regions such as the Midwestern and Eastern United States. In an attempt to increase both flower colonization by A. pullulans and disease control efficacy, we applied a contact sterilant to clear the flower niche of native microbial populations 4 hr prior to application of Blossom Protect. Results from four years of field testing showed that application of the contact sterilant resulted in a significant reduction in populations of bacteria, fungi, and native yeast populations; however, all of these microbial populations recovered after 24 h. Examination of fire blight incidence revealed that use of the contact sterilant did not significantly impact disease control. Two applications of Blossom Protect, at 70–80% bloom and full bloom, exhibited the best efficacy in disease control over four years. In addition, we observed marginal differences in the marketability of the final fruit between treatments, each with less than 8% deemed unmarketable due to russet. Our results indicate that niche-clearing of apple flowers did not enhance flower colonization by A. pullulans, nor produce an increase in biological control efficacy. However, our current experimental results (2014–2018) do indicate consistency and an increase in efficacy of Blossom Protect compared to results from previous years.

Dust-Associated Airborne Microbes Affect Primary and Bacterial Production Rates, and Eukaryotes Diversity, in the Northern Red Sea: A Mesocosm Approach

The northern Red Sea (NRS) is a low-nutrient, low-chlorophyll (LNLC) ecosystem with high rates of atmospheric deposition due to its proximity to arid regions. Impacts of atmospheric deposition on LNLC ecosystems have been attributed to the chemical constituents of dust, while overlooking bioaerosols. Understanding how these vast areas of the ocean will respond to future climate and anthropogenic change hinges on the response of microbial communities to these changes. We tested the impacts of bioaerosols on the surface water microbial diversity and the primary and bacterial production rates in the NRS, a system representative of other LNLC oceanic regions, using a mesocosm bioassay experiment. By treating NRS surface seawater with dust, which contained nutrients, metals, and viable organisms, and “UV-treated dust” (which contained only nutrients and metals), we were able to assess the impacts of bioaerosols on local natural microbial populations. Following amendments (20 and 44 h) the incubations treated with “live dust” showed different responses than those with UV-treated dust. After 44 h, primary production was suppressed (as much as 50%), and bacterial production increased (as much as 55%) in the live dust treatments relative to incubations amended with UV-treated dust or the control. The diversity of eukaryotes was lower in treatments with airborne microbes. These results suggest that the airborne microorganisms and viruses alter the surface microbial ecology of the NRS. These results may have implications for the carbon cycle in LNLC ecosystems, which are expanding and are especially important since dust storms are predicted to increase in the future due to desertification and expansion of arid regions.

Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy.

The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.

Spatial Heterogeneity of Vibrio spp. in Sediments of Chinese Marginal Seas.

Vibrio spp. are ubiquitous marine bacteria with high metabolism flexibility and genome plasticity. Previous studies have revealed the dynamics of planktonic vibrios in relation to environmental forces, such as temperature and salinity. However, little is known about Vibrio ecology in benthic environments. Here, we elucidate the abundance, diversity, and spatial distribution of Vibrio spp. in sediments of the Chinese marginal seas, with a wide spatial range from north to south covering the Yellow Sea (YS), East China Sea (ECS), and South China Sea (SCS). Quantitative analysis showed that Vibrio spp. were most abundant in the SCS (∼9.04 × 105 copies/g) compared to the YS (∼1.00 × 105 copies/g) and ECS (∼8.86 × 105 copies/g). Vibrio community compositions derived from Illumina sequencing of Vibrio-specific 16S rRNA genes varied significantly between sampling areas, which was reflected by a strong distance-decay pattern. The spatial distribution of Vibrio was governed by a joint effect of spatial and environmental factors (especially temperature, salinity, and SiO32-), and their respective pure effects explained only a small fraction of the community variation. Moreover, we identified the most prominent operational taxonomic units (OTUs) that were partitioned in these sea areas. Whereas Vibrionaceae OTU20 and Photobacterium lipolyticum were prevalent in the YS, Vibrio gigantis and Photobacterium piscicola, and P. piscicola, Photobacterium lutimaris, and Photobacterium alginatilyticum were prevalent in the ECS and SCS, respectively. Our study demonstrated clear spatial heterogeneity of Vibrio spp. in sediments of the Chinese marginal seas, laying a foundation for fully understanding the marine Vibrio ecology and the ecological roles of the species.IMPORTANCEVibrio is an important component of natural marine microbial populations in terms of pathogenicity and roles in carbon cycling. Compared to the marine pelagic environment, our knowledge of the diversity and distribution pattern of Vibrio spp. in sediment is limited. Here, we show higher Vibrio abundance in Chinese marginal seas than in other studied sediments. There was a clear spatial differentiation of Vibrio abundance and community composition in different sea areas. The benthic Vibrio community displayed a strong distance-decay pattern across a wide spatial range, which was formed under the combined effects of spatial and environmental factors. These results provide deep insights into the ecological dynamics of Vibrio and its environmental controls, facilitating a more comprehensive understanding of the marine Vibrio ecology.

Chemical mixtures and fluorescence in situ hybridization analysis of natural microbial community in the Tiber river

The Water Framework Directive (WFD) regulates freshwater and coastal water quality assessment in Europe. Chemical and ecological water quality status is based on measurements of chemical pollutants in water and biota together with other indicators such as temperature, nutrients, species compositions (phytoplankton, microalgae, benthos and fish) and hydromorphological conditions. However, in the current strategy a link between the chemical and the ecological status is missing. In the present WFD, no microbiological indicators are foreseen for integrating the different anthropogenic pressures, including mixtures of chemicals, nutrients and temperature changes, to provide a holistic view of the freshwater ecosystem water quality. The main aim of this work was to evaluate if natural microbial populations can be valuable indicators of multiple stressors (e.g. chemical pollutants, temperature, nutrients etc.) to guide preventive and remediation actions by water authorities. A preliminary survey was conducted to identify four sites reflecting a contamination gradient from the source to the mouth of a river suitable to the objectives of the European Marie Curie project, MicroCoKit. The River Tiber (Italy) was selected as a pilot case study to investigate the correlation between bacteria taxa and the chemical status of the river. The main physicochemical parameters, inorganic elements, organic pollutants and natural microbial community composition were assessed at four selected sites corresponding to pristine, agricultural, industrial and urban areas for three consecutive years.The overall chemical results indicated a correspondence between different groups of contaminants and the main contamination sources at the selected sampling points. Phylogenetic analysis of the microbial community analyzed by Fluorescence In Situ Hybridization method (FISH) revealed differences among the four sampling sites which could reflect an adaptive bacterial response to the different anthropogenic pressures.

Systematic application of slightly acidic electrolyzed water (SAEW) for natural microbial reduction of buckwheat sprouts

The systematic application of slightly acidic electrolyzed water (SAEW) for natural microbial reduction of buckwheat sprouts were investigated including seed-dipping, germination and sprouts-washing in the present study. The results show that all the three SAEW treatments with similar pH value (approximately 6.0) used in the study resulted in the reduction of the natural moulds and yeasts and total bacteria counts in buckwheat seeds and harvested sprouts in spite of their different available chlorine concentration (ACC, approximately 10, 28 and 92 mg/L respectively), which was equivalent or high disinfectant efficacy for buckwheat seeds and sprouts compared to NaClO solutions and acidic electrolyzed water (AEW). Moreover, SAEW treatments could control the growth of natural microbial populations during germination and decrease the E. coli O78 and L. monocytogenes counts on 8-day-old sprouts by 1.10–2.74 and 1.85–2.46 log10 CFU/g, respectively. However, too high ACC (91.96 mg/L) in SAEW had adverse effect on the sprouts length. SAEW with appropriate ACC (10–28 mg/L) could be considered in the whole process of sprouts industry because of its strong disinfection efficacy and less adverse effect on the sprouts growth than NaClO solutions and AEW.

Probing the ecological and evolutionary history of a thermophilic cyanobacterial population via statistical properties of its microdiversity.

Despite extensive DNA sequencing data derived from natural microbial communities, it remains a major challenge to identify the key evolutionary and ecological forces that shape microbial populations. We have focused on the extensive microdiversity of the cyanobacterium Synechococcus sp., which is a dominant member of the dense phototrophic biofilms in the hot springs of Yellowstone National Park. From deep amplicon sequencing of many loci and statistical analyses of these data, we showed previously that the population has undergone an unexpectedly high degree of homologous recombination, unlinking synonymous SNP-pair correlations even on intragenic length scales. Here, we analyze the genic amino acid diversity, which provides new evidence of selection and insights into the evolutionary history of the population. Surprisingly, some features of the data, including the spectrum of distances between genic-alleles, appear consistent with primarily asexual neutral drift. Yet the non-synonymous site frequency spectrum has too large an excess of low-frequency polymorphisms to result from negative selection on deleterious mutations given the distribution of coalescent times that we infer. And our previous analyses showed that the population is not asexual. Taken together, these apparently contradictory data suggest that selection, epistasis, and hitchhiking all play essential roles in generating and stabilizing the diversity. We discuss these as well as potential roles of ecological niches at genomic and genic levels. From quantitative properties of the diversity and comparative genomic data, we infer aspects of the history and inter-spring dispersal of the meta-population since it was established in the Yellowstone Caldera. Our investigations illustrate the need for combining multiple types of sequencing data and quantitative statistical analyses to develop an understanding of microdiversity in natural microbial populations.

Microbial Strategies for Cellulase and Xylanase Production through Solid-State Fermentation of Digestate from Biowaste

Solid-state fermentation (SSF) is a promising technology for producing bioproducts from organic wastes. The objective of this study is to assess the feasibility of using digestate as substrate to produce hydrolytic enzymes, mainly cellulase and xylanase, by exploring three different inoculation strategies: (i) SSF with autochthonous microbiota; (ii) non-sterile SSF inoculated with Trichoderma reesei and (iii) sequential batch operation to select a specialized inoculum, testing two different residence times. Native microbial population did not show a significant cellulase production, suggesting the need for a specialized inoculum. The inoculation of Trichoderma reesei did not improve the enzymatic activity. On the other hand, inconsistent operation was achieved during sequential batch reactor in terms of specific oxygen uptake rate, temperature and enzymatic activity profile. Low cellulase and xylanase activities were attained and the main hypotheses are non-appropriate biomass selection and some degree of hydrolysis by non-targeted proteases produced during fermentation.

Natural attenuation, biostimulation and bioaugmentation of landfill leachate management

Landfills used for solid waste management will lead to leachate production. Proper leachate management is highly essential to be paid attention to protect the environment and living organisms’ health and safety. In this study, the remedial strategies used for leachate management were natural attenuation, biostimulation and bioaugmentation. All treatment samples were treated via 42-days combined anaerobic-aerobic treatment and the treatment efficiency was studied by measuring the removal rate of COD and ammonia nitrogen. In this study, all remedial strategies showed different degrees of contaminants removal. Lowest contaminants removal rate was achieved via bioaugmentation of B. panacihumi strain ZB1, which were 39.4% of COD and 37.6% of ammonia nitrogen removed from the leachate sample. Higher contaminants removal rate was achieved via natural attenuation and biostimulation. Native microbial population was able to remove 41% of COD and 59% of ammonia nitrogen from the leachate sample. The removal efficiency could be further improved via biostimulation to trigger microbial growth and decontamination rate. Through biostimulation, 58% of COD and 51.8% of ammonia nitrogen were removed from the leachate sample. In conclusion, natural attenuation and biostimulation should be the main choice for leachate management to avoid any unexpected impacts due to introduction of exogenous species.

Multilevel characterization of marine microbial biodegradation potentiality by means of flow-modulated comprehensive two-dimensional gas chromatography combined with a triple quadrupole mass spectrometer

The present research is focused on the use of a triple quadrupole mass spectrometer (QqQ MS) coupled with flow modulated comprehensive two-dimensional gas chromatography (FM GC × GC) for a multilevel elucidation of biodegradation potentiality of natural marine microbial populations during a bioremediation (biostimulation) treatment. The crude oil used for the evaluation of the bioremediation process, namely Dansk Blend Pier E1, represents a very complex sample. Hence, in order to understand the metabolic activity of microbial populations during the bioremediation process, a GC × GC system was used. The high separation power has allowed a detailed characterization of the different chemical families; moreover, thanks to the high acquisition frequency of the QqQ MS spectrometer, both full scan and multiple reaction monitoring (MRM) data were acquired in the same run. By using this system, both qualitative analysis of untargeted hydrocarbons mixture (crude oil) and qualitative analysis of biomarker compounds, present in low amount and often hindered under the bulk of the sample (i.e. adamantanes, diamantanes, steranes and hopanes), were performed simultaneously.The bioremediation capability of biostimulated bacteria was evaluated at four (T4), eight (T8) and fourteen (T14) days. Progressive degradation of linear, branched, and aromatic hydrocarbons, adamantanes, and diamantanes has been showed, whereas, results underline the lack of any kind of activity against steranes, and hopanes.

Speciation dynamics of oxyanion contaminants (As, Sb, Cr) in argillaceous suspensions during oxic-anoxic cycles

Argillaceous geological formations are considered promising repositories for waste containing inorganic contaminants. However, the sequestration capacity of an argillaceous natural barrier may change as a result of dynamic environmental conditions, in particular changes in redox state. Here, we imposed redox cycles to argillaceous suspensions amended with a mixture of the inorganic contaminants As(V), Sb(V), Cr(VI), by alternating 7-day cycles of sparging with either oxic or anoxic gas mixtures. During the redox cycles, we assessed the relative importance of different contaminant sequestration mechanisms under sterile and non-sterile conditions. The non-sterile experiments were carried out 1) with the argillaceous material as is, that is, containing the native microbial population, 2) with the addition of ethanol as a source of labile organic carbon, and 3) with the addition of both ethanol and a soil microbial inoculum. In order to capture the observed solid-solution partitioning trends, a series of mixed thermodynamic-kinetic models representing the dynamic conditions in the experiments were developed using PHREEQC. Parameter values for processes such as adsorption, which occurred in all experiments, were kept constant across all the simulations. Additional formulations were introduced as needed to account for the microbial detoxification and respiration of the contaminants in the increasing complexity experiments. Abiotic adsorption of As and abiotic reductive precipitation of Cr dominated sequestration of these two contaminants under all experimental conditions, whereas the presence of microorganisms was essential to decrease the aqueous Sb concentration. Once reduced, As(III), Sb(III), and Cr(III) were not re-oxidized upon exposure to dissolved O2 in any of the experiments. Neither the mineralogy nor the native microbiota catalysed contaminant oxidation processes. Thus, kinetically, the reduction of As(V), Sb(V), and Cr(VI) was irreversible over the experimental duration (49 days). The capacity of the argillaceous matrix to reduce and sequester the aqueous contaminants, without subsequent remobilization to the aqueous phase during the oxic periods, supports the use of argillaceous barriers for geologic waste storage.

Developing methanogenic microbial consortia from diverse coal sources and environments

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations under initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. To evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH4 and CO2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft3/ton or 4.8 scm3/g) for methane and 176,370 ppm (31 sft3/ton or 0.9 scm3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor - were used to identify trends and levels of significance or impact of the consortia enrichment. It was demonstrated that microbial communities from coal and lake sediments can be enriched and adapted to effectively generate methane under initial atmospheric exposure. The development and enrichment of these methanogenic consortia is described.

<b>Population density of <i>Beauveria bassiana</i> in soil under the action of fungicides and native microbial populations

This study investigated whether populations of naturally-occurring soil bacteria, fungi and actinomycetes influence the effect of fungicides on the survival and growth of Beauveria bassiana . The toxicity of methyl thiophanate, pyraclostrobin, mancozeb and copper oxychloride at the recommended doses was analyzed in culture medium and in soil inoculated with fungus at various time points after addition of fungicides. All fungicides completely inhibited the growth and sporulation of B. bassiana in the culture medium. The fungicides were less toxic in soil, emphasizing the action of the microbial populations, which interfered with the toxic effects of these products to the fungus. Actinomycetes had the greatest influence on the entomopathogen, inhibiting it or degrading the fungicides to contribute to the survival and growth of B. bassiana in soil. Native populations of fungi and bacteria had a smaller influence on the population density of B. bassiana and the action of fungicides towards entomopathogen. The toxic effect of the fungicides was greater when added to the soil one hour before or after inoculation than at 48h after inoculation.

The anaerobic corrosion of carbon steel in compacted bentonite exposed to natural Opalinus Clay porewater containing native microbial populations

ABSTRACTA long-term in situ corrosion experiment is ongoing in the Mont Terri Underground Research Laboratory in Switzerland to (i) measure the in situ corrosion behaviour of carbon steel in compacted bentonite under simulated repository conditions, (ii) study the effect of the bentonite buffer density on microbial activity and microbially influenced corrosion and (iii) study the effect of welding on the corrosion rate. Carbon steel corrosion coupons, with and without welds, were surrounded by compacted bentonite with a range of dry densities and mounted in modules allowing free exchange with the local anoxic groundwater. After about 20 months of exposure, corrosion coupons and bentonite were sampled. A complex corrosion product was identified, consisting predominantly of magnetite. The bentonite adjacent to the metal was finer grained, more dispersed and enriched in iron. Aerobic, anaerobic and sulphate-reducing bacteria were identified both in the porewater surrounding the modules and in the bentonite.This paper is part of a supplement on the 6th International Workshop on Long-Term Prediction of Corrosion Damage in Nuclear Waste Systems.

The underlying process of early ecological and genetic differentiation in a facultative mutualistic Sinorhizobium meliloti population

The question of how genotypic and ecological units arise and spread in natural microbial populations remains controversial in the field of evolutionary biology. Here, we investigated the early stages of ecological and genetic differentiation in a highly clonal sympatric Sinorhizobium meliloti population. Whole-genome sequencing revealed that a large DNA region of the symbiotic plasmid pSymB was replaced in some isolates with a similar synteny block carrying densely clustered SNPs and displaying gene acquisition and loss. Two different versions of this genomic island of differentiation (GID) generated by multiple genetic exchanges over time appear to have arisen recently, through recombination in a particular clade within this population. In addition, these isolates display resistance to phages from the same geographic region, probably due to the modification of surface components by the acquired genes. Our results suggest that an underlying process of early ecological and genetic differentiation in S. meliloti is primarily triggered by acquisition of genes that confer resistance to soil phages within particular large genomic DNA regions prone to recombination.

Dual effects of acidic electrolyzed water treatments on the microbial reduction and control of enzymatic browning for fresh‐cut lotus root

AbstractThe disinfection efficacy of acidic electrolyzed water including slightly acidic electrolyzed water (SAEW) and strongly acidic electrolyzed water (AEW) on the fresh‐cut lotus roots and their effects on the appearance quality of fresh‐cut lotus root were evaluated in the present paper. The results showed that SAEW treatment could reduce the natural microbial flora populations as well as the inoculated populations of fresh‐cut lotus roots significantly. Also, our results obtained from the present study suggested that SAEW treatment could maintain the appearance quality and market values more effectively than acidic electrolyzed water (AEW) treatment. Considering that SAEW is environmentally friendly and has dual efficacy of disinfection and browning‐prevention, it may be a better choice in the processing of fresh‐cut lotus roots. The results implied that SAEW could inhibit the polyphenol oxidase (PPO) activity, thus keep the overall visual quality. However, how SAEW treatments affect PPO activity of the fresh‐cut lotus roots is still unknown and further research is needed.Practical applicationsHow to prevent the quality deterioration of fresh‐cut lotus root, which limited its safety and processing, had become a serious problem. In the past, the strong disinfection efficacy of acidic electrolyzed water (AEW) and its application in food industry including the disinfection of fruits and vegetables were widely reported. Due to its neutral pH and lower available chlorine concentration (10–30 mg/L), slightly acidic electrolyzed water (SAEW) showed a promising prospect in the agriculture and food industry. In the present study, the disinfection efficacy of SAEW on the fresh‐cut lotus roots was investigated. Moreover, the effect of SAEW treatment on the appearance quality of fresh‐cut lotus root was evaluated. This study confirmed that SAEW treatment might have a high potential for practical use in the processing fresh‐cut lotus roots processing.

Correlated Mutations and Homologous Recombination Within Bacterial Populations.

Inferring the rate of homologous recombination within a bacterial population remains a key challenge in quantifying the basic parameters of bacterial evolution. Due to the high sequence similarity within a clonal population, and unique aspects of bacterial DNA transfer processes, detecting recombination events based on phylogenetic reconstruction is often difficult, and estimating recombination rates using coalescent model-based methods is computationally expensive, and often infeasible for large sequencing data sets. Here, we present an efficient solution by introducing a set of mutational correlation functions computed using pairwise sequence comparison, which characterize various facets of bacterial recombination. We provide analytical expressions for these functions, which precisely recapitulate simulation results of neutral and adapting populations under different coalescent models. We used these to fit correlation functions measured at synonymous substitutions using whole-genome data on Escherichia coli and Streptococcus pneumoniae populations. We calculated and corrected for the effect of sample selection bias, i.e., the uneven sampling of individuals from natural microbial populations that exists in most datasets. Our method is fast and efficient, and does not employ phylogenetic inference or other computationally intensive numerics. By simply fitting analytical forms to measurements from sequence data, we show that recombination rates can be inferred, and the relative ages of different samples can be estimated. Our approach, which is based on population genetic modeling, is broadly applicable to a wide variety of data, and its computational efficiency makes it particularly attractive for use in the analysis of large sequencing datasets.

Evidence for microbial local adaptation in nature.

Local adaptation is an outcome of divergent selection on microbial populations and has been linked to the immense genetic diversity of microbes observed in nature. Because it is difficult to study microbes in their natural habitats, most tests of microbial local adaptation have been performed in model laboratory systems; as a result, microbiologists have limited understanding of local adaptation among natural microbial populations. In this review, we summarize the evidence for microbial local adaptation in nature. Local adaptation has been most frequently studied, and most frequently found, in host-pathogen systems. We argue that more research is needed to understand the prevalence of local adaptation in free-living microbial populations. However, researchers will need to overcome a variety of logistical and conceptual challenges when studying natural microbial local adaptation, including a lack of solid understanding of many microbes' natural histories. We propose strategies to facilitate future natural history research on divergent selection. We also summarize laboratory experimental work investigating the ecological and evolutionary processes leading to local adaptation. Microbiologists' ongoing challenge is to integrate the valuable knowledge gained from laboratory experiments into well-designed field experiments. Such integration will help us understand the prevalence of, and circumstances leading to, local adaptation among microorganisms.

Evolution of Mutation Rates in Rapidly Adapting Asexual Populations.

Mutator and antimutator alleles often arise and spread in both natural microbial populations and laboratory evolution experiments. The evolutionary dynamics of these mutation rate modifiers are determined by indirect selection on linked beneficial and deleterious mutations. These indirect selection pressures have been the focus of much earlier theoretical and empirical work, but we still have a limited analytical understanding of how the interplay between hitchhiking and deleterious load influences the fates of modifier alleles. Our understanding is particularly limited when clonal interference is common, which is the regime of primary interest in laboratory microbial evolution experiments. Here, we calculate the fixation probability of a mutator or antimutator allele in a rapidly adapting asexual population, and we show how this quantity depends on the population size, the beneficial and deleterious mutation rates, and the strength of a typical driver mutation. In the absence of deleterious mutations, we find that clonal interference enhances the fixation probability of mutators, even as they provide a diminishing benefit to the overall rate of adaptation. When deleterious mutations are included, natural selection pushes the population toward a stable mutation rate that can be suboptimal for the adaptation of the population as a whole. The approach to this stable mutation rate is not necessarily monotonic: even in the absence of epistasis, selection can favor mutator and antimutator alleles that "overshoot" the stable mutation rate by substantial amounts.