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Davide Zannoni - One of the best experts on this subject based on the ideXlab platform.
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Acetate permease (ActP) Is responsible for tellurite (TeO32-) uptake and resistance in cells of the facultative Phototroph Rhodobacter capsulatus.
Applied and Environmental Microbiology, 2009Co-Authors: Roberto Borghese, Davide ZannoniAbstract:The highly toxic oxyanion tellurite has to enter the cytoplasm of microbial cells in order to fully express its toxicity. Here we show that in the Phototroph Rhodobacter capsulatus, tellurite exploits acetate permease (ActP) to get into the cytoplasm and that the levels of resistance and uptake are linked.
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effects of the metalloid oxyanion tellurite teo32 on growth characteristics of the Phototrophic bacterium rhodobacter capsulatus
Applied and Environmental Microbiology, 2004Co-Authors: Roberto Borghese, Francesca Borsetti, Paola Foladori, G. Ziglio, Davide ZannoniAbstract:This work examines the effects of potassium tellurite (K2TeO3) on the cell viability of the facultative Phototroph Rhodobacter capsulatus. There was a growth mode-dependent response in which cultures anaerobically grown in the light tolerate the presence of up to 250 to 300 μg of tellurite (TeO32−) per ml, while dark-grown aerobic cells were inhibited at tellurite levels as low as 2 μg/ml. The tellurite sensitivity of aerobic cultures was evident only for growth on minimal salt medium, whereas it was not seen during growth on complex medium. Notably, through the use of flow cytometry, we show that the cell membrane integrity was strongly affected by tellurite during the early growth phase (≤50% viable cells); however, at the end of the growth period and in parallel with massive tellurite intracellular accumulation as elemental Te0 crystallites, recovery of cytoplasmic membrane integrity was apparent (≥90% viable cells), which was supported by the development of a significant membrane potential (Δψ = 120 mV). These data are taken as evidence that in anaerobic aquatic habitats, the facultative Phototroph R. capsulatus might act as a natural scavenger of the highly soluble and toxic oxyanion tellurite.
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the electron transport system of the facultative Phototroph rhodoferax fermentans i a functional thermodynamic and spectroscopic study of the respiratory chain of dark and light grown cells
Biochimica et Biophysica Acta, 1995Co-Authors: Alejandro Hochkoeppler, Giovanni Moschettini, Davide ZannoniAbstract:Abstract Membranes isolated from light- and dark-grown cells of the recently established new taxon of the purple nonsulfur bacteria, Rhodoferax fermentans , gen. nov., sp. nov., have been examined. The results have been interpreted to show that the oxidative electron transport chain is branched at the ubiquinone level and does not involve rhodoquinone. Dark-grown membranes contain four b -type and three c -type membrane-bound cytochromes with E m7.0 of +371, +315, +76 and −18 mV and +298, +201 and +44 mV, respectively. No significant amount of soluble c was found in aerobic cells. Conversely, photosynthetically grown cells contain a soluble c -type haem ( α max at 551 nm, E m7.0 = +287 mV), four membrane-bound c -type haems with E m7.0 of +358, +296, +78 and −1 mV and three cytochromes b with E m7.0 of +320, +30 and −50 mV. Notably, the absence of cyt b -371 from light-grown membranes parallels the very low rate of cyt c oxidase activity catalyzed by this type of membrane. Oxido-reduction kinetics demonstrated that most of the c -type haems detected in light-grown membranes are not involved in respiration. These data suggest that the facultative Phototroph Rf. fermentans is endowed with an electron transport system different rrom that of typical facultative Phototrophs, e.g., Rhodobacter and Rhodospirillum species, but similar to that of green- and purple-nonsulfur genera such as Chloroflexus, Rhodocyclus and Rhodopseudomonas .
Lewis M. Ward - One of the best experts on this subject based on the ideXlab platform.
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granick revisited synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer
bioRxiv, 2020Co-Authors: Lewis M. Ward, Patrick M ShihAbstract: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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Microbial mats in the Turks and Caicos Islands reveal diversity and evolution of Phototrophy in the Chloroflexota order Aggregatilineales
Environmental Microbiome, 2020Co-Authors: Lewis M. Ward, Usha F. Lingappa, John P. Grotzinger, Woodward W. FischerAbstract: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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evolutionary implications of anoxygenic Phototrophy in the bacterial phylum candidatus eremiobacterota wps 2
Frontiers in Microbiology, 2019Co-Authors: Lewis M. Ward, Tanai Cardona, Hannah HollandmoritzAbstract:Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including Phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Candidatus Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of Phototrophic WPS-2. We demonstrate that Phototrophic WPS-2 show significant genetic and metabolic divergence from other Phototrophic and non-Phototrophic lineages. The genomes of these organisms encode a new family of anoxygenic Type II photochemical reaction centers and other Phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described Phototrophs. We propose the name Candidatus Baltobacterales for the order-level aerobic WPS-2 clade which contains Phototrophic lineages, from the Greek for "bog" or "swamp," in reference to the typical habitat of Phototrophic members of this clade.
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Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Palusbacterota (WPS-2)
2019Co-Authors: Lewis M. Ward, Tanai Cardona, Hannah Holland-moritzAbstract:Abstract Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including Phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been found in the uncultured bacterial WPS-2 clade that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of Phototrophic WPS-2. We demonstrate that Phototrophic WPS-2 show significant genetic and metabolic divergence from other Phototrophic and non-Phototrophic lineages. The genomes of these organisms encode a completely new family of anoxygenic Type II photochemical reaction centers and other Phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described Phototrophs. We propose the name Candidatus Palusbacterota for the phylum-level aerobic WPS-2 clade which contains Phototrophic lineages, from the Latin for “bog bacteria”, distinguishing it from the anaerobic, non-Phototrophic sister phylum Candidatus Eremiobacterota for “desert bacteria”, typically found in dry environments.
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Phototrophic Methane Oxidation in a Member of the Chloroflexi Phylum
2019Co-Authors: Lewis M. Ward, Patrick M Shih, Woodward W. Fischer, James Hemp, Takeshi Kakegawa, Shawn E. McglynnAbstract:Biological methane cycling plays an important role in Earth's climate and the global carbon cycle, with biological methane oxidation (methanotrophy) modulating methane release from numerous environments including soils, sediments, and water columns. Methanotrophy is typically coupled to aerobic respiration or anaerobically via the reduction of sulfate, nitrate, or metal oxides, and while the possibility of coupling methane oxidation to Phototrophy (photomethanotrophy) has been proposed, no organism has ever been described that is capable of this metabolism. Here we described a new bacterial genome from a member of the Chloroflexi phylum--termed here Candidatus Chlorolinea photomethanotrophicum--with cooccurring methanotrophy and Phototrophy pathways, suggesting a novel link between these two metabolisms. Recovered as a metagenome-assembled genome from microbial mats in an iron-rich hot spring in Japan, Ca. "C. photomethanotrophicum" forms a new lineage within the Chloroflexi phylum and expands the known metabolic diversity of this already diverse clade. Ca. "C. photomethanotrophicum" appears to be metabolically versatile, capable of Phototrophy (via a Type 2 reaction center), aerobic respiration, nitrite reduction, oxidation of methane and carbon monoxide, and potentially carbon fixation via a novel pathway composed of hybridized components of the serine cycle and the 3-hydroxypropionate bicycle. The biochemical network of this organism is constructed from components from multiple organisms and pathways, further demonstrating the modular nature of metabolic machinery and the ecological and evolutionary importance of horizontal gene transfer in the establishment of novel pathways.
Hannah Hollandmoritz - One of the best experts on this subject based on the ideXlab platform.
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evolutionary implications of anoxygenic Phototrophy in the bacterial phylum candidatus eremiobacterota wps 2
Frontiers in Microbiology, 2019Co-Authors: Lewis M. Ward, Tanai Cardona, Hannah HollandmoritzAbstract:Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including Phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Candidatus Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of Phototrophic WPS-2. We demonstrate that Phototrophic WPS-2 show significant genetic and metabolic divergence from other Phototrophic and non-Phototrophic lineages. The genomes of these organisms encode a new family of anoxygenic Type II photochemical reaction centers and other Phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described Phototrophs. We propose the name Candidatus Baltobacterales for the order-level aerobic WPS-2 clade which contains Phototrophic lineages, from the Greek for "bog" or "swamp," in reference to the typical habitat of Phototrophic members of this clade.
Enrique Lara - One of the best experts on this subject based on the ideXlab platform.
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Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling
Soil Biology & Biochemistry, 2017Co-Authors: Christophe Victor W. Seppey, Bertrand Fournier, Kenneth Dumack, Lassaad Belbahri, Edward A D Mitchell, David Singer, Enrique LaraAbstract:Abstract High-throughput sequencing (HTS) of soil environmental DNA (eDNA) allows assessing the full diversity of soil micro-eukaryotes. The resulting operational taxonomic units (OTUs) can be assigned to potential taxonomic and functional identities using increasingly complete reference databases. HTS of soil eDNA is revealing a high diversity and abundance of potential eukaryovorous protists, thus challenging the paradigm of the predominantly bacterivorous function of soil phagotrophic protists (i.e. microbial loop). Using Illumina sequencing of soil eDNA and targeting the V9 region of the SSU rRNA gene, we investigated the taxonomic and functional diversities, distribution and co-occurrence patterns of soil micro-eukaryotes in three land-use categories: forests, meadows and croplands located in Switzerland. Each OTU was assigned to a broad functional category (Phototrophs, phagotrophs, osmotrophs, or parasites). Total OTU richness was similar in the three land-use categories, but community composition differed significantly between forests and other land-uses. The proportion of fungal sequences (especially Basidiomycota) was highest, and Phototroph (i.e. soil microalgae) sequences least abundant in forests. Seven OTUs representing phagotrophic protists, together accounting for >25% of all phagotroph sequences, were significantly correlated to the total number of Phototroph sequences, thus suggesting algivory. At least three of these OTUs corresponded to known algal predators. These results suggest that beyond plants, soil microalgae represent a functionally significant but rarely considered input of carbon in soils that should be taken into account when modelling soil nutrient cycling.
Woodward W. Fischer - One of the best experts on this subject based on the ideXlab platform.
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Microbial mats in the Turks and Caicos Islands reveal diversity and evolution of Phototrophy in the Chloroflexota order Aggregatilineales
Environmental Microbiome, 2020Co-Authors: Lewis M. Ward, Usha F. Lingappa, John P. Grotzinger, Woodward W. FischerAbstract: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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Phototrophic Methane Oxidation in a Member of the Chloroflexi Phylum
2019Co-Authors: Lewis M. Ward, Patrick M Shih, Woodward W. Fischer, James Hemp, Takeshi Kakegawa, Shawn E. McglynnAbstract:Biological methane cycling plays an important role in Earth's climate and the global carbon cycle, with biological methane oxidation (methanotrophy) modulating methane release from numerous environments including soils, sediments, and water columns. Methanotrophy is typically coupled to aerobic respiration or anaerobically via the reduction of sulfate, nitrate, or metal oxides, and while the possibility of coupling methane oxidation to Phototrophy (photomethanotrophy) has been proposed, no organism has ever been described that is capable of this metabolism. Here we described a new bacterial genome from a member of the Chloroflexi phylum--termed here Candidatus Chlorolinea photomethanotrophicum--with cooccurring methanotrophy and Phototrophy pathways, suggesting a novel link between these two metabolisms. Recovered as a metagenome-assembled genome from microbial mats in an iron-rich hot spring in Japan, Ca. "C. photomethanotrophicum" forms a new lineage within the Chloroflexi phylum and expands the known metabolic diversity of this already diverse clade. Ca. "C. photomethanotrophicum" appears to be metabolically versatile, capable of Phototrophy (via a Type 2 reaction center), aerobic respiration, nitrite reduction, oxidation of methane and carbon monoxide, and potentially carbon fixation via a novel pathway composed of hybridized components of the serine cycle and the 3-hydroxypropionate bicycle. The biochemical network of this organism is constructed from components from multiple organisms and pathways, further demonstrating the modular nature of metabolic machinery and the ecological and evolutionary importance of horizontal gene transfer in the establishment of novel pathways.
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Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer.
Frontiers in microbiology, 2018Co-Authors: Lewis M. Ward, Patrick M Shih, James Hemp, Shawn E. Mcglynn, Woodward W. FischerAbstract:The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of Phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant Phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the Phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal) and Phototrophy (reaction center and bacteriochlorophyll synthesis) protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired Phototrophy independently via horizontal gene transfer (HGT) from different ancestral donors within the classically Phototrophic Chloroflexia class. These results illustrate a complex history of Phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of Phototrophy in many of the extant clades in which it appears.
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Genomics of a Phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification
The ISME journal, 2016Co-Authors: James Hemp, Sebastian Lücker, Joachim Schott, Laura A. Pace, Jena E. Johnson, Bernhard Schink, Holger Daims, Woodward W. FischerAbstract:Oxygenic photosynthesis evolved from anoxygenic ancestors before the rise of oxygen ~2.32 billion years ago; however, little is known about this transition. A high redox potential reaction center is a prerequisite for the evolution of the water-oxidizing complex of photosystem II. Therefore, it is likely that high-potential Phototrophy originally evolved to oxidize alternative electron donors that utilized simpler redox chemistry, such as nitrite or Mn. To determine whether nitrite could have had a role in the transition to high-potential Phototrophy, we sequenced and analyzed the genome of Thiocapsa KS1, a Gammaproteobacteria capable of anoxygenic Phototrophic nitrite oxidation. The genome revealed a high metabolic flexibility, which likely allows Thiocapsa KS1 to colonize a great variety of habitats and to persist under fluctuating environmental conditions. We demonstrate that Thiocapsa KS1 does not utilize a high-potential reaction center for Phototrophic nitrite oxidation, which suggests that this type of Phototrophic nitrite oxidation did not drive the evolution of high-potential Phototrophy. In addition, phylogenetic and biochemical analyses of the nitrite oxidoreductase (NXR) from Thiocapsa KS1 illuminate a complex evolutionary history of nitrite oxidation. Our results indicate that the NXR in Thiocapsa originates from a different nitrate reductase clade than the NXRs in chemolithotrophic nitrite oxidizers, suggesting that multiple evolutionary trajectories led to modern nitrite-oxidizing bacteria.