Structure and dynamics of genome-wide diversity in Prochlorococcus

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2008.Includes bibliographical references.The capability of microbes to thrive in myriad environments has its foundation in the diversity of microbial genomes. Here we explore adaptation and diversification through the lens of the marine cyanobacterium Prochlorococcus, which comprises a group of closely-related ecotypes that together perform most of the primary production in low-nutrient regions of the world oceans. Prochlorococcus was one of the first microbes in which a genomic basis for ecological differentiation was characterized, in the distinction between high- and low-light adapted ecotypes. It is clear, however, that other axes of differentiation are important, including temperature, nutrient availability, and biotic interactions. This thesis seeks to characterize salient aspects of genomic diversity in Prochlorococcus and to advance understanding of the ecological and evolutionary forces that shape this variation. We show that closely related isolates harbor remarkably dissimilar gene complements, and much of this variation is concentrated in specific genome regions, termed islands, that appear to have arisen through phage-mediated gene transfer. Several island-encoded genes likely play important metabolic roles, as inferred from their strong and specific upregulation under stress conditions. A region of the genome involved in phosphate assimilation has highly variable gene content that appears to reflect oceanic phosphate availability. Accordingly, we find extreme differences between strains in the transcriptional response to phosphate starvation. Using metagenomics approaches, we describe high coexisting diversity in natural Prochlorococcus populations. Nevertheless, this diversity is structured: a core genome of universal single-copy genes is augmented by a flexible genome.(cont.) The population genome changes with water depth, reflecting genotypic variation among ecotypes and within the dominant ecotype. Finally, we show that the transcriptomes of wild Prochlorococcus correlate strongly with transcriptomes in culture as measured by microarrays. Genes of unknown function are among the most highly expressed in the wild. Several highly expressed genes show signatures of intragenic recombination, a process that likely influences their diversity and function. Overall, this work demonstrates that environmental factors such as light, temperature, nutrient availability, and interspecies interactions each leave different marks in the genome over different scales of time and space. Understanding microbial evolution requires that we dissect diversity over these multiple scales.by Maureen Lynn Coleman.Ph.D

Diverse and Variable Community Structure of Picophytoplankton across the Laurentian Great Lakes

The Laurentian Great Lakes provide economic support to millions of people, drive biogeochemical cycling, and are an important natural laboratory for characterizing the fundamental components of aquatic ecosystems. Small phytoplankton are important contributors to the food web in much of the Laurentian Great Lakes. Here, for the first time, we reveal and quantify eight phenotypically distinct picophytoplankton populations across the Lakes using a multilaser flow cytometry approach, which distinguishes cells based on their pigment phenotype. The distributions and diversity of picophytoplankton flow populations varied across lakes and depths, with Lake Erie standing out with the highest diversity. By sequencing sorted cells, we identified several distinct lineages of Synechococcales spanning Subclusters 5.2 and 5.3. Distinct genotypic clusters mapped to phenotypically similar flow populations, suggesting that there may not be a clear one-to-one mapping between genotypes and phenotypes. This suggests genome-level differentiation between lakes but some degree of phenotypic convergence in pigment characteristics. Our results demonstrate that ecological selection for locally adapted populations may outpace homogenization by physical transport in this interconnected system. Given the reliance of the Lakes on in situ primary production as a source for organic carbon, this work sets the foundation to test how the community structure of small primary producers corresponds to biogeochemical and food web functions of the Great Lakes and other freshwater systems

Body size shapes inter-specific migratory behaviour: evidence from individual tracks of long-distance migratory shorebirds

Migration is a common phenomenon across many animal taxa. Understanding how migration scales with body size across species is fundamental in the development of migration theory and in making size‐related predictions. Although aerodynamic theory and ecophysiological scaling laws have assisted greatly in generating such predictions, their verifications have been limited by a lack of empirical data across a range of body sizes. The recent development of ultra‐light tracking devices and its rapid application to migration now allows us to put theory to the test. We used tracking data of seven closely related migratory sandpiper species (family Scolopacidae) along the East Asian‐Australasian Flyway to compare their migratory behaviour when migrating towards the breeding grounds as a function of size (50–750 g). We found a marked decline in migration speed (migration distance divided by total migration duration, including time at stopover sites and in flight) with size. Departure date from the non‐breeding (i.e. wintering) ground and arrival date at the breeding ground also scaled negatively with size. Total migration duration, migration distance, total staging duration (the number of days staying at stopover sites plus days preparing, i.e. fuelling, prior to initial migration) and step length (distance covered within one migratory leg) were not significantly related with size. Correction for phylogeny showed consistent results for all variables. Besides improving our fundamental understanding of inter‐specific variation in migration behaviours, the finding of a clear scaling with size in migration speed and migration timing highlight differential size related capabilities and constraints of migrants. Migratory birds, including sandpipers, are declining on a global scale and particularly along the East Asian‐Australasian Flyway. This notion of size‐dependency in migratory traits may have a bearing on their vulnerability to specific environmental disturbances along their flyways

Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater

© 2018, International Society for Microbial Ecology. Bacterial genomes evolve in complex ecosystems and are best understood in this natural context, but replicating such conditions in the lab is challenging. We used transposon sequencing to define the fitness consequences of gene disruption in the bacterium Caulobacter crescentus grown in natural freshwater, compared with axenic growth in common laboratory media. Gene disruptions in amino-acid and nucleotide sugar biosynthesis pathways and in metabolic substrate transport machinery impaired fitness in both lake water and defined minimal medium relative to complex peptone broth. Fitness in lake water was enhanced by insertions in genes required for flagellum biosynthesis and reduced by insertions in genes involved in biosynthesis of the holdfast surface adhesin. We further uncovered numerous hypothetical and uncharacterized genes for which disruption impaired fitness in lake water, defined minimal medium, or both. At the genome scale, the fitness profile of mutants cultivated in lake water was more similar to that in complex peptone broth than in defined minimal medium. Microfiltration of lake water did not significantly affect the terminal cell density or the fitness profile of the transposon mutant pool, suggesting that Caulobacter does not strongly interact with other microbes in this ecosystem on the measured timescale. Fitness of select mutants with defects in cell surface biosynthesis and environmental sensing were significantly more variable across days in lake water than in defined medium, presumably owing to day-to-day heterogeneity in the lake environment. This study reveals genetic interactions between Caulobacter and a natural freshwater environment, and provides a new avenue to study gene function in complex ecosystems

Disturbance regimes predictably alter diversity in an ecologically complex bacterial system

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 7 (2016): e01372-16, doi:10.1128/mBio.01372-16.Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems

Iron and Copper Act Synergistically To Delay Anaerobic Growth of Bacteria

Transition metals are known to cause toxic effects through their interaction with oxygen, but toxicity under anoxic conditions is poorly understood. Here we investigated the effects of iron (Fe) and copper (Cu) on the anaerobic growth and gene expression of the purple phototrophic bacterium Rhodopseudomonas palustris TIE-1. We found that Fe(II) and Cu(II) act synergistically to delay anaerobic growth at environmentally relevant metal concentrations. Cu(I) and Cu(II) had similar effects both alone and in the presence of ascorbate, a Cu(II) reductant, indicating that reduction of Cu(II) to Cu(I) by Fe(II) is not sufficient to explain the growth inhibition. Addition of Cu(II) increased the toxicity of Co(II) and Ni(II); in contrast, Ni(II) toxicity was diminished in the presence of Fe(II). The synergistic anaerobic toxicity of Fe(II) and Cu(II) was also observed for Escherichia coli MG1655, Shewanella oneidensis MR-1, and Rhodobacter capsulatus SB1003. Gene expression analyses for R. palustris identified three regulatory genes that respond to Cu(II) and not to Fe(II): homologs of cueR and cusR, two known proteobacterial copper homeostasis regulators, and csoR, a copper regulator recently identified in Mycobacterium tuberculosis. Two P-type ATPase efflux pumps, along with an F_oF_1 ATP synthase, were also upregulated by Cu(II) but not by Fe(II). An Escherichia coli mutant deficient in copA, cus, and cueO showed a smaller synergistic effect, indicating that iron might interfere with one or more of the copper homeostasis systems. Our results suggest that interactive effects of transition metals on microbial physiology may be widespread under anoxic conditions, although the molecular mechanisms remain to be more fully elucidated

Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche

Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant–microbe interactions (P-value<10^−6); in addition, we observed diverse hpnP types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche

Correlates of Complete Childhood Vaccination in East African Countries.

Despite the benefits of childhood vaccinations, vaccination rates in low-income countries (LICs) vary widely. Increasing coverage of vaccines to 90% in the poorest countries over the next 10 years has been estimated to prevent 426 million cases of illness and avert nearly 6.4 million childhood deaths worldwide. Consequently, we sought to provide a comprehensive examination of contemporary vaccination patterns in East Africa and to identify common and country-specific barriers to complete childhood vaccination. Using data from the Demographic and Health Surveys (DHS) for Burundi, Ethiopia, Kenya, Rwanda, Tanzania, and Uganda, we looked at the prevalence of complete vaccination for polio, measles, Bacillus Calmette-Guérin (BCG) and DTwPHibHep (DTP) as recommended by the WHO among children ages 12 to 23 months. We conducted multivariable logistic regression within each country to estimate associations between complete vaccination status and health care access and sociodemographic variables using backwards stepwise regression. Vaccination varied significantly by country. In all countries, the majority of children received at least one dose of a WHO recommended vaccine; however, in Ethiopia, Tanzania, and Uganda less than 50% of children received a complete schedule of recommended vaccines. Being delivered in a public or private institution compared with being delivered at home was associated with increased odds of complete vaccination status. Sociodemographic covariates were not consistently associated with complete vaccination status across countries. Although no consistent set of predictors accounted for complete vaccination status, we observed differences based on region and the location of delivery. These differences point to the need to examine the historical, political, and economic context of each country in order to maximize vaccination coverage. Vaccination against these childhood diseases is a critical step towards reaching the Millennium Development Goal of reducing under-five mortality by two-thirds by 2015 and thus should be a global priority