scholarly journals Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Eric W. Getz ◽  
Saima Sultana Tithi ◽  
Liqing Zhang ◽  
Frank O. Aylward
Keyword(s):  
Nutrient Dynamics ◽  
Parallel Evolution ◽  
Biogeochemical Cycles ◽  
Microbial Evolution ◽  
Global Ocean ◽  
Microbial Life ◽  
Respiratory Complex ◽  
Evolutionary Forces ◽  
Cellular Bioenergetics ◽  
Key Features

ABSTRACTDiverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track the genome evolution of the globally abundant marine bacterial phylumMarinimicrobiaacross its diversification into modern marine environments and demonstrate that extant lineages are partitioned between epipelagic and mesopelagic habitats. Moreover, we show that these habitat preferences are associated with fundamental differences in genomic organization, cellular bioenergetics, and metabolic modalities. Multiple lineages present in epipelagic niches independently acquired genes necessary for phototrophy and environmental stress mitigation, and their genomes convergently evolved key features associated with genome streamlining. In contrast, lineages residing in mesopelagic waters independently acquired nitrate respiratory machinery and a variety of cytochromes, consistent with the use of alternative terminal electron acceptors in oxygen minimum zones (OMZs). Further, while epipelagic clades have retained an ancestral Na+-pumping respiratory complex, mesopelagic lineages have largely replaced this complex with canonical H+-pumping respiratory complex I, potentially due to the increased efficiency of the latter together with the presence of the more energy-limiting environments deep in the ocean’s interior. These parallel evolutionary trends indicate that key features of genomic streamlining and cellular bioenergetics have occurred repeatedly and congruently in disparate clades and underscore the importance of environmental conditions and nutrient dynamics in driving the evolution of diverse bacterioplankton lineages in similar ways throughout the global ocean.IMPORTANCEUnderstanding long-term patterns of microbial evolution is critical to advancing our knowledge of past and present role microbial life in driving global biogeochemical cycles. Historically, it has been challenging to study the evolution of environmental microbes due to difficulties in obtaining genome sequences from lineages that could not be cultivated, but recent advances in metagenomics and single-cell genomics have begun to obviate many of these hurdles. Here we present an evolutionary genomic analysis of theMarinimicrobia, a diverse bacterial group that is abundant in the global ocean. We demonstrate that distantly relatedMarinimicrobiaspecies that reside in similar habitats have converged to assume similar genome architectures and cellular bioenergetics, suggesting that common factors shape the evolution of a broad array of marine lineages. These findings broaden our understanding of the evolutionary forces that have given rise to microbial life in the contemporary ocean.

scholarly journals Parallel Evolution of Key Genomic Features and Cellular Bioenergetics Across the Marine Radiation of a Bacterial Phylum

2018 ◽  
Author(s):  
Eric W. Getz ◽  
Saima Sultana Tithi ◽  
Liqing Zhang ◽  
Frank O. Aylward
Keyword(s):  
Nutrient Dynamics ◽  
Genomic Organization ◽  
Parallel Evolution ◽  
Global Ocean ◽  
Oxygen Minimum Zones ◽  
Respiratory Complex ◽  
Respiratory Complex I ◽  
Cellular Bioenergetics ◽  
Key Features ◽  
Oxygen Minimum

AbstractDiverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track the genome evolution of the globally-abundant marine bacterial phylum Marinimicrobia across its diversification into modern marine environments and demonstrate that extant lineages have repeatedly switched between epipelagic and mesopelagic habitats. Moreover, we show that these habitat transitions have been accompanied by repeated and fundamental shifts in genomic organization, cellular bioenergetics, and metabolic modalities. Lineages present in epipelagic niches independently acquired genes necessary for phototrophy and environmental stress mitigation, and their genomes convergently evolved key features associated with genome streamlining. Conversely, lineages residing in mesopelagic waters independently acquired nitrate respiratory machinery and a variety of cytochromes, consistent with the use of alternative terminal electron acceptors in oxygen minimum zones (OMZs). Further, while surface water clades have retained an ancestral Na+-pumping respiratory complex, deep water lineages have largely replaced this complex with a canonical H+-pumping respiratory complex I, potentially due to the increased efficiency of the latter together with more energy-limiting environments deep in the ocean’s interior. These parallel evolutionary trends across disparate clades suggest that the evolution of key features of genomic organization and cellular bioenergetics in abundant marine lineages may in some ways be predictable and driven largely by environmental conditions and nutrient dynamics.

The Role of Restricted Basins in Global Biogeochemical Cycles

2020 ◽  
Author(s):  
Alexandra Turchyn
Keyword(s):  
Isotopic Composition ◽  
Chemical Weathering ◽  
Biogeochemical Cycles ◽  
Biogeochemical Cycle ◽  
Global Ocean ◽  
Sulfur Isotopic Composition ◽  
Sediment Biogeochemistry ◽  
Shelf Slope ◽  
Salt Deposits ◽  
Global Biogeochemical Cycles

<p>The formation of restricted basins isolates seawater from the global ocean and allows the formation of salt deposits, often because restricted basins can have minor connectivity to the global ocean and thus can fill and evaporate many times over. The formation of salts removes ions from the global ocean, potentially decreasing their concentration elsewhere and leading to an alteration of their biogeochemical cycle.  The subsequent exposure and chemical weathering of these salt deposits changes the source of these elements back into the global ocean and can influence their biogeochemical cycles for a long time after the formation of the restricted basin.   Sediment biogeochemistry in restricted basins also differs from most global continental shelf, slope, and deep-sea sediments. The formation of sedimentary minerals and their subsequent diagenesis means that the amount and isotopic composition of deposited minerals in restricted basins can differ greatly from those in the global ocean. In this talk I am going to explore how the formation of restricted basins, including epicontinental seas and isolated seas, has influenced the biogeochemical cycle of carbon and sulfur over the course of the last 65 million years.  I am going to use a combination of new measurements on the carbon and sulfur isotopic composition of the ocean over this time to explore how different types of restricted basins influence global biogeochemical cycles in the rest of the ocean. I will argue that the formation of restricted basins has been important in driving changes in the carbon and sulfur isotopic composition of the ocean over time, linking changes in ocean chemistry to tectonics.</p>

scholarly journals Adaptation of Escherichia coli to Long-Term Serial Passage in Complex Medium: Evidence of Parallel Evolution

mSystems ◽  
2017 ◽  
Vol 2 (2) ◽  
Author(s):  
Karin E. Kram ◽  
Christopher Geiger ◽  
Wazim Mohammed Ismail ◽  
Heewook Lee ◽  
Haixu Tang ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Parallel Evolution ◽  
Microbial Evolution ◽  
Complex Medium ◽  
Evolutionary Mechanisms ◽  
Adaptive Mutations ◽  
Experimental Systems ◽  
Experimental Laboratory ◽  
Five Phases

ABSTRACT With a growing body of work directed toward understanding the mechanisms of evolution using experimental systems, it is crucial to decipher what effects the experimental setup has on the outcome. If the goal of experimental laboratory evolution is to elucidate underlying evolutionary mechanisms and trends, these must be demonstrated in a variety of systems and environments. Here, we perform experimental evolution in a complex medium allowing the cells to transition through all five phases of growth, including death phase and long-term stationary phase. We show that the swiftness of selection and the specific targets of adaptive evolution are different in this system compared to others. We also observe parallel evolution where different mutations in the same genes are under positive natural selection. Together, these data show that while some outcomes of microbial evolution experiments may be generalizable, many outcomes will be environment or system specific. Experimental evolution of bacterial populations in the laboratory has led to identification of several themes, including parallel evolution of populations adapting to carbon starvation, heat stress, and pH stress. However, most of these experiments study growth in defined and/or constant environments. We hypothesized that while there would likely continue to be parallelism in more complex and changing environments, there would also be more variation in what types of mutations would benefit the cells. In order to test our hypothesis, we serially passaged Escherichia coli in a complex medium (Luria-Bertani broth) throughout the five phases of bacterial growth. This passaging scheme allowed cells to experience a wide variety of stresses, including nutrient limitation, oxidative stress, and pH variation, and therefore allowed them to adapt to several conditions. After every ~30 generations of growth, for a total of ~300 generations, we compared both the growth phenotypes and genotypes of aged populations to the parent population. After as few as 30 generations, populations exhibit changes in growth phenotype and accumulate potentially adaptive mutations. There were many genes with mutant alleles in different populations, indicating potential parallel evolution. We examined 8 of these alleles by constructing the point mutations in the parental genetic background and competed those cells with the parent population; five of these alleles were found to be adaptive. The variety and swiftness of adaptive mutations arising in the populations indicate that the cells are adapting to a complex set of stresses, while the parallel nature of several of the mutations indicates that this behavior may be generalized to bacterial evolution. IMPORTANCE With a growing body of work directed toward understanding the mechanisms of evolution using experimental systems, it is crucial to decipher what effects the experimental setup has on the outcome. If the goal of experimental laboratory evolution is to elucidate underlying evolutionary mechanisms and trends, these must be demonstrated in a variety of systems and environments. Here, we perform experimental evolution in a complex medium allowing the cells to transition through all five phases of growth, including death phase and long-term stationary phase. We show that the swiftness of selection and the specific targets of adaptive evolution are different in this system compared to others. We also observe parallel evolution where different mutations in the same genes are under positive natural selection. Together, these data show that while some outcomes of microbial evolution experiments may be generalizable, many outcomes will be environment or system specific.

scholarly journals From extreme environments to human pathogens: an evolutionary journey

2017 ◽  
Vol 39 (6) ◽  
pp. 4-9
Author(s):  
Donato Giovannelli ◽  
Costantino Vetriani
Keyword(s):  
Unsolved Problem ◽  
Extreme Environments ◽  
Microbial Metabolism ◽  
Microbial Evolution ◽  
Human Pathogens ◽  
Environmental Niche ◽  
Microbial Life ◽  
Evolution Of Life ◽  
History Of ◽  
Anoxic Environment

The history of our planet is underpinned by roughly 4 billion years of microbial evolution. From its emergence in a (probably) hot and anoxic environment, microbial life has evolved to colonize every available niche on our planet, including the inside and outside of other organisms. Yet, the emergence and evolution of microbial metabolism remains a major unsolved problem. How have microbes adapted to colonize every available environmental niche, including other organisms? How did they evolve to colonize mammals and our human ancestors? Answers to these questions will allow us to understand the emergence and evolution of life on our planet, inform the search for life elsewhere and, in the making, reveal important insight that will help us fight infections.

scholarly journals Illuminating the Virosphere Through Global Metagenomics

2021 ◽  
Vol 4 (1) ◽  
pp. 369-391
Author(s):  
Lee Call ◽  
Stephen Nayfach ◽  
Nikos C. Kyrpides
Keyword(s):  
Biogeochemical Cycles ◽  
Microbial Evolution ◽  
Biological Entity ◽  
Careful Study ◽  
Viral Sequence ◽  
Biomedical Sciences ◽  
Modern Biology ◽  
Domains Of Life ◽  
Viral Sequences

Viruses are the most abundant biological entity on Earth, infect cellular organisms from all domains of life, and are central players in the global biosphere. Over the last century, the discovery and characterization of viruses have progressed steadily alongside much of modern biology. In terms of outright numbers of novel viruses discovered, however, the last few years have been by far the most transformative for the field. Advances in methods for identifying viral sequences in genomic and metagenomic datasets, coupled to the exponential growth of environmental sequencing, have greatly expanded the catalog of known viruses and fueled the tremendous growth of viral sequence databases. Development and implementation of new standards, along with careful study of the newly discovered viruses, have transformed and will continue to transform our understanding of microbial evolution, ecology, and biogeochemical cycles, leading to new biotechnological innovations across many diverse fields, including environmental, agricultural, and biomedical sciences.

scholarly journals Spatial structure affects evolutionary dynamics and drives genomic diversity in experimental populations of Pseudomonas fluorescens

2021 ◽  
Author(s):  
Susan F Bailey ◽  
Andrew Trudeau ◽  
Katherine Tulowiecki ◽  
Morgan McGrath ◽  
Aria Belle ◽  
...  
Keyword(s):  
Spatial Structure ◽  
Pseudomonas Fluorescens ◽  
Evolutionary Dynamics ◽  
Parallel Evolution ◽  
Theoretical Models ◽  
Microbial Evolution ◽  
Genomic Diversity ◽  
Genomic Changes ◽  
Evolution Experiment ◽  
Semi Solid

Most populations live in spatially structured environments and that structure has the potential to impact the evolutionary dynamics in a number of important ways. Theoretical models tracking evolution in structured environments using a range of different approaches, suggest that local interactions and spatial heterogeneity can increase the adaptive benefits of motility, impact both the rate and extent of adaptation, and increase the probability of parallel evolution. We test these general predictions in a microbial evolution experiment tracking phenotypic and genomic changes in replicate populations of Pseudomonas fluorescens evolved in both well-mixed and spatially-structured environments, where spatial structure was generated through the addition of semi-solid agar. In contrast to the well-mixed environment, populations evolved in the spatially-structured environment adapted more slowly, retained the ability to disperse more rapidly, and had a greater putatively neutral population genomic diversity. The degree of parallel evolution measured at the gene-level, did not differ across these two types of experimental environments, perhaps because the populations had not evolved for long enough to near their fitness optima. These results confirm important general impacts of spatial structure on evolutionary dynamics at both the phenotypic and genomic level.

scholarly journals Re-Thinking the Roles of Pathogens and Mutualists: Exploring the Continuum of Symbiosis in the Context of Microbial Ecology and Evolution

2022 ◽  
Author(s):  
Ashley Stengel ◽  
Rhae Drijber ◽  
Erin Carr ◽  
Thais Egreja ◽  
Edward Hillman ◽  
...  
Keyword(s):  
Ecological Factors ◽  
Plant Host ◽  
Holistic View ◽  
Microbial Life ◽  
Evolutionary Forces ◽  
Dynamic Relationship ◽  
Research Activities ◽  
Host Microbe Interactions ◽  
Static Conditions ◽  
The Continuum

Systems of classification are important for guiding research activities and providing a common platform for discussion and investigation. One such system is assigning microbial taxa to the roles of mutualists and pathogens. Yet, there are often challenges and even inconsistencies in reports of research findings when microbial taxa display behaviors outside of these two static conditions (e.g. commensal). Over the last two decades, there has been some effort to highlight a continuum of symbiosis, wherein certain microbial taxa may exhibit mutualistic or pathogenic traits depending on environmental contexts, life stages, and plant host associations. However, gaps remain in understanding how to apply the continuum approach to host-microbe pairs across a range of environmental and ecological factors. This commentary presents an alternative framework for evaluating the continuum of symbiosis using dominant archetypes that define symbiotic ranges. We focus particularly on fungi and bacteria, though we recognize that archaea and other microeukaryotes play important roles in host-microbe interactions that may be described by this approach. This framework is centered in eco-evolutionary theory and aims to enhance communication among researchers, as well as prioritize holistic consideration of the factors shaping microbial life strategies. We discuss the influence of plant-mediated factors, habitat constraints, co-evolutionary forces, and the genetic contributions which shape different microbial lifestyles. Looking to the future, using a continuum of symbiosis paradigm will enable greater flexibility in defining the roles of target microbes and facilitate a more holistic view of the complex and dynamic relationship between microbes and plants.

scholarly journals Quantification and Trend Analysis of Multidecadal Global Dissolved Oxygen Changes

2021 ◽  
Author(s):  
Ayush Agrawal ◽  
James Swift
Keyword(s):  
Dissolved Oxygen ◽  
Water Column ◽  
Large Scale ◽  
Average Rate ◽  
Biogeochemical Cycles ◽  
Global Ocean ◽  
Climate Fluctuations ◽  
Ocean Productivity ◽  
Using Data ◽  
Thick Layers

Abstract Previous studies have found there to be measurable deoxygenation in regions of the world’s oceans, with changes linked to biogeochemical cycles, changes in ocean productivity, and climate fluctuations. Here, we investigated multidecadal large-scale dissolved oxygen trends in the principal basins of the Atlantic, Pacific, and Indian Oceans using data from WOCE, CLIVAR, and GO-SHIP cruises, representing some of the highest quality available water column data. We differenced spatially coincident older and more recent data, averaged differences in geographic subregions, and integrated results on 500-dbar thick layers from 500 dbar to 3500 dbar, with bottom levels extending to 6000 dbar. Overall, we found a deoxygenation below 500 dbar across all major basins at a global average rate of -0.06 µmol kg−1 year−1, with important variations between regions and layers. Our research demonstrates a deoxygenation trend coincident with the global ocean warming and increased stratification trends documented in other studies.

Conserving the Oceans

2021 ◽  
Author(s):  
Justin Alger
Keyword(s):  
Protected Areas ◽  
Marine Protected Areas ◽  
Environmental Policies ◽  
Global Ocean ◽  
The Political ◽  
Extractive Industry ◽  
The Us ◽  
Political Economies ◽  
Advocacy Campaigns ◽  
Key Features

Conserving the Oceans: The Politics of Large Marine Protected Areas documents the efforts of activists and states to increase the pace and scale of global ocean protections, leading to a new global norm in ocean conservation of large marine protected areas (MPAs) exceeding 200,000 km2. Through an analysis of domestic political economies, the book explains how states have protected millions of square kilometers of ocean space while remaining highly responsive to the interests of businesses. It argues that states design environmental policies above all around two key features of a given space: (1) the composition of extractive versus non-extractive industry interests; and (2) the salience of various industry interests, defined as the degree to which businesses would suffer tangible and significant costs in response to new environmental regulations. Through an analysis of large MPA advocacy campaigns in Australia, Palau, and the US, this book demonstrates how the political economy of a given marine space shapes how governments align their environmental and economic goals, sometimes strengthening conservation but more often than not undermining it. While recognizing important global progress and growing ambition to conserve ocean ecosystems, Conserving the Oceans demonstrates that even ambitious large MPAs have so far not fundamentally challenged a neoliberal paradigm of environmentalism that has caused considerable ecological harm.

Avaliação de Produção de Serapilheira em Planície Inundável no Pantanal Mato-Grossense

2018 ◽  
Vol 21 (3) ◽  
pp. 148
Author(s):  
Ana Carolina Amorim Marques ◽  
Osvaldo Borges Pinto Junior ◽  
George Louis Vourlitis
Keyword(s):  
Rainy Season ◽  
Nutrient Dynamics ◽  
Biogeochemical Cycles ◽  
Sensu Stricto ◽  
Dry Season ◽  
Litter Production ◽  
Distilled Water ◽  
Leaf Production ◽  
Shoot Production

A pesquisa teve como objetivo avaliar a produção de serapilheira (litter) em planície inundável, em duas áreas distintas, sendo de fitofisionomia denominada Cerrado sensu stricto e uma área com dominância de Scheelea phalerata (Arecaceae), popularmente conhecida como acuri, localizada no município de Poconé MT.Para a coleta de dados da serapilheira produzida foram distribuídos, sistematicamente, seis coletoresnas duas áreas de estudo, totalizando 12 unidades amostrais. O material foi recolhido, mensalmente, durante 10 meses. Todas as amostras de serapilheira foram recolhidas, mensalmente, e levadas ao laboratório para lavagem com água destilada, posteriormente, sendo separada em folhas, galhos, flores, frutos e sementes, e estes levados para secagem em estufa a 65 - 70 °C por 72 horas e, posterior pesagem em balança digital. A produção de folhas foi maior na área de cerrado durante a estação da seca, contudo, a produção de galhos teve maior percentual na área de acuri na estação chuvosa, as flores se mostraram em maior quantidade na área de cerrado se comparada ao acuri (estação chuvosa), a presença de frutos somente pode ser denotada na área de acuri e as sementes apresentaram maior quantidade na área de acuri. Observou-se que a produção de serapilheira apresentou sazonalidade, ao longo do ano, sendo a maior produção no período de junho a novembro (estação seca).Palavras-chave: Ciclos Biogeoquímicos. Dinâmica de Nutrientes. Sazonalidade.AbstractThe objective of this work was to evaluate the litter production in floodplain, in two distinct areas, being of phytophysiognomy called Cerrado sensu stricto and an area identified as by Scheelea phalerata (Arecaceae), popularly known as acuri, located in the municipality of Poconé MT. In order to collect data from the litter produced, six collectors were systematically distributed in the two study areas, totaling 12 sample units. The material was collected monthly for 10 months. All litter samples were collected monthly and taken to the laboratory for washing with distilled water, then separated into leaves, branches, flowers, fruits and seeds, and oven dried at 65-70 ° C for 72 hours and subsequently weighed in digital scale. Leaf production was higher in the cerrado area during the dry season, however, the shoot production had a higher percentage in the acuri area during the rainy season, the flowers were larger in the cerrado area when compared to acuri (rainy season ), the presence of fruits could only be denoted in the acuri area and the seeds showed more quantity in the acuri area. It was observed that litter production presented seasonality throughout the year, with the highest production in the period from June to November (dry season).Keywords: Biogeochemical Cycles. Nutrient Dynamics. Seasonality.Palavras-chave: Ciclos biogeoquímicos, Dinâmica de nutrientes, Sazonalidade.

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