Microbial mats in the Turks and Caicos Islands reveal diversity and evolution of phototrophy in the Chloroflexota order Aggregatilineales

10.21203/rs.2.21749/v1 ◽

2020 ◽

Author(s):

Lewis M Ward ◽

Ush Lingappa ◽

John Grotzinger ◽

Woodward Fischer

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Metabolic Pathways ◽

Microbial Mats ◽

Accurate Determination ◽

Metagenomic Sequencing ◽

Turks And Caicos Islands ◽

History Of

Abstract Genome-resolved metagenomic sequencing approaches have led to a substantial increase in the recognized diversity of microorganisms; this included the discovery of novel metabolic pathways in previously recognized clades, and has enabled a more accurate determination of the extant distribution of key metabolisms and how they evolved over Earth history. Here, we present metagenome-assembled genomes of members of the Chloroflexota (formerly Chloroflexi or Green Nonsulfur Bacteria) order Aggregatilineales (formerly SBR1031 or Thermofonsia) discovered from sequencing of thick and expansive microbial mats present in an intertidal lagoon on Little Ambergris Cay in the Turks and Caicos Islands. These taxa included multiple new lineages of Type 2 reaction center-containing phototrophs that were not closely related to previously described phototrophic Chloroflexota—revealing a rich and intricate history of horizontal gene transfer and the evolution of phototrophy and other core metabolic pathways within this widespread phylum.

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Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer

PLoS ONE ◽

10.1371/journal.pone.0239248 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0239248 ◽

Cited By ~ 1

Author(s):

Lewis M. Ward ◽

Patrick M. Shih

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

Photosynthetic Bacteria ◽

Photosynthetic Apparatus ◽

Metagenomic Sequencing ◽

Crown Group ◽

Environmental Diversity ◽

Chlorophyll Pigments ◽

History Of

Photosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

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Granick Revisited: Synthesizing Evolutionary and Ecological Evidence for the Late Origin of Bacteriochlorophyll via Ghost Lineages and Horizontal Gene Transfer

10.1101/2020.09.01.277905 ◽

2020 ◽

Cited By ~ 2

Author(s):

Lewis M. Ward ◽

Patrick M. Shih

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

Photosynthetic Bacteria ◽

Photosynthetic Apparatus ◽

Metagenomic Sequencing ◽

Crown Group ◽

Environmental Diversity ◽

Chlorophyll Pigments ◽

History Of

AbstractPhotosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

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Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

Genes ◽

10.3390/genes10080569 ◽

2019 ◽

Vol 10 (8) ◽

pp. 569 ◽

Cited By ~ 7

Author(s):

Phale ◽

Shah ◽

Malhotra

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Food Web ◽

Microbial Communities ◽

Metabolic Pathways ◽

Anthropogenic Activities ◽

Genetic Material ◽

Genomic Islands ◽

Biochemical Pathways ◽

Integrative Conjugative Elements

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

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Adaptation by Ancient Horizontal Acquisition of Butyrate Metabolism Genes in Aggregatibacter actinomycetemcomitans

mBio ◽

10.1128/mbio.03581-20 ◽

2021 ◽

Vol 12 (2) ◽

Author(s):

Ahmed M. Moustafa ◽

Senthil Kumar Velusamy ◽

Lidiya Denu ◽

Apurva Narechania ◽

Daniel H. Fine ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Strong Association ◽

Aggregatibacter Actinomycetemcomitans ◽

Short Chain ◽

Oral Microbiota ◽

Content Type ◽

History Of ◽

The Impact

ABSTRACT Like the bacterial residents of the human gut, it is likely that many of the species in the human oral microbiota have evolved to better occupy and persist in their niche. Aggregatibacter actinomycetemcomitans (Aa) is both a common colonizer of the oral cavity and has been implicated in the pathogenesis of periodontal disease. Here, we present a whole-genome phylogenetic analysis of Aa isolates from humans and nonhuman primates that revealed an ancient origin for this species and a long history of association with the Catarrhini, the lineage that includes Old World monkeys (OWM) and humans. Further genomic analysis showed a strong association with the presence of a short-chain fatty acid (SCFA) catabolism locus (atoRDAEB) in many human isolates that was absent in almost all nonhuman OWM isolates. We show that this locus was likely acquired through horizontal gene transfer. When grown under conditions that are similar to those at the subgingival site of periodontitis (anaerobic, SCFA replete), Aa strains with atoRDAEB formed robust biofilms and showed upregulation of genes involved in virulence, colonization, and immune evasion. Both an isogenic deletion mutant and nonhuman primate isolates lacking the ato locus failed to grow in a robust biofilm under these conditions, but grew well under the carbohydrate-rich conditions similar to those found above the gumline. We propose that the acquisition of the ato locus was a key evolutionary step allowing Aa to utilize SCFAs, adapt, and modulate subgingival disease. IMPORTANCE There has been considerable interest in the impact of short-chain fatty acids (SCFAs) on inflammatory effects related to the microbiome. Here, we present evidence that SCFAs may also be important in disease by providing an energy source or disease-associated cue for colonizing pathogens. We propose that SCFAs allow Aggregatibacter actinomycetemcomitans (Aa) to adapt to the subgingival anaerobic environment, which is the site of human periodontitis. Under anaerobic, SCFA-rich conditions, human-derived Aa strains that possess butyrate metabolism genes form strong biofilms and upregulate virulence genes. Our phylogenetic analysis highlights a long history of evolution of Aa with its primate hosts and suggests that the acquisition of butyrate metabolism genes may have been a critical step in allowing Aa to colonize a new niche and cause disease in humans. Overall, this study highlights the important role that horizontal gene transfer may play in microbial adaptation and the evolution of infectious disease.

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The Linguistics of Bacterial Conflict Systems Reveal Ancient Origins of Eukaryotic Innate Immunity

Journal of Bacteriology ◽

10.1128/jb.00507-20 ◽

2020 ◽

Vol 202 (24) ◽

Author(s):

Emily M. Kibby ◽

Aaron T. Whiteley

Keyword(s):

Innate Immunity ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

Protein Domains ◽

Arms Race ◽

Bacterial Populations ◽

Defense Systems ◽

History Of ◽

Novel Protein

ABSTRACT The arms race between bacteria and their competitors has produced an astounding variety of conflict systems that are shared via horizontal gene transfer across bacterial populations. In this issue of the Journal of Bacteriology, Burroughs and Aravind investigate how these biological conflict systems have been mixed and matched into new configurations, often with novel protein domains (A. M. Burroughs and L. Aravind, J Bacteriol 202:e00365-20, 2020, https://doi.org/10.1128/JB.00365-20). The authors additionally characterize the evolutionary history of genes in eukaryotes that appear to have been acquired from these prokaryotic defense systems.

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Nisin Influence on the Antimicrobial Resistance Ability of Canine Oral Enterococci

Antibiotics ◽

10.3390/antibiotics9120890 ◽

2020 ◽

Vol 9 (12) ◽

pp. 890

Author(s):

Eva Cunha ◽

Rita Janela ◽

Margarida Costa ◽

Luís Tavares ◽

Ana Salomé Veiga ◽

...

Keyword(s):

Gene Transfer ◽

Antimicrobial Resistance ◽

Horizontal Gene Transfer ◽

Selective Pressure ◽

Vana Gene ◽

Selection Window ◽

Antimicrobial Resistance Profile ◽

Mutant Prevention Concentration ◽

Amoxicillin Clavulanate

Periodontal disease (PD) is one of the most common diseases in dogs. Although previous studies have shown the potential of the antimicrobial peptide nisin for PD control, there is no information regarding its influence in the development of antimicrobial resistance or horizontal gene transfer (HGT). Nisin’s mutant prevention concentration (MPC) and selection window (MSW) were determined for a collection of canine oral enterococci. Isolates recovered after the determination of the MPC values were characterized for their antimicrobial profile and its nisin minimum inhibitory and bactericidal concentrations. The potential of vanA HGT between Enterococcus faecium CCGU36804 and nine clinical canine staphylococci and enterococci was evaluated. Nisin MPC values ranged from 400 to more than 600 μg/mL. In comparison with the original enterococci collection, the isolates recovered after the determination of the nisin MPC showed increased resistance towards amoxicillin/clavulanate (5%), vancomycin (5%), enrofloxacin (10%), gentamicin (10%) and imipenem (15%). The HGT of vanA gene was not observed. This work showed that nisin selective pressure may induce changes in the bacteria’s antimicrobial resistance profile but does not influence horizontal transfer of vanA gene. To our knowledge, this is the first report of nisin’s MPC and MSW determination regarding canine enterococci.

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Horizontal Gene Transfers from Bacteria toEntamoebaComplex: A Strategy for Dating Events along Species Divergence

Journal of Parasitology Research ◽

10.1155/2016/3241027 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 2

Author(s):

Miguel Romero ◽

R. Cerritos ◽

Cecilia Ximenez

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Entamoeba Histolytica ◽

Lateral Gene Transfer ◽

Adaptive Radiation ◽

Fossil Record ◽

Evolutionary History ◽

Divergence Time ◽

Eukaryotic Evolution ◽

History Of

Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasiteEntamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genusEntamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of someEntamoebaspecies was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence betweenE. histolyticaandE. nuttalliiprobably occurred 5.93 million years ago (Mya); this lineage diverged fromE. dispar9.97 Mya, while the ancestor of the latter separated fromE. invadens68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of theEntamoebagenus.

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Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea

BMC Evolutionary Biology ◽

10.1186/1471-2148-12-226 ◽

2012 ◽

Vol 12 (1) ◽

pp. 226 ◽

Cited By ~ 24

Author(s):

Céline Petitjean ◽

David Moreira ◽

Purificación López-García ◽

Céline Brochier-Armanet

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

History Of

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Fuzzy Tuned PID Controller for Envisioned Agricultural Manipulator

International Journal of Automation and Computing ◽

10.1007/s11633-021-1280-5 ◽

2021 ◽

Author(s):

Satyam Paul ◽

Ajay Arunachalam ◽

Davood Khodadad ◽

Henrik Andreasson ◽

Olena Rubanenko

Keyword(s):

Pid Controller ◽

Control Strategies ◽

Low Cost ◽

Accurate Determination ◽

Agricultural Practices ◽

Science Research ◽

Vibration Attenuation

AbstractThe implementation of image-based phenotyping systems has become an important aspect of crop and plant science research which has shown tremendous growth over the years. Accurate determination of features using images requires stable imaging and very precise processing. By installing a camera on a mechanical arm driven by motor, the maintenance of accuracy and stability becomes non-trivial. As per the state-of-the-art, the issue of external camera shake incurred due to vibration is a great concern in capturing accurate images, which may be induced by the driving motor of the manipulator. So, there is a requirement for a stable active controller for sufficient vibration attenuation of the manipulator. However, there are very few reports in agricultural practices which use control algorithms. Although, many control strategies have been utilized to control the vibration in manipulators associated to various applications, no control strategy with validated stability has been provided to control the vibration in such envisioned agricultural manipulator with simple low-cost hardware devices with the compensation of non-linearities. So, in this work, the combination of proportional-integral-differential (PID) control with type-2 fuzzy logic (T2-F-PID) is implemented for vibration control. The validation of the controller stability using Lyapunov analysis is established. A torsional actuator (TA) is applied for mitigating torsional vibration, which is a new contribution in the area of agricultural manipulators. Also, to prove the effectiveness of the controller, the vibration attenuation results with T2-F-PID is compared with conventional PD/PID controllers, and a type-1 fuzzy PID (T1-F-PID) controller.

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