scholarly journals Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

2006 ◽  
Vol 361 (1475) ◽  
pp. 2009-2021 ◽  
Author(s):  
Martin F Polz ◽  
Dana E Hunt ◽  
Sarah P Preheim ◽  
Daniel M Weinreich
Keyword(s):  
Microbial Communities ◽  
Division Of Labour ◽  
Population Diversity ◽  
Nutrient Concentrations ◽  
Emergent Properties ◽  
Marine Microbes ◽  
Whole Genomes ◽  
Population Sizes ◽  
Underlying Mechanisms ◽  
Diverse Groups

Microbes in the ocean dominate biogeochemical processes and are far more diverse than anticipated. Thus, in order to understand the ocean system, we need to delineate microbial populations with predictable ecological functions. Recent observations suggest that ocean communities comprise diverse groups of bacteria organized into genotypic (and phenotypic) clusters of closely related organisms. Although such patterns are similar to metazoan communities, the underlying mechanisms for microbial communities may differ substantially. Indeed, the potential among ocean microbes for vast population sizes, extensive migration and both homologous and illegitimate genetic recombinations, which are uncoupled from reproduction, challenges classical population models primarily developed for sexually reproducing animals. We examine possible mechanisms leading to the formation of genotypic clusters and consider alternative population genetic models for differentiation at individual loci as well as gene content at the level of whole genomes. We further suggest that ocean bacteria follow at least two different adaptive strategies, which constrain rates and bounds of evolutionary processes: the ‘opportuni-troph’, exploiting spatially and temporally variable resources; and the passive oligotroph, efficiently using low nutrient concentrations. These ecological lifestyle differences may represent a fundamental divide with major consequences for growth and predation rates, genome evolution and population diversity, as emergent properties driving the division of labour within microbial communities.

scholarly journals Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

2020 ◽  
Vol 8 (11) ◽  
pp. 1657
Author(s):  
Abdul-Salam Juhmani ◽  
Alessandro Vezzi ◽  
Mohammad Wahsha ◽  
Alessandro Buosi ◽  
Fabio De Pascale ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Response ◽  
Environmental Parameters ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Concentrations ◽  
Lagoon Of Venice ◽  
Anthropogenic Stressors ◽  
Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

scholarly journals Temporally selective modification of the tomato rhizosphere and root microbiome by a dacitic tuff breccia (volcanic ash) containing minerals and trace elements.

2021 ◽  
Author(s):  
Elijah C. Mehlferber ◽  
Kent F. McCue ◽  
Jon E. Ferrel ◽  
Britt Koskella ◽  
Rajnish Khanna
Keyword(s):  
Microbial Communities ◽  
Volcanic Ash ◽  
Crop Productivity ◽  
Growth Stress ◽  
Microbial Composition ◽  
Nutrient Environment ◽  
Ash Deposit ◽  
Phosphorus And Potassium ◽  
Underlying Mechanisms ◽  
Functional Pathway

Abstract Food crops are grown with fertilizers containing nitrogen, phosphorus, and potassium (macronutrients), along with magnesium, calcium, boron, and zinc (micronutrients) at different ratios during their cultivation. Soil and plant associated microbes have been implicated to promote plant growth, stress tolerance, and productivity. However, the high degree of variability across agricultural environments makes it difficult to assess the possible influences of nutrient fertilizers on these microbial communities. Uncovering the underlying mechanisms could lead us to achieving consistently improved food quality and productivity with minimal environmental impacts. For this purpose, we tested a commercially available fertilizer (surface-mined 38-million-year-old volcanic ash deposit AZOMITE®), applied as a supplement to the normal fertilizer program to tomato plants grown in the greenhouse. We examined its impact on the composition of below-ground microbial communities, focusing on those members we identified as "core taxa" that were enriched in the rhizosphere and root endosphere compared to bulk soil, and appeared above their predicted neutral distribution levels in control and treated samples. This analysis revealed that Azomite had little effect on soil or rhizosphere microbial composition overall, but it had a significant, temporally selective influence on the rhizosphere and root associated core taxa. Changes in the composition of the core taxa were correlated to associated functional pathway enrichment of carbohydrate metabolism over shorter chain carbon metabolism, suggesting a conversion of available microbial nutrient source within the roots. This finding exemplifies how the nutrient environment can specifically alter the functional capacity of root-associated bacterial taxa, with potential to improve crop productivity.

scholarly journals Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment

2020 ◽  
Vol 367 (1) ◽  
Author(s):  
Jeffrey J Marlow ◽  
Isabella Colocci ◽  
Sean P Jungbluth ◽  
Nils Moritz Weber ◽  
Amy Gartman ◽  
...  
Keyword(s):  
Structure Function ◽  
Microbial Communities ◽  
Metabolic Activity ◽  
Point Sources ◽  
Emergent Properties ◽  
Spatial Relationships ◽  
Environmental Regime ◽  
Novel Approach ◽  
Stable Conditions ◽  
Metabolite Exchange

ABSTRACT Interactions among microorganisms and their mineralogical substrates govern the structure, function and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2 and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities ‘as they really are’ and explore determinants of metabolic activity across a range of microbiomes.

Shape Homeostasis in Virtual Embryos

2009 ◽  
Vol 15 (2) ◽  
pp. 161-183 ◽  
Author(s):  
Tim Andersen ◽  
Richard Newman ◽  
Tim Otter
Keyword(s):  
Regulatory Networks ◽  
Developmental Process ◽  
Three Dimensional ◽  
High Capacity ◽  
Cellular Systems ◽  
Emergent Properties ◽  
Complex Interactions ◽  
Self Repair ◽  
Underlying Mechanisms ◽  
Cellular Components

We have constructed a computational platform suitable for examining emergence of shape homeostasis in simple three-dimensional cellular systems. An embryo phenotype results from a developmental process starting with a single cell and its genome. When coupled to an evolutionary search, this platform can evolve embryos with particular stable shapes and high capacity for self-repair, even though repair is not genetically encoded or part of the fitness criteria. With respect to the genome, embryo shape and self-repair are emergent properties that arise from complex interactions among cells and cellular components via signaling and gene regulatory networks, during development or during repair. This report analyzes these networks and the underlying mechanisms that control embryo growth, organization, stability, and robustness to injury.

scholarly journals Population diversity and relatedness in Sugarbirds (Promeropidae:Promeropsspp.)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5000
Author(s):  
Evan S. Haworth ◽  
Michael J. Cunningham ◽  
Kathleen M. Calf Tjorve
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Gene ◽  
Conservation Status ◽  
Tail Length ◽  
Population Diversity ◽  
Breeding Systems ◽  
Effective Population ◽  
Socially Monogamous ◽  
Population Sizes ◽  
Polymorphic Microsatellite

Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops caferandP. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data,P. gurneyiare in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity inP. caferfrom Helderberg Nature Reserve andP. gurneyifrom Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes.

scholarly journals From numbers to ecosystems and biodiversity: A mechanistic approach to monitoring

Koedoe ◽  
2011 ◽  
Vol 53 (2) ◽  
Author(s):  
Sam Ferreira ◽  
Andrew Deacon ◽  
Hendrik Sithole ◽  
Hugo Bezuidenhout ◽  
Mahlomola Daemane ◽  
...  
Keyword(s):  
National Parks ◽  
Information Needs ◽  
Biological Diversity ◽  
Habitat Preferences ◽  
Management Strategies ◽  
Conservation Implications ◽  
Trade Offs ◽  
Population Sizes ◽  
Underlying Mechanisms ◽  
Analytical Approaches

Diverse political, cultural and biological needs epitomise the contrasting demands impacting on the mandate of the South African National Parks (SANParks) to maintain biological diversity. Systems-based approaches and strategic adaptive management (learn by doing) enable SANParks to accommodate these demands. However, such a management strategy creates new information needs, which require an appropriate analytical approach. We use conceptual links between objectives, indicators, mechanisms and modulators to identify key concerns in the context of and related to management objectives. Although our suggested monitoring designs are based mostly on defined or predicted underlying mechanisms of a concern, SANParks requires inventory monitoring to evaluate its key mandate. We therefore propose a predictive inventory approach based on species assemblages related to habitat preferences. Inventories alone may not always adequately serve unpacking of mechanisms: in some cases population size needs to be estimated to meet the information needs of management strategies, but actual population sizes may indirectly affect how the species impact on other values. In addition, ecosystem objectives require multivariate assessments of key communities, which can be used in trend analysis. SANParks therefore needs to know how to detect and define trends efficiently, which, in turn, requires precision of measures of variables. Conservation implications: Current research needs with regard to monitoring should focus on defining designs to yield optimal precision whilst taking methodology, survey trade-offs and analytical approaches into account. Use of these directives and research will guide monitoring during evaluation of SANParks objectives at various scales.

scholarly journals Human Lung Microbiome on the Way to Cancer

2019 ◽  
Vol 2019 ◽  
pp. 1-6 ◽  
Author(s):  
Olga V. Kovaleva ◽  
Daniil Romashin ◽  
Irina B. Zborovskaya ◽  
Mikhail M. Davydov ◽  
Murat S. Shogenov ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Helicobacter Pylori ◽  
Tumor Progression ◽  
Microbial Communities ◽  
Cancer Progression ◽  
Human Lung ◽  
Lung Microbiome ◽  
Long Time ◽  
Underlying Mechanisms ◽  
Proinflammatory Factors

Recent research on cancer-associated microbial communities led to the accumulation of data on the interplay between bacteria, immune and tumor cells, the pathways of bacterial induction of carcinogenesis, and its meaningfulness for medicine. Microbial communities that have any kind of impact on tumor progression and microorganisms associated with tumors have been defined as oncobiome. Over the last decades, a number of studies were dedicated to Helicobacter pylori and its role in the progression of stomach tumors, so this correlation can be regarded as proven. Involvement of bacteria in the induction of lung cancer has been largely ignored for a long time, though some correlations between this type of cancer and lung microbiome were established. Despite the fact that in the present the microbial impact on lung cancer progression has many confirmations, the underlying mechanisms are poorly understood. Microorganisms can contribute to tumor initiation and progression through production of bacteriotoxins and other proinflammatory factors. The purpose of this review is to organize the available data on lung cancer microbiome and its role in malignant tumor progression.

Emergent properties of microbial communities drive accelerated biogeochemical cycling in disturbed temperate forests

Ecology ◽  
2021 ◽  
Author(s):  
Ernest D Osburn ◽  
Brian D Badgley ◽  
Brian D Strahm ◽  
Frank O Aylward ◽  
J E Barrett
Keyword(s):  
Microbial Communities ◽  
Temperate Forests ◽  
Biogeochemical Cycling ◽  
Emergent Properties

scholarly journals Understanding predicted shifts in diazotroph biogeography using resource competition theory

2014 ◽  
Vol 11 (19) ◽  
pp. 5445-5461 ◽  
Author(s):  
S. Dutkiewicz ◽  
B. A. Ward ◽  
J. R. Scott ◽  
M. J. Follows
Keyword(s):  
Global Change ◽  
Resource Competition ◽  
Nutrient Concentrations ◽  
Change Models ◽  
Competition Theory ◽  
Nitrogen Fixers ◽  
Warming Climate ◽  
Model Predictions ◽  
Underlying Mechanisms ◽  
Central Atlantic

Abstract. We examine the sensitivity of the biogeography of nitrogen fixers to a warming climate and increased aeolian iron deposition in the context of a global earth system model. We employ concepts from the resource-ratio theory to provide a simplifying and transparent interpretation of the results. First we demonstrate that a set of clearly defined, easily diagnosed provinces are consistent with the theory. Using this framework we show that the regions most vulnerable to province shifts and changes in diazotroph biogeography are the equatorial and South Pacific, and central Atlantic. Warmer and dustier climates favor diazotrophs due to an increase in the ratio of supply rate of iron to fixed nitrogen. We suggest that the emergent provinces could be a standard diagnostic for global change models, allowing for rapid and transparent interpretation and comparison of model predictions and the underlying mechanisms. The analysis suggests that monitoring of real world province boundaries, indicated by transitions in surface nutrient concentrations, would provide a clear and easily interpreted indicator of ongoing global change.

scholarly journals Metapopulation stability in branching river networks

2018 ◽  
Vol 115 (26) ◽  
pp. E5963-E5969 ◽  
Author(s):  
Akira Terui ◽  
Nobuo Ishiyama ◽  
Hirokazu Urabe ◽  
Satoru Ono ◽  
Jacques C. Finlay ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Strong Association ◽  
Network Size ◽  
Population Diversity ◽  
River Networks ◽  
Emergent Properties ◽  
2D Systems ◽  
Scale Invariant ◽  
Ecosystem Size ◽  
Theoretical Predictions

Intraspecific population diversity (specifically, spatial asynchrony of population dynamics) is an essential component of metapopulation stability and persistence in nature. In 2D systems, theory predicts that metapopulation stability should increase with ecosystem size (or habitat network size): Larger ecosystems will harbor more diverse subpopulations with more stable aggregate dynamics. However, current theories developed in simplified landscapes may be inadequate to predict emergent properties of branching ecosystems, an overlooked but widespread habitat geometry. Here, we combine theory and analyses of a unique long-term dataset to show that a scale-invariant characteristic of fractal river networks, branching complexity (measured as branching probability), stabilizes watershed metapopulations. In riverine systems, each branch (i.e., tributary) exhibits distinctive ecological dynamics, and confluences serve as “merging” points of those branches. Hence, increased levels of branching complexity should confer a greater likelihood of integrating asynchronous dynamics over the landscape. We theoretically revealed that the stabilizing effect of branching complexity is a consequence of purely probabilistic processes in natural conditions, where within-branch synchrony exceeds among-branch synchrony. Contrary to current theories developed in 2D systems, metapopulation size (a variable closely related to ecosystem size) had vague effects on metapopulation stability. These theoretical predictions were supported by 18-y observations of fish populations across 31 watersheds: Our cross-watershed comparisons revealed consistent stabilizing effects of branching complexity on metapopulations of very different riverine fishes. A strong association between branching complexity and metapopulation stability is likely to be a pervasive feature of branching networks that strongly affects species persistence during rapid environmental changes.

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