scholarly journals The diversity and evolution of microbial dissimilatory phosphite oxidation

2021 ◽  
Vol 118 (11) ◽  
pp. e2020024118
Author(s):  
Sophia D. Ewens ◽  
Alexa F. S. Gomberg ◽  
Tyler P. Barnum ◽  
Mikayla A. Borton ◽  
Hans K. Carlson ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Phylogenetic Analyses ◽  
Taxonomic Diversity ◽  
Metagenomic Sequencing ◽  
Low Oxygen ◽  
Cell Potential ◽  
Environmental Distribution ◽  
Metabolic Versatility ◽  
Anoxic Environments

Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (Eo′) of −650 mV for the PO43−/PO33− couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOMs) have remained enigmatic, as only two species have been identified. Here, metagenomic sequencing of phosphite-enriched microbial communities enabled the genome reconstruction and metabolic characterization of 21 additional DPOMs. These DPOMs spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria, and Desulfomonilia_A. Comparing the DPO genes from the genomes of enriched organisms with over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on Earth.

scholarly journals The Diversity and Evolution of Microbial Dissimilatory Phosphite Oxidation

2020 ◽  
Author(s):  
Sophia D. Ewens ◽  
Alexa F. S. Gomberg ◽  
Tyler P. Barnum ◽  
Mikayla A. Borton ◽  
Hans K. Carlson ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Phylogenetic Analyses ◽  
Taxonomic Diversity ◽  
Metagenomic Sequencing ◽  
Low Oxygen ◽  
Cell Potential ◽  
Environmental Distribution ◽  
Metabolic Versatility ◽  
Anoxic Environments ◽  
Geochemical Models

AbstractPhosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (E°’) of −650 mV for the PO43-/PO33- couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOM) has remained enigmatic and only two species have been identified. Here metagenomic sequencing of phosphite enriched microbial communities enabled the reconstruction and metabolic characterization of 21 novel DPOM. These DPOM spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria and Desulfomonilia_A. Comparing the DPO genes from the genomes of enriched organisms to over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on earth.Significance StatementGeochemical models of the phosphorus (P) cycle uniquely ignore microbial redox transformations. Yet phosphite is a reduced P source that has been detected in several environments at concentrations that suggest a contemporary P redox cycle. Microbial dissimilatory phosphite oxidation (DPO) converts soluble phosphite into phosphate, and a false notion of rarity has limited our understanding of its diversity and environmental distribution. Here we demonstrate that DPO is an ancient energy metabolism hosted by taxonomically diverse, autotrophic bacteria that exist globally throughout anoxic environments. DPO microorganisms are therefore likely to have provided bioavailable phosphate and fixed carbon to anoxic ecosystems throughout Earth’s history and continue to do so in contemporary environments.

scholarly journals Geochemical and metagenomic characterization of Jinata Onsen, a Proterozoic-analog hot spring, reveals novel microbial diversity including iron-tolerant phototrophs and thermophilic lithotrophs

2018 ◽  
Author(s):  
Lewis M. Ward ◽  
Airi Idei ◽  
Mayuko Nakagawa ◽  
Yuichiro Ueno ◽  
Woodward W. Fischer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Ferrous Iron ◽  
Hot Springs ◽  
Hot Spring ◽  
Spatial Scales ◽  
Oxygenic Photosynthesis ◽  
Metagenomic Sequencing ◽  
Geochemical Conditions

AbstractHydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interaction between the reducing hydrothermal fluids, the oxygenated atmosphere, and in some cases seawater. At Jinata Onsen, on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating a diversity of chemical potentials and redox pairs over a distance ~10 m. We characterized the geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse via 16S rDNA amplicon and genome-resolved shotgun metagenomic sequencing. The microbial community changed significantly downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Near the spring source, biomass is limited relative to downstream, and primary productivity may be fueled by oxidation of ferrous iron and molecular hydrogen by members of the Zetaproteobacteria and Aquificae. Downstream, the microbial community is dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the Chloroflexi and Caldithrichaeota phyla, positioning Jinata Onsen as a valuable site for future characterization of these clades.ImportanceHigh temperatures and reducing conditions allow hot springs to support microbial communities that are very different from those found elsewhere on the surface of the Earth today; in some ways, these environments and the communities they support can be similar to environments that existed on the early Earth and that may exist on other planets. Here, we describe a novel hot spring system where hot, iron-rich but oxygen-poor water flows into the ocean, supporting a range of unique microbial communities. Metagenomic sequencing recovered many novel microbial lineages, including deep-branching and uniquely thermotolerant members of known groups. Comparison of the biological communities in the upstream part of the hot spring, potentially supported by biological iron and hydrogen oxidizing metabolisms, to downstream microbial mats, supported by oxygenic photosynthesis, provides insight into the potential productivity of life during Proterozoic time and on other planets where oxygenic photosynthesis is not possible.

scholarly journals Human Adenovirus Type 7 Infections in Hubei, China During 2018-2019: Epidemic Features and Genetic Characterization of the Detected Viruses

2021 ◽  
Vol 11 ◽  
Author(s):  
Ying Li ◽  
Decheng Wang ◽  
Jingjing Zhang ◽  
Peiqi Huang ◽  
Hui Du ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Human Adenovirus ◽  
Adenovirus Type ◽  
Restriction Endonuclease Analysis ◽  
Metagenomic Sequencing ◽  
Clinical Indicators ◽  
Genome Variation ◽  
The Public ◽  
Stable Genome

Human adenoviruses (HAdVs) type 7 can cause severe respiratory disease. During the period between December 2018 and August 2019, HAdV-7 infection was identified in 129 patients in Wuhan Children’s Hospital, Hubei Province, China. Samples were collected from hospitalized children and metagenomic sequencing was applied to detect the HAdV infections. Hemophagocytic lymphohistiocystosis (HLH) related to HAdV infections was observed in some patients clinically and patients were divided into two groups based on this to test the differences among clinical indicators. Genome variation, in silico restriction endonuclease analysis (REA), and phylogenetic analyses were carried out to show the genome characterization of HAdV-7 in this study. It was found that many indicators, such as all blood routine indicators, in patients of the HLH group showed significant levels. In this study, REA revealed that HAdV-7 might belong to genome 7d and genome variation analysis displayed the stable genome of HAdV. HAdV-7 is an ongoing threat to the public, and global surveillance should be established.

scholarly journals Living to the high extreme: unraveling the composition, structure, and functional insights of bacterial communities thriving in the arsenic-rich Salar de Huasco – Altiplanic ecosystem.

2021 ◽  
Author(s):  
Juan Castro-Severyn ◽  
Coral Pardo-Esté ◽  
Katterinne N. Mendez ◽  
Jonathan Fortt ◽  
Sebastián Márquez ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Extreme Environments ◽  
Taxonomic Diversity ◽  
Functional Categories ◽  
Bacterial Composition ◽  
Functional Potential ◽  
Metabolic Versatility ◽  
Composition Structure ◽  
Metagenomic Approach

Microbial communities inhabiting extreme environments like Salar de Huasco (SH) are adapted to thrive while exposed to several abiotic pressures and the presence of toxic elements like arsenic (As). Hence, we aimed to uncover the role of arsenic in shaping bacterial composition, structure, and functional potential in five different sites in this Altiplanic wetland using a shotgun metagenomic approach. The sites exhibit wide gradients of arsenic (9 to 321 mg/kg), and our results showed highly diverse communities and a clear dominance exerted by the Proteobacteria and Bacteroidetes phyla. Functional potential analyses showed broadly convergent patterns, contrasting with their great taxonomic variability. Arsenic-related metabolism is different among the five communities, as well as other functional categories like those related to the CH4 and S cycles. Particularly, we found that the distribution and abundance of As-related genes increase, following along the As concentration gradient. Approximately 75% of the detected genes for As-metabolism belong to expulsion mechanisms, being arsJ and arsP pumps related to sites with higher As concentrations and present almost exclusively in Proteobacteria. Furthermore, taxonomic diversity and functional potential are reflected in the 12 reconstructed high-quality MAGs (Metagenome Assembled Genomes) belonging to the Bacteroidetes (5), Proteobacteria (5), Cyanobacteria (1) and Gemmatimonadota (1) phyla. We conclude that SH microbial communities are diverse and possess a broad genetic repertoire to thrive under extreme conditions, including increasing concentrations of the highly toxic As. Finally, this environment represents a reservoir of unknown and undescribed microorganisms, with a great metabolic versatility, which needs further study.

scholarly journals Polyphasic characterization of Trichocoleus desertorum sp. nov. (Pseudanabaenales, Cyanobacteria) from desert soils and phylogenetic placement of the genus Trichocoleus

Phytotaxa ◽  
2014 ◽  
Vol 163 (5) ◽  
pp. 241 ◽  
Author(s):  
Radka Muhlsteinova ◽  
Jeffrey R. Johansen ◽  
Nicole Pietrasiak ◽  
Michael P. Martin ◽  
Karina Osorio-Santos ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Its Region ◽  
Taxonomic Diversity ◽  
Morphological Description ◽  
Rrna Gene ◽  
New Taxon ◽  
Desert Soils ◽  
Phylogenetic Placement ◽  
Polyphasic Characterization

Little is known about the taxonomic diversity of cyanobacteria in deserts, despite their important ecological roles in these ecosystems. In this study, cyanobacterial strains from the Atacama, Colorado, and Mojave Deserts were isolated and characterized using molecular, morphological, and ecological information. Phylogenetic placement of these strains was revealed through Bayesian and parsimony-based phylogenetic analyses utilizing sequences of the 16S rRNA gene and the associated 16S–23S ITS region. Based on the combined evidence of this polyphasic approach, a new species from desert soils morphologically corresponding to the genus Trichocoleus was described. Trichocoleus desertorum sp. nov. Mühlsteinová, Johansen et Pietrasiak was used to obtain a phylogenetic reference point for Trichocoleus, a genus so far characterized by morphological description only. Through characterization of this new taxon in desert soils we hope to contribute to the general understanding of cyanobacterial diversity in extreme arid habitats.

scholarly journals Physiological, Ecological, and Phylogenetic Characterization of Stappia, a Marine CO-Oxidizing Bacterial Genus

2006 ◽  
Vol 73 (4) ◽  
pp. 1266-1276 ◽  
Author(s):  
Carolyn F. Weber ◽  
Gary M. King
Keyword(s):  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Membrane Lipid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Bisphosphate Carboxylase ◽  
Phylogenetic Characterization ◽  
Metabolic Versatility ◽  
Wide Range

ABSTRACT Bacteria play a major role in marine CO cycling, yet very little is known about the microbes involved. Thirteen CO-oxidizing Stappia isolates obtained from existing cultures, macroalgae, or surf samples representing geographically and ecologically diverse habitats were characterized using biochemical, physiological, and phylogenetic approaches. All isolates were aerobic chemoorganotrophs that oxidized CO at elevated (1,000 ppm) and ambient-to-subambient concentrations (<0.3 ppm). All contained the form I (OMP) coxL gene for aerobic CO dehydrogenase and also the form II (BMS) putative coxL gene. In addition, some strains possessed cbbL, the large subunit gene for ribulose-1,5-bisphosphate carboxylase/oxygenase, suggesting the possibility of lithotrophic or mixotrophic metabolism. All isolates used a wide range of sugars, organic acids, amino acids, and aromatics for growth and grew at salinities from 5 to 45 ppt. All but one isolate denitrified or respired nitrate. Phylogenetic analyses based on 16S rRNA gene sequences indicated that several isolates could not be distinguished from Stappia aggregata and contributed to a widely distributed species complex. Four isolates (of strains GA15, HI, MIO, and M4) were phylogenetically distinct from validly described Stappia species and closely related genera (e.g., Ahrensia, Pannonibacter, Pseudovibrio, and Roseibium). Substrate utilization profiles, enzymatic activity, and membrane lipid composition further distinguished these isolates and supported their designations as new Stappia species. The observed metabolic versatility of Stappia likely accounts for its cosmopolitan distribution and its ability to contribute to CO cycling as well as other important biogeochemical cycles.

scholarly journals Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

2011 ◽  
Vol 77 (11) ◽  
pp. 3846-3852 ◽  
Author(s):  
Andrea K. Bartram ◽  
Michael D. J. Lynch ◽  
Jennifer C. Stearns ◽  
Gabriel Moreno-Hagelsieb ◽  
Josh D. Neufeld
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Diversity ◽  
Illumina Genome Analyzer ◽  
Rrna Gene ◽  
Variable Regions ◽  
Gene Libraries

ABSTRACTMicrobial communities host unparalleled taxonomic diversity. Adequate characterization of environmental and host-associated samples remains a challenge for microbiologists, despite the advent of 16S rRNA gene sequencing. In order to increase the depth of sampling for diverse bacterial communities, we developed a method for sequencing and assembling millions of paired-end reads from the 16S rRNA gene (spanning the V3 region; ∼200 nucleotides) by using an Illumina genome analyzer. To confirm reproducibility and to identify a suitable computational pipeline for data analysis, sequence libraries were prepared in duplicate for both a defined mixture of DNAs from known cultured bacterial isolates (>1 million postassembly sequences) and an Arctic tundra soil sample (>6 million postassembly sequences). The Illumina 16S rRNA gene libraries represent a substantial increase in number of sequences over all extant next-generation sequencing approaches (e.g., 454 pyrosequencing), while the assembly of paired-end 125-base reads offers a methodological advantage by incorporating an initial quality control step for each 16S rRNA gene sequence. This method incorporates indexed primers to enable the characterization of multiple microbial communities in a single flow cell lane, may be modified readily to target other variable regions or genes, and demonstrates unprecedented and economical access to DNAs from organisms that exist at low relative abundances.

scholarly journals Bark from avocado trees of different geographic locations have consistent microbial communities

2020 ◽  
Author(s):  
Eneas Aguirre-von-Wobeser ◽  
Alexandro Alonso-Sánchez ◽  
Alfonso Méndez-Bravo ◽  
Luis Alberto Villanueva Espino ◽  
Frédérique Reverchon
Keyword(s):  
Microbial Communities ◽  
Persea Americana ◽  
Microbial Colonization ◽  
Taxonomic Structure ◽  
Metagenomic Sequencing ◽  
Important Species ◽  
Pests And Diseases ◽  
Shotgun Metagenomic Sequencing ◽  
Taxonomic Groups

AbstractBark is a permanent surface for microbial colonization at the interface of trees and the surrounding air. However, little is known about the microbial communities harbored on these tissues. Studies on bark microbial ecology show a dominance of bacteria from a few phyla. Bark microbial communities of avocado (Persea americana) could have implications for tree health, as a first barrier for defense against certain pests and diseases in this economically important species. We used shotgun metagenomic sequencing to analyze the bark microbial communities of avocado trees from two orchards, and compared one of them to rhizospheric soil. Our results show that the microbial communities of avocado bark have a well-defined taxonomic structure, with consistent patterns of abundance of bacteria, fungi and archaea, even in trees from two different locations. Bacteria in avocado bark were dominated by Proteobacteria (particularly Alphaproteobacteria), Actinobacteria and Bacteroidetes, consistently with bark communities in other trees. Fungal members were dominated by Ascomycota and Basidiomycota, while most Archaea in bark were Euryarchaeota. We can conclude that avocado bark is a well-defined environment, providing niches for specific taxonomic groups. The present in-depth characterization of bark microbial communities can form a basis for their future manipulation for agronomical purposes.

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